Comparative Study of Neural Network Frameworks for the Next Generation of Adaptive Optics Systems.

PubMed

González-Gutiérrez, Carlos; Santos, Jesús Daniel; Martínez-Zarzuela, Mario; Basden, Alistair G; Osborn, James; Díaz-Pernas, Francisco Javier; De Cos Juez, Francisco Javier

2017-06-02

Many of the next generation of adaptive optics systems on large and extremely large telescopes require tomographic techniques in order to correct for atmospheric turbulence over a large field of view. Multi-object adaptive optics is one such technique. In this paper, different implementations of a tomographic reconstructor based on a machine learning architecture named "CARMEN" are presented. Basic concepts of adaptive optics are introduced first, with a short explanation of three different control systems used on real telescopes and the sensors utilised. The operation of the reconstructor, along with the three neural network frameworks used, and the developed CUDA code are detailed. Changes to the size of the reconstructor influence the training and execution time of the neural network. The native CUDA code turns out to be the best choice for all the systems, although some of the other frameworks offer good performance under certain circumstances.

Comparative Study of Neural Network Frameworks for the Next Generation of Adaptive Optics Systems

PubMed Central

González-Gutiérrez, Carlos; Santos, Jesús Daniel; Martínez-Zarzuela, Mario; Basden, Alistair G.; Osborn, James; Díaz-Pernas, Francisco Javier; De Cos Juez, Francisco Javier

2017-01-01

Many of the next generation of adaptive optics systems on large and extremely large telescopes require tomographic techniques in order to correct for atmospheric turbulence over a large field of view. Multi-object adaptive optics is one such technique. In this paper, different implementations of a tomographic reconstructor based on a machine learning architecture named “CARMEN” are presented. Basic concepts of adaptive optics are introduced first, with a short explanation of three different control systems used on real telescopes and the sensors utilised. The operation of the reconstructor, along with the three neural network frameworks used, and the developed CUDA code are detailed. Changes to the size of the reconstructor influence the training and execution time of the neural network. The native CUDA code turns out to be the best choice for all the systems, although some of the other frameworks offer good performance under certain circumstances. PMID:28574426

Haemophilus ducreyi Outer Membrane Determinants, Including DsrA, Define Two Clonal Populations

PubMed Central

White, Catherine Dinitra; Leduc, Isabelle; Olsen, Bonnie; Jeter, Chrystina; Harris, Chavala; Elkins, Christopher

2005-01-01

The Haemophilus ducreyi outer membrane component DsrA (for ducreyi serum resistance A) is necessary for complete resistance to normal human serum (NHS). When DsrA expression in 19 temporally and geographically diverse clinical isolates of H. ducreyi was examined by Western blotting, 5 of the strains expressed a different immunotype of the DsrA protein (DsrAII) than the well-characterized prototypical strain 35000HP (DsrAI). The predicted DsrA proteins expressed by the DsrAII strains were 100% identical to each other but only 48% identical to that of strain 35000HP. In addition to the DsrAII protein, class II strains also expressed variant forms of other outer membrane proteins (OMPs) including NcaA (necessary for collagen adhesion A), DltA (ducreyi lectin A), Hlp (H. ducreyi lipoprotein), major OMP, and/or OmpA2 (for OMP A2) and synthesized a distinct, faster-migrating lipooligosaccharide. Based on these data, strains expressing DsrAI were termed class I, and those expressing DsrAII were termed class II. Expression of dsrAII from strain CIP 542 ATCC in the class I dsrAI mutant FX517 (35000HP background), which does not express a DsrA protein, rendered this strain resistant to 50% NHS. This demonstrates that DsrAII protein is also critical to serum resistance. Taken together, these results indicate that there are two clonal populations of H. ducreyi. The implications of two classes of H. ducreyi strains differing in important antigenic outer membrane components are discussed. PMID:15784585

Implementation of Branch-Point-Tolerant Wavefront Reconstructor for Strong Turbulence Compensation

DTIC Science & Technology

2012-06-14

Strehl ratio. Strehl ratio is defined as [38] S = ∫ ∞ −∞ ∫ ∞ −∞H( fx , fy) d fx d fy∫ ∞ −∞ ∫ ∞ −∞ Hdl( fx , fy) d fx d fy , (2.36) where H( fx , fy) is the...aberrated optical transfer function (OTF) [18] and Hdl( fx , fy) is the diffraction limited OTF. Both of these OTF’s are in terms of their spatial...frequencies fx and fy. There are several approximations to this form that better suit various applications or measurement techniques [25, 38]. For this

Thiosulfate Transfer Mediated by DsrE/TusA Homologs from Acidothermophilic Sulfur-oxidizing Archaeon Metallosphaera cuprina*

PubMed Central

Liu, Li-Jun; Stockdreher, Yvonne; Koch, Tobias; Sun, Shu-Tao; Fan, Zheng; Josten, Michaele; Sahl, Hans-Georg; Wang, Qian; Luo, Yuan-Ming; Liu, Shuang-Jiang; Dahl, Christiane; Jiang, Cheng-Ying

2014-01-01

Conserved clusters of genes encoding DsrE and TusA homologs occur in many archaeal and bacterial sulfur oxidizers. TusA has a well documented function as a sulfurtransferase in tRNA modification and molybdenum cofactor biosynthesis in Escherichia coli, and DsrE is an active site subunit of the DsrEFH complex that is essential for sulfur trafficking in the phototrophic sulfur-oxidizing Allochromatium vinosum. In the acidothermophilic sulfur (S0)- and tetrathionate (S4O62−)-oxidizing Metallosphaera cuprina Ar-4, a dsrE3A-dsrE2B-tusA arrangement is situated immediately between genes encoding dihydrolipoamide dehydrogenase and a heterodisulfide reductase-like complex. In this study, the biochemical features and sulfur transferring abilities of the DsrE2B, DsrE3A, and TusA proteins were investigated. DsrE3A and TusA proved to react with tetrathionate but not with NaSH, glutathione persulfide, polysulfide, thiosulfate, or sulfite. The products were identified as protein-Cys-S-thiosulfonates. DsrE3A was also able to cleave the thiosulfate group from TusA-Cys18-S-thiosulfonate. DsrE2B did not react with any of the sulfur compounds tested. DsrE3A and TusA interacted physically with each other and formed a heterocomplex. The cysteine residue (Cys18) of TusA is crucial for this interaction. The single cysteine mutants DsrE3A-C93S and DsrE3A-C101S retained the ability to transfer the thiosulfonate group to TusA. TusA-C18S neither reacted with tetrathionate nor was it loaded with thiosulfate with DsrE3A-Cys-S-thiosulfonate as the donor. The transfer of thiosulfate, mediated by a DsrE-like protein and TusA, is unprecedented not only in M. cuprina but also in other sulfur-oxidizing prokaryotes. The results of this study provide new knowledge on oxidative microbial sulfur metabolism. PMID:25122768

Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction

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

Venceslau, Sofia S.; Cort, John R.; Baker, Erin Shammel

2013-11-29

Dissimilatory reduction of sulfite is carried out by the siroheme enzyme DsrAB, with the involvement of the protein DsrC having two conserved cysteine residues. Here, we report a study of the distribution of DsrC in cell extracts, a cysteine-labelling gel-shift assay to monitor its redox state and behaviour, and procedures to produce the different redox forms. We show that, in the model sulfate reducer Desulfovibrio vulgaris, the majority of DsrC is not associated with DsrAB and is thus free to interact with other proteins. In addition, we successfully produced DsrC with an intramolecular disulfide bond (oxidized state) by treatment withmore » arginine.« less

New Proteins Involved in Sulfur Trafficking in the Cytoplasm of Allochromatium vinosum*

PubMed Central

Stockdreher, Yvonne; Sturm, Marga; Josten, Michaele; Sahl, Hans-Georg; Dobler, Nadine; Zigann, Renate; Dahl, Christiane

2014-01-01

The formation of periplasmic sulfur globules is an intermediate step during the oxidation of reduced sulfur compounds in various sulfur-oxidizing microorganisms. The mechanism of how this sulfur is activated and crosses the cytoplasmic membrane for further oxidation to sulfite by the dissimilatory reductase DsrAB is incompletely understood, but it has been well documented that the pathway involves sulfur trafficking mediated by sulfur-carrying proteins. So far sulfur transfer from DsrEFH to DsrC has been established. Persulfurated DsrC very probably serves as a direct substrate for DsrAB. Here, we introduce further important players in oxidative sulfur metabolism; the proteins Rhd_2599, TusA, and DsrE2 are strictly conserved in the Chromatiaceae, Chlorobiaceae, and Acidithiobacillaceae families of sulfur-oxidizing bacteria and are linked to genes encoding complexes involved in sulfur oxidation (Dsr or Hdr) in the latter two. Here we show via relative quantitative real-time PCR and microarray analysis an increase of mRNA levels under sulfur-oxidizing conditions for rhd_2599, tusA, and dsrE2 in Allochromatium vinosum. Transcriptomic patterns for the three genes match those of major genes for the sulfur-oxidizing machinery rather than those involved in biosynthesis of sulfur-containing biomolecules. TusA appears to be one of the major proteins in A. vinosum. A rhd_2599-tusA-dsrE2-deficient mutant strain, although not viable in liquid culture, was clearly sulfur oxidation negative upon growth on solid media containing sulfide. Rhd_2599, TusA, and DsrE2 bind sulfur atoms via conserved cysteine residues, and experimental evidence is provided for the transfer of sulfur between these proteins as well as to DsrEFH and DsrC. PMID:24648525

Lander Trajectory Reconstruction computer program

NASA Technical Reports Server (NTRS)

Adams, G. L.; Bradt, A. J.; Ferguson, J. B.; Schnelker, H. J.

1971-01-01

The Lander Trajectory Reconstruction (LTR) computer program is a tool for analysis of the planetary entry trajectory and atmosphere reconstruction process for a lander or probe. The program can be divided into two parts: (1) the data generator and (2) the reconstructor. The data generator provides the real environment in which the lander or probe is presumed to find itself. The reconstructor reconstructs the entry trajectory and atmosphere using sensor data generated by the data generator and a Kalman-Schmidt consider filter. A wide variety of vehicle and environmental parameters may be either solved-for or considered in the filter process.

Physical And Medical Attributes Of Six Contemporary Noninvasive Imaging Techniques

NASA Astrophysics Data System (ADS)

Budinger, Thomas F.

1981-11-01

Digital subtraction angiography(DSA)is compared to five other noninvasive imaging methods with respect to physical attributes and medical applications. 1) Digital subtraction angiography measures flow channel (vessel) anatomy and vascular leaks in regions where signals from under and overlying vascular pools do not conflict in strength with the vessel or tissue of interest. 2) X-ray computed tomography, in principle, can separate the under and overlying signals, yet presently it is limited in speed, axial coverage, and computational burden for tasks DSA can efficiently perform. Possible exceptions are the dynamic spatial reconstructor (DSR) of Mayo Clinic and the system under construction at the University of California, San Francisco. 3) Heavy ion imaging measures electron density and is less sensitive to injected contrast than x-ray imaging which has the advantage of the photoelectric effect. A unique attribute of heavy ion imaging is its potential for treatment planning and the fact that beam hardening is not a physical problem. 4) Ultrasound detects surfaces, bulk tissue characteristics, and blood velocity. Doppler ultrasound competes with DSA in some regions of the body and generally involves less equipment and patient procedures. Ultrasound vessel imaging and range-gated Doppler have limitations due to sound absorption by atheromatous tissue and available imaging windows. 5) Emission tomography measures receptor site distribution, metabolism, permeability, and tissue perfusion. Resolution is limited to 7mm full width half maximum (FWHM) in the near future, and extraction of metabolic and perfusion information usually requires kinetic analyses with statistically poor data. The ability of positron tomography to measure metabolism (sugar, fatty acid, and oxygen utilization) and the ability to measure tissue perfusion with single photon tomography (17 mm FWHM) or PET (7 mm FWHM) using non-cyclotron produced radionuclides are the major unique features of emission tomography. 6) Nuclear magnetic resonance procedures measure the concentration of some nuclei (e.g., 1H, 23Na, 32P) as well as their chemical state and the local physical-chemical environment of the resolution volume. Velocity and diffusion are also potential measurements. Two unique capabilities of contemporary interest are the ability to image the spatial distribu-tion of relaxation parameters which give information about the local tissue characteristics, and the ability of NMR spectroscopy to sample (not image) the energy state of phosphorous in selected regions of the body. A third attribute of importance is that possible tissue heating seems to be the only hazard and this can be controlled.

DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli.

PubMed

Lalaouna, David; Morissette, Audrey; Carrier, Marie-Claude; Massé, Eric

2015-10-01

The 87 nucleotide long DsrA sRNA has been mostly studied for its translational activation of the transcriptional regulator RpoS. However, it also represses hns mRNA, which encodes H-NS, a major regulator that affects expression of nearly 5% of Escherichia coli genes. A speculative model previously suggested that DsrA would block hns mRNA translation by binding simultaneously to start and stop codon regions of hns mRNA (coaxial model). Here, we show that DsrA efficiently blocked translation of hns mRNA by base-pairing immediately downstream of the start codon. In addition, DsrA induced hns mRNA degradation by actively recruiting the RNA degradosome complex. Data presented here led to a model of DsrA action on hns mRNA, which supports a canonical mechanism of sRNA-induced mRNA degradation by binding to the translation initiation region. Furthermore, using MS2-affinity purification coupled with RNA sequencing technology (MAPS), we also demonstrated that DsrA targets rbsD mRNA, involved in ribose utilization. Surprisingly, DsrA base pairs far downstream of rbsD start codon and induces rapid degradation of the transcript. Thus, our study enables us to draw an extended DsrA targetome. © 2015 John Wiley & Sons Ltd.

Defining Potential Vaccine Targets of Haemophilus ducreyi Trimeric Autotransporter Adhesin DsrA

PubMed Central

Fusco, William G.; Choudhary, Neelima R.; Stewart, Shelley M.; Alam, S. Munir; Sempowski, Gregory D.; Elkins, Christopher

2015-01-01

Haemophilus ducreyi is the causative agent of the sexually transmitted genital ulcer disease chancroid. Strains of H. ducreyi are grouped in two classes (I and II) based on genotypic and phenotypic differences, including those found in DsrA, an outer membrane protein belonging to the family of multifunctional trimeric autotransporter adhesins. DsrA is a key serum resistance factor of H. ducreyi that prevents binding of natural IgM at the bacterial surface and functions as an adhesin to fibronectin, fibrinogen, vitronectin, and human keratinocytes. Monoclonal antibodies (MAbs) were developed to recombinant DsrA (DsrAI) from prototypical class I strain 35000HP to define targets for vaccine and/or therapeutics. Two anti-DsrAI MAbs bound monomers and multimers of DsrA from genital and non-genital/cutaneous H. ducreyi strains in a Western blot and reacted to the surface of the genital strains; however, these MAbs did not recognize denatured or native DsrA from class II strains. In a modified extracellular matrix protein binding assay using viable H. ducreyi, one of the MAbs partially inhibited binding of fibronectin, fibrinogen, and vitronectin to class I H. ducreyi strain 35000HP, suggesting a role for anti-DsrA antibodies in preventing binding of H. ducreyi to extracellular matrix proteins. Standard ELISA and surface plasmon resonance using a peptide library representing full-length, mature DsrAI revealed the smallest nominal epitope bound by one of the MAbs to be MEQNTHNINKLS. Taken together, our findings suggest that this epitope is a potential target for an H. ducreyi vaccine. PMID:25897604

Defining Potential Vaccine Targets of Haemophilus ducreyi Trimeric Autotransporter Adhesin DsrA.

PubMed

Fusco, William G; Choudhary, Neelima R; Stewart, Shelley M; Alam, S Munir; Sempowski, Gregory D; Elkins, Christopher; Leduc, Isabelle

2015-04-01

Haemophilus ducreyi is the causative agent of the sexually transmitted genital ulcer disease chancroid. Strains of H. ducreyi are grouped in two classes (I and II) based on genotypic and phenotypic differences, including those found in DsrA, an outer membrane protein belonging to the family of multifunctional trimeric autotransporter adhesins. DsrA is a key serum resistance factor of H. ducreyi that prevents binding of natural IgM at the bacterial surface and functions as an adhesin to fibronectin, fibrinogen, vitronectin, and human keratinocytes. Monoclonal antibodies (MAbs) were developed to recombinant DsrA (DsrA(I)) from prototypical class I strain 35000HP to define targets for vaccine and/or therapeutics. Two anti-DsrAI MAbs bound monomers and multimers of DsrA from genital and non-genital/cutaneous H. ducreyi strains in a Western blot and reacted to the surface of the genital strains; however, these MAbs did not recognize denatured or native DsrA from class II strains. In a modified extracellular matrix protein binding assay using viable H. ducreyi, one of the MAbs partially inhibited binding of fibronectin, fibrinogen, and vitronectin to class I H. ducreyi strain 35000HP, suggesting a role for anti-DsrA antibodies in preventing binding of H. ducreyi to extracellular matrix proteins. Standard ELISA and surface plasmon resonance using a peptide library representing full-length, mature DsrAI revealed the smallest nominal epitope bound by one of the MAbs to be MEQNTHNINKLS. Taken together, our findings suggest that this epitope is a potential target for an H. ducreyi vaccine.

Insight into the molecular mechanism of the sulfur oxidation process by reverse sulfite reductase (rSiR) from sulfur oxidizer Allochromatium vinosum.

PubMed

Ghosh, Semanti; Bagchi, Angshuman

2018-04-26

Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex. However, there are practically no reports to elucidate the molecular mechanism of the sulfur oxidation process by the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum. In the present context, we tried to analyze the structural details of the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum by molecular dynamics simulations. The molecular dynamics simulation results revealed the various types of molecular interactions between DsrA and DsrB proteins during the formation of DsrAB protein complex. We, for the first time, predicted the mode of binding interactions between the co-factor and DsrAB protein complex from Allochromatium vinosum. We also compared the binding interfaces of DsrAB from sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris. This study is the first to provide a comparative aspect of binding modes of sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris.

Peatland Acidobacteria with a dissimilatory sulfur metabolism.

PubMed

Hausmann, Bela; Pelikan, Claus; Herbold, Craig W; Köstlbacher, Stephan; Albertsen, Mads; Eichorst, Stephanie A; Glavina Del Rio, Tijana; Huemer, Martin; Nielsen, Per H; Rattei, Thomas; Stingl, Ulrich; Tringe, Susannah G; Trojan, Daniela; Wentrup, Cecilia; Woebken, Dagmar; Pester, Michael; Loy, Alexander

2018-02-23

Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.

The emergence of a temporally extended self and factors that contribute to its development: from theoretical and empirical perspectives.

PubMed

2013-04-01

The main aims of the current research were to determine when children develop a temporally extended self (TES) and what factors contribute to its development. However, in order to address these aims it was important to, first, assess whether the test of delayed self-recognition (DSR) is a valid measure for the development of the TES, and, second, to propose and evaluate a theoretical model that describes what factors influence the development of the TES. The validity of the DSR test was verified by comparing the performance of 57 children on the DSR test to their performance on a meta-representational task (modified false belief task) and to a task that was essentially the same as the DSR test but was specifically designed to rely on the capacity to entertain secondary representations (i.e., surprise body task). Longitudinal testing of the children showed that at the mental age (MA) of 2.5 years they failed the DSR test, despite training them to understand the intended functions of the medium used in the DSR test; whereas, with training, children at the MA of 3.0 and 3.5 years exhibited DSR. Children at the MA of 4 years exhibited DSR without any training. Finally, results suggest that children's meta-representational ability was the only factor that contributed to the prediction of successful performance on the DSR test, and thus to the emergence of the TES. Furthermore, prospective longitudinal data revealed that caregiver conversational style was the only factor that contributed to the prediction of level of training required to pass the DSR test. That is, children of low-elaborative caregivers required significantly more training to pass the DSR test than children of high-elaborative caregivers, indicating that children who received more elaborative conversational input from their caregivers had a more advanced understanding of their TES. © 2013 The Society for Research in Child Development, Inc.

The Haemophilus ducreyi trimeric autotransporter adhesin DsrA protects against an experimental infection in the swine model of chancroid.

PubMed

Fusco, William G; Choudhary, Neelima R; Routh, Patty A; Ventevogel, Melissa S; Smith, Valerie A; Koch, Gary G; Almond, Glen W; Orndorff, Paul E; Sempowski, Gregory D; Leduc, Isabelle

2014-06-24

Adherence of pathogens to cellular targets is required to initiate most infections. Defining strategies that interfere with adhesion is therefore important for the development of preventative measures against infectious diseases. As an adhesin to host extracellular matrix proteins and human keratinocytes, the trimeric autotransporter adhesin DsrA, a proven virulence factor of the Gram-negative bacterium Haemophilus ducreyi, is a potential target for vaccine development. A recombinant form of the N-terminal passenger domain of DsrA from H. ducreyi class I strain 35000HP, termed rNT-DsrAI, was tested as a vaccine immunogen in the experimental swine model of H. ducreyi infection. Viable homologous H. ducreyi was not recovered from any animal receiving four doses of rNT-DsrAI administered with Freund's adjuvant at two-week intervals. Control pigs receiving adjuvant only were all infected. All animals receiving the rNT-DsrAI vaccine developed antibody endpoint titers between 3.5 and 5 logs. All rNT-DsrAI antisera bound the surface of the two H. ducreyi strains used to challenge immunized pigs. Purified anti-rNT-DsrAI IgG partially blocked binding of fibrinogen at the surface of viable H. ducreyi. Overall, immunization with the passenger domain of the trimeric autotransporter adhesin DsrA accelerated clearance of H. ducreyi in experimental lesions, possibly by interfering with fibrinogen binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Targeted investment improves access to hospice and palliative care.

PubMed

Abernethy, Amy P; Bull, Janet; Whitten, Elizabeth; Shelby, Rebecca; Wheeler, Jane L; Taylor, Donald H

2013-11-01

Availability of hospice and palliative care is increasing, despite lack of a clear national strategy for developing and evaluating their penetration into and impact on the target population. To determine whether targeted investment (i.e., strategic grants made by one charitable foundation) in hospice and palliative care in one U.S. state (North Carolina [NC]) led to improved access to end-of-life care services as indicated by hospice utilization. Access was measured by the death service ratio (DSR), defined as the proportion of people who died and were served by hospice for at least one day before death. Calculation of the DSR is based on counts of patients accessing hospice by county in a given year (numerator) and U.S. Census projected population data for that county (denominator). Multilevel modeling was the primary analytic strategy used to generate two models: 1) comparison of the DSR in counties with vs. without philanthropic funding and 2) relationship between years since receipt of a philanthropic grant and DSR. In NC, the average DSR increased from 20.7% in 2003 to 35.8% in 2009 (55% increase). In 2009, 82 of 100 NC counties had a DSR below the U.S. average (41.6%). In Model 1, significant associations were found between county population and DSR (P=0.03) and between receipt of philanthropic funding and DSR (P=0.01); on average, funded counties had a DSR that was 2.63 percentage points higher than unfunded counties. Receipt of philanthropic funding appeared to be associated with improved access to palliative care and hospice services in NC. Copyright © 2013 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.

Reduction of produced elementary sulfur in denitrifying sulfide removal process.

PubMed

Zhou, Xu; Liu, Lihong; Chen, Chuan; Ren, Nanqi; Wang, Aijie; Lee, Duu-Jong

2011-05-01

Denitrifying sulfide removal (DSR) processes simultaneously convert sulfide, nitrate, and chemical oxygen demand from industrial wastewater into elemental sulfur, dinitrogen gas, and carbon dioxide, respectively. The failure of a DSR process is signaled by high concentrations of sulfide in reactor effluent. Conventionally, DSR reactor failure is blamed for overcompetition for heterotroph to autotroph communities. This study indicates that the elementary sulfur produced by oxidizing sulfide that is a recoverable resource from sulfide-laden wastewaters can be reduced back to sulfide by sulfur-reducing Methanobacterium sp. The Methanobacterium sp. was stimulated with excess organic carbon (acetate) when nitrite was completely consumed by heterotrophic denitrifiers. Adjusting hydraulic retention time of a DSR reactor when nitrite is completely consumed provides an additional control variable for maximizing DSR performance.

Elementary sulfur in effluent from denitrifying sulfide removal process as adsorbent for zinc(II).

PubMed

Chen, Chuan; Zhou, Xu; Wang, Aijie; Wu, Dong-hai; Liu, Li-hong; Ren, Nanqi; Lee, Duu-Jong

2012-10-01

The denitrifying sulfide removal (DSR) process can simultaneously convert sulfide, nitrate and organic compounds into elementary sulfur (S(0)), di-nitrogen gas and carbon dioxide, respectively. However, the S(0) formed in the DSR process are micro-sized colloids with negatively charged surface, making isolation of S(0) colloids from other biological cells and metabolites difficult. This study proposed the use of S(0) in DSR effluent as a novel adsorbent for zinc removal from wastewaters. Batch and continuous tests were conducted for efficient zinc removal with S(0)-containing DSR effluent. At pH<7.5, removal rates of zinc(II) were increased with increasing pH. The formed S(0) colloids carried negative charge onto which zinc(II) ions could be adsorbed via electrostatic interactions. The zinc(II) adsorbed S(0) colloids further enhanced coagulation-sedimentation efficiency of suspended solids in DSR effluents. The DSR effluent presents a promising coagulant for zinc(II) containing wastewaters. Copyright © 2012 Elsevier Ltd. All rights reserved.

MPH-M, AODV-M and DSR-M Performance Evaluation under Jamming Attacks.

PubMed

Del-Valle-Soto, Carolina; Mex-Perera, Carlos; Monroy, Raul; Nolazco-Flores, Juan A

2017-07-05

In this work, we present the design of a mitigation scheme for jamming attacks integrated to the routing protocols MPH, AODV, and DSR. The resulting protocols are named MPH-M (Multi-Parent Hierarchical - Modified), AODV-M (Ad hoc On Demand Distance Vector - Modified), and DSR-M (Dynamic Source Routing - Modified). For the mitigation algorithm, if the detection algorithm running locally in each node produces a positive result then the node is isolated; second, the routing protocol adapts their paths avoiding the isolated nodes. We evaluated how jamming attacks affect different metrics for all these modified protocols. The metrics we employ to detect jamming attack are number of packet retransmissions, number of CSMA/CA (Carrier Sense Multiple Access with Collision Avoidance) retries while waiting for an idle channel and the energy wasted by the node. The metrics to evaluate the performance of the modified routing protocols are the throughput and resilience of the system and the energy used by the nodes. We evaluated all the modified protocols when the attacker position was set near, middle and far of the collector node. The results of our evaluation show that performance for MPH-M is much better than AODV-M and DSR-M. For example, the node energy for MPH-M is 138.13% better than AODV-M and 126.07% better than DSR-M. Moreover, we also find that MPH-M benefits much more of the mitigation scheme than AODV-M and DSR-M. For example, the node energy consumption is 34.61% lower for MPH-M and only 3.92% and 3.42% for AODV-M and DSR-M, respectively. On throughput, the MPH protocol presents a packet reception efficiency at the collector node of 16.4% on to AODV and DSR when there is no mitigation mechanism. Moreover, MPH-M has an efficiency greater than 7.7% with respect to AODV-M and DSR-M when there is a mitigation scheme. In addition, we have that with the mitigation mechanism AODV-M and DSR-M do not present noticeable modification. However, MPH-M improves its efficiency by 8.4%. We also measure the resilience of these algorithms from the average packet re-transmissions perspective, and we find that MPH-M has around a 15% lower change rate than AODV-M and DSR-M. The MPH-M recovery time is 5 s faster than AODV-M and 2 s faster than DSR-M.

MPH-M, AODV-M and DSR-M Performance Evaluation under Jamming Attacks

PubMed Central

Del-Valle-Soto, Carolina

2017-01-01

In this work, we present the design of a mitigation scheme for jamming attacks integrated to the routing protocols MPH, AODV, and DSR. The resulting protocols are named MPH-M (Multi-Parent Hierarchical - Modified), AODV-M (Ad hoc On Demand Distance Vector - Modified), and DSR-M (Dynamic Source Routing - Modified). For the mitigation algorithm, if the detection algorithm running locally in each node produces a positive result then the node is isolated; second, the routing protocol adapts their paths avoiding the isolated nodes. We evaluated how jamming attacks affect different metrics for all these modified protocols. The metrics we employ to detect jamming attack are number of packet retransmissions, number of CSMA/CA (Carrier Sense Multiple Access with Collision Avoidance) retries while waiting for an idle channel and the energy wasted by the node. The metrics to evaluate the performance of the modified routing protocols are the throughput and resilience of the system and the energy used by the nodes. We evaluated all the modified protocols when the attacker position was set near, middle and far of the collector node. The results of our evaluation show that performance for MPH-M is much better than AODV-M and DSR-M. For example, the node energy for MPH-M is 138.13% better than AODV-M and 126.07% better than DSR-M. Moreover, we also find that MPH-M benefits much more of the mitigation scheme than AODV-M and DSR-M. For example, the node energy consumption is 34.61% lower for MPH-M and only 3.92% and 3.42% for AODV-M and DSR-M, respectively. On throughput, the MPH protocol presents a packet reception efficiency at the collector node of 16.4% on to AODV and DSR when there is no mitigation mechanism. Moreover, MPH-M has an efficiency greater than 7.7% with respect to AODV-M and DSR-M when there is a mitigation scheme. In addition, we have that with the mitigation mechanism AODV-M and DSR-M do not present noticeable modification. However, MPH-M improves its efficiency by 8.4%. We also measure the resilience of these algorithms from the average packet re-transmissions perspective, and we find that MPH-M has around a 15% lower change rate than AODV-M and DSR-M. The MPH-M recovery time is 5 s faster than AODV-M and 2 s faster than DSR-M. PMID:28678180

Reconstructing spatial organizations of chromosomes through manifold learning

PubMed Central

Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

2018-01-01

Abstract Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data. PMID:29408992

Reconstructing spatial organizations of chromosomes through manifold learning.

PubMed

Zhu, Guangxiang; Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

2018-05-04

Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data.

Combining Imaging and Non-Imaging Observations for Improved Space-Object Identification

DTIC Science & Technology

2011-09-27

Optical and Digital Superresolution Early in the project, we expolited Fisher information (FI) to characterize the extent of spatial-frequency...extrapolation beyond the diffraction-limited optical bandwidth when the support of the object is known a priori. This support-assisted optical superresolution ...both digital (DSR) and optical superresolution (OSR). Indeed, by analyzing a se- quence of sub-pixel-shifted undersampled images one can show the

Phase discrepancy induced from least squares wavefront reconstruction of wrapped phase measurements with high noise or large localized wavefront gradients

NASA Astrophysics Data System (ADS)

Steinbock, Michael J.; Hyde, Milo W.

2012-10-01

Adaptive optics is used in applications such as laser communication, remote sensing, and laser weapon systems to estimate and correct for atmospheric distortions of propagated light in real-time. Within an adaptive optics system, a reconstruction process interprets the raw wavefront sensor measurements and calculates an estimate for the unwrapped phase function to be sent through a control law and applied to a wavefront correction device. This research is focused on adaptive optics using a self-referencing interferometer wavefront sensor, which directly measures the wrapped wavefront phase. Therefore, its measurements must be reconstructed for use on a continuous facesheet deformable mirror. In testing and evaluating a novel class of branch-point- tolerant wavefront reconstructors based on the post-processing congruence operation technique, an increase in Strehl ratio compared to a traditional least squares reconstructor was noted even in non-scintillated fields. To investigate this further, this paper uses wave-optics simulations to eliminate many of the variables from a hardware adaptive optics system, so as to focus on the reconstruction techniques alone. The simulation results along with a discussion of the physical reasoning for this phenomenon are provided. For any applications using a self-referencing interferometer wavefront sensor with low signal levels or high localized wavefront gradients, understanding this phenomena is critical when applying a traditional least squares wavefront reconstructor.

DSR-98776, a novel selective mGlu5 receptor negative allosteric modulator with potent antidepressant and antimanic activity.

PubMed

Kato, Taro; Takata, Makoto; Kitaichi, Maiko; Kassai, Momoe; Inoue, Mitsuhiro; Ishikawa, Chihiro; Hirose, Wataru; Yoshida, Kozo; Shimizu, Isao

2015-06-15

Modulation of monoaminergic systems has been the main stream of treatment for patients with mood disorders. However, recent evidence suggests that the glutamatergic system plays an important role in the pathophysiology of these disorders. This study pharmacologically characterized a structurally novel metabotropic glutamate 5 (mGlu5) receptor negative allosteric modulator, DSR-98776, and evaluated its effect on rodent models of depression and mania. First, DSR-98776 in vitro profile was assessed using intracellular calcium and radioligand binding assays. This compound showed dose-dependent inhibitory activity for mGlu5 receptors by binding to the same allosteric site as 2-methyl-6-(phenylethynyl)-pyridine (MPEP), a known mGlu5 inhibitor. The in vivo therapeutic benefits of DSR-98776 were evaluated in common rodent models of depression and mania. In the rat forced swimming test, DSR-98776 (1-3mg/kg) significantly reduced rats immobility time after treatment for 7 consecutive days, while paroxetine (3 and 10mg/kg) required administration for 2 consecutive weeks to reduce rats immobility time. In the mouse forced swimming test, acute administration of DSR-98776 (10-30 mg/kg) significantly reduced immobility time. This effect was not influenced by 4-chloro-DL-phenylalanine methyl ester hydrochloride-induced 5-HT depletion. Finally, DSR-98776 (30 mg/kg) significantly decreased methamphetamine/chlordiazepoxide-induced hyperactivity in mice, which reflects this compound antimanic-like effect. These results indicate that DSR-98776 acts as an orally potent antidepressant and antimanic in rodent models and can be a promising therapeutic option for the treatment of a broad range of mood disorders with depressive and manic states. Copyright © 2015 Elsevier B.V. All rights reserved.

Functional consortium for denitrifying sulfide removal process.

PubMed

Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

2010-03-01

Denitrifying sulfide removal (DSR) process simultaneously converts sulfide, nitrate, and chemical oxygen demand from industrial wastewaters to elemental sulfur, nitrogen gas, and carbon dioxide, respectively. This investigation utilizes a dilution-to-extinction approach at 10(-2) to 10(-6) dilutions to elucidate the correlation between the composition of the microbial community and the DSR performance. In the original suspension and in 10(-2) dilution, the strains Stenotrophomonas sp., Thauera sp., and Azoarcus sp. are the heterotrophic denitrifiers and the strains Paracoccus sp. and Pseudomonas sp. are the sulfide-oxidizing denitrifers. The 10(-4) dilution is identified as the functional consortium for the present DSR system, which comprises two functional strains, Stenotrophomonas sp. strain Paracoccus sp. At 10(-6) dilution, all DSR performance was lost. The functions of the constituent cells in the DSR granules were discussed based on data obtained using the dilution-to-extinction approach.

Enhanced performance of denitrifying sulfide removal process at high carbon to nitrogen ratios under micro-aerobic condition.

PubMed

Chen, Chuan; Zhang, Ruo-Chen; Xu, Xi-Jun; Fang, Ning; Wang, Ai-Jie; Ren, Nan-Qi; Lee, Duu-Jong

2017-05-01

The success of denitrifying sulfide removal (DSR) processes, which simultaneously degrade sulfide, nitrate and organic carbon in the same reactor, counts on synergetic growths of autotrophic and heterotrophic denitrifiers. Feeding wastewaters at high C/N ratio would stimulate overgrowth of heterotrophic bacteria in the DSR reactor so deteriorating the growth of autotrophic denitrifiers. The DSR tests at C/N=1.26:1, 2:1 or 3:1 and S/N =5:6 or 5:8 under anaerobic (control) or micro-aerobic conditions were conducted. Anaerobic DSR process has <50% sulfide removal with no elemental sulfur transformation. Under micro-aerobic condition to remove <5% sulfide by chemical oxidation pathway, 100% sulfide removal is achieved by the DSR consortia. Continuous-flow tests under micro-aerobic condition have 70% sulfide removal and 55% elemental sulfur recovery. Trace oxygen enhances activity of sulfide-oxidizing, nitrate-reducing bacteria to accommodate properly the wastewater with high C/N ratios. Copyright © 2017 Elsevier Ltd. All rights reserved.

Domain Evolution and Functional Diversification of Sulfite Reductases

NASA Astrophysics Data System (ADS)

Dhillon, Ashita; Goswami, Sulip; Riley, Monica; Teske, Andreas; Sogin, Mitchell

2005-02-01

Sulfite reductases are key enzymes of assimilatory and dissimilatory sulfur metabolism, which occur in diverse bacterial and archaeal lineages. They share a highly conserved domain "C-X5-C-n-C-X3-C" for binding siroheme and iron-sulfur clusters that facilitate electron transfer to the substrate. For each sulfite reductase cluster, the siroheme-binding domain is positioned slightly differently at the N-terminus of dsrA and dsrB, while in the assimilatory proteins the siroheme domain is located at the C-terminus. Our sequence and phylogenetic analysis of the siroheme-binding domain shows that sulfite reductase sequences diverged from a common ancestor into four separate clusters (aSir, alSir, dsr, and asrC) that are biochemically distinct; each serves a different assimilatory or dissimilatory role in sulfur metabolism. The phylogenetic distribution and functional grouping in sulfite reductase clusters (dsrA and dsrB vs. aSiR, asrC, and alSir) suggest that their functional diversification during evolution may have preceded the bacterial/archaeal divergence.

Sharing behavioral data through a grid infrastructure using data standards

PubMed Central

Min, Hua; Ohira, Riki; Collins, Michael A; Bondy, Jessica; Avis, Nancy E; Tchuvatkina, Olga; Courtney, Paul K; Moser, Richard P; Shaikh, Abdul R; Hesse, Bradford W; Cooper, Mary; Reeves, Dianne; Lanese, Bob; Helba, Cindy; Miller, Suzanne M; Ross, Eric A

2014-01-01

Objective In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). Methods The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. Results UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. Conclusions Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data. PMID:24076749

Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin

NASA Technical Reports Server (NTRS)

Dhillon, Ashita; Teske, Andreas; Dillon, Jesse; Stahl, David A.; Sogin, Mitchell L.

2003-01-01

The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

Convolution- and Fourier-transform-based reconstructors for pyramid wavefront sensor.

PubMed

Shatokhina, Iuliia; Ramlau, Ronny

2017-08-01

In this paper, we present two novel algorithms for wavefront reconstruction from pyramid-type wavefront sensor data. An overview of the current state-of-the-art in the application of pyramid-type wavefront sensors shows that the novel algorithms can be applied in various scientific fields such as astronomy, ophthalmology, and microscopy. Assuming a computationally very challenging setting corresponding to the extreme adaptive optics (XAO) on the European Extremely Large Telescope, we present the results of the performed end-to-end simulations and compare the achieved AO correction quality (in terms of the long-exposure Strehl ratio) to other methods, such as matrix-vector multiplication and preprocessed cumulative reconstructor with domain decomposition. Also, we provide a comparison in terms of applicability and computational complexity and closed-loop performance of our novel algorithms to other methods existing for this type of sensor.

Evidence of Sr/Ca and Mg/Ca Temperature Invariance in Live Aragonitic Hoeglundina elegans Tests from the Little Bahama Bank

NASA Astrophysics Data System (ADS)

Blanks, J. K.; Hintz, C. J.; Chandler, G. T.; Shaw, T. J.; McCorkle, D. C.; Bernhard, J. M.

2007-12-01

Mg/Ca and Sr/Ca were analyzed from core-top individual Hoeglundina elegans aragonitic tests collected from three continental slope depths within the South Carolina and Little Bahama Bank continental slope environs (220 m to 1084 m). Our study utilized only individuals that labeled with the vital probe CellTracker Green - unlike bulk core-top material often stained with Rose Bengal, which has known inconsistencies in distinguishing live from dead foraminifera. DSr x 10 values were consistently 1.74 $ pm 0.23 across all sampling depths. The analytical error in DSr values (0.7%) determined by ICP-MS between repeated measurements on individual H. elegans tests across all depths was less than analytical error on repeated measurements from standards. Variation in DSr values was not directly explained by a linear temperature relationship (p=0.0003, R2=0.44) over the temperature range of 4.9-11.4°C with a sensitivity of 59.8 μmol/mol/1°C. The standard error by regressing DSr across temperature yields + 3.4°C, which is nearly 3x greater that reported in previous studies. Sr/Ca was more sensitive for calibrating temperature than Mg/Ca in H. elegans. Observed scatter in DSr was too great across individuals of the same size and of different sizes to resolve ontogenetic effects. However, higher DSr values were associated with smaller individuals and warmer/shallower sampling depths. The highest DSr values were observed at the intermediate sampling depth (~600 m). No significant ontogenetic relationship was found across DSr values in different sized individuals due to tighter overall constrained variance; however lower DSr values were observed from several smaller individuals. Several dead tests of H. elegans showed no significant differences in DSr values compared to live specimens cleaned by standard cleaning methods, unlike higher dead than live DMg values observed for the same individuals. There were no significant deviations in DSr across batches cleaned on separate days, unlike the observed sensitivity of DMg across batches. A subset of samples were reductively cleaned (hydrazine solution); and exhibited DMg values within analytical precision of those observed for non-reductively cleaned samples. Therefore, deviations in DMg values resulting from the removal of the reductive cleaning step did not explain analytical errors greater than published values for Mg/Ca or the high variance across same sized individuals. Variation in DMg values across the same cleaning methods and from dead individuals suggests the need for a careful look into how foraminiferal aragonite should be processed. These findings provide evidence that both Mg and Sr in benthic foraminiferal aragonite reflect factors in addition to temperature and pressure that may interfere with absolute temperature calibrations. Funded by NSF OCE 0351029, OCE 0437366, and OCE-0350794.

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

PubMed Central

Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

2014-01-01

Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere. PMID:24624126

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes.

PubMed

Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

2014-01-01

Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.

Sharing behavioral data through a grid infrastructure using data standards.

PubMed

Min, Hua; Ohira, Riki; Collins, Michael A; Bondy, Jessica; Avis, Nancy E; Tchuvatkina, Olga; Courtney, Paul K; Moser, Richard P; Shaikh, Abdul R; Hesse, Bradford W; Cooper, Mary; Reeves, Dianne; Lanese, Bob; Helba, Cindy; Miller, Suzanne M; Ross, Eric A

2014-01-01

In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Vector dissipative soliton resonance in a fiber laser.

PubMed

Luo, Zhi-Chao; Ning, Qiu-Yi; Mo, Hai-Lan; Cui, Hu; Liu, Jin; Wu, Li-Jun; Luo, Ai-Ping; Xu, Wen-Cheng

2013-04-22

We report on the vector nature of rectangular pulse operating in dissipative soliton resonance (DSR) region in a passively mode-locked fiber laser. Apart from the typical signatures of DSR, the rectangular pulse trapping of two polarization components centered at different wavelengths was observed and they propagated as a group-velocity locked vector soliton. Moreover, the polarization resolved soliton spectra show different spectral distributions. The observed results will enhance the understanding of fundamental physics of DSR phenomenon.

Multiparticle states in deformed special relativity

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

Hossenfelder, S.

2007-05-15

We investigate the properties of multiparticle states in deformed special relativity (DSR). Starting from the Lagrangian formalism with an energy dependent metric, the conserved Noether current can be derived which is additive in the usual way. The integrated Noether current had previously been discarded as a conserved quantity, because it was correctly realized that it does no longer obey the DSR transformations. We identify the reason for this mismatch in the fact that DSR depends only on the extensive quantity of total four momentum instead of the energy-momentum densities as would be appropriate for a field theory. We argue thatmore » the reason for the failure of DSR to reproduce the standard transformation behavior in the well established limits is due to the missing sensitivity to the volume inside which energy is accumulated. We show that the soccer-ball problem is absent if one formulates DSR instead for the field densities. As a consequence, estimates for predicted effects have to be corrected by many orders of magnitude. Further, we derive that the modified quantum field theory implies a locality bound.« less

Computer simulations and real-time control of ELT AO systems using graphical processing units

NASA Astrophysics Data System (ADS)

Wang, Lianqi; Ellerbroek, Brent

2012-07-01

The adaptive optics (AO) simulations at the Thirty Meter Telescope (TMT) have been carried out using the efficient, C based multi-threaded adaptive optics simulator (MAOS, http://github.com/lianqiw/maos). By porting time-critical parts of MAOS to graphical processing units (GPU) using NVIDIA CUDA technology, we achieved a 10 fold speed up for each GTX 580 GPU used compared to a modern quad core CPU. Each time step of full scale end to end simulation for the TMT narrow field infrared AO system (NFIRAOS) takes only 0.11 second in a desktop with two GTX 580s. We also demonstrate that the TMT minimum variance reconstructor can be assembled in matrix vector multiply (MVM) format in 8 seconds with 8 GTX 580 GPUs, meeting the TMT requirement for updating the reconstructor. Analysis show that it is also possible to apply the MVM using 8 GTX 580s within the required latency.

An ANN-Based Smart Tomographic Reconstructor in a Dynamic Environment

PubMed Central

de Cos Juez, Francisco J.; Lasheras, Fernando Sánchez; Roqueñí, Nieves; Osborn, James

2012-01-01

In astronomy, the light emitted by an object travels through the vacuum of space and then the turbulent atmosphere before arriving at a ground based telescope. By passing through the atmosphere a series of turbulent layers modify the light's wave-front in such a way that Adaptive Optics reconstruction techniques are needed to improve the image quality. A novel reconstruction technique based in Artificial Neural Networks (ANN) is proposed. The network is designed to use the local tilts of the wave-front measured by a Shack Hartmann Wave-front Sensor (SHWFS) as inputs and estimate the turbulence in terms of Zernike coefficients. The ANN used is a Multi-Layer Perceptron (MLP) trained with simulated data with one turbulent layer changing in altitude. The reconstructor was tested using three different atmospheric profiles and compared with two existing reconstruction techniques: Least Squares type Matrix Vector Multiplication (LS) and Learn and Apply (L + A). PMID:23012524

How to introduce demand side resources in the design of low-carbon power systems in China

NASA Astrophysics Data System (ADS)

Zhou, Pengcheng; Liu, Yiqun; Zeng, Ming; Sun, Chenjun

2018-04-01

Nowadays, China's energy demand sustained rapid growth, and the coal-based energy structure has adverse effects on the environment. The flexibility of demand side resource (DSR) will be greatly improved, and DSR can reduce electricity consumption actively and temporarily, and realize energy saving and emission reduction. But there are still some problems to introduce DSR in China. This paper proposes three practices for introducing demand side resources to improve the flexibility of power systems through demand resources.

Sulfur Isotope Effects of Dissimilatory Sulfite Reductase

PubMed Central

Leavitt, William D.; Bradley, Alexander S.; Santos, André A.; Pereira, Inês A. C.; Johnston, David T.

2015-01-01

The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/32S, 36S/32S) sulfur isotope fractionations imparted by a central enzyme in the energy metabolism of sulfate reducers, dissimilatory sulfite reductase (DsrAB). Results from in vitro sulfite reduction experiments allow us to calculate the in vitro DsrAB isotope effect in 34S/32S (hereafter, 34εDsrAB) to be 15.3 ± 2‰, 2σ. The accompanying minor isotope effect in 33S, described as 33λDsrAB, is calculated to be 0.5150 ± 0.0012, 2σ. These observations facilitate a rigorous evaluation of the isotopic fractionation associated with the dissimilatory MSR pathway, as well as of the environmental variables that govern the overall magnitude of fractionation by natural communities of sulfate reducers. The isotope effect induced by DsrAB upon sulfite reduction is a factor of 0.3–0.6 times prior indirect estimates, which have ranged from 25 to 53‰ in 34εDsrAB. The minor isotope fractionation observed from DsrAB is consistent with a kinetic or equilibrium effect. Our in vitro constraints on the magnitude of 34εDsrAB is similar to the median value of experimental observations compiled from all known published work, where 34εr−p = 16.1‰ (r–p indicates reactant vs. product, n = 648). This value closely matches those of MSR operating at high sulfate reduction rates in both laboratory chemostat experiments (34εSO4−H2S =  17.3 ± 1.5‰, 2σ) and in modern marine sediments (34εSO4−H2S =  17.3 ± 3.8‰). Targeting the direct isotopic consequences of a specific enzymatic processes is a fundamental step toward a biochemical foundation for reinterpreting the biogeochemical and geobiological sulfur isotope records in modern and ancient environments. PMID:26733949

Identifying and Addressing Stakeholder Interests in Design Science Research: An Analysis Using Critical Systems Heuristics

NASA Astrophysics Data System (ADS)

Venable, John R.

This paper utilises the Critical Systems Heuristics (CSH) framework developed by Werner Ulrich to critically consider the stakeholders and design goals that should be considered as relevant by researchers conducing Design Science Research (DSR). CSH provides a philosophically and theoretically grounded framework and means for critical consideration of the choices of stakeholders considered to be relevant to any system under design consideration. The paper recommends that legitimately undertaken DSR should include witnesses to represent the interests of the future consumers of the outcomes of DSR, i.e., the future clients, decision makers, professionals, and other non-included stakeholders in the future use of the solution technologies to be invented in DSR. The paper further discusses options for how witnesses might be included, who should be witnessed for and obstacles to implementing the recommendations.

Neutron spectrometry - An essential tool for diagnosing implosions at the National Ignition Facility

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

Mackinnon, A J; Johnson, M G; Frenje, J A

DT neutron yield (Y{sub n}), ion temperature (T{sub i}) and down-scatter ratio (dsr) determined from measured neutron spectra are essential metrics for diagnosing the performance of Inertial Confinement Fusion (ICF) implosions at the National Ignition Facility (NIF). A suite of neutron-Time-Of-Flight (nTOF) spectrometers and a Magnetic Recoil Spectrometer (MRS) have been implemented in different locations around the NIF target chamber, providing good implosion coverage and the redundancy required for reliable measurements of Yn, Ti and dsr. From the measured dsr value, an areal density ({rho}R) is determined from the relationship {rho}R{sub tot} (g/cm{sup 2}) = (20.4 {+-} 0.6) x dsr{submore » 10-12 MeV}. The proportionality constant is determined considering implosion geometry, neutron attenuation and energy range used for the dsr measurement. To ensure high accuracy in the measurements, a series of commissioning experiments using exploding pushers have been used for in situ calibration. The spectrometers are now performing to the required accuracy, as indicated by the good agreement between the different measurements over several commissioning shots. In addition, recent data obtained with the MRS and nTOFs indicate that the implosion performance of cryogenically layered DT implosions, characterized by the experimental Ignition Threshold Factor (ITFx) which is a function of dsr (or fuel {rho}R) and Y{sub n}, has improved almost two orders of magnitude since the first shot in September, 2010.« less

Neutron spectrometry-An essential tool for diagnosing implosions at the National Ignition Facility (invited)

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

Johnson, M. Gatu; Frenje, J. A.; Casey, D. T.

2012-10-15

DT neutron yield (Y{sub n}), ion temperature (T{sub i}), and down-scatter ratio (dsr) determined from measured neutron spectra are essential metrics for diagnosing the performance of inertial confinement fusion (ICF) implosions at the National Ignition Facility (NIF). A suite of neutron-time-of-flight (nTOF) spectrometers and a magnetic recoil spectrometer (MRS) have been implemented in different locations around the NIF target chamber, providing good implosion coverage and the complementarity required for reliable measurements of Y{sub n}, T{sub i}, and dsr. From the measured dsr value, an areal density ({rho}R) is determined through the relationship {rho}R{sub tot} (g/cm{sup 2}) = (20.4 {+-} 0.6)more » Multiplication-Sign dsr{sub 10-12MeV}. The proportionality constant is determined considering implosion geometry, neutron attenuation, and energy range used for the dsr measurement. To ensure high accuracy in the measurements, a series of commissioning experiments using exploding pushers have been used for in situ calibration of the as-built spectrometers, which are now performing to the required accuracy. Recent data obtained with the MRS and nTOFs indicate that the implosion performance of cryogenically layered DT implosions, characterized by the experimental ignition threshold factor (ITFx), which is a function of dsr (or fuel {rho}R) and Y{sub n}, has improved almost two orders of magnitude since the first shot in September, 2010.« less

Transfer of function and prior derived-relations testing.

PubMed

Doughty, Adam H; Best, Lauren

2017-10-01

This experiment assessed transfer of function through equivalence relations with and without prior derived-stimulus-relations (DSR) testing. In a DSR-Testing Group, eight college students learned A-B and A-C discriminations in baseline. They then derived the B-C and C-B equivalence relations before being exposed to a transfer-of-function manipulation and test. Eight participants in a No-DSR Testing Group were exposed to the transfer-of-function manipulation and test immediately after learning the baseline discriminations (i.e., B-C and C-B testing were omitted). In the transfer-of-function manipulation, participants learned to respond differently in the presence of B1 and B2 to avoid money loss. In the transfer-of-function test, responding in the presence of C1 and C2 was measured in the absence of differential consequences. Transfer of function occurred reliably only in the DSR-Testing Group (i.e., participants responding to C1 and C2 in the manner they learned to respond to B1 and B2, respectively). These findings support the notion that prior DSR testing can be critical to observing transfer of function. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of the left ventricular shape and motion with a limited number of slices

NASA Astrophysics Data System (ADS)

Robert, Anne; Schmitt, Francis J. M.; Mousseaux, Elie

1996-04-01

In this paper, we describe a method for the reconstruction of the surface of the left ventricle from a set of lacunary data (that is an incomplete, unevenly sampled and unstructured data set). Global models, because they compress the properties of a surface into a small set of parameters, have a strong regularizing power and are therefore very well suited to lacunary data. Globally deformable superquadrics are particularly attractive, because of their simplicity. This model can be fitted to the data using the Levenberg-Marquardt algorithm for non-linear optimization. However, the difficulties we experienced to get temporally consistent solutions as well as the intrinsic 4D character of the data led us to generalize the classical 3D superquadric model to 4D. We present results on a 4D sequence from the Dynamic Spatial Reconstructor of the Mayo Clinic, and on a 4D IRM sequence.

Trimeric autotransporter DsrA is a major mediator of fibrinogen binding in Haemophilus ducreyi.

PubMed

Fusco, William G; Elkins, Christopher; Leduc, Isabelle

2013-12-01

Haemophilus ducreyi is the etiologic agent of the sexually transmitted genital ulcer disease chancroid. In both natural and experimental chancroid, H. ducreyi colocalizes with fibrin at the base of the ulcer. Fibrin is obtained by cleavage of the serum glycoprotein fibrinogen (Fg) by thrombin to initiate formation of the blood clot. Fg binding proteins are critical virulence factors in medically important Gram-positive bacteria. H. ducreyi has previously been shown to bind Fg in an agglutination assay, and the H. ducreyi Fg binding protein FgbA was identified in ligand blotting with denatured proteins. To better characterize the interaction of H. ducreyi with Fg, we examined Fg binding to intact, viable H. ducreyi bacteria and identified a novel Fg binding protein. H. ducreyi bound unlabeled Fg in a dose-dependent manner, as measured by two different methods. In ligand blotting with total denatured cellular proteins, digoxigenin (DIG)-Fg bound only two H. ducreyi proteins, the trimeric autotransporter DsrA and the lectin DltA; however, only the isogenic dsrA mutant had significantly less cell-associated Fg than parental strains in Fg binding assays with intact bacteria. Furthermore, expression of DsrA, but not DltA or an empty vector, rendered the non-Fg-binding H. influenzae strain Rd capable of binding Fg. A 13-amino-acid sequence in the C-terminal section of the passenger domain of DsrA appears to be involved in Fg binding by H. ducreyi. Taken together, these data suggest that the trimeric autotransporter DsrA is a major determinant of Fg binding at the surface of H. ducreyi.

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.

PubMed

Yu, Hao; Chen, Chuan; Ma, Jincai; Liu, Wenzong; Zhou, Jizhong; Lee, Duu-Jong; Ren, Nanqi; Wang, Aijie

2014-07-01

The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process. Copyright © 2014. Published by Elsevier B.V.

Functional analysis of truncated and site-directed mutagenesis dextransucrases to produce different type dextrans.

PubMed

Wang, Chao; Zhang, Hong-Bin; Li, Meng-Qi; Hu, Xue-Qin; Li, Yao

2017-07-01

Dextrans with distinct molecular size and structure are increasingly being used in the food and pharmaceutical industries. Dextran is produced by dextransucrase (DSR, EC2.4.5.1), which is produced by Leuconostoc mesenteroides. DSR belongs to glycosyl hydrolase family (GH70) and synthesizes branched α-glucan (dextran) with both 5% α(1-3) and 95% α(1-6) glycosidic linkages. The DSR gene dex-YG (Genebank, Accession No. DQ345760) was cloned from the wild strain Leuconostoc mesenteroides 0326. This study generated a series of C-terminally truncated variants of dextransucrase and substituting the amino-acid residues in the active site of DSR. With shorter length of DSR, its polysaccharide-synthesizing capability was impaired heavily, whereas oligosaccharide (acting as prebiotics)-synthesizing capability increased significantly, efficiently producing special sizes of dextran. All truncated mutant enzymes were active. Results demonstrated that the catalytic domain dextransucrase was likely in 800 aa or less. Based on the three-dimensional structure model of dextransucrase built through homology modeling methods, the DSR and its mutants with the acceptor substrate of maltose and donor substrate of sucrose were studied by molecular-docking method. Substituting these amino-acid residues significantly affected enzyme activities. Compared with the wild-type dextran, mutant enzymes catalyzed the synthesis of a-glucan with 1-9% α(1-3) and 90-98% α(1-6) branching linkages. Some mutants introduced a small amount of α(1-4) linkages and α(1-2) linkages. This strategy can be effectively used for the rational protein design of dextransucrase. Copyright © 2017 Elsevier Inc. All rights reserved.

Detector, collimator and real-time reconstructor for a new scanning-beam digital x-ray (SBDX) prototype.

PubMed

Speidel, Michael A; Tomkowiak, Michael T; Raval, Amish N; Dunkerley, David A P; Slagowski, Jordan M; Kahn, Paul; Ku, Jamie; Funk, Tobias

Scanning-beam digital x-ray (SBDX) is an inverse geometry fluoroscopy system for low dose cardiac imaging. The use of a narrow scanned x-ray beam in SBDX reduces detected x-ray scatter and improves dose efficiency, however the tight beam collimation also limits the maximum achievable x-ray fluence. To increase the fluence available for imaging, we have constructed a new SBDX prototype with a wider x-ray beam, larger-area detector, and new real-time image reconstructor. Imaging is performed with a scanning source that generates 40,328 narrow overlapping projections from 71 × 71 focal spot positions for every 1/15 s scan period. A high speed 2-mm thick CdTe photon counting detector was constructed with 320×160 elements and 10.6 cm × 5.3 cm area (full readout every 1.28 μs), providing an 86% increase in area over the previous SBDX prototype. A matching multihole collimator was fabricated from layers of tungsten, brass, and lead, and a multi-GPU reconstructor was assembled to reconstruct the stream of captured detector images into full field-of-view images in real time. Thirty-two tomosynthetic planes spaced by 5 mm plus a multiplane composite image are produced for each scan frame. Noise equivalent quanta on the new SBDX prototype measured 63%-71% higher than the previous prototype. X-ray scatter fraction was 3.9-7.8% when imaging 23.3-32.6 cm acrylic phantoms, versus 2.3-4.2% with the previous prototype. Coronary angiographic imaging at 15 frame/s was successfully performed on the new SBDX prototype, with live display of either a multiplane composite or single plane image.

Quantitative three-dimensional dynamic imaging of structure and function of the cardiopulmonary and circulatory systems in all regions of the body

NASA Technical Reports Server (NTRS)

Sturm, R. E.; Ritman, E. L.; Wood, E. H.

1975-01-01

The background for, and design of a third generation, general purpose, all electronic spatial scanning system, the DSR is described. Its specified performance capabilities provide dynamic and stop action three dimensional spatial reconstructions of any portion of the body based on a minimum exposure time of 0.01 second for each 28 multiplanar 180 deg scanning set, a maximum scan repetition rate of sixty 28 multiplane scan sets per second, each scan set consisting of a maximum of 240 parallel cross sections of a minimum thickness of 0.9 mm, and encompassing a maximum cylindrical volume about 23 cm in length and up to 38 cm in diameter.

Trimeric Autotransporter DsrA Is a Major Mediator of Fibrinogen Binding in Haemophilus ducreyi

PubMed Central

Fusco, William G.; Elkins, Christopher

2013-01-01

Haemophilus ducreyi is the etiologic agent of the sexually transmitted genital ulcer disease chancroid. In both natural and experimental chancroid, H. ducreyi colocalizes with fibrin at the base of the ulcer. Fibrin is obtained by cleavage of the serum glycoprotein fibrinogen (Fg) by thrombin to initiate formation of the blood clot. Fg binding proteins are critical virulence factors in medically important Gram-positive bacteria. H. ducreyi has previously been shown to bind Fg in an agglutination assay, and the H. ducreyi Fg binding protein FgbA was identified in ligand blotting with denatured proteins. To better characterize the interaction of H. ducreyi with Fg, we examined Fg binding to intact, viable H. ducreyi bacteria and identified a novel Fg binding protein. H. ducreyi bound unlabeled Fg in a dose-dependent manner, as measured by two different methods. In ligand blotting with total denatured cellular proteins, digoxigenin (DIG)-Fg bound only two H. ducreyi proteins, the trimeric autotransporter DsrA and the lectin DltA; however, only the isogenic dsrA mutant had significantly less cell-associated Fg than parental strains in Fg binding assays with intact bacteria. Furthermore, expression of DsrA, but not DltA or an empty vector, rendered the non-Fg-binding H. influenzae strain Rd capable of binding Fg. A 13-amino-acid sequence in the C-terminal section of the passenger domain of DsrA appears to be involved in Fg binding by H. ducreyi. Taken together, these data suggest that the trimeric autotransporter DsrA is a major determinant of Fg binding at the surface of H. ducreyi. PMID:24042118

Dextransucrase Expression Is Concomitant with that of Replication and Maintenance Functions of the pMN1 Plasmid in Lactobacillus sakei MN1

PubMed Central

Nácher-Vázquez, Montserrat; Ruiz-Masó, José A.; Mohedano, María L.; del Solar, Gloria; Aznar, Rosa; López, Paloma

2017-01-01

The exopolysaccharide synthesized by Lactobacillus sakei MN1 is a dextran with antiviral and immunomodulatory properties of potential utility in aquaculture. In this work we have investigated the genetic basis of dextran production by this bacterium. Southern blot hybridization experiments demonstrated the plasmidic location of the dsrLS gene, which encodes the dextransucrase involved in dextran synthesis. DNA sequencing of the 11,126 kbp plasmid (pMN1) revealed that it belongs to a family which replicates by the theta mechanism, whose prototype is pUCL287. The plasmid comprises the origin of replication, repA, repB, and dsrLS genes, as well as seven open reading frames of uncharacterized function. Lb. sakei MN1 produces dextran when sucrose, but not glucose, is present in the growth medium. Therefore, plasmid copy number and stability, as well as dsrLS expression, were investigated in cultures grown in the presence of either sucrose or glucose. The results revealed that pMN1 is a stable low-copy-number plasmid in both conditions. Gene expression studies showed that dsrLS is constitutively expressed, irrespective of the carbon source present in the medium. Moreover, dsrLS is expressed from a monocistronic transcript as well as from a polycistronic repA-repB-orf1-dsrLS mRNA. To our knowledge, this is the first report of a plasmid-borne dextransucrase-encoding gene, as well as the first time that co-transcription of genes involved in plasmid maintenance and replication with a gene encoding an enzyme has been established. PMID:29209293

Psychological factors associated with delayed symptom resolution in children with concussion

PubMed Central

Grubenhoff, Joseph A.; Currie, Dustin; Comstock, R. Dawn; Juarez-Colunga, Elizabeth; Bajaj, Lalit; Kirkwood, Michael W.

2016-01-01

Objective To characterize t h e psychological factors associated with persistent symptoms following pediatric concussion. Study design Longitudinal cohort study of 179 concussed children 8–18 years old evaluated in a pediatric emergency department. Participants were followed for one month for delayed symptom resolution defined as ≥3 symptoms that were new/worse than pre-injury symptoms measured using graded symptom inventory. Pre-injury psychological traits were measured by parental report on subscales of the Personality Inventory for Children-2 (maladjustment, cognitive abilities, somatization). Child report of post-injury anxiety and injury perception were measured using State-Trait Anxiety Inventory for Children (STAIC) and Children’s Illness Perception Questionnaire. Psychological instrument scores were compared between those with and without DSR using a Kruskal-Wallis test. Associations between psychological traits and DSR were investigated using logistic regression. Results DSR occurred in 21% of participants. Score distributions were significantly worse on the STAIC [38 (IQR 33–40) vs 35 (IQR 31–39); p=0.04] and somatization subscale [1 (IQR 0–3) vs 1 (IQR 0–1); p=0.01] among children with DSR compared with children with early symptom resolution (ESR). Somatization was associated with DSR [adjusted odds ratio (OR) 1.35, 95% CI: 1.08– 1.69]. The proportion of children with abnormal somatization scores was significantly higher in the DSR group (34.2%) than the ESR group (12.8%; p<0.01). Other psychological measures were not different between groups. Conclusion Somatization is associated with delayed symptom resolution in this cohort of concussed children. Post-concussive symptoms lasting at least one month may warrant referral to a neuropsychologist familiar with post-concussion care. PMID:27079963

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

PubMed Central

Cooper, Myriel; Schreiber, Lars; Lloyd, Karen G.; Baker, Brett J.; Petersen, Dorthe G.; Jørgensen, Bo Barker; Stepanauskas, Ramunas; Reinhardt, Richard; Schramm, Andreas; Loy, Alexander; Adrian, Lorenz

2016-01-01

ABSTRACT The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH. PMID:27143384

Characterization and compression of dissipative-soliton-resonance pulses in fiber lasers

PubMed Central

Li, Daojing; Li, Lei; Zhou, Junyu; Zhao, Luming; Tang, Dingyuan; Shen, Deyuan

2016-01-01

We report numerical and experimental studies of dissipative-soliton-resonance (DSR) in a fiber laser with a nonlinear optical loop mirror. The DSR pulse presents temporally a flat-top profile and a clamped peak power. Its spectrum has a rectangle profile with characteristic steep edges. It shows a unique behavior as pulse energy increases: The rectangle part of the spectrum is unchanged while the newly emerging spectrum sits on the center part and forms a peak. Experimental observations match well with the numerical results. Moreover, the detailed evolution of the DSR pulse compression is both numerically and experimentally demonstrated for the first time. An experimentally obtained DSR pulse of 63 ps duration is compressed down to 760 fs, with low-intensity pedestals using a grating pair. Before being compressed to its narrowest width, the pulse firstly evolves into a cat-ear profile, and the corresponding autocorrelation trace shows a crown shape, which distinguishes itself from properties of other solitons formed in fiber lasers. PMID:27025189

The Chinese version of story recall: a useful screening tool for mild cognitive impairment and Alzheimer's disease in the elderly.

PubMed

Shi, Jing; Wei, Mingqing; Tian, Jinzhou; Snowden, Julie; Zhang, Xuekai; Ni, Jingnian; Li, Ting; Jian, Wenjia; Ma, Congcong; Tong, Yanping; Liu, Jianping; Liu, Tonghua; Wang, Pengwen; Wang, Yongyan

2014-03-10

Decline in verbal episodic memory is a core feature of amnestic mild cognitive impairment (aMCI). The delayed story recall (DSR) test from the Adult Memory and Information Processing Battery (AMIPB) discriminates MCI from normal aging and predicts its conversion to Alzheimer's dementia. However, there is no study that validates the Chinese version of the DSR and reports cut-off scores in the Chinese population. A total of 631 subjects were screened in the memory clinics of Dongzhimen Hospital, Beijing University of Chinese Medicine, China. 249 were considered to have normal cognition (NC), 134 met diagnostic criteria for MCI according to the MCI Working Group of the European Consortium on Alzheimer's Disease, and 97 met criteria for probable Alzheimer's disease (AD) according to the NINCDS/ADRDA criteria, 14 exhibited vascular dementia (VaD), and 50 had a diagnosis of another type of dementia. Receiver operating characteristic (ROC) curve analyses were used to calculate the story recall cutoff score for detecting MCI and AD. Normative data in the NC group were obtained as a function of age and education. In this Chinese sample, the normative mean DSR score was 28.10 ± 8.54 in the 50-64 year-old group, 26.22 ± 8.38 in the 65-74 year-old group, and 24.42 ± 8.38 in the 75-85 year-old group. DSR performance was influenced by age and education. The DSR test had high sensitivity (0.899) and specificity (0.799) in the detection of MCI from NC using a cut-off score of 15.5. When the cutoff score was 10.5, the DSR test obtained optimal sensitivity (0.980) and specificity (0.938) in the discrimination of AD from NC. Cutoff scores and diagnostic values were calculated stratified by age and education. The Chinese version of the DSR can be used as a screening tool to detect MCI and AD with high sensitivity and specificity, and it could be used to identify people at high risk of cognitive impairment.

Effects of an extended flexible regimen of an oral contraceptive pill containing 20 μg ethinylestradiol and 3 mg drospirenone on menstrual-related symptoms: a randomised controlled trial.

PubMed

Machado, Rogério Bonassi; Pompei, Luciano Melo; Badalotti, Mariangela; Ferriani, Rui; Cruz, Achilles M; Nahas, Eliana; Maia, Hugo

2017-02-01

The aim of the study was to assess the efficacy for menstrual-related symptoms of an extended flexible regimen of an oral contraceptive pill containing 20 μg ethinylestradiol and 3 mg drospirenone in comparison with a 24/4 d cyclical regimen of the same formulation. This randomised, non-inferiority, open-label, multicentre study was conducted in women aged 18-39 years. Their menstrual-related symptoms were assessed using the Penn Daily Symptom Rating (DSR17). Participants were randomised to use an extended flexible regimen of 20 μg ethinylestradiol and 3 mg drospirenone (EE/DRSP e.flex ), comprising 168 consecutive days with a 4-d hormone-free interval (HFI, allowing for management of unexpected bleeding) or a conventional 24/4 cyclical regimen of the same pill (EE/DRSP 24/4 ). The primary measure of efficacy was the percentage change in DSR17 total score from baseline to cycle 6. The secondary measures of efficacy were the percentage changes in DSR17 total score from baseline after each 28-d interval throughout the entire study and in the scores for individual DSR17 symptoms. The primary analysis demonstrated that EE/DRSP e.flex was not inferior to EE/DRSP 24/4 (Mean DSR17 score 9.1; 95% confidence interval (CI) - 2.5, 20.6; p = 0.123). Analysis at intervals throughout the entire evaluation period showed greater reduction in DSR17 total score for EE/DRSP e.flex than for the 24/4 regimen (p < 0.001). The decreases in individual scores for the symptoms 'poor coordination' and 'depression/feeling sad/down or blue' were greater for the extended flexible regimen than for the cyclical regimen (p < 0.05). The extended flexible regimen was not inferior to the 24/4 cyclical regimen in terms of the primary endpoint. It significantly improved symptoms in the interval analysis, and the effects on specific DSR17 symptoms, compared with the cyclical regimen.

Procuring load curtailment from local customers under uncertainty.

PubMed

Mijatović, Aleksandar; Moriarty, John; Vogrinc, Jure

2017-08-13

Demand side response (DSR) provides a flexible approach to managing constrained power network assets. This is valuable if future asset utilization is uncertain. However there may be uncertainty over the process of procurement of DSR from customers. In this context we combine probabilistic modelling, simulation and optimization to identify economically optimal procurement policies from heterogeneous customers local to the asset, under chance constraints on the adequacy of the procured DSR. Mathematically this gives rise to a search over permutations, and we provide an illustrative example implementation and case study.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'. © 2017 The Author(s).

Enhanced performance of denitrifying sulfide removal process under micro-aerobic condition.

PubMed

Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

2010-07-15

The denitrifying sulfide removal (DSR) process with bio-granules comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide and acetate into di-nitrogen gas, elementary sulfur and carbon dioxide, respectively, at high loading rates. This study determines the reaction rate of sulfide oxidized into sulfur, as well as the reduction of nitrate to nitrite, would be enhanced under a micro-aerobic condition. The presence of limited oxygen mitigated the inhibition effects of sulfide on denitrifier activities, and enhanced the performance of DSR granules. The advantages and disadvantages of applying the micro-aerobic condition to the DSR process are discussed. 2010 Elsevier B.V. All rights reserved.

Intrusion Detection for Defense at the MAC and Routing Layers of Wireless Networks

DTIC Science & Technology

2007-01-01

Space DoS Denial of Service DSR Dynamic Source Routing IDS Intrusion Detection System LAR Location-Aided Routing MAC Media Access Control MACA Multiple...different mobility parameters. 10 They simulate interaction between three MAC protocols ( MACA , 802.11 and CSMA) and three routing protocols (AODV, DSR

Secreted expression of Leuconostoc mesenteroides glucansucrase in Lactococcus lactis for the production of insoluble glucans

USDA-ARS?s Scientific Manuscript database

We expressed a glucansucrase, DsrI, from Leuconostoc mesenteroides that catalyzes formation of water-insoluble glucans from sucrose in Lactococcus lactis using a nisin-controlled gene expression system. Production of DsrI was optimized using several different background vectors, signal peptides, str...

Enhanced Weight based DSR for Mobile Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Verma, Samant; Jain, Sweta

2011-12-01

Routing in ad hoc network is a great problematic, since a good routing protocol must ensure fast and efficient packet forwarding, which isn't evident in ad hoc networks. In literature there exists lot of routing protocols however they don't include all the aspects of ad hoc networks as mobility, device and medium constraints which make these protocols not efficient for some configuration and categories of ad hoc networks. Thus in this paper we propose an improvement of Weight Based DSR in order to include some of the aspects of ad hoc networks as stability, remaining battery power, load and trust factor and proposing a new approach Enhanced Weight Based DSR.

Denitrifying sulfide removal process on high-salinity wastewaters.

PubMed

Liu, Chunshuang; Zhao, Chaocheng; Wang, Aijie; Guo, Yadong; Lee, Duu-Jong

2015-08-01

Denitrifying sulfide removal (DSR) process comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide, and acetate into nitrogen gas, elemental sulfur (S(0)), and carbon dioxide, respectively. Sulfide- and nitrate-laden wastewaters at 2-35 g/L NaCl were treated by DSR process. A C/N ratio of 3:1 was proposed to maintain high S(0) conversion rate. The granular sludge with a compact structure and smooth outer surface was formed. The microbial communities of DSR consortium via high-throughput sequencing method suggested that salinity shifts the predominating heterotrophic denitrifiers at <10 g/L NaCl to autotrophic denitrifiers at >10 g/L NaCl.

Delayed Video Self-Recognition in Children with High Vo Functioning Autism and Asperger's Disorder

ERIC Educational Resources Information Center

Dissanayake, Cheryl; Shembrey, Joh; Suddendorf, Thomas

2010-01-01

Two studies are reported which investigate delayed video self-recognition (DSR) in children with autistic disorder and Asperger's disorder relative to one another and to their typically developing peers. A secondary aim was to establish whether DSR ability is dependent on metarepresentational ability. Children's verbal and affective responses to…

2 µm high-power dissipative soliton resonance in a compact σ-shaped Tm-doped double-clad fiber laser

NASA Astrophysics Data System (ADS)

Du, Tuanjie; Li, Weiwei; Ruan, Qiujun; Wang, Kaijie; Chen, Nan; Luo, Zhengqian

2018-05-01

We report direct generation of a high-power, large-energy dissipative soliton resonance (DSR) in a 2 µm Tm-doped double-clad fiber laser. A compact σ-shaped cavity is formed by a fiber Bragg grating and a 10/90 fiber loop mirror (FLM). The 10/90 FLM is not only used as an output mirror, but also acts as a nonlinear optical loop mirror for initiating mode locking. The mode-locked laser can deliver high-power, nanosecond DSR pulses at 2005.9 nm. We further perform a comparison study of the effect of the FLM’s loop length on the mode-locking threshold, peak power, pulse energy, and optical spectrum of the DSR pulses. We achieve a maximum average output power as high as 1.4 W, a maximum pulse energy of 353 nJ, and a maximum peak power of 84 W. This is, to the best of our knowledge, the highest power for 2 µm DSR pulses obtained in a mode-locked fiber laser.

Semi-arid grassland bird responses to patch-burn grazing and drought

USGS Publications Warehouse

Skagen, Susan K.; Augustine, David J.; Derner, Justin D.

2018-01-01

As grassland birds of central North America experience steep population declines with changes in land use, management of remaining tracts becomes increasingly important for population viability. The integrated use of fire and grazing may enhance vegetation heterogeneity and diversity in breeding birds, but the subsequent effects on reproduction are unknown. We examined the influence of patch-burn grazing management in shortgrass steppe in eastern Colorado on habitat use and reproductive success of 3 grassland bird species, horned lark (Eremophila alpestris), lark bunting (Calamospiza melanocorys), and McCown’s longspur (Rhynchophanes mccownii), at several spatial scales during 2011 and 2012. Although no simple direct relationship to patch-burn grazing treatment existed, habitat selection depended on precipitation- and management-induced vegetation conditions and spatial scale. All species selected taller-than-expected vegetation at the nest site, whereas at the territory scale, horned larks and McCown’s longspurs selected areas with low vegetation height and sparse cover of tall plants (taller than the dominant shortgrasses). Buntings nested primarily in unburned grassland under average rainfall. Larks and longspurs shifted activity from patch burns during average precipitation (2011) to unburned pastures during drought (2012). Daily survival rate (DSR) of nests varied with time in season, species, weather, and vegetation structure. Daily survival rate of McCown’s longspur nests did not vary with foliar cover of relatively tall vegetation at the nest under average precipitation but declined with increasing cover during drought. At the 200-m scale, increasing cover of shortgrasses, rather than taller plant species, improved DSR of larks and longspurs. These birds experience tradeoffs in the selection of habitat at different spatial scales: tall structure at nests may reduce visual detection by predators and provide protection from sun, wind, and rain, yet taller structure surrounding territories may host nest predators. Patch-burn grazing management in combination with other strategies that retain taller-structured vegetation may help sustain a diversity of breeding habitats for shortgrass birds under varying weather conditions.

Peritumoral stromal remodeling, pattern of invasion and expression of c-met/HGF in advanced squamous cell carcinoma of the cervix uteri, FIGO stages III and IV.

PubMed

Horn, L-C; Hommel, N; Roschlau, U; Bilek, K; Hentschel, B; Einenkel, J

2012-07-01

Different patterns of invasion (PIs) have prognostic impact in several types of cancer and are associated with different grades of peritumoral stromal remodeling, characterized by the desmoplastic stromal response (DSR). One key regulator influencing cellular motility and peritumoral stromal response is c-met/HGF. This study evaluates the association between different PI, peritumoral DSR and its correlation to the expression of c-met/HGF in squamous cell carcinomas of the uterine cervix (CX). 131 advanced stage CX (FIGO III/IV) were re-evaluated histologically regarding PI, using a two-level scoring system. The tumor grows in solid cords/trabeculae in finger-like PI and in very small groups or single cells in spray-like PI. DSR was categorized as none/weak and moderate/strong. The tumors were stained with antibodies against c-met and HGF. The staining of >30% of tumor cells was defined as overexpression. The PI was correlated to the prognostic outcome, different categories of DSR and expression status of c-met and HGF. 66.4% of the tumors showed a finger-like, and 33.6% a spray-like PI. The spray-like PI showed a reduced two-year overall survival when compared to the finger-like PI (14.0% vs. 29.1%, respectively; p=0.012), and was associated with moderate/strong DSR. The majority of the tumors showed overexpression of c-met (85.4%) and HGF (74.8%). There was no correlation between the expression status of c-met/HGF and the FIGO stage, peritumoral DSR or the prognostic outcome. Spray-like PI is of prognostic impact in cervical carcinoma FIGO III/IV and is associated with strong peritumoral stromal remodeling. There is no prognostic impact of the immunohistochemical expression of c-met/HGF in advanced stage cervical carcinomas. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice (Oryza sativa L.)

PubMed Central

Yadav, Shailesh; Singh, Uma M.; Naik, Shilpa M.; Venkateshwarlu, Challa; Ramayya, Perumalla J.; Raman, K. Anitha; Sandhu, Nitika; Kumar, Arvind

2017-01-01

Dry direct-seeded rice (DSR) is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL), culm diameter (qCD), and culm strength (qCS)] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10%) and qCS1.1 (with R2 of 14%) on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772) were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength) and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR. PMID:28871266

Adaptive optics; Proceedings of the Meeting, Arlington, VA, April 10, 11, 1985

NASA Astrophysics Data System (ADS)

Ludman, J. E.

Papers are presented on the directed energy program for ballistic missile defense, a self-referencing wavefront interferometer for laser sources, the effects of mirror grating distortions on diffraction spots at wavefront sensors, and the optical design of an all-reflecting, high-resolution camera for active-optics on ground-based telescopes. Also considered are transverse coherence length observations, time dependent statistics of upper atmosphere optical turbulence, high altitude acoustic soundings, and the Cramer-Rao lower bound on wavefront sensor error. Other topics include wavefront reconstruction from noisy slope or difference data using the discrete Fourier transform, acoustooptic adaptive signal processing, the recording of phase deformations on a PLZT wafer for holographic and spatial light modulator applications, and an optical phase reconstructor using a multiplier-accumulator approach. Papers are also presented on an integrated optics wavefront measurement sensor, a new optical preprocessor for automatic vision systems, a model for predicting infrared atmospheric emission fluctuations, and optical logic gates and flip-flops based on polarization-bistable semiconductor lasers.

Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA.

PubMed

Cayrol, Bastien; Fortas, Emilie; Martret, Claire; Cech, Grzegorz; Kloska, Anna; Caulet, Stephane; Barbet, Marion; Trépout, Sylvain; Marco, Sergio; Taghbalout, Aziz; Busi, Florent; Wegrzyn, Grzegorz; Arluison, Véronique

2015-01-01

The bacterial actin-homolog MreB is a key player in bacterial cell-wall biosynthesis and is required for the maintenance of the rod-like morphology of Escherichia coli. However, how MreB cellular levels are adjusted to growth conditions is poorly understood. Here, we show that DsrA, an E. coli small noncoding RNA (sRNA), is involved in the post-transcriptional regulation of mreB. DsrA is required for the downregulation of MreB cellular concentration during environmentally induced slow growth-rates, mainly growth at low temperature and during the stationary phase. DsrA interacts in an Hfq-dependent manner with the 5' region of mreB mRNA, which contains signals for translation initiation and thereby affects mreB translation and stability. Moreover, as DsrA is also involved in the regulation of two transcriptional regulators, σ(S) and the nucleoid associated protein H-NS, which negatively regulate mreB transcription, it also indirectly contributes to mreB transcriptional down-regulation. By using quantitative analyses, our results evidence the complexity of this regulation and the tangled interplay between transcriptional and post-transcriptional control. As transcription factors and sRNA-mediated post-transcriptional regulators use different timescales, we propose that the sRNA pathway helps to adapt to changes in temperature, but also indirectly mediates long-term regulation of MreB concentration. The tight regulation and fine-tuning of mreB gene expression in response to cellular stresses is discussed in regard to the effect of the MreB protein on cell elongation.

Analysis of the neutron time-of-flight spectra from inertial confinement fusion experiments

NASA Astrophysics Data System (ADS)

Hatarik, R.; Sayre, D. B.; Caggiano, J. A.; Phillips, T.; Eckart, M. J.; Bond, E. J.; Cerjan, C.; Grim, G. P.; Hartouni, E. P.; Knauer, J. P.; Mcnaney, J. M.; Munro, D. H.

2015-11-01

Neutron time-of-flight diagnostics have long been used to characterize the neutron spectrum produced by inertial confinement fusion experiments. The primary diagnostic goals are to extract the d + t → n + α (DT) and d + d → n + 3He (DD) neutron yields and peak widths, and the amount DT scattering relative to its unscattered yield, also known as the down-scatter ratio (DSR). These quantities are used to infer yield weighted plasma conditions, such as ion temperature (Tion) and cold fuel areal density. We report on novel methodologies used to determine neutron yield, apparent Tion, and DSR. These methods invoke a single temperature, static fluid model to describe the neutron peaks from DD and DT reactions and a spline description of the DT spectrum to determine the DSR. Both measurements are performed using a forward modeling technique that includes corrections for line-of-sight attenuation and impulse response of the detection system. These methods produce typical uncertainties for DT Tion of 250 eV, 7% for DSR, and 9% for the DT neutron yield. For the DD values, the uncertainties are 290 eV for Tion and 10% for the neutron yield.

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

Girelli, Florian; Livine, Etera R.; Laboratoire de Physique, ENS Lyon, CNRS UMR 5672, 46 Allee d'Italie, 69007 Lyon

Deformed special relativity (DSR) is obtained by imposing a maximal energy to special relativity and deforming the Lorentz symmetry (more exactly, the Poincare symmetry) to accommodate this requirement. One can apply the same procedure in the context of Galilean relativity by imposing a maximal speed (the speed of light). Effectively, one deforms the Galilean group and this leads to a noncommutative space structure, together with the deformations of composition of speed and conservation of energy momentum. In doing so, one runs into most of the ambiguities that one stumbles onto in the DSR context. However, this time, special relativity ismore » there to tell us what is the underlying physics, in such a way we can understand and interpret these ambiguities. We use these insights to comment on the physics of DSR.« less

High Resolution Imaging Testbed Utilizing Sodium Laser Guide Star Adaptive Optics: The Real Time Wavefront Reconstructor Computer

DTIC Science & Technology

2008-07-31

Unlike the Lyrtech, each DSP on a Bittware board offers 3 MB of on-chip memory and 3 GFLOPs of 32-bit peak processing power. Based on the performance...Each NVIDIA 8800 Ultra features 576 GFLOPS on 128 612-MHz single-precision floating-point SIMD processors, arranged in 16 clusters of eight. Each

Engagement with Novel Virtual Environments: The Role of Perceived Novelty and Flow in the Development of the Deficient Self-Regulation of Internet Use and Media Habits

ERIC Educational Resources Information Center

Tokunaga, Robert Shota

2013-01-01

This article extends theory on the deficient self-regulation (DSR) of Internet use and media habits by integrating predictors relevant to technology use. It introduces novelty perceptions of a technology and flow as conditions that increase the likelihood of experiencing DSR and media habits. An experiment, with between- and within-subjects…

Analysis of the neutron time-of-flight spectra from inertial confinement fusion experiments

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

Hatarik, R., E-mail: hatarik1@llnl.gov; Sayre, D. B.; Caggiano, J. A.

2015-11-14

Neutron time-of-flight diagnostics have long been used to characterize the neutron spectrum produced by inertial confinement fusion experiments. The primary diagnostic goals are to extract the d + t → n + α (DT) and d + d → n + {sup 3}He (DD) neutron yields and peak widths, and the amount DT scattering relative to its unscattered yield, also known as the down-scatter ratio (DSR). These quantities are used to infer yield weighted plasma conditions, such as ion temperature (T{sub ion}) and cold fuel areal density. We report on novel methodologies used to determine neutron yield, apparent T{sub ion}, and DSR. These methods invoke a single temperature,more » static fluid model to describe the neutron peaks from DD and DT reactions and a spline description of the DT spectrum to determine the DSR. Both measurements are performed using a forward modeling technique that includes corrections for line-of-sight attenuation and impulse response of the detection system. These methods produce typical uncertainties for DT T{sub ion} of 250 eV, 7% for DSR, and 9% for the DT neutron yield. For the DD values, the uncertainties are 290 eV for T{sub ion} and 10% for the neutron yield.« less

Simulation of dissipative-soliton-resonance generation in a passively mode-locked Yb-doped fiber laser

NASA Astrophysics Data System (ADS)

Du, Wenxiong; Li, Heping; Liu, Cong; Shen, Shengnan; Zhang, Shangjian; Liu, Yong

2017-10-01

We present a numerical investigation of dissipative-soliton-resonance (DSR) generation in an all-normal-dispersion Ybdoped fiber laser mode-locked by a real saturable absorber (SA). In the simulation model, the SA includes both the saturable absorption and excited-state absorption (ESA) effects. The intra-cavity pulse evolution is numerically simulated with different transmission functions of SA. When omitting the ESA effect, the transmissivity of SA increases monotonically with the input pulse power. The noise-like pulse (NLP) operation in the cavity is obtained at high pump power, which is attributed to the spectral filtering effect. When the ESA effect is activated, higher instantaneous power part of pulse encounters larger loss induced by SA, causing that the pulse peak power is clamped at a certain fixed value. With increasing pump, the pulse starts to extend in the time domain while the pulse spectrum is considerably narrowed. In this case, the NLP operation state induced by the spectral filtering effect is avoided and the DSR is generated. Our simulation results indicate that the ESA effect in the SA plays a dominant role in generating the DSR pulses, which will be conducive to comprehending the mechanism of DSR generation in passively mode-locked fiber lasers.

Teaching neuroscience through Web adventures: adolescents reconstruct the history and science of opioids.

PubMed

Miller, Leslie; Schweingruber, Heidi; Oliver, Robert; Mayes, Janice; Smith, Donna

2002-02-01

New technological and cultural developments surrounding adolescents' use of the World Wide Web offer an opportunity for turning aspects of the Internet gaming phenomenon to the advantage of neuroscience education. Specifically, an experimental project to transmit aspects of problem-based learning and the National Science Standards through an interactive Web adventure is reported here. The Reconstructors is an episodic Web-based adventure series entitled Medicinal Mysteries from History. It is funded by the National Institute on Drug Abuse, and the first series focuses on opioids. It was created with the input of middle school students and teachers. Through the use of multimedia technologies, middle school students enter a futuristic world in which they become "reconstructors," members of an elite scientific unit charged with recovering lost medical knowledge about analgesic drugs. Two of the four episodes have been evaluated through a comprehensive review process involving middle school students, teachers, neuroscience researchers, and clinicians. Analysis of the pretest and posttest scores demonstrated significant knowledge gain that validly can be attributed to use of the game. These data provide evidence that science content can be transmitted through innovative online techniques without sacrificing compelling content or effective pedagogical strategies.

Pilot Metabolome-Wide Association Study of Benzo(a)pyrene in Serum from Military Personnel

PubMed Central

Walker, Douglas I.; Pennell, Kurt D.; Uppal, Karan; Xia, Xiaoyan; Hopke, Philip K.; Utell, Mark J.; Phipps, Richard P.; Sime, Patricia J.; Rohrbeck, Patricia; Mallon, COL Timothy M.; Jones, Dean P.

2016-01-01

Objective A pilot study was conducted to test the feasibility of using Department of Defense Serum Repository (DoDSR) samples to study health and exposure-related effects. Methods Thirty unidentified human serum samples were obtained from the DoDSR and analyzed for normal serum metabolites with high-resolution mass spectrometry and serum levels of free benzo(a)pyrene (BaP) by gas chromatography-mass spectrometry. Metabolic associations with BaP were determined using a metabolome wide association study (MWAS) and metabolic pathway enrichment. Results The serum analysis detected normal ranges of glucose, selected amino acids, fatty acids, and creatinine. Free BaP was detected in a broad concentration range. MWAS of BaP showed associations with lipids, fatty acids, and sulfur amino acid metabolic pathways. Conclusion The results show the DoDSR samples are of sufficient quality for chemical profiling of DoD personnel. PMID:27501104

Pilot Metabolome-Wide Association Study of Benzo(a)pyrene in Serum From Military Personnel.

PubMed

Walker, Douglas I; Pennell, Kurt D; Uppal, Karan; Xia, Xiaoyan; Hopke, Philip K; Utell, Mark J; Phipps, Richard P; Sime, Patricia J; Rohrbeck, Patricia; Mallon, Col Timothy M; Jones, Dean P

2016-08-01

A pilot study was conducted to test the feasibility of using Department of Defense Serum Repository (DoDSR) samples to study health and exposure-related effects. Thirty unidentified human serum samples were obtained from the DoDSR and analyzed for normal serum metabolites with high-resolution mass spectrometry and serum levels of free benzo(a)pyrene (BaP) by gas chromatography-mass spectrometry. Metabolic associations with BaP were determined using a metabolome-wide association study (MWAS) and metabolic pathway enrichment. The serum analysis detected normal ranges of glucose, selected amino acids, fatty acids, and creatinine. Free BaP was detected in a broad concentration range. MWAS of BaP showed associations with lipids, fatty acids, and sulfur amino acid metabolic pathways. The results show that the DoDSR samples are of sufficient quality for chemical profiling of DoD personnel.

Fourier transform-wavefront reconstruction for the pyramid wavefront sensor

NASA Astrophysics Data System (ADS)

Quirós-Pacheco, Fernando; Correia, Carlos; Esposito, Simone

The application of Fourier-transform reconstruction techniques to the pyramid wavefront sensor has been investigated. A preliminary study based on end-to-end simulations of an adaptive optics system with ≈40x40 subapertures and actuators shows that the performance of the Fourier-transform reconstructor (FTR) is of the same order of magnitude than the one obtained with a conventional matrix-vector multiply (MVM) method.

dsrAB-based analysis of sulphate-reducing bacteria in moving bed biofilm reactor (MBBR) wastewater treatment plants.

PubMed

Biswas, Kristi; Taylor, Michael W; Turner, Susan J

2014-08-01

Sulphate-reducing bacteria (SRB) are important members of the sulphur cycle in wastewater treatment plants (WWTPs). In this study, we investigate the diversity and activity of SRB within the developing and established biofilm of two moving bed biofilm reactor (MBBR) systems treating municipal wastewater in New Zealand. The larger of the two WWTPs (Moa Point) generates high levels of sulphide relative to the smaller Karori plant. Clone libraries of the dissimilatory (bi)sulphite reductase (dsrAB) genes and quantitative real-time PCR targeting dsrA transcripts were used to compare SRB communities between the two WWTPs. Desulfobulbus (35-53 % of total SRB sequences) and genera belonging to the family Desulfobacteraceae (27-41 %) dominated the SRB fraction of the developing biofilm on deployed plastic carriers at both sites, whereas Desulfovibrio and Desulfomicrobium were exclusively found at Moa Point. In contrast, the established biofilms from resident MBBR carriers were largely dominated by Desulfomonile tiedjei-like organisms (58-100 % of SRB sequences). The relative transcript abundance of dsrA genes (signifying active SRBs) increased with biofilm weight yet remained low overall, even in the mature biofilm stage. Our results indicate that although SRB are both present and active in the microbial community at both MBBR study sites, differences in the availability of sulphate may be contributing to the observed differences in sulphide production at these two plants.

Fine-tuning key parameters of an integrated reactor system for the simultaneous removal of COD, sulfate and ammonium and elemental sulfur reclamation.

PubMed

Yuan, Ye; Chen, Chuan; Liang, Bin; Huang, Cong; Zhao, Youkang; Xu, Xijun; Tan, Wenbo; Zhou, Xu; Gao, Shuang; Sun, Dezhi; Lee, Duujong; Zhou, Jizhong; Wang, Aijie

2014-03-30

In this paper, we proposed an integrated reactor system for simultaneous removal of COD, sulfate and ammonium (integrated C-S-N removal system) and investigated the key parameters of the system for a high level of elemental sulfur (S(0)) production. The system consisted of 4 main units: sulfate reduction and organic carbon removal (SR-CR), autotrophic and heterotrophic denitrifying sulfide removal (A&H-DSR), sulfur reclamation (SR), and aerated filter for aerobic nitrification (AN). In the system, the effects of key operational parameters on production of elemental sulfur were investigated, including hydraulic retention time (HRT) of each unit, sulfide/nitrate (S(2-)-S/NO3(-)-N) ratios, reflux ratios between the A&H-DSR and AN units, and loading rates of chemical oxygen demand (COD), sulfate and ammonium. Physico-chemical characteristics of biosulfur were studied for acquiring efficient S(0) recovery. The experiments successfully explored the optimum parameters for each unit and demonstrated 98% COD, 98% sulfate and 78% nitrogen removal efficiency. The optimum HRTs for SR-CR, A&H-DSR and AN were 12h, 3h and 3h, respectively. The reflux ratio of 3 could provide adequate S(2-)-S/NO3(-)-N ratio (approximately 1:1) to the A&H-DSR unit for obtaining maximum sulfur production. In this system, the maximum production of S(0) reached 90%, but only 60% S(0) was reclaimed from effluent. The S(0) that adhered to the outer layer of granules was deposited in the bottom of the A&H-DSR unit. Finally, the microbial community structure of the corresponding unit at different operational stage were analyzed by 16S rRNA gene based high throughput Illumina MiSeq sequencing and the potential function of dominant species were discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

Biogeochemical and Molecular Signatures of Anaerobic Methane Oxidation in a Marine Sediment

PubMed Central

Thomsen, Trine R.; Finster, Kai; Ramsing, Niels B.

2001-01-01

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802–805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin. PMID:11282617

Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment.

PubMed

Thomsen, T R; Finster, K; Ramsing, N B

2001-04-01

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802-805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.

Regulation of Mammary Progenitor Cells by p53 and Parity

DTIC Science & Technology

2011-01-01

quantitative PCR system (Stratagene). To knockdown Notch1 in TM40A cells, siRNA (s70698 and s70700) were purchased from Ambion. s70698 siRNA sense sequence: 5...hours after transfect ion and real-tim e quantitative P CR was used to confirm the knockdown efficiency. Results Label and chase progenitor cells...cells contained 0.8% o f DsRed positiv e (DsR +) progenitor cells (Fig. 1B). The mammosphere-forming capacity of DsR+ cells is 3.8-fold greater

Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer.

PubMed

Bagwell, Christopher E; Liu, Xuaduan; Wu, Liyou; Zhou, Jizhong

2006-03-01

The impact of legacy nuclear waste on the compositional diversity and distribution of sulfate-reducing bacteria in a heavily contaminated subsurface aquifer was examined. dsrAB clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis used to evaluate genetic variation between sampling wells. Principal component analysis identified nickel, nitrate, technetium, and organic carbon as the primary variables contributing to well-to-well geochemical variability, although comparative sequence analysis showed the sulfate-reducing bacteria community structure to be consistent throughout contaminated and uncontaminated regions of the aquifer. Only 3% of recovered dsrAB gene sequences showed apparent membership to the Deltaproteobacteria. The remainder of recovered sequences may represent novel, deep-branching lineages that, to our knowledge, do not presently contain any cultivated members; although corresponding phylotypes have recently been reported from several different marine ecosystems. These findings imply resiliency and adaptability of sulfate-reducing bacteria to extremes in environmental conditions, although the possibility for horizontal transfer of dsrAB is also discussed.

A Magnetic Suspension and Excitation System for Spin Vibration Testing of Turbomachinery Blades

NASA Technical Reports Server (NTRS)

Johnson, Dexter; Brown, Gerald V.; Mehmed, Oral

1998-01-01

The Dynamic Spin Rig (DSR) is used to perform vibration tests of turbomachinery blades and components under spinning conditions in a vacuum. A heteropolar radial active magnetic bearing was integrated into the DSR to provide non-contact magnetic suspension and mechanical excitation of the rotor to induce turbomachinery blade vibrations. The magnetic bearing replaces one of the two existing conventional radial ball bearings. Prior operation of the DSR used two voice-coil type linear electromagnetic shakers which provided axial excitation of the rotor. The new magnetic suspension and excitation system has provided enhanced testing capabilities. Tests were performed at high rotational speeds for longer duration and higher vibration amplitudes. Some characteristics of the system include magnetic bearing stiffness values up to 60,000 lb./in., closed loop control bandwidth around 500 Hz, and multi-directional radial excitation of the rotor. This paper reports on the implementation and operation of this system and presents some test results using this system.

Survival of juvenile ring-necked ducks on wetlands of different pH

USGS Publications Warehouse

McAuley, D.G.; Longcore, J.R.

1988-01-01

Brood and duckling survival of ring-necked ducks (Aythya collaris) was examined in relation to wetland water chemistry in eastcentral Maine during 1983-85. Daily survival rates (DSR) of broods and ducklings were determined for 381 ducklings from 64 broods by counts of each brood at 6-10-day intervals during broodrearing. Twelve of 64 females lost entire broods. Only 176 of 381 (46%) ducklings survived to fledge. Brood survival for the 45-day rearing period was 0.7731; duckling survival was 0.3707. Young ducklings (25 days) ducklings (0.9818/day) (P = 0.002). Survival rates of broods and ducklings did not differ among wetlands of high and low alkalinities. Brood survival did not differ among wetlands of different pH, but DSR of ducklings was lower (0.9763/day) on low-pH (6.1) wetlands (0.9816/day) (P = 0.049). Class lIb-III (25-45 days old) ducklings from the lowest-pH wetlands(6.5) had the highest DSR (0.9856) (P = 0.009).

Denitrifying sulfide removal process on high-tetracycline wastewater.

PubMed

Liu, Chunshuang; Xu, Jian; Lee, Duu-Jong; Yu, Daoyong; Liu, Lihong

2016-04-01

Antibiotics wastewater from tetracycline (TC) production unit can have high levels of chemical oxygen demand, ammonium and sulfate and up to a few hundreds of milligrams per liter of TC. Denitrifying sulfide removal (DSR) process is set up for simultaneously removal of sulfur, carbon and nitrogen from waters. The DSR process was for the first time studied for treating TC wastewaters. The TC stress has no adverse effects on removal rates of nitrate and acetate; however, it moderately deteriorated sulfide removal rates and S(0) accumulation rates when the concentration is higher than 100mgL(-1) TC. The Thauera sp., and Pseudomonas sp. present the heterotrophs and Sulfurovum sp. presented the autotroph for the present DSR reactions. The high tolerance of TC stress by the tested consortium was explained by the excess production of extracellular polymeric substances at high TC concentration, which can bind with TC for minimizing its inhibition effects. Copyright © 2016 Elsevier Ltd. All rights reserved.

The acute effect of different warm-up protocols on anaerobic performance in elite youth soccer players.

PubMed

Needham, Robert A; Morse, Christopher I; Degens, Hans

2009-12-01

The purpose of the study was to investigate the acute effect of different warm-up protocols on anaerobic performance in elite youth soccer players. Twenty elite youth soccer players (mean age 17.2 +/- 1.2 years) performed 3 different warm-up protocols in a random order on nonconsecutive days. Each warm-up protocol consisted of a 5-minute low-intensity jog followed by 10 minutes of static stretching (SS), dynamic stretching (DS), or dynamic stretching followed by 8 front squats + 20% body mass (DSR). Subjects performed a countermovement jump followed by a 10- and 20-m sprint test immediately and at 3 and 6 minutes after each warm-up protocol. Vertical jump performance following DSR was better at 3 and 6 minutes than after DS, which in turn was better than after SS at 0, 3, and 6 minutes (p < 0.05). Jump performance was better at 3 minutes than immediately after, and this improvement was maintained at 6 minutes after DSR (p < 0.05). A better sprint performance was observed after DSR and DS compared with SS immediately and at 3 and 6 minutes following each warm-up protocol (p < 0.05). The results of the study suggest that a dynamic warm-up with the inclusion of resistance enhances jumping ability more than dynamic exercise alone. In addition, a dynamic warm-up produces a superior sprint and jump performance compared to a warm-up consisting of static stretching.

Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific.

PubMed

Nakagawa, Tatsunori; Ishibashi, Jun-Ichiro; Maruyama, Akihiko; Yamanaka, Toshiro; Morimoto, Yusuke; Kimura, Hiroyuki; Urabe, Tetsuro; Fukui, Manabu

2004-01-01

This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5 degrees C and natural vent fluids at 7 degrees C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and gamma- and epsilon-Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with "Nanoarchaeota." The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300 degrees C were affiliated with the delta-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4 degrees C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments.

Effect of weed management and seed rate on crop growth under direct dry seeded rice systems in Bangladesh.

PubMed

Ahmed, Sharif; Salim, Muhammad; Chauhan, Bhagirath S

2014-01-01

Weeds are a major constraint to the success of dry-seeded rice (DSR). The main means of managing these in a DSR system is through chemical weed control using herbicides. However, the use of herbicides alone may not be sustainable in the long term. Approaches that aim for high crop competitiveness therefore need to be exploited. One such approach is the use of high rice seeding rates. Experiments were conducted in the aman (wet) seasons of 2012 and 2013 in Bangladesh to evaluate the effect of weed infestation level (partially-weedy and weed-free) and rice seeding rate (20, 40, 60, 80, and 100 kg ha(-1)) on weed and crop growth in DSR. Under weed-free conditions, higher crop yields (5.1 and 5.2 t ha(-1) in the 2012 and 2013 seasons, respectively) were obtained at the seeding rate of 40 kg ha(-1) and thereafter, yield decreased slightly beyond 40 kg seed ha(-1). Under partially-weedy conditions, yield increased by 30 to 33% (2.0-2.2 and 2.9-3.2 t ha(-1) in the 2012 and 2013 seasons, respectively) with increase in seeding rate from 20 to 100 kg ha(-1). In the partially-weedy plots, weed biomass decreased by 41-60% and 54-56% at 35 days after sowing and at crop anthesis, respectively, when seeding rate increased from 20 to 100 kg ha(-1). Results from our study suggest that increasing seeding rates in DSR can suppress weed growth and reduce grain yield losses from weed competition.

Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields.

PubMed

Priha, Outi; Nyyssönen, Mari; Bomberg, Malin; Laitila, Arja; Simell, Jaakko; Kapanen, Anu; Juvonen, Riikka

2013-09-01

Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10(1) to 6 × 10(5) dsrB gene copies ml(-1). DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different dsrB compositions were detected at different geographical locations. The identified dsrB gene sequences belonged to several phylogenetic groups, such as Desulfovibrio, Desulfococcus, Desulfomicrobium, Desulfobulbus, Desulfotignum, Desulfonatronovibrio, and Desulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.

Adolescent social instability stress increases aggression in a food competition task in adult male Long-Evans rats.

PubMed

Cumming, Mark J; Thompson, Madison A; McCormick, Cheryl M

2014-11-01

Adolescent social instability stress (SS; daily 1 hr isolation + new cage partners postnatal days 30-45; thereafter with original cage partner, also in the SS condition) and control (CTL) rats competed for access to a preferred food in five sessions against their cage partner. In the first session, SS pairs displayed more aggression (face whacks, p = .02; rear attacks, p = .03), were less likely to relinquish access to the food voluntarily (p = .03), spent more time at the feeder than CTL pairs (p = .06), but did not differ in latency to access the feeder (p = .41). Pairs were considered in dominant-submissive relationships (DSR) if one rat spent significantly more time at the feeder than the other; 8 of 12 SS and 8 of 12 CTL pairs displayed DSRs (remaining: no-DSR). Aggression increased from the 1st to 5th session (p < .001), was greater in no-DSR than DSR pairs (p = .04; consistent with the proposed function of DSRs to be the reduction of aggression in groups), and was higher in SS than CTL pairs (p = .05). Because the increased aggression of SS compared with CTL pairs did not result in a significant increase in their time at the feeder, the increased aggression may be considered maladaptive, and may reflect an increased motivation for food reward. These results add to evidence that SS in adolescence modifies the adult social repertoire of rats and highlight the importance of adolescent social experiences for adult behavior. © 2014 Wiley Periodicals, Inc.

Daily survival rate for nests and chicks of Least Terns (Sternula antillarum) at natural nest sites in South Carolina

USGS Publications Warehouse

Brooks, Gillian L.; Sanders, Felicia J.; Gerard, Patrick D.; Jodice, Patrick G.R.

2013-01-01

Although a species of conservation concern, little is known about the reproductive success of Least Terns (Sternula antillarum) throughout the southeastern USA where availability of natural beaches for nesting is limited. Daily survival rate (DSR) of nests and chicks was examined at four natural nesting sites in Cape Romain National Wildlife Refuge, South Carolina, 2009–2010. Measures of nest success (n = 257 nests) ranged from 0–93% among colony sites. The DSR of nests was primarily related to colony site, but year and estimates of predation risk also were related to DSR. Predation was the principal cause of identifiable nest loss, accounting for 47% of nest failures when the two years of data were pooled. The probability (± SE) of a chick surviving from hatching to fledging = 0.449 ± 0.01 (n = 92 chicks). DSR of chicks was negatively related to tide height and rainfall. Therefore, productivity of Least Terns is being lost during both the nesting and chick stage through a combination of biotic and abiotic factors that may prove difficult to fully mitigate or manage. Although natural nesting sites within Cape Romain National Wildlife Refuge intermittently produce successful nests, the consistency of productivity over the long term is still unknown. Given that the long term availability of anthropogenic nest sites (e.g., rooftops, dredge-spoil islands) for Least Terns is questionable, further research is required both locally and throughout the region to assess the extent to which natural sites act as population sources or sinks.

Salicylic Acid-Dependent Plant Stress Signaling via Mitochondrial Succinate Dehydrogenase1[OPEN

PubMed Central

Thatcher, Louise F.

2017-01-01

Mitochondria are known for their role in ATP production and generation of reactive oxygen species, but little is known about the mechanism of their early involvement in plant stress signaling. The role of mitochondrial succinate dehydrogenase (SDH) in salicylic acid (SA) signaling was analyzed using two mutants: disrupted in stress response1 (dsr1), which is a point mutation in SDH1 identified in a loss of SA signaling screen, and a knockdown mutant (sdhaf2) for SDH assembly factor 2 that is required for FAD insertion into SDH1. Both mutants showed strongly decreased SA-inducible stress promoter responses and low SDH maximum capacity compared to wild type, while dsr1 also showed low succinate affinity, low catalytic efficiency, and increased resistance to SDH competitive inhibitors. The SA-induced promoter responses could be partially rescued in sdhaf2, but not in dsr1, by supplementing the plant growth media with succinate. Kinetic characterization showed that low concentrations of either SA or ubiquinone binding site inhibitors increased SDH activity and induced mitochondrial H2O2 production. Both dsr1 and sdhaf2 showed lower rates of SA-dependent H2O2 production in vitro in line with their low SA-dependent stress signaling responses in vivo. This provides quantitative and kinetic evidence that SA acts at or near the ubiquinone binding site of SDH to stimulate activity and contributes to plant stress signaling by increased rates of mitochondrial H2O2 production, leading to part of the SA-dependent transcriptional response in plant cells. PMID:28209841

Understanding diversity–stability relationships: towards a unified model of portfolio effects

PubMed Central

Thibaut, Loïc M; Connolly, Sean R; He, Fangliang

2013-01-01

A major ecosystem effect of biodiversity is to stabilise assemblages that perform particular functions. However, diversity–stability relationships (DSRs) are analysed using a variety of different population and community properties, most of which are adopted from theory that makes several restrictive assumptions that are unlikely to be reflected in nature. Here, we construct a simple synthesis and generalisation of previous theory for the DSR. We show that community stability is a product of two quantities: the synchrony of population fluctuations, and an average species-level population stability that is weighted by relative abundance. Weighted average population stability can be decomposed to consider effects of the mean-variance scaling of abundance, changes in mean abundance with diversity and differences in species' mean abundance in monoculture. Our framework makes explicit how unevenness in the abundances of species in real communities influences the DSR, which occurs both through effects on community synchrony, and effects on weighted average population variability. This theory provides a more robust framework for analysing the results of empirical studies of the DSR, and facilitates the integration of findings from real and model communities. PMID:23095077

A differential spectral responsivity measurement system constructed for determining of the spectral responsivity of a single- and triple-junction photovoltaic cells

NASA Astrophysics Data System (ADS)

Sametoglu, Ferhat; Celikel, Oguz; Witt, Florian

2017-10-01

A differential spectral responsivity (DSR) measurement system has been designed and constructed at National Metrology Institute of Turkey (TUBITAK UME) to determine the spectral responsivity (SR) of a single- or a multi-junction photovoltaic device (solar cell). The DSR setup contains a broad band light bias source composed of a constructed Solar Simulator based on a 1000 W Xe-arc lamp owning a AM-1.5 filter and 250 W quartz-tungsten-halogen lamp, a designed and constructed LED-based Bias Light Sources, a DC voltage bias circuit, and a probe beam optical power tracking and correction circuit controlled with an ADuC847 microcontroller card together with an embedded C based software, designed and constructed in TUBITAK UME under this project. By using the constructed DSR measurement system, the SR calibration of solar cells, the monolitic triple-junction solar cell GaInP/GaInAs/Ge and its corresponding component cells have been performed within the EURAMET Joint Research Project SolCell.

Water treatment capacity of forward osmosis systems utilizing power plant waste heat

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

Zhou, Xingshi; Gingerich, Daniel B.; Mauter, Meagan S.

Forward osmosis (FO) has the potential to improve the energy efficiency of membrane-based water treatment by leveraging waste heat from steam electric power generation as the primary driving force for separation. In this study, we develop a comprehensive FO process model, consisting of membrane separation, heat recovery, and draw solute regeneration (DSR) models. We quantitatively characterize three alternative processes for DSR: distillation, steam stripping, and air stripping. We then construct a mathematical model of the distillation process for DSR that incorporates hydrodynamics, mass and heat transport resistances, and reaction kinetics, and we integrate this into a model for the fullmore » FO process. Finally, we utilize this FO process model to derive a first-order approximation of the water production capacity given the rejected heat quantity and quality available at U.S. electric power facilities. We find that the upper bound of FO water treatment capacity using low-grade heat sources at electric power facilities exceeds process water treatment demand for boiler water make-up and flue gas desulfurization wastewater systems.« less

Biosorption of Cu(II) by powdered anaerobic granular sludge from aqueous medium.

PubMed

Zhou, Xu; Chen, Chuan; Wang, Aijie; Jiang, Guangming; Liu, Lihong; Xu, Xijun; Yuan, Ye; Lee, Duu-Jung; Ren, Nanqi

2013-01-01

Copper(II) biosorption processes by two pre-treated powdered anaerobic granular sludges (PAGS) (original sludges were methanogenic anaerobic granules and denitrifying sulfide removal (DSR) anaerobic granules) were investigated through batch tests. Factors affecting the biosorption process, such as pH, temperature and initial copper concentrations, were examined. Also, the physico-chemical characteristics of the anaerobic sludge were analyzed by Fourier transform infrared spectroscopy, scanning electron microscopy image, surface area and elemental analysis. A second-order kinetic model was applied to describe the biosorption process, and the model could fit the biosorption process. The Freundlich model was used for describing the adsorption equilibrium data and could fit the equilibrium data well. It was found that the methanogenic PAGS was more effective in Copper(II) biosorption process than the DSR PAGS, whose maximum biosorption capacity was 39.6% lower. The mechanisms of the biosorption capacities for different PAGS were discussed, and the conclusion suggested that the environment and biochemical reactions during the growth of biomass may have affected the structure of the PAGS. The methanogenic PAGS had larger specific surface area and more biosorption capacity than the DSR PAGS.

Water treatment capacity of forward osmosis systems utilizing power plant waste heat

DOE PAGES

Zhou, Xingshi; Gingerich, Daniel B.; Mauter, Meagan S.

2015-06-11

Forward osmosis (FO) has the potential to improve the energy efficiency of membrane-based water treatment by leveraging waste heat from steam electric power generation as the primary driving force for separation. In this study, we develop a comprehensive FO process model, consisting of membrane separation, heat recovery, and draw solute regeneration (DSR) models. We quantitatively characterize three alternative processes for DSR: distillation, steam stripping, and air stripping. We then construct a mathematical model of the distillation process for DSR that incorporates hydrodynamics, mass and heat transport resistances, and reaction kinetics, and we integrate this into a model for the fullmore » FO process. Finally, we utilize this FO process model to derive a first-order approximation of the water production capacity given the rejected heat quantity and quality available at U.S. electric power facilities. We find that the upper bound of FO water treatment capacity using low-grade heat sources at electric power facilities exceeds process water treatment demand for boiler water make-up and flue gas desulfurization wastewater systems.« less

Branch point reconstructors for discontinuous light phase functions

NASA Astrophysics Data System (ADS)

Le Bigot, Eric O.; Wild, Walter J.; Kibblewhite, Edward J.

1998-09-01

The study of phase discontinuities caused by atmospheric turbulence is a recent research topic; their study might yield significant improvements in high-quality adaptive optics systems, laser weapons and laser communication. We present in this paper an introduction to discontinuities in the light phase. We also provide a geometrical description of phase discontinuities, a study of their effect on Hartmann-Shack sensor measurements, as well as algorithms for measuring discontinuous light phases and the position of phase discontinuities.

Effect of ecological restoration programs on dust concentrations in the North China Plain: a case study

NASA Astrophysics Data System (ADS)

Long, Xin; Tie, Xuexi; Li, Guohui; Cao, Junji; Feng, Tian; Zhao, Shuyu; Xing, Li; An, Zhisheng

2018-05-01

In recent decades, the Chinese government has made a great effort in initiating large-scale ecological restoration programs (ERPs) to reduce the dust concentrations in China, especially for dust storm episodes. Using the Moderate Resolution Imaging Spectroradiometer (MODIS) land cover product, the ERP-induced land cover changes are quantitatively evaluated in this study. Two obvious vegetation protective barriers arise throughout China from the southwest to the northeast, which are well known as the Green Great Wall (GGW). Both the grass GGW and forest GGW are located between the dust source region (DSR) and the densely populated North China Plain (NCP). To assess the effect of ERPs on dust concentrations, a regional transport/dust model (WRF-DUST, Weather Research and Forecast model with dust) is applied to investigate the evolution of dust plumes during a strong dust storm episode from 2 to 8 March 2016. The WRF-DUST model generally performs reasonably well in reproducing the temporal variations and spatial distributions of near-surface [PMC] (mass concentration of particulate matter with aerodynamic diameter between 2.5 and 10 µm) during the dust storm event. Sensitivity experiments have indicated that the ERP-induced GGWs help to reduce the dust concentration in the NCP, especially in BTH (Beijing, Tianjin, and Hebei). When the dust storm is transported from the upwind DSR to the downwind NCP, the [PMC] reduction ranges from -5 to -15 % in the NCP, with a maximum reduction of -12.4 % (-19.2 µg m-3) in BTH and -7.6 % (-10.1 µg m-3) in the NCP. We find the dust plumes move up to the upper atmosphere and are transported from the upwind DSR to the downwind NCP, accompanied by dust decrease. During the episode, the forest GGW is nonsignificant in dust concentration control because it is of benefit for dry deposition and not for emission. Conversely, the grass GGW is beneficial in controlling dust erosion and is the dominant reason for [PMC] decrease in the NCP. Because the air pollution is severe in eastern China, especially in the NCP, and the contribution of dust episodes is significant, the reduction of dust concentrations will have important effects on severe air pollution. This study illustrates the considerable contribution of ERPs to the control of air pollution in China, especially in springtime.

Modeling astronomical adaptive optics performance with temporally filtered Wiener reconstruction of slope data

NASA Astrophysics Data System (ADS)

Correia, Carlos M.; Bond, Charlotte Z.; Sauvage, Jean-François; Fusco, Thierry; Conan, Rodolphe; Wizinowich, Peter L.

2017-10-01

We build on a long-standing tradition in astronomical adaptive optics (AO) of specifying performance metrics and error budgets using linear systems modeling in the spatial-frequency domain. Our goal is to provide a comprehensive tool for the calculation of error budgets in terms of residual temporally filtered phase power spectral densities and variances. In addition, the fast simulation of AO-corrected point spread functions (PSFs) provided by this method can be used as inputs for simulations of science observations with next-generation instruments and telescopes, in particular to predict post-coronagraphic contrast improvements for planet finder systems. We extend the previous results and propose the synthesis of a distributed Kalman filter to mitigate both aniso-servo-lag and aliasing errors whilst minimizing the overall residual variance. We discuss applications to (i) analytic AO-corrected PSF modeling in the spatial-frequency domain, (ii) post-coronagraphic contrast enhancement, (iii) filter optimization for real-time wavefront reconstruction, and (iv) PSF reconstruction from system telemetry. Under perfect knowledge of wind velocities, we show that $\\sim$60 nm rms error reduction can be achieved with the distributed Kalman filter embodying anti- aliasing reconstructors on 10 m class high-order AO systems, leading to contrast improvement factors of up to three orders of magnitude at few ${\\lambda}/D$ separations ($\\sim1-5{\\lambda}/D$) for a 0 magnitude star and reaching close to one order of magnitude for a 12 magnitude star.

Ecological Restoration Programs Induced Amelioration of the Dust Pollution in North China Plain

NASA Astrophysics Data System (ADS)

Long, X.; Tie, X.; Li, G.; Junji, C.

2017-12-01

With Moderate Resolution Imaging Spectroradiometer (MODIS) land cover product (MCD12Q1), we quantitatively evaluate the ecological restoration programs (ERP) induced land cover change in China by calculating gridded the land use fraction (LUF). We clearly capture two obvious vegetation (grass and forest) protective barriers arise between the dust source region DSR and North China Plain NCP from 2011 to 2013. The WRF-DUST model is applied to investigate the impact of ERPs on dust pollution from 2 to 8 March 2016, corresponding to a national dust storm event over China. Despite some model biases, the WRF-DUST model reasonably reproduced the temporal variations of dust storm event, involving IOA of 0.96 and NMB of 2% for DSR, with IOA of 0.83 and NMB of -15% for downwind area of NCP. Generally, the WRF-DUST model well capture the spatial variations and evolutions of dust storm events with episode-average [PMC] correlation coefficient (R) of 0.77, especially the dust storm outbreak and transport evolution, involving daily average [PMC] R of 0.9 and 0.73 on 4-5 March, respectively. It is found that the ERPs generally reduce the dust pollution in NCP, especially for BTH, involving upper dust pollution control benefits of -15.3% (-21.0 μg m-3) for BTH, and -6.2% (-9.3 μg m-3) for NCP. We are the first to conduct model sensitivity studies to quantitatively evaluate the impacts of the ERPs on the dust pollution in NCP. And our narrative is independently based on first-hand sources, whereas government statistics.

Analysis of Dissimilatory Sulfite Reductase and 16S rRNA Gene Fragments from Deep-Sea Hydrothermal Sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific

PubMed Central

Nakagawa, Tatsunori; Ishibashi, Jun-Ichiro; Maruyama, Akihiko; Yamanaka, Toshiro; Morimoto, Yusuke; Kimura, Hiroyuki; Urabe, Tetsuro; Fukui, Manabu

2004-01-01

This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5°C and natural vent fluids at 7°C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and γ- and ɛ-Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with “Nanoarchaeota.” The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300°C were affiliated with the δ-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4°C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments. PMID:14711668

The effect of changing seawater Ca and Mg concentrations upon the distribution coefficients of Mg and Sr in the skeletons of the scleractinian coral Pocillopora damicornis

NASA Astrophysics Data System (ADS)

Giri, Sharmila J.; Swart, Peter K.; Devlin, Quinn B.

2018-02-01

The skeletal composition of calcifying organisms, in particular Mg/Ca and Sr/Ca ratios, have been widely used to understand fluctuations in seawater chemistry throughout the Phanerozoic. While the success of applying these data to the geologic record depends on a knowledge of the distribution coefficients for these elements (DMg and DSr), there are scarcely any studies which have described how these values vary as a result of changing seawater Mg/Ca ratios. To address this, we have cultured the scleractinian coral, Pocillopora damicornis, in seawater with ranges of Mg and Ca concentrations. Here, we demonstrate that Mg/Ca and Sr/Ca ratios of coral skeletons correlate with total seawater Mg/Ca and Sr/Ca molar ratios, but that apparent DMg and DSr values do not remain constant across the range of experimental seawater treatments, with DMg values significantly increasing with seawater Mg/Ca ratios and DSr values significantly increasing with seawater Ca concentrations. These trends are not rate dependent and may be best explained by a Rayleigh distillation model, in which the calcifying space is semi-isolated from seawater during skeletogenesis (i.e. leaky). As there is a slight increase in DMg and decrease in DSr values between our "Jurassic" and "Modern" seawater treatments, the application of a constant distribution coefficient to estimate changes in ancient seawater chemistry may underestimate seawater Mg/Ca ratios and overestimate Sr/Ca throughout the Mesozoic and Cenozoic. We suggest that interpretations of seawater chemistry from fossil corals may be improved by using the relationships derived for skeletal and seawater Mg/Ca and Sr/Ca ratios established by our experiments, as they incorporate the effect of seawater Mg/Ca ratios on skeletal Mg/Ca and Sr/Ca ratios.

Effect of Weed Management and Seed Rate on Crop Growth under Direct Dry Seeded Rice Systems in Bangladesh

PubMed Central

Ahmed, Sharif; Salim, Muhammad; Chauhan, Bhagirath S.

2014-01-01

Weeds are a major constraint to the success of dry-seeded rice (DSR). The main means of managing these in a DSR system is through chemical weed control using herbicides. However, the use of herbicides alone may not be sustainable in the long term. Approaches that aim for high crop competitiveness therefore need to be exploited. One such approach is the use of high rice seeding rates. Experiments were conducted in the aman (wet) seasons of 2012 and 2013 in Bangladesh to evaluate the effect of weed infestation level (partially-weedy and weed-free) and rice seeding rate (20, 40, 60, 80, and 100 kg ha−1) on weed and crop growth in DSR. Under weed-free conditions, higher crop yields (5.1 and 5.2 t ha−1 in the 2012 and 2013 seasons, respectively) were obtained at the seeding rate of 40 kg ha−1 and thereafter, yield decreased slightly beyond 40 kg seed ha−1. Under partially-weedy conditions, yield increased by 30 to 33% (2.0–2.2 and 2.9–3.2 t ha−1 in the 2012 and 2013 seasons, respectively) with increase in seeding rate from 20 to 100 kg ha−1. In the partially-weedy plots, weed biomass decreased by 41–60% and 54–56% at 35 days after sowing and at crop anthesis, respectively, when seeding rate increased from 20 to 100 kg ha−1. Results from our study suggest that increasing seeding rates in DSR can suppress weed growth and reduce grain yield losses from weed competition. PMID:25000520

Dietary sodium restriction reverses vascular endothelial dysfunction in middle-aged/older adults with moderately elevated systolic blood pressure

PubMed Central

Jablonski, Kristen L.; Racine, Matthew L.; Geolfos, Candace J.; Gates, Phillip E.; Chonchol, Michel; McQueen, Matthew B.; Seals, Douglas R.

2013-01-01

Objectives We determined the efficacy of dietary sodium restriction (DSR) for improving vascular endothelial dysfunction in middle-aged/older adults with moderately elevated systolic blood pressure (SBP; 130–159 mmHg) and the associated physiological mechanisms. Background Vascular endothelial dysfunction develops with advancing age and elevated SBP, contributing to increased cardiovascular risk. DSR lowers BP, but its effect on vascular endothelial function and mechanisms involved are unknown. Methods Seventeen subjects (11M/6F; 62±7 yrs, mean±S.D.) completed a randomized, crossover study of 4 weeks of both low and normal sodium intake. Vascular endothelial function (endothelium-dependent dilation; EDD), nitric oxide (NO)/tetrahydrobiopterin (BH4) bioavailability and oxidative stress-associated mechanisms were assessed following each condition. Results Urinary sodium excretion was reduced by ~50% (to 70±30 mmol/day), and conduit (brachial artery flow-mediated dilation [FMDBA]) and resistance (forearm blood flow responses to acetylcholine [FBFACh]) artery EDD were 68% and 42% (peak FBFACh) higher following the low sodium diet (p<0.005). Low sodium markedly enhanced NO- mediated EDD (greater ΔFBFACh with endothelial NO synthase [eNOS] inhibition) without changing eNOS expression/activation (Ser1177 phosphorylation), restored BH4 bioactivity (less ΔFMDBA with acute BH4), abolished tonic superoxide suppression of EDD (less ΔFMDBA and ΔFBFACh with ascorbic acid infusion), and increased circulating superoxide dismutase activity (p<0.05). These effects were independent of ΔSBP. Other subject characteristics/dietary factors and endothelium-independent dilation were unchanged. Conclusions DSR largely reverses both macro- and microvascular endothelial dysfunction by enhancing NO and BH4 bioavailability and reducing oxidative stress. Our findings support the emerging concept that DSR induces “vascular protection” beyond that attributable to its BP-lowering effects. PMID:23141486

A 32 mm  ×  32 mm  ×  22 mm monolithic LYSO:Ce detector with dual-sided digital photon counter readout for ultrahigh-performance TOF-PET and TOF-PET/MRI

NASA Astrophysics Data System (ADS)

Borghi, Giacomo; Peet, Bart Jan; Tabacchini, Valerio; Schaart, Dennis R.

2016-07-01

New applications for positron emission tomography (PET) and combined PET/magnetic resonance imaging (MRI) are currently emerging, for example in the fields of neurological, breast, and pediatric imaging. Such applications require improved image quality, reduced dose, shorter scanning times, and more precise quantification. This can be achieved by means of dedicated scanners based on ultrahigh-performance detectors, which should provide excellent spatial resolution, precise depth-of-interaction (DOI) estimation, outstanding time-of-flight (TOF) capability, and high detection efficiency. Here, we introduce such an ultrahigh-performance TOF/DOI PET detector, based on a 32 mm  ×  32 mm  ×  22 mm monolithic LYSO:Ce crystal. The 32 mm  ×  32 mm front and back faces of the crystal are coupled to a digital photon counter (DPC) array, in so-called dual-sided readout (DSR) configuration. The fully digital detector offers a spatial resolution of ~1.1 mm full width at half maximum (FWHM)/~1.2 mm mean absolute error, together with a DOI resolution of ~2.4 mm FWHM, an energy resolution of 10.2% FWHM, and a coincidence resolving time of 147 ps FWHM. The time resolution closely approaches the best results (135 ps FWHM) obtained to date with small crystals made from the same material coupled to the same DPC arrays, illustrating the excellent correction for optical and electronic transit time spreads that can be achieved in monolithic scintillators using maximum-likelihood techniques for estimating the time of interaction. The performance barely degrades for events with missing data (up to 6 out of 32 DPC dies missing), permitting the use of almost all events registered under realistic acquisition conditions. Moreover, the calibration procedures and computational methods used for position and time estimation follow recently made improvements that make them fast and practical, opening up realistic perspectives for using DSR monolithic scintillator detectors in TOF-PET and TOF-PET/MRI systems.

Analysis of the neutron time-of-flight spectra from inertial confinement fusion experiments

DOE PAGES

Hatarik, R.; Sayre, D. B.; Caggiano, J. A.; ...

2015-11-12

For a long time, neutron time-of-flight diagnostics been used to characterize the neutron spectrum produced by inertial confinement fusion experiments. The primary diagnostic goals are to extract the d+t→n+α (DT) and d+d→n+³He (DD) neutron yields and peak widths, and the amount DT scattering relative to its unscattered yield, which is also known as the down-scatter ratio (DSR). These quantities are used to infer yield weighted plasma conditions, such as ion temperature (T ion) and cold fuel areal density. We explain such novel methodologies used to determine neutron yield, apparent T ion and DSR.

Maximizing the Utility of the Serum Repository With Current Technologies and Recommendations to Meet Future Needs: Report of the Technical Panel.

PubMed

Baird, Coleen P

2015-10-01

The Department of Defense Serum Repository (DoDSR) of the Armed Forces Health Surveillance Center (AFHSC), Silver Spring, Maryland, has over 55 million specimens. Over 80% of these specimens are linked to individual health data. In response to Congressional and Department of Defense (DoD) concern about toxic exposures of deployed Service members and rapidly developing laboratory capabilities that may identify those exposed, the AFHSC hosted two panels in 2013. The first, the Needs Panel, focused on assessing the needs of the DoD that may be met using the current DoDSR and an enhanced repository. The second panel, the Technical Panel, focused on identifying the emerging laboratory technologies that are or will be available to DoD public health workers and researchers. This report summarizes the recommendations of the Technical Panel, to include identified gaps in the ability of the current DoDSR to address questions of interest to the DoD, the availability of laboratory technology to address these needs, and the types and quality of specimens required from Service members possibly exposed. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Ethics, Human Use, and the Department of Defense Serum Repository.

PubMed

Pavlin, Julie A; Welch, Robert A

2015-10-01

The Department of Defense Serum Repository (DoDSR) contains a growing archive of sera from service members collected to perform medical surveillance, clinical diagnosis, and epidemiologic studies to identify, prevent, and control diseases associated with military service. The specimens are a mandatory collection under DoD and U.S. regulations and do not include informed consent for uses beyond force health protection. Any use of the specimens for research requires deidentification of the samples and must be approved by Institutional Review Boards. However, as expansion of the DoDSR is contemplated, ethical considerations of sample collection, storage, and use must be carefully reconsidered. Other similar programs for research use of specimens collected for public health purpose are also undergoing similar reviews. It is recommended that at a minimum, service members are informed of the potential storage and use of their specimens and are allowed to opt out of additional use, or a broad informed consent is provided. The DoDSR provides a tremendous resource to the DoD and global health community, and to ensure its continued existence and improvement, the DoD must stay consistent with all principles of research ethics. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

A cross-shear deformation for optimizing the strength and ductility of AZ31 magnesium alloys

PubMed Central

Hamad, Kotiba; Ko, Young Gun

2016-01-01

Magnesium alloys have recently attracted great interest due their lightweight and high specific strength. However, because of their hexagonal close-packed structure, they have few active slip systems, resulting in poor ductility and high mechanical anisotropy at room temperature. In the present work, we used a cross-shear deformation imposed by a differential speed rolling (DSR) technique to improve the room temperature strength and ductility of AZ31 magnesium alloy sheets. To introduce the cross-shear deformation, the sheets were rotated 180° around their longitudinal axis between the adjacent passes of DSR. The sheets of the AZ31 alloy subjected to the cross-shear deformation showed a uniform fine microstructure (1.2 ± 0.1 μm) with weak basal textures. The fabricated sheets showed a simultaneous high ultimate tensile strength and elongation-to-failure, i.e., ~333 MPa and ~21%, respectively. These were explained based on the structural features evolved due to the cross-shear deformation by DSR. The high strength was attributed to the uniform fine microstructure, whereas the high ductility was explained based on the basal texture weakening. PMID:27406685

Temporal and spatial resolution required for imaging myocardial function

NASA Astrophysics Data System (ADS)

Eusemann, Christian D.; Robb, Richard A.

2004-05-01

4-D functional analysis of myocardial mechanics is an area of significant interest and research in cardiology and vascular/interventional radiology. Current multidimensional analysis is limited by insufficient temporal resolution of x-ray and magnetic resonance based techniques, but recent improvements in system design holds hope for faster and higher resolution scans to improve images of moving structures allowing more accurate functional studies, such as in the heart. This paper provides a basis for the requisite temporal and spatial resolution for useful imaging during individual segments of the cardiac cycle. Multiple sample rates during systole and diastole are compared to determine an adequate sample frequency to reduce regional myocardial tracking errors. Concurrently, out-of-plane resolution has to be sufficiently high to minimize partial volume effect. Temporal resolution and out-of-plane spatial resolution are related factors that must be considered together. The data used for this study is a DSR dynamic volume image dataset with high temporal and spatial resolution using implanted fiducial markers to track myocardial motion. The results of this study suggest a reduced exposure and scan time for x-ray and magnetic resonance imaging methods, since a lower sample rate during systole is sufficient, whereas the period of rapid filling during diastole requires higher sampling. This could potentially reduce the cost of these procedures and allow higher patient throughput.

Efficient reconstruction method for ground layer adaptive optics with mixed natural and laser guide stars.

PubMed

Wagner, Roland; Helin, Tapio; Obereder, Andreas; Ramlau, Ronny

2016-02-20

The imaging quality of modern ground-based telescopes such as the planned European Extremely Large Telescope is affected by atmospheric turbulence. In consequence, they heavily depend on stable and high-performance adaptive optics (AO) systems. Using measurements of incoming light from guide stars, an AO system compensates for the effects of turbulence by adjusting so-called deformable mirror(s) (DMs) in real time. In this paper, we introduce a novel reconstruction method for ground layer adaptive optics. In the literature, a common approach to this problem is to use Bayesian inference in order to model the specific noise structure appearing due to spot elongation. This approach leads to large coupled systems with high computational effort. Recently, fast solvers of linear order, i.e., with computational complexity O(n), where n is the number of DM actuators, have emerged. However, the quality of such methods typically degrades in low flux conditions. Our key contribution is to achieve the high quality of the standard Bayesian approach while at the same time maintaining the linear order speed of the recent solvers. Our method is based on performing a separate preprocessing step before applying the cumulative reconstructor (CuReD). The efficiency and performance of the new reconstructor are demonstrated using the OCTOPUS, the official end-to-end simulation environment of the ESO for extremely large telescopes. For more specific simulations we also use the MOST toolbox.

Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted.

PubMed

Chi Fru, E

2011-07-01

Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.

Transgenic rice expressing a codon-modified synthetic CP4-EPSPS confers tolerance to broad-spectrum herbicide, glyphosate.

PubMed

Chhapekar, Sushil; Raghavendrarao, Sanagala; Pavan, Gadamchetty; Ramakrishna, Chopperla; Singh, Vivek Kumar; Phanindra, Mullapudi Lakshmi Venkata; Dhandapani, Gurusamy; Sreevathsa, Rohini; Ananda Kumar, Polumetla

2015-05-01

Highly tolerant herbicide-resistant transgenic rice was developed by expressing codon-modified synthetic CP4--EPSPS. The transformants could tolerate up to 1% commercial glyphosate and has the potential to be used for DSR (direct-seeded rice). Weed infestation is one of the major biotic stress factors that is responsible for yield loss in direct-seeded rice (DSR). Herbicide-resistant rice has potential to improve the efficiency of weed management under DSR. Hence, the popular indica rice cultivar IR64, was genetically modified using Agrobacterium-mediated transformation with a codon-optimized CP4-EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene, with N-terminal chloroplast targeting peptide from Petunia hybrida. Integration of the transgenes in the selected rice plants was confirmed by Southern hybridization and expression by Northern and herbicide tolerance assays. Transgenic plants showed EPSPS enzyme activity even at high concentrations of glyphosate, compared to untransformed control plants. T0, T1 and T2 lines were tested by herbicide bioassay and it was confirmed that the transgenic rice could tolerate up to 1% of commercial Roundup, which is five times more in dose used to kill weeds under field condition. All together, the transgenic rice plants developed in the present study could be used efficiently to overcome weed menace.

Diversity and degradation mechanism of an anaerobic bacterial community treating phenolic wastewater with sulfate as an electron acceptor.

PubMed

Guo, X J; Lu, Z Y; Wang, P; Li, H; Huang, Z Z; Lin, K F; Liu, Y D

2015-10-01

Petrochemical wastewater often contains high concentrations of phenol and sulfate that must be properly treated to meet discharge standards. This study acclimated anaerobic-activated sludge to treat saline phenolic wastewater with sulfate reduction and clarified the diversity and degradation mechanism of the microbial community. The active sludge in an upflow anaerobic sludge blanket (UASB) reactor could remove 90 % of phenol and maintain the effluent concentration of SO4 (2-) below 400 mg/L. Cloning and sequencing showed that Clostridium spp. and Desulfotomaculum spp. were major phenol-degrading bacteria. Phenol was probably degraded through the carboxylation pathway and sulfate reduction catalyzed by adenosine-5'-phosphosulfate (APS) reductase and dissimilatory sulfite reductase (DSR). A real-time polymerase chain reaction (RT-PCR) showed that as phenol concentration increased, the quantities of 16S rRNA gene, dsrB, and mcrA in the sludge all decreased. The relative abundance of dsrB dropped to 12.46 %, while that of mcrA increased to 56.18 %. The change in the electron flow ratio suggested that the chemical oxygen demand (COD) was removed mainly by sulfate-reducing bacteria under a phenol concentration of 420 mg/L, whereas it was removed mainly by methanogens above 630 mg/L.

New insights into the rate dependence of sulfur isotope fractionation during dissimilatory sulfate reduction

NASA Astrophysics Data System (ADS)

Giannetta, M.; Druhan, J. L.; Sanford, R. A.

2016-12-01

The vast majority of experiments concerning the isotope partitioning of sulfate reducing bacteria (SRB) are conducted under artificially optimized growth conditions. In contrast, many natural environments supporting SRB reflect limited nutrient availability. In this study, we couple the cell-specific reduction rate of a common SRB to the characteristic partitioning of stable sulfur isotopes. However, our method is novel in that we regulate the addition of electron donor such that cell growth is minimized and cell-specific reduction rates are constant, thus simulating the low reactivity characteristic of natural conditions. Anoxic bioreactors containing equal amounts of Desulfovibrio vulgariswere continuously injected with formate to control the rate of dissimilatory sulfate reduction (DSR). Cell growth was minimized through two means, (1) a high initial culture density ensured the ratio of nutrients per cell was low; (2) the oxidation state of carbon in formate is unfavorable to cell biomass accumulation. Negligible cell growth was verified by flow cytometry. Four controlled DSR rates ranging from 0.32 to 1.8 µmole/hour exhibited fractionation factor (ɛ) values ranging from 9‰ to 4‰ over 1200 to 300 hours, respectively. These results demonstrate a unique value of ɛ for each rate of DSR, where larger S isotope partitioning is characteristic of a slower cell-specific rate of sulfate reduction. The results of this study provide a unique dataset that can be used to constrain variations in ɛ as a function of DSR rate. Specifically, the dataset offers a foundation to test recently proposed analytical models and predict variations in observed ɛ as a result of a multi-step reactive pathway. Based on these results, we suggest a novel rate expression for incorporation into reactive transport models. Such a rate law supports extrapolation of experimental behavior into natural conditions over modern to geologic timescales.

Apical Transportation, Centering Ratio, and Volume Increase after Manual, Rotary, and Reciprocating Instrumentation in Curved Root Canals: Analysis by Micro-computed Tomographic and Digital Subtraction Radiography.

PubMed

Zanesco, Caroline; Só, Marcus Vinicius Reis; Schmidt, Sabrina; Fontanella, Vania Regina Camargo; Grazziotin-Soares, Renata; Barletta, Fernando Branco

2017-03-01

This study aimed to evaluate apical transportation (AT), centering ratio (CR), and volume increase (VI) produced after instrumentation of mesiobuccal canals of maxillary molars with hand files, rotary, and reciprocating instruments using micro-computed tomographic (micro-CT) imaging and to demonstrate the ability of digital subtraction radiography (DSR) to evaluate AT. Forty-five canals were randomly assigned to either group K, manual K-files; PTN, ProTaper Next (Dentsply Maillefer, Ballaigues, Switzerland); or Rec, Reciproc (n = 15 for each group) for preparation. Master apical files were #25, X2 (#25/06), and R25 (#25/08), respectively. Micro-CT imaging was used to measure AT (mm) and CR (mm) at 3 different locations (1, 4, and 7 mm from the apex). VI (mm 3 ) was measured for each root third and for the whole canal. DSR (mesiodistal and buccolingual projections) was used to measure AT at 1 mm from the apex. AT and CR values were statistically similar across the groups at 1, 4, and 7 mm. AT results obtained for the different locations were similar within each group; CR, in turn, showed statistically lower values at 1 mm. VI was statistically similar in all groups. Both DSR and micro-CT imaging showed that AT always occurred on the outside of canal curvature. The highest mean value obtained for AT was 0.215 mm. AT, CR, and VI were similar for the K, PTN, and Rec groups. AT results were clinically irrelevant. DSR was as effective as micro-CT imaging in AT analysis and could be considered as an alternative method for assessing this outcome. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Impact of the Conservation Reserve Program on duck recruitment in the U.S. Prairie Pothole Region

USGS Publications Warehouse

Reynolds, Ronald E.; Shaffer, Terry L.; Renner, Randy W.; Newton, Wesley E.; Batt, Bruce D.J.

2001-01-01

The U.S. Department of Agriculture (USDA)'s Conservation Reserve Program (CRP) resulted in the conversion of about 1.9 million ha of cropland to perennial grass cover in the Prairie Pothole Region of North Dakota, South Dakota, and northeastern Montana by 1992. Many wildlife managers believed this cover would provide benefits to wildlife, including upland nesting ducks. During 1992-1995, we evaluated success of 5 duck species nesting in CRP fields and nearby Waterfowl Production Areas (WPA) throughout the region. We examined relationships between daily survival rates (DSR) of duck nests in CRP cover and landscape-level habitat and population parameters. We computed DSR of duck nests in other major cover types in our study area from data collected during 1980-1984 (pre-CRP) and 1990-1994 (CRP) periods. We then applied recruitment models to estimate duck production in our study area during peak CRP years (1992-1997) and compared these results with those that simulated the scenario in which cropland was in place of CRP cover (i.e., the CRP had not occurred). DSR were higher in all habitats combined during the CRP period compared to the pre-CRP period. Regressions of DSR in CRP cover on the percent of each study plot in perennial cover and geographic location were significant (P < 0.01) for 4 of 5 duck (Anas spp.) species. Estimated nest success and recruitment rates for the 5 species combined during 1992-1997 were 46% and 30% higher, respectively, with CRP cover on the landscape compared to a scenario where we simulated cropland in place of CRP. Our model estimated an additional 12.4 million recruits from our study area to the fall flight as a consequence of the CRP during 1992-1997. Our results document benefits to 5 duck species in the northern plains associated with a farm program that provided financial incentives to landowners for planting undisturbed grass cover as an alternative to annual crops.

Calcium and strontium isotope fractionation during precipitation from aqueous solutions as a function of temperature and reaction rate; II. Aragonite

NASA Astrophysics Data System (ADS)

AlKhatib, Mahmoud; Eisenhauer, Anton

2017-07-01

In order to study Strontium (Sr) partitioning and isotope fractionation of Sr and Calcium (Ca) in aragonite we performed precipitation experiments decoupling temperature and precipitation rates (R∗, μmol/m2 h) in the interval of about 2.3-4.5 μmol/m2 h. Aragonite is the only pure solid phase precipitated from a stirred solutions exposed to an atmosphere of NH3 and CO2 gases throughout the spontaneous decomposition of (NH4)2CO3. The order of reaction with respect to Ca ions is one and independent of temperature. However, the order of reaction with respect to the dissolved inorganic carbon (DIC) is temperature dependent and decreases from three via two to one as temperature increases from 12.5 and 25.0 to 37.5 °C, respectively. Strontium distribution coefficient (DSr) increases with decreasing temperature. However, R∗ responds differently depending on the initial Sr/Ca concentration and temperature: at 37.5 °C DSr increase as a function of increasing R∗ but decrease for 12.5 and 25 °C. Not seen at 12.5 and 37.5 °C but at 25 °C the DSr-R∗ gradient is also changing sign depending on the initial Sr/Ca ratio. Magnesium (Mg) adsorption coefficient between aragonite and aqueous solution (DMg) decreases with temperature but increases with R∗ in the range of 2.4-3.8 μmol/m2 h. Strontium isotope fractionation (Δ88/86Sraragonite-aq) follows the kinetic type of fractionation and become increasingly negative as a function of R∗ for all temperatures. In contrast Ca isotope fractionation (Δ44/40Caaragonite-aq) shows a different behavior than the Sr isotopes. At low temperatures (12.5 and 25 °C) Ca isotope fractionation (Δ44/40Caaragonite-aq) becomes positive as a function of R∗. In contrast, at 37.5 °C and as a function of increasing R∗ the Δ44/40Caaragonite-aq show a Sr type like behavior and becomes increasingly negative. Concerning both the discrepant behavior of DSr as a function of temperature as well as for the Ca isotope fractionation as a function of temperature we infer that the switch of sign in the trace element partitioning as well as in the direction of the Ca isotope fractionation is probably due to the switch of complexation from a Ca2+-NH3 complexation at and below 25 °C to an Ca2+-H2O aquacomplex at 37.5 °C. The DSr-Δ88/86Srcalcite-aq correlation for calcite is independent of temperature in contrast to aragonite. We interpreted the strong DSr-temperature dependency of aragonite, the smaller range of Sr isotope fractionation as well as the shallower Δ88/86Srcalcite-aq-R∗ gradients to be a consequence of the increased aragonite solubility and the "Mg blocking effect". In contrast to Sr the Ca isotope fractionation values in calcite and aragonite depend both on the complexation in solution and independent on polymorphism.

Dynamic Reconstruction and Multivariable Control for Force-Actuated, Thin Facesheet Adaptive Optics

NASA Technical Reports Server (NTRS)

Grocott, Simon C. O.; Miller, David W.

1997-01-01

The Multiple Mirror Telescope (MMT) under development at the University of Arizona takes a new approach in adaptive optics placing a large (0.65 m) force-actuated, thin facesheet deformable mirror at the secondary of an astronomical telescope, thus reducing the effects of emissivity which are important in IR astronomy. However, The large size of the mirror and low stiffness actuators used drive the natural frequencies of the mirror down into the bandwidth of the atmospheric distortion. Conventional adaptive optics takes a quasi-static approach to controlling the, deformable mirror. However, flexibility within the control bandwidth calls for a new approach to adaptive optics. Dynamic influence functions are used to characterize the influence of each actuator on the surface of the deformable mirror. A linearized model of atmospheric distortion is combined with dynamic influence functions to produce a dynamic reconstructor. This dynamic reconstructor is recognized as an optimal control problem. Solving the optimal control problem for a system with hundreds of actuators and sensors is formidable. Exploiting the circularly symmetric geometry of the mirror, and a suitable model of atmospheric distortion, the control problem is divided into a number of smaller decoupled control problems using circulant matrix theory. A hierarchic control scheme which seeks to emulate the quasi-static control approach that is generally used in adaptive optics is compared to the proposed dynamic reconstruction technique. Although dynamic reconstruction requires somewhat more computational power to implement, it achieves better performance with less power usage, and is less sensitive than the hierarchic technique.

Elimination of sulphur odours at landfills by bioconversion and the corona discharge plasma technique.

PubMed

Xia, Fangfang; Liu, Xin; Kang, Ying; He, Ruo; Wu, Zucheng

2015-01-01

Hydrogen sulphide (H2S) contributes a lot to odours at landfills, which is a threat to the environment and the health of the staff therein. To mitigate its emission, the bioconversion within landfill cover soils (LCSs) was introduced. H2S emission and concentration both in the field air above the landfill and in microcosm testing were surveyed. Results indicated that H2S emission and concentration in the landfill varied with landfill seasons and sites. There existed relationship between H2S concentration and fluxes spatially and temporally. To characterize and assess the spatial and temporal diversity of sulphur-oxidizing bacteria (SOB) and sulphate-reducing bacteria (SRB) in the LCSs, the terminal-restriction fragment length polymorphism technique was employed. Using the functional genes of dsrB and soxB, SOB, including Halothiobacillus, Rhodothalassium, Paracocccus, Allochromatium, and Thiobacillus, and SRB, including Desulfovibrio, Syntrophobacter, Desulfomonile and Desulfobacca, were identical and exhibited the dominant role in the LCSs. By employing an alternative available corona reactor, more than 90% removal efficiencies of sulphides were demonstrated, suggesting that the LCSs for eliminating odours in a lower concentration would be feasible.

Bacterial community structure and activity of sulfate reducing bacteria in a membrane aerated biofilm analyzed by microsensor and molecular techniques.

PubMed

Liu, Hong; Tan, Shuying; Sheng, Zhiya; Liu, Yang; Yu, Tong

2014-11-01

The activities and vertical spatial distribution of sulfate reducing bacteria (SRB) in an oxygen (O2 )-based membrane aerated biofilm (MAB) were investigated using microsensor (O2 and H2 S) measurements and molecular techniques (polymerase chain reaction-denaturing gradient gel electrophoresis [PCR-DGGE] and fluorescence in situ hybridization [FISH]). The O2 concentration profile revealed that O2 penetrated from the bottom (substratum) of the gas permeable membrane, and was gradually consumed within the biofilm until it was completely depleted near the biofilm/bulk liquid interface, indicating oxic and anoxic zone in the MAB. The H2 S concentration profile showed that H2 S production was found in the upper 285 µm of the biofilm, indicating a high activity of SRB in this region. The results from DGGE of the PCR-amplified dissimilatory sulfite reductase subunit B (dsrB) gene and FISH showed an uneven spatial distribution of SRB. The maximum SRB biomass was located in the upper biofilm. The information from the molecular analysis can be supplemented with that from microsensor measurements to better understand the microbial community and activity of SRB in the MAB. © 2014 Wiley Periodicals, Inc.

Solid solution partitioning of Sr2+, Ba2+, and Cd2+ to calcite

USGS Publications Warehouse

Tesoriero, A.J.; Pankow, J.F.

1996-01-01

Although solid solutions play important roles in controlling the concentrations of minor metal ions in natural waters, uncertainties regarding their compositions, thermodynamics, and kinetics usually prevent them from being considered. A range of precipitation rates was used here to study the nonequilibrium and equilibrium partitioning behaviors of Sr2+, Ba2+, and Cd2+ to calcite (CaCO3(s)). The distribution coefficient of a divalent metal ion Me2+ for partitioning from an aqueous solution into calcite is given by DMe = (XMeCO3(s)/[Me2+])/(XCaCO3(s)/[Ca 2+]). The X values are solid-phase mole fractions; the bracketed values are the aqueous molal concentrations. In agreement with prior work, at intermediate to high precipitation rates R (nmol/mg-min), DSr, DBa, and DCd were found to depend strongly on R. At low R, the values of DSr, DBa, and DCd became constant with R. At 25??C, the equilibrium values for DSr, DBa, and DCd for dilute solid solutions were estimated to be 0.021 ?? 0.003, 0.012 ?? 0.005, and 1240 ?? 300, respectively. Calculations using these values were made to illustrate the likely importance of partitioning of these ions to calcite in groundwater systems. Due to its large equilibrium DMe value, movement of Cd2+ will be strongly retarded in aquifers containing calcite; Sr2+ and Ba2+ will not be retarded nearly as much.

Deep Soil Recharge in Arid and Semi-Arid Regions: New Evidences in MU-US Sandy Land of China

NASA Astrophysics Data System (ADS)

Cheng, Y.; Yang, W.; Zhan, H.

2017-12-01

Precipitation induced recharge is an important source of groundwater budget but it is very difficult to quantify in arid and semiarid regions. In this study, a newly invented lysimeter was used to monitor deep soil recharge (DSR) under 200 cm depth in MU-US sandy land in western China under three kinds of landforms (mobile dune, semi-fixed dune, and fixed dune). We found that the annual DSRs in such three different kinds of landforms varied significantly. Specifically, the annual DSRs were 224.1 mm (50.5% of the annual precipitation), 71.1 mm (50.5% of the annual precipitation), and 1.3 mm (0.3% of the annual precipitation) in mobile dune, semi-fixed dune, and fixed dune, respectively. We also found that vegetation coverage and precipitation pattern significantly affected DSR. A 24-hr precipitation event with the precipitation amount greater than 8 mm was able to infiltrate soil deeper than 200 cm and contributed to ground water recharge directly. Vegetation was a dominant factor influencing infiltration in the fixed sand dune. Our research revealed that precipitation induced DSR in arid and semi-arid regions was a complex process that required long-term monitoring and innovative system analysis of interrelated factors such as precipitation strength and pattern, meteorological parameters, and dynamic soil moisture. Key words: Precipitation pattern, sand dune groundwater, deep soil recharge, infiltration.

Multigrid preconditioned conjugate-gradient method for large-scale wave-front reconstruction.

PubMed

Gilles, Luc; Vogel, Curtis R; Ellerbroek, Brent L

2002-09-01

We introduce a multigrid preconditioned conjugate-gradient (MGCG) iterative scheme for computing open-loop wave-front reconstructors for extreme adaptive optics systems. We present numerical simulations for a 17-m class telescope with n = 48756 sensor measurement grid points within the aperture, which indicate that our MGCG method has a rapid convergence rate for a wide range of subaperture average slope measurement signal-to-noise ratios. The total computational cost is of order n log n. Hence our scheme provides for fast wave-front simulation and control in large-scale adaptive optics systems.

Comparison between a model-based and a conventional pyramid sensor reconstructor.

PubMed

Korkiakoski, Visa; Vérinaud, Christophe; Le Louarn, Miska; Conan, Rodolphe

2007-08-20

A model of a non-modulated pyramid wavefront sensor (P-WFS) based on Fourier optics has been presented. Linearizations of the model represented as Jacobian matrices are used to improve the P-WFS phase estimates. It has been shown in simulations that a linear approximation of the P-WFS is sufficient in closed-loop adaptive optics. Also a method to compute model-based synthetic P-WFS command matrices is shown, and its performance is compared to the conventional calibration. It was observed that in poor visibility the new calibration is better than the conventional.

Display system replacement baseline research report.

DOT National Transportation Integrated Search

2000-12-01

This report provides baseline measurements on the Display System Replacement (DSR). These measurements followed six constructs: : safety, capacity, performance, workload, usability, and simulation fidelity. To collect these measurements, human factor...

Intelligent Sensing and Classification in DSR-Based Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Dempsey, Tae; Sahin, Gokhan; Morton, Yu T. (Jade

Wireless ad hoc networks have fundamentally altered today's battlefield, with applications ranging from unmanned air vehicles to randomly deployed sensor networks. Security and vulnerabilities in wireless ad hoc networks have been considered at different layers, and many attack strategies have been proposed, including denial of service (DoS) through the intelligent jamming of the most critical packet types of flows in a network. This paper investigates the effectiveness of intelligent jamming in wireless ad hoc networks using the Dynamic Source Routing (DSR) and TCP protocols and introduces an intelligent classifier to facilitate the jamming of such networks. Assuming encrypted packet headers and contents, our classifier is based solely on the observable characteristics of size, inter-arrival timing, and direction and classifies packets with up to 99.4% accuracy in our experiments.

Passive and Active Analysis in DSR-Based Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Dempsey, Tae; Sahin, Gokhan; Morton, Y. T. (Jade)

Security and vulnerabilities in wireless ad hoc networks have been considered at different layers, and many attack strategies have been proposed, including denial of service (DoS) through the intelligent jamming of the most critical packet types of flows in a network. This paper investigates the effectiveness of intelligent jamming in wireless ad hoc networks using the Dynamic Source Routing (DSR) and TCP protocols and introduces an intelligent classifier to facilitate the jamming of such networks. Assuming encrypted packet headers and contents, our classifier is based solely on the observable characteristics of size, inter-arrival timing, and direction and classifies packets with up to 99.4% accuracy in our experiments. Furthermore, we investigate active analysis, which is the combination of a classifier and intelligent jammer to invoke specific responses from a victim network.

Denitrifying sulfide removal process on high-salinity wastewaters in the presence of Halomonas sp.

PubMed

Liu, Chunshuang; Zhao, Dongfeng; Ma, Wenjuan; Guo, Yadong; Wang, Aijie; Wang, Qilin; Lee, Duu-Jong

2016-02-01

Biological conversion of sulfide, acetate, and nitrate to, respectively, elemental sulfur (S(0)), carbon dioxide, and nitrogen-containing gas (such as N2) at NaCl concentration of 35-70 g/L was achieved in an expanded granular sludge bed (EGSB) reactor. A C/N ratio of 1:1 was noted to achieve high sulfide removal and S(0) conversion rate at high salinity. The extracellular polymeric substance (EPS) quantities were increased with NaCl concentration, being 11.4-mg/g volatile-suspended solids at 70 mg/L NaCl. The denitrifying sulfide removal (DSR) consortium incorporated Thauera sp. and Halomonas sp. as the heterotrophs and Azoarcus sp. being the autotrophs at high salinity condition. Halomonas sp. correlates with the enhanced DSR performance at high salinity.

Colorstratigraphy; A New Stratigraphic Correlation Technique

NASA Astrophysics Data System (ADS)

Nanayakkara, N. U.; Ranasinghage, P. N.; Priyantha, C.; Abillapitiya, T.

2016-12-01

Here we introduce a novel stratigraphic technique namely colorstratigraphy for correlating sedimentary sequences. Minihagalkanda is about 1 km long amphitheater like sedimentary terrain, situated at the southeastern coast of Sri Lanka. It has Miocene sedimentary sequences, separated in to 10-12 m high small hillocks by erosion, and bounded by about 30 m high escarpment. Sandstone, yellowish sandy clay, greenish silty clay sequences are capped by 4-5 m limestone bed in these hillocks but not at the boundary escarpment. Stratigraphic profiles at two hillocks and the boundary escarpment, separated each other by 200-300 m, were selected to test the new colorstartigraphic correlation technique. Color reflectance (DSR) was measured at four samples in each sequence at every profile and hence altogether 36 reflectance measurements were taken using Minolta 2500D hand-held color spectrophotometer. The first-derivative of the reflectance spectra (dR/dλ) defines the "spectral shape" of the sample. Therefore, DSR data (360-740 nm) measured at 10 nm resolution were used to calculate a center-weighted, first-derivative spectra for each reflectance sample consisting of 39 channels. Particle size of each sequence was measured at all 03 profiles using laser particle size analyzer to verify the stratigraphic correlation. Mean reflectance spectrum for each sequence at all 03 profiles were plotted on the same graph for comparison. Same was done for the grain size spectrums. Discriminant function analysis was performed separately for dsr data and grain size data using a number assigned to each sedimentary sequence as the grouping variable Color spectrums of sandstone, yellowish sandy clay, and greenish silty clay sequences at all three profiles perfectly match showing clear stratigraphic correlation among these three stratigraphic profiles. Matching grain size distribution curves of the three sequence at the three profiles verify the stratigraphic correlation. Perfect 100 % discrimination of the three sequences with color reflectance data proves the accuracy of the correlation. Similar 100 % discrimination resulted with grain size data further verifies the results. Therefore, colorstratigraphy based on DSR can be introduced as a quick and easy technique for stratigraphic correlation of sedimentary sequences.

Compact all-fiber figure-9 dissipative soliton resonance mode-locked double-clad Er:Yb laser.

PubMed

Krzempek, Karol; Sotor, Jaroslaw; Abramski, Krzysztof

2016-11-01

The first demonstration of a compact all-fiber figure-9 double-clad erbium-ytterbium laser working in the dissipative soliton resonance (DSR) regime is presented. Mode-locking was achieved using a nonlinear amplifying loop (NALM) resonator configuration. The laser was assembled with an additional 475 m long spool of SMF28 fiber in the NALM loop in order to obtain large net-anomalous cavity dispersion (-10.4  ps²), and therefore ensure that DSR would be the dominant mode-locking mechanism. At maximum pump power (4.78 W) the laser generated rectangular-shaped pulses with 455 ns duration and an average power of 950 mW, which at a repetition frequency of 412 kHz corresponds to a record energy of 2.3 μJ per pulse.

On the routing protocol influence on the resilience of wireless sensor networks to jamming attacks.

PubMed

Del-Valle-Soto, Carolina; Mex-Perera, Carlos; Monroy, Raul; Nolazco-Flores, Juan Arturo

2015-03-27

In this work, we compare a recently proposed routing protocol, the multi-parent hierarchical (MPH) protocol, with two well-known protocols, the ad hoc on-demand distance vector (AODV) and dynamic source routing (DSR). For this purpose, we have developed a simulator, which faithfully reifies the workings of a given protocol, considering a fixed, reconfigurable ad hoc network given by the number and location of participants, and general network conditions. We consider a scenario that can be found in a large number of wireless sensor network applications, a single sink node that collects all of the information generated by the sensors. The metrics used to compare the protocols were the number of packet retransmissions, carrier sense multiple access (CSMA) inner loop retries, the number of nodes answering the queries from the coordinator (sink) node and the energy consumption. We tested the network under ordinary (without attacks) conditions (and combinations thereof) and when it is subject to different types of jamming attacks (in particular, random and reactive jamming attacks), considering several positions for the jammer. Our results report that MPH has a greater ability to tolerate such attacks than DSR and AODV, since it minimizes and encapsulates the network segment under attack. The self-configuring capabilities of MPH derived from a combination of a proactive routes update, on a periodic-time basis, and a reactive behavior provide higher resilience while offering a better performance (overhead and energy consumption) than AODV and DSR, as shown in our simulation results.

On the MAC/network/energy performance evaluation of Wireless Sensor Networks: Contrasting MPH, AODV, DSR and ZTR routing protocols.

PubMed

Del-Valle-Soto, Carolina; Mex-Perera, Carlos; Orozco-Lugo, Aldo; Lara, Mauricio; Galván-Tejada, Giselle M; Olmedo, Oscar

2014-12-02

Wireless Sensor Networks deliver valuable information for long periods, then it is desirable to have optimum performance, reduced delays, low overhead, and reliable delivery of information. In this work, proposed metrics that influence energy consumption are used for a performance comparison among our proposed routing protocol, called Multi-Parent Hierarchical (MPH), the well-known protocols for sensor networks, Ad hoc On-Demand Distance Vector (AODV), Dynamic Source Routing (DSR), and Zigbee Tree Routing (ZTR), all of them working with the IEEE 802.15.4 MAC layer. Results show how some communication metrics affect performance, throughput, reliability and energy consumption. It can be concluded that MPH is an efficient protocol since it reaches the best performance against the other three protocols under evaluation, such as 19.3% reduction of packet retransmissions, 26.9% decrease of overhead, and 41.2% improvement on the capacity of the protocol for recovering the topology from failures with respect to AODV protocol. We implemented and tested MPH in a real network of 99 nodes during ten days and analyzed parameters as number of hops, connectivity and delay, in order to validate our Sensors 2014, 14 22812 simulator and obtain reliable results. Moreover, an energy model of CC2530 chip is proposed and used for simulations of the four aforementioned protocols, showing that MPH has 15.9% reduction of energy consumption with respect to AODV, 13.7% versus DSR, and 5% against ZTR.

Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments.

PubMed

Varon-Lopez, Maryeimy; Dias, Armando Cavalcante Franco; Fasanella, Cristiane Cipolla; Durrer, Ademir; Melo, Itamar Soares; Kuramae, Eiko Eurya; Andreote, Fernando Dini

2014-03-01

Mangrove soils are anaerobic environments rich in sulphate and organic matter. Although the sulphur cycle is one of the major actors in this ecosystem, little is known regarding the sulphur bacteria communities in mangrove soils. We investigated the abundance, composition and diversity of sulphur-oxidizing (SOB) and sulphate-reducing (SRB) bacteria in sediments from three Brazilian mangrove communities: two contaminated, one with oil (OilMgv) and one with urban waste and sludge (AntMgv), and one pristine (PrsMgv). The community structures were assessed using quantitative real-time polymerase chain reaction (qPCR), polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries, using genes for the enzymes adenosine-5'-phosphosulphate reductase (aprA) and sulphite reductase (Dsr) (dsrB). The abundance for qPCR showed the ratio dsrB/aprA to be variable among mangroves and higher according to the gradient observed for oil contamination in the OilMgv. The PCR-DGGE patterns analysed by Nonmetric Multidimensional Scaling revealed differences among the structures of the three mangrove communities. The clone libraries showed that Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were the most abundant groups associated with sulphur cycling in mangrove sediments. We conclude that the microbial SOB and SRB communities in mangrove soils are different in each mangrove forest and that such microbial communities could possibly be used as a proxy for contamination in mangrove forests. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment

PubMed Central

2012-01-01

Background Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Results Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Conclusions Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other. PMID:22935169

Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment.

PubMed

Andrade, Luiza L; Leite, Deborah C A; Ferreira, Edir M; Ferreira, Lívia Q; Paula, Geraldo R; Maguire, Michael J; Hubert, Casey R J; Peixoto, Raquel S; Domingues, Regina M C P; Rosado, Alexandre S

2012-08-30

Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Mangrove sediment was sampled from 0-5, 15-20 and 35-40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0-5 cm) being greater than in both deeper sediment layers (15-20 and 35-40 cm), which were similar to each other.

Interactive models of depression vulnerability: the role of childhood trauma, dysfunctional attitudes, and coping.

PubMed

Morris, Matthew C; Kouros, Chrystyna D; Fox, Kathryn R; Rao, Uma; Garber, Judy

2014-06-01

This prospective study investigated whether within-individual relations between depression vulnerability factors (childhood trauma, dysfunctional attitudes, maladaptive coping) and depressive symptom trajectories varied as a function of the number of prior major depressive episodes (MDEs) experienced in their lifetime. Participants were 68 young adults who varied with regard to their history of depression; 32 were remitted depressed and 36 were never depressed. Depressive symptoms and disorders were assessed using semi-structured psychiatric interviews conducted twice over a 6-month period; interviews yielded weekly ratings of depressive symptoms during the follow-up interval. Childhood trauma, dysfunctional attitudes and coping were assessed with self-report measures. Data analyses were conducted using time-lagged multilevel models. Individuals with more previous MDEs who reported greater childhood trauma exposure, more dysfunctional attitudes, or greater use of maladaptive coping strategies experienced more rapid increases in depressive symptoms during the follow-up period. A significant interaction of coping, number of previous MDEs, and time was found indicating that among individuals with less adaptive coping (i.e., lower primary or lower secondary control coping scores), depressive symptoms rating (DSR) increased significantly in relation to number of prior depressive episodes; no change in DSR was observed for never-depressed individuals. Among individuals with higher primary control coping scores, significant increases in DSR scores were observed for individuals with ≥3 prior MDEs only. Findings highlight the need for treatment and prevention programmes that target stress reactivity and coping strategies early in the course of depression. © 2013 The British Psychological Society.

Interactive models of depression vulnerability: The role of childhood trauma, dysfunctional attitudes, and coping

PubMed Central

Morris, Matthew C.; Kouros, Chrystyna D.; Fox, Kathryn R.; Rao, Uma; Garber, Judy

2013-01-01

Objectives This prospective study investigated whether within-individual relations between depression vulnerability factors (childhood trauma, dysfunctional attitudes, maladaptive coping) and depressive symptom trajectories varied as a function of the number of prior major depressive episodes experienced in their lifetime. Design Participants were 68 young adults who varied with regard to their history of depression; 32 were remitted depressed and 36 were never depressed Methods Depressive symptoms and disorders were assessed using semi-structured psychiatric interviews conducted twice over a 6-month period; interviews yielded weekly ratings of depressive symptoms during the follow-up interval. Childhood trauma, dysfunctional attitudes and coping were assessed with self-report measures. Data analyses were conducted using time-lagged multilevel models. Results Individuals with more previous major depressive episodes (MDEs) who reported greater childhood trauma exposure, more dysfunctional attitudes, or greater use of maladaptive coping strategies experienced more rapid increases in depressive symptoms during the follow-up period. A significant interaction of coping, number of previous MDEs, and time was found indicating that among individuals with less adaptive coping (i.e., lower primary or lower secondary control coping scores), depressive symptoms (DSR) increased significantly in relation to number of prior depressive episodes; no change in DSR was observed for never-depressed individuals. Among individuals with higher primary control coping scores, significant increases in DSR scores were observed for individuals with ≥ 3 prior MDEs only. Conclusions Findings highlight the need for treatment and prevention programs that target stress reactivity and coping strategies early in the course of depression. PMID:24372468

Differential response in chick survival to diet in least and crested auklets

USGS Publications Warehouse

Gall, Adrian E.; Roby, D.D.; Irons, D.B.; Rose, I.C.

2006-01-01

Least auklets Aethia pusilla and crested auklets A. cristatella are abundant planktivorous seabirds found throughout the Bering Sea and are inextricably linked to the secondary productivity of this northern marine ecosystem. We assessed the relationship between productivity and diet in least and crested auklets by examining breeding chronology, daily survival rates (DSR) of chicks, and nestling diet composition at 2 mixed colonies on St. Lawrence Island in the northern Bering Sea during the 2000 to 2002 breeding seasons. Nestlings of both least and crested auklets hatched earlier, had higher survival rates, and were fed more of the large, oceanic copepod Neocalanus cristatus in 2002 compared to the 2 yr of lower chick survival. In contrast, during the year of lowest DSR for both auklet species (2001), the small copepod Calanus marshallae was more prevalent in the diet of least auklets and the mid-sized copepod N. flemingeri was more prevalent in the diet of crested auklets compared to the other 2 yr. The prevalence of oceanic copepods in meals fed to chicks explained much of the annual variation in DSR in least auklets. Interannual differences in timing of nest initiation, nest survival, and diet of least and crested auklets may be associated with the strength of the cold, nutrient-rich Anadyr Current, which passes in close proximity to St. Lawrence Island and has important influences on zooplankton productivity and distribution. Auklet productivity and diet composition may serve as key indicators in the overall effort to monitor the impact of climate change on the productivity of the Bering Sea.

Optimization of arsenic removal water treatment system through characterization of terminal electron accepting processes.

PubMed

Upadhyaya, Giridhar; Clancy, Tara M; Brown, Jess; Hayes, Kim F; Raskin, Lutgarde

2012-11-06

Terminal electron accepting process (TEAP) zones developed when a simulated groundwater containing dissolved oxygen (DO), nitrate, arsenate, and sulfate was treated in a fixed-bed bioreactor system consisting of two reactors (reactors A and B) in series. When the reactors were operated with an empty bed contact time (EBCT) of 20 min each, DO-, nitrate-, sulfate-, and arsenate-reducing TEAP zones were located within reactor A. As a consequence, sulfate reduction and subsequent arsenic removal through arsenic sulfide precipitation and/or arsenic adsorption on or coprecipitation with iron sulfides occurred in reactor A. This resulted in the removal of arsenic-laden solids during backwashing of reactor A. To minimize this by shifting the sulfate-reducing zone to reactor B, the EBCT of reactor A was sequentially lowered from 20 min to 15, 10, and 7 min. While 50 mg/L (0.81 mM) nitrate was completely removed at all EBCTs, more than 90% of 300 μg/L (4 μM) arsenic was removed with the total EBCT as low as 27 min. Sulfate- and arsenate-reducing bacteria were identified throughout the system through clone libraries and quantitative PCR targeting the 16S rRNA, dissimilatory (bi)sulfite reductase (dsrAB), and dissimilatory arsenate reductase (arrA) genes. Results of reverse transcriptase (RT) qPCR of partial dsrAB (i.e., dsrA) and arrA transcripts corresponded with system performance. The RT qPCR results indicated colocation of sulfate- and arsenate-reducing activities, in the presence of iron(II), suggesting their importance in arsenic removal.

Provenance of Holocene sediment on the Chukchi-Alaskan margin based on combined diffuse spectral reflectance and quantitative X-Ray Diffraction analysis

USGS Publications Warehouse

Ortiz, J.D.; Polyak, L.; Grebmeier, J.M.; Darby, D.; Eberl, D.D.; Naidu, S.; Nof, D.

2009-01-01

Sediment clay and silt mineral assemblages provide an excellent means of assessing the provenance of fine-grained Arctic sediment especially when a unique mineral assemblage can be tied to specific source areas. The diffuse spectral reflectance (DSR) first derivative measurements and quantitative X-Ray Diffraction (qXRD) on a high-resolution sediment core from the continental slope north of Alaska constrain the sediment mineralogy. DSR results are augmented by measurements on several adjacent cores and compared to surface sediment samples from the northern Alaskan shelf and slope. Using Principal Component Analysis (PCA), we infer that the three leading DSR modes relate to mixtures of smectite + dolomite, illite + goethite, and chlorite + muscovite. This interpretation is consistent with the down core qXRD results. While the smectite + dolomite, and illite + goethite factors show increased variability down core, the chlorite + muscovite factor had highest positive loadings in the middle Holocene, between ca. 6.0 and 3.6??ka. Because the most likely source of the chlorite + muscovite suite in this vicinity lies in the North Pacific, we argue that the oscillations in chlorite + muscovite values likely reflect an increase in the inflow of Pacific water to the Arctic through the Bering Strait. The time interval of this event is associated in other parts of the globe with a non-linear response of the climate system to the decrease in insolation, which may be related to changes in water exchange between the Pacific and Arctic Ocean. ?? 2009 Elsevier B.V.

Performance evaluation and specification of trackless tack : [project summary].

DOT National Transportation Integrated Search

2016-09-01

Researchers compared two tracking resistance tests for tack: a track-free time test and a modified dynamic shear rheometer (DSR) tackiness test. : Researchers compared four bond strength tests: interface shear, pull-off, torque, and Arcan. Then, usin...

Evaluation of dynamic shear rheometer tests for emulsions.

DOT National Transportation Integrated Search

2014-12-01

DSR-based rheological tests of 20 different : asphalt emulsion residues were : performed and relationships : with elastic recovery (A : ASHTO : T301) and force ductility (AASHTO T : 300) were investigated. In stra : in sweep test from 2% to 52% : , i...

Comparison of scales for evaluating premenstrual symptoms in women using oral contraceptives.

PubMed

Coffee, Andrea L; Kuehl, Thomas J; Sulak, Patricia J

2008-05-01

To compare two scales used in research to evaluate daily premenstrual mood symptoms during use of a monophasic oral contraceptive. Subanalysis of data from a prospective study. University-affiliated medical center. SUBJECTS; One hundred two reproductive-aged (18-48 yrs) women taking a monophasic oral contraceptive containing ethinyl estradiol and drospirenone in the standard 21-7 fashion (21 days of hormones followed by 7 days of placebo), and who had self-identified premenstrual symptoms of headache, mood changes, or pelvic pain. Subjects completed a single-item questionnaire, the Scott & White Daily Diary of Symptoms, and a multiple-item questionnaire, the Penn State Daily Symptom Report (DSR), to assess their premenstrual symptoms. The Scott & White diary used a visual analog scale of 0-10 to assess pelvic pain, headache, and mood (a composite of anxiety, depression, and irritability). The Penn State DSR contained 17 items: 10 behavioral and seven physical components, each rated on a scale of 0-4, with one item that specifically rated mood swings. Scores from the two scales were compared by using Spearman correlation coefficients, the Kendall W for concordance, and linear regression of ranked sums for study cycles. The Scott & White mood score significantly correlated with the total of the 17 items on the Penn State DSR, as well as the 10 behavioral items, the seven physical items, and the single mood-swing item (p<0.0001); specific coefficients of concordance were 0.44, 0.23, 0.10, and 0.28, respectively, and R2 values were 0.39, 0.39, 0.30, and 0.34, respectively. The daily Scott & White mood score was positively correlated with all 17 elements of the Penn State DSR (0.25-0.57). The greatest correlation was seen with the mood-swing element. Both instruments demonstrated the same patterns during the 21-7 oral contraceptive cycle, with symptoms increasing immediately before and peaking during the 7-day hormone-free interval. A single-item daily mood score using a rating scale of 0-10 was concordant with a relatively complex 17-element symptom index and demonstrated the same pattern of change during cycles of oral contraception. The simple scoring system offers an advantage, especially in clinical studies of long duration.

Productivity trade-off with different water regimes and genotypes of rice under non-puddled conditions in Eastern India.

PubMed

Kar, Ipsita; Sudhir-Yadav; Mishra, Amit; Behera, Basudev; Khanda, Chandramani; Kumar, Virender; Kumar, Ashok

2018-06-01

Increasing farm labor scarcity and depletion of natural resources such as water are posing a major threat to the sustainability of traditional puddled transplanted rice (PTR) farming in Eastern India. Dry-seeded rice (DSR) or non-puddled transplanted rice (NPTR) could be used as an alternative to PTR. To understand the trade-off with different water management and rice genotypes under non-puddled conditions, a field experiment was conducted during 2014-2015 on a sandy clay loam soil of Bhubaneswar, Odisha. The treatments for water regimes were based on soil water tension (no stress, 10 kPa, and 40 kPa) at 15-cm soil depth and the cultivars used in the study were inbreds (Lalat and Sahbhagi Dhan) and hybrids (Arize ® 6129, 6444, and US 323). In both years, rice yields were higher in the dry season than in the wet season. However, both establishment methods performed similarly in all the seasons. With an increase in water stress, there was a significant decline in yield and yield attributes in the dry season. Irrigation input in the dry season was roughly more than double that in the wet season. Irrigation input was relatively higher in DSR than in NPTR in all the seasons, which might be because of an extra irrigation required for DSR crop establishment than for transplanting in non-puddled conditions where watering is done only for ease of transplanting. There was irrigation saving of 25% and 58% in 10 kPa and 40 kPa, respectively, compared to no stress in the dry season. A consistent trend of an increase in irrigation water productivity (WP I ) and input water productivity (WP I+R ) was observed with an increase in stress. Arize ® 6444 produced the highest grain yield, irrigation and input water productivity, and its performance was also better in terms of tiller density, LAI, and biomass. Our findings highlight the potential of hybrids compared with inbreds and their performance under DSR was found to be superior. Even though the yield in no stress was slightly higher than in 10and kPa, the irrigation water savings in 10 kPa were distinctly significant.

Forced virus evolution reveals functional crosstalk between the disulfide bonded region and membrane proximal ectodomain region of HIV-1 gp41

PubMed Central

2013-01-01

Background The disulfide-bonded region (DSR) of HIV-1 gp41 mediates association with gp120 and plays a role in transmission of receptor-induced conformational changes in gp120 to gp41 that activate membrane fusion function. In this study, forced viral evolution of a DSR mutant that sheds gp120 was employed to identify domains within gp120-gp41 that are functionally linked to the glycoprotein association site. Results The HIV-1AD8 mutant, W596L/K601D, was serially passaged in U87.CD4.CCR5 cells until replication was restored. Whereas the W596L mutation persisted throughout the cultures, a D601H pseudoreversion in the DSR partially restored cell-free virus infectivity and virion gp120-gp41 association, with further improvements to cell-free virus infectivity following a 2nd-site D674E mutation in the membrane-proximal external region (MPER) of gp41. In an independent culture, D601H appeared with a deletion in V4 (Thr-394-Trp-395) and a D674N substitution in the MPER, however this MPER mutation was inhibitory to W596L/K601H cell-free virus infectivity. While cell-free virus infectivity was not fully restored for the revertant genotypes, their cell-to-cell transmission approached the levels observed for WT. Interestingly, the functional boost associated with the addition of D674E to W596L/K601H was not observed for cell-cell fusion where the cell-surface expressed glycoproteins function independently of virion assembly. The W596L/K601H and W596L/K601H/D674E viruses exhibited greater sensitivity to neutralization by the broadly reactive MPER directed monoclonal antibodies, 2F5 and 4E10, indicating that the reverting mutations increase the availability of conserved neutralization epitopes in the MPER. Conclusions The data indicate for the first time that functional crosstalk between the DSR and MPER operates in the context of assembled virions, with the Leu-596-His-601-Glu-674 combination optimizing viral spread via the cell-to-cell route. Our data also indicate that changes in the gp120-gp41 association site may increase the exposure of conserved MPER neutralization epitopes in virus. PMID:23618462

Evaluation of Thermal Oxidative Aging Effect on the Rheological Performance of Modified Asphalt Binders

NASA Astrophysics Data System (ADS)

Zhu, Cheng

Modified asphalt binder, which is combined by base binder and additive modifier, has been implemented in pavement industry for more than 30 years. Recently, the oxidative aging mechanism of asphalt binder has been studied for several decades, and appreciable finding results of asphalt binder aging mechanism were achieved from the chemistry and rheological performance aspects. However, most of these studies were conducted with neat binders, the research of aging mechanism of modified asphalt binder was limited. Nowadays, it is still highly necessary to clarify how the asphalt binder aging happens with the modified asphalt binder, what is the effect of the different modifiers (additives) on the binder aging process, how the rheological performance changes under the thermal oxidative aging conditions and so on. The objective of this study was to investigate the effect of isothermal oxidative aging conditions on the rheological performance change of the modified and controlled asphalt binders. There were totally 14 different sorts of asphalt binders had been aged in the PAV pans in the air-force drafted ovens at 50°C, 60°C and 85°C for 0.5 day to 240 days. The Fourier-Transform Infrared Spectroscopy (FT-IR) and Dynamic Shear Rheometer (DSR) were used to perform the experiments. The analysis of rheological indices (Low shear viscosity-LSV, Crossover modulus-G*c, Glover-Rowe Parameter-G-R, DSR function-DSR Fn) as a function of carbonyl area (CA) was conducted. With the SBS modification, both of the hardening susceptibility of the rheological index-LSV and G-R decreases compared with the corresponding base binder. The TR increased the hardening susceptibility of all the rheological indexes. While for the G*c, SBS increases the slope of the most modified asphalt binders except A and B_TR_X series binders. The multiple linear regression statistical analysis results indicate that the oxidative aging conditions play an important role on the CA, and rheological performance indexes. The modifiers-SBS and TR have different directional effect on these parameters. The field asphalt binder carbonyl area prediction was conducted. The pavement temperatures which were calculated by TEMP software were input into MATLAB(TM) as a parameter with other factors, e.g the asphalt binder oxidative aging parameters, the binder film thickness, the air void radius, etc., to calculate the field asphalt CA value as a function of time out to 20 years. It was found that the different rheological index method resulted different conclusion with the asphalt binder. The SBS modified asphalt binders of A, C version and B version had close average increasing rate of LSV, higher average decreasing rate of G*c, lower average increasing rate of DSR Fn compared with the corresponding base binders. D_HPM had lower average increasing rate of LSV, G*c and DSR Fn than base binder Base D. The tire rubber modified binder B_TR had higher average increasing rate of LSV, DSR Fn, and higher average decreasing rate of G*c than base binder Base B. The main finding of this study was that the modifier SBS and tire rubber can reduce the thermal oxidation aging rate (kf and kc) compared with the corresponding base binder, the activation energy was asphalt binder source dependent. For the hardening susceptibility, the modifiers-SBS, X, Y, Z reduced the HS of LSV and G-R. The tire rubber slightly increased the HS of LSV and G-R. A_PM, B_TR_X_PM reduced the HS of G*c and other modified binders increased the HS of G*c.

Central Federal Lands Division data collection packages : final report.

DOT National Transportation Integrated Search

2011-03-31

The purpose of this research study was to develop a proof of concept, prototype electronic data-collection and reporting system to facilitate the completion of Emergency Relief for Federally Owned (ERFO) Roads Damage Site Reports (DSR). The system wo...

A model of the human supervisor

NASA Technical Reports Server (NTRS)

Kok, J. J.; Vanwijk, R. A.

1977-01-01

A general model of the human supervisor's behavior is given. Submechanisms of the model include: the observer/reconstructor; decision-making; and controller. A set of hypothesis is postulated for the relations between the task variables and the parameters of the different submechanisms of the model. Verification of the model hypotheses is considered using variations in the task variables. An approach is suggested for the identification of the model parameters which makes use of a multidimensional error criterion. Each of the elements of this multidimensional criterion corresponds to a certain aspect of the supervisor's behavior, and is directly related to a particular part of the model and its parameters. This approach offers good possibilities for an efficient parameter adjustment procedure.

Fast algorithm for wavefront reconstruction in XAO/SCAO with pyramid wavefront sensor

NASA Astrophysics Data System (ADS)

Shatokhina, Iuliia; Obereder, Andreas; Ramlau, Ronny

2014-08-01

We present a fast wavefront reconstruction algorithm developed for an extreme adaptive optics system equipped with a pyramid wavefront sensor on a 42m telescope. The method is called the Preprocessed Cumulative Reconstructor with domain decomposition (P-CuReD). The algorithm is based on the theoretical relationship between pyramid and Shack-Hartmann wavefront sensor data. The algorithm consists of two consecutive steps - a data preprocessing, and an application of the CuReD algorithm, which is a fast method for wavefront reconstruction from Shack-Hartmann sensor data. The closed loop simulation results show that the P-CuReD method provides the same reconstruction quality and is significantly faster than an MVM.

Grade determination of crumb rubber-modified performance graded asphalt binder.

DOT National Transportation Integrated Search

2013-08-01

Due to particulates common in crumb rubber-modified asphalt binders, conventional PG grading using the Dynamic Shear Rheometer (DSR) with a gap height of 1.0 mm may not be valid and in accordance with current specifications. Asphalt binder testing an...

Grade determination of crumb rubber-modified performance graded asphalt binder.

DOT National Transportation Integrated Search

2013-08-01

Due to particulates common in crumb rubber-modified asphalt binders, conventional PG grading using the Dynamic : Shear Rheometer (DSR) with a gap height of 1.0 mm may not be valid and in accordance with current specifications. : Asphalt binder testin...

Plankton Production Biology

DTIC Science & Technology

2013-09-30

population dynamics (growth rate, production, mortality) of copepod nauplii in the field or captured water columns (mesocosms). Since biology...36-45, doi:10.1016/j.dsr.2012.03.001, 2012. PUBLICATIONS Banse, K., Naqvi, S.W.A., Narvekar, P.V., Postel, J.R., Jayakumar , D.A. Oxygen minimum

The generalized liquid drop model alpha-decay formula: Predictability analysis and superheavy element alpha half-lives

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

Dasgupta-Schubert, N.; Reyes, M.A.

2007-11-15

The predictive accuracy of the generalized liquid drop model (GLDM) formula for alpha-decay half-lives has been investigated in a detailed manner and a variant of the formula with improved coefficients is proposed. The method employs the experimental alpha half-lives of the well-known alpha standards to obtain the coefficients of the analytical formula using the experimental Q{sub {alpha}} values (the DSR-E formula), as well as the finite range droplet model (FRDM) derived Q{sub {alpha}} values (the FRDM-FRDM formula). The predictive accuracy of these formulae was checked against the experimental alpha half-lives of an independent set of nuclei (TEST) that span approximatelymore » the same Z, A region as the standards and possess reliable alpha spectroscopic data, and were found to yield good results for the DSR-E formula but not for the FRDM-FRDM formula. The two formulae were used to obtain the alpha half-lives of superheavy elements (SHE) and heavy nuclides where the relative accuracy was found to be markedly improved for the FRDM-FRDM formula, which corroborates the appropriateness of the FRDM masses and the GLDM prescription for high Z, A nuclides. Further improvement resulted, especially for the FRDM-FRDM formula, after a simple linear optimization over the calculated and experimental half-lives of TEST was used to re-calculate the half-lives of the SHE and heavy nuclides. The advantage of this optimization was that it required no re-calculation of the coefficients of the basic DSR-E or FRDM-FRDM formulae. The half-lives for 324 medium-mass to superheavy alpha decaying nuclides, calculated using these formulae and the comparison with experimental half-lives, are presented.« less

Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site

PubMed Central

Chang, Yun-Juan; Peacock, Aaron D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Macnaughton, Sarah J.; Hussain, A. K. M. Anwar; Saxton, Arnold M.; White, David C.

2001-01-01

Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from δ-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within δ-Proteobacteria were mainly recovered from low-uranium (≤302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. PMID:11425735

Influence of COD/sulfate ratios on the integrated reactor system for simultaneous removal of carbon, sulfur and nitrogen.

PubMed

Yuan, Ye; Chen, Chuan; Zhao, Youkang; Wang, Aijie; Sun, Dezhi; Huang, Cong; Liang, Bin; Tan, Wenbo; Xu, Xijun; Zhou, Xu; Lee, Duu-Jung; Ren, Nanqi

2015-01-01

An integrated reactor system was developed for the simultaneous removal of carbon, sulfur and nitrogen from sulfate-laden wastewater and for elemental sulfur (S°) reclamation. The system mainly consisted of an expanded granular sludge bed (EGSB) for sulfate reduction and organic carbon removal (SR-CR), an EGSB for denitrifying sulfide removal (DSR), a biological aerated filter for nitrification and a sedimentation tank for sulfur reclamation. This work investigated the influence of chemical oxygen demand (COD)/sulfate ratios on the performance of the system. Influent sulfate and ammonium were fixed to the level of 600 mg SO(4)(2-) L⁻¹ and 120 mg NH(4)(+) L⁻¹, respectively. Lactate was introduced to generate COD/SO(4)(2-) = 0.5:1, 1:1, 1.5:1, 2:1, 3:1, 3.5:1 and 4:1. The experimental results indicated that sulfate could be efficiently reduced in the SR-CR unit when the COD/SO(4)(2-) ratio was between 1:1 and 3:1, and sulfate reduction was inhibited by the growth of methanogenic bacteria when the COD/SO(4)(2-) ratio was between 3.5:1 and 4:1. Meanwhile, the Org-C/S²⁻/NO(3)(-) ratios affected the S(0) reclamation efficiency in the DSR unit. When the influent COD/SO(4)(2-) ratio was between 1:1 and 3:1, appropriate Org-C/S²⁻/NO(3)(-) ratios could be achieved to obtain a maximum S° recovery in the DSR unit. For the microbial community of the SR-CR unit at different COD/SO(4)(2-) ratios, 16S rRNA gene-based high throughput Illumina MiSeq sequencing was used to analyze the diversity and potential function of the dominant species.

Quantitative assessment of the presence of a single leg separation in Björk-Shiley convexoconcave prosthetic heart valves.

PubMed

Vrooman, H A; Maliepaard, C; van der Linden, L P; Jessurun, E R; Ludwig, J W; Plokker, H W; Schalij, M J; Weeda, H W; Laufer, J L; Huysmans, H A; Reiber, J H

1997-09-01

The authors developed an analytic software package for the objective and reproducible assessment of a single leg separation (SLS) in the outlet strut of Björk-Shiley convexoconcave (BSCC) prosthetic heart valves. The radiographic cinefilm recordings of 18 phantom valves (12 intact and 6 SLS) and of 43 patient valves were acquired. After digitization of regions of interest in a cineframe, several processing steps were carried out to obtain a one-dimensional corrected and averaged density profile along the central axis of each strut leg. To characterize the degree of possible separation, two quantitative measures were introduced: the normalized pit depth (NPD) and the depth-sigma ratio (DSR). The group of 43 patient studies was divided into a learning set (25 patients) and a test set (18 patients). All phantom valves with an SLS were detected (sensitivity, 100%) at a specificity of 100%. The threshold values for the NPD and the DSR to decide whether a fracture was present or not were 3.6 and 2.5, respectively. On the basis of the visual interpretations of the 25 patient studies (learning set) by an expert panel, it was concluded that none of the patients had an SLS. To achieve a 100% specificity by quantitative analysis, the threshold values for the NPD and the DSR were set at 5.8 and 2.5, respectively, for the patient data. Based on these threshold values, the analysis of patient data from the test set resulted in one false-negative detection and three false-positive detections. An analytic software package for the detection of an SLS was developed. Phantom data showed excellent sensitivity (100%) and specificity (100%). Further research and software development is needed to increase the sensitivity and specificity for patient data.

Using well casing as an electrical source to monitor hydraulic fracture fluid injection

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

Wilt, Michael; Nieuwenhuis, Greg; MacLennan, Kris

2016-03-09

The depth to surface resistivity (DSR) method transmits current from a source located in a cased or openhole well to a distant surface return electrode while electric field measurements are made at the surface over the target of interest. This paper presents both numerical modelling results and measured data from a hydraulic fracturing field test where conductive water was injected into a resistive shale reservoir during a hydraulic fracturing operation. Modelling experiments show that anomalies due to hydraulic fracturing are small but measureable with highly sensitive sensor technology. The field measurements confirm the model results,showing that measured differences in themore » surface fields due to hydraulic fracturing have been detected above the noise floor. Our results show that the DSR method is sensitive to the injection of frac fluids; they are detectable above the noise floor in a commercially active hydraulic fracturing operation, and therefore this method can be used for monitoring fracture fluid movement.« less

A Comparison Study of Magnetic Bearing Controllers for a Fully Suspended Dynamic Spin Rig

NASA Technical Reports Server (NTRS)

Choi, Benjamin; Johnson, Dexter; Morrison, Carlos; Mehmed, Oral; Huff, Dennis (Technical Monitor)

2002-01-01

NASA Glenn Research Center (GRC) has developed a fully suspended magnetic bearing system for the Dynamic Spin Rig (DSR) that is used to perform vibration tests of turbomachinery blades and components under spinning conditions in a vacuum. Two heteropolar radial magnetic bearings and a thrust bearing and the associated control system were integrated into the DSR to provide noncontact magnetic suspension and mechanical excitation of the 35 lb vertical rotor with blades to induce turbomachinery blade vibration. A simple proportional-integral-derivative (PID) controller with a special feature for multidirectional radial excitation worked very well to both support and shake the shaft with blades. However, more advanced controllers were developed and successfully tested to determine the optimal controller in terms of sensor and processing noise reduction, smaller rotor orbits, and energy savings for the system. The test results of a variety of controllers we demonstrated up to the rig's maximum allowable speed of 10,000 rpm are shown.

Psychometric Properties of the Dietary Salt Reduction Self-Care Behavior Scale.

PubMed

Srikan, Pratsani; Phillips, Kenneth D

2014-07-01

Valid, reliable, and culturally-specific scales to measure salt reduction self-care behavior in older adults are needed. The purpose of this study was to develop the Dietary Salt Reduction Self-Care Behavior Scale (DSR-SCB) for use in hypertensive older adults with Orem's self-care deficit theory as a base. Exploratory factor analysis, Rasch modeling, and reliability were performed on data from 242 older Thai adults. Nine items loaded on one factor (factor loadings = 0.63 to 0.79) and accounted for 52.28% of the variance (Eigenvalue = 4.71). The Kaiser-Meyer-Olkin method of sampling adequacy was 0.89, and the Bartlett's test showed significance (χ 2 ( df =36 ) = 916.48, p < 0.0001). Infit and outfit mean squares ranged from 0.81 to 1.25, while infit and outfit standardized mean squares were located at ±2. Cronbach's alpha was 0.88. The 9-item DSR-SCB is a short and reliable scale. © The Author(s) 2014.

Detection of Serum microRNAs From Department of Defense Serum Repository

PubMed Central

Woeller, Collynn F.; Thatcher, Thomas H.; Van Twisk, Daniel; Pollock, Stephen J.; Croasdell, Amanda; Kim, Nina; Hopke, Philip K.; Xia, Xiaoyan; Thakar, Juilee; Mallon, COL Timothy M.; Utell, Mark J.; Phipps, Richard P.

2017-01-01

Objective The aim of this study was to investigate whether serum samples from the Department of Defense Serum Repository (DoDSR) are of sufficient quality to detect microRNAs (miRNAs), cytokines, immunoglobulin E (IgE), and polycyclic aromatic hydrocarbons (PAHs). Methods MiRNAs were isolated and quantified by polymerase chain reaction (PCR) array. Cytokines and chemokines related to inflammation were measured using multiplex immunoassays. Cotinine and IgE were detected by enzyme-linked immunoassay (ELISA) and PAHs were detected by Liquid Chromatography/Mass Spectroscopy. Results We detected miRNAs, cytokines, IgE, and PAHs with high sensitivity. Eleven of 30 samples tested positive for cotinine suggesting tobacco exposure. Significant associations between serum cotinine, cytokine, IgE, PAHs, and miRNA were discovered. Conclusion We successfully quantified over 200 potential biomarkers of occupational exposure from DoDSR samples. The stored serum samples were not affected by hemolysis and represent a powerful tool for biomarker discovery and analysis in retrospective studies. PMID:27501106

MicroRNA Expression Profiling of the Armed Forces Health Surveillance Branch Cohort for Identification of "Enviro-miRs" Associated With Deployment-Based Environmental Exposure.

PubMed

Dalgard, Clifton L; Polston, Keith F; Sukumar, Gauthaman; Mallon, Col Timothy M; Wilkerson, Matthew D; Pollard, Harvey B

2016-08-01

The aim of this study was to identify serum microRNA (miRNA) biomarkers that indicate deployment-associated exposures in service members at military installations with open burn pits. Another objective was to determine detection rates of miRNAs in Department of Defense Serum Repository (DoDSR) samples with a high-throughput methodology. Low-volume serum samples (n = 800) were profiled by miRNA-capture isolation, pre-amplification, and measurement by a quantitative PCR-based OpenArray platform. Normalized quantitative cycle values were used for differential expression analysis between groups. Assay specificity, dynamic range, reproducibility, and detection rates by OpenArray passed target desired specifications. Serum abundant miRNAs were consistently measured in study specimens. Four miRNAs were differentially expressed in the case deployment group subjects. miRNAs are suitable RNA species for biomarker discovery in the DoDSR serum specimens. Serum miRNAs are candidate biomarkers for deployment and environmental exposure in military service members.

76 FR 37192 - Lake Providence Port Commission-Trackage Rights Exemption-Delta Southern Railroad, Inc.

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-24

... exemption is void ab initio. Petitions to revoke the exemption under 49 U.S.C. 10502(d) may be filed at any... will acquire from DSR. See Delta Southern R.R.--Aban. Exemption--in E. Carroll Parish, La., AB 384 (Sub...

Spatial distributions of sulphur species and sulphate-reducing bacteria provide insights into sulphur redox cycling and biodegradation hot-spots in a hydrocarbon-contaminated aquifer

NASA Astrophysics Data System (ADS)

Einsiedl, Florian; Pilloni, Giovanni; Ruth-Anneser, Bettina; Lueders, Tillman; Griebler, Christian

2015-05-01

Dissimilatory sulphate reduction (DSR) has been proven to be one of the most relevant redox reactions in the biodegradation of contaminants in groundwater. However, the possible role of sulphur species of intermediate oxidation state, as well as the role of potential re-oxidative sulphur cycling in biodegradation particularly at the groundwater table are still poorly understood. Here we used a combination of stable isotope measurements of SO42-, H2S, and S0 as well as geochemical profiling of sulphur intermediates with special emphasis on SO32-, S2O32-, and S0 to unravel possible sulphur cycling in the biodegradation of aromatics in a hydrocarbon-contaminated porous aquifer. By linking these results to the quantification of total bacterial rRNA genes and respiratory genes of sulphate reducers, as well as pyrotag sequencing of bacterial communities over depth, light is shed on possible key-organisms involved. Our results substantiate the role of DSR in biodegradation of hydrocarbons (mainly toluene) in the highly active plume fringes above and beneath the plume core. In both zones the concentration of sulphur intermediates (S0, SO32- and S2O32-) was almost twice that of other sampling-depths, indicating intense sulphur redox cycling. The dual isotopic fingerprint of oxygen and sulphur in dissolved sulphate suggested a re-oxidation of reduced sulphur compounds to sulphate especially at the upper fringe zone. An isotopic shift in δ34S of S0 of nearly +4‰ compared to the δ34S values of H2S from the same depth linked to a high abundance (∼10%) of sequence reads related to Sulphuricurvum spp. (Epsilonproteobacteria) in the same depth were indicative of intensive oxidation of S0 to sulphate in this zone. At the lower plume fringe S0 constituted the main inorganic sulphur species, possibly formed by abiotic re-oxidation of H2S with Fe(III)oxides subsequent to sulphate reduction. These results provide first insights into intense sulphur redox cycling in a hydrocarbon contaminant plume, which widens the perspective of redox processes and microbial interactions ongoing in contaminated aquifers.

A Black Hole Attack Model for Reactive Ad-Hoc Protocols

DTIC Science & Technology

2012-03-01

Technology Conference. IEEE, 2003. pp. 2286-2290. [BhS09] N. Bhalaji, and A. Shanmugam. "Association Between Nodes to Combat Blackhole Attack in DSR...2012. 102 [PSA09] A. Prathapani, L. Santhanam, and P. Agrawal. "Intelligent Honeypot Agent for Blackhole Attack Detection in Wireless Mesh

Reduced posting and marking of flight progress strips for en route air traffic control : final report.

DOT National Transportation Integrated Search

2000-02-01

The new Display System Replacement (DSR) being implemented in air route traffic control centers (ARTCCs) will allow the data-side controller less room to post Flight Progress Strips (FPSs). We tested a new FPS marking and posting procedure designed t...

Delayed Self-Recognition in Children with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Lind, Sophie E.; Bowler, Dermot M.

2009-01-01

This study aimed to investigate temporally extended self-awareness (awareness of one's place in and continued existence through time) in autism spectrum disorder (ASD), using the delayed self-recognition (DSR) paradigm (Povinelli et al., Child Development 67:1540-1554, 1996). Relative to age and verbal ability matched comparison children, children…

Crystal-chemical controls on the partitioning of Sr and Ba between plagioclase feldspar, silicate melts, and hydrothermal solutions

NASA Astrophysics Data System (ADS)

Blundy, Jonathan D.; Wood, Bernard J.

1991-01-01

The isothermal (750°C) experiments of LAGACHE and DUJON (1987) reveal that the partitioning of Sr between plagioclase feldspar and hydrothermal solutions is a funtion of the anorthite (An) content of the plagioclase, indicating that crystal chemistry may exert a powerful influence on trace element partitioning. In order to compare these results with those on trace element partitioning between plagioclase and silicate melts we have compiled from the literature a large dataset of experimental and volcanic distribution coefficients ( D's) for Sr (and Ba). These data, which span a compositional range from lunar basalt to high silica rhyolite and a temperature range of over 650°C, show a relationship between DSr (and DBa) and mole fraction An ( XAn) which is similar to that exhibited by the hydrothermal results obtained at constant temperature. Plots of In DSr and In DBa versus XAn are linear with negative slope, indicating that both elements are more compatible in albite than anorthite. In terms of molar distribution coefficients ( D Sr∗) the hydrothermal and silicate melt data display an identical linear relationship between RT In D Sr∗ (where T is the absolute temperature in K and R is the gas constant, 8.314 JK -1 mol -1) and XAn. We conclude therefore that crystal chemistry provides the dominant control on partitioning of Sr and Ba into plagioclase and that the effects of temperature, pressure, and fluid composition are minor. Apparent relationships between DSr (and DBa) and the reciprocal temperature (1/ T) are artefacts of the linear relationships between XAn and 1/ T in the experimental studies. By defining a Henry's law standard state for the silicate melts and hydrothermal solutions, and considering plagioclases to be ternary regular solutions, we are able to relate the observed relationships between RT In D i∗ (where i is Ba or Sr) and XAn to the excess free energies of the trace element partitioning reactions between plagioclase and melt or hydrothermal solution. The interaction parameters are consistent with simple models in which the larger Ba or Sr cations are accommodated by lattice strain in the host plagioclase lattice, which is assumed to be perfectly elastic and isotropic. Thus D i∗ is a function of the Young's modulus of the host crystal and the size mismatch between trace and host cations. The greater elasticity of albite relative to anorthite accounts for the observed preference of Sr and Ba for sodic plagioclases over calcic plagioclases. For geochemical purposes the weight fraction partition coefficient Di is of more value than its molar counterpart. Regression of the Di data versus XAn yields the semi-empirical relationships RTIn DSr = 26,800 - 26,700 · XAnRTIn DBa = 10,200 - 38,200 · XAn. Thus measurement of the An and trace element (Ba, Sr) contents of a magmatic plagioclase enables calculation of the Ba and Sr contents of the coexisting liquid, which can be extremely important in the deciphering of igneous processes. By reference to plagioclase fractionation in the simple An-Ab binary we show that failure to take into account the compositional dependence of DSr can result in erroneous interpretations of geochemical trends. We also consider applications to three natural igneous suites: the Aden Volcanics; the layered Kiglapait Intrusion, Labrador; and the southern Actamello Massif, Italy.

Effects of mutations on the insoluble glucan synthesized by Leuconostoc mesenteroides NRRL B-1118 glucansucrase

USDA-ARS?s Scientific Manuscript database

Twelve different amino acids were each substituted for Threonine-654 in a cloned glucansucrase from Leuconostoc mesenteroides NRRL B-1118 (DSR-I). The native enzyme produces a water-insoluble glucan containing approximately 44 mol% 1,3-disubstituted a-D-glucopyranosyl units and 29 mol% 1,6-disubstit...

RT-PCR FOR DETECTING EXPRESSION OF THE DISSIMILATORY BISULFITE REDUCTASE DSR GENE IN THE SEAGRASS RHIZOSPHERE

EPA Science Inventory

Sulfate-reducing bacteria (SRB) colonize the epidermis and cortex layers in roots of the seagrass, Halodule wrightii. The purpose of this study is to determine whether SRB reduces sulfate to sulfide within these roots. Summer lac-1 is a lactate-utilizing SRB isolated from the ro...

Simultaneous acquisition of EEG and NIRS during cognitive tasks for an open access dataset.

PubMed

Shin, Jaeyoung; von Lühmann, Alexander; Kim, Do-Won; Mehnert, Jan; Hwang, Han-Jeong; Müller, Klaus-Robert

2018-02-13

We provide an open access multimodal brain-imaging dataset of simultaneous electroencephalography (EEG) and near-infrared spectroscopy (NIRS) recordings. Twenty-six healthy participants performed three cognitive tasks: 1) n-back (0-, 2- and 3-back), 2) discrimination/selection response task (DSR) and 3) word generation (WG) tasks. The data provided includes: 1) measured data, 2) demographic data, and 3) basic analysis results. For n-back (dataset A) and DSR tasks (dataset B), event-related potential (ERP) analysis was performed, and spatiotemporal characteristics and classification results for 'target' versus 'non-target' (dataset A) and symbol 'O' versus symbol 'X' (dataset B) are provided. Time-frequency analysis was performed to show the EEG spectral power to differentiate the task-relevant activations. Spatiotemporal characteristics of hemodynamic responses are also shown. For the WG task (dataset C), the EEG spectral power and spatiotemporal characteristics of hemodynamic responses are analyzed, and the potential merit of hybrid EEG-NIRS BCIs was validated with respect to classification accuracy. We expect that the dataset provided will facilitate performance evaluation and comparison of many neuroimaging analysis techniques.

Simultaneous acquisition of EEG and NIRS during cognitive tasks for an open access dataset

PubMed Central

Shin, Jaeyoung; von Lühmann, Alexander; Kim, Do-Won; Mehnert, Jan; Hwang, Han-Jeong; Müller, Klaus-Robert

2018-01-01

We provide an open access multimodal brain-imaging dataset of simultaneous electroencephalography (EEG) and near-infrared spectroscopy (NIRS) recordings. Twenty-six healthy participants performed three cognitive tasks: 1) n-back (0-, 2- and 3-back), 2) discrimination/selection response task (DSR) and 3) word generation (WG) tasks. The data provided includes: 1) measured data, 2) demographic data, and 3) basic analysis results. For n-back (dataset A) and DSR tasks (dataset B), event-related potential (ERP) analysis was performed, and spatiotemporal characteristics and classification results for ‘target’ versus ‘non-target’ (dataset A) and symbol ‘O’ versus symbol ‘X’ (dataset B) are provided. Time-frequency analysis was performed to show the EEG spectral power to differentiate the task-relevant activations. Spatiotemporal characteristics of hemodynamic responses are also shown. For the WG task (dataset C), the EEG spectral power and spatiotemporal characteristics of hemodynamic responses are analyzed, and the potential merit of hybrid EEG-NIRS BCIs was validated with respect to classification accuracy. We expect that the dataset provided will facilitate performance evaluation and comparison of many neuroimaging analysis techniques. PMID:29437166

Physical and rheological properties of Titanium Dioxide modified asphalt

NASA Astrophysics Data System (ADS)

Buhari, Rosnawati; Ezree Abdullah, Mohd; Khairul Ahmad, Mohd; Chong, Ai Ling; Haini, Rosli; Khatijah Abu Bakar, Siti

2018-03-01

Titanium Dioxide (TiO2) has been known as a useful photocatalytic material that is attributed to the several characteristics includes high photocatalytic activity compared with other metal oxide photocatalysts, compatible with traditional construction materials without changing any original performance. This study investigates the physical and rheological properties of modified asphalt with TiO2. Five samples of asphalt with different concentration of TiO2 were studied, namely asphalt 2%, 4%, 6% 8% and 10% TiO2. The tests includes are penetration, softening point, ductility, rotational viscosity and dynamic shear rheometer (DSR) test. From the results of this study, it is noted that addition of TiO2 has significant effect on the physical properties of asphalt. The viscosity tests revealed that asphalt 10% TiO2 has good workability among with reducing approximately 15°C compared to base asphalt. Based on the results from DSR measurements, asphalt 10% TiO2 has reduced temperature susceptibility and increase stiffness and elastic behaviour in comparison to base asphalt. As a result, TiO2 can be considered to be an additive to modify the properties of asphalt.

Effect of fast pyrolysis bio-oil from palm oil empty fruit bunch on bitumen properties

NASA Astrophysics Data System (ADS)

Poh, Chia Chin; Hassan, Norhidayah Abdul; Raman, Noor Azah Abdul; Shukry, Nurul Athma Mohd; Warid, Muhammad Naqiuddin Mohd; Satar, Mohd Khairul Idham Mohd; Ros Ismail, Che; Asmah Hassan, Sitti; Mashros, Nordiana

2018-04-01

Bitumen shortage has triggered the exploration of another alternative waste material that can be blended with conventional bitumen. This study presents the performance of pyrolysis bio-oil from palm oil empty fruit bunch (EFB) as an alternative binder in modified bitumen mixtures. The palm oil EFB was first pyrolyzed using auger pyrolyzer to extract the bio-oil. Conventional bitumen 80/100 penetration grade was used as a control sample and compared with samples that were modified with different percentages, i.e., 5% and 10%, of pyrolysis EFB bio-oil. The physical and rheological properties of the control and modified bitumen samples were investigated using penetration, softening point, viscosity and dynamic shear rheometer (DSR) tests. Results showed that the addition of EFB bio-oil softened the bitumen with high penetration and a reduction in softening point, penetration index, and viscosity. However, the DSR results showed a comparable rutting resistance between the bitumen samples containing EFB bio-oil and virgin bitumen with a failure temperature achieved greater than 64°C.

Control Study for Five-axis Dynamic Spin Rig Using Magnetic Bearings

NASA Technical Reports Server (NTRS)

Choi, Benjamin; Johnson, Dexter; Provenza, Andrew; Morrison, Carlos; Montague, Gerald

2003-01-01

The NASA Glenn Research Center (GRC) has developed a magnetic bearing system for the Dynamic Spin Rig (DSR) with a fully suspended shaft that is used to perform vibration tests of turbomachinery blades and components under spinning conditions in a vacuum. Two heteropolar radial magnetic bearings and a thrust magnetic bearing and the associated control system were integrated into the DSR to provide magnetic excitation as well as non-contact mag- netic suspension of a 15.88 kg (35 lb) vertical rotor with blades to induce turbomachinery blade vibration. For rotor levitation, a proportional-integral-derivative (PID) controller with a special feature for multidirectional radial excitation worked well to both support and shake the shaft with blades. However, more advanced controllers were developed and successfully tested to determine the optimal controller in terms of sensor and processing noise reduction, smaller rotor orbits, more blade vibration amplitude, and energy savings for the system. The test results of a variety of controllers that were demonstrated up to 10.000 rpm are shown. Furthermore, rotor excitation operation and conceptual study of active blade vibration control are addressed.

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

PubMed Central

Thorup, Casper; Schramm, Andreas

2017-01-01

ABSTRACT This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus. Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase. PMID:28720728

Influence of selected test parameters on measured values during the MSCR test

NASA Astrophysics Data System (ADS)

Benešová, Lucie; Valentin, Jan

2017-09-01

One of today’s most commonly used test on a Dynamic Shear Rheometer (DSR) is the Multiple Stress Creep Recovery (MSCR) test. The test is described in the standard EN 16659, which is valid in the Czech Republic since October 2016. The principle of the test is based on repeated loading and recovering of a bitumen sample, according to which it is possible to determine the percentage of elastic recovery (R) and non-recoverable creep compliance (Jnr) of the bituminous binder. This method has been recently promoted as the most suitable test for assessing the resistance of bituminous binders to permanent deformation. The test is performed at higher temperatures and is particularly suitable for modified bituminous binders. The paper deals with the comparison of the different input parameters set on the DSR device - different levels of stress, temperature of test, the geometry of the measuring device and also a comparison of the results for a different number of loading cycles. The research study was focused mainly on modified bituminous binders, but to compare the MSCR test it is performed even with conventional paving grade binders.

Multi-conjugate AO for the European Solar Telescope

NASA Astrophysics Data System (ADS)

Montilla, I.; Béchet, C.; Le Louarn, M.; Tallon, M.; Sánchez-Capuchino, J.; Collados Vera, M.

2012-07-01

The European Solar Telescope (EST) will be a 4-meter diameter world-class facility, optimized for studies of the magnetic coupling between the deep photosphere and upper chromosphere. It will specialize in high spatial resolution observations and therefore it has been designed to incorporate an innovative built-in Multi-Conjugate Adaptive Optics system (MCAO). It combines a narrow field high order sensor that will provide the information to correct the ground layer and a wide field low order sensor for the high altitude mirrors used in the MCAO mode. One of the challenging particularities of solar AO is that it has to be able to correct the turbulence for a wide range of observing elevations, from zenith to almost horizon. Also, seeing is usually worse at day-time, and most science is done at visible wavelengths. Therefore, the system has to include a large number of high altitude deformable mirrors. In the case of the EST, an arrangement of 4 high altitude DMs is used. Controlling such a number of mirrors makes it necessary to use fast reconstruction algorithms to deal with such large amount of degrees of freedom. For this reason, we have studied the performance of the Fractal Iterative Method (FriM) and the Fourier Transform Reconstructor (FTR), to the EST MCAO case. Using OCTOPUS, the end-to-end simulator of the European Southern Observatory, we have performed several simulations with both algorithms, being able to reach the science requirement of a homogeneous Strehl higher that 50% all over the 1 arcmin field of view.

Display And Analysis Of Tomographic Volumetric Images Utilizing A Vari-Focal Mirror

NASA Astrophysics Data System (ADS)

Harris, L. D.; Camp, J. J.

1984-10-01

A system for the three-dimensional (3-D) display and analysis of stacks of tomographic images is described. The device utilizes the principle of a variable focal (vari-focal) length optical element in the form of an aluminized membrane stretched over a loudspeaker to generate a virtual 3-D image which is a visible representation of a 3-D array of image elements (voxels). The system displays 500,000 voxels per mirror cycle in a 3-D raster which appears continuous and demonstrates no distracting artifacts. The display is bright enough so that portions of the image can be dimmed without compromising the number of shades of gray. For x-ray CT, a displayed volume image looks like a 3-D radiograph which appears to be in the space directly behind the mirror. The viewer sees new views by moving his/her head from side to side or up and down. The system facilitates a variety of operator interactive functions which allow the user to point at objects within the image, control the orientation and location of brightened oblique planes within the volume, numerically dissect away selected image regions, and control intensity window levels. Photographs of example volume images displayed on the system illustrate, to the degree possible in a flat picture, the nature of displayed images and the capabilities of the system. Preliminary application of the display device to the analysis of volume reconstructions obtained from the Dynamic Spatial Reconstructor indicates significant utility of the system in selecting oblique sections and gaining an appreciation of the shape and dimensions of complex organ systems.

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

PubMed Central

2010-01-01

Background Some of the recent investigations in systems biology have revealed the existence of a complex regulatory network between genes, microRNAs (miRNAs) and transcription factors (TFs). In this paper, we focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. A putative TF of an miRNA is considered here as those binding within the close genomic locality of that miRNA with respect to its starting or ending base pair on the chromosome. Recent studies suggest that these putative TFs are possible regulators of those miRNAs. Description The interface is built around two datasets that consist of the exhaustive lists of putative TFs binding respectively in the 10 kb upstream region (USR) and downstream region (DSR) of human miRNAs. A web server, named as PuTmiR, is designed. It provides an option for extracting the putative TFs for human miRNAs, as per the requirement of a user, based on genomic locality, i.e., any upstream or downstream region of interest less than 10 kb. The degree distributions of the number of putative TFs and miRNAs against each other for the 10 kb USR and DSR are analyzed from the data and they explore some interesting results. We also report about the finding of a significant regulatory activity of the YY1 protein over a set of oncomiRNAs related to the colon cancer. Conclusion The interface provided by the PuTmiR web server provides an important resource for analyzing the direct and indirect regulation of human miRNAs. While it is already an established fact that miRNAs are regulated by TFs binding to their USR, this database might possibly help to study whether an miRNA can also be regulated by the TFs binding to their DSR. PMID:20398296

Representation of Time-Relevant Common Data Elements in the Cancer Data Standards Repository: Statistical Evaluation of an Ontological Approach

PubMed Central

Chen, Henry W; Du, Jingcheng; Song, Hsing-Yi; Liu, Xiangyu; Jiang, Guoqian

2018-01-01

Background Today, there is an increasing need to centralize and standardize electronic health data within clinical research as the volume of data continues to balloon. Domain-specific common data elements (CDEs) are emerging as a standard approach to clinical research data capturing and reporting. Recent efforts to standardize clinical study CDEs have been of great benefit in facilitating data integration and data sharing. The importance of the temporal dimension of clinical research studies has been well recognized; however, very few studies have focused on the formal representation of temporal constraints and temporal relationships within clinical research data in the biomedical research community. In particular, temporal information can be extremely powerful to enable high-quality cancer research. Objective The objective of the study was to develop and evaluate an ontological approach to represent the temporal aspects of cancer study CDEs. Methods We used CDEs recorded in the National Cancer Institute (NCI) Cancer Data Standards Repository (caDSR) and created a CDE parser to extract time-relevant CDEs from the caDSR. Using the Web Ontology Language (OWL)–based Time Event Ontology (TEO), we manually derived representative patterns to semantically model the temporal components of the CDEs using an observing set of randomly selected time-related CDEs (n=600) to create a set of TEO ontological representation patterns. In evaluating TEO’s ability to represent the temporal components of the CDEs, this set of representation patterns was tested against two test sets of randomly selected time-related CDEs (n=425). Results It was found that 94.2% (801/850) of the CDEs in the test sets could be represented by the TEO representation patterns. Conclusions In conclusion, TEO is a good ontological model for representing the temporal components of the CDEs recorded in caDSR. Our representative model can harness the Semantic Web reasoning and inferencing functionalities and present a means for temporal CDEs to be machine-readable, streamlining meaningful searches. PMID:29472179

Anti-Cyclic Citrullinated Peptide Assays Differ in Subjects at Elevated Risk for Rheumatoid Arthritis and Subjects with Established Disease

PubMed Central

Demoruelle, M. Kristen; Parish, Mark C.; Derber, Lezlie A.; Kolfenbach, Jason R.; Hughes-Austin, Jan M.; Weisman, Michael H.; Gilliland, William; Edison, Jess D.; Buckner, Jane H.; Mikuls, Ted R.; O’Dell, James R.; Keating, Richard M.; Gregersen, Peter K.; Norris, Jill M.; Holers, V. Michael; Deane, Kevin D.

2013-01-01

Objective To compare commonly-available tests for antibodies to citrullinated protein antigens (ACPAs) for diagnostic accuracy and assay agreement in established rheumatoid arthritis (RA) and subjects at elevated risk for RA. Methods ELISA testing for anti-cyclic citrullinated peptide (anti-CCP) antibodies was performed using CCP2 (Axis-Shield) and CCP3.1 (IgA/IgG INOVA) in the following subjects: 1) probands with established RA (N=340) from the Studies of the Etiology of RA (SERA), 2) first degree relatives (FDRs) without RA (family members of SERA RA probands; N=681), 3) Department of Defense Serum Repository (DoDSR) RA cases with pre-diagnosis samples (N=83; 47/83 also had post-diagnosis samples), and 4) blood-donor and DoDSR controls (N=283). Results In established RA, CCP2 was more specific (99.2% vs. 93.1%, p<0.01), but less sensitive (58.7% vs. 67.4%, p=0.01) than CCP3.1, with specificity of CCP3.1 increasing to 97.2% if levels ≥3 times the standard cut-off level were considered. In all subjects, at standard cut-off levels, CCP3.1 positivity was more prevalent. In DoDSR cases, CCP2 was more specific than CCP3.1 for a future diagnosis of RA, and higher CCP levels trended towards greater specificity for disease onset within 2 years. At standard cut-off levels, assay agreement was good in established RA (kappa=0.76), but poor in FDRs without inflammatory arthritis (kappa=0.25). Conclusion Anti-CCP assays differ to an extent that may be meaningful in diagnosing RA in patients with inflammatory arthritis, and in evaluating the natural history of RA development in subjects at-risk for future RA. Mechanisms underlying these differences in test performance need further investigation. PMID:23686569

LensEnt2: Maximum-entropy weak lens reconstruction

NASA Astrophysics Data System (ADS)

Marshall, P. J.; Hobson, M. P.; Gull, S. F.; Bridle, S. L.

2013-08-01

LensEnt2 is a maximum entropy reconstructor of weak lensing mass maps. The method takes each galaxy shape as an independent estimator of the reduced shear field and incorporates an intrinsic smoothness, determined by Bayesian methods, into the reconstruction. The uncertainties from both the intrinsic distribution of galaxy shapes and galaxy shape estimation are carried through to the final mass reconstruction, and the mass within arbitrarily shaped apertures are calculated with corresponding uncertainties. The input is a galaxy ellipticity catalog with each measured galaxy shape treated as a noisy tracer of the reduced shear field, which is inferred on a fine pixel grid assuming positivity, and smoothness on scales of w arcsec where w is an input parameter. The ICF width w can be chosen by computing the evidence for it.

Fourier transform wavefront control with adaptive prediction of the atmosphere.

PubMed

Poyneer, Lisa A; Macintosh, Bruce A; Véran, Jean-Pierre

2007-09-01

Predictive Fourier control is a temporal power spectral density-based adaptive method for adaptive optics that predicts the atmosphere under the assumption of frozen flow. The predictive controller is based on Kalman filtering and a Fourier decomposition of atmospheric turbulence using the Fourier transform reconstructor. It provides a stable way to compensate for arbitrary numbers of atmospheric layers. For each Fourier mode, efficient and accurate algorithms estimate the necessary atmospheric parameters from closed-loop telemetry and determine the predictive filter, adjusting as conditions change. This prediction improves atmospheric rejection, leading to significant improvements in system performance. For a 48x48 actuator system operating at 2 kHz, five-layer prediction for all modes is achievable in under 2x10(9) floating-point operations/s.

Exploring Undergraduate Student Attitudes toward Persons with Disabilities: Application of the Disability Social Relationship Scale

ERIC Educational Resources Information Center

Hergenrather, Kenneth; Rhodes, Scott

2007-01-01

The Disability Social Relations Generalized Disability (DSRGD) Scale was used to explore the influence of the social context on attitudes toward persons with disabilities. The DSRGD Scale was based on the Disability Social Relationship (DSR) Scale (Grand, Bernier, & Strohmer, 1982; Strohmer, Grand, & Purcell, 1984). A sample of 1,013 undergraduate…

77 FR 64815 - Eunice Kennedy Shriver National Institute of Child Health & Human Development; Notice of Closed...

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2012-10-23

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76 FR 76169 - Eunice Kennedy Shriver National Institute of Child Health & Human Development Notice of Meeting

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2011-12-06

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2012-10-23

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2011-07-29

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2012-04-26

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2011-11-28

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Factors Affecting Florida Scrub-Jay Nest Survival on Ocala National Forest, Florida

Treesearch

Kathleen Franzreb; Stan Zarnoch

2011-01-01

One of the main populations of the Florida scrub-jay (Aphelocoma coerulescens), a federally threatened species, occurs on Ocala National Forest, Florida. We determined the nest survival rate (DSR) of 474 nests of Florida scrub-jays in stands subject to sand pine reforestation management after timber harvesting or wildfire on Ocala National Forest. We used the...

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2012-06-21

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77 FR 16247 - Eunice Kennedy Shriver National Institute of Child Health and Human Development; Notice of Closed...

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2012-03-20

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2012-06-06

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Relationships between menopausal and mood symptoms and EEG sleep measures in a multi-ethnic sample of middle-aged women: the SWAN sleep study.

PubMed

Kravitz, Howard M; Avery, Elizabeth; Sowers, Maryfran; Bromberger, Joyce T; Owens, Jane F; Matthews, Karen A; Hall, Martica; Zheng, Huiyong; Gold, Ellen B; Buysse, Daniel J

2011-09-01

Examine associations of vasomotor and mood symptoms with visually scored and computer-generated measures of EEG sleep. Cross-sectional analysis. Community-based in-home polysomnography (PSG). 343 African American, Caucasian, and Chinese women; ages 48-58 years; pre-, peri- or post-menopausal; participating in the Study of Women's Health Across the Nation Sleep Study (SWAN Sleep Study). None. Measures included PSG-assessed sleep duration, continuity, and architecture, delta sleep ratio (DSR) computed from automated counts of delta wave activity, daily diary-assessed vasomotor symptoms (VMS), questionnaires to collect mood (depression, anxiety) symptoms, medication, and lifestyle information, and menopausal status using bleeding criteria. Sleep outcomes were modeled using linear regression. Nocturnal VMS were associated with longer sleep time. Higher anxiety symptom scores were associated with longer sleep latency and lower sleep efficiency, but only in women reporting nocturnal VMS. Contrary to expectations, VMS and mood symptoms were unrelated to either DSR or REM latency. Vasomotor symptoms moderated associations of anxiety with EEG sleep measures of sleep latency and sleep efficiency and was associated with longer sleep duration in this multi-ethnic sample of midlife women.

An overview of four studies of a continuous oral contraceptive (levonorgestrel 90 mcg/ethinyl estradiol 20 mcg) on premenstrual dysphoric disorder and premenstrual syndrome.

PubMed

Freeman, Ellen W; Halbreich, Uriel; Grubb, Gary S; Rapkin, Andrea J; Skouby, Sven O; Smith, Lynne; Mirkin, Sebastian; Constantine, Ginger D

2012-05-01

This article presents an overview of four studies that evaluated a continuous oral contraceptive (OC) containing levonorgestrel (90 mcg) and ethinyl estradiol (20 mcg; LNG/EE) for managing premenstrual dysphoric disorder (PMDD) and premenstrual syndrome (PMS). Three randomized, double-blind, placebo-controlled trials and one open-label, single-treatment substudy examined mean changes from baseline in the Daily Record of Severity of Problems (DRSP) or Penn Daily Symptom Rating (DSR). Improvements from baseline in mean DRSP and DSR scores were observed, but results were not consistent among the studies. Mean percent improvement of premenstrual symptoms ranged from 30% to 59% in controlled trials and 56% to 81% in an open-label substudy. A large placebo effect was also observed in the placebo-controlled studies. Continuous LNG/EE yielded a favorable safety profile. These data, although not consistent, indicate that continuous LNG/EE may reduce the symptoms of PMDD and PMS, providing an option for women who are appropriate candidates for a continuous OC as a contraceptive, the approved indication for this medication. Copyright © 2012 Elsevier Inc. All rights reserved.

Daily survival rate and habitat characteristics of nests of Wilson's Plover

USGS Publications Warehouse

Zinsser, Elizabeth; Sanders, Felicia J.; Gerard, Patrick D.; Jodice, Patrick G.R.

2017-01-01

We assessed habitat characteristics and measured daily survival rate of 72 nests of Charadrius wilsonia (Wilson's Plover) during 2012 and 2013 on South Island and Sand Island on the central coast of South Carolina. At both study areas, nest sites were located at slightly higher elevations (i.e., small platforms of sand) relative to randomly selected nearby unused sites, and nests at each study area also appeared to be situated to enhance crypsis and/or vigilance. Daily survival rate (DSR) of nests ranged from 0.969 to 0.988 among study sites and years, and the probability of nest survival ranged from 0.405 to 0.764. Flooding and predation were the most common causes of nest failure at both sites. At South Island, DSR was most strongly related to maximum tide height, which suggests that flooding and overwash may be common causes of nest loss for Wilson's Plovers at these study sites. The difference in model results between the 2 nearby study sites may be partially due to more-frequent flooding at Sand Island because of some underlying yet unmeasured physiographic feature. Remaining data gaps for the species include regional assessments of nest and chick survival and habitat requirements during chick rearing.

Smart Wire Grid: Resisting Expectations

ScienceCinema

Ramsay, Stewart; Lowe, DeJim

2018-05-30

Smart Wire Grid's DSR technology (Discrete Series Reactor) can be quickly deployed on electrical transmission lines to create intelligent mesh networks capable of quickly rerouting electricity to get power where and when it's needed the most. With their recent ARPA-E funding, Smart Wire Grid has been able to move from prototype and field testing to building out a US manufacturing operation in just under a year.

77 FR 43344 - Eunice Kennedy Shriver National Institute of Child Health and Human Development; Notice of Closed...

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2012-07-24

... National Institute of Child Health and Human Development; Notice of Closed Meeting Pursuant to section 10(d... Health and Human Development Special Emphasis Panel; ZHD1 DSR-Z 42 2. Date: August 8, 2012. Time: 1:30 p... Institute of Child Health and Human Development, NIH, 6100 Executive Boulevard, Room 5B01, Bethesda, MD...

AD HOC Networks for the Autonomous Car

NASA Astrophysics Data System (ADS)

Ron, Davidescu; Negrus, Eugen

2017-10-01

The future of the vehicle is made of cars, roads and infrastructures connected in a two way automated communication in a holistic system. It is a mandatory to use Encryption to maintain Confidentiality, Integrity and Availability in an ad hoc vehicle network. Vehicle to Vehicle communication, requires multichannel interaction between mobile, moving and changing parties to insure the full benefit from data sharing and real time decision making, a network of such users referred as mobile ad hoc network (MANET), however as ad hoc networks were not implemented in such a scale, it is not clear what is the best method and protocol to apply. Furthermore the visibility of secure preferred asymmetric encrypted ad hoc networks in a real time environment of dense moving autonomous vehicles has to be demonstrated, In order to evaluate the performance of Ad Hoc networks in changing conditions a simulation of multiple protocols was performed on large number of mobile nodes. The following common routing protocols were tested, DSDV is a proactive protocol, every mobile station maintains a routing table with all available destinations, DSR is a reactive routing protocol which allows nodes in the MANET to dynamically discover a source route across multiple network hops, AODV is a reactive routing protocol Instead of being proactive. It minimizes the number of broadcasts by creating routes based on demand, SAODV is a secure version of AODV, requires heavyweight asymmetric cryptographic, ARIANDE is a routing protocol that relies on highly efficient symmetric cryptography the concept is primarily based on DSR. A methodical evolution was performed in a various density of transportation, based on known communication bench mark parameters including, Throughput Vs. time, Routing Load per packets and bytes. Out of the none encrypted protocols, It is clear that in terms of performance of throughput and routing load DSR protocol has a clear advantage the high node number mode. The encrypted protocols show lower performance with ARIANDE being superior to SAODV and SRP. Nevertheless all protocol simulation proved it to match required real time performance.

Characterization and Modeling of Asphalt Binder Fatigue

NASA Astrophysics Data System (ADS)

Safaei, Farinaz

Fatigue cracking is a primary distress in asphalt pavements caused by the accumulation of damage under repeated traffic loading. Many factors influence fatigue damage in pavements, including pavement structure, environmental conditions, and asphalt mixture volumetric properties. Asphalt binder is the weakest asphalt concrete constituent and, thus, plays a critical role in determining the fatigue resistance of pavements. Therefore, the ability to characterize and model the inherent fatigue performance of an asphalt binder is a necessary first step to design. A comprehensive understanding and prediction of asphalt binder fatigue performance require a suitable experiment coupled with a model to predict how the binder will perform under various traffic, temperature, and structural conditions encountered in the field. The simplified viscoelastic continuum damage (S-VECD) model has been used successfully by researchers to predict the damage evolution in asphalt mixtures for various traffic and climatic conditions using limited uniaxial test data. Although the literature shows promise for applying VECD modeling to asphalt binder fatigue, the past efforts have several shortcomings. It has been demonstrated that flow and adhesion loss can impede DSR fatigue test results. Thus, definition of test conditions (e.g., temperature) where cyclic DSR tests are appropriate for fatigue characterization of binders is necessary. In addition, the applicability of the model to predict fatigue performance under varying loading and thermal history has not been rigorously evaluated. Furthermore, the effects of material nonlinearity have been largely neglected in past modeling efforts for simplicity. In addition, past efforts have employed the parallel plate DSR geometry for the fatigue characterization of asphalt binders. In the parallel plate geometry, the strain depends on the radial distance from the specimen center. Therefore, the material will fail at different rates as a function of radial location. Past efforts have neglected the radial strain gradient, using the apparent shear stress at the sample edge to infer fatigue damage and derive S-VECD model parameters. Apparent edge stress is calculated using linear mapping to the total torque, which is erroneous in the presence of material or geometric nonlinearities (such as cracking). This study seeks to overcome the aforementioned shortcomings of past efforts to improve the ability to characterize and predict asphalt binder fatigue.

Changes in the Indian summer monsoon intensity in Sri Lanka during the last 30 ky - A multiproxy record from a marine sediment core.

NASA Astrophysics Data System (ADS)

Ranasinghage, P. N.; Nanayakkara, N. U.; Kodithuwakku, S.; Siriwardana, S.; Luo, C.; Fenghua, Z.

2016-12-01

Indian monsoon plays a vital role in determining climate events happening in the Asian region. There is no sufficient work in Sri Lanka to fully understand how the summer monsoonal variability affected Sri Lanka during the quaternary. Sri Lanka is situated at an ideal location with a unique geography to isolate Indian summer monsoon record from iris counterpart, Indian winter monsoon. Therefore, this study was carried out to investigate its variability and understand the forcing factors. For this purpose a 1.82 m long gravity core, extracted from western continental shelf off Colombo, Sri Lanka by Shiyan 1 research vessel, was used. Particle size, chemical composition and colour reflectance were measured using laser particle size analyzer at 2 cm resolution, X-Ray Fluorescence spectrometer (XRF) at 2 cm resolution, and color spectrophotometer at 1 cm resolution respectively. Radio carbon dating of foraminifera tests by gas bench technique yielded the sediment age. Finally, principal component analysis (PCA) of XRF and color reflectance (DSR) data was performed to identify groups of correlating elements and mineralogical composition of sediments. Particle size results indicate that Increasing temperature and strengthening monsoonal rainfall after around 18000 yrs BP, at the end of last glacial period, enhanced chemical weathering over physical weathering. Proxies for terrestrial influx (XRF PC1, DSR PC1) and upwelling and nutrient supply driven marine productivity (XRF PC3 and DSR PC2) indicate that strengthening of summer monsoon started around 15000 yrs BP and maximized around 8000-10000 yrs BP after a short period of weakening during Younger Dryas (around 11000 yrs BP). The 8.2 cold event was recorded as a period of low terrestrial influx indicating weakening of rainfall. After that terrestrial input was low till around 2000 yrs BP indicating decrease in rainfall. However, marine productivity remained increasing throughout the Holocene indicating an increase in monsoonal driven upwelling. Authors recorded similar increase in monsoonal wind strength during the late Holocene, with no increase in rainfall in another sediment core extracted from the western continental shelf of Sri Lanka.

Simulation results for a finite element-based cumulative reconstructor

NASA Astrophysics Data System (ADS)

Wagner, Roland; Neubauer, Andreas; Ramlau, Ronny

2017-10-01

Modern ground-based telescopes rely on adaptive optics (AO) systems for the compensation of image degradation caused by atmospheric turbulences. Within an AO system, measurements of incoming light from guide stars are used to adjust deformable mirror(s) in real time that correct for atmospheric distortions. The incoming wavefront has to be derived from sensor measurements, and this intermediate result is then translated into the shape(s) of the deformable mirror(s). Rapid changes of the atmosphere lead to the need for fast wavefront reconstruction algorithms. We review a fast matrix-free algorithm that was developed by Neubauer to reconstruct the incoming wavefront from Shack-Hartmann measurements based on a finite element discretization of the telescope aperture. The method is enhanced by a domain decomposition ansatz. We show that this algorithm reaches the quality of standard approaches in end-to-end simulation while at the same time maintaining the speed of recently introduced solvers with linear order speed.

Newtonian CAFE: a new ideal MHD code to study the solar atmosphere

NASA Astrophysics Data System (ADS)

González, J. J.; Guzmán, F.

2015-12-01

In this work we present a new independent code designed to solve the equations of classical ideal magnetohydrodynamics (MHD) in three dimensions, submitted to a constant gravitational field. The purpose of the code centers on the analysis of solar phenomena within the photosphere-corona region. In special the code is capable to simulate the propagation of impulsively generated linear and non-linear MHD waves in the non-isothermal solar atmosphere. We present 1D and 2D standard tests to demonstrate the quality of the numerical results obtained with our code. As 3D tests we present the propagation of MHD-gravity waves and vortices in the solar atmosphere. The code is based on high-resolution shock-capturing methods, uses the HLLE flux formula combined with Minmod, MC and WENO5 reconstructors. The divergence free magnetic field constraint is controlled using the Flux Constrained Transport method.

Newtonian CAFE: a new ideal MHD code to study the solar atmosphere

NASA Astrophysics Data System (ADS)

González-Avilés, J. J.; Cruz-Osorio, A.; Lora-Clavijo, F. D.; Guzmán, F. S.

2015-12-01

We present a new code designed to solve the equations of classical ideal magnetohydrodynamics (MHD) in three dimensions, submitted to a constant gravitational field. The purpose of the code centres on the analysis of solar phenomena within the photosphere-corona region. We present 1D and 2D standard tests to demonstrate the quality of the numerical results obtained with our code. As solar tests we present the transverse oscillations of Alfvénic pulses in coronal loops using a 2.5D model, and as 3D tests we present the propagation of impulsively generated MHD-gravity waves and vortices in the solar atmosphere. The code is based on high-resolution shock-capturing methods, uses the Harten-Lax-van Leer-Einfeldt (HLLE) flux formula combined with Minmod, MC, and WENO5 reconstructors. The divergence free magnetic field constraint is controlled using the Flux Constrained Transport method.

The Emergence of a Temporally Extended Self and Factors that Contribute to Its Development: From Theoretical and Empirical Perspectives

ERIC Educational Resources Information Center

Lazaridis, Mary

2013-01-01

The main aims of the current research were to determine when children develop a temporally extended self (TES) and what factors contribute to its development. However, in order to address these aims it was important to, first, assess whether the test of delayed self-recognition (DSR) is a valid measure for the development of the TES, and, second,…

78 FR 44576 - Eunice Kennedy Shriver National Institute of Child Health & Human Development; Notice of Closed...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-24

... sections 552b(c)(4) and 552b(c)(6), Title 5 U.S.C., as amended. The grant applications and the discussions... Health and Human Development Special Emphasis Panel; ZHD1 DSR-H GS 1. Date: August 15, 2013. Time: 3:15 p...) of the Federal Advisory Committee Act, as amended (5 U.S.C. App.), notice is hereby given of the...

An artificial immune system approach with secondary response for misbehavior detection in mobile ad hoc networks.

PubMed

Sarafijanović, Slavisa; Le Boudec, Jean-Yves

2005-09-01

In mobile ad hoc networks, nodes act both as terminals and information relays, and they participate in a common routing protocol, such as dynamic source routing (DSR). The network is vulnerable to routing misbehavior, due to faulty or malicious nodes. Misbehavior detection systems aim at removing this vulnerability. In this paper, we investigate the use of an artificial immune system (AIS) to detect node misbehavior in a mobile ad hoc network using DSR. The system is inspired by the natural immune system (IS) of vertebrates. Our goal is to build a system that, like its natural counterpart, automatically learns, and detects new misbehavior. We describe our solution for the classification task of the AIS; it employs negative selection and clonal selection, the algorithms for learning and adaptation used by the natural IS. We define how we map the natural IS concepts such as self, antigen, and antibody to a mobile ad hoc network and give the resulting algorithm for classifying nodes as misbehaving. We implemented the system in the network simulator Glomosim; we present detection results and discuss how the system parameters affect the performance of primary and secondary response. Further steps will extend the design by using an analogy to the innate system, danger signal, and memory cells.

Discrete Element Method Modeling of the Rheological Properties of Coke/Pitch Mixtures

PubMed Central

Majidi, Behzad; Taghavi, Seyed Mohammad; Fafard, Mario; Ziegler, Donald P.; Alamdari, Houshang

2016-01-01

Rheological properties of pitch and pitch/coke mixtures at temperatures around 150 °C are of great interest for the carbon anode manufacturing process in the aluminum industry. In the present work, a cohesive viscoelastic contact model based on Burger’s model is developed using the discrete element method (DEM) on the YADE, the open-source DEM software. A dynamic shear rheometer (DSR) is used to measure the viscoelastic properties of pitch at 150 °C. The experimental data obtained is then used to estimate the Burger’s model parameters and calibrate the DEM model. The DSR tests were then simulated by a three-dimensional model. Very good agreement was observed between the experimental data and simulation results. Coke aggregates were modeled by overlapping spheres in the DEM model. Coke/pitch mixtures were numerically created by adding 5, 10, 20, and 30 percent of coke aggregates of the size range of 0.297–0.595 mm (−30 + 50 mesh) to pitch. Adding up to 30% of coke aggregates to pitch can increase its complex shear modulus at 60 Hz from 273 Pa to 1557 Pa. Results also showed that adding coke particles increases both storage and loss moduli, while it does not have a meaningful effect on the phase angle of pitch. PMID:28773459

Discrete Element Method Modeling of the Rheological Properties of Coke/Pitch Mixtures.

PubMed

Majidi, Behzad; Taghavi, Seyed Mohammad; Fafard, Mario; Ziegler, Donald P; Alamdari, Houshang

2016-05-04

Rheological properties of pitch and pitch/coke mixtures at temperatures around 150 °C are of great interest for the carbon anode manufacturing process in the aluminum industry. In the present work, a cohesive viscoelastic contact model based on Burger's model is developed using the discrete element method (DEM) on the YADE, the open-source DEM software. A dynamic shear rheometer (DSR) is used to measure the viscoelastic properties of pitch at 150 °C. The experimental data obtained is then used to estimate the Burger's model parameters and calibrate the DEM model. The DSR tests were then simulated by a three-dimensional model. Very good agreement was observed between the experimental data and simulation results. Coke aggregates were modeled by overlapping spheres in the DEM model. Coke/pitch mixtures were numerically created by adding 5, 10, 20, and 30 percent of coke aggregates of the size range of 0.297-0.595 mm (-30 + 50 mesh) to pitch. Adding up to 30% of coke aggregates to pitch can increase its complex shear modulus at 60 Hz from 273 Pa to 1557 Pa. Results also showed that adding coke particles increases both storage and loss moduli, while it does not have a meaningful effect on the phase angle of pitch.

Cloning and characterization of a Weissella confusa dextransucrase and its application in high fibre baking.

PubMed

Kajala, Ilkka; Shi, Qiao; Nyyssölä, Antti; Maina, Ndegwa Henry; Hou, Yaxi; Katina, Kati; Tenkanen, Maija; Juvonen, Riikka

2015-01-01

Wheat bran offers health benefits as a baking ingredient, but is detrimental to bread textural quality. Dextran production by microbial fermentation improves sourdough bread volume and freshness, but extensive acid production during fermentation may negate this effect. Enzymatic production of dextran in wheat bran was tested to determine if dextran-containing bran could be used in baking without disrupting bread texture. The Weissella confusa VTT E-90392 dextransucrase gene was sequenced and His-tagged dextransucrase Wc392-rDSR was produced in Lactococcus lactis. Purified enzyme was characterized using (14)C-sucrose radioisotope and reducing value-based assays, the former yielding K(m) and V(max) values of 14.7 mM and 8.2 μmol/(mg ∙ min), respectively, at the pH optimum of 5.4. The structure and size of in vitro dextran product was similar to dextran produced in vivo. Dextran (8.1% dry weight) was produced in wheat bran in 6 h using Wc392-rDSR. Bran with and without dextran was used in wheat baking at 20% supplementation level. Dextran presence improved bread softness and neutralized bran-induced volume loss, clearly demonstrating the potential of using dextransucrases in bran bioprocessing for use in baking.

Cloning and Characterization of a Weissella confusa Dextransucrase and Its Application in High Fibre Baking

PubMed Central

Kajala, Ilkka; Shi, Qiao; Nyyssölä, Antti; Maina, Ndegwa Henry; Hou, Yaxi; Katina, Kati; Tenkanen, Maija; Juvonen, Riikka

2015-01-01

Wheat bran offers health benefits as a baking ingredient, but is detrimental to bread textural quality. Dextran production by microbial fermentation improves sourdough bread volume and freshness, but extensive acid production during fermentation may negate this effect. Enzymatic production of dextran in wheat bran was tested to determine if dextran-containing bran could be used in baking without disrupting bread texture. The Weissella confusa VTT E-90392 dextransucrase gene was sequenced and His-tagged dextransucrase Wc392-rDSR was produced in Lactococcus lactis. Purified enzyme was characterized using 14C-sucrose radioisotope and reducing value-based assays, the former yielding K m and V max values of 14.7 mM and 8.2 μmol/(mg∙min), respectively, at the pH optimum of 5.4. The structure and size of in vitro dextran product was similar to dextran produced in vivo. Dextran (8.1% dry weight) was produced in wheat bran in 6 h using Wc392-rDSR. Bran with and without dextran was used in wheat baking at 20% supplementation level. Dextran presence improved bread softness and neutralized bran-induced volume loss, clearly demonstrating the potential of using dextransucrases in bran bioprocessing for use in baking. PMID:25603169

Thermodynamics and luminosities of rainbow black holes

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

Mu, Benrong; Wang, Peng; Yang, Haitang, E-mail: mubenrong@uestc.edu.cn, E-mail: pengw@scu.edu.cn, E-mail: hyanga@scu.edu.cn

2015-11-01

Doubly special relativity (DSR) is an effective model for encoding quantum gravity in flat spacetime. As result of the nonlinearity of the Lorentz transformation, the energy-momentum dispersion relation is modified. One simple way to import DSR to curved spacetime is ''Gravity's rainbow'', where the spacetime background felt by a test particle would depend on its energy. Focusing on the ''Amelino-Camelia dispersion relation'' which is E{sup 2} = m{sup 2}+p{sup 2}[1−η(E/m{sub p}){sup n}] with n > 0, we investigate the thermodynamical properties of a Schwarzschild black hole and a static uncharged black string for all possible values of η and n in the framework ofmore » rainbow gravity. It shows that there are non-vanishing minimum masses for these two black holes in the cases with η < 0 and n ≥ 2. Considering effects of rainbow gravity on both the Hawking temperature and radius of the event horizon, we use the geometric optics approximation to compute luminosities of a 2D black hole, a Schwarzschild one and a static uncharged black string. It is found that the luminosities can be significantly suppressed or boosted depending on the values of η and n.« less

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

PubMed Central

Robador, Alberto; Jungbluth, Sean P.; LaRowe, Douglas E.; Bowers, Robert M.; Rappé, Michael S.; Amend, Jan P.; Cowen, James P.

2015-01-01

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling. PMID:25642212

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

PubMed Central

Bomberg, Malin; Nyyssönen, Mari; Pitkänen, Petteri; Lehtinen, Anne; Itävaara, Merja

2015-01-01

Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing ε-proteobacteria (Sulfurimonas sp.) dominated in the SMMZ and γ-proteobacteria (Pseudomonas spp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, α-, β- and δ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems. PMID:26425566

Productivity of forest birds at Hakalau Forest NWR

USGS Publications Warehouse

Paxton, Eben H.; Cummins, George C; Kendall, Steven J.

2014-01-01

Hawai‘i has some of the most endangered avian species in the world, which face numerous threats from habitat loss, disease, climate change, and introduced species. This report details the results of a two-year productivity study of all forest bird species at Hakalau National Wildlife Refuge, Hawai‘i Island. We found and monitored nests from seven native species and three common non-native species of forest birds at three sites across the refuge. In addition to gathering important baseline information on productivity of forest birds, we examined differences in productivity between years, sites, and as a function of nest height. The weather differed greatly between the two years, with much more rain occurring in 2014. The daily survival rate (DSR) of nests was found to have an inverse relationship with the amount of rainfall, and accordingly was much lower in 2014 compared to 2013. Nest success was lower at a regenerating forest site compared with mature rainforest, indicating negative environmental factors affecting nest success may be exacerbated in reforested areas which have lower canopies. Nest success was also impacted by nest height, with a positive relationship in the drier 2013, and a negative relationship in 2014 for the canopy nesting honeycreepers. The large difference in weather and DSR between years illustrates the need for long term demographic studies that can capture the vital rates of this community of birds.

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan.

PubMed

Nunoura, Takuro; Takaki, Yoshihiro; Shimamura, Shigeru; Kakuta, Jungo; Kazama, Hiromi; Hirai, Miho; Masui, Noriaki; Tomaru, Hitoshi; Morono, Yuki; Imachi, Hiroyuki; Inagaki, Fumio; Takai, Ken

2016-06-01

Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Corporate Repair Philosophy and Measuring for Continuous Improvement at Philadelphia Naval Shipyard

DTIC Science & Technology

1992-09-01

processes and products of Improvement Program (NIIP) vegan a series Wavy depot-level activities, of discussions which centered on the development of a...alteration project have been made at the and workforce. Prior to entering the shipyard. These changes and their effect planning stages fortheUSS...the in CKO at 80% is slightly less for CV-64 "rippling effects " of a DSR submittal when compared to CV-63 at its 80% point such as work stoppage

Airborne Network Data Availability Using Peer to Peer Database Replication on a Distributed Hash Table

DTIC Science & Technology

2013-03-01

DSR Dynamic Source Routing DSSS Direct -sequence spread spectrum GUID Globally Unique ID MANET Mobile Ad-hoc Network NS3 Network Simulator 3 OLSR...networking schemes for safe maneuvering and data communication. Imagine needing to maintain an operational picture of an overall environment using a...as simple as O(n) where every node is sequentially queried to O log(n), or O(1). These schemes will be discussed with each individual DHT. Four of the

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

Hurricane, O. A.; Clark, D. S.

The work is summarized from several perspectives: 1D simulation perspective: Post-shot models agree with yield data to within a factor of ~2 at low implosion velocities, but the models diverge from the data as the velocity and convergence ratio increase. 2D simulation perspective: Integrated hohlraum-capsule post-shot models agree with primary data for most implosions, but overpredict yield and DSR for a few of the highest velocity implosions. High-resolution 3D post-shot capsule-only modeling captures much of the delivered performance of the one shot currently simulated.

Derivative plumbing: redesigning washrooms, bodies, and trans affects in ds+r's Brasserie.

PubMed

Crawford, Lucas Cassidy

2014-01-01

diller scofidio + renfro's Brasserie restaurant sets the scene for this article's overarching question: what are the stakes of absorbing "the washroom" into our affective habits as trans people? This article uses architectural theory to show that some hygienic models of transgender-such as "original plumbing"-are less about explaining our genders to ourselves and more about (1) communicating our "fuckability" to (presumably non-trans) others and (2) codifying subtle and often problematic beliefs about the relationship between architecture and the body.

Manual for Calculating the Seepage Strength of Earthfill Dams,

DTIC Science & Technology

1976-07-01

gravity of material of soil particles; d--diameter of soil particles; dio...d 17 ...dsr-diameters of soil particles, the smallest of which in its...compcsition may be present as 10... 17 ...60% by weight; dci--diameter of (piping) particles of soil which may be carried away by the seepage flow; -dso Y1 d...should, however, be reduced, assuming: k" onnfrmsi S(Jk)dnonuniform soil = [(Jk)d]uniform soil ( 17 ) where 7is the coefficient of reduction (less than

The Cultural Resources Investigation of the Wild Rice River - South Branch and Felton Ditch Flood Control Project Area, Clay and Norman Counties, Minnesota,

DTIC Science & Technology

1980-01-01

1979. Principal Investigator: An Archaeological Investigation of the Proposed Lagoon Site, Dam Site Recreation Area, Coralville Lake, ! Iowa River, Iowa ...Proposed Lagoon Site, Coralville Lake, Iowa . Winter, 1979. I Analysis of Material from the Site Survey of Blue Earth City Park, Faribault County...t Site Recreation Area, Coralville Lake, Iowa . With Richard A. Strachan. For the Rock Island DsrFct, U. S. Acmy Corps of Engineers. With Richard A

Turbulence profiling for adaptive optics tomographic reconstructors

NASA Astrophysics Data System (ADS)

Laidlaw, Douglas J.; Osborn, James; Wilson, Richard W.; Morris, Timothy J.; Butterley, Timothy; Reeves, Andrew P.; Townson, Matthew J.; Gendron, Éric; Vidal, Fabrice; Morel, Carine

2016-07-01

To approach optimal performance advanced Adaptive Optics (AO) systems deployed on ground-based telescopes must have accurate knowledge of atmospheric turbulence as a function of altitude. Stereo-SCIDAR is a high-resolution stereoscopic instrument dedicated to this measure. Here, its profiles are directly compared to internal AO telemetry atmospheric profiling techniques for CANARY (Vidal et al. 20141), a Multi-Object AO (MOAO) pathfinder on the William Herschel Telescope (WHT), La Palma. In total twenty datasets are analysed across July and October of 2014. Levenberg-Marquardt fitting algorithms dubbed Direct Fitting and Learn 2 Step (L2S; Martin 20142) are used in the recovery of profile information via covariance matrices - respectively attaining average Pearson product-moment correlation coefficients with stereo-SCIDAR of 0.2 and 0.74. By excluding the measure of covariance between orthogonal Wavefront Sensor (WFS) slopes these results have revised values of 0.65 and 0.2. A data analysis technique that combines L2S and SLODAR is subsequently introduced that achieves a correlation coefficient of 0.76.

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

PubMed Central

Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.; Chanton, Jeffrey P.; Pizarro, Oscar; Teske, Andreas

2010-01-01

Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes. PMID:20090951

Anti-Myeloperoxidase Antibodies Associate with Future Proliferative Lupus Nephritis

PubMed Central

Lee, J. J.; Poirier, M.; Little, D. J.; Prince, L. K.; Baker, T. P.; Edison, J. D.; Abbott, K. C.

2017-01-01

Background The subclinical pathophysiology of proliferative lupus nephritis (PLN) has not been fully elucidated. Myeloperoxidase anti-neutrophil cytoplasmic antibody (MPO-ANCA) is associated with PLN, but prediagnostic levels have not been reported. Methods We performed a retrospective case-control Department of Defense Serum Repository (DoDSR) study comparing MPO-ANCA levels in longitudinal prediagnostic serum samples for 23 biopsy confirmed proliferative lupus nephritis (PLN) patients to DoDSR identified age, sex, race, and age of serum matched healthy and SLE without LN disease controls. We also compared the temporal relationship of MPO-ANCA to anti-double stranded DNA antibodies (dsDNAab). Results A greater proportion of PLN patients had prediagnostic MPO-ANCA levels above ≥3 U/mL and ≥6 U/mL compared to SLE without LN (91% versus 43%, p < 0.001; 57% versus 5%, p < 0.001, resp.). In subgroup analysis, the MPO-ANCA threshold of ≥3 U/mL was significant at <1 year (88% versus 39%, p = 0.007) and 1–4 years (87% versus 38%, p = 0.009) prior to diagnosis. Statistically significant subclinical MPO-ANCA levels (≥3 U/mL) occurred prior to statistically significant dsDNAab ≥ 3 IU/ml (89% versus 11%, p = 0.003). Conclusions Subclinical MPO-ANCA levels could distinguish future PLN from SLE without LN. MPO-ANCA manifests prior to clinical disease and subclinical dsDNAab to suggest that it may contribute directly to PLN pathogenicity. PMID:29435367

Test of the FLRW Metric and Curvature with Strong Lens Time Delays

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

Liao, Kai; Li, Zhengxiang; Wang, Guo-Jian

We present a new model-independent strategy for testing the Friedmann–Lemaître–Robertson–Walker (FLRW) metric and constraining cosmic curvature, based on future time-delay measurements of strongly lensed quasar-elliptical galaxy systems from the Large Synoptic Survey Telescope and supernova observations from the Dark Energy Survey. The test only relies on geometric optics. It is independent of the energy contents of the universe and the validity of the Einstein equation on cosmological scales. The study comprises two levels: testing the FLRW metric through the distance sum rule (DSR) and determining/constraining cosmic curvature. We propose an effective and efficient (redshift) evolution model for performing the formermore » test, which allows us to concretely specify the violation criterion for the FLRW DSR. If the FLRW metric is consistent with the observations, then on the second level the cosmic curvature parameter will be constrained to ∼0.057 or ∼0.041 (1 σ ), depending on the availability of high-redshift supernovae, which is much more stringent than current model-independent techniques. We also show that the bias in the time-delay method might be well controlled, leading to robust results. The proposed method is a new independent tool for both testing the fundamental assumptions of homogeneity and isotropy in cosmology and for determining cosmic curvature. It is complementary to cosmic microwave background plus baryon acoustic oscillation analyses, which normally assume a cosmological model with dark energy domination in the late-time universe.« less

Can herbicide safeners allow selective control of weedy rice infesting rice crops?

PubMed

Busi, Roberto; Nguyen, Nghia K; Chauhan, Bhagirath S; Vidotto, Francesco; Tabacchi, Maurizio; Powles, Stephen B

2017-01-01

Rice is a major field crop of paramount importance for global food security. However, the increased adoption of more profitable and resource-efficient direct-seeded rice (DSR) systems has contributed to greater weed infestations, including weedy rice, which has become a severe problem in several Asian regions. In this study we have developed a conceptually novel method to protect rice plants at high doses of clomazone and triallate. The insecticide phorate applied to rice seeds provided a substantial level of protection against the herbicides clomazone or triallate. A quantity of 15 kg phorate ha -1 significantly increased the LD 50 values, which were more than twofold greater than for rice plants treated only with clomazone. A quantity of 20 kg phorate ha -1 in combination with 2000 g triallate ha -1 safened rice plants (80% survival) with LD 50 >3.4-fold greater than in phorate-untreated rice. Weed control efficacy was not lowered by the presence of phorate-treated rice seeds. Weedy rice is one of the most damaging global weeds and a major threat to DSR systems. In this study we have developed a proof-of-concept method to allow selective weedy rice control in rice crops. We call for herbicide discovery programmes and research to identify candidate safener and herbicide combinations to achieve selective herbicide control of weedy rice and alleviate weed infestations in global rice crops. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Nest survival of piping plovers at a dynamic reservoir indicates an ecological trap for a threatened population

USGS Publications Warehouse

Anteau, Michael J.; Shaffer, Terry L.; Sherfy, Mark H.; Sovada, Marsha A.; Stucker, Jennifer H.; Wiltermuth, Mark T.

2012-01-01

In the past 60 years, reservoirs have reshaped riverine ecosystems and transformed breeding habitats used by the threatened piping plover (Charadrius melodus; hereafter plover). Currently, 29% of the Northern Great Plains plover population nests at reservoirs that might function as ecological traps because reservoirs have more diverse habitat features and greater dynamics in water levels than habitats historically used by breeding plovers. We examined factors influencing daily survival rates (DSR) of 346 plover nests at Lake Sakakawea (SAK; reservoir) during 2006–2009 by evaluating multiple a priori models, and we used our best model to hindcast nest success of plovers during 1985–2009. Our observed and hindcast estimates of nest success were low compared to published estimates. Previous findings indicate that plovers prefer nest sites that are low relative to water level. We found that elevation of nests above the water level had a strong positive correlation with DSR because water levels of SAK typically increased throughout the nesting period. Habitat characteristics on the reservoir differ from those that shaped nest-site selection for plovers. Accordingly, extraordinary nest loss occurs there in many years, largely due to inundation of nests, and based on low fledging rates those losses were not compensated by potential changes in chick survival. Therefore, our example supports the concept of ecological traps in birds because it addresses quantitative assessments of habitat preference and productivity over 25 years (since species listing) and affects a large portion of the population.

Mercury methylation in Sphagnum moss mats and its association with sulfate-reducing bacteria in an acidic Adirondack forest lake wetland.

PubMed

Yu, Ri-Qing; Adatto, Isaac; Montesdeoca, Mario R; Driscoll, Charles T; Hines, Mark E; Barkay, Tamar

2010-12-01

Processes leading to the bioaccumulation of methylmercury (MeHg) in northern wetlands are largely unknown. We have studied various ecological niches within a remote, acidic forested lake ecosystem in the southwestern Adirondacks, NY, to discover that mats comprised of Sphagnum moss were a hot spot for mercury (Hg) and MeHg accumulation (190.5 and 18.6 ng g⁻¹ dw, respectively). Furthermore, significantly higher potential methylation rates were measured in Sphagnum mats as compared with other sites within Sunday Lake's ecosystem. Although MPN estimates showed a low biomass of sulfate-reducing bacteria (SRB), 2.8 × 10⁴ cells mL⁻¹ in mat samples, evidence consisting of (1) a twofold stimulation of potential methylation by the addition of sulfate, (2) a significant decrease in Hg methylation in the presence of the sulfate reduction inhibitor molybdate, and (3) presence of dsrAB-like genes in mat DNA extracts, suggested that SRB were involved in Hg methylation. Sequencing of dsrB genes indicated that novel SRB, incomplete oxidizers including Desulfobulbus spp. and Desulfovibrio spp., and syntrophs dominated the sulfate-reducing guild in the Sphagnum moss mat. Sphagnum, a bryophyte dominating boreal peatlands, and its associated microbial communities appear to play an important role in the production and accumulation of MeHg in high-latitude ecosystems. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A single exposure of sediment sulphate-reducing bacteria to oxytetracycline concentrations relevant to aquaculture enduringly disturbed their activity, abundance and community structure.

PubMed

Fernández, M L; Granados-Chinchilla, F; Rodríguez, C

2015-08-01

Although feed medicated with antibiotics is widely used in animal production to prevent and treat bacterial infections, the effect of these drugs on nontarget anaerobic bacteria is unknown. We aimed to clarify whether a single exposure of sulphate-reducing bacteria (SRB) from a tilapia pond to oxytetracycline (OTC) concentrations relevant to aquaculture impacts their function, abundance and community structure. To demonstrate changes in SO4(2-) content, SRB abundance, dsrB copy number and SRB diversity, sediment mesocosms were spiked with 5, 25, 50 and 75 mg OTC kg(-1) and examined for 30 days by means of ion chromatography, qPCR, cultivation and fluorescent in situ hybridization (FISH). On day 3, we measured higher SO4(2-) concentrations (ca. two-fold) and a reduction in dsrB copy numbers of approximately 50% in the treatments compared to the controls. After 30 days, a subtle yet measurable enrichment of bacteria from the order Desulfovibrionales occurred in mesocosms receiving ≥ 50 mg OTC kg(-1), notwithstanding that SRB counts decreased two orders of magnitude. OTC was dynamically and reversibly converted into 4-epioxytetracycline and other related compounds in a dose-dependent manner during the experiment. A single exposure to rather high OTC concentrations triggered functional and structural changes in a SRB community that manifested quickly and persisted for a month. This study improves our limited knowledge on the ecotoxicology of antibiotics in anaerobic environments. © 2015 The Society for Applied Microbiology.

Daily survival rates for nests of Black Skimmers from a core breeding area of the Southeastern USA

USGS Publications Warehouse

Brooks, Gillian L.; Sanders, Felicia J.; Gerard, Patrick D.; Jodice, Patrick G.R.

2014-01-01

Little is known about the reproductive success of Black Skimmers (Rynchops niger) throughout the southeastern USA where availability of undisturbed beaches for nesting is limited. Daily survival rates (DSR) of nests were examined at three nesting sites in Cape Romain National Wildlife Refuge (CRNWR), South Carolina, USA, 2009–2010. The percent of successful nests (n  =  346 nests) ranged from 42–69% among colony sites when data were pooled across both years. The DSR of nests was primarily related to colony site, predation risk, height of high tide, and clutch size. Predation and overwash were the principal causes of identifiable nest loss, each accounting for ∼33% of nest failures during the two study years. Because of the challenges of resighting skimmer chicks, we were not able to measure chick survival effectively and therefore accurate measures of productivity remain elusive. High variability in nest success among sites within close proximity to each other (<20 km) suggests factors at local scales such as disturbance, predation, and overwash events strongly influenced nest success of Black Skimmers during these 2 years as opposed to more region-wide stressors such as tropical storms or food availability. Although time-intensive techniques to control predators do exist, management options to limit flooding and overwash are far more limited. Conservation of Black Skimmers in the southeastern USA would benefit from coordinated, multi-state efforts to measure nest and chick survival.

Genome Wide Screening of Candidate Genes for Improving Piglet Birth Weight Using High and Low Estimated Breeding Value Populations

PubMed Central

Zhang, Lifan; Zhou, Xiang; Michal, Jennifer J.; Ding, Bo; Li, Rui; Jiang, Zhihua

2014-01-01

Birth weight is an economically important trait in pig production because it directly impacts piglet growth and survival rate. In the present study, we performed a genome wide survey of candidate genes and pathways associated with individual birth weight (IBW) using the Illumina PorcineSNP60 BeadChip on 24 high (HEBV) and 24 low estimated breeding value (LEBV) animals. These animals were selected from a reference population of 522 individuals produced by three sires and six dam lines, which were crossbreds with multiple breeds. After quality-control, 43,257 SNPs (single nucleotide polymorphisms), including 42,243 autosomal SNPs and 1,014 SNPs on chromosome X, were used in the data analysis. A total of 27 differentially selected regions (DSRs), including 1 on Sus scrofa chromosome 1 (SSC1), 1 on SSC4, 2 on SSC5, 4 on SSC6, 2 on SSC7, 5 on SSC8, 3 on SSC9, 1 on SSC14, 3 on SSC18, and 5 on SSCX, were identified to show the genome wide separations between the HEBV and LEBV groups for IBW in piglets. A DSR with the most number of significant SNPs (including 7 top 0.1% and 31 top 5% SNPs) was located on SSC6, while another DSR with the largest genetic differences in FST was found on SSC18. These regions harbor known functionally important genes involved in growth and development, such as TNFRSF9 (tumor necrosis factor receptor superfamily member 9), CA6 (carbonic anhydrase VI) and MDFIC (MyoD family inhibitor domain containing). A DSR rich in imprinting genes appeared on SSC9, which included PEG10 (paternally expressed 10), SGCE (sarcoglycan, epsilon), PPP1R9A (protein phosphatase 1, regulatory subunit 9A) and ASB4 (ankyrin repeat and SOCS box containing 4). More importantly, our present study provided evidence to support six quantitative trait loci (QTL) regions for pig birth weight, six QTL regions for average birth weight (ABW) and three QTL regions for litter birth weight (LBW) reported previously by other groups. Furthermore, gene ontology analysis with 183 genes harbored in these 27 DSRs suggested that protein, metal, ion and ATP binding, viral process and innate immune response present important pathways for deciphering their roles in fetal growth or development. Overall, our study provides useful information on candidate genes and pathways for regulating birth weight in piglets, thus improving our understanding of the genetic mechanisms involved in porcine embryonic or fetal development. PMID:24644423

Cigarette smoking and alveolar bone in young adults: a study using digitized radiographs.

PubMed

Rosa, Guillermo M; Lucas, Gabriela Q; Lucas, Oscar N

2008-02-01

Evidence indicates that cigarette smoking is one of the most significant risk factors for periodontal diseases; however, there have been few radiographic prospective studies of alveolar bone in young populations. The purpose of this study was to evaluate the effect of smoking on alveolar bone in young adults. Eighty-one dental students (mean age: 20.5 years), considered not to have periodontitis according to clinical criteria, participated in this study. Forty-two subjects were smokers (mean consumption was 14.1 cigarettes/day for > or =2 years), and 39 subjects had never smoked. A parallel-arm prospective design was used. All subjects took part in a dental hygiene program (DHP) that included oral hygiene instructions, mechanical debridement, and polishing. The following clinical variables were measured before and after the DHP: plaque index (PI), gingival crevicular fluid (GCF) flow rate, gingival index (GI), probing depth, and clinical attachment level (CAL). Standardized posterior vertical bitewing radiographs were taken and digitized preexperimentally and on days 180, 365, and 545. The following analyses were performed: bone height measurement (BHM), computer-assisted densitometric image analysis (CADIA), and qualitative analysis of digital subtraction radiography (DSR). Repeated-measures multiple-way analysis of variance (ANOVA) was performed between the groups, and one-way ANOVA was performed within the groups. The mean PI and GI were significantly greater in the smokers (P <0.01). The mean GCF flow rate was significantly lower in the smokers (P <0.01). CAL and the number of sites with recession were significantly greater in the smokers (P <0.001). The BHM indicated a significantly lower mean alveolar bone height in the smokers (P <0.01). The smokers showed significantly lower CADIA values, which indicated a lower bone density on days 0 (P <0.05), 180, 365, and 545 (P <0.01). CADIA values decreased during the study in the smokers, with significant differences on day 545 (P <0.05). The smokers had a significantly higher mean percentage of sites that had decreased density, as assessed by DSR (P <0.001). In the smokers, the mean percentage of sites with decreased density, as assessed by DSR, had increased significantly by days 365 (P <0.05) and 545 (P <0.01). Smoking produces an adverse effect on clinical periodontal variables and alveolar bone height and density, acting as a potential risk factor for alveolar bone loss, even at an early age with low tobacco consumption. It is very important to inform young smokers about the risk of this habit in relation to periodontal health.

Sight Impairment registration due to stroke-A small yet significant rise?

PubMed

Bunce, Catey; Zekite, Antra; Wormald, Richard; Rowe, Fiona

2017-12-01

In the United Kingdom, when an individual's sight falls to and remains at a certain threshold, they may be offered registration as sight impaired. Recent analysis of causes of registrable sight impairment in England/Wales indicated that visual impairment due to stroke had increased as a proportionate cause of sight loss. We aim to assess whether there is evidence of an increase in incidence of certification for sight impairment due to stroke in England/Wales between 2008 and 2014. The number of certifications with a main cause of sight impairment being stroke was obtained from the Certifications Office London. Directly standardized rates per 100,000 were computed with 95% confidence intervals and examined. Poisson regression was used to assess evidence of trend over time. In the year ending 31st March 2008, 992 people were newly certified with stroke with an estimated DSR of 2.1 (2.0 to 2.2) per 100,000 persons at risk. In the year ending March 31st 2014, there were 1310 certifications with a DSR of 2.5 (2.4 to 2.7). Figures were higher for men than women. Poisson regression indicated an estimated incidence rate ratio of 1.03 per year with 95% confidence intervals of 1.028 to 1.051, P  < .001. These data suggest a small but statistically significant increase in the incidence of certifiable visual impairment due to stroke between 2008 and 2014. Figures are, however, considerably lower than estimated, perhaps suggesting that more should be done to address the visual needs of those who have suffered stroke.

Relationships of habitat patch size to predator community and survival of duck nests

USGS Publications Warehouse

Sovada, M.A.; Zicus, M.C.; Greenwood, R.J.; Rave, D.P.; Newton, W.E.; Woodward, R.O.; Beiser, J.A.

2000-01-01

We studied duck nest success and predator community composition in relation to size of discrete patches of nesting cover in the Prairie Pothole Region (PPR) of the United States in 1993-95. We focused on nests in uplands that were seeded to perennial grasses and forbs and enrolled in the Conservation Reserve Program (CRP) in Minnesota, North Dakota, and South Dakota. We estimated daily survival rates (DSRs) of upland duck nests and indices of activity for red foxes (Vulpes vulpes), coyotes (Canis latrans), American badgers (Taxidea taxus), striped skunks (Mephitis mephitis), and Franklin's ground squirrels (Spermophilus franklinii), and related these variables to habitat patch size. The effect of patch size (small vs. large) on estimated annual mean DSR was dependent on date of nest initiation (early vs. late) and year. Examination of within-year comparisons for early and late nests suggested that DSR was generally greater in larger habitat patches. Activity indices for the 5 mammalian nest predators were influenced differently by year, location, and patch size. Activity indices of the red fox were greatest in small patches. Coyote indices were the most inconsistent, demonstrating a year X location X patch size interaction. Activity indices of the striped skunk and American badger varied only among years. Franklin's ground squirrel indices were affected by study area location, with higher indices in the southeast than the northwest. Red fox activity was weakly correlated with that of the striped skunk and coyote. Although a positive relationship between habitat patch size and nest success probably exists, we believe the experiment to fully test this hypothesis will continue to be elusive.

Effect of deformation path on microstructure, microhardness and texture evolution of interstitial free steel fabricated by differential speed rolling

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

Hamad, Kotiba; Chung, Bong Kwon; Ko, Young Gun, E-mail: younggun@ynu.ac.kr

2014-08-15

This paper reports the effect of the deformation path on the microstructure, microhardness, and texture evolution of interstitial free (IF) steel processed by differential speed rolling (DSR) method. For this purpose, total height reductions of 50% and 75% were imposed on the samples by a series of differential speed rolling operations with various height reductions per pass (deformation levels) ranging from 10 to 50% under a fixed roll speed ratio of 1:4 for the upper and lower rolls, respectively. Microstructural observations using transmission electron microscopy and electron backscattered diffraction measurements showed that the samples rolled at deformation level of 50%more » had the finest mean grain size (∼ 0.5 μm) compared to the other counterparts; also the samples rolled at deformation level of 50% showed a more uniform microstructure. Based on the microhardness measurements along the thickness direction of the deformed samples, gradual evolution of the microhardness value and its homogeneity was observed with the increase of the deformation level per pass. Texture analysis showed that, as the deformation level per pass increased, the fraction of alpha fiber and gamma fiber in the deformed samples increased. The textures obtained by the differential speed rolling process under the lubricated condition would be equivalent to those obtained by the conventional rolling. - Highlights: • Effect of DSR deformation path on microstructure of IF steel is significant. • IF steel rolled at deformation level of 50% has the ultrafine grains of ∼ 0.5 μm. • Rolling texture components are pronounced with increasing deformation level.« less

Longitudinal plasma metanephrines preceding pheochromocytoma diagnosis: a retrospective case-control serum repository study.

PubMed

Olson, S W; Yoon, S; Baker, T; Prince, L K; Oliver, D; Abbott, K C

2016-03-01

Plasma metanephrines (PMN) are highly sensitive for diagnosis of pheochromocytoma, but the natural history of PMN before pheochromocytoma diagnosis has not been previously described. The aim of the study was to compare the progression of PMN before pheochromocytoma diagnosis to matched healthy and essential hypertension disease controls. A retrospective case-control Department of Defense Serum Repository (DoDSR) study. We performed a DoDSR study that compared three longitudinal pre-diagnostic PMN for 30 biopsy-proven pheochromocytoma cases to three longitudinal PMN for age, sex, race, and age of serum sample matched healthy and essential hypertension disease controls. Predominant metanephrine (MN) or normetanephrine (NMN) production was identified for each case and converted to a percentage of the upper limit of normal to allow analysis of all cases together. PMN were measured by Quest Diagnostics. The predominant plasma metanephrine (PPM) was >100 and 300% of the upper limit of normal a median of 6.6 and 4.1 years before diagnosis respectively. A greater percentage of pheochromocytoma patients had a PPM >100 and >300% of the upper limit of normal compared with combined healthy and essential hypertension disease controls <2, 2-8, and >8 years prior to diagnosis. For patients with a baseline PPM 90-300% of the upper limit of normal, a 25% rate of rise per year was 100% specific for pheochromocytoma. PPMs elevate years before diagnosis which suggests that delayed diagnoses are common. For mild PMN elevations, follow-up longitudinal PMN trends may provide a highly specific and economical diagnostic tool. © 2016 European Society of Endocrinology.

Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan.

PubMed

Green-Saxena, A; Feyzullayev, A; Hubert, C R J; Kallmeyer, J; Krueger, M; Sauer, P; Schulz, H-M; Orphan, V J

2012-12-01

Terrestrial mud volcanoes (TMVs) represent geochemically diverse habitats with varying sulfur sources and yet sulfur cycling in these environments remains largely unexplored. Here we characterized the sulfur-metabolizing microorganisms and activity in four TMVs in Azerbaijan. A combination of geochemical analyses, biological rate measurements and molecular diversity surveys (targeting metabolic genes aprA and dsrA and SSU ribosomal RNA) supported the presence of active sulfur-oxidizing and sulfate-reducing guilds in all four TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. The TMVs varied in potential sulfate reduction rates (SRR) by up to four orders of magnitude with highest SRR observed in sediments where in situ sulfate concentrations were highest. Maximum temperatures at which SRR were measured was 60°C in two TMVs. Corresponding with these trends in SRR, members of the potentially thermophilic, spore-forming, Desulfotomaculum were detected in these TMVs by targeted 16S rRNA analysis. Additional sulfate-reducing bacterial lineages included members of the Desulfobacteraceae and Desulfobulbaceae detected by aprA and dsrA analyses and likely contributing to the mesophilic SRR measured. Phylotypes affiliated with sulfide-oxidizing Gamma- and Betaproteobacteria were abundant in aprA libraries from low sulfate TMVs, while the highest sulfate TMV harboured 16S rRNA phylotypes associated with sulfur-oxidizing Epsilonproteobacteria. Altogether, the biogeochemical and microbiological data indicate these unique terrestrial habitats support diverse active sulfur-cycling microorganisms reflecting the in situ geochemical environment. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Hybrid suboptimal control of multi-rate multi-loop sampled-data systems

NASA Technical Reports Server (NTRS)

Shieh, Leang S.; Chen, Gwangchywan; Tsai, Jason S. H.

1992-01-01

A hybrid state-space controller is developed for suboptimal digital control of multirate multiloop multivariable continuous-time systems. First, an LQR is designed for a continuous-time subsystem which has a large bandwidth and is connnected in the inner loop of the overall system. The designed LQR would optimally place the eigenvalues of a closed-loop subsystem in the common region of an open sector bounded by sector angles + or - pi/2k for k = 2 or 3 from the negative real axis and the left-hand side of a vertical line on the negative real axis in the s-plane. Then, the developed continuous-time state-feedback gain is converted into an equivalent fast-rate discrete-time state-feedback gain via a digital redesign technique (Tsai et al. 1989, Shieh et al. 1990) reviewed here. A real state reconstructor is redeveloped utilizing the fast-rate input-output data of the system of interest. The design procedure of multiloop multivariable systems using multirate samplers is shown, and a terminal homing missile system example is used to demonstrate the effectiveness of the proposed method.

(t, n) Threshold d-Level Quantum Secret Sharing.

PubMed

Song, Xiu-Li; Liu, Yan-Bing; Deng, Hong-Yao; Xiao, Yong-Gang

2017-07-25

Most of Quantum Secret Sharing(QSS) are (n, n) threshold 2-level schemes, in which the 2-level secret cannot be reconstructed until all n shares are collected. In this paper, we propose a (t, n) threshold d-level QSS scheme, in which the d-level secret can be reconstructed only if at least t shares are collected. Compared with (n, n) threshold 2-level QSS, the proposed QSS provides better universality, flexibility, and practicability. Moreover, in this scheme, any one of the participants does not know the other participants' shares, even the trusted reconstructor Bob 1 is no exception. The transformation of the particles includes some simple operations such as d-level CNOT, Quantum Fourier Transform(QFT), Inverse Quantum Fourier Transform(IQFT), and generalized Pauli operator. The transformed particles need not to be transmitted from one participant to another in the quantum channel. Security analysis shows that the proposed scheme can resist intercept-resend attack, entangle-measure attack, collusion attack, and forgery attack. Performance comparison shows that it has lower computation and communication costs than other similar schemes when 2 < t < n - 1.

Implementation of the pyramid wavefront sensor as a direct phase detector for large amplitude aberrations

NASA Astrophysics Data System (ADS)

Kupke, Renate; Gavel, Don; Johnson, Jess; Reinig, Marc

2008-07-01

We investigate the non-modulating pyramid wave-front sensor's (P-WFS) implementation in the context of Lick Observatory's Villages visible light AO system on the Nickel 1-meter telescope. A complete adaptive optics correction, using a non-modulated P-WFS in slope sensing mode as a boot-strap to a regime in which the P-WFS can act as a direct phase sensor is explored. An iterative approach to reconstructing the wave-front phase, given the pyramid wave-front sensor's non-linear signal, is developed. Using Monte Carlo simulations, the iterative reconstruction method's photon noise propagation behavior is compared to both the pyramid sensor used in slope-sensing mode, and the traditional Shack Hartmann sensor's theoretical performance limits. We determine that bootstrapping using the P-WFS as a slope sensor does not offer enough correction to bring the phase residuals into a regime in which the iterative algorithm can provide much improvement in phase measurement. It is found that both the iterative phase reconstructor and the slope reconstruction methods offer an advantage in noise propagation over Shack Hartmann sensors.

Sulfur cycling in wetland peat of the New Jersey Pinelands and its effect on stream water chemistry

NASA Astrophysics Data System (ADS)

Mandernack, Kevin W.; Lynch, L.; Krouse, H. R.; Morgan, M. D.

2000-12-01

The dynamics of sulfur cycling in wetland peat along an elevational transect at high, intermediate, and low locations (MS, NW, and LB sites, respectively) was investigated in the watershed of McDonalds Branch within the New Jersey Pinelands, by utilizing both soil incubation experiments (with 35SO 42- as a radiotracer) and stable isotope (δ 34S and δ 18O) analyses of soil, rain, and streamwater. The results indicate that sulfur cycling can vary greatly among different portions of the watershed and this can have large effects on streamwater chemistry and δ 34S values over distances as short as 1 km. Laboratory incubations of peat samples collected in July 1993 revealed the co-occurrence of dissimilatory sulfate reduction (DSR; rates ranging from 0.2 to 22.1 nmol/wet g/day) and net generation of sulfate (NaH 2PO 4 extractable) in the porewater. Generation of sulfate, which was most pronounced at the LB site, may involve oxidation of reduced sulfur in the peat and/or hydrolysis of ester sulfates (ES). Seasonal changes in streamwater SO 42-/Cl - molar ratios were similar at LB and NW, being low during the summer and high in the winter, probably a result of higher rates of DSR within the peat during the summer. Consistent with this, higher δ 34S values of sulfate in streamwater at NW during the summer are attributable to kinetic isotope effects associated with DSR. In contrast to NW, δ 34S values of streamwater sulfate at LB were consistently lower, fluctuated little throughout the year, and were most negative during the summer (as much as 9‰ lower than streamwater at NW 1 km upstream). In comparison to NW, SO 42-/Cl - ratios were lower in streamwater at LB throughout most of the year except for reversals during the summer, which coincided with the lowest δ 34S values. In addition, there was a marked difference in the relationship of δ 18O vs. δ 34S of sulfate in LB and NW streamwater, further suggesting that sulfur cycling varies greatly over relatively short distances within this watershed. In order to explain some of these site-specific differences in streamwater SO 42-/Cl - ratios, δ 34S, and δ 18O values, we hypothesize that the ES pool at LB may, by means of hydrolysis or isotopic exchange with streamwater sulfate, serve as an additional source of isotopically light sulfate to streamwater throughout most of the year. During the summer, drier conditions lower the water table at LB and enhance oxidation of reduced sulfur which releases a pulse of even isotopically lighter sulfate to the stream.

Distribution of clay minerals on the Alaskan margin near Barrow Canyon revealed by Diffuse Spectral Reflectance measurements

NASA Astrophysics Data System (ADS)

Orsburn, C.; Ortiz, J. D.; Polyak, L.; Grebmeier, J. M.; Darby, D.

2007-12-01

Sediment clay mineral assemblages provide an excellent means of assessing the provenance of Arctic sediment due to the variety of sediment transport mechanisms at work and the existence of distinct weathering sources from differing bedrock geology. During HOTRAX Leg 1 aboard the USCG Ice breaker Healy (cruise HLY0501), we collected jumbo piston cores on the Alaskan margin near Barrow Canyon which provide detailed Holocene sedimentary records. Measurements of Diffuse Spectral Reflectance (DSR) were collected at 1cm resolution from the split surface of the cores using a Minolta CM-2600d UV/VIS spectrophotometer (400-700nm wavelength range; 10nm resolution; 3mm spot size). To interpret the resulting downcore records, we present a preliminary study using 28 coretop sediment samples collected by the Shelf-Basin Interaction program in 2004 arrayed in four transects across the shelf near Barrow Canyon. The samples were analyzed using an ASD Labspec Pro FR UV/VIS/NIR spectrometer (250-2500nm wavelength range, 2-10nm resolution; 20mm spot size). Our results indicate that the measurements from the two instruments are offset by constant factors, but can be easily compared. To estimate the clay mineralogy of the cores, we decomposed the matrix of DSR measurements from the coretop and downcore samples using principle component analysis and compared the resulting factor score patterns with mineral diffuse spectral reflectance signatures from known samples measured in our lab or available from version 5 of the USGS Digital Spectral Library. The three leading modes extracted by principle component analysis of the downcore samples are applicable to the coretops. We infer that the first principle component mode relates to smectite, the second to chlorite, and the third to a mixture of illite and goethite (herein referred to as illite - goethite). The geographic and bathymetric trends in the coretop data indicate that (1) the smectite and illite - goethite components both increase with depth and reach greater values in the two western transects than in the two eastern transects closest to the coast and Barrow Canyon, (2) the smectite and illite- goethite components are anticorrelated in the two western transects, but not in the two eastern transects, (3) chlorite decreases with depth and is highest in the two transects closest to Barrow Canyon. These results suggest that the chlorite on the Alaskan margin is transported by nearshore currents from the Bering Straight and then by bottom currents flowing through the Barrow Canyon. Accordingly, we interpret downcore chlorite peaks inferred from DSR measurements in our sediment cores as evidence of times of enhanced input of Pacific water to the Alaskan Margin.

Incorporating natural hazard assessments into municipal master-plans; case-studies from Israel

NASA Astrophysics Data System (ADS)

Katz, Oded

2010-05-01

The active Dead Sea Rift (DSR) runs along the length of Israel, making the entire state susceptible to earthquake-related hazards. Current building codes generally acknowledge seismic hazards and direct engineers towards earthquake-resistant structures. However, hazard mapping on a scale fit for municipal/governmental planning is subject to local initiative and is currently not mandatory as seems necessary. In the following, a few cases of seismic-hazard evaluation made by the Geological Survey of Israel are presented, emphasizing the reasons for their initiation and the way results were incorporated (or not). The first case is a seismic hazard qualitative micro-zonation invited by the municipality of Jerusalem as part of a new master plan. This work resulted in maps (1:50,000; GIS format) identifying areas prone to (1) amplification of seismic shaking due to site characteristics (outcrops of soft rocks or steep topography) and (2) sites with earthquake induced landslide (EILS) hazard. Results were validated using reports from the 1927, M=6.2 earthquake that originated along the DSR about 30km east of Jerusalem. Although the hazard maps were accepted by municipal authorities, practical use by geotechnical engineers working within the frame of the new master-plan was not significant. The main reason for that is apparently a difference of opinion between the city-engineers responsible for implementing the new master-plan and the geologists responsible of the hazard evaluation. The second case involves evaluation of EILS hazard for two towns located further north along the DSR, Zefat and Tiberias. Both were heavily damaged more than once by strong earthquakes in past centuries. Work was carried out as part of a governmental seismic-hazard reduction program. The results include maps (1:10,000 scales) of sites with high EILS hazard identified within city limits. Maps (in GIS format) were sent to city engineers with reports explaining the methods and results. As far as we know, widespread implementation of the maps within municipal master plans never came about, and there was no open discussion between city engineers and the Geological Survey. The main reasons apparently are (1) a lack, until recently, of mandatory building codes requiring incorporation of EILS hazard; (2) budget priorities; (3) failure to involve municipality personnel in planning and executing the EILS hazard evaluation. These cases demonstrate that for seismic hazard data to be incorporated and implemented within municipal master-plans there needs to be (1) active involvement of municipal officials and engineers from the early planning stages of the evaluation campaign, and (2) a-priori dedication of funds towards implementation of evaluation results.

Observation-based estimation of aerosol-induced reduction of planetary boundary layer height

NASA Astrophysics Data System (ADS)

Zou, Jun; Sun, Jianning; Ding, Aijun; Wang, Minghuai; Guo, Weidong; Fu, Congbin

2017-09-01

Radiative aerosols are known to influence the surface energy budget and hence the evolution of the planetary boundary layer. In this study, we develop a method to estimate the aerosol-induced reduction in the planetary boundary layer height (PBLH) based on two years of ground-based measurements at a site, the Station for Observing Regional Processes of the Earth System (SORPES), at Nanjing University, China, and radiosonde data from the meteorological station of Nanjing. The observations show that increased aerosol loads lead to a mean decrease of 67.1 W m-2 for downward shortwave radiation (DSR) and a mean increase of 19.2 W m-2 for downward longwave radiation (DLR), as well as a mean decrease of 9.6 Wm-2 for the surface sensible heat flux (SHF) in the daytime. The relative variations of DSR, DLR and SHF are shown as a function of the increment of column mass concentration of particulate matter (PM2.5). High aerosol loading can significantly increase the atmospheric stability in the planetary boundary layer during both daytime and nighttime. Based on the statistical relationship between SHF and PM2.5 column mass concentrations, the SHF under clean atmospheric conditions (same as the background days) is derived. In this case, the derived SHF, together with observed SHF, are then used to estimate changes in the PBLH related to aerosols. Our results suggest that the PBLH decreases more rapidly with increasing aerosol loading at high aerosol loading. When the daytime mean column mass concentration of PM2.5 reaches 200 mg m-2, the decrease in the PBLH at 1600 LST (local standard time) is about 450 m.

Montreal Cognitive Assessment (MoCA) screening mild cognitive impairment in patients with chronic kidney disease (CKD) pre-dialysis.

PubMed

Paraizo, Marilise de Andrade; Almeida, Ana Laura Maciel; Pires, Leopoldo Antônio; Abrita, Renata Silva Almeida; Crivellari, Mary Hellen Teixeira; Pereira, Beatriz Dos Santos; Fernandes, Natália Maria da Silva; Bastos, Marcus Gomes

2016-03-01

Individuals with chronic kidney disease (CKD) are at higher risk of developing cognitive impairment (CI), initially mild (MCI), potentially identifiable, but still poorly diagnosed and treated. The Montreal Cognitive Assessment (MoCA) has been indicated for MCI screening in CKD. To assess MCI in patients with CKD not yet on dialysis. Study conducted in 72 non-elderly subjects with pre-dialysis CKD. The neuropsychological assessment included: The global cognitive assessment test MoCA; the clock drawing (CD); the digit span forward (DSF) and reverse (DSR); phonemic verbal (VF) fluency (FAS) and semantics (animals); the fist-edge-palm (FEP); and the memory 10 pictures. The average age of the participants was 56.74 ± 7.63 years, with predominance of male sex (55.6%), mainly with ≥ 4 years of education (84.3%), with CKD cathegories 1, 2 and 3a and 3b (67.6%), hypertension (93.1%) and diabetes mellitus (52.1%). MCI (MoCA ≤ 24) was observed in 73.6% of the patients. We did not find association among MCI with demographic and clinical variables, but a tendency to association with age (p = 0.07), educational level (p= 0.06) and diabetes (0.06). The executive function tests CD, DS-reverse and FEP, individually were able to identify CI with good sensibility and negative predictive value compared to MoCA and together, showed the same capability to identify MCI when compared to MoCA. The MCI is common in non-elderly patients with CKD not yet on dialysis. Together, the CD, DSR and FEP showed similar performance in identify MCI in this population when compared to MoCA, suggesting impairment of executive functions.

Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil.

PubMed

Sitte, Jana; Akob, Denise M; Kaufmann, Christian; Finster, Kai; Banerjee, Dipanjan; Burkhardt, Eva-Maria; Kostka, Joel E; Scheinost, Andreas C; Büchel, Georg; Küsel, Kirsten

2010-05-01

Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the (35)SO(4)(2-) radiotracer method, was restricted to reduced soil horizons with rates of < or =142 +/- 20 nmol cm(-3) day(-1). Concentrations of heavy metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that approximately 80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone libraries were dominated by sequences affiliated with members of the Desulfobacterales but also the Desulfovibrionales, Syntrophobacteraceae, and Clostridiales. [(13)C]acetate- and [(13)C]lactate-biostimulated soil microcosms were dominated by sulfate and Fe(III) reduction. These processes were associated with enrichment of SRB and Geobacteraceae; enriched SRB were closely related to organisms detected in soils by using the dsrAB marker. Concentrations of soluble nickel, cobalt, and occasionally zinc declined < or =100% during anoxic soil incubations. In contrast to results in other studies, soluble uranium increased in carbon-amended treatments, reaching < or =1,407 nM in solution. Our results suggest that (i) ongoing sulfate reduction in contaminated soil resulted in in situ metal attenuation and (ii) the fate of uranium mobility is not predictable and may lead to downstream contamination of adjacent ecosystems.

Microbial Links between Sulfate Reduction and Metal Retention in Uranium- and Heavy Metal-Contaminated Soil▿

PubMed Central

Sitte, Jana; Akob, Denise M.; Kaufmann, Christian; Finster, Kai; Banerjee, Dipanjan; Burkhardt, Eva-Maria; Kostka, Joel E.; Scheinost, Andreas C.; Büchel, Georg; Küsel, Kirsten

2010-01-01

Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the 35SO42− radiotracer method, was restricted to reduced soil horizons with rates of ≤142 ± 20 nmol cm−3 day−1. Concentrations of heavy metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that ∼80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone libraries were dominated by sequences affiliated with members of the Desulfobacterales but also the Desulfovibrionales, Syntrophobacteraceae, and Clostridiales. [13C]acetate- and [13C]lactate-biostimulated soil microcosms were dominated by sulfate and Fe(III) reduction. These processes were associated with enrichment of SRB and Geobacteraceae; enriched SRB were closely related to organisms detected in soils by using the dsrAB marker. Concentrations of soluble nickel, cobalt, and occasionally zinc declined ≤100% during anoxic soil incubations. In contrast to results in other studies, soluble uranium increased in carbon-amended treatments, reaching ≤1,407 nM in solution. Our results suggest that (i) ongoing sulfate reduction in contaminated soil resulted in in situ metal attenuation and (ii) the fate of uranium mobility is not predictable and may lead to downstream contamination of adjacent ecosystems. PMID:20363796

Sediment Cd and Mo accumulation in the oxygen-minimum zone off western Baja California linked to global climate over the past 52 kyr

USGS Publications Warehouse

Dean, W.E.; Zheng, Yen; Ortiz, J.D.; VanGeen, A.

2006-01-01

Concentrations of organic carbon (orgC), cadmium (Cd), and molybdenum (Mo) were measured in two sediment cores raised from depths of 430 and 700 m within the oxygen-minimum zone (OMZ) off southern Baja California at a temporal resolution of e10.5 kyr over the past 52 kyr. These records are supplemented with diffuse spectral reflectance (DSR) measurements obtained on board ship soon after collection at a resolution of e10.05 kyr. In the core from 700 m depth, a component extracted from the DSR data and the three geochemical proxies generally vary in concert with each other and over a wide range (4-22% orgC; 1-40 mg/kg Cd; 5-120 mg/kg Mo). Intervals of increased orgC, Cd, and Mo accumulation generally correspond to warm periods recorded in the oxygen-isotopic composition of Greenland ice, with the exception of the Bolling/Allerod which is only weakly expressed off Baja California. Concentrations of the biogenic proxies are higher in the core from 430 m depth, but erratic sediment accumulation before 15 ka precludes dating of the older intervals that are laminated and contain elevated orgC, Cd, and Mo concentrations. The new data provide further evidence of an intimate teleconnection between global climate and the intensity of the OMZ and/or productivity along the western margin of North America. On the basis of a comparison with Cd and Mo records collected elsewhere in the region, we conclude that productivity may actually have varied off southern Baja California by no more than a factor of 2 over the past 52 kyr. Copyright 2006 by the American Geophysical Union.

Temporal variability of mass transport across Canary Islands Channels

NASA Astrophysics Data System (ADS)

Marrero-Díaz, Ángeles; Rodríguez-Santana, Ángel; José Machín, Francisco; García-Weil, Luis; Sangrà, Pablo; Vélez-Belchí, Pedro; Fraile-Nuez, Eugenio

2014-05-01

The equatorward flowing Canary Current (CC) is the main feature of the circulation in the Canary Islands region. The CC flow perturbation by the Canary Islands originate the Canary Eddy Corridor which is the major pathway for long lived eddies in the subtropical North Atlantic (Sangrà et al., 2009, DSR). Therefore the variability of the CC passing through the Canary Archipelago will have both local and regional importance. Past studies on the CC variability trough the Canary Islands point out a clearly seasonal variability (Fraile-Nuez et al, 2010 (JGR); Hernández-Guerra et al, 2002 (DSR)). However those studies where focused on the eastern islands channels missing the variability through the western island channels which are the main source of long lived eddies. In order to fill this gap from November 2012 until September 2013 we conducted trimonthly surveys crossing the whole islands channels using opportunity ships (Naviera Armas Ferries). XBT and XCTD where launched along the cross channels transects. Additionally a closed box circling the Archipelago was performed on October 2013 as part of the cruise RAPROCAN-2013 (IEO) using also XBT and XCTD. Dynamical variables where derived inferring salinity from S(T,p) analytical relationships for the region updated with new XCTD data. High resolution, vertical sections of temperature, potential density, geostrophic velocity and transport where obtained. Our preliminary results suggest that the CC suffer a noticeable acceleration in those islands channels where eddy shedding is more frequent. They also indicate a clearly seasonal variability of the flows passing the islands channels. With this regard we observed significant differences on the obtained seasonal variability with respect the cited past studies on the eastern islands channel (Lanzarote / Fuerteventura - Africa coast). This work was co-funded by Canary Government (TRAMIC project: PROID20100092) and the European Union (FEDER).

Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

PubMed Central

Weissgerber, Thomas; Dobler, Nadine; Polen, Tino; Latus, Jeanette; Stockdreher, Yvonne

2013-01-01

The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to photoorganoheterotrophic growth on malate. Differential expression of 1,178 genes was observed, corresponding to 30% of the A. vinosum genome. Relative transcription of 551 genes increased significantly during growth on one of the different sulfur sources, while the relative transcript abundance of 627 genes decreased. A significant number of genes that revealed strongly enhanced relative transcription levels have documented sulfur metabolism-related functions. Among these are the dsr genes, including dsrAB for dissimilatory sulfite reductase, and the sgp genes for the proteins of the sulfur globule envelope, thus confirming former results. In addition, we identified new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Those four genes for hypothetical proteins that exhibited the strongest increases of mRNA levels on sulfide and elemental sulfur, respectively, were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for sulfur globule formation during the oxidation of sulfide and thiosulfate and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria. PMID:23873913

Composition and Function of Sulfate-Reducing Prokaryotes in Eutrophic and Pristine Areas of the Florida Everglades†

PubMed Central

Castro, Hector; Reddy, K. R.; Ogram, Andrew

2002-01-01

As a result of agricultural activities in regions adjacent to the northern boundary of the Florida Everglades, a nutrient gradient developed that resulted in physicochemical and ecological changes from the original system. Sulfate input from agricultural runoff and groundwater is present in soils of the Northern Everglades, and sulfate-reducing prokaryotes (SRP) may play an important role in biogeochemical processes such as carbon cycling. The goal of this project was to utilize culture-based and non-culture-based approaches to study differences between the composition of assemblages of SRP in eutrophic and pristine areas of the Everglades. Sulfate reduction rates and most-probable-number enumerations revealed SRP populations and activities to be greater in eutrophic zones than in more pristine soils. In eutrophic regions, methanogenesis rates were higher, the addition of acetate stimulated methanogenesis, and SRP able to utilize acetate competed to a limited degree with acetoclastic methanogens. A surprising amount of diversity within clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) genes was observed, and the majority of DSR sequences were associated with gram-positive spore-forming Desulfotomaculum and uncultured microorganisms. Sequences associated with Desulfotomaculum fall into two categories: in the eutrophic regions, 94.7% of the sequences related to Desulfotomaculum were associated with those able to completely oxidize substrates, and in samples from pristine regions, all Desulfotomaculum-like sequences were related to incomplete oxidizers. This metabolic selection may be linked to the types of substrates that Desulfotomaculum spp. utilize; it may be that complete oxidizers are more versatile and likelier to proliferate in nutrient-rich zones of the Everglades. Desulfotomaculum incomplete oxidizers may outcompete complete oxidizers for substrates such as hydrogen in pristine zones where diverse carbon sources are less available. PMID:12450837

Distribution of microbial biomass and potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment.

PubMed

Lin, Xueju; Kennedy, David; Peacock, Aaron; McKinley, James; Resch, Charles T; Fredrickson, James; Konopka, Allan

2012-02-01

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.

Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment

PubMed Central

Lin, Xueju; Kennedy, David; Peacock, Aaron; McKinley, James; Resch, Charles T.; Fredrickson, James

2012-01-01

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling. PMID:22138990

Clinical Subtypes of Premenstrual Syndrome and Responses to Sertraline Treatment

PubMed Central

Freeman, Ellen W.; Sammel, Mary D.; Lin, Hui; Rickels, Karl; Sondheimer, Steven J.

2011-01-01

OBJECTIVE To estimate response of diagnosis and symptom-based subtypes to sertraline treatment. METHODS This was a secondary data analysis for women who were diagnosed with premenstrual syndrome (PMS) or premenstrual dysphoric disorder and treated in three National Institutes of Health-supported clinical trials (N=447). Three PMS subtypes were identified based on predominance of psychological, physical, or both symptom types. Scores for each symptom and a total premenstrual score at baseline and endpoint were calculated from daily symptom diaries. Change from baseline after three treated menstrual cycles (or endpoint if sooner) was estimated using linear regression models adjusted for baseline severity. RESULTS The PMS and premenstrual dysphoric disorder diagnoses improved similarly with sertraline relative to placebo, while symptom-based subtypes had differential responses to treatment. The mixed symptom subtype had the strongest response to sertraline relative to placebo (Daily Symptom Rating [DSR] difference 33.80, 95% CI: 17.16, 50.44, P<0.001), and the physical symptom subtype had the poorest response to sertraline (DSR difference 9.50, 95% CI: −16.29, 35.28, P=0.470). Results based on clinical improvement (50% decrease from baseline) indicated that 8.3 participants in the mixed symptom subtype, 3.9 in the psychological subtype, and 7.1 in the physical subtype are needed to observe one woman in the subtype who would achieve clinical improvement. CONCLUSION The PMS and premenstrual dysphoric disorder diagnoses have similar response to sertraline treatment, but symptom-based subtypes have significantly different responses to this treatment. Mixed and psychological symptom subtypes improved while the physical symptom subtype did not improve significantly. Identifying the patient’s predominant symptoms, and their severity is important for individualized treatment and possible response to a selective serotonin reuptake inhibitor. PMID:22105258

Significant role of organic sulfur in supporting sedimentary sulfate reduction in low-sulfate environments

NASA Astrophysics Data System (ADS)

Fakhraee, Mojtaba; Li, Jiying; Katsev, Sergei

2017-09-01

Dissimilatory sulfate reduction (DSR) is a major carbon mineralization pathway in aquatic sediments, soils, and groundwater, which regulates the production of hydrogen sulfide and the mobilization rates of biologically important elements such as phosphorus and mercury. It has been widely assumed that water-column sulfate is the main sulfur source to fuel this reaction in sediments. While this assumption may be justified in high-sulfate environments such as modern seawater, we argue that in low-sulfate environments mineralization of organic sulfur compounds can be an important source of sulfate. Using a reaction-transport model, we investigate the production of sulfate from sulfur-containing organic matter for a range of environments. The results show that in low sulfate environments (<500 μM) the in-sediment production of sulfate can support a substantial portion (>50%) of sulfate reduction. In well-oxygenated systems, porewater sulfate profiles often exhibit sub-interface peaks so that sulfate fluxes are directed out of the sediment. Our measurements in Lake Superior, the world's largest lake, corroborate this conclusion: offshore sediments act as sources rather than sinks of sulfate for the water column, and sediment DSR is supported entirely by the in-sediment production of sulfate. Sulfate reduction rates are correlated to the depth of oxygen penetration and strongly regulated by the supply of reactive organic matter; rate co-regulation by sulfate availability becomes appreciable below 500 μM level. The results indicate the need to consider the mineralization of organic sulfur in the biogeochemical cycling in low-sulfate environments, including several of the world's largest freshwater bodies, deep subsurface, and possibly the sulfate-poor oceans of the Early Earth.

Choroïdopathie du lupus érythémateux systémique, à propos d'un cas

PubMed Central

Idriss, Benatiya Andaloussi; Fouad, Chraibi; Salima, Bhallil; Meryem, Abdellaoui; Hicham, Tahri

2013-01-01

Le lupus érythémateux systémique (LES) est une maladie auto-immune multi systémique d’étiologie inconnue. Nous rapportons une manifestation très rare du LES représentée par une choroidopathie bilatérale sans hypertension artérielle associée. Il s'agit d'une patiente âgée de 45 ans, suivie pour un LES depuis 5 ans, qui présente une baisse de l'acuité visuelle bilatérale et progressive depuis 3 mois. L'examen du fond d’œil, complété l'angiographie à la fluorescéine et la tomographie en cohérence optique, retrouve un décollement séreux rétinien (DSR) multifocal et bilatéral. L’évolution après corticothérapie systémique est marquée par une amélioration de l'acuité visuelle et une régression du DSR. L'atteinte oculaire au cours du LED est dominée par la kérato-conjonctivite sèche (1/4 à 1/3 des cas). La choroïdopathie est plus rare: seulement une trentaine de cas sont rapportés dans littérature. Elle se manifeste par un décollement séreux rétinien et est habituellement observée chez les patients présentant une néphropathie ou une hypertension artérielle, ce qui n'est pas le cas de notre observation. L'apparition d'une atteinte oculaire au cours du LES peut annoncer une poussée d'atteinte systémique et doit susciter une enquête appropriée. PMID:23717732

Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years.

PubMed

de Rezende, Júlia Rosa; Kjeldsen, Kasper Urup; Hubert, Casey R J; Finster, Kai; Loy, Alexander; Jørgensen, Bo Barker

2013-01-01

Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 10(4) per cm(3) at the surface and decreased exponentially to 10(0) per cm(3) at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments.

Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years

PubMed Central

de Rezende, Júlia Rosa; Kjeldsen, Kasper Urup; Hubert, Casey R J; Finster, Kai; Loy, Alexander; Jørgensen, Bo Barker

2013-01-01

Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 104 per cm3 at the surface and decreased exponentially to 100 per cm3 at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments. PMID:22832348

Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed

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

Kovacik, William P.; Scholten, Johannes C.; Culley, David E.

2010-08-01

The complexity and diversity of the microbial communities in biogranules from an upflow anaerobic sludge blanket (UASB) bioreactor were determined in response to short-term changes in substrate feeds. The reactor was fed simulated brewery wastewater (SBWW) (70% ethanol, 15% acetate, 15% propionate) for 1.5 months (phase 1), acetate / sulfate for 2 months (phase 2), acetate-alone for 3 months (phase 3), and then a return to SBWW for 2 months (phase 4). Performance of the reactor remained relatively stable throughout the experiment as shown by COD removal and gas production. 16S rDNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB genes weremore » PCR amplified, then cloned and sequenced. Sequence analysis of 16S clone libraries showed a relatively simple community composed mainly of the methanogenic Archaea (Methanobacterium and Methanosaeta), members of the Green Non-Sulfur (Chloroflexi) group of Bacteria, followed by fewer numbers of Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related Bacterial sequences. Methanogen-related mcrA clone libraries were dominated throughout by Methanobacter and Methanospirillum related sequences. Although not numerous enough to be detected in our 16S rDNA libraries, sulfate reducers were detected in dsrAB clone libraries, with sequences related to Desulfovibrio and Desulfomonile. Community diversity levels (Shannon-Weiner index) generally decreased for all libraries in response to a change from SBWW to acetate-alone feed. But there was a large transitory increase noted in 16S diversity at the two-month sampling on acetate-alone, entirely related to an increase in Bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels.« less

Effect of tailored on-road driving lessons on driving safety in older adults: A randomised controlled trial.

PubMed

Anstey, Kaarin J; Eramudugolla, Ranmalee; Kiely, Kim M; Price, Jasmine

2018-06-01

We evaluated the effectiveness of individually tailored driving lessons compared with a road rules refresher course for improving older driver safety. Two arm parallel randomised controlled trial, involving current drivers aged 65 and older (Mean age 72.0, 47.4% male) residing in Canberra, Australia. The intervention group (n = 28) received a two-hour class-based road rules refresher course, and two one-hour driving lessons tailored to improve poor driving skills and habits identified in a baseline on-road assessment. The control group (n = 29) received the road rules refresher course only. Tests of cognitive performance, and on-road driving were conducted at baseline and at 12-weeks. Main outcome measure was the Driver safety rating (DSR) on the on-road driving test. The number of Critical Errors made during the on-road was also recorded. 55 drivers completed the trial (intervention group: 27, control group: 28). Both groups showed reduction in dangerous/hazardous driver errors that required instructor intervention. From baseline to follow-up there was a greater reduction in the number of critical errors made by the intervention group relative to the control group (IRR = 0.53, SE = 0.1, p = .008). The intervention group improved on the DSR more than the control group (intervention mean change = 1.07 SD = 2.00, control group mean change = 0.32 SD = 1.61). The intervention group had 64% remediation of unsafe driving, where drivers who achieved a score of 'fail' at baseline, 'passed' at follow-up. The control group had 25% remediation. Tailored driving lessons reduced the critical driving errors made by older adults. Longer term follow-up and larger trials are required. Copyright © 2018 Elsevier Ltd. All rights reserved.

The tragic fire event of June 17, 2017 in Portugal: the meteorological perspective

NASA Astrophysics Data System (ADS)

DaCamara, C.; Trigo, R. M.; Pinto, M. M.; Nunes, S. A.; Trigo, I. F.

2017-12-01

Like Mediterranean Europe, Portugal is prone to the occurrence of large and destructive wildfires that have serious impacts at the socio-economic and ecological levels. A tragic example is the episode of June 17, 2017 at Pedrógão Grande-Góis, with an official death toll of 64 people, almost 500 buildings destroyed and a continuous patch of more than 42 thousand hectares burned in one week. Climate and meteorology play a determinant role in the onset and spreading of large wildfire events in the Mediterranean basin. Two main kinds of atmospheric mechanisms may be identified. At the regional and the seasonal levels, a wetter-than usual winter followed by a warmer and drier than average spring makes the landscape prone to the occurrence of large fires. At the local and the daily scales, extreme weather conditions favor the ignition and spread of wildfires. This dual role may be assessed by means of indices of meteorological fire danger like FWI and DSR. We show that the severity of the 2017 fire season was correctly anticipated by means of a statistical model based on cumulated values of DSR starting on April 1. We then show that extreme danger of fire on June 17 was correctly forecasted for the area of Pedrógão Grande-Góis, based on values of estimated probability of exceedance of daily released energy by active fires. These two statistical approaches are on the basis of a website developed at Instituto Dom Luiz (IDL) at the Faculty of Sciences of the University of Lisbon. With more than 400 registered users, the website relies on products disseminated by the Land Surface Analysis Satellite Application Facility (LSA SAF), coordinated by IPMA, the Portuguese Weather Service.

Reducing the costs of meeting regional water demand through risk-based transfer agreements.

PubMed

Palmer, Reed N; Characklis, Gregory W

2009-04-01

Transfers of treated water among inter-connected utilities is becoming more common as the cost of developing new supplies grows, and transfer agreements require well developed rules describing when and how much water will be transferred. The nature of the decision rules governing an agreement must also be coordinated with respect to the treatment and conveyance capacity required to execute the transfers. This study explores different combinations of infrastructure and agreement type that define three different transfer programs, describing the frequency and volume of transfers associated with each, as well as their costs. The agreements are described in terms of the type of decision rule employed: Take-or-Pay, where the timing and quantity of transfers is fixed; Days of Supply Remaining (DSR), which uses a static hydrologic indicator to trigger transfers; and Risk-of-Failure, a probability-based decision rule that involves consideration of both supply and demand. This analysis is conducted within the context of the Research Triangle area of North Carolina (USA), a rapidly growing area that is beginning to approach the practical limits of water resource development. The Risk-of-Failure agreement is shown to reduce the average volume of transfers by over 80% compared to a Take-or-Pay agreement and by roughly half relative to the DSR agreement, leading to significant cost reductions. A utility's willingness to accept something less than guaranteed access to a specified quantity of water (i.e. an interruption) also has a significant impact on cost. Interruptions do not necessarily lead to lower reliability, but rather to the purchasing utility acquiring more water during off-peak periods when the seller has excess treatment capacity available. The lowest cost guaranteed agreement is 40-50% more expensive than the lowest cost interruptible contract.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

PubMed

Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

2018-04-01

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

WE-AB-207A-08: BEST IN PHYSICS (IMAGING): Advanced Scatter Correction and Iterative Reconstruction for Improved Cone-Beam CT Imaging On the TrueBeam Radiotherapy Machine

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

Wang, A; Paysan, P; Brehm, M

2016-06-15

Purpose: To improve CBCT image quality for image-guided radiotherapy by applying advanced reconstruction algorithms to overcome scatter, noise, and artifact limitations Methods: CBCT is used extensively for patient setup in radiotherapy. However, image quality generally falls short of diagnostic CT, limiting soft-tissue based positioning and potential applications such as adaptive radiotherapy. The conventional TrueBeam CBCT reconstructor uses a basic scatter correction and FDK reconstruction, resulting in residual scatter artifacts, suboptimal image noise characteristics, and other artifacts like cone-beam artifacts. We have developed an advanced scatter correction that uses a finite-element solver (AcurosCTS) to model the behavior of photons as theymore » pass (and scatter) through the object. Furthermore, iterative reconstruction is applied to the scatter-corrected projections, enforcing data consistency with statistical weighting and applying an edge-preserving image regularizer to reduce image noise. The combined algorithms have been implemented on a GPU. CBCT projections from clinically operating TrueBeam systems have been used to compare image quality between the conventional and improved reconstruction methods. Planning CT images of the same patients have also been compared. Results: The advanced scatter correction removes shading and inhomogeneity artifacts, reducing the scatter artifact from 99.5 HU to 13.7 HU in a typical pelvis case. Iterative reconstruction provides further benefit by reducing image noise and eliminating streak artifacts, thereby improving soft-tissue visualization. In a clinical head and pelvis CBCT, the noise was reduced by 43% and 48%, respectively, with no change in spatial resolution (assessed visually). Additional benefits include reduction of cone-beam artifacts and reduction of metal artifacts due to intrinsic downweighting of corrupted rays. Conclusion: The combination of an advanced scatter correction with iterative reconstruction substantially improves CBCT image quality. It is anticipated that clinically acceptable reconstruction times will result from a multi-GPU implementation (the algorithms are under active development and not yet commercially available). All authors are employees of and (may) own stock of Varian Medical Systems.« less

AOF LTAO mode: reconstruction strategy and first test results

NASA Astrophysics Data System (ADS)

Oberti, Sylvain; Kolb, Johann; Le Louarn, Miska; La Penna, Paolo; Madec, Pierre-Yves; Neichel, Benoit; Sauvage, Jean-François; Fusco, Thierry; Donaldson, Robert; Soenke, Christian; Suárez Valles, Marcos; Arsenault, Robin

2016-07-01

GALACSI is the Adaptive Optics (AO) system serving the instrument MUSE in the framework of the Adaptive Optics Facility (AOF) project. Its Narrow Field Mode (NFM) is a Laser Tomography AO (LTAO) mode delivering high resolution in the visible across a small Field of View (FoV) of 7.5" diameter around the optical axis. From a reconstruction standpoint, GALACSI NFM intends to optimize the correction on axis by estimating the turbulence in volume via a tomographic process, then projecting the turbulence profile onto one single Deformable Mirror (DM) located in the pupil, close to the ground. In this paper, the laser tomographic reconstruction process is described. Several methods (virtual DM, virtual layer projection) are studied, under the constraint of a single matrix vector multiplication. The pseudo-synthetic interaction matrix model and the LTAO reconstructor design are analysed. Moreover, the reconstruction parameter space is explored, in particular the regularization terms. Furthermore, we present here the strategy to define the modal control basis and split the reconstruction between the Low Order (LO) loop and the High Order (HO) loop. Finally, closed loop performance obtained with a 3D turbulence generator will be analysed with respect to the most relevant system parameters to be tuned.

Laser guide star wavefront sensing for ground-layer adaptive optics on extremely large telescopes.

PubMed

Clare, Richard M; Le Louarn, Miska; Béchet, Clementine

2011-02-01

We propose ground-layer adaptive optics (GLAO) to improve the seeing on the 42 m European Extremely Large Telescope. Shack-Hartmann wavefront sensors (WFSs) with laser guide stars (LGSs) will experience significant spot elongation due to off-axis observation. This spot elongation influences the design of the laser launch location, laser power, WFS detector, and centroiding algorithm for LGS GLAO on an extremely large telescope. We show, using end-to-end numerical simulations, that with a noise-weighted matrix-vector-multiply reconstructor, the performance in terms of 50% ensquared energy (EE) of the side and central launch of the lasers is equivalent, the matched filter and weighted center of gravity centroiding algorithms are the most promising, and approximately 10×10 undersampled pixels are optimal. Significant improvement in the 50% EE can be observed with a few tens of photons/subaperture/frame, and no significant gain is seen by adding more than 200 photons/subaperture/frame. The LGS GLAO is not particularly sensitive to the sodium profile present in the mesosphere nor to a short-timescale (less than 100 s) evolution of the sodium profile. The performance of LGS GLAO is, however, sensitive to the atmospheric turbulence profile.

Waffle mode error in the AEOS adaptive optics point-spread function

NASA Astrophysics Data System (ADS)

Makidon, Russell B.; Sivaramakrishnan, Anand; Roberts, Lewis C., Jr.; Oppenheimer, Ben R.; Graham, James R.

2003-02-01

Adaptive optics (AO) systems have improved astronomical imaging capabilities significantly over the last decade, and have the potential to revolutionize the kinds of science done with 4-5m class ground-based telescopes. However, provided sufficient detailed study and analysis, existing AO systems can be improved beyond their original specified error budgets. Indeed, modeling AO systems has been a major activity in the past decade: sources of noise in the atmosphere and the wavefront sensing WFS) control loop have received a great deal of attention, and many detailed and sophisticated control-theoretic and numerical models predicting AO performance are already in existence. However, in terms of AO system performance improvements, wavefront reconstruction (WFR) and wavefront calibration techniques have commanded relatively little attention. We elucidate the nature of some of these reconstruction problems, and demonstrate their existence in data from the AEOS AO system. We simulate the AO correction of AEOS in the I-band, and show that the magnitude of the `waffle mode' error in the AEOS reconstructor is considerably larger than expected. We suggest ways of reducing the magnitude of this error, and, in doing so, open up ways of understanding how wavefront reconstruction might handle bad actuators and partially-illuminated WFS subapertures.

An Online, Interactive Approach to Teaching Neuroscience to Adolescents

PubMed Central

Moreno, Janette; Willcockson, Irmgard; Smith, Donna; Mayes, Janice

2006-01-01

Most of today's students are skilled in instant messaging, Web browsing, online games, and blogs. These have become part of the social landscape and have changed how we learn and where we learn. The question becomes how to harness the attractiveness and ubiquity of electronic venues toward the goal of teaching neuroscience. At the Rice University Center for Technology in Teaching and Learning, a central focus is the creation of innovative materials that appeal to middle school students. A recent project was undertaken through a Science Education Drug Abuse Partnership Award (R25 DA15063) from the National Institute on Drug Abuse to inform adolescents about the neurobiology of substance abuse and the current research dealing with a class of drugs known as club drugs. Problem-based learning, multimedia pedagogy, and the National Science Content Standards were integrated to produce The Reconstructors™, an episodic series available via the World Wide Web at http://reconstructors.rice.edu. A field test of students from five schools assessed the retention of content after “playing” The Reconstructors™ series titled Nothing to Rave About. Gain scores indicated that middle school students' knowledge about club drugs and the basic neuroscience concepts that explain their effects improved significantly. PMID:17012204

Anticipating the severity of the fire season in Northern Portugal using statistical models based on meteorological indices of fire danger

NASA Astrophysics Data System (ADS)

Nunes, Sílvia A.; DaCamara, Carlos C.; Turkman, Kamil F.; Ermida, Sofia L.; Calado, Teresa J.

2017-04-01

Like in other regions of Mediterranean Europe, climate and weather are major drivers of fire activity in Portugal. The aim of the present study is to assess the role played by meteorological factors on inter-annual variability of burned area over a region of Portugal characterized by large fire activity. Monthly cumulated values of burned area in August are obtained from the fire database of ICNF, the Portuguese authority for forests. The role of meteorological factors is characterized by means of Daily Severity Rating, DSR, an index of meteorological fire danger, which is derived from meteorological fields as obtained from ECMWF Interim Reanalysis. The study area is characterized by the predominance of forest, with high percentages of maritime pine and eucalyptus, two species with high flammability in summer. The time series of recorded burned area in August during 1980-2011 is highly correlated (correlation coefficient of 0.93) with the one for whole Portugal. First, a normal distribution model is fitted to the 32-year sample of decimal logarithms of monthly burned area. The model is improved by introducing two covariates:(1) the top-down meteorological factor (DSRtd) which consists of daily cumulated values of DSR since April 1 to July 31 and may be viewed as the cumulated stress on vegetation due to meteorological conditions during the pre-fire season; (2) the bottom-up factor (DSRbu) which consists of the square root of the mean of the squared daily deviations (restricted to days with positive departures of DSR from the corresponding long term mean) and may be viewed as the contribution of days characterized by extreme weather conditions favoring the onset and spreading of wildfires. Three different statistical models are then developed: the "climate anomaly" model, using DSRtd as covariate, the "weather anomaly", using DSRbu as covariate, and the "combined" model using both variables as covariates. These models are used to define background fire danger, fire weather danger and combined fire danger, respectively quantifying the contribution of DSRtd, DSRbu and both covariates to increasing or decreasing the probability of having extremely high/low values of burned area in August. Using the information obtained by the "combined" model it is possible to calculate the minimum/ maximum value of DSRbu for a given year to be modelled as severe/weak. The probability is then made using a normal distribution of the data series of DSRbu, if the probability is below 20% than the year will be considered as not belonging to that classification. This classification is able to correctly identify 34 out of the 36 years studied. This results can be of extreme use to forest managers and firefighters when deciding which the best fire preventing measures are and where to allocate the resources.

Comparison of the egg flotation and egg candling techniques for estimating incubation day of Canada Goose nests

USGS Publications Warehouse

Reiter, M.E.; Andersen, D.E.

2008-01-01

Both egg flotation and egg candling have been used to estimate incubation day (often termed nest age) in nesting birds, but little is known about the relative accuracy of these two techniques. We used both egg flotation and egg candling to estimate incubation day for Canada Geese (Branta canadensis interior) nesting near Cape Churchill, Manitoba, from 2000 to 2007. We modeled variation in the difference between estimates of incubation day using each technique as a function of true incubation day, as well as, variation in error rates with each technique as a function of the true incubation day. We also evaluated the effect of error in the estimated incubation day on estimates of daily survival rate (DSR) and nest success using simulations. The mean difference between concurrent estimates of incubation day based on egg flotation minus egg candling at the same nest was 0.85 ?? 0.06 (SE) days. The positive difference in favor of egg flotation and the magnitude of the difference in estimates of incubation day did not vary as a function of true incubation day. Overall, both egg flotation and egg candling overestimated incubation day early in incubation and underestimated incubation day later in incubation. The average difference between true hatch date and estimated hatch date did not differ from zero (days) for egg flotation, but egg candling overestimated true hatch date by about 1 d (true - estimated; days). Our simulations suggested that error associated with estimating the incubation day of nests and subsequently exposure days using either egg candling or egg flotation would have minimal effects on estimates of DSR and nest success. Although egg flotation was slightly less biased, both methods provided comparable and accurate estimates of incubation day and subsequent estimates of hatch date and nest success throughout the entire incubation period. ?? 2008 Association of Field Ornithologists.

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin

PubMed Central

Sharrar, Allison M.; Flood, Beverly E.; Bailey, Jake V.; Jones, Daniel S.; Biddanda, Bopaiah A.; Ruberg, Steven A.; Marcus, Daniel N.; Dick, Gregory J.

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea. PMID:28533768

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.

PubMed

Sharrar, Allison M; Flood, Beverly E; Bailey, Jake V; Jones, Daniel S; Biddanda, Bopaiah A; Ruberg, Steven A; Marcus, Daniel N; Dick, Gregory J

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H 2 -based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H 2 oxidation via Ni-Fe hydrogenases, and the use of O 2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction ( sat, apr , and dsr ) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea.

caCORE: a common infrastructure for cancer informatics.

PubMed

Covitz, Peter A; Hartel, Frank; Schaefer, Carl; De Coronado, Sherri; Fragoso, Gilberto; Sahni, Himanso; Gustafson, Scott; Buetow, Kenneth H

2003-12-12

Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).

Microbiological Monitoring in Geothermal Plants

NASA Astrophysics Data System (ADS)

Alawi, M.; Lerm, S.; Linder, R.; Vetter, A.; Vieth-Hillebrand, A.; Miethling-Graff, R.; Seibt, A.; Wolfgramm, M.; Wuerdemann, H.

2010-12-01

In the scope of the research projects “AquiScreen” and “MiProTherm” we investigated geothermally used groundwater systems under microbial, geochemical, mineralogical and petrological aspects. On one side an enhanced process understanding of engineered geothermal systems is mandatory to optimize plant reliability and economy, on the other side this study provides insights into the microbiology of terrestrial thermal systems. Geothermal systems located in the North German Basin and the Molasse Basin were analyzed by sampling of fluids and solid phases. The investigated sites were characterized by different temperatures, salinities and potential microbial substrates. The microbial population was monitored by the use of genetic fingerprinting techniques and PCR-cloning based on PCR-amplified 16S rRNA and dissimilatory sulfite reductase (DSR) genes. DNA-sequences of fingerprints and cloned PCR-products were compared to public databases and correlated with metabolic classes to provide information about the biogeochemical processes. In all investigated geothermal plants, covering a temperature range from 5° to 120°C, microorganisms were found. Phylogenetic gene analyses indicate a broad diversity of microorganisms adapted to the specific conditions in the engineered system. Beside characterized bacteria like Thermus scotoductus, Siderooxidans lithoautotrophicus and the archaeon Methanothermobacter thermoautotrophicus a high number of so far uncultivated microorganisms was detected. As it is known that - in addition to abiotic factors - microbes like sulfate-reducing bacteria (SRB) are involved in the processes of corrosion and scaling in plant components, we identified SRB by specific analyses of DSR genes. The SRB detected are closely related to thermotolerant and thermophilic species of Desulfotomaculum, Thermodesulfovibrio, Desulfohalobium and Thermodesulfobacterium, respectively. Overall, the detection of microbes known to be involved in biocorrosion and the examined precipitation products like iron sulfides are indicating that microorganisms play an important role for the understanding of processes in engineered geothermal systems. The further identification of crucial process parameters influencing microbial activities will help to develop appropriate counter measures against microbial induced clogging and corrosion.

Normal reference values of diastolic strain rate in healthy individuals: Chronological trends and the comparison according to genders.

PubMed

Sun, Byung Joo; Park, Jae-Hyeong; Kim, Jeongai; Choi, Jin-Oh; Lee, Ju-Hee; Shin, Mi-Seung; Kim, Mi-Jeong; Jung, Hae Ok; Park, Jeong Rang; Sohn, Il Suk; Kim, Hyungseop; Kim, Hyung-Kwan; Cho, Goo-Yeong; Park, Jin-Sun; Shim, Chi Young; Shin, Sung Hee; Kim, Kye Hun; Kim, Woo-Shik; Park, Seung Woo

2018-06-19

Recently, the diastolic strain rate (DSR) utilizing speckle-tracking echocardiography has been proposed as a novel parameter for left ventricular diastolic function. We aimed to present normal reference data for those in a large-sized, selected group of healthy individuals. The current study was a part of the Normal echOcardiogRaphic Measurements in KoreAn popuLation (NORMAL), a prospective nationwide survey from 23 centers in Korea. We analyzed 447 subjects (age 48 ± 15 years, 234 females) without any history of cardiovascular disease and presented the early and late DSRs (SR e and SR a , respectively) in a total and gender-/age-specified groups. Among the total subjects, the mean SR e and SR a were 1.6 ± 0.4 S -1 and 0.8 ± 0.3 S -1 , respectively. With increasing age, there were significant trends of decreasing SR e and increasing SR a . Although both gender groups showed comparable age, the female group presented significantly higher SR e compared to male subjects with age of 20-59 years, which diminished after the age of 60 years. However, the SR a was comparable between genders in all age groups. On multiple linear regression, age showed independent associations with both SR e (β = -0.132, P = .010) and SR a (β = 0.440, P < .001), whereas gender did not show any association with SR e or SR a . We present normal reference data of a novel parameter, DSR, in a large-sized selected group with healthy Korean subjects. Additionally, we present significant age-related changes both in SR e and SR a without the impact of their gender. © 2018 Wiley Periodicals, Inc.

Balloon dilation of the esophago-gastric junction affects lower and upper esophageal sphincter function in achalasia.

PubMed

Wauters, L; Van Oudenhove, L; Selleslagh, M; Vanuytsel, T; Boeckxstaens, G; Tack, J; Omari, T; Rommel, N

2014-01-01

Pneumatic dilation of the lower esophageal sphincter (LES) in achalasia has an unappreciated effect on upper esophageal sphincter (UES) function. We studied UES pressure patterns at baseline and alterations in UES parameters resulting from therapy. High-resolution manometry (HRM) tracings from 50 achalasia patients, seen at a tertiary center between January 2009 and July 2011, were reviewed. Manometric parameters studied were (i) LES: resting pressure (restP), 4-second integrated relaxation pressure (IRP4); (ii) UES: resting pressure (restP), minimal relaxation pressure (MRP), peak pressure (PP), relaxation interval (RI), intrabolus pressure (IBP), and deglutitive sphincter resistance (DSR). Mixed models analyses with LES and UES parameters as dependent variables and treatment stage as within-subject independent variable of interest were used. Correlations between treatment-induced changes in LES, UES, and esophageal body (EB) parameters were performed. Pre- and posttreatment HRM tracings were available from 50 patients (mean age 52.7 ± 18.6 years, 29 men). Upper esophageal sphincter parameters MRP (17.9 ± 1.2 vs 15.2 ± 0.9 mmHg; p = 0.02) and IBP (31.5 ± 1.5 vs 27.4 ± 1.2 mmHg; p = 0.009) were significantly reduced after initial balloon dilation and this effect was significant in type II achalasia (p = 0.002 and p = 0.0006). Peak pressure, RI, and DSR were not. The therapeutic effect on LES IRP4 correlated significantly with the change in UES MRP, statistically mediated by the change in EB deglutitive pressure (p = 0.004 and p = 0.0002). We present the first HRM study demonstrating that pneumatic dilation of the LES affects intraesophageal and UES pressures in patients with achalasia. © 2013 John Wiley & Sons Ltd.

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings.

PubMed

An, Xinli; Baker, Paul; Li, Hu; Su, Jianqiang; Yu, Changping; Cai, Chao

2016-11-01

Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO 4 2- concentrations exerted a significant effect on the variation of the bacterial community (P < 0.05), with higher concentrations of sulfate reducing the microbial diversity (H' index), indicating that human activity (e.g., mining industries) was a possible factor disturbing the structure of the bacterial community. Quantitative analysis of the functional genes showed that the proportions of dsrB to total bacteria were 0.002-2.85 %, and the sulfate-reducing bacteria (SRB) were predominant within the prokaryotic community in the groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe-environment interactions and provide a strong foundation for qualitative exploration of the bacterial diversity in rare earth tailings groundwater that might ultimately be incorporated into the remediation of environmental contamination.

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies.

PubMed

Gangaiah, Dharanesh; Spinola, Stanley M

2016-12-01

Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities.

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate.

PubMed

Thorup, Casper; Schramm, Andreas; Findlay, Alyssa J; Finster, Kai W; Schreiber, Lars

2017-07-18

This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase. IMPORTANCE Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as D. alkaliphilus , with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, D. alkaliphilus is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, D. alkaliphilus may represent an exciting model organism in which to study the physiology of this process. Copyright © 2017 Thorup et al.

RNA-based molecular survey of biodiversity of limestone tombstone microbiota in response to atmospheric sulphur pollution.

PubMed

Villa, F; Vasanthakumar, A; Mitchell, R; Cappitelli, F

2015-01-01

Outdoor stoneworks sustain biofilm formation and are constantly at risk of deterioration by micro-organisms. In this study, the biofilm microflora of historic limestone tombstones located in a highly polluted urban environment (Cambridge, MA) and in a less polluted location (Lexington, MA) were compared using comprehensive RNA-based molecular analyses of 16S rRNA gene sequences as well as sequences of genes for different pathways of sulphur metabolism (soxB, apsA, dsrA). The metabolically active micro-organisms detected by denaturing gradient gel electrophoresis analysis of 16S rRNA fragments were predominantly represented by cyanobacteria (belonging to the family Nostocaceae and to the genus Chroococcidiopsis) in both polluted and unpolluted environments. The investigation of soxB, apsA, dsrA transcripts reflected the abundance and the diversity of sulphur-oxidizing and sulphate-reducing bacteria in the Cambridge samples in comparison with the Lexington samples. The investigation revealed that in addition to phototrophic sulphur bacteria belonging to the genera Thiocapsa, Halochromatium, Allochromatium, Thiococcus and Thermochromatium, other sulphate-oxidizing prokaryotes (e.g. the genus Thiobacillus) as well as sequences of Deltaproteobacteria from the genus Desulfovibrio occurred at the polluted urban site. The interactions between the main functional groups retrieved from the limestone tombstones were discussed. The biofilm microflora inhabiting historic limestones are a multi-component open ecosystem sensitively reacting to all environmental factors including air pollutants. Little is known about specific target groups that are active in the biofilm and their physiological functions. For the first time, transcripts involved in important energy-yielding processes were investigated to reveal the metabolic capabilities of the microflora in response to atmospheric sulphur pollution. This work provides novel and important information about the ecology of limestone tombstone microbiota and its complex interaction with the external environment. © 2014 The Society for Applied Microbiology.

Dispatchable hydrogen production at the forecourt for electricity grid balancing

NASA Astrophysics Data System (ADS)

Rahil, Abdulla; Gammon, Rupert; Brown, Neil

2017-02-01

The rapid growth of renewable energy (RE) generation and its integration into electricity grids has been motivated by environmental issues and the depletion of fossil fuels. For the same reasons, an alternative to hydrocarbon fuels is needed for vehicles; hence the anticipated uptake of electric and fuel cell vehicles. High penetrations of RE generators with variable and intermittent output threaten to destabilise electricity networks by reducing the ability to balance electricity supply and demand. This can be greatly mitigated by the use of energy storage and demand-side response (DSR) techniques. Hydrogen production by electrolysis is a promising option for providing DSR as well as an emission-free vehicle fuel. Tariff structures can be used to incentivise the operating of electrolysers as controllable (dispatchable) loads. This paper compares the cost of hydrogen production by electrolysis at garage forecourts under both dispatchable and continuous operation, while ensuring no interruption of fuel supply to fuel cell vehicles. An optimisation algorithm is applied to investigate a hydrogen refueling station in both dispatchable and continuous operation. Three scenarios are tested to see whether a reduced off-peak electricity price could lower the cost of electrolytic hydrogen. These scenarios are: 1) "Standard Continuous", where the electrolyser is operated continuously on a standard all-day tariff of 12p/kWh; 2) "Off-peak Only", where it runs only during off-peak periods in a 2-tier tariff system at the lower price of 5p/kWh; and 3) "2-Tier Continuous", operating continuously and paying a low tariff at off- peak times and a high tariff at other times. This study uses the Libyan coastal city of Derna as a case study. The cheapest electricity cost per kg of hydrogen produced was £2.8, which occurred in Scenario 2. The next cheapest, at £5.8 - £6.3, was in Scenario 3, and the most expensive was £6.8/kg in Scenario 1.

Temporal Changes in Microbial Metagenomic Signatures and Lipid Profiles After Fracturing in the Marcellus Shale

NASA Astrophysics Data System (ADS)

Trexler, R.; Wrighton, K. C.; Pfiffner, S. M.; Wilkins, M.; Daly, R. A.; Mouser, P. J.

2014-12-01

Shale gas formations represent understudied deep biosphere ecosystems with important implications to terrestrial biogeochemical cycles and global energy resources. Recent 16S rRNA gene studies examining temporal microbial community dynamics of returned fluids from hydraulically fractured wells in the Marcellus Shale indicate ecosystem changes from aerobic, low-salt associated microbes in injected fluids to anaerobic, halophilic taxa in produced fluids several months after fracturing. To further characterize changes in the ecology, functional potential and biosignatures of observed taxa, we sequenced genomic DNA from three key time points after fracturing (T7, T82, and T328; Tn, n = days) and analyzed their lipid signatures. The metagenomic profiles verify 16S rRNA gene trends, revealing strain-type changes in dominant Bacteria of Marinobacter, Halomonas, and Halanaerobium and the Archaeal genus Methanolobus through time. Novel species within the γ-Proteobacteria were also observed. Reconstructed genomes show as bioavailable N decreases through time, genes associated with N2 fixing and obtaining N from organic pools (ncd2, nit1, and eutCB) increase in T82 and T328 samples after oxidized nitrogen species (NO3) are depleted. Further, S oxidizing genes were only detected in the T7 sample with incomplete pathways for dissimilatory sulfate reduction (DSR). Later time points showed an increase in abundance of sulfonate importer genes and the anaerobic DSR gene, asrA, suggesting the use of sulfite and sulfonates for S acquisition after sulfate is depleted. Lipid analyses confirmed distinct profiles between T82 and T328 and revealed differences in 16 and 18 C monounsaturated fatty acids, indicative of gram (-) bacteria. The lipid profile from T328 was markedly less diverse than that of T82 and indicated a very limited community, as supported by the 16S rRNA gene and metagenomic data. This research integrates metagenomic data with lipid profiles to characterize temporal changes in biosignatures and the functional potential of N and S metabolic genes of deep shale microbes.

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

PubMed Central

Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

2013-01-01

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669

Parallel image reconstruction for 3D positron emission tomography from incomplete 2D projection data

NASA Astrophysics Data System (ADS)

Guerrero, Thomas M.; Ricci, Anthony R.; Dahlbom, Magnus; Cherry, Simon R.; Hoffman, Edward T.

1993-07-01

The problem of excessive computational time in 3D Positron Emission Tomography (3D PET) reconstruction is defined, and we present an approach for solving this problem through the construction of an inexpensive parallel processing system and the adoption of the FAVOR algorithm. Currently, the 3D reconstruction of the 610 images of a total body procedure would require 80 hours and the 3D reconstruction of the 620 images of a dynamic study would require 110 hours. An inexpensive parallel processing system for 3D PET reconstruction is constructed from the integration of board level products from multiple vendors. The system achieves its computational performance through the use of 6U VME four i860 processor boards, the processor boards from five manufacturers are discussed from our perspective. The new 3D PET reconstruction algorithm FAVOR, FAst VOlume Reconstructor, that promises a substantial speed improvement is adopted. Preliminary results from parallelizing FAVOR are utilized in formulating architectural improvements for this problem. In summary, we are addressing the problem of excessive computational time in 3D PET image reconstruction, through the construction of an inexpensive parallel processing system and the parallelization of a 3D reconstruction algorithm that uses the incomplete data set that is produced by current PET systems.

Development of a scalable generic platform for adaptive optics real time control

NASA Astrophysics Data System (ADS)

Surendran, Avinash; Burse, Mahesh P.; Ramaprakash, A. N.; Parihar, Padmakar

2015-06-01

The main objective of the present project is to explore the viability of an adaptive optics control system based exclusively on Field Programmable Gate Arrays (FPGAs), making strong use of their parallel processing capability. In an Adaptive Optics (AO) system, the generation of the Deformable Mirror (DM) control voltages from the Wavefront Sensor (WFS) measurements is usually through the multiplication of the wavefront slopes with a predetermined reconstructor matrix. The ability to access several hundred hard multipliers and memories concurrently in an FPGA allows performance far beyond that of a modern CPU or GPU for tasks with a well-defined structure such as Adaptive Optics control. The target of the current project is to generate a signal for a real time wavefront correction, from the signals coming from a Wavefront Sensor, wherein the system would be flexible to accommodate all the current Wavefront Sensing techniques and also the different methods which are used for wavefront compensation. The system should also accommodate for different data transmission protocols (like Ethernet, USB, IEEE 1394 etc.) for transmitting data to and from the FPGA device, thus providing a more flexible platform for Adaptive Optics control. Preliminary simulation results for the formulation of the platform, and a design of a fully scalable slope computer is presented.

CAFE: A New Relativistic MHD Code

NASA Astrophysics Data System (ADS)

Lora-Clavijo, F. D.; Cruz-Osorio, A.; Guzmán, F. S.

2015-06-01

We introduce CAFE, a new independent code designed to solve the equations of relativistic ideal magnetohydrodynamics (RMHD) in three dimensions. We present the standard tests for an RMHD code and for the relativistic hydrodynamics regime because we have not reported them before. The tests include the one-dimensional Riemann problems related to blast waves, head-on collisions of streams, and states with transverse velocities, with and without magnetic field, which is aligned or transverse, constant or discontinuous across the initial discontinuity. Among the two-dimensional (2D) and 3D tests without magnetic field, we include the 2D Riemann problem, a one-dimensional shock tube along a diagonal, the high-speed Emery wind tunnel, the Kelvin-Helmholtz (KH) instability, a set of jets, and a 3D spherical blast wave, whereas in the presence of a magnetic field we show the magnetic rotor, the cylindrical explosion, a case of Kelvin-Helmholtz instability, and a 3D magnetic field advection loop. The code uses high-resolution shock-capturing methods, and we present the error analysis for a combination that uses the Harten, Lax, van Leer, and Einfeldt (HLLE) flux formula combined with a linear, piecewise parabolic method and fifth-order weighted essentially nonoscillatory reconstructors. We use the flux-constrained transport and the divergence cleaning methods to control the divergence-free magnetic field constraint.

Horizontal Line-of-Sight Turbulence Over Near-Ground Paths and Implications for Adaptive Optics Corrections in Laser Communications.

PubMed

Levine, B M; Martinsen, E A; Wirth, A; Jankevics, A; Toledo-Quinones, M; Landers, F; Bruno, T L

1998-07-20

Atmospheric turbulence over long horizontal paths perturbs phase and can also cause severe intensity scintillation in the pupil of an optical communications receiver, which limits the data rate over which intensity-based modulation schemes can operate. The feasibility of using low-order adaptive optics by applying phase-only corrections over horizontal propagation paths is investigated. A Shack-Hartmann wave-front sensor was built and data were gathered on paths 1 m above ground and between a 1- and 2.5-km range. Both intensity fluctuations and optical path fluctuation statistics were gathered within a single frame, and the wave-front reconstructor was modified to allow for scintillated data. The temporal power spectral density for various Zernike polynomial modes was used to determine the effects of the expected corrections by adaptive optics. The slopes of the inertial subrange of turbulence were found to be less than predicted by Kolmogorov theory with an infinite outer scale, and the distribution of variance explained by increasing order was also found to be different. Statistical analysis of these data in the 1-km range indicates that at communications wavelengths of 1.3 mum, a significant improvement in transmitted beam quality could be expected most of the time, to a performance of 10% Strehl ratio or better.

Duque performs VIDEO-2 (VID-01) experiment

NASA Image and Video Library

2003-10-23

ISS007-E-17848 (23 October 2003) --- Cosmonaut Alexander Y. Kaleri (right), Expedition 8 flight engineer, uses a camera to film a scientific experiment performed by European Space Agency (ESA) astronaut Pedro Duque of Spain in the Zvezda Service Module on the International Space Station (ISS). Kaleri represents Rosaviakosmos. Duque and Kaleri performed the European educational VIDEO-2 (VID-01) experiment, which uses the Russian DSR PD-150P digital video camcorder for recording demos of several basic physical phenomena, viz., Isaac Newton's three motion laws, with narration. [The demo made use of a sealed bag containing coffee and a syringe to fill one of two hollow balls with the brown liquid (to provide "mass", as opposed to the other, "mass-less" ball).

Duque and Kaleri in Zvezda Service module with video camera

NASA Image and Video Library

2003-10-23

ISS007-E-17842 (23 October 2003) --- European Space Agency (ESA) astronaut Pedro Duque (left) of Spain and cosmonaut Alexander Y. Kaleri, Expedition 8 flight engineer representing Rosaviakosmos, work with a scientific experiment in the Zvezda Service Module on the International Space Station (ISS). Duque and Kaleri performed the European educational VIDEO-2 (VID-01) experiment, which uses the Russian DSR PD-150P digital video camcorder for recording demos of several basic physical phenomena, viz., Isaac Newton's three motion laws, with narration. [The demo made use of a sealed bag containing coffee and a syringe to fill one of two hollow balls with the brown liquid (to provide "mass", as opposed to the other, "mass-less" ball).

Analysis of BigFoot HDC SymCap experiment N161205 on NIF

NASA Astrophysics Data System (ADS)

Dittrich, T. R.; Baker, K. L.; Thomas, C. A.; Berzak Hopkins, L. F.; Harte, J. A.; Zimmerman, G. B.; Woods, D. T.; Kritcher, A. L.; Ho, D. D.; Weber, C. R.; Kyrala, G.

2017-10-01

Analysis of NIF implosion experiment N161205 provides insight into both hohlraum and capsule performance. This experiment used an undoped High Density Carbon (HDC) ablator driven by a BigFoot x-ray profile in a Au hohlraum. Observations from this experiment include DT fusion yield, bang time, DSR, Tion and time-resolved x-ray emission images around bang time. These observations are all consistent with an x-ray spectrum having significantly reduced Au m-band emission that is present in a standard hohlraum simulation. Attempts to justify the observations using several other simulation modifications will be presented. This work was performed under the auspices of the Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344.

Five-Axis, Three-Magnetic-Bearing Dynamic Spin Rig

NASA Technical Reports Server (NTRS)

Morrison, Carlos R.; Provenza, Andrew; Kurkov, Anatole; Mehmed, Oral; Johnson, Dexter; Montague, Gerald; Duffy, Kirsten; Jansen, Ralph

2005-01-01

The Five-Axis, Three-Magnetic-Bearing Dynamic Spin Rig is an apparatus for vibration testing of turbomachine blades in a vacuum at rotational speeds from 0 to 40,000 rpm. This rig includes (1) a vertically oriented shaft on which is mounted an assembly comprising a rotor holding the blades to be tested, (2) two actively controlled heteropolar radial magnetic bearings at opposite ends of the shaft, and (3) an actively controlled magnetic thrust bearing at the upper end of the shaft. This rig is a more capable successor to a prior apparatus, denoted the Dynamic Spin Rig (DSR), that included a vertically oriented shaft with a mechanical thrust bearing at the upper end and a single actively controlled heteropolar radial magnetic bearing at the lower end.

Palatini actions and quantum gravity phenomenology

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

Olmo, Gonzalo J., E-mail: gonzalo.olmo@csic.es

2011-10-01

We show that an invariant an universal length scale can be consistently introduced in a generally covariant theory through the gravitational sector using the Palatini approach. The resulting theory is able to capture different aspects of quantum gravity phenomenology in a single framework. In particular, it is found that in this theory field excitations propagating with different energy-densities perceive different background metrics, which is a fundamental characteristic of the DSR and Rainbow Gravity approaches. We illustrate these properties with a particular gravitational model and explicitly show how the soccer ball problem is avoided in this framework. The isotropic and anisotropicmore » cosmologies of this model also avoid the big bang singularity by means of a big bounce.« less

Spatial patterns of denitrification and its functional genes in peatlands

NASA Astrophysics Data System (ADS)

Mander, Ülo; Ligi, Teele; Truu, Marika; Truu, Jaak; Pärn, Jaan; Egorov, Sergey; Järveoja, Järvi; Vohla, Christina; Maddison, Martin; Soosaar, Kaido; Oopkaup, Kristjan; Teemusk, Alar; Preem, Jens-Konrad; Uuemaa, Evelyn

2014-05-01

This study is aimed to analyse relationships between the environmental factors and the spatial distribution of the main functional genes nirS, nirK, and nosZ regulating the denitrification process. Variations in hydrological regime, soil temperature and peat quality have been taken into the consideration at both local and global scale. Measurements of greenhouse gas (GHG) emissions using static chambers, groundwater analysis, gas and peat sampling for further laboratory analysis has been conducted in various peatlands in Iceland (two study areas, 2011), Transylvania/Romania (2012), Santa Catarina/Brazil (2012), Quebec/Canada (2012), Bashkortostan/Russian Federation (two study areas, 2012), Sichuan/China (2012), Estonia (two study areas, 2012), Florida/USA (2013, Sologne/France (2013), Jugra in West Siberia/Russia (2013), Uganda (2013), French Guyana (two study areas, 2013), Tasmania (two study areas, 2014) and New Zealand (two study areas, 2014). In each study area at least 2 transects along the groundwater depth gradient, one preferably in undisturbed, another one in drained area, and at least 3 rows of sampling sites (3-5 replicate chambers and 1 piezometer and soil sampling plot in each) in both has been established for studies. In each transect GHG emission was measured during 2-3 days in at least 5 sessions. In addition, organic sediments from the artificial riverine wetlands in Ohio/USA in 2009 and relevant gas emission studies have been used in the analyses. In the laboratories of Estonian University of Life Sciences and the University of Tartu, the peat chemical quality (pH, N, P, C, NH4, NO3) and N2O, CO2, and CH4 concentration in gas samples (50mL glass bottles and exetainers) were analysed. The peat samples for further pyrosequencing and qPCR analyses are stored in fridge by -22oC. This presentation will consider the variation of GHG emissions and hydrological conditions in the study sites. In addition, several selected biophysical factors will be taken into account. Further study will include peatland sites in Montana/USA, Columbia (Andes), Tierra del Fuego/Argentina, Pyrenees/Spain, Savo/Finland, the Netherlands, Okawango/Botswana, Heilongjiang/China, and Kamchatka/Russian Federation. Also, additional analysis will be conducted on the relationships between the intensity of CH4 emissions and methanogenesis regulating functional genes mcrA, pmoA, and dsrAB.

High-Resolution Metabolomics Assessment of Military Personnel: Evaluating Analytical Strategies for Chemical Detection.

PubMed

Liu, Ken H; Walker, Douglas I; Uppal, Karan; Tran, ViLinh; Rohrbeck, Patricia; Mallon, Timothy M; Jones, Dean P

2016-08-01

The aim of this study was to maximize detection of serum metabolites with high-resolution metabolomics (HRM). Department of Defense Serum Repository (DoDSR) samples were analyzed using ultrahigh resolution mass spectrometry with three complementary chromatographic phases and four ionization modes. Chemical coverage was evaluated by number of ions detected and accurate mass matches to a human metabolomics database. Individual HRM platforms provided accurate mass matches for up to 58% of the KEGG metabolite database. Combining two analytical methods increased matches to 72% and included metabolites in most major human metabolic pathways and chemical classes. Detection and feature quality varied by analytical configuration. Dual chromatography HRM with positive and negative electrospray ionization provides an effective generalized method for metabolic assessment of military personnel.

High-resolution metabolomics assessment of military personnel: Evaluating analytical strategies for chemical detection

PubMed Central

Liu, Ken H.; Walker, Douglas I.; Uppal, Karan; Tran, ViLinh; Rohrbeck, Patricia; Mallon, Timothy M.; Jones, Dean P.

2016-01-01

Objective To maximize detection of serum metabolites with high-resolution metabolomics (HRM). Methods Department of Defense Serum Repository (DoDSR) samples were analyzed using ultra-high resolution mass spectrometry with three complementary chromatographic phases and four ionization modes. Chemical coverage was evaluated by number of ions detected and accurate mass matches to a human metabolomics database. Results Individual HRM platforms provided accurate mass matches for up to 58% of the KEGG metabolite database. Combining two analytical methods increased matches to 72%, and included metabolites in most major human metabolic pathways and chemical classes. Detection and feature quality varied by analytical configuration. Conclusions Dual chromatography HRM with positive and negative electrospray ionization provides an effective generalized method for metabolic assessment of military personnel. PMID:27501105

Meta-Transcriptomic Analysis of a Chromate-Reducing Aquifer Microbial Community

NASA Astrophysics Data System (ADS)

Beller, H. R.; Brodie, E. L.; Han, R.; Karaoz, U.

2010-12-01

A major challenge for microbial ecology that has become more tractable in the advent of new molecular techniques is characterizing gene expression in complex microbial communities. We are using meta-transcriptomic analysis to characterize functional changes in an aquifer-derived, chromate-reducing microbial community as it transitions through various electron-accepting conditions. We inoculated anaerobic microcosms with groundwater from the Cr-contaminated Hanford 100H site and supplemented them with lactate and electron acceptors present at the site, namely, nitrate, sulfate, and Fe(III). The microcosms progressed successively through various electron-accepting conditions (e.g., denitrifying, sulfate-reducing, and ferric iron-reducing conditions, as well as nitrate-dependent, chemolithotrophic Fe(II)-oxidizing conditions). Cr(VI) was rapidly reduced initially and again upon further Cr(VI) amendments. Extensive geochemical sampling and analysis (e.g., lactate, acetate, chloride, nitrate, nitrite, sulfate, dissolved Cr(VI), total Fe(II)), RNA/DNA harvesting, and PhyloChip analyses were conducted. Methods were developed for removal of rRNA from total RNA in preparation for meta-transcriptome sequencing. To date, samples representing denitrifying and fermentative/sulfate-reducing conditions have been sequenced using 454 Titanium technology. Of the non-rRNA related reads for the denitrifying sample (which was also actively reducing chromate), ca. 8% were associated with denitrification and ca. 0.9% were associated with chromate resistance/transport, in contrast to the fermentative/sulfate-reducing sample (in which chromate had already been reduced), which had zero reads associated with either of these categories but many predicted proteins associated with sulfate-reducing bacteria. We observed sequences for key functional transcripts that were unique at the nucleotide level compared to the GenBank non-redundant database [such as L-lactate dehydrogenase (iron-sulfur-cluster-binding subunit), cytochrome cd1 nitrite reductase (nirS) (from the denitrifying phase), and dissimilatory sulfite reductase (dsrA, dsrB) (from the sulfate-reducing phase)]. One potential advantage of this approach is that such important genes may not have been detected using more traditional techniques, including PCR-based methods and a priori functional microarrays.

230Th and 231Pa: Tracers for Deep Water Circulation and Particle Fluxes in the Arctic Ocean

NASA Astrophysics Data System (ADS)

Valk, O.; Rutgers van der Loeff, M.; Puigcorbe Lacueva, V.; Paffrath, R.; Gdaniec, S.

2016-02-01

230Th and 231Pa data from the central Arctic Ocean is very limited. 230Th and 231Pa are produced at a constant rate in the water column by radioactive decay of Uranium isotopes (234U and 235U respectively) (e.g. Anderson et al., 1983). They are both particle reactive and are scavenged on settling particles. As 230Th is more particle reactive than 231Pa, their distribution in the water column and activity ratio give us information about particle fluxes and circulation patterns and -intensities (Henderson et al., 1999; Scholten et al., 2001). The Arctic Ocean is an almost landlocked ocean with limited connections to the Atlantic and Pacific and a high input of river water. About 10 % of the global river run-off is delivered to the Arctic Ocean. Due to climate change the Arctic Ocean will undergo dramatic changes in sea ice cover and supply of fresh water, while increasing coastal erosion will cause an increased input of terrestrial material (Peterson et al., 2002). This will influence the biogeochemical cycling and transport of carbon, nutrients and trace elements (IPCC, 2007). We expect that the distribution of 230Th and 231Pa will reflect changes in particle fluxes and shelf-basin exchange (Roy-Barman, 2009). We will present the first results of 230Th and 231Pa, in combination with on board measured particulate 234Th, collected during the 2015 Polarstern section (GEOTRACES section GN04 2015) through the Nansen, Amundsen, and Makarov Basins. Anderson, R. F., et al. (1983). EPSL 62: 7-23. Henderson, G. M., et al. (1999). DSR I 46: 1861-1893. IPCC, 2007. Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S. et al.]. Cambridge University Press. Peterson, B. J., et al. (2002). Science 298: 2171-2173. Roy-Barman, M. (2009). Biogeosciences 6: 3091-3107. Scholten, J. C., et al. (2001). DSR II 48: 2383-2408.

Microbial ecology of soda lakes: investigating sulfur and nitrogen cycling at Mono Lake, CA, USA

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Phillips, A. A.; Wells, M.; Bao, R.; Fullerton, K. M.; Stamps, B. W.; Speth, D. R.; Johnson, H.; Sessions, A. L.

2017-12-01

Soda lakes represent unique ecosystems characterized by extremes of pH, salinity and distinct geochemical cycling. Despite these extreme conditions, soda lakes are important repositories of biological adaptation and have a highly functional microbial system. We investigated the biogeochemical cycling of sulfur and nitrogen compounds in Mono Lake, California, located east of the Sierra Nevada mountains. Mono lake is characterized by hyperalkaline, hypersaline and high sulfate concentrations and can enter prolonged periods of meromixis due to freshwater inflow. Typically, the microbial sulfur cycle is highly active in soda lakes with both oxidation and reduction of sulfur compounds. However, the biological sulfur cycle is connected to many other main elemental cycles such as carbon, nitrogen and metals. Here we investigated the interaction between sulfur and nitrogen cycling in Mono lake using a combination of molecular, isotopic, and geochemical observations to explore the links between microbial phylogenetic composition and functionality. Metagenomic and 16S rRNA gene amplicon sequencing were determined at two locations and five depths in May 2017. 16S rRNA gene amplicon sequencing analysis revealed organisms capable of both sulfur and nitrogen cycling. The relative abundance and distribution of functional genes (dsrA, soxAB, nifH, etc) were also determined. These genetic markers indicate the potential in situ relevance of specific carbon, nitrogen, and sulfur pathways in the water column prior to the transition to meromictic stratification. However, genes for sulfide oxidation, denitrification, and ammonification were present. Genome binning guided by the most abundant dsrA sequences, GC content, and abundance with depth identified a Thioalkalivibrio paradoxus bin containing genes capable of sulfur oxidation, denitrification, and nitrate reduction. The presence of a large number of sulfur and nitrogen cycling genes associated with Thioalkalivibrio paradoxus suggests thiosulfate oxidation may be coupled to nitrate reduction despite the extremely low level of nitrate in Mono Lake. Our results illustrate the centrality of living organisms in both shaping and responding to geochemical cycles, as well as future directions for exploring coupled biogeochemical cycles in Mono Lake.

Effect of platelet-rich plasma in the treatment of periodontal intrabony defects in humans.

PubMed

Ouyang, Xiang-ying; Qiao, Jing

2006-09-20

Platelet-rich plasma (PRP) is a kind of natural source of autologous growth factors, and has been used successfully in medical community. However, the effect of PRP in periodontal regeneration is not clear yet. This study was designed to evaluate the effectiveness of PRP as an adjunct to bovine porous bone mineral (BPBM) graft in the treatment of human intrabony defects. Seventeen intrabony defects in 10 periodontitis patients were randomly treated either with PRP and BPBM (test group, n = 9) or with BPBM alone (control group, n = 8). Clinical parameters were evaluated including changes in probing depth, relative attachment level (measured by Florida Probe and a stent), and bone probing level between baseline and 1 year postoperatively. Standardized periapical radiographs of each defect were taken at baseline, 2 weeks, and 1 year postoperatively, and analyzed by digital subtraction radiography (DSR). Both treatment modalities resulted in significant attachment gain, reduction of probing depth, and bone probing level at 1-year post-surgery compared to baseline. The test group exhibited statistically significant improvement compared to the control sites in probing depth reduction: (4.78 +/- 0.95) mm versus (3.48 +/- 0.41) mm (P < 0.01); clinical attachment gain: (4.52 +/- 1.14) mm versus (2.85 +/- 0.80) mm (P < 0.01); bone probing reduction: (4.56 +/- 1.04) mm versus (2.88 +/- 0.79) mm (P < 0.01); and defect bone fill: (73.41 +/- 14.78)% versus (47.32 +/- 11.47)% (P < 0.01). DSR analysis of baseline and 1 year postoperatively also showed greater radiographic gains in alveolar bone mass in the test group than in the control group: gray increase (580 +/- 50) grays versus (220 +/- 32) grays (P = 0.0001); area with increased gray were (5.21 +/- 1.25) mm(2) versus (3.02 +/- 1.22) mm(2) (P = 0.0001). The treatment with a combination of PRP and BPBM led to a significantly favorable clinical improvement in periodontal intrabony defects compared to using BPBM alone. Further studies are necessary to assess the long-term effectiveness of PRP, and a larger sample size is needed.

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies

PubMed Central

Gangaiah, Dharanesh

2016-01-01

Background Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. Methodology/Principal Findings We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. Conclusions/Significance CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities. PMID:28027326

Expanding diversity of potential bacterial partners of the methanotrophic ANME archaea using Magneto-FISH

NASA Astrophysics Data System (ADS)

Trembath-Reichert, E.; Green-Saxena, A.; Steele, J. A.; Orphan, V. J.

2012-12-01

Sulfate-coupled anaerobic oxidation of methane (AOM) in marine sediments is the major sink for methane in the oceans. This process is believed to be catalyzed by as yet uncultured syntrophic consortia of ANME archaea (affiliated with the Methanosarcinales) and sulfate-reducing bacteria belonging to the Desulfosarcina/Desulfococcus and Desulfobulbaceae. These syntrophic consortia have been described from methane-rich habitats worldwide and appear to be most concentrated in areas of high methane flux, such as cold seeps along continental margins. The extent of the diversity and ecophysiological potential of these microbial associations is still poorly constrained. In an effort to better characterize the diversity of microorganisms forming associations with different clades of methanotrophic ANME archaea (ANME-1, ANME-2a/b/c, ANME-3) and link these organisms to potentially diagnostic metabolic genes (e.g. mcrA, dsrAB, aprA), we employed a unique culture-independent whole cell capture technique which combines Fluorescence In Situ Hybridization with immuno-magnetic cell capture (Magneto-FISH). We used Magneto-FISH for targeted enrichment of specific ANME groups and their associated bacteria directly from formalin- and ethanol-fixed methane seep sediment. The identity and metabolic gene diversity of captured microorganisms were then assessed by clone library construction and sequencing. Diversity recovered from Magneto-FISH experiments using general and clade-specific ANME targeted probes show both the expected selectivity of the FISH probes (i.e. predominately ANME-2c subclade captured with an ANME-2c probe and multiple ANME groups recovered with the general probe targeting most ANME). Follow up FISH experiments were conducted to confirm physical associations between ANME and unique bacterial members (deltaproteobacteria and other non-sulfate reducing groups) that were common to multiple Magneto-FISH capture experiments. Analyses of metabolic gene diversity for archaeal (mcrA) and sulfate-reducing (aprA and dsrAB) members of the consortia were generally consistent with the diversity observed by 16S rRNA from individual Magneto-FISH experiments. Together, this data indicates a role for the involvement of additional microbial groups in the AOM symbioses at methane seeps.

Iterative reconstruction methods in atmospheric tomography: FEWHA, Kaczmarz and Gradient-based algorithm

NASA Astrophysics Data System (ADS)

Ramlau, R.; Saxenhuber, D.; Yudytskiy, M.

2014-07-01

The problem of atmospheric tomography arises in ground-based telescope imaging with adaptive optics (AO), where one aims to compensate in real-time for the rapidly changing optical distortions in the atmosphere. Many of these systems depend on a sufficient reconstruction of the turbulence profiles in order to obtain a good correction. Due to steadily growing telescope sizes, there is a strong increase in the computational load for atmospheric reconstruction with current methods, first and foremost the MVM. In this paper we present and compare three novel iterative reconstruction methods. The first iterative approach is the Finite Element- Wavelet Hybrid Algorithm (FEWHA), which combines wavelet-based techniques and conjugate gradient schemes to efficiently and accurately tackle the problem of atmospheric reconstruction. The method is extremely fast, highly flexible and yields superior quality. Another novel iterative reconstruction algorithm is the three step approach which decouples the problem in the reconstruction of the incoming wavefronts, the reconstruction of the turbulent layers (atmospheric tomography) and the computation of the best mirror correction (fitting step). For the atmospheric tomography problem within the three step approach, the Kaczmarz algorithm and the Gradient-based method have been developed. We present a detailed comparison of our reconstructors both in terms of quality and speed performance in the context of a Multi-Object Adaptive Optics (MOAO) system for the E-ELT setting on OCTOPUS, the ESO end-to-end simulation tool.

Parallel Implementation of a Frozen Flow Based Wavefront Reconstructor

NASA Astrophysics Data System (ADS)

Nagy, J.; Kelly, K.

2013-09-01

Obtaining high resolution images of space objects from ground based telescopes is challenging, often requiring the use of a multi-frame blind deconvolution (MFBD) algorithm to remove blur caused by atmospheric turbulence. In order for an MFBD algorithm to be effective, it is necessary to obtain a good initial estimate of the wavefront phase. Although wavefront sensors work well in low turbulence situations, they are less effective in high turbulence, such as when imaging in daylight, or when imaging objects that are close to the Earth's horizon. One promising approach, which has been shown to work very well in high turbulence settings, uses a frozen flow assumption on the atmosphere to capture the inherent temporal correlations present in consecutive frames of wavefront data. Exploiting these correlations can lead to more accurate estimation of the wavefront phase, and the associated PSF, which leads to more effective MFBD algorithms. However, with the current serial implementation, the approach can be prohibitively expensive in situations when it is necessary to use a large number of frames. In this poster we describe a parallel implementation that overcomes this constraint. The parallel implementation exploits sparse matrix computations, and uses the Trilinos package developed at Sandia National Laboratories. Trilinos provides a variety of core mathematical software for parallel architectures that have been designed using high quality software engineering practices, The package is open source, and portable to a variety of high-performance computing architectures.

High speed real-time wavefront processing system for a solid-state laser system

NASA Astrophysics Data System (ADS)

Liu, Yuan; Yang, Ping; Chen, Shanqiu; Ma, Lifang; Xu, Bing

2008-03-01

A high speed real-time wavefront processing system for a solid-state laser beam cleanup system has been built. This system consists of a core2 Industrial PC (IPC) using Linux and real-time Linux (RT-Linux) operation system (OS), a PCI image grabber, a D/A card. More often than not, the phase aberrations of the output beam from solid-state lasers vary fast with intracavity thermal effects and environmental influence. To compensate the phase aberrations of solid-state lasers successfully, a high speed real-time wavefront processing system is presented. Compared to former systems, this system can improve the speed efficiently. In the new system, the acquisition of image data, the output of control voltage data and the implementation of reconstructor control algorithm are treated as real-time tasks in kernel-space, the display of wavefront information and man-machine conversation are treated as non real-time tasks in user-space. The parallel processing of real-time tasks in Symmetric Multi Processors (SMP) mode is the main strategy of improving the speed. In this paper, the performance and efficiency of this wavefront processing system are analyzed. The opened-loop experimental results show that the sampling frequency of this system is up to 3300Hz, and this system can well deal with phase aberrations from solid-state lasers.

Analytical study of Cattaneo-Christov heat flux model for a boundary layer flow of Oldroyd-B fluid

NASA Astrophysics Data System (ADS)

F, M. Abbasi; M, Mustafa; S, A. Shehzad; M, S. Alhuthali; T, Hayat

2016-01-01

We investigate the Cattaneo-Christov heat flux model for a two-dimensional laminar boundary layer flow of an incompressible Oldroyd-B fluid over a linearly stretching sheet. Mathematical formulation of the boundary layer problems is given. The nonlinear partial differential equations are converted into the ordinary differential equations using similarity transformations. The dimensionless velocity and temperature profiles are obtained through optimal homotopy analysis method (OHAM). The influences of the physical parameters on the velocity and the temperature are pointed out. The results show that the temperature and the thermal boundary layer thickness are smaller in the Cattaneo-Christov heat flux model than those in the Fourier’s law of heat conduction. Project supported by the Deanship of Scientific Research (DSR) King Abdulaziz University, Jeddah, Saudi Arabia (Grant No. 32-130-36-HiCi).

Mechanical Performance of Asphalt Mortar Containing Hydrated Lime and EAFSS at Low and High Temperatures.

PubMed

Moon, Ki Hoon; Falchetto, Augusto Cannone; Wang, Di; Riccardi, Chiara; Wistuba, Michael P

2017-07-03

In this paper, the possibility of improving the global response of asphalt materials for pavement applications through the use of hydrated lime and Electric Arc-Furnace Steel Slag (EAFSS) was investigated. For this purpose, a set of asphalt mortars was prepared by mixing two different asphalt binders with fine granite aggregate together with hydrated lime or EAFSS at three different percentages. Bending Beam Rheometer (BBR) creep tests and Dynamic Shear Rheometer (DSR) complex modulus tests were performed to evaluate the material response both at low and high temperature. Then, the rheological Huet model was fitted to the BBR creep results for estimating the impact of filler content on the model parameters. It was found that an addition of hydrated lime and EAFSS up to 10% and 5%, respectively, results in satisfactory low-temperature performance with a substantial improvement of the high-temperature behavior.

A sulfate-reducing bacterium with unusual growing capacity in moderately acidic conditions.

PubMed

Rampinelli, L R; Azevedo, R D; Teixeira, M C; Guerra-Sá, R; Leão, V A

2008-09-01

The use of sulfate-reducing bacteria (SRB) is a cost-effective route to treat sulfate- contaminated waters and precipitate metals. The isolation and characterization of a SRB strain from an AMD in a Brazilian tropical region site was carried out. With a moderately acidic pH (5.5), the C.1 strain began its growth and with continued growth, modified the pH accordingly. The strain under these conditions reduced sulfate at the same rate as an experiment performed using an initial pH of 7.0. The dsrB gene-based molecular approach was used for the characterization of this strain and its phylogenetic affiliation was similar to genus Desulfovibrio sp. The results show an SRB isolate with unexpected sulfate reducing capacity in moderately acidic conditions, bringing new possibilities for the treatment of AMD, as acid water would be neutralized to a mildly acidic condition.

Mechanical Performance of Asphalt Mortar Containing Hydrated Lime and EAFSS at Low and High Temperatures

PubMed Central

Moon, Ki Hoon; Wang, Di; Riccardi, Chiara; Wistuba, Michael P.

2017-01-01

In this paper, the possibility of improving the global response of asphalt materials for pavement applications through the use of hydrated lime and Electric Arc-Furnace Steel Slag (EAFSS) was investigated. For this purpose, a set of asphalt mortars was prepared by mixing two different asphalt binders with fine granite aggregate together with hydrated lime or EAFSS at three different percentages. Bending Beam Rheometer (BBR) creep tests and Dynamic Shear Rheometer (DSR) complex modulus tests were performed to evaluate the material response both at low and high temperature. Then, the rheological Huet model was fitted to the BBR creep results for estimating the impact of filler content on the model parameters. It was found that an addition of hydrated lime and EAFSS up to 10% and 5%, respectively, results in satisfactory low-temperature performance with a substantial improvement of the high-temperature behavior. PMID:28773100

High-Resolution Metabolomics for Nutrition and Health Assessment of Armed Forces Personnel.

PubMed

Accardi, Carolyn Jonas; Walker, Douglas I; Uppal, Karan; Quyyumi, Arshed A; Rohrbeck, Patricia; Pennell, Kurt D; Mallon, Col Timothy M; Jones, Dean P

2016-08-01

The aim of this study was to test the utility of high-resolution metabolomics (HRM) for analysis of nutritional status and health indicators in military personnel. Serum samples from 400 military personnel were obtained from the Department of Defense Serum Repository (DoDSR) and analyzed for metabolites related to nutrition and health status. Metabolic profile organization was studied using modulated modularity clustering (MMC). HRM provided quantitative measures of 61 metabolites across chemical classes for use as nutritional and clinical biomarkers. Levels were comparable to reported values except for arginine and glutamine, which were above and below reference ranges, respectively. MMC generated five clusters, three of which were associated and contained amino acids. The others contained lipids and mitochondria-related metabolites. HRM analysis of serum is suitable for real-time and/or retrospective evaluation of nutrition and health status of specific military cohorts.

Gene expression in the deep biosphere.

PubMed

Orsi, William D; Edgcomb, Virginia P; Christman, Glenn D; Biddle, Jennifer F

2013-07-11

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles, but deep biosphere activities are not well understood. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

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

Herbert, J.H.

This brief note describes the probabilistic structure of the Arps/Roberts (A/R) model of petroleum discovery. A model similar to the A/R model is derived from probabilistic propositions demonstrated to be similar to the E. Barouch/G.M. Kaufman (B/K) model, and also demonstrated to be similar to the Drew, Schuenemeyer, and Root (D/S/R) model. This note attempts to elucidate and to simplify some fundamental ideas contained in an unpublished paper by Barouch and Kaufman. This note and its predecessor paper does not attempt to address a wide variety of statistical approaches for estimating petroleum resource availability. Rather, an attempt is made tomore » draw attention to characteristics of certain methods that are commonly used, both formally and informally, to estimate a petroleum resource base for a basin or a nation. Some of these characteristics are statistical, but many are not, except in the broadest sense of the term.« less

Causal Conceptions in Social Explanation and Moral Evaluation: A Historical Tour.

PubMed

Alicke, Mark D; Mandel, David R; Hilton, Denis J; Gerstenberg, Tobias; Lagnado, David A

2015-11-01

Understanding the causes of human behavior is essential for advancing one's interests and for coordinating social relations. The scientific study of how people arrive at such understandings or explanations has unfolded in four distinguishable epochs in psychology, each characterized by a different metaphor that researchers have used to represent how people think as they attribute causality and blame to other individuals. The first epoch was guided by an "intuitive scientist" metaphor, which emphasized whether observers perceived behavior to be caused by the unique tendencies of the actor or by common reactions to the requirements of the situation. This metaphor was displaced in the second epoch by an "intuitive lawyer" depiction that focused on the need to hold people responsible for their misdeeds. The third epoch was dominated by theories of counterfactual thinking, which conveyed a "person as reconstructor" approach that emphasized the antecedents and consequences of imagining alternatives to events, especially harmful ones. With the current upsurge in moral psychology, the fourth epoch emphasizes the moral-evaluative aspect of causal judgment, reflected in a "person as moralist" metaphor. By tracing the progression from the person-environment distinction in early attribution theories to present concerns with moral judgment, our goal is to clarify how causal constructs have been used, how they relate to one another, and what unique attributional problems each addresses. © Her Majesty the Queen in Right of Canada, as represented by Defence Research and Development Canada 2015.

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

PubMed

Tranchida-Lombardo, Valentina; Aiese Cigliano, Riccardo; Anzar, Irantzu; Landi, Simone; Palombieri, Samuela; Colantuono, Chiara; Bostan, Hamed; Termolino, Pasquale; Aversano, Riccardo; Batelli, Giorgia; Cammareri, Maria; Carputo, Domenico; Chiusano, Maria Luisa; Conicella, Clara; Consiglio, Federica; D'Agostino, Nunzio; De Palma, Monica; Di Matteo, Antonio; Grandillo, Silvana; Sanseverino, Walter; Tucci, Marina; Grillo, Stefania

2017-11-14

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8 M and 56.4 M of 30-150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Dynamics of biogeochemical sulfur cycling in Mono Lake

NASA Astrophysics Data System (ADS)

Phillips, A. A.; Fairbanks, D.; Wells, M.; Fullerton, K. M.; Bao, R.; Johnson, H.; Speth, D. R.; Stamps, B. W.; Miller, L.; Sessions, A. L.

2017-12-01

Mono Lake, California is a closed-basin soda lake (pH 9.8) with high sulfate (120mM), and is an ideal natural laboratory for studying microbial sulfur cycling. Mono Lake is typically thermally stratified in summer while mixing completely in winter. However, large snowmelt inputs may induce salinity stratification that persists for up to five years, causing meromixis. During the California drought of 2014-16, the lake has mixed thoroughly each winter, but the abundant 2017 snowmelt may usher in a multi-year stratification. This natural experiment provides an opportunity to investigate the temporal relationship between microbial sulfur cycling and lake biogeochemistry. We analyzed water samples from five depths at two stations in May of 2017, before the onset of meromixis. Water column sulfate isotope values were generally constant with depth, centering at a δ34SVCDT of 17.39 ± 0.06‰. Organic sulfur isotopes were consistently lighter than lake sulfate, with a δ34SVCDT of 15.59 ± 0.56‰. This significant offset between organic and inorganic sulfur contradicts the minimal isotope effect associated with sulfate assimilation. Sediment push core organic values were further depleted, ranging between δ34SVCDT of -8.94‰ and +0.23‰, implying rapid turnover of Mono Lake sulfur pools. Both lipid biomarkers and 16S rRNA gene amplicons identify Picocystis salinarum, a unicellular green alga, as the dominant member of the microbial community. However, bacterial biomarkers and 16S rRNA genes point to microbes capable of sulfur cycling. We found that dsrA increased with depth (R2 = 0.9008, p < 0.05). Phylogenetic analysis clustered dsrA with reversible dissimilatory sulfite reductases, suggesting sulfide oxidation rather than sulfate reduction. These findings are only partially consistent with a previous observation of Mono Lake from 2012, which identified a zoned assemblage of sulfate reducers and sulfide oxidizers after >1 year of stratification. We saw no evidence in May of 2017 of sulfate reducing bacteria across the oxycline. Additionally, no sulfide was detectable in lake bottom waters despite oxygen below 6.25 µM. Preliminary results suggest a dynamic interplay between sulfide oxidation, sulfate reduction, and the onset of lake stratification. Additional data from September 2017 sampling will be presented.

Can productivity and profitability be enhanced in intensively managed cereal systems while reducing the environmental footprint of production? Assessing sustainable intensification options in the breadbasket of India.

PubMed

Kumar, Virender; Jat, Hanuman S; Sharma, Parbodh C; Balwinder-Singh; Gathala, Mahesh K; Malik, Ram K; Kamboj, Baldev R; Yadav, Arvind K; Ladha, Jagdish K; Raman, Anitha; Sharma, D K; McDonald, Andrew

2018-01-15

In the most productive area of the Indo-Gangetic Plains in Northwest India where high yields of rice and wheat are commonplace, a medium-term cropping system trial was conducted in Haryana State. The goal of the study was to identify integrated management options for further improving productivity and profitability while rationalizing resource use and reducing environmental externalities (i.e., "sustainable intensification", SI) by drawing on the principles of diversification, precision management, and conservation agriculture. Four scenarios were evaluated: Scenario 1 - "business-as-usual" [conventional puddled transplanted rice (PTR) followed by ( fb ) conventional-till wheat]; Scenario 2 - reduced tillage with opportunistic diversification and precision resource management [PTR fb zero-till (ZT) wheat fb ZT mungbean]; Scenario 3 - ZT for all crops with opportunistic diversification and precision resource management [ZT direct-seeded rice (ZT-DSR) fb ZT wheat fb ZT mungbean]; and Scenario 4 - ZT for all crops with strategic diversification and precision resource management [ZT maize fb ZT wheat fb ZT mungbean]. Results of this five-year study strongly suggest that, compared with business-as-usual practices, SI strategies that incorporate multi-objective yield, economic, and environmental criteria can be more productive when used in these production environments. For Scenarios 2, 3, and 4, system-level increases in productivity (10-17%) and profitability (24-50%) were observed while using less irrigation water (15-71% reduction) and energy (17-47% reduction), leading to 15-30% lower global warming potential (GWP), with the ranges reflecting the implications of specific innovations. Scenario 3, where early wheat sowing was combined with ZT along with no puddling during the rice phase, resulted in a 13% gain in wheat yield compared with Scenario 2. A similar gain in wheat yield was observed in Scenario 4 vis-à-vis Scenario 2. Compared to Scenario 1, wheat yields in Scenarios 3 and 4 were 15-17% higher, whereas, in Scenario 2, yield was either similar in normal years or higher in warmer years. During the rainy ( kharif ) season, ZT-DSR provided yields similar to or higher than those of PTR in the first three years and lower (11-30%) in Years 4 and 5, a result that provides a note of caution for interpreting technology performance through short-term trials or simply averaging results over several years. The resource use and economic and environmental advantages of DSR were more stable through time, including reductions in irrigation water (22-40%), production cost (11-17%), energy inputs (13-34%), and total GWP (14-32%). The integration of "best practices" in PTR in Scenario 2 resulted in reductions of 24% in irrigation water and 21% in GWP, with a positive impact on yield (0.9 t/ha) and profitability compared to conventional PTR, demonstrating the power of simple management changes to generate improved SI outcomes. When ZT maize was used as a diversification option instead of rice in Scenario 4, reductions in resource use jumped to 82-89% for irrigation water and 49-66% for energy inputs, with 13-40% lower GWP, similar or higher rice equivalent yield, and higher profitability (27-73%) in comparison to the rice-based scenarios. Despite these advantages, maize value chains are not robust in this part of India and public procurement is absent. Results do demonstrate that transformative opportunities exist to break the cycle of stagnating yields and inefficient resource use in the most productive cereal-based cropping systems of South Asia. However, these SI entry points need to be placed in the context of the major drivers of change in the region, including market conditions, risks, and declining labor availability, and matching with the needs and interests of different types of farmers.

Comparison of Reconstruction and Control algorithms on the ESO end-to-end simulator OCTOPUS

NASA Astrophysics Data System (ADS)

Montilla, I.; Béchet, C.; Lelouarn, M.; Correia, C.; Tallon, M.; Reyes, M.; Thiébaut, É.

Extremely Large Telescopes are very challenging concerning their Adaptive Optics requirements. Their diameters, the specifications demanded by the science for which they are being designed for, and the planned use of Extreme Adaptive Optics systems, imply a huge increment in the number of degrees of freedom in the deformable mirrors. It is necessary to study new reconstruction algorithms to implement the real time control in Adaptive Optics at the required speed. We have studied the performance, applied to the case of the European ELT, of three different algorithms: the matrix-vector multiplication (MVM) algorithm, considered as a reference; the Fractal Iterative Method (FrIM); and the Fourier Transform Reconstructor (FTR). The algorithms have been tested on ESO's OCTOPUS software, which simulates the atmosphere, the deformable mirror, the sensor and the closed-loop control. The MVM is the default reconstruction and control method implemented in OCTOPUS, but it scales in O(N2) operations per loop so it is not considered as a fast algorithm for wave-front reconstruction and control on an Extremely Large Telescope. The two other methods are the fast algorithms studied in the E-ELT Design Study. The performance, as well as their response in the presence of noise and with various atmospheric conditions, has been compared using a Single Conjugate Adaptive Optics configuration for a 42 m diameter ELT, with a total amount of 5402 actuators. Those comparisons made on a common simulator allow to enhance the pros and cons of the various methods, and give us a better understanding of the type of reconstruction algorithm that an ELT demands.

Preconditioned conjugate gradient wave-front reconstructors for multiconjugate adaptive optics

NASA Astrophysics Data System (ADS)

Gilles, Luc; Ellerbroek, Brent L.; Vogel, Curtis R.

2003-09-01

Multiconjugate adaptive optics (MCAO) systems with 104-105 degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wave-front control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of adaptive optics degrees of freedom. We develop scalable open-loop iterative sparse matrix implementations of minimum variance wave-front reconstruction for telescope diameters up to 32 m with more than 104 actuators. The basic approach is the preconditioned conjugate gradient method with an efficient preconditioner, whose block structure is defined by the atmospheric turbulent layers very much like the layer-oriented MCAO algorithms of current interest. Two cost-effective preconditioners are investigated: a multigrid solver and a simpler block symmetric Gauss-Seidel (BSGS) sweep. Both options require off-line sparse Cholesky factorizations of the diagonal blocks of the matrix system. The cost to precompute these factors scales approximately as the three-halves power of the number of estimated phase grid points per atmospheric layer, and their average update rate is typically of the order of 10-2 Hz, i.e., 4-5 orders of magnitude lower than the typical 103 Hz temporal sampling rate. All other computations scale almost linearly with the total number of estimated phase grid points. We present numerical simulation results to illustrate algorithm convergence. Convergence rates of both preconditioners are similar, regardless of measurement noise level, indicating that the layer-oriented BSGS sweep is as effective as the more elaborated multiresolution preconditioner.

Correlated Time-Variation of Asphalt Rheology and Bulk Microstructure

NASA Astrophysics Data System (ADS)

Ramm, Adam; Nazmus, Sakib; Bhasin, Amit; Downer, Michael

We use noncontact optical microscopy and optical scattering in the visible and near-infrared spectrum on Performance Grade (PG) asphalt binder to confirm the existence of microstructures in the bulk. The number of visible microstructures increases linearly as penetration depth of the incident radiation increases, which verifies a uniform volume distribution of microstructures. We use dark field optical scatter in the near-infrared to measure the temperature dependent behavior of the bulk microstructures and compare this behavior with Dynamic Shear Rheometer (DSR) measurements of the bulk complex shear modulus | G* (T) | . The main findings are: (1) After reaching thermal equilibrium, both temperature dependent optical scatter intensity (I (T)) and bulk shear modulus (| G* (T) |) continue to change appreciably for times much greater than thermal equilibration times. (2) The hysteresis behavior during a complete temperature cycle seen in previous work derives from a larger time dependence in the cooling step compared with the heating step. (3) Different binder aging conditions show different thermal time-variations for both I (T) and | G* (T) | .

Biocorrosion and biofilm formation in a nutrient limited heating system subjected to alternating microaerophilic conditions.

PubMed

Kjellerup, B V; Kjeldsen, K U; Lopes, F; Abildgaard, L; Ingvorsen, K; Frølund, B; Sowers, K R; Nielsen, P H

2009-11-01

Severe biofilm formation and biocorrosion have been observed in heating systems even when the water quality complied with existing standards. The coupling between water chemistry, biofilm formation, species composition, and biocorrosion in a heating system was investigated by adding low concentrations of nutrients and oxygen under continuous and alternating dosing regimes. Molecular analysis of 16S rRNA gene fragments demonstrated that the amendments did not cause changes in the overall bacterial community composition. The combined alternating dosing of nutrients and oxygen caused increased rates of pitting (bio-) corrosion. Detection of bacteria involved in sulfide production and oxidation by retrieval of the functional dsrAB and apsA genes revealed the presence of Gram-positive sulfate- and sulfite-reducers and an unknown sulfur-oxidizer. Therefore, to control biocorrosion, sources of oxygen and nutrients must be limited, since the effect of the alternating operational conditions apparently is more important than the presence of potentially corrosive biofilm bacteria.

Achieving interoperability for metadata registries using comparative object modeling.

PubMed

Park, Yu Rang; Kim, Ju Han

2010-01-01

Achieving data interoperability between organizations relies upon agreed meaning and representation (metadata) of data. For managing and registering metadata, many organizations have built metadata registries (MDRs) in various domains based on international standard for MDR framework, ISO/IEC 11179. Following this trend, two pubic MDRs in biomedical domain have been created, United States Health Information Knowledgebase (USHIK) and cancer Data Standards Registry and Repository (caDSR), from U.S. Department of Health & Human Services and National Cancer Institute (NCI), respectively. Most MDRs are implemented with indiscriminate extending for satisfying organization-specific needs and solving semantic and structural limitation of ISO/IEC 11179. As a result it is difficult to address interoperability among multiple MDRs. In this paper, we propose an integrated metadata object model for achieving interoperability among multiple MDRs. To evaluate this model, we developed an XML Schema Definition (XSD)-based metadata exchange format. We created an XSD-based metadata exporter, supporting both the integrated metadata object model and organization-specific MDR formats.

UMDR: Multi-Path Routing Protocol for Underwater Ad Hoc Networks with Directional Antenna

NASA Astrophysics Data System (ADS)

Yang, Jianmin; Liu, Songzuo; Liu, Qipei; Qiao, Gang

2018-01-01

This paper presents a new routing scheme for underwater ad hoc networks based on directional antennas. Ad hoc networks with directional antennas have become a hot research topic because of space reuse may increase networks capacity. At present, researchers have applied traditional self-organizing routing protocols (such as DSR, AODV) [1] [2] on this type of networks, and the routing scheme is based on the shortest path metric. However, such routing schemes often suffer from long transmission delays and frequent link fragmentation along the intermediate nodes of the selected route. This is caused by a unique feature of directional transmission, often called as “deafness”. In this paper, we take a different approach to explore the advantages of space reuse through multipath routing. This paper introduces the validity of the conventional routing scheme in underwater ad hoc networks with directional antennas, and presents a special design of multipath routing algorithm for directional transmission. The experimental results show a significant performance improvement in throughput and latency.

Multi-hop routing mechanism for reliable sensor computing.

PubMed

Chen, Jiann-Liang; Ma, Yi-Wei; Lai, Chia-Ping; Hu, Chia-Cheng; Huang, Yueh-Min

2009-01-01

Current research on routing in wireless sensor computing concentrates on increasing the service lifetime, enabling scalability for large number of sensors and supporting fault tolerance for battery exhaustion and broken nodes. A sensor node is naturally exposed to various sources of unreliable communication channels and node failures. Sensor nodes have many failure modes, and each failure degrades the network performance. This work develops a novel mechanism, called Reliable Routing Mechanism (RRM), based on a hybrid cluster-based routing protocol to specify the best reliable routing path for sensor computing. Table-driven intra-cluster routing and on-demand inter-cluster routing are combined by changing the relationship between clusters for sensor computing. Applying a reliable routing mechanism in sensor computing can improve routing reliability, maintain low packet loss, minimize management overhead and save energy consumption. Simulation results indicate that the reliability of the proposed RRM mechanism is around 25% higher than that of the Dynamic Source Routing (DSR) and ad hoc On-demand Distance Vector routing (AODV) mechanisms.

Evaluation and development the routing protocol of a fully functional simulation environment for VANETs

NASA Astrophysics Data System (ADS)

Ali, Azhar Tareq; Warip, Mohd Nazri Mohd; Yaakob, Naimah; Abduljabbar, Waleed Khalid; Atta, Abdu Mohammed Ali

2017-11-01

Vehicular Ad-hoc Networks (VANETs) is an area of wireless technologies that is attracting a great deal of interest. There are still several areas of VANETS, such as security and routing protocols, medium access control, that lack large amounts of research. There is also a lack of freely available simulators that can quickly and accurately simulate VANETs. The main goal of this paper is to develop a freely available VANETS simulator and to evaluate popular mobile ad-hoc network routing protocols in several VANETS scenarios. The VANETS simulator consisted of a network simulator, traffic (mobility simulator) and used a client-server application to keep the two simulators in sync. The VANETS simulator also models buildings to create a more realistic wireless network environment. Ad-Hoc Distance Vector routing (AODV), Dynamic Source Routing (DSR) and Dynamic MANET On-demand (DYMO) were initially simulated in a city, country, and highway environment to provide an overall evaluation.

Evaluating the Rheological Properties of Waste Natural Rubber Latex Modified Binder

NASA Astrophysics Data System (ADS)

Khatijah Abu Bakar, Siti; Ezree Abdulah, Mohd; Mustafa Kamal, Mazlina; Rahman, Raha Abd; Arifin Hadithon, Kamarul; Buhari, Rosnawati; Tajudin, Saiful Azhar Ahmad

2018-03-01

Road surface is designed to be the durable surface material to sustain the traffic loading. However, due to physical and mechanical stress, pavement deterioration is accelerated. Thus, modifying conventional bitumen by improving its properties is seen as the best method to prolong pavement in-service life. The purpose of this paper is to study the effect of waste natural rubber (NR) latex on rheological properties of bitumen. Conventional bitumen PEN 80/100 was modified with different content of waste NR latex using a high shear mixer at temperature of 150°C. The modified binder properties were characterized by conducting physical test (i.e. softening point, penetration and penetration index) and rheological test (i.e. dynamic shear rheometer, DSR). Results showed that, the addition of waste NR latex improved the rheology properties, which indicates by improving of rutting factor (G*/sin δ). This properties improvement has also shows a potential to resist deformation on road surface despite of high traffic loading.

Structural and magnetic properties of epitaxial delafossite CuFeO2 thin films grown by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Senty, Tess; Joshi, Toyanath; Trappen, Robbyn; Zhou, Jinling; Chen, Song; Ferrari, Piero; Borisov, Pavel; Song, Xueyan; Holcomb, Mikel; Bristow, Alan; Cabrera, Alejandro; Lederman, David

2015-03-01

Growth of pure phase delafossite CuFeO2 thin films on Al2O3 (00.1) substrates by pulsed laser deposition was systematically investigated as function of growth temperature and oxygen pressure. X-ray diffraction, transmission electron microscopy, Raman scattering, and x-ray absorption spectroscopy confirmed the existence of the delafossite phase. Infrared reflectivity spectra determined a band edge at 1.15 eV, in agreement with the bulk delafossite data. Magnetization measurements on CuFeO2 films demonstrated a phase transition at TC = 15K, which agrees with the first antiferromagnetic transition at 14K in the bulk CuFeO2. Low temperature magnetic phase is best described by commensurate, weak ferromagnetic spin ordering along the c-axis. This work was supported by a Research Challenge Grant from the West Virginia Higher Education Policy Commission (HEPC.dsr.12.29) and the Microelectronics Advanced Research Corporation (Contract #2013-MA-2382) at WVU. Work at PUC was supported by FONDECyT.

Effect of functional monomers in all-in-one adhesive systems on formation of enamel/dentin acid-base resistant zone.

PubMed

Nikaido, Toru; Ichikawa, Chiaki; Li, Na; Takagaki, Tomohiro; Sadr, Alireza; Yoshida, Yasuhiro; Suzuki, Kazuomi; Tagami, Junji

2011-01-01

This study aimed at evaluating the effect of functional monomers in all-in-one adhesive systems on formation of acid-base resistant zone (ABRZ) in enamel and dentin. Experimental adhesive systems containing one of three functional monomers; MDP, 3D-SR and 4-META were applied to enamel or dentin surface and light-cured. A universal resin composite was then placed. The specimens were subjected to a demineralizing solution (pH 4.5) and 5% NaClO for acid-base challenge and then observed by SEM. The ABRZ was clearly observed in both enamel and dentin interfaces. However, enamel ABRZ was thinner than dentin ABRZ in all adhesives. Morphology of the ABRZ was different between enamel and dentin, and also among the adhesives. Funnel-shaped erosion was observed only in the enamel specimen with the 4-META adhesive. The formation of enamel/dentin ABRZ was confirmed in all adhesives, but the morphology was influenced by the functional monomers.

Analysis of power management and system latency in wireless sensor networks

NASA Astrophysics Data System (ADS)

Oswald, Matthew T.; Rohwer, Judd A.; Forman, Michael A.

2004-08-01

Successful power management in a wireless sensor network requires optimization of the protocols which affect energy-consumption on each node and the aggregate effects across the larger network. System optimization for a given deployment scenario requires an analysis and trade off of desired node and network features with their associated costs. The sleep protocol for an energy-efficient wireless sensor network for event detection, target classification, and target tracking developed at Sandia National Laboratories is presented. The dynamic source routing (DSR) algorithm is chosen to reduce network maintenance overhead, while providing a self-configuring and self-healing network architecture. A method for determining the optimal sleep time is developed and presented, providing reference data which spans several orders of magnitude. Message timing diagrams show, that a node in a five-node cluster, employing an optimal cyclic single-radio sleep protocol, consumes 3% more energy and incurs a 16-s increase latency than nodes employing the more complex dual-radio STEM protocol.

Current Highlights on ESA's Planetary Technology Reference Studies

NASA Astrophysics Data System (ADS)

Falkner, P.

The concept of Technology Reference Studies has been introduced already at EGU05, where the Venus Entry Probe (VEP), the Jupiter Minisat Explorer (JME), the Deimos Sample Return (DSR) and the Interstellar Heliopause Probe (IHP) have been presented in detail. At the EGU06 the new studies in reaction to the Cosmic Vision exercise have been introduced. The formulation of themes and mapping into potential future missions has been taken as basis in the planning of additional new and adaptation of existing TRS's to cover areas, which have not yet been addressed by any TRS. These new ongoing studies are progressing well and current highlights will be presented in the paper in further detail as well as an overview on supporting technology studies and Concurrent Design Facility (CDF) sessions. The Jupiter System Explorer (JSE) study investigates mission concepts with up to two Magnetospheric Orbiters placed in a highly elliptical Jovian orbit and the possibility to deploy a Jovian Entry Probe. The mission profile is based on a solar powered concept launched on a Soyuz-Fregat launcher. Mission analysis and the application of a new Jovian radiation model are supporting the study activities. The Near-Earth Asteroid Sample Return (NEA-SR) concept explores the possibilities of sample return or in-situ mission profiles with visits to up to two NEA targets. Due to the assumed low cost cap a trade between a sample return and remote/in-situ exploration concept has a high attention in the study. The Cross Scale TRS (CS-TRS) is intended to simultaneously investigate magnetospheric and plasma processes in three spatial scales with a formation flight of up to 12 spacecraft, orbiting on deep elliptical orbits around Earth. One of the major challenges is the launch of that number of spacecraft on a single launcher and the collisionless deployment of the formation at the target orbit. The scope if the GeoSail TRS is to demonstrate deployment, attitude control and navigation concepts for a solar sailing mission as required by Interstellar Heliopause Probe (IHP) or Solar Polar Orbiter (SPO) mission concepts and to investigate the potential influence of the extended sail for science measurements.

A Survey of Light Pollution in the Rogue Valley, Southwest Oregon, By St. Mary’s School, Medford, Oregon

NASA Astrophysics Data System (ADS)

Bensel, Holly; Arianna Ashby, Colin Cai, Thomas Cox, Genna Dorrell, Gabe FitzPatrick, Meaghan FitzPatrick, Jason Mars Liu, Mitchell Moczygemba, Kieran Rooney, Emry Timmons,; Ray You, students, (St. Mary's. School)

2015-01-01

Rural areas in Oregon, including the Rogue Valley, are renowned for beautiful dark skies. Electric light came to Medford, Oregon, the largest town in the Rogue Valley, in 1894. During the past 100 years the Rogue Valley grew from 2,500 individuals in 1895 to a population of 76,462 and a metropolitan area population of 208,545, in 2012. The increased population density resulted in increased light pollution. A light pollution chart using DMSP, Defense Meteorological Satellite Program, data was published in 2006, but did not show the spatial variation in detail. In the spring of 2014, the 9th grade physics students, astronomy students, and members of the Astronomy Club from St. Mary's School conducted the first detailed night sky survey. The purpose of the survey is to create a baseline of the variations in light pollution in the Rogue Valley.The project started with a talk by Steve Bosbach, former Texas IDA coordinator, on the topic of light pollution and how it affects our lives and the environment. Groups of students were given the tasks of measuring the night sky brightness in the Rogue Valley, doing a light audit in an area of their choice, and researching what light pollution is and its effects on the environment. From this they created a presentation for a final physics grade. The basis for this project, along with procedures can be found on the Globe at Night (www.globeatnight.org) website. The light audit and research portion were developed from the Dark Sky Rangers section (www.globeatnight.org/dsr/) of the website. In the fall of 2014, astronomy students and club members extended this study to the town of Ashland and the Sothern Oregon University campus, areas of the valley not surveyed in the Spring.This survey will increase awareness of light pollution in the Rogue Valley, as well as educate developers and city planners on the impact that light pollution has on the environment in Southern Oregon. It will help determine areas of concern and areas of dark sky compliant lighting, which could spur appropriate regulation regarding outdoor lighting.

A Survey of Light Pollution in the Rogue Valley, Southwest Oregon, by St. Mary's School, Medford, Oregon

NASA Astrophysics Data System (ADS)

Bensel, Holly; Dorrell, Genna; Feng, James; Hicks, Sean; Mars Liu, Jason; Liu, Steven; Moczygemba, Mitchell; Sheng, Jason; Sternenburg, Leah; Than, Emi; Timmons, Emry; Wen, Jerry; Yaeger, Bella; You, Ruiyang

2016-01-01

The Rogue Valley in Southwest Oregon was known for its beautiful dark skies, but due to population growth the dark skies are vanishing. A light pollution chart using Defense Meteorological Satellite Program (DMSP) data was published in 2006, but did not show the spatial variation in detail. In the spring of 2014, the 9th grade physics students, astronomy students, and members of the Astronomy Club from St. Mary's School conducted the first detailed night sky survey. The purpose of the survey is to create a baseline of the variations in light pollution in the Rogue Valley.The project continued into 2015, incorporating suggestions made at the 2014 AAS Conference to improve the study by including more light meter data and community outreach. Students used light meters, Loss of the Night app, and the Dark Sky meter app. Students researched light pollution and its effects on the environment, measured night sky brightness in the Rogue Valley, and completed a light audit in an area of their choice. They created a presentation for a final physics grade. The basis for this project, along with procedures can be found on the GaN, Globe at Night, (www.globeatnight.org) website. The light audit and research portion were developed from the Dark Sky Rangers section of the website (www.globeatnight.org/dsr/).The 2014 survey and public outreach increased awareness of light pollution in the Rogue Valley and around the state of Oregon. Examples include a local senior project to change lighting at a baseball stadium and a 4-H club in Northeast Oregon starting a GaN survey in their area. GaN shows growth in the amount of data collected in Oregon from 8 data points in 2006 to 193 in 2014. The Rogue Valley magnitude data from the spring of 2015 indicates a drop from an average magnitude of 4 to an average magnitude of 2. This is due to hazy skies from smoke drifting into the valley from a Siberian wildfire. Data collection during the summer and fall was hampered due to smoke from local wildfires.

Metabolic Strategies in Energy-Limited Microbial Communities in the Anoxic Subsurface (Frasassi Cave System, Italy)

NASA Astrophysics Data System (ADS)

McCauley, R. L.; Jones, D. S.; Schaperdoth, I.; Steinberg, L.; Macalady, J. L.

2010-12-01

Two major sources of energy, light and chemical potential, are available to microorganisms. However, energy is not always abundant and is often a limiting factor in microbial survival and replication. The anoxic, terrestrial subsurface offers a unique opportunity to study microorganisms and their potentially novel metabolic strategies that are relevant for understanding biogeochemistry and biosignatures as related to the non-photosynthetic, energy-limited environments on the modern and ancient Earth and elsewhere in the solar system. Geochemical data collected in a remote stratified lake 600 m below ground surface in the sulfidic Frasassi cave system (Italy) suggest that little redox energy is available for life, consistent with low signal from domain-specific FISH probes. The carbon isotope signatures of biofilms (-33‰) and DIC (-9‰) in the anoxic water suggest in situ production by lithoautotrophs using RuBisCO. 16S rDNA libraries constructed from the biofilm are dominated by diverse sulfate reducing bacteria. The remaining bacterial and archaeal clones affiliate with more than 11 major uncultivated or novel prokaryotic lineages. Diverse dsrAB gene sequences are consistent with high sulfate concentrations and undetectable or extremely low oxygen, nitrate, and iron concentrations. However, the electron donor for sulfate reduction is unclear. Methane is detectable in the anoxic water although no 16S rDNA sequences associated with known methanogens or anaerobic methane oxidizers were retrieved. mcrA gene sequences retrieved from the biofilm by cloning are not related to cultivated methanogens or to known anaerobic methane oxidizers. Non-purgable organic carbon (NPOC) is below detection limits (i.e. <42 μM acetate) suggesting that alternative electron donors or novel metabolisms may be important. A sample collected by cave divers in October 2009 was pyrosequenced at the Pennsylvania State University Genomics Core Facility using Titanium chemistry (454 Life Sciences). We retrieved more than 420,000 metagenomic reads, of which 46% have significant homology to sequences in NCBI’s non-redundant protein database and 3% could be assigned using the Clusters of Orthologous Groups of proteins (COGs) classification system. 16S (174 reads) and 23S (283 reads) rDNA sequences in the metagenome imply a phylogenetically diverse community dominated by Deltaproteobacteria and Firmicutes. We also identified 15 metagenome sequences with homology to known dsrAB genes. Further work will identify additional genes for specific energy and nutrient metabolisms in the community, as well as use comparative analyses to determine overrepresented functions that are characteristic of life in the oligotrophic, euxinic cave environment.

Diversity and composition of sulfate- and sulfite-reducing prokaryotes as affected by marine-freshwater gradient and sulfate availability.

PubMed

Fan, Lan-Feng; Tang, Sen-Lin; Chen, Chang-Po; Hsieh, Hwey-Lian

2012-01-01

Sulfate- and sulfite-reducing prokaryotes (SSRP) communities play a key role in both sulfur and carbon cycles. In estuarine ecosystems, sulfate concentrations change with tides and could be limited in tidal freshwater reach or deep sediments. In a subtropical estuary of northern Taiwan in December 2007, we examined the compositional changes of SSRP communities. We examined three sites: from the lower estuarine brackish-water reach (site GR and mangrove vegetation site, GM) to the upper estuarine tidal freshwater reach (site HR), as well as from surface to a 50-cm depth. The partial sequence of sulfite reductase (dsrB) genes was used as a molecular marker of SSRP, linked to polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE) techniques. SSRP communities of the DGGE profiles varied with sites according to one-way analyses of similarities (Global R = 0.69, P = 0.001). Using cluster analysis, the DGGE profile was found to show site-specific clusters and a distinct depth zonation (five, six, and two SSRP communities at the GM, GR, and HR sites, respectively). SSRP composition was highly correlated to the combination of salinity, reduced sulfur, and total organic carbon contents (BIO-ENV analysis, r ( s ) = 0.56). After analyzing a total of 35 dsrB sequences in the DGGE gel, six groups with 15 phylotypes were found, which were closely related to marine-freshwater gradient. Moreover, sequences neighboring sulfite-reducing prokaryotes were observed, in addition to those affiliated to sulfate-reducing prokaryotes. Four phylotypes harvested in HR resembled the genus Desulfitobacterium, a sulfite-reducing prokaryote, which failed to use sulfate as an electron acceptor and were active in freshwater and sulfate-limited habitat. The other five phylotypes in the HR reach belonged to the sulfate-reducing prokaryotes of the genera Desulfatiferula, Desulfosarcina, Desulfovibrio, and Desulfotomaculum, which appeared to tolerate low salinity and low sulfate supply. SSRP phylotypes at the mangrove-vegetated GM site (five phylotypes in two groups) were phylogenetically less diverse, when compared with those at the non-mangrove-vegetated GR site (three phylotypes in three groups) and the tidally influenced freshwater HR site (nine phylotypes in five groups). Phylotypes found at GR and GM were all affiliated to marine sulfate-reducing prokaryote strains of the genera Desulfofaba, Desulfobotulus, Desulfatiferula, Desulfosarcina, and Desulfotomaculum. Notably, a phylotype recorded in the surface sediment at GR resembled the genus Desulfobulbus, which was recorded from freshwater environment consisting of the freshwater input at GR during ebb tides.

Preconditioned conjugate gradient wave-front reconstructors for multiconjugate adaptive optics.

PubMed

Gilles, Luc; Ellerbroek, Brent L; Vogel, Curtis R

2003-09-10

Multiconjugate adaptive optics (MCAO) systems with 10(4)-10(5) degrees of freedom have been proposed for future giant telescopes. Using standard matrix methods to compute, optimize, and implement wavefront control algorithms for these systems is impractical, since the number of calculations required to compute and apply the reconstruction matrix scales respectively with the cube and the square of the number of adaptive optics degrees of freedom. We develop scalable open-loop iterative sparse matrix implementations of minimum variance wave-front reconstruction for telescope diameters up to 32 m with more than 10(4) actuators. The basic approach is the preconditioned conjugate gradient method with an efficient preconditioner, whose block structure is defined by the atmospheric turbulent layers very much like the layer-oriented MCAO algorithms of current interest. Two cost-effective preconditioners are investigated: a multigrid solver and a simpler block symmetric Gauss-Seidel (BSGS) sweep. Both options require off-line sparse Cholesky factorizations of the diagonal blocks of the matrix system. The cost to precompute these factors scales approximately as the three-halves power of the number of estimated phase grid points per atmospheric layer, and their average update rate is typically of the order of 10(-2) Hz, i.e., 4-5 orders of magnitude lower than the typical 10(3) Hz temporal sampling rate. All other computations scale almost linearly with the total number of estimated phase grid points. We present numerical simulation results to illustrate algorithm convergence. Convergence rates of both preconditioners are similar, regardless of measurement noise level, indicating that the layer-oriented BSGS sweep is as effective as the more elaborated multiresolution preconditioner.

Efficacy of MedMyst: an Internet Teaching Tool for Middle School Microbiology.

PubMed

Miller, Leslie M; Moreno, Janette; Estrera, Vicky; Lane, David

2004-05-01

Can web-based technology be used to effectively introduce or reinforce aspects of microbiology to middle school students? This central hypothesis examines whether brief exposure to a web adventure format containing virtual lab experiments and computer games within an engaging story line can impact student learning. An episodic adventure series, MedMyst (http://medmyst.rice.edu), focuses on infectious diseases and the microbes that cause them. The website is not intended to replace classroom instruction, but rather to engage students in problem-solving activities not likely to be encountered elsewhere. It also provides scientists with a resource to introduce microbiology to adolescent audiences through outreach activities. In the online adventure, the player (student) enters a futuristic world in which he or she becomes a "Reconstructor," a member of an elite team charged with preventing the spread of infectious disease. The series consists of three "missions," each lasting approximately 30 to 40 minutes and designed to address a limited set of learning objectives. Middle school students participated in the creation of the characters and the stylized design through focus groups. Classroom teachers oversaw the alignment of the web adventure objectives with the National Science Content Standards. Scientists and clinicians reviewed the web adventure for content and accuracy. A field test involving over 700 students from nine different schools assessed the knowledge gains attributable to playing MedMyst. Gain scores from pretest to posttest indicated that middle school students retained important information by interacting with the online material for as little as 30 minutes per adventure; however, gains for high school students were less persuasive, perhaps indicating a different learning tool or content is required for this age audience.

Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

PubMed Central

Loy, Alexander; Lehner, Angelika; Lee, Natuschka; Adamczyk, Justyna; Meier, Harald; Ernst, Jens; Schleifer, Karl-Heinz; Wagner, Michael

2002-01-01

For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB). PMID:12324358

Mesoporous CdS via Network of Self-Assembled Nanocrystals: Synthesis, Characterization and Enhanced Photoconducting Property.

PubMed

Patra, Astam K; Banerjee, Biplab; Bhaumik, Asim

2018-01-01

Semiconduction nanoparticles are intensively studied due to their huge potential in optoelctronic applications. Here we report an efficient chemical route for hydrothermal synthesis of aggregated mesoporous cadmium sulfide (CdS) nanoparticles using supramolecular-assembly of ionic and water soluble sodium salicylate as the capping agent. The nanostructure, mesophase, optical property and photoconductivity of these mesoporous CdS materials have been characterized by using small and wide angle powder X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), N2-sorption, Raman analysis, Fourier transformed infrared (FT-IR), UV-Visible DSR spectroscopy, and photoconductivity measurement. Wide angle XRD pattern and high resolution TEM image analysis suggested that the particle size of the materials is within 10 nm and the nanoparticles are in well-crystallized cubic phase. Mesoporous CdS nanoparticles showed drastically enhanced photoelectrochemical response under visible light irradiation on entrapping a photosensitizer (dye) molecule in the interparticle spaces. Efficient synthesis strategy and the enhanced photo response in the mesoporous CdS material could facilitate the designing of other porous semiconductor oxide/sulfide and their applications in photon-to-electron conversion processes.

Sulfate-reducing bacteria inhabiting natural corrosion deposits from marine steel structures.

PubMed

Païssé, Sandrine; Ghiglione, Jean-François; Marty, Florence; Abbas, Ben; Gueuné, Hervé; Amaya, José Maria Sanchez; Muyzer, Gerard; Quillet, Laurent

2013-08-01

In the present study, investigations were conducted on natural corrosion deposits to better understand the role of sulfate-reducing bacteria (SRB) in the accelerated corrosion process of carbon steel sheet piles in port environments. We describe the abundance and diversity of total and metabolically active SRB within five natural corrosion deposits located within tidal or low water zone and showing either normal or accelerated corrosion. By using molecular techniques, such as quantitative real-time polymerase chain reaction, denaturing gel gradient electrophoresis, and sequence cloning based on 16S rRNA, dsrB genes, and their transcripts, we demonstrated a clear distinction between SRB population structure inhabiting normal or accelerated low-water corrosion deposits. Although SRB were present in both normal and accelerated low-water corrosion deposits, they dominated and were exclusively active in the inner and intermediate layers of accelerated corrosion deposits. We also highlighted that some of these SRB populations are specific to the accelerated low-water corrosion deposit environment in which they probably play a dominant role in the sulfured corrosion product enrichment.

Effects of plant downtime on the microbial community composition in the highly saline brine of a geothermal plant in the North German Basin.

PubMed

Westphal, Anke; Lerm, Stephanie; Miethling-Graff, Rona; Seibt, Andrea; Wolfgramm, Markus; Würdemann, Hilke

2016-04-01

The microbial biocenosis in highly saline fluids produced from the cold well of a deep geothermal heat store located in the North German Basin was characterized during regular plant operation and immediately after plant downtime phases. Genetic fingerprinting revealed the dominance of sulfate-reducing bacteria (SRB) and fermentative Halanaerobiaceae during regular plant operation, whereas after shutdown phases, sequences of sulfur-oxidizing bacteria (SOB) were also detected. The detection of SOB indicated oxygen ingress into the well during the downtime phase. High 16S ribosomal RNA (rRNA) and dsrA gene copy numbers at the beginning of the restart process showed an enrichment of bacteria, SRB, and SOB during stagnant conditions consistent with higher concentrations of dissolved organic carbon (DOC), sulfate, and hydrogen sulfide in the produced fluids. The interaction of SRB and SOB during plant downtimes might have enhanced the corrosion processes occurring in the well. It was shown that scale content of fluids was significantly increased after stagnant phases. Moreover, the sulfur isotopic signature of the mineral scales indicated microbial influence on scale formation.

Impact of oxygen on the coexistence of nitrification, denitrification, and sulfate reduction in oxygen-based membrane aerated biofilm.

PubMed

Liu, Hong; Tan, Shuying; Sheng, Zhiya; Yu, Tong; Liu, Yang

2015-03-01

Membrane aerated biofilms (MABs) are subject to "counter diffusion" of oxygen and substrates. In a membrane aerated biofilm reactor, gases (e.g., oxygen) diffuse through the membrane into the MAB, and liquid substrates pass from the bulk liquid into the MAB. This behavior can result in a unique biofilm structure in terms of microbial composition, distribution, and community activity in the MAB. Previous studies have shown simultaneous aerobic oxidation, nitrification, and denitrification within a single MAB. Using molecular techniques, we investigated the growth of sulfate-reducing bacteria (SRB) in the oxygen-based MAB attached to a flat sheet membrane. Denaturing gradient gel electrophoresis of the amplified 16S rRNA gene fragments and functional gene fragments specific for ammonia-oxidizing bacteria (amoA), denitrifying bacteria (nirK), and SRB (dsrB) demonstrated the coexistence of nitrifiers, denitrifiers, and SRB communities within a single MAB. The functional diversities of SRB and denitrifiers decreased with an increase in the oxygen concentration in the bulk water of the reactor.

Wireless Inductive Power Device Suppresses Blade Vibrations

NASA Technical Reports Server (NTRS)

Morrison, Carlos R.; Provenza, Andrew J.; Choi, Benjamin B.; Bakhle, Milind A.; Min, James B.; Stefko, George L.; Duffy, Kirsten P.; Fougers, Alan J.

2011-01-01

Vibration in turbomachinery can cause blade failures and leads to the use of heavier, thicker blades that result in lower aerodynamic efficiency and increased noise. Metal and/or composite fatigue in the blades of jet engines has resulted in blade destruction and loss of lives. Techniques for suppressing low-frequency blade vibration, such as gtuned circuit resistive dissipation of vibratory energy, h or simply "passive damping," can require electronics incorporating coils of unwieldy dimensions and adding unwanted weight to the rotor. Other approaches, using vibration-dampening devices or damping material, could add undesirable weight to the blades or hub, making them less efficient. A wireless inductive power device (WIPD) was designed, fabricated, and developed for use in the NASA Glenn's "Dynamic Spin Rig" (DSR) facility. The DSR is used to simulate the functionality of turbomachinery. The relatively small and lightweight device [10 lb (approx.=4.5 kg)] replaces the existing venerable and bulky slip-ring. The goal is the eventual integration of this technology into actual turbomachinery such as jet engines or electric power generators, wherein the device will facilitate the suppression of potentially destructive vibrations in fan blades. This technology obviates slip rings, which require cooling and can prove unreliable or be problematic over time. The WIPD consists of two parts: a remote element, which is positioned on the rotor and provides up to 100 W of electrical power to thin, lightweight piezoelectric patches strategically placed on/in fan blades; and a stationary base unit that wirelessly communicates with the remote unit. The base unit supplies inductive power, and also acts as an input and output corridor for wireless measurement, and active control command to the remote unit. Efficient engine operation necessitates minimal disturbance to the gas flow across the turbine blades in any effort to moderate blade vibration. This innovation makes it possible to moderate vibration on or in turbomachinery blades by providing 100 W of wireless electrical power and actuation control to thin, lightweight vibration-suppressing piezoelectric patches (eight actuation and eight sensor patches in this prototype, for a total of 16 channels) positioned strategically on the surface of, or within, titanium fan blades, or embedded in composite fan blades. This approach moves significantly closer to the ultimate integration of "active" vibration suppression technology into jet engines and other turbomachinery devices such as turbine electrical generators used in the power industry. The novel feature of this device is in its utilization of wireless technology to simultaneously sense and actively control vibration in rotating or stationary turbomachinery blades using piezoelectric patches. In the past, wireless technology was used solely for sensing and diagnostics. This technology, however, will accomplish much more, in terms of simultaneously sensing, suppressing blade vibration, and making it possible for detailed study of vibration impact in turbomachinery blades.

Microbial Dynamics During a Temporal Sequence of Bioreduction Stimulated by Emulsified Vegetable Oil

NASA Astrophysics Data System (ADS)

Schadt, C. W.; Gihring, T. M.; Yang, Z.; Wu, W.; Green, S.; Overholt, W.; Zhang, G.; Brandt, C. C.; Campbell, J. H.; Carroll, S. C.; Criddle, C.; Jardine, P. M.; Lowe, K.; Mehlhorn, T.; Kostka, J. E.; Watson, D. B.; Brooks, S. C.

2011-12-01

Amendments of slow-release substrates (e.g. emulsified vegetable oil; EVO) are potentially pragmatic alternatives to short-lived labile substrates for sustained uranium bioimmobilization within groundwater systems. The spatial and temporal dynamics of geochemical and microbial community changes during EVO amendment are likely to differ significantly from populations stimulated by readily utilizable soluble substrates (e.g. ethanol or acetate). We tracked dynamic changes in geochemistry and microbial communities for 270 days following a one-time EVO injection at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site that resulted in decreased groundwater U concentrations for ~4 months. Pyrosequencing and quantitative PCR of 16S rRNA and dissimilatory sulfite reductase (dsrA) genes from monitoring well samples revealed a rapid decline in bacterial community richness and evenness after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group consisting of 10-15 dominant OTUs, rather than a broad community stimulation. By association of the known physiology of close relatives identified in the pyrosequencing analysis, it is possible to infer a hypothesized sequence of microbial functions leading the major changes in electron donors and acceptors in the system. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition and utilized the glycerol associated with the oils. Sulfate-reducing bacteria from the genus Desulforegula, known for LCFA oxidation to acetate, also dominated shortly after EVO amendment and are thought to catalyze this process. Acetate and H2 production during LCFA degradation appeared to stimulate NO3-, Fe(III), U(VI), and SO42- reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late in the experiment and in some samples constituted over 25 % of the total microbial community. Bacterial richness rebounded after nine months, although community composition remained distinct from the pre-amendment conditions. Subsequent to the experiment we have isolated several of these organisms into pure culture including representatives of probable new species of Geobacter, Desulforegula and Desulfovibrio. A hypothesized model for the functioning of these limited communities will be verified in the laboratory using defined combinations of isolates from the field where possible. These results demonstrated EVO serves as an effective electron donor source for in situ U(VI) bioreduction, and subsurface EVO degradation and metal reduction was likely mediated by successive identifiable guilds of organisms.

Predicting fundamental frequency from mel-frequency cepstral coefficients to enable speech reconstruction.

PubMed

Shao, Xu; Milner, Ben

2005-08-01

This work proposes a method to reconstruct an acoustic speech signal solely from a stream of mel-frequency cepstral coefficients (MFCCs) as may be encountered in a distributed speech recognition (DSR) system. Previous methods for speech reconstruction have required, in addition to the MFCC vectors, fundamental frequency and voicing components. In this work the voicing classification and fundamental frequency are predicted from the MFCC vectors themselves using two maximum a posteriori (MAP) methods. The first method enables fundamental frequency prediction by modeling the joint density of MFCCs and fundamental frequency using a single Gaussian mixture model (GMM). The second scheme uses a set of hidden Markov models (HMMs) to link together a set of state-dependent GMMs, which enables a more localized modeling of the joint density of MFCCs and fundamental frequency. Experimental results on speaker-independent male and female speech show that accurate voicing classification and fundamental frequency prediction is attained when compared to hand-corrected reference fundamental frequency measurements. The use of the predicted fundamental frequency and voicing for speech reconstruction is shown to give very similar speech quality to that obtained using the reference fundamental frequency and voicing.

Evaluation of Asphalt Mixture Low-Temperature Performance in Bending Beam Creep Test.

PubMed

Pszczola, Marek; Jaczewski, Mariusz; Rys, Dawid; Jaskula, Piotr; Szydlowski, Cezary

2018-01-10

Low-temperature cracking is one of the most common road pavement distress types in Poland. While bitumen performance can be evaluated in detail using bending beam rheometer (BBR) or dynamic shear rheometer (DSR) tests, none of the normalized test methods gives a comprehensive representation of low-temperature performance of the asphalt mixtures. This article presents the Bending Beam Creep test performed at temperatures from -20 °C to +10 °C in order to evaluate the low-temperature performance of asphalt mixtures. Both validation of the method and its utilization for the assessment of eight types of wearing courses commonly used in Poland were described. The performed test indicated that the source of bitumen and its production process (and not necessarily only bitumen penetration) had a significant impact on the low-temperature performance of the asphalt mixtures, comparable to the impact of binder modification (neat, polymer-modified, highly modified) and the aggregate skeleton used in the mixture (Stone Mastic Asphalt (SMA) vs. Asphalt Concrete (AC)). Obtained Bending Beam Creep test results were compared with the BBR bitumen test. Regression analysis confirmed that performing solely bitumen tests is insufficient for comprehensive low-temperature performance analysis.

Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach

PubMed Central

Jiang, Guoqian; Solbrig, Harold R.; Prud’hommeaux, Eric; Tao, Cui; Weng, Chunhua; Chute, Christopher G.

2015-01-01

Domain-specific common data elements (CDEs) are emerging as an effective approach to standards-based clinical research data storage and retrieval. A limiting factor, however, is the lack of robust automated quality assurance (QA) tools for the CDEs in clinical study domains. The objectives of the present study are to prototype and evaluate a QA tool for the study of cancer CDEs using a post-coordination approach. The study starts by integrating the NCI caDSR CDEs and The Cancer Genome Atlas (TCGA) data dictionaries in a single Resource Description Framework (RDF) data store. We designed a compositional expression pattern based on the Data Element Concept model structure informed by ISO/IEC 11179, and developed a transformation tool that converts the pattern-based compositional expressions into the Web Ontology Language (OWL) syntax. Invoking reasoning and explanation services, we tested the system utilizing the CDEs extracted from two TCGA clinical cancer study domains. The system could automatically identify duplicate CDEs, and detect CDE modeling errors. In conclusion, compositional expressions not only enable reuse of existing ontology codes to define new domain concepts, but also provide an automated mechanism for QA of terminological annotations for CDEs. PMID:26958201

Autonomic correlates of physical and moral disgust.

PubMed

Ottaviani, Cristina; Mancini, Francesco; Petrocchi, Nicola; Medea, Barbara; Couyoumdjian, Alessandro

2013-07-01

Given that the hypothesis of a common origin of physical and moral disgust has received sparse empirical support, this study aimed to shed light on the subjective and autonomic signatures of these two facets of the same emotional response. Participants (20 men, 20 women) were randomly assigned to physical or moral disgust induction by the use of audio scripts while their electrocardiogram was continuously recorded. Affect ratings were obtained before and after the induction. Time and frequency domain heart rate variability (HRV) measures were obtained. After controlling for disgust sensitivity (DS-R) and obsessive-compulsive (OCI-R) tendencies, both scripts elicited disgust but whereas the physical script elicited a feeling of dirtiness, the moral script evoked more indignation and contempt. The disgust-induced subjective responses were associated with opposite patterns of autonomic reactivity: enhanced activity of the parasympathetic nervous system without concurrent changes in heart rate (HR) for physical disgust and decreased vagal tone and increased HR and autonomic imbalance for moral disgust. Results suggest that immorality relies on the same biological root of physical disgust only in subjects with obsessive compulsive tendencies. Disgust appears to be a heterogeneous response that varies based on the individuals' contamination-based appraisal. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of black rice husk ash on the physical and rheological properties of bitumen

NASA Astrophysics Data System (ADS)

Romastarika, Raissa; Jaya, Ramadhansyah Putra; Yaacob, Haryati; Nazri, Fadzli Mohamed; Agussabti, Ichwana, Jayanti, Dewi Sri

2017-08-01

Black rice husk ash (BRHA) waste product is inexpensive and can be obtained from rice mills. Reuse of waste product is ideal to reduce pollution, because disposal is decreased or eliminated. The commercial value of BRHA has increased, and it is suitable for use in road construction. In this study, BRHA waste was ground using a grinding ball mill for 120 min to form fine powder. BRHA was then sieved to less than 75 µm. At the laboratory, BRHA was mixed with bitumen to replace 2%, 4%, and 6% of the total weight, whereas 0% represented the control sample. The penetration, softening point, dynamic shear rheometer (DSR) and rolling thin film oven (RTFO) were investigated in this study. Results showed that bitumen became harder, whereas the rate of penetration decreased when the replacement amount of BRHA increased. Softening point test of bitumen also revealed an increase. The short-term aging test revealed that modification of bitumen could relieve the effect of aging. BRHA waste added into bitumen improved the performance of bitumen. Therefore, the usage of BRHA could help improve the performance of road pavement and reduce the rutting effect.

Facile Quantification and Identification Techniques for Reducing Gases over a Wide Concentration Range Using a MOS Sensor in Temperature-Cycled Operation.

PubMed

Schultealbert, Caroline; Baur, Tobias; Schütze, Andreas; Sauerwald, Tilman

2018-03-01

Dedicated methods for quantification and identification of reducing gases based on model-based temperature-cycled operation (TCO) using a single commercial MOS gas sensor are presented. During high temperature phases the sensor surface is highly oxidized, yielding a significant sensitivity increase after switching to lower temperatures (differential surface reduction, DSR). For low concentrations, the slope of the logarithmic conductance during this low-temperature phase is evaluated and can directly be used for quantification. For higher concentrations, the time constant for reaching a stable conductance during the same low-temperature phase is evaluated. Both signals represent the reaction rate of the reducing gas on the strongly oxidized surface at this low temperature and provide a linear calibration curve, which is exceptional for MOS sensors. By determining these reaction rates on different low-temperature plateaus and applying pattern recognition, the resulting footprint can be used for identification of different gases. All methods are tested over a wide concentration range from 10 ppb to 100 ppm (4 orders of magnitude) for four different reducing gases (CO, H₂, ammonia and benzene) using randomized gas exposures.

Variation in the biomass density and demography of Antarctic krill in the vicinity of the South Shetland Islands during the 1999/2000 austral summer

NASA Astrophysics Data System (ADS)

Hewitt, R. P.; Kim, S.; Naganobu, M.; Gutierrez, M.; Kang, D.; Takao, Y.; Quinones, J.; Lee, Y.-H.; Shin, H.-C.; Kawaguchi, S.; Emery, J. H.; Demer, D. A.; Loeb, V. J.

2004-06-01

Vessels from Japan, Peru, and the USA conducted four sequential surveys designed to estimate the biomass density and demography of Antarctic krill in the vicinity of the South Shetland Islands between late December 1999 and early March 2000. The surveys were conducted during the same austral summer as the CCAMLR 2000 Survey in the Scotia Sea (Watkins et al., Deep-Sea Research, II, this issue [doi: 10.1016/j.dsr2.2004.06.010]), and the data were analyzed in a similar manner. Biomass densities were not significantly different between the surveys and averaged 49 g m -2. Maps of krill biomass indicate three areas of consistently high density: one near the eastern end of Elephant Island, one mid-way between Elephant Island and King George Island, and one near Cape Shirreff on the north side of Livingston Island. The areas of highest krill density appeared to move closer to the shelf break as the season progressed. This apparent movement was accompanied by a change in the demographic structure of the population, with smaller krill absent and a larger proportion of sexually mature animals present in late summer.

Evaluation of Asphalt Mixture Low-Temperature Performance in Bending Beam Creep Test

PubMed Central

Rys, Dawid; Jaskula, Piotr; Szydlowski, Cezary

2018-01-01

Low-temperature cracking is one of the most common road pavement distress types in Poland. While bitumen performance can be evaluated in detail using bending beam rheometer (BBR) or dynamic shear rheometer (DSR) tests, none of the normalized test methods gives a comprehensive representation of low-temperature performance of the asphalt mixtures. This article presents the Bending Beam Creep test performed at temperatures from −20 °C to +10 °C in order to evaluate the low-temperature performance of asphalt mixtures. Both validation of the method and its utilization for the assessment of eight types of wearing courses commonly used in Poland were described. The performed test indicated that the source of bitumen and its production process (and not necessarily only bitumen penetration) had a significant impact on the low-temperature performance of the asphalt mixtures, comparable to the impact of binder modification (neat, polymer-modified, highly modified) and the aggregate skeleton used in the mixture (Stone Mastic Asphalt (SMA) vs. Asphalt Concrete (AC)). Obtained Bending Beam Creep test results were compared with the BBR bitumen test. Regression analysis confirmed that performing solely bitumen tests is insufficient for comprehensive low-temperature performance analysis. PMID:29320443

Facile Quantification and Identification Techniques for Reducing Gases over a Wide Concentration Range Using a MOS Sensor in Temperature-Cycled Operation

PubMed Central

Schultealbert, Caroline; Baur, Tobias; Schütze, Andreas; Sauerwald, Tilman

2018-01-01

Dedicated methods for quantification and identification of reducing gases based on model-based temperature-cycled operation (TCO) using a single commercial MOS gas sensor are presented. During high temperature phases the sensor surface is highly oxidized, yielding a significant sensitivity increase after switching to lower temperatures (differential surface reduction, DSR). For low concentrations, the slope of the logarithmic conductance during this low-temperature phase is evaluated and can directly be used for quantification. For higher concentrations, the time constant for reaching a stable conductance during the same low-temperature phase is evaluated. Both signals represent the reaction rate of the reducing gas on the strongly oxidized surface at this low temperature and provide a linear calibration curve, which is exceptional for MOS sensors. By determining these reaction rates on different low-temperature plateaus and applying pattern recognition, the resulting footprint can be used for identification of different gases. All methods are tested over a wide concentration range from 10 ppb to 100 ppm (4 orders of magnitude) for four different reducing gases (CO, H2, ammonia and benzene) using randomized gas exposures. PMID:29494545

Perception of tourists regarding the smoke-free policy at Suvarnabhumi International Airport, Bangkok, Thailand.

PubMed

Sirichotiratana, Nithat; Yogi, Subash; Prutipinyo, Chardsumon

2013-08-30

This study was conducted during February-March 2012 to determine the perception and support regarding smoke-free policy among tourists at Suvarnabhumi International Airport, Bangkok, Thailand. In this cross-sectional study, 200 tourists (n = 200) were enrolled by convenience sampling and interviewed by structured questionnaire. Descriptive statistics, chi-square, and multinomial logistic regression were adopted in the study. Results revealed that half (50%) of the tourists were current smokers and 55% had visited Thailand twice or more. Three quarter (76%) of tourists indicated that they would visit Thailand again even if it had a 100% smoke-free regulation. Almost all (99%) of the tourists had supported for the smoke-free policy (partial ban and total ban), and current smokers had higher percentage of support than non-smokers. Two factors, current smoking status and knowledge level, were significantly associated with perception level. After analysis with Multinomial Logistic Regression, it was found that perception, country group, and presence of designated smoking room (DSR) were associated with smoke-free policy. Recommendation is that, at institution level effective monitoring system is needed at the airport. At policy level, the recommendation is that effective comprehensive policy needed to be emphasized to ensure smoke-free airport environment.

Paleoenvironmental reconstruction of lagoonal strata from Sri Lanka using multiple physical properties proxies to assure stratigraphic continuity

NASA Astrophysics Data System (ADS)

Ranasinghage, P. N.; Ortiz, J. D.; Moore, A.; Siriwardana, C.

2009-12-01

Core collapsing is a common problem in studies of lagoonal sediment cores. Coring liquefied sediments below the water table can lead to collapse of material from upper core drives in to the hole. This can be prevented by casing the hole. But casing is not always possible due to practical issues such as coring device type, resources, or time constraints. In such cases identifying the collapsed material in each drive is necessary to ensure accurate results. Direct visual identification of collapsed portion is not always possible and may not be precise. This study successfully recognized collapsed material using a suite of physical properties measurements including: visible (VIS) reflectance spectroscopy, magnetic susceptibility and grain size spectra. This enables us to use the verified stratigraphically continuous records for paleo-environmental studies. Sediment cores were collected from three coastal lagoons and a swale along south eastern and eastern Sri Lanka. Cores were collected using a customized AMS soil coring device with a 1-m long sample barrel. The metal barrel of this instrument collects a 2.5 cm diameter sample in 1-m long plastic tubes. Coring was conducted to refusal, with a maximum depth of 5 m. Casing was not applied to the holes due to small core diameter and time constrains. Drill holes were placed at locations situated both below and above the water level of the lagoons. A total of 100 m of sediment core were obtained from these locations. After opening the cores, suspected collapsed material was initially identified by visual observation using a high power binocular microscope. Particle size, magnetic susceptibility, X-ray fluorescence (XRF) and Diffuse Spectral Reflectance (DSR) was then measured on all cores at 1-2 cm resolution to precisely define the repeated sediment intervals. Down core variation plots of magnetic susceptibility, CIE L* (lightness), a*(red/green difference), b* (blue and yellow difference) clearly record abrupt changes at core drive boundaries at the presence of collapsed material. The correlation of grain-size spectra from the bottom and top of consecutive drives was used to precisely determine the thickness of the collapsed material between drives. Our analysis of 48 m of core material thus far indicates that ~4.4m or ~9% of the record represents collapsed material which can be excluded from further study. The remaining continuous record was analyzed for paleoenvironmental studies. Down core variation of grain size, geochemical ratios, principle components of DSR and geochemical data, and magnetic susceptibility from all locations indicate a gradual filling of these deep lagoons and a transition from reducing to oxic conditions. According to an age model constructed for a nearby lagoon the onset of regression began ~6,000 years BP. Several instantaneous sedimentation events were recorded in all lagoons. Further studies will be carried out to determine whether these represent tsunami, storm surge, or flood deposits.

Calcium and strontium isotope fractionation in aqueous solutions as a function of temperature and reaction rate; I. Calcite

NASA Astrophysics Data System (ADS)

AlKhatib, Mahmoud; Eisenhauer, Anton

2017-07-01

In order to study Strontium (Sr) partitioning and isotope fractionation of Sr and Calcium (Ca) in calcite we performed precipitation (T) experiments decoupling temperature and precipitation rate (R∗). Calcite was precipitated at 12.5, 25.0 and 37.5 °C by diffusing NH3 and CO2 gases into aqueous solutions closely following the experimental setup of Lemarchand et al. (2004). The precipitation rate (R∗) for every sample was determined applying the initial rate method and from the specific surface area of almost all samples for each reaction. The order of reaction with respect to Ca2+ ions was determined to be one and independent of T. However, the order of reaction with respect to HCO3- changed from three to one as temperature increases from 12.5, 25 °C and 37.5 °C. Strontium incorporated into calcite (expressed as DSr = [Sr/Ca]calcite/[Sr/Ca]solution) was found to be R∗ and T dependent. As a function of increasing R∗ the Δ88/86Sr-values become more negative and as temperature increases the Δ88/86Sr values also increase at constant R∗. The DSr and Δ88/86Sr-values are correlated to a high degree and depend only on R∗ being independent of temperature, complexation and varying initial ratios. Latter observation may have important implications for the study of diagenesis, the paleo-sciences and the reconstruction of past environmental conditions. Calcium isotope fractionation (Δ44/40Ca) was also found to be R∗ and T dependent. For 12.5 and 25.0 °C we observe a general increase of the Δ44/40Ca values as a function of R∗ (Lemarchand et al. type behavior, Lemarchand et al. (2004)). Whereas at 37.5 °C a significant decreasing Δ44/40Ca is observed relative to increasing R∗ (Tang et al. type behavior, Tang et al. (2008)). In order to reconcile the discrepant observations we suggest that the temperature triggered change from a Ca2+-NH3-aquacomplex covalent controlled bonding to a Ca2+-H2O-aquacomplex van-der-Waals controlled bonding caused the change in sign of the R∗ - Δ44/40Ca slope due to the switch of an equilibrium type of isotope fractionation related to the covalent bonding during lower temperatures to a kinetic type of isotope fractionation at higher temperatures. This is supported by the observation that the Δ44/40Ca ratios tend to depend on the [Ca]:[DIC] ratio at 12.5 and 25 °C but is highly independent at 37.5 °C. Our observations imply the chemical fluid composition and temperature dependent complexation controls the amount and direction of Ca isotope fractionation in contrast to the Sr isotopes which do not show any change of its fractionation behavior as a function of complexation in the liquid phase.

Quantitative digital subtraction radiography in the assessment of external apical root resorption induced by orthodontic therapy: a retrospective study.

PubMed

Sunku, Raghavendra; Roopesh, R; Kancherla, Pavan; Perumalla, Kiran Kumar; Yudhistar, Palla Venkata; Reddy, V Sridhar

2011-11-01

The objective of this study was to evaluate density changes around the apices of teeth during orthodontic treatment by using digital subtraction radiography to measure the densities around six teeth (maxilla central incisors, lateral incisors, and canines) before and after orthodontic treatment in 36 patients and also assess treatment variables and their coorelation with root resorption. A total of 36 consecutive patient files were selected initially. The selected patients presented with a class I or II relationship and were treated with or without premolar extractions and fixed appliances. Some class II patients were treated additionally with extraoral forces or functional appliances. External apical root resorption (EARR) per tooth in millimeters was calculated and was also expressed as a percentage of the original root length. Image reconstruction and subtraction were performed using the software Regeemy Image Registration and Mosaicing (version 0.2.43-RCB, DPI-INPE, Sao Jose dos Campos, Sao Paulo, Brazil) by a single operator. A region of interest (ROI) was defined in the apical third of the root and density calibration was made in Image J® using enamel (gray value = 255) as reference in the same image. The mean gray values in the ROIs were reflective of the change in the density values between the two images. The root resorption of the tooth and the factors of malocclusion were analyzed with a one-way ANOVA. An independent t-test was performed to compare the mean amount of resorption between male and female, between extraction and nonextraction cases. The density changes after orthodontic treatment were analyzed using the Wilcoxon signedrank test. In addition, the density changes in different teeth were analyzed using the Kruskal-Wallis test. The cut-off for statistical significance was a p-value of 0.05. All the statistical analyses were carried out using SPSS (version 13.0 for Windows, Chicago, IL, USA). Gender, the age at which treatment was started and Angle's classification was not statistically related with observed root resorption. The mean percentage density reduction as assessed by DSR was greatest in both central incisor: by 27.2 and 25.2% in the upper-right and upper-left central incisors, respectively, followed by the upper-right and upper-left canine teeth (23.5 and 21.0%) and then the upper-right and upper-left lateral incisors (19.1 and 17.4%). Tooth extraction prior to treatment initiation and the duration of orthodontic treatment was positively correlated with the amount of root resorption. DSR is useful for evaluating density changes around teeth during orthodontic treatment. The density around the apices of teeth reduced significantly after the application of orthodontic forces during treatment. Assessment of density changes on treatment radiographs of patients undergoing orthodontic therapy may help in the monitoring of external apical root resorption during course of treatment.

Why humans do not make good vampires. Testing the ability of humans to detect true blood.

PubMed

De Smet, Delphine; Van Speybroeck, Linda; Verplaetse, Jan

2012-01-01

Research indicating the effects of real blood or of its iconic representation on human behaviour has thus far concentrated on phobia and aggressiveness. Little is known about other responses or, more fundamentally, about the biological basis of all such responses. In this study it is examined whether or not humans are able to detect real blood. Human subjects (n = 89) were asked to distinguish different kinds of blood from red control fluids under varying visual and choice conditions. Relevant differences between subjects were tested for through written questionnaires, including standardized scales for disgust sensitivity (DS-R) and blood phobia (MBPI) and performance on two clinical olfactory tests. Analysis of variance shows that humans are excellent detectors of animal blood (in casu pig blood), whereas the ability of detecting human blood is much less developed. Surprisingly, differences in olfactory capacities and personal experience with blood have no effect on blood detection, while blood fear lowers and disgust sensitivity ameliorates this performance. This study allows further mapping of the exact role of disgust sensitivity in human behaviour, as well as a deliberate choice of materials in blood-related experiments. It is imperative for further research on the behavioural and psychological impact 'blood' resorts on humans.

Desulfatiferula berrensis sp. nov., a n-alkene-degrading sulfate-reducing bacterium isolated from estuarine sediments.

PubMed

Hakil, Florence; Amin-Ali, Oulfat; Hirschler-Réa, Agnès; Mollex, Damien; Grossi, Vincent; Duran, Robert; Matheron, Robert; Cravo-Laureau, Cristiana

2014-02-01

A novel sulfate-reducing bacterium designated strain BE2801(T) was isolated from oil-polluted estuarine sediments (Berre Lagoon, France). Cells were Gram-stain-negative, motile, slightly curved or vibrioid rods. Optimal growth of strain BE2801(T) occurred at 30-32 °C, 0.5-1.5% NaCl (w/v) and pH 7.2-7.4. Strain BE2801(T) grew with C4 to C20 fatty acids or C12 to C20 n-alkenes as electron donors. Acetate and carbon dioxide were the oxidation products. The major cellular fatty acids were C16 : 0, C(16 : 1)ω7c and C(18 : 1)ω7. The DNA G+C content was 50.2 mol%. 16S rRNA and dsrAB gene sequence analysis indicated that strain BE2801(T) was a member of the family Desulfobacteraceae within the class Deltaproteobacteria. DNA-DNA hybridization with the most closely related taxon demonstrated 14.8 % relatedness. Based on phenotypic and phylogenetic evidence, strain BE2801(T) ( = DSM 25524(T) = JCM 18157(T)) is proposed to be a representative of a novel species of the genus Desulfatiferula, for which the name Desulfatiferula berrensis sp. nov. is suggested.

An approach to the usage of polyethylene terephthalate (PET) waste as roadway pavement material.

PubMed

Gürü, Metin; Çubuk, M Kürşat; Arslan, Deniz; Farzanian, S Ali; Bilici, İbrahim

2014-08-30

This study investigates an application area for Polyethylene Terephthalate (PET) bottle waste which has become an environmental problem in recent decades as being a considerable part of the total plastic waste bulk. Two novel additive materials, namely Thin Liquid Polyol PET (TLPP) and Viscous Polyol PET (VPP), were chemically derived from waste PET bottles and used to modify the base asphalt separately for this aim. The effects of TLPP and VPP on the asphalt and hot mix asphalt (HMA) mixture properties were detected through conventional tests (Penetration, Softening Point, Ductility, Marshall Stability, Nicholson Stripping) and Superpave methods (Rotational Viscosity, Dynamic Shear Rheometer (DSR), Bending Beam Rheometer (BBR)). Also, chemical structures were described by Scanning Electron Microscope (SEM) equipped with Energy Dispersive Spectrometer (EDS) and Fourier Transform Infrared (FTIR) techniques. Since TLPP and VPP were determined to improve the low temperature performance and fatigue resistance of the asphalt as well as the Marshall Stability and stripping resistance of the HMA mixtures based on the results of the applied tests, the usage of PET waste as an asphalt roadway pavement material offers an alternative and a beneficial way of disposal of this ecologically hazardous material. Copyright © 2014 Elsevier B.V. All rights reserved.

Performance analysis of routing protocols for IoT

NASA Astrophysics Data System (ADS)

Manda, Sridhar; Nalini, N.

2018-04-01

Internet of Things (IoT) is an arrangement of advancements that are between disciplinary. It is utilized to have compelling combination of both physical and computerized things. With IoT physical things can have personal virtual identities and participate in distributed computing. Realization of IoT needs the usage of sensors based on the sector for which IoT is integrated. For instance, in healthcare domain, IoT needs to have integration with wearable sensors used by patients. As sensor devices produce huge amount of data, often called big data, there should be efficient routing protocols in place. To the extent remote systems is worried there are some current protocols, for example, OLSR, DSR and AODV. It additionally tosses light into Trust based routing protocol for low-power and lossy systems (TRPL) for IoT. These are broadly utilized remote directing protocols. As IoT is developing round the corner, it is basic to investigate routing protocols that and evaluate their execution regarding throughput, end to end delay, and directing overhead. The execution experiences can help in settling on very much educated choices while incorporating remote systems with IoT. In this paper, we analyzed different routing protocols and their performance is compared. It is found that AODV showed better performance than other routing protocols aforementioned.

Experiences of offspring searching for and contacting their donor siblings and donor.

PubMed

Jadva, Vasanti; Freeman, Tabitha; Kramer, Wendy; Golombok, Susan

2010-04-01

This study investigates a new phenomenon whereby individuals conceived by donor insemination are searching for and contacting their donor and/or 'donor siblings' (i.e. donor offspring conceived by the same donor who are their genetic half siblings). On-line questionnaires were completed by members of the Donor Sibling Registry (DSR), a US-based registry that facilitates contact between donor conception families who share the same donor. Of the 165 donor offspring who completed the survey, 15% were searching for their donor siblings, 13% were searching for their donor, and 64% were searching for both. Differences were found according to family type and age of disclosure. Fewer offspring from heterosexual couple families had told their father about their search when compared with offspring from lesbian couple families who had told their co-parent. Offspring who had found out about their conception after age 18 were more likely to be searching for medical reasons, whereas those who had found out before age 18 tended to be searching out of curiosity. Some offspring had discovered large numbers of half siblings (maximum=13). The majority of offspring who had found their donor relations reported positive experiences and remained in regular contact with them. Copyright (c) 2010 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Mathematical modeling of simultaneous carbon-nitrogen-sulfur removal from industrial wastewater.

PubMed

Xu, Xi-Jun; Chen, Chuan; Wang, Ai-Jie; Ni, Bing-Jie; Guo, Wan-Qian; Yuan, Ye; Huang, Cong; Zhou, Xu; Wu, Dong-Hai; Lee, Duu-Jong; Ren, Nan-Qi

2017-01-05

A mathematical model of carbon, nitrogen and sulfur removal (C-N-S) from industrial wastewater was constructed considering the interactions of sulfate-reducing bacteria (SRB), sulfide-oxidizing bacteria (SOB), nitrate-reducing bacteria (NRB), facultative bacteria (FB), and methane producing archaea (MPA). For the kinetic network, the bioconversion of C-N by heterotrophic denitrifiers (NO 3 - →NO 2 - →N 2 ), and that of C-S by SRB (SO 4 2- →S 2- ) and SOB (S 2- →S 0 ) was proposed and calibrated based on batch experimental data. The model closely predicted the profiles of nitrate, nitrite, sulfate, sulfide, lactate, acetate, methane and oxygen under both anaerobic and micro-aerobic conditions. The best-fit kinetic parameters had small 95% confidence regions with mean values approximately at the center. The model was further validated using independent data sets generated under different operating conditions. This work was the first successful mathematical modeling of simultaneous C-N-S removal from industrial wastewater and more importantly, the proposed model was proven feasible to simulate other relevant processes, such as sulfate-reducing, sulfide-oxidizing process (SR-SO) and denitrifying sulfide removal (DSR) process. The model developed is expected to enhance our ability to predict the treatment of carbon-nitrogen-sulfur contaminated industrial wastewater. Copyright © 2016 Elsevier B.V. All rights reserved.

Host-pathogen interplay of Haemophilus ducreyi.

PubMed

Janowicz, Diane M; Li, Wei; Bauer, Margaret E

2010-02-01

Haemophilus ducreyi, the causative agent of the sexually transmitted infection chancroid, is primarily a pathogen of human skin. During infection, H. ducreyi thrives extracellularly in a milieu of professional phagocytes and other antibacterial components of the innate and adaptive immune responses. This review summarizes our understanding of the interplay between this pathogen and its host that leads to development and persistence of disease. H. ducreyi expresses key virulence mechanisms to resist host defenses. The secreted LspA proteins are tyrosine-phosphorylated by host kinases, which may contribute to their antiphagocytic effector function. The serum resistance and adherence functions of DsrA map to separate domains of this multifunctional virulence factor. An influx transporter protects H. ducreyi from killing by the antimicrobial peptide LL37. Regulatory genes have been identified that may coordinate virulence factor expression during disease. Dendritic cells and natural killer cells respond to H. ducreyi and may be involved in determining the differential outcomes of infection observed in humans. A human model of H. ducreyi infection has provided insights into virulence mechanisms that allow this human-specific pathogen to survive immune pressures. Components of the human innate immune system may also determine the ultimate fate of H. ducreyi infection by driving either clearance of the organism or an ineffective response that allows disease progression.

Determination of band gap in epitaxial delafossite Cu oxide using optical techniques

NASA Astrophysics Data System (ADS)

Cabrera, Alejandro; Wheatley, R.; Seifert, B.; Wallentowitz, S.; Joshi, T.; Lederman, D.

Highly epitaxial delafossite CuFeO2 and CuFe1-xGaxO2 films were grown using Pulsed Laser Deposition techniques. The sample thicknesses were estimated to be 21 nm, 75 nm.The estimated gallium fraction of substituted ferric atoms was x =0.25 for the composite sample. We present the study of the fundamental band gap(s) for each sample via observation of their respective optical absorption properties in the NIR-VIS region using transmittance and diffuse reflection spectroscopy. Predominant absorption edges measured were between 1.1eV and 3.1eV from transmittance spectra. The sample of CuFe1-xGaxO2 showed measurable absorption features located at 2.4eV and 2.8eV. This study also found evidence of changes between apparent absorption edges between transmittance and diffuse reflectance spectroscopies of each sample and it may be resultant from absorption channels via surface states. Future photoluminescence experiments are planned to determine the photo-induced semiconductor behavior of these materials. ACNOWLEDGEMENTS: This work was supported by FONDECyT 1130372 and Proyecto Anillo ACT1409 at PUC and supported in part by the WV Higher Education Policy Commission (Grant HEPC.dsr.12.29) and by FAME sponsored by MARCO and DARPA (contract # 2013-MA-2382).

Generation and evolution of mode-locked noise-like square-wave pulses in a large-anomalous-dispersion Er-doped ring fiber laser.

PubMed

Liu, Jun; Chen, Yu; Tang, Pinghua; Xu, Changwen; Zhao, Chujun; Zhang, Han; Wen, Shuangchun

2015-03-09

In a passively mode-locked Erbium-doped fiber laser with large anomalous-dispersion, we experimentally demonstrate the formation of noise-like square-wave pulse, which shows quite different features from conventional dissipative soliton resonance (DSR). The corresponding temporal and spectral characteristics of a variety of operation states, including Q-switched mode-locking, continuous-wave mode-locking and Raman-induced noise-like pulse near the lasing threshold, are also investigated. Stable noise-like square-wave mode-locked pulses can be obtained at a fundamental repetition frequency of 195 kHz, with pulse packet duration tunable from 15 ns to 306 ns and per-pulse energy up to 200 nJ. By reducing the linear cavity loss, stable higher-order harmonic mode-locking had also been observed, with pulse duration ranging from 37 ns at the 21st order harmonic wave to 320 ns at the fundamental order. After propagating along a piece of long telecom fiber, the generated square-wave pulses do not show any obvious change, indicating that the generated noise-like square-wave pulse can be considered as high-energy pulse packet for some promising applications. These experimental results should shed some light on the further understanding of the mechanism and characteristics of noise-like square-wave pulses.

Perception of Tourists Regarding the Smoke-Free Policy at Suvarnabhumi International Airport, Bangkok, Thailand

PubMed Central

Sirichotiratana, Nithat; Yogi, Subash; Prutipinyo, Chardsumon

2013-01-01

This study was conducted during February-March 2012 to determine the perception and support regarding smoke-free policy among tourists at Suvarnabhumi International Airport, Bangkok, Thailand. In this cross-sectional study, 200 tourists (n = 200) were enrolled by convenience sampling and interviewed by structured questionnaire. Descriptive statistics, chi-square, and multinomial logistic regression were adopted in the study. Results revealed that half (50%) of the tourists were current smokers and 55% had visited Thailand twice or more. Three quarter (76%) of tourists indicated that they would visit Thailand again even if it had a 100% smoke-free regulation. Almost all (99%) of the tourists had supported for the smoke-free policy (partial ban and total ban), and current smokers had higher percentage of support than non-smokers. Two factors, current smoking status and knowledge level, were significantly associated with perception level. After analysis with Multinomial Logistic Regression, it was found that perception, country group, and presence of designated smoking room (DSR) were associated with smoke-free policy. Recommendation is that, at institution level effective monitoring system is needed at the airport. At policy level, the recommendation is that effective comprehensive policy needed to be emphasized to ensure smoke-free airport environment. PMID:23999549

Multiferroic fluoride BaCoF4 Thin Films Grown Via Molecular Beam Epitaxy

NASA Astrophysics Data System (ADS)

Borisov, Pavel; Johnson, Trent; García-Castro, Camilo; Kc, Amit; Schrecongost, Dustin; Cen, Cheng; Romero, Aldo; Lederman, David

Multiferroic materials exhibit exciting physics related to the simultaneous presence of multiple long-range orders, in many cases consisting of antiferromagnetic (AF) and ferroelectric (FE) orderings. In order to provide a new, promising route for fluoride-based multiferroic material engineering, we grew multiferroic fluoride BaCoF4 in thin film form on Al2O3 (0001) substrates by molecular beam epitaxy. The films grow with the orthorhombic b-axis out-of-plane and with three in-plane structural twin domains along the polar c-axis directions. The FE ordering in thin films was verified by FE remanent hysteresis loops measurements at T = 14 K and by room temperature piezoresponse force microscopy (PFM). An AF behavior was found below Neel temperature TN ~ 80 K, which is in agreement with the bulk properties. At lower temperatures two additional magnetic phase transitions at 19 K and 41 K were found. First-principles calculations demonstrated that the growth strain applied to the bulk BaCoF4 indeed favors two canted spin orders, along the b- and a-axes, respectively, in addition to the main AF spin order along the c-axis. Supported by FAME (Contract 2013-MA-2382), WV Research Challenge Grant (HEPC.dsr.12.29), and DMREF-NSF 1434897.

Effect of Combined Use of Calcium and Vitamin B6 on Premenstrual Syndrome Symptoms: a Randomized Clinical Trial.

PubMed

Masoumi, Seyedeh Zahra; Ataollahi, Maryam; Oshvandi, Khodayar

2016-03-01

Premenstrual syndrome is one of the most common disorders in women, which includes a group of psychological and physical symptoms. The aim of this study was to examine the impact of combined use of calcium and vitamin B6 on premenstrual syndrome symptoms. This double blind randomized controlled was carried out on 76 students of Hamadan University of Medical Sciences. Students were randomly allocated to two groups. (38 people in each group). Student in intervention groups received calcium tablet (500mg) and vitamin B6 (40 mg) and student in intervention groups received only vitamin B6 twice a day for two consecutive months. The symptoms were assessed by Beck depression inventory (BDI) and daily symptom records (DSR) questionnaires. Analyses were carried out by test-retest method, Chi-square, Mann-Whitney, Independent t-test, and paired t-test using SPSS software ver.13. Results The result showed that although the severity of symptoms decreased in both groups, but this reduction was more significant in the combined calcium and vitamin B6 group. According to the result, using of combination of calcium and vitamin B6 leads to better controlling of the premenstrual syndrome symptoms. Therefore it is recommended for women who suffer from these syndromes.

A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries.

PubMed

Webster, Gordon; Watt, Lynsey C; Rinna, Joachim; Fry, John C; Evershed, Richard P; Parkes, R John; Weightman, Andrew J

2006-09-01

Marine sediment slurries enriched for anaerobic, sulfate-reducing prokaryotic communities utilizing glucose and acetate were used to provide the first comparison between stable-isotope probing (SIP) of phospholipid fatty acids (PLFA) and DNA (16S rRNA and dsrA genes) biomarkers. Different 13C-labelled substrates (glucose, acetate and pyruvate) at low concentrations (100 microM) were used over a 7-day incubation to follow and identify carbon flow into different members of the community. Limited changes in total PLFA and bacterial 16S rRNA gene DGGE profiles over 7 days suggested the presence of a stable bacterial community. A broad range of PLFA were rapidly labelled (within 12 h) in the 13C-glucose slurry but this changed with time, suggesting the presence of an active glucose-utilizing population and later development of another population able to utilize glucose metabolites. The identity of the major glucose-utilizers was unclear as 13C-enriched PLFA were common (16:0, 16:1, 18:1omega7, highest incorporation) and there was little difference between 12C- and 13C-DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. Seemingly glucose, a readily utilizable substrate, resulted in widespread incorporation consistent with the higher extent of 13C-incorporation (approximately 10 times) into PLFA compared with 13C-acetate or 13C-pyruvate. 13C-PLFA in the 13C-acetate and 13C-pyruvate slurries were similar to each other and to those that developed in the 13C-glucose slurry after 4 days. These were more diagnostic, with branched odd-chain fatty acids (i15:0, a15:0 and 15:1omega6) possibly indicating the presence of Desulfococcus or Desulfosarcina sulfate-reducing bacteria (SRB) and sequences related to these SRB were in the 13C-acetate-DNA dsrA gene library. The 13C-acetate-DNA 16S rRNA gene library also contained sequences closely related to SRB, but these were the acetate-utilizing Desulfobacter sp., as well as a broad range of uncultured Bacteria. In contrast, analysis of DGGE bands from 13C-DNA demonstrated that the candidate division JS1 and Firmicutes were actively assimilating 13C-acetate. Denaturing gradient gel electrophoresis also confirmed the presence of JS1 in the 13C-DNA from the 13C-glucose slurry. These results demonstrate that JS1, originally found in deep subsurface sediments, is more widely distributed in marine sediments and provides the first indication of its metabolism; incorporation of acetate and glucose (or glucose metabolites) under anaerobic, sulfate-reducing conditions. Here we demonstrate that PLFA- and DNA-SIP can be used together in a sedimentary system, with low concentrations of 13C-substrate and overlapping incubation times (up to 7 days) to provide complementary, although not identical, information on carbon flow and the identity of active members of an anaerobic prokaryotic community.

Subcellular localization of proteins in the anaerobic sulfate reducer Desulfovibrio vulgaris via SNAP-tag labeling and photoconversion

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

Gorur, A.; Leung, C. M.; Jorgens, D.

2010-06-01

Systems Biology studies the temporal and spatial 3D distribution of macromolecular complexes with the aim that such knowledge will allow more accurate modeling of biological function and will allow mathematical prediction of cellular behavior. However, in order to accomplish accurate modeling precise knowledge of spatial 3D organization and distribution inside cells is necessary. And while a number of macromolecular complexes may be identified by its 3D structure and molecular characteristics alone, the overwhelming number of proteins will need to be localized using a reporter tag. GFP and its derivatives (XFPs) have been traditionally employed for subcelllar localization using photoconversion approaches,more » but this approach cannot be taken for obligate anaerobic bacteria, where the intolerance towards oxygen prevents XFP approaches. As part of the GTL-funded PCAP project (now ENIGMA) genetic tools have been developed for the anaerobe sulfate reducer Desulfovibrio vulgaris that allow the high-throughput generation of tagged-protein mutant strains, with a focus on the commercially available SNAP-tag cell system (New England Biolabs, Ipswich, MA), which is based on a modified O6-alkylguanine-DNA alkyltransferase (AGT) tag, that has a dead-end reaction with a modified O6-benzylguanine (BG) derivative and has been shown to function under anaerobic conditions. After initial challenges with respect to variability, robustness and specificity of the labeling signal we have optimized the labeling. Over the last year, as a result of the optimized labeling protocol, we now obtain robust labeling of 20 out of 31 SNAP strains. Labeling for 13 strains were confirmed at least five times. We have also successfully performed photoconversion on 5 of these 13 strains, with distinct labeling patterns for different strains. For example, DsrC robustly localizes to the periplasmic portion of the inner membrane, where as a DNA-binding protein localizes to the center of the cell, where the chromosome is located. Two other proteins - Thiosulfate reductase and ATP binding protein were found to be cytoplasmically distributed, whereas a molybdenum transporter was found to locate to the cell periphery. We judge labeling outcome by (1) SDS gel electrophoresis, followed by direct fluorescence imaging of the gel to address specificity of labeling/confirm expected molecular weight, and subsequent Coomassie analysis to ensure comparable protein levels (2) fluorescence intensity of culture by plate reader for statistical sampling (after adjustment for respective cell numbers) and (3) fluorescence microscopy for addressing cell-to-cell signal variation and potential localization patterns. All three assays were usually found to be consistent with one another. While we have been able to improve the efficacy of photoconversion by drastically reducing (eliminating) non-specific binding with our altered labeling protocol, we are currently working on reducing non-specific photoconversion reaction arising occasionally in non-labeled cells. In addition, we have confirmed the presence of SNAP tagged constructs in three recently cloned E.coli strains under promotor control, and are in the process of utilizing them for evaluating the sensitivity of the photoconversion protocol. Fluorescent Activated Cell Sorting was successfully applied to labeled E.coli cells containing SNAP tagged AtpA protein. Different batches of sorted cells, representing low and high labeling intensity, were re-grown and re-labeled and displayed a labeling efficiency similar to the starter culture, supporting the notion that cell-to-cell differences in labeling reflect difference in protein expression, rather then genetic differences.« less

The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow.

PubMed

Nobu, Masaru K; Narihiro, Takashi; Hideyuki, Tamaki; Qiu, Yan-Ling; Sekiguchi, Yuji; Woyke, Tanja; Goodwin, Lynne; Davenport, Karen W; Kamagata, Yoichi; Liu, Wen-Tso

2015-12-01

How aromatic compounds are degraded in various anaerobic ecosystems (e.g. groundwater, sediments, soils and wastewater) is currently poorly understood. Under methanogenic conditions (i.e. groundwater and wastewater treatment), syntrophic metabolizers are known to play an important role. This study explored the draft genome of Syntrophorhabdus aromaticivorans strain UI and identified the first syntrophic phenol-degrading phenylphosphate synthase (PpsAB) and phenylphosphate carboxylase (PpcABCD) and syntrophic terephthalate-degrading decarboxylase complexes. The strain UI genome also encodes benzoate degradation through hydration of the dienoyl-coenzyme A intermediate as observed in Geobacter metallireducens and Syntrophus aciditrophicus. Strain UI possesses electron transfer flavoproteins, hydrogenases and formate dehydrogenases essential for syntrophic metabolism. However, the biochemical mechanisms for electron transport between these H2 /formate-generating proteins and syntrophic substrate degradation remain unknown for many syntrophic metabolizers, including strain UI. Analysis of the strain UI genome revealed that heterodisulfide reductases (HdrABC), which are poorly understood electron transfer genes, may contribute to syntrophic H2 and formate generation. The genome analysis further identified a putative ion-translocating ferredoxin : NADH oxidoreductase (IfoAB) that may interact with HdrABC and dissimilatory sulfite reductase gamma subunit (DsrC) to perform novel electron transfer mechanisms associated with syntrophic metabolism. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

A Scoping Review of Empirical Research Relating to Quality and Effectiveness of Research Ethics Review.

PubMed

Nicholls, Stuart G; Hayes, Tavis P; Brehaut, Jamie C; McDonald, Michael; Weijer, Charles; Saginur, Raphael; Fergusson, Dean

2015-01-01

To date there is no established consensus of assessment criteria for evaluating research ethics review. We conducted a scoping review of empirical research assessing ethics review processes in order to identify common elements assessed, research foci, and research gaps to aid in the development of assessment criteria. Electronic searches of Ovid Medline, PsychInfo, and the Cochrane DSR, ACP Journal Club, DARE, CCTR, CMR, HTA, and NHSEED, were conducted. After de-duplication, 4234 titles and abstracts were reviewed. Altogether 4036 articles were excluded following screening of titles, abstracts and full text. A total of 198 articles included for final data extraction. Few studies originated from outside North America and Europe. No study reported using an underlying theory or framework of quality/effectiveness to guide study design or analyses. We did not identify any studies that had involved a controlled trial--randomised or otherwise--of ethics review procedures or processes. Studies varied substantially with respect to outcomes assessed, although tended to focus on structure and timeliness of ethics review. Our findings indicate a lack of consensus on appropriate assessment criteria, exemplified by the varied study outcomes identified, but also a fragmented body of research. To date research has been largely quantitative, with little attention given to stakeholder experiences, and is largely cross sectional. A lack of longitudinal research to date precludes analyses of change or assessment of quality improvement in ethics review.

Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park

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

Hamilton-Brehm, Scott D.; Gibson, Robert A.; Green, Stefan J.

2013-01-24

A novel sulfate-reducing bacterium designated OPF15T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70 90 C and an optimum of 83 C. Optimal pH was around 6.5 7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve asmore » electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15T was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15T representing the type strain.« less

Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park.

PubMed

Hamilton-Brehm, Scott D; Gibson, Robert A; Green, Stefan J; Hopmans, Ellen C; Schouten, Stefan; van der Meer, Marcel T J; Shields, John P; Damsté, Jaap S S; Elkins, James G

2013-03-01

A novel sulfate-reducing bacterium designated OPF15(T) was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15(T) was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15(T) representing the type strain.

Combined 34S, 33S and 18O isotope fractionations record different intracellular steps of microbial sulfate reduction

NASA Astrophysics Data System (ADS)

Antler, Gilad; Turchyn, Alexandra V.; Ono, Shuhei; Sivan, Orit; Bosak, Tanja

2017-04-01

Several enzymatic steps in microbial sulfate reduction (MSR) fractionate the isotope ratios of 33S/32S, 34S/32S and 18O/16O in extracellular sulfate, but the effects of different intracellular processes on the isotopic composition of residual sulfate are still not well quantified. We measured combined multiple sulfur (33S/32S, 34S/32S) and oxygen (18O/16O) isotope ratios of sulfate in pure cultures of a marine sulfate reducing bacterium Desulfovibrio sp. DMSS-1 grown on different organic substrates. These measurements are consistent with the previously reported correlations of oxygen and sulfur isotope fractionations with the cell-specific rate of MSR: faster reduction rates produced smaller isotopic fractionations for all isotopes. Combined isotope fractionation of oxygen and multiple sulfur isotopes are also consistent with the relationship between the rate limiting step during microbial sulfate reduction and the availability of the DsrC subunit. These experiments help reconstruct and interpret processes that operate in natural pore waters characterized by high 18O/16O and moderate 34S/32S ratios and suggest that some multiple isotope signals in the environment cannot be explained by microbial sulfate reduction alone. Instead, these signals support the presence of active, but slow sulfate reduction as well as the reoxidation of sulfide.

Combining in situ chemical oxidation, stabilization, and anaerobic bioremediation in a single application to reduce contaminant mass and leachability in soil.

PubMed

Cassidy, Daniel P; Srivastava, Vipul J; Dombrowski, Frank J; Lingle, James W

2015-10-30

Laboratory batch reactors were maintained for 32 weeks to test the potential for an in situ remedy that combines chemical oxidation, stabilization, and anaerobic bioremediation in a single application to treat soil from a manufactured gas plant, contaminated with polycyclic aromatic hydrocarbons (PAH) and benzene, toluene, ethylbenzene, and xylenes (BTEX). Portland cement and slaked lime were used to activate the persulfate and to stabilize/encapsulate the contaminants that were not chemically oxidized. Native sulfate-reducing bacteria degraded residual contaminants using the sulfate left after persulfate activation. The ability of the combined remedy to reduce contaminant mass and leachability was compared with NaOH-activated persulfate, stabilization, and sulfate-reducing bioremediation as stand-alone technologies. The stabilization amendments increased pH and temperature sufficiently to activate the persulfate within 1 week. Activation with both stabilization amendments and NaOH removed between 55% and 70% of PAH and BTEX. However, combined persulfate and stabilization significantly reduced the leachability of residual BTEX and PAH compared with NaOH activation. Sulfide, 2-naphthoic acid, and the abundance of subunit A of the dissimilatory sulfite reductase gene (dsrA) were used to monitor native sulfate-reducing bacteria, which were negatively impacted by activated persulfate, but recovered completely within weeks. Copyright © 2015 Elsevier B.V. All rights reserved.

Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation.

PubMed

Hücker, Sarah Maria; Simon, Svenja; Scherer, Siegfried; Neuhaus, Klaus

2017-01-01

The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively. Indeed, cold and osmotic stress related genes are simultaneously regulated at both levels, but translational regulation clearly dominates. Special emphasis was given to genes regulated by RNA secondary structures in their 5 ' UTRs, such as RNA thermometers and riboswitches, or genes controlled by small RNAs encoded in trans The results reveal large differences in gene expression between short-time shock compared to adaptation in combined cold and osmotic stress. Whereas the majority of cold shock proteins, such as CspA, are translationally downregulated after adaptation, many osmotic stress genes are still significantly upregulated mainly translationally, but several also transcriptionally. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307)

PubMed Central

Webster, Gordon; Blazejak, Anna; Cragg, Barry A; Schippers, Axel; Sass, Henrik; Rinna, Joachim; Tang, Xiaohong; Mathes, Falko; Ferdelman, Timothy G; Fry, John C; Weightman, Andrew J; Parkes, R John

2009-01-01

The Porcupine Seabight Challenger Mound is the first carbonate mound to be drilled (∼270 m) and analyzed in detail microbiologically and biogeochemically. Two mound sites and a non-mound Reference site were analyzed with a range of molecular techniques [catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative PCR (16S rRNA and functional genes, dsrA and mcrA), and 16S rRNA gene PCR-DGGE] to assess prokaryotic diversity, and this was compared with the distribution of total and culturable cell counts, radiotracer activity measurements and geochemistry. There was a significant and active prokaryotic community both within and beneath the carbonate mound. Although total cell numbers at certain depths were lower than the global average for other subseafloor sediments and prokaryotic activities were relatively low (iron and sulfate reduction, acetate oxidation, methanogenesis) they were significantly enhanced compared with the Reference site. In addition, there was some stimulation of prokaryotic activity in the deepest sediments (Miocene, > 10 Ma) including potential for anaerobic oxidation of methane activity below the mound base. Both Bacteria and Archaea were present, with neither dominant, and these were related to sequences commonly found in other subseafloor sediments. With an estimate of some 1600 mounds in the Porcupine Basin alone, carbonate mounds may represent a significant prokaryotic subseafloor habitat. PMID:18826439

Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

PubMed Central

Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.; Peacock, Aaron D.; Deng, Ye; Long, Philip E.; Resch, C. Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C.; Lovley, Derek R.

2012-01-01

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

Molecular phylogenetic analysis of non-sexually transmitted strains of Haemophilus ducreyi.

PubMed

Gaston, Jordan R; Roberts, Sally A; Humphreys, Tricia L

2015-01-01

Haemophilus ducreyi, the etiologic agent of chancroid, has been previously reported to show genetic variance in several key virulence factors, placing strains of the bacterium into two genetically distinct classes. Recent studies done in yaws-endemic areas of the South Pacific have shown that H. ducreyi is also a major cause of cutaneous limb ulcers (CLU) that are not sexually transmitted. To genetically assess CLU strains relative to the previously described class I, class II phylogenetic hierarchy, we examined nucleotide sequence diversity at 11 H. ducreyi loci, including virulence and housekeeping genes, which encompass approximately 1% of the H. ducreyi genome. Sequences for all 11 loci indicated that strains collected from leg ulcers exhibit DNA sequences homologous to class I strains of H. ducreyi. However, sequences for 3 loci, including a hemoglobin receptor (hgbA), serum resistance protein (dsrA), and a collagen adhesin (ncaA) contained informative amounts of variation. Phylogenetic analyses suggest that these non-sexually transmitted strains of H. ducreyi comprise a sub-clonal population within class I strains of H. ducreyi. Molecular dating suggests that CLU strains are the most recently developed, having diverged approximately 0.355 million years ago, fourteen times more recently than the class I/class II divergence. The CLU strains' divergence falls after the divergence of humans from chimpanzees, making it the first known H. ducreyi divergence event directly influenced by the selective pressures accompanying human hosts.

Pulsed Laser Deposition Growth of Delafossite (CuFeO2) thin films and multilayers

NASA Astrophysics Data System (ADS)

Joshi, Toyanath; Ferrari, Piero; Borisov, Pavel; Cabrera, Alejandro; Lederman, David

2014-03-01

Owing to its narrow band gap (<2 eV) and p-type conductivity delafossite CuFeO2 is attractive for applications in the field of solar energy conversion. Obtaining pure phase CuFeO2 thin films, however, is relatively difficult. It is necessary to maintain the lowest possible Cu valency (+1) in order to avoid forming the comparably stable spinel compound CuFe2O4. We present a systematic study of the pulsed laser deposition (PLD) growth conditions for epitaxial (00.1) oriented CuFeO2 thin films on Al2O3 (00.1) substrates. The secondary impurity phase, CuFe2O4, was removed completely by optimizing the growth conditions. RHEED, XRD and TEM showed that the pure phase delafossite films are highly epitaxial to the substrate. The chemical purity was verified by Raman and XPS. The indirect bandgap of 1.15 eV was measured using infrared reflectivity, and is in agreement with the CuFeO2 bulk value. Finally, we discuss the growth and structural characterization of delafossite multilayers, CuFeO2/CuGaO2. This work was supported by a Research Challenge Grant from the West Virginia Higher Education Policy Commission (HEPC.dsr.12.29) and the Microelectronics Advanced Research Corporation (Contract # 2013-MA-2382) at WVU.

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor.

PubMed

Orsi, William D; Barker Jørgensen, Bo; Biddle, Jennifer F

2016-08-01

Sulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ-Proteobacteria peak at 90 m below seafloor (mbsf) within a deep sulfate methane transition zone. This coincides with isotopically heavy δ(34) S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0-5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α-subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low-energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Influence of Water Solute Exposure on the Chemical Evolution and Rheological Properties of Asphalt.

PubMed

Pang, Ling; Zhang, Xuemei; Wu, Shaopeng; Ye, Yong; Li, Yuanyuan

2018-06-11

The properties of asphalt pavement are damaged under the effects of moisture. The pH value and salt concentration of water are the key factors that affect the chemical and rheological properties of asphalt during moisture damage. Four kinds of water solutions, including distilled water, an acidic solution, alkaline solution and saline solution were used to investigate the effects of aqueous solute compositions on the chemical and rheological properties of asphalt. Thin-layer chromatography with flame ionization detection (TLC-FID), Fourier transform infrared (FTIR) spectroscopy and dynamic shear rheometer (DSR) were applied to investigate the components, chemistry and rheology characteristics of asphalt specimens before and after water solute exposure. The experimental results show that moisture damage of asphalt is not only associated with an oxidation process between asphalt with oxygen, but it is also highly dependent on some compounds of asphalt dissolving and being removed in the water solutions. In detail, after immersion in water solute, the fraction of saturates, aromatics and resins in asphalt binders decreased, while asphaltenes increased; an increase in the carbonyl and sulphoxide indices, and a decrease in the butadiene index were also found from the FTIR analyzer test. The rheological properties of asphalt are sensitive to water solute immersing. The addition of aqueous solutes causes more serious moisture damage on asphalt binders, with the pH11 solution presenting as the most destructive during water solute exposure.

Review article: cinnamon- and benzoate-free diet as a primary treatment for orofacial granulomatosis.

PubMed

Campbell, H E; Escudier, M P; Patel, P; Challacombe, S J; Sanderson, J D; Lomer, M C E

2011-10-01

Orofacial granulomatosis is a rare chronic granulomatous inflammatory disease of the lips, face and mouth. The aetiology remains unclear but may involve an allergic component. Improvements have been reported with cinnamon- and benzoate-free diets. To explore the prevalence of compound and food sensitivity and examine the dietary treatments used in orofacial granulomatosis. A comprehensive literature search was carried out and relevant studies from January 1933 to January 2010 were identified using the electronic database search engines; AGRIS 1991-2008, AMED 1985-2008, British Nursing and Index archive 1985-2008, EMBASE 1980-2008, evidence based medicine review databases (e.g. Cochrane DSR), International Pharmaceutical and Medline 1950-2008. Common sensitivities identified, predominantly through patch testing, were to benzoic acid (36%) food additives (33%), perfumes and flavourings (28%), cinnamaldehyde (27%), cinnamon (17%), benzoates (17%) and chocolate (11%). The cinnamon- and benzoate-free diet has been shown to provide benefit in 54-78% of patients with 23% requiring no adjunctive therapies. A negative or positive patch test result to cinnamaldehyde, and benzoates did not predict dietary outcome. The most concentrated source of benzoate exposure is from food preservatives. Use of liquid enteral formulas can offer a further dietary therapy, particularly in children with orofacial granulomatosis. Management of orofacial granulomatosis is challenging but cinnamon- and benzoate-free diets appear to have a definite role to play. © 2011 Blackwell Publishing Ltd.

Expansion of Phragmites australis alters methane dynamics and methanogen, methanotroph, and sulfate reducing bacteria communities in tidal marsh in Korea

NASA Astrophysics Data System (ADS)

Kim, J.; Lee, J.; Kim, H.; Gauhar, M.; Kang, H.

2016-12-01

Plant invasion is known to change substantially methane dynamics in tidal marshes. However, the exact mechanisms related to methane dynamics change due to plant invasion have not been fully understood. In Suncheon Bay, South Korea, Phragmites australis has invaded the habitat of native species, Suaeda japonica, and becomes dominant vegetation in this area. We measured methane fluxes, soil biogeochemistry, and microbial communities from both vegetation sites throughout a growing season and conducted a chronosequence analysis in order to illustrate the effect of plant invasion on methane dynamics and microbial communities. For analyzing microbial communities, we collected 1m intact soil cores and conducted functional gene-targeted real-time qPCR, T-RFLP, and PLFA. P. australis invasion significantly increased methane emission in a summer season, accompanied by greater dissolved organic carbon and soil water content. Methanogen, methanotroph, and sulfate reducing bacterial communities were gradually changed along with the invasion periods. In particular, abundances ratio of mcrA/pmoA and mcrA/dsrA had a positive correlation with methane emission, which indicates that P. australis invasion reduces methane oxidation by methanotroph, and competitive inhibition between methanogen and sulfate reducing bacteria. In conclusion, P. australis invasion on S. japonica significantly increased methane emission in tidal marsh by altering the microbial communities in a way that C decomposition would be dominated by methanogenesis.

Constitutive modeling of polycarbonate over a wide range of strain rates and temperatures

NASA Astrophysics Data System (ADS)

Wang, Haitao; Zhou, Huamin; Huang, Zhigao; Zhang, Yun; Zhao, Xiaoxuan

2017-02-01

The mechanical behavior of polycarbonate was experimentally investigated over a wide range of strain rates (10^{-4} to 5× 103 s^{-1}) and temperatures (293 to 353 K). Compression tests under these conditions were performed using a SHIMADZU universal testing machine and a split Hopkinson pressure bar. Falling weight impact testing was carried out on an Instron Dynatup 9200 drop tower system. The rate- and temperature-dependent deformation behavior of polycarbonate was discussed in detail. Dynamic mechanical analysis (DMA) tests were utilized to observe the glass (α ) transition and the secondary (β ) transition of polycarbonate. The DMA results indicate that the α and β transitions have a dramatic influence on the mechanical behavior of polycarbonate. The decompose/shift/reconstruct (DSR) method was utilized to decompose the storage modulus into the α and β components and extrapolate the entire modulus, the α-component modulus and the β-component modulus. Based on three previous models, namely, Mulliken-Boyce, G'Sell-Jonas and DSGZ, an adiabatic model is proposed to predict the mechanical behavior of polycarbonate. The model considers the contributions of both the α and β transitions to the mechanical behavior, and it has been implemented in ABAQUS/Explicit through a user material subroutine VUMAT. The model predictions are proven to essentially coincide with the experimental results during compression testing and falling weight impact testing.

Interventions to improve hemodialysis adherence: a systematic review of randomized-controlled trials.

PubMed

Matteson, Michelle L; Russell, Cynthia

2010-10-01

Over 485,000 people in the United States have chronic kidney disease, a progressive kidney disease that may lead to hemodialysis. Hemodialysis involves a complex regimen of treatment, medication, fluid, and diet management. In 2005, over 312,000 patients were undergoing hemodialysis in the United States. Dialysis nonadherence rates range from 8.5% to 86%. Dialysis therapy treatment nonadherence, including treatment, medication, fluid, and diet nonadherence, significantly increases the risk of morbidity and mortality. The purpose of this paper is to systematically review randomized-controlled trial intervention studies designed to increase treatment, medication, fluid, and diet adherence in adult hemodialysis patients. A search of Cumulative Index of Nursing and Allied Health Literature (CINAHL) (1982 to May 2008), MEDLINE (1950 to May 2008), PsycINFO (1806 to May 2008), and all Evidence-Based Medicine (EBM) Reviews (Cochran DSR, ACP Journal Club, DARE, and CCTR) was conducted to identify randomized-controlled studies that tested the efficacy of interventions to improve adherence in adult hemodialysis patients. Eight randomized-controlled trials met criteria for inclusion. Six of the 8 studies found statistically significant improvement in adherence with the intervention. Of these 6 intervention studies, all studies had a cognitive component, with 3 studies utilizing cognitive/behavioral intervention strategies. Based on this systematic review, interventions utilizing a cognitive or cognitive/behavioral component appear to show the most promise for future study. © 2010 The Authors. Hemodialysis International © 2010 International Society for Hemodialysis.

Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California

USGS Publications Warehouse

Blum, Jodi Switzer; Kulp, Thomas R.; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad W.; Stolz, John F.; Miller, Laurence G.; Oremland, Ronald S.

2012-01-01

A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

An alternative marker for the effectiveness of water fluoridation: hospital extraction rates for dental decay, a two-region study.

PubMed

Elmer, T B; Langford, J W; Morris, A J

2014-03-01

Contemporary evidence for the effectiveness of water fluoridation schemes in the U.K. is sparse. The utility of routinely collected data in providing evidence warrants further research. To examine inpatient hospital episodes statistics for dental extractions as an alternative population marker for the effectiveness of water fluoridation by comparing hospital admissions between two major strategic health authority (SHA) areas, the West Midlands SHA-largely fluoridated--and the North West SHA--largely unfluoridated. Hospital episodes statistics (HES) were interrogated to provide data on admissions for simple and surgical dental extractions, which had a primary diagnostic code of either dental caries or diseases of pulp and periapical tissues for financial years 2006/7, 2007/8 and 2008/9. Data was aggregated by SHA area and quinary age group. Directly standardised rates (DSR) of admissions purchased for each primary care trust (PCT) were calculated and ranked by index of multiple deprivation (IMD). A significant difference in DSRs of admission between PCTs in the West Midlands and North West was observed (Mann-Whitney U test [p <0.0001]) irrespective of IMD ranking. The difference in rates between the two most deprived PCTs was 27-fold. After ranking by IMD, DSRs of hospital admissions for the extraction of decayed or pulpally/periapically involved teeth is lower in areas with a fluoridated water supply. The analysis of routinely collected HES data may help identify the impact of water fluoridation schemes.

An evaluation of the schemes of ocean surface albedo parameterization in shortwave radiation estimation

NASA Astrophysics Data System (ADS)

Niu, Hailin; Zhang, Xiaotong; Liu, Qiang; Feng, Youbin; Li, Xiuhong; Zhang, Jialin; Cai, Erli

2015-12-01

The ocean surface albedo (OSA) is a deciding factor on ocean net surface shortwave radiation (ONSSR) estimation. Several OSA schemes have been proposed successively, but there is not a conclusion for the best OSA scheme of estimating the ONSSR. On the base of analyzing currently existing OSA parameterization, including Briegleb et al.(B), Taylor et al.(T), Hansen et al.(H), Jin et al.(J), Preisendorfer and Mobley(PM86), Feng's scheme(F), this study discusses the difference of OSA's impact on ONSSR estimation in condition of actual downward shortwave radiation(DSR). Then we discussed the necessity and applicability for the climate models to integrate the more complicated OSA scheme. It is concluded that the SZA and the wind speed are the two most significant effect factor to broadband OSA, thus the different OSA parameterizations varies violently in the regions of both high latitudes and strong winds. The OSA schemes can lead the ONSSR results difference of the order of 20 w m-2. The Taylor's scheme shows the best estimate, and Feng's result just following Taylor's. However, the accuracy of the estimated instantaneous OSA changes at different local time. Jin's scheme has the best performance generally at noon and in the afternoon, and PM86's is the best of all in the morning, which indicate that the more complicated OSA schemes reflect the temporal variation of OWA better than the simple ones.

Fluoxetine versus Vitex agnus castus extract in the treatment of premenstrual dysphoric disorder.

PubMed

Atmaca, Murad; Kumru, Selahattin; Tezcan, Ertan

2003-04-01

Clinical trials have demonstrated that serotonin reuptake inhibitors (SRIs) and the extract of Vitex agnus castus are effective for the treatment of premenstrual dysphoric disorder (PMDD). However, to the best of our knowledge, there has been no study comparing the efficacy of the SRIs with Vitex agnus castus (AC) extract. Therefore, the aim of the present study was to compare the efficacy of fluoxetine, a selective serotonin reuptake inhibitor (SSRI), with that of the AC extract, a natural choice. After a period of 2 screening months to screen the patients for suitability, 41 patients with PMDD according to DSM-IV were recruited into the study. The patients were randomized to fluoxetine or AC for 2 months of single-blind, rater- blinded and prospective treatment period. The outcome measures included the Penn daily symptom report (DSR), the Hamilton depression rating scale (HAM-D), and the clinical global impression-severity of illness (CGI-SI) and -improvement (CGI-I) scales. At endpoint, using the clinical criterion for improvement, a similar percentage of patients responded to fluoxetine (68.4%, n = 13) and AC (57.9%, n = 11). There was no statistically significant difference between the groups with respect to the rate of responders. This preliminary study suggests that patients with PMDD respond well to treatment with both fluoxetine and AC. However, fluoxetine was more effective for psychological symptoms while the extract diminished the physical symptoms. Copyright 2002 John Wiley & Sons, Ltd.

Comparison of the time taken for localised breast surgery pre- and post-introduction of intra-operative digital specimen mammography.

PubMed

Carraro do Nascimento, Vinicius; Bourke, Anita G

2018-02-01

More than half of the patients with an impalpable malignant breast lesion have a mammographically detected and imaged-guided localisation, which can be technically challenging for the breast surgeon. Specimen imaging is used to confirm successful excision of the localised index lesion and has improved the operating list efficiency resulting in a higher number of excisions per surgical list. The aim of this study was to evaluate whether introducing IDSM (intra-operative digital specimen mammography) saved operation time for localised breast surgery. A single-centre retrospective review was undertaken to compare the operation time (from incision to wound closure) taken for excision of 114 consecutive image-guided localised impalpable breast lesions, performed using departmental specimen radiography (DSR), 6 months prior to the introduction of IDSM (Hologic, Trident ® ) in March 2013, with the theatre time taken for excision of 121 consecutive image-guided localised impalpable breast lesions in the 6 months following introduction of IDSM. There was no significant difference in mean surgical time, which were 47.8 (±27.3) minutes in the CSR group and 48.8 (±25.7) minutes in the IDSM group. We were expecting to confirm a reduction in theatre time with the introduction of IDSM. Surprisingly, no difference in operating times was demonstrated. Factors that influenced the impact of IDSM included the proximity of the imaging department to the operating theatre. © 2017 The Royal Australian and New Zealand College of Radiologists.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

PubMed

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage▿

PubMed Central

Kock, Dagmar; Schippers, Axel

2008-01-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

A Scoping Review of Empirical Research Relating to Quality and Effectiveness of Research Ethics Review

PubMed Central

Nicholls, Stuart G.; Hayes, Tavis P.; Brehaut, Jamie C.; McDonald, Michael; Weijer, Charles; Saginur, Raphael; Fergusson, Dean

2015-01-01

Background To date there is no established consensus of assessment criteria for evaluating research ethics review. Methods We conducted a scoping review of empirical research assessing ethics review processes in order to identify common elements assessed, research foci, and research gaps to aid in the development of assessment criteria. Electronic searches of Ovid Medline, PsychInfo, and the Cochrane DSR, ACP Journal Club, DARE, CCTR, CMR, HTA, and NHSEED, were conducted. After de-duplication, 4234 titles and abstracts were reviewed. Altogether 4036 articles were excluded following screening of titles, abstracts and full text. A total of 198 articles included for final data extraction. Results Few studies originated from outside North America and Europe. No study reported using an underlying theory or framework of quality/effectiveness to guide study design or analyses. We did not identify any studies that had involved a controlled trial - randomised or otherwise – of ethics review procedures or processes. Studies varied substantially with respect to outcomes assessed, although tended to focus on structure and timeliness of ethics review. Discussion Our findings indicate a lack of consensus on appropriate assessment criteria, exemplified by the varied study outcomes identified, but also a fragmented body of research. To date research has been largely quantitative, with little attention given to stakeholder experiences, and is largely cross sectional. A lack of longitudinal research to date precludes analyses of change or assessment of quality improvement in ethics review. PMID:26225553

Compositions and Abundances of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Water-Flooded Petroleum Reservoirs with Different Temperatures in China

PubMed Central

Tian, Huimei; Gao, Peike; Chen, Zhaohui; Li, Yanshu; Li, Yan; Wang, Yansen; Zhou, Jiefang; Li, Guoqiang; Ma, Ting

2017-01-01

Sulfate-reducing bacteria (SRB) have been studied extensively in the petroleum industry due to their role in corrosion, but very little is known about sulfur-oxidizing bacteria (SOB), which drive the oxidization of sulfur-compounds produced by the activity of SRB in petroleum reservoirs. Here, we surveyed the community structure, diversity and abundance of SRB and SOB simultaneously based on 16S rRNA, dsrB and soxB gene sequencing, and quantitative PCR analyses, respectively in petroleum reservoirs with different physicochemical properties. Similar to SRB, SOB were found widely inhabiting the analyzed reservoirs with high diversity and different structures. The dominant SRB belonged to the classes Deltaproteobacteria and Clostridia, and included the Desulfotignum, Desulfotomaculum, Desulfovibrio, Desulfobulbus, and Desulfomicrobium genera. The most frequently detected potential SOB were Sulfurimonas, Thiobacillus, Thioclava, Thiohalomonas and Dechloromonas, and belonged to Betaproteobacteria, Alphaproteobacteria, and Epsilonproteobacteria. Among them, Desulfovibrio, Desulfomicrobium, Thioclava, and Sulfurimonas were highly abundant in the low-temperature reservoirs, while Desulfotomaculum, Desulfotignum, Thiobacillus, and Dechloromonas were more often present in high-temperature reservoirs. The relative abundances of SRB and SOB varied and were present at higher proportions in the relatively high-temperature reservoirs. Canonical correspondence analysis also revealed that the SRB and SOB communities in reservoirs displayed high niche specificity and were closely related to reservoir temperature, pH of the formation brine, and sulfate concentration. In conclusion, this study extends our knowledge about the distribution of SRB and SOB communities in petroleum reservoirs. PMID:28210252

Anodes Stimulate Anaerobic Toluene Degradation via Sulfur Cycling in Marine Sediments

PubMed Central

Daghio, Matteo; Vaiopoulou, Eleni; Patil, Sunil A.; Suárez-Suárez, Ana; Head, Ian M.

2015-01-01

Hydrocarbons released during oil spills are persistent in marine sediments due to the absence of suitable electron acceptors below the oxic zone. Here, we investigated an alternative bioremediation strategy to remove toluene, a model monoaromatic hydrocarbon, using a bioanode. Bioelectrochemical reactors were inoculated with sediment collected from a hydrocarbon-contaminated marine site, and anodes were polarized at 0 mV and +300 mV (versus an Ag/AgCl [3 M KCl] reference electrode). The degradation of toluene was directly linked to current generation of up to 301 mA m−2 and 431 mA m−2 for the bioanodes polarized at 0 mV and +300 mV, respectively. Peak currents decreased over time even after periodic spiking with toluene. The monitoring of sulfate concentrations during bioelectrochemical experiments suggested that sulfur metabolism was involved in toluene degradation at bioanodes. 16S rRNA gene-based Illumina sequencing of the bulk anolyte and anode samples revealed enrichment with electrocatalytically active microorganisms, toluene degraders, and sulfate-reducing microorganisms. Quantitative PCR targeting the α-subunit of the dissimilatory sulfite reductase (encoded by dsrA) and the α-subunit of the benzylsuccinate synthase (encoded by bssA) confirmed these findings. In particular, members of the family Desulfobulbaceae were enriched concomitantly with current production and toluene degradation. Based on these observations, we propose two mechanisms for bioelectrochemical toluene degradation: (i) direct electron transfer to the anode and/or (ii) sulfide-mediated electron transfer. PMID:26497463

Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough

NASA Astrophysics Data System (ADS)

Wang, Long; Yu, Min; Liu, Yan; Liu, Jiwen; Wu, Yonghua; Li, Li; Liu, Jihua; Wang, Min; Zhang, Xiao-Hua

2018-04-01

As an ideal place to study back-arc basins and hydrothermal eco-system, Okinawa Trough has attracted the interests of scientists for decades. However, there are still no in-depth studies targeting the bacterial community of the seafloor sediments and hydrothermal deposits in Okinawa Trough. In the present study, we reported the bacterial community of the surface deposits of a newly found hydrothermal field in the southern Okinawa Trough, and the horizontal and vertical variation of bacterial communities in the sediments of the northern Okinawa Trough. The hydrothermal deposits had a relatively high 16S rRNA gene abundance but low bacterial richness and diversity. Epsilonproteobacteria and Bacteroidetes were predominant in hydrothermal deposits whereas Deltaproteobacteria, Gammaproteobacteria and Chloroflexi were abundant across all samples. The bacterial distribution in the seafloor of Okinawa Trough was significantly correlated to the content of total nitrogen, and had consistent relationship with total carbon. Gradual changes of sulfur-oxidizing bacteria were found with the distance away from hydrothermal fields, while the hydrothermal activity did not influence the distribution of the major clades of sulfate-reducing bacteria. Higher abundance of the sulfur cycle related genes (aprA and dsrB), and lower abundance of the bacterial ammonia-oxidizing related gene (amoA) were quantified in hydrothermal deposits. In addition, the present study also compared the inter-field variation of Epsilonproteobacteria among multi-types of hydrothermal vents, revealing that the proportion and diversity of this clade were quite various.

Grid-enabled measures: using Science 2.0 to standardize measures and share data.

PubMed

Moser, Richard P; Hesse, Bradford W; Shaikh, Abdul R; Courtney, Paul; Morgan, Glen; Augustson, Erik; Kobrin, Sarah; Levin, Kerry Y; Helba, Cynthia; Garner, David; Dunn, Marsha; Coa, Kisha

2011-05-01

Scientists are taking advantage of the Internet and collaborative web technology to accelerate discovery in a massively connected, participative environment--a phenomenon referred to by some as Science 2.0. As a new way of doing science, this phenomenon has the potential to push science forward in a more efficient manner than was previously possible. The Grid-Enabled Measures (GEM) database has been conceptualized as an instantiation of Science 2.0 principles by the National Cancer Institute (NCI) with two overarching goals: (1) promote the use of standardized measures, which are tied to theoretically based constructs; and (2) facilitate the ability to share harmonized data resulting from the use of standardized measures. The first is accomplished by creating an online venue where a virtual community of researchers can collaborate together and come to consensus on measures by rating, commenting on, and viewing meta-data about the measures and associated constructs. The second is accomplished by connecting the constructs and measures to an ontological framework with data standards and common data elements such as the NCI Enterprise Vocabulary System (EVS) and the cancer Data Standards Repository (caDSR). This paper will describe the web 2.0 principles on which the GEM database is based, describe its functionality, and discuss some of the important issues involved with creating the GEM database such as the role of mutually agreed-on ontologies (i.e., knowledge categories and the relationships among these categories--for data sharing). Published by Elsevier Inc.

The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough.

PubMed

Ramos, Ana Raquel; Grein, Fabian; Oliveira, Gonçalo P; Venceslau, Sofia S; Keller, Kimberly L; Wall, Judy D; Pereira, Inês A C

2015-07-01

Flavin-based electron bifurcation (FBEB) is an important mechanism for the energy metabolism of anaerobes. A new family of NADH dehydrogenases, the flavin oxidoreductase (FlxABCD, previously called FloxABCD), was proposed to perform FBEB in sulphate-reducing organisms coupled with heterodisulfide reductase (HdrABC). We found that the hdrABC-flxABCD gene cluster is widespread among anaerobic bacteria, pointing to a general and important role in their bioenergetics. In this work, we studied FlxABCD of Desulfovibrio vulgaris Hildenborough. The hdr-flx genes are part of the same transcriptional unit and are increased in transcription during growth in ethanol-sulfate, and to a less extent during pyruvate fermentation. Two mutant strains were generated: one where expression of the hdr-flx genes was interrupted and another lacking the flxA gene. Both strains were unable to grow with ethanol-sulfate, whereas growth was restored in a flxA-complemented strain. The mutant strains also produced very reduced amounts of ethanol compared with the wild type during pyruvate fermentation. Our results show that in D. vulgaris, the FlxABCD-HdrABC proteins are essential for NADH oxidation during growth on ethanol, probably involving a FBEB mechanism that leads to reduction of ferredoxin and the small protein DsrC, while in fermentation they operate in reverse, reducing NAD(+) for ethanol production. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of two warm-mix additives on aging, rheological and failure properties of asphalt cements

NASA Astrophysics Data System (ADS)

Omari, Isaac Obeng

Sustainable road construction and maintenance could be supported when excellent warm-mix additives are employed in the modification of asphalt. These warm-mix additives provide remedies for today's requirements such as fatigue cracking resistance, durability, thermal cracking resistance, rutting resistance and resistance to moisture damage. Warm-mix additives are based on waxes and surfactants which reduce energy consumption and carbon dioxide emissions significantly during the construction phase of the pavement. In this study, the effects of two warm mix additives, siloxane and oxidised polyethylene wax, on roofing asphalt flux (RAF) and asphalt modified with waste engine oil (655-7) were investigated to evaluate the rheological, aging and failure properties of the asphalt binders. In terms of the properties of these two different asphalts, RAF has proved to be superior quality asphalt whereas 655-7 is poor quality asphalt. The properties of the modified asphalt samples were measured by Superpave(TM) tests such as Dynamic Shear Rheometer (DSR) test and Bending Beam Rheometer (BBR) test as well as modified protocols such as the extended BBR (eBBR) test (LS-308) and the Double- Edge-Notched Tension (DENT) test (LS-299) after laboratory aging. In addition, the Avrami theory was used to gain an insight on the crystallization of asphalt or the waxes within the asphalt binder. This study has however shown that the eBBR and DENT tests are better tools for providing accurate specification tests to curb thermal and fatigue cracking in contemporary asphalt pavements.

Structural and electrical characterization of NbO2 vertical devices grown on TiN coated SiO2/Si substrate

NASA Astrophysics Data System (ADS)

Joshi, Toyanath; Borisov, Pavel; Lederman, David

Due to its relatively high MIT temperature (1081 K) and current-controlled negative differential resistance, NbO2 is a robust candidate for memory devices and electrical switching applications. In this work, we present in-depth analysis of NbO2 thin film vertical devices grown on TiN coated SiO2/Si substrates using pulsed laser deposition (PLD). Two of the films grown in 1 mTorr and 10 mTorr O2/Ar (~7% O2) mixed growth pressures were studied. The formation of NbO2 phase was confirmed by Grazing Incidence X-ray Diffractometry (GIXRD), X-ray Photoelectron Spectroscopy (XPS) and current vs. voltage measurements. A probe station tip (tip size ~2 μm) or conductive AFM tip was used as a top and TiN bottom layer was used as a bottom contact. Device conductivity showed film thickness and contact size dependence. Current pulse measurements, performed in response to applied triangular voltage pulses, showed a non-linear threshold switching behavior for voltage pulse durations of ~100 ns and above. Self-sustained current oscillations were analyzed in terms of defect density presented in the film. Supported by FAME (sponsored by MARCO and DARPA, Contract 2013-MA-2382), WV Higher Education Policy Commission Grant (HEPC.dsr.12.29), and WVU SRF. We also thank S. Kramer from Micron for providing the TiN-coated Si substrates.

Modelling the petrogenesis of high Rb/Sr silicic magmas

USGS Publications Warehouse

Halliday, A.N.; Davidson, J.P.; Hildreth, W.; Holden, P.

1991-01-01

Rhyolites can be highly evolved with Sr contents as low as 0.1 ppm and Rb Sr > 2,000. In contrast, granite batholiths are commonly comprised of rocks with Rb Sr 100. Mass-balance modelling of source compositions, differentiation and contamination using the trace-element geochemistry of granites are therefore commonly in error because of the failure to account for evolved differentiates that may have been erupted from the system. Rhyolitic magmas with very low Sr concentrations (???1 ppm) cannot be explained by any partial melting models involving typical crustal source compositions. The only plausible mechanism for the production of such rhyolites is Rayleigh fractional crystallization involving substantial volumes of cumulates. A variety of methods for modelling the differentiation of magmas with extremely high Rb/Sr is discussed. In each case it is concluded that the bulk partition coefficients for Sr have to be large. In the simplest models, the bulk DSr of the most evolved types is modelled as > 50. Evidence from phenocryst/glass/whole-rock concentrations supports high Sr partition coefficients in feldspars from high silica rhyolites. However, the low modal abundance of plagioclase commonly observed in such rocks is difficult to reconcile with such simple fractionation models of the observed trace-element trends. In certain cases, this may be because the apparent trace-element trend defined by the suite of cognetic rhyolites is the product of different batches of magma with separate differentiation histories accumulating in the magma chamber roof zone. ?? 1991.

Nucleic acid based quantitative microbial community analysis in different marine and terrestrial sediments

NASA Astrophysics Data System (ADS)

Schippers, A.; Blazejak, A.; Köweker, G.

2009-12-01

Sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This immense cell number is calculated from numerous microscopic cell counts (AODC) in ODP sediment cores. Since AODC can not differentiate between living or dead cells, the population size of living microorganisms and the abundance of different prokaryotic groups are unknown. Recent molecular nucleic acid and biomarker analyses showed that a high proportion of the cells are alive and that the microbial communities of deep marine sediments harbour members of distinct, uncultured bacterial and archaeal lineages. The main objective of our project is the quantification of living prokaryotes in various sediments. Deep sediment samples from the Pacific and the Atlantic Oceans (ODP Legs 201 and 207, IODP Exp. 307 and 308), sediments from the Indian Ocean (RV Sonne 189-2) and the Black Sea (RV Meteor 51/4) as well as terrestrial Chesapeake Bay Sediments (ICDP) were analyzed using Catalyzed Reporter Deposition - Fluorescence In Situ Hybridisation (CARD - FISH) and quantitative, real-time PCR (Q-PCR), targeting either the 16S rRNA gene or the functional genes dsrA, mcrA and aprA to quantify microorganisms of various phylogenetic or physiological groups (e.g. JS1 cluster and Chloroflexi). At all sediment sites, cell numbers decreased with depth, however, the abundance of particular microbial groups varied at different sites and depths. The results indicate that global estimates of the deep biosphere should be reconsidered.

Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage.

PubMed

Kock, Dagmar; Schippers, Axel

2008-08-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

Sulfate-reducing bacteria mediate thionation of diphenylarsinic acid under anaerobic conditions.

PubMed

Guan, Ling; Shiiya, Ayaka; Hisatomi, Shihoko; Fujii, Kunihiko; Nonaka, Masanori; Harada, Naoki

2015-02-01

Diphenylarsinic acid (DPAA) is often found as a toxic intermediate metabolite of diphenylchloroarsine or diphenylcyanoarsine that were produced as chemical warfare agents and were buried in soil after the World Wars. In our previous study Guan et al. (J Hazard Mater 241-242:355-362, 2012), after application of sulfate and carbon sources, anaerobic transformation of DPAA in soil was enhanced with the production of diphenylthioarsinic acid (DPTAA) as a main metabolite. This study aimed to isolate and characterize anaerobic soil microorganisms responsible for the metabolism of DPAA. First, we obtained four microbial consortia capable of transforming DPAA to DPTAA at a high transformation rate of more than 80% after 4 weeks of incubation. Sequencing for the bacterial 16S rRNA gene clone libraries constructed from the consortia revealed that all the positive consortia contained Desulfotomaculum acetoxidans species. In contrast, the absence of dissimilatory sulfite reductase gene (dsrAB) which is unique to sulfate-reducing bacteria was confirmed in the negative consortia showing no DPAA reduction. Finally, strain DEA14 showing transformation of DPAA to DPTAA was isolated from one of the positive consortia. The isolate was assigned to D. acetoxidans based on the partial 16S rDNA sequence analysis. Thionation of DPAA was also carried out in a pure culture of a known sulfate-reducing bacterial strain, Desulfovibrio aerotolerans JCM 12613(T). These facts indicate that sulfate-reducing bacteria are microorganisms responsible for the transformation of DPAA to DPTAA under anaerobic conditions.

Building Specialized Multilingual Lexical Graphs Using Community Resources

NASA Astrophysics Data System (ADS)

Daoud, Mohammad; Boitet, Christian; Kageura, Kyo; Kitamoto, Asanobu; Mangeot, Mathieu; Daoud, Daoud

We are describing methods for compiling domain-dedicated multilingual terminological data from various resources. We focus on collecting data from online community users as a main source, therefore, our approach depends on acquiring contributions from volunteers (explicit approach), and it depends on analyzing users' behaviors to extract interesting patterns and facts (implicit approach). As a generic repository that can handle the collected multilingual terminological data, we are describing the concept of dedicated Multilingual Preterminological Graphs MPGs, and some automatic approaches for constructing them by analyzing the behavior of online community users. A Multilingual Preterminological Graph is a special lexical resource that contains massive amount of terms related to a special domain. We call it preterminological, because it is a raw material that can be used to build a standardized terminological repository. Building such a graph is difficult using traditional approaches, as it needs huge efforts by domain specialists and terminologists. In our approach, we build such a graph by analyzing the access log files of the website of the community, and by finding the important terms that have been used to search in that website, and their association with each other. We aim at making this graph as a seed repository so multilingual volunteers can contribute. We are experimenting this approach with the Digital Silk Road Project. We have used its access log files since its beginning in 2003, and obtained an initial graph of around 116000 terms. As an application, we used this graph to obtain a preterminological multilingual database that is serving a CLIR system for the DSR project.

Effect of naphtha diluent on greenhouse gases and reduced sulfur compounds emissions from oil sands tailings.

PubMed

Gee, Kathleen F; Poon, Ho Yin; Hashisho, Zaher; Ulrich, Ania C

2017-11-15

The long-term storage of oil sands tailings has resulted in the evolution of greenhouse gases (CH 4 and CO 2 ) as a result of residual organics biodegradation. Recent studies have identified black, sulfidic zones below the tailings-water interface, which may be producing toxic sulfur-containing gases. An anaerobic mesocosm study was conducted over an 11-week period to characterize the evolution of CH 4 , CO 2 and reduced sulfur compounds (RSCs) (including H 2 S) in tailings as it relates to naphtha-containing diluent concentrations (0.2, 0.8, and 1.5% w/v) and microbial activity. Our results showed that RSCs were produced first at 0.12μmol°RSCs/mL MFT (1.5% w/v diluent treatment). RSCs contribution (from highest to lowest) was H 2 S and 2-methylthiophene>2.5-dimethylthiophene>3-methylthiophene>thiofuran>butyl mercaptan>carbonyl sulfide, where H 2 S and 2-methylthiophene contributed 81% of the gas produced. CH 4 and CO 2 production occurred after week 5 at 40.7μmolCH 4 /mL MFT and 5.9μmolCO 2 /mL MFT (1.5% w/v diluent treatment). The amount of H 2 S and CH 4 generated is correlated to the amount of diluent present and to microbial activity as shown by corresponding increases in sulfate-reducers' Dissimilatory sulfite reductase (DsrAB) gene and methanogens' methyl-coenzyme M reductase (MCR) gene. Copyright © 2017 Elsevier B.V. All rights reserved.

Study on viscosity of conventional and polymer modified asphalt binders in steady and dynamic shear domain

NASA Astrophysics Data System (ADS)

Saboo, Nikhil; Singh, Bhupendra; Kumar, Praveen; Vikram, Durgesh

2018-02-01

This study focuses on evaluating the flow behavior of conventional and polymer modified asphalt binders in steady- and dynamic-shear domain, for a temperature range of 20-70 °C, using a Dynamic Shear Rheometer (DSR). Steady-shear viscosity and frequency sweep tests were carried out on two conventional (VG 10 and VG 30) and two polymer (SBS and EVA) modified asphalt binders. Applicability of the Cox-Merz principle was evaluated and complex viscosity master curves were analyzed at five different reference temperatures. Cross model was used to simulate the complex viscosity master curves at different temperatures. It was found that asphalt binders exhibited shear-thinning behavior at all the test temperatures. The critical shear rate increased with increase in temperature and was found to be lowest for plastomeric modified asphalt binder. The Cox-Merz principle was found to be valid in the zero-shear viscosity (ZSV) domain and deviated at higher frequency/shear rate for all the binders. Results from the study indicated that the ratio of ZSV can be successfully used as shift factors for construction of master curves at different reference temperatures. Cross model was found to be suitable in simulating the complex viscosity master curves at all the test temperatures. Analysis of model parameters indicated that a strong relationship exists between ZSV and the critical shear rate. ZSV and critical shear rate varied exponentially with temperature. This relationship was used to propose a simple equation for assessing the shift factors for construction of master curves.

Quantitative Financial Analysis of Alternative Energy Efficiency Shareholder Incentive Mechanisms

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

Cappers, Peter; Goldman, Charles; Chait, Michele

2008-08-03

Rising energy prices and climate change are central issues in the debate about our nation's energy policy. Many are demanding increased energy efficiency as a way to help reduce greenhouse gas emissions and lower the total cost of electricity and energy services for consumers and businesses. Yet, as the National Action Plan on Energy Efficiency (NAPEE) pointed out, many utilities continue to shy away from seriously expanding their energy efficiency program offerings because they claim there is insufficient profit-motivation, or even a financial disincentive, when compared to supply-side investments. With the recent introduction of Duke Energy's Save-a-Watt incentive mechanism andmore » ongoing discussions about decoupling, regulators and policymakers are now faced with an expanded and diverse landscape of financial incentive mechanisms, Determining the 'right' way forward to promote deep and sustainable demand side resource programs is challenging. Due to the renaissance that energy efficiency is currently experiencing, many want to better understand the tradeoffs in stakeholder benefits between these alternative incentive structures before aggressively embarking on a path for which course corrections can be time-consuming and costly. Using a prototypical Southwest utility and a publicly available financial model, we show how various stakeholders (e.g. shareholders, ratepayers, etc.) are affected by these different types of shareholder incentive mechanisms under varying assumptions about program portfolios. This quantitative analysis compares the financial consequences associated with a wide range of alternative incentive structures. The results will help regulators and policymakers better understand the financial implications of DSR program incentive regulation.« less

The health economics of ankle and foot sprains and fractures: A systematic review of English-language published papers. Part 1: Overview and critical appraisal.

PubMed

Bielska, Iwona A; Wang, Xiang; Lee, Raymond; Johnson, Ana P

2017-07-01

Ankle and foot sprains and fractures are common injuries affecting many individuals, often requiring considerable and costly medical interventions. The objectives of this systematic review are to collect, assess, and critically appraise the published literature on the health economics of ankle and foot injury (sprain and fracture) treatment. A systematic literature review of Ovid MEDLINE, EMBASE, Cochrane DSR, ACP Journal Club, AMED, Ovid Healthstar, and CINAHL was conducted for English-language studies on the costs of treating ankle and foot sprains and fractures published from January 1980 to December 2014. Two reviewers assessed the articles for study quality and abstracted data. The literature search identified 2047 studies of which 32 were analyzed. A majority of the studies were published in the last decade. A number of the studies did not report full economic information, including the sources of the direct and indirect costs, as suggested in the guidelines. The perspective used in the analysis was missing in numerous studies, as was the follow-up time period of participants. Only five of the studies undertook a sensitivity analysis which is required whenever there are uncertainties regarding cost data. This systematic review found that publications do not consistently report on the components of health economics methodology, which in turn limits the quality of information. Future studies undertaking economic evaluations should ensure that their methods are transparent and understandable so as to yield accurate interpretation for assistance in forthcoming economic evaluations and policy decision-making. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA.

PubMed

Edwardson, Christian F; Hollibaugh, James T

2017-10-01

This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.

Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies.

PubMed

Sharma, Deepak K; Solbrig, Harold R; Tao, Cui; Weng, Chunhua; Chute, Christopher G; Jiang, Guoqian

2017-06-05

Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/ITEM_GROUP pattern defined in the latest CIMI Reference Model is used to represent reusable model elements (mini-Archetypes). We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. We performed a case study of the domain "clinical pharmaceutical" in the TCGA data dictionary and demonstrated enriched data elements in the metadata repository are very useful in support of building detailed clinical models. Our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMI-compliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.

Activation of the Glutamic Acid-Dependent Acid Resistance System in Escherichia coli BL21(DE3) Leads to Increase of the Fatty Acid Biotransformation Activity.

PubMed

Woo, Ji-Min; Kim, Ji-Won; Song, Ji-Won; Blank, Lars M; Park, Jin-Byung

The biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. The productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. Here, we have investigated factors that influence the tolerance of Escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. The metabolic and genomic responses of E. coli BL21(DE3) and MG1655 grown in the presence of n-heptanoic acid indicated that the GadA/B-based glutamic acid-dependent acid resistance (GDAR) system might be critical for cellular tolerance. The GDAR system, which is responsible for scavenging intracellular protons by catalyzing decarboxylation of glutamic acid, was inactive in E. coli BL21(DE3). Activation of the GDAR system in this strain by overexpressing the rcsB and dsrA genes, of which the gene products are involved in the activation of GadE and RpoS, respectively, resulted in acid tolerance not only to HCl but also to n-heptanoic acid. Furthermore, activation of the GDAR system allowed the recombinant E. coli BL21(DE3) expressing the alcohol dehydrogenase of Micrococcus luteus and the Baeyer-Villiger monooxygenase of Pseudomonas putida to reach 60% greater product concentration in the biotransformation of ricinoleic acid (i.e., 12-hydroxyoctadec-9-enoic acid (1)) into n-heptanoic acid (5) and 11-hydroxyundec-9-enoic acid (4). This study may contribute to engineering E. coli-based biocatalysts for the production of carboxylic acids from renewable biomass.

A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

PubMed Central

Weissgerber, Thomas; Sylvester, Marc; Kröninger, Lena

2014-01-01

In the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified A. vinosum proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515). PMID:24487535

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

PubMed Central

Li, Xiao-Xiao; Liu, Jin-Feng; Zhou, Lei; Mbadinga, Serge M.; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2017-01-01

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5′-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs. PMID:28638372

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer.

PubMed

Zhang, Ping; He, Zhili; Van Nostrand, Joy D; Qin, Yujia; Deng, Ye; Wu, Liyou; Tu, Qichao; Wang, Jianjun; Schadt, Christopher W; W Fields, Matthew; Hazen, Terry C; Arkin, Adam P; Stahl, David A; Zhou, Jizhong

2017-04-04

To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H 2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO 4 -2 , U(VI), NO 3 - , Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4-31 days, whereas Desulfobacterium became dominant at 80-140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing

PubMed Central

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas. PMID:26020967

Fully Suspended, Five-Axis, Three-Magnetic-Bearing Dynamic Spin Rig With Forced Excitation

NASA Technical Reports Server (NTRS)

Morrison, Carlos R.; Provenza, Andrew; Kurkov, Anatole; Montague, Gerald; Duffy, Kirsten; Mehmed, Oral; Johnson, Dexter; Jansen, Ralph

2004-01-01

The Five-Axis, Three-Magnetic-Bearing Dynamic Spin Rig, a significant advancement in the Dynamic Spin Rig (DSR), is used to perform vibration tests of turbomachinery blades and components under rotating and nonrotating conditions in a vacuum. The rig has as its critical components three magnetic bearings: two heteropolar radial active magnetic bearings and a magnetic thrust bearing. The bearing configuration allows full vertical rotor magnetic suspension along with a feed-forward control feature, which will enable the excitation of various natural blade modes in bladed disk test articles. The theoretical, mechanical, electrical, and electronic aspects of the rig are discussed. Also presented are the forced-excitation results of a fully levitated, rotating and nonrotating, unbladed rotor and a fully levitated, rotating and nonrotating, bladed rotor in which a pair of blades was arranged 180 degrees apart from each other. These tests include the bounce mode excitation of the rotor in which the rotor was excited at the blade natural frequency of 144 Hz. The rotor natural mode frequency of 355 Hz was discerned from the plot of acceleration versus frequency. For nonrotating blades, a blade-tip excitation amplitude of approximately 100 g/A was achieved at the first-bending critical (approximately 144 Hz) and at the first-torsional and second-bending blade modes. A blade-tip displacement of 70 mils was achieved at the first-bending critical by exciting the blades at a forced-excitation phase angle of 908 relative to the vertical plane containing the blades while simultaneously rotating the shaft at 3000 rpm.

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere.

PubMed

Venkatachalam, S; Ranjan, K; Prasanna, R; Ramakrishnan, B; Thapa, S; Kanchan, A

2016-07-01

The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi-controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field-grown plants under a conventional flooded system of rice intensification (SRI) and in dry-seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α-proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2 μg·ml(-1) ) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non-heterocystous filaments under aerobic as well as anaerobic conditions. PCR-DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

Analyzing the effect of routing protocols on media access control protocols in radio networks

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

Barrett, C. L.; Drozda, M.; Marathe, A.

2002-01-01

We study the effect of routing protocols on the performance of media access control (MAC) protocols in wireless radio networks. Three well known MAC protocols: 802.11, CSMA, and MACA are considered. Similarly three recently proposed routing protocols: AODV, DSR and LAR scheme 1 are considered. The experimental analysis was carried out using GloMoSim: a tool for simulating wireless networks. The main focus of our experiments was to study how the routing protocols affect the performance of the MAC protocols when the underlying network and traffic parameters are varied. The performance of the protocols was measured w.r.t. five important parameters: (i)more » number of received packets, (ii) average latency of each packet, (iii) throughput (iv) long term fairness and (v) number of control packets at the MAC layer level. Our results show that combinations of routing and MAC protocols yield varying performance under varying network topology and traffic situations. The result has an important implication; no combination of routing protocol and MAC protocol is the best over all situations. Also, the performance analysis of protocols at a given level in the protocol stack needs to be studied not locally in isolation but as a part of the complete protocol stack. A novel aspect of our work is the use of statistical technique, ANOVA (Analysis of Variance) to characterize the effect of routing protocols on MAC protocols. This technique is of independent interest and can be utilized in several other simulation and empirical studies.« less

The "ick" Factor Matters: Disgust Prospectively Predicts Avoidance in Chemotherapy Patients.

PubMed

Reynolds, Lisa M; Bissett, Ian P; Porter, David; Consedine, Nathan S

2016-12-01

Chemotherapy can be physically and psychologically demanding. Avoidance and withdrawal are common among patients coping with these demands. This report compares established emotional predictors of avoidance during chemotherapy (embarrassment; distress) with an emotion (disgust) that has been unstudied in this context. This report outlines secondary analyses of an RCT where 68 cancer patients undergoing chemotherapy were randomized to mindfulness or relaxation interventions. Self-reported baseline disgust (DS-R), embarrassment (SES-SF), and distress (Distress Thermometer) were used to prospectively predict multiple classes of avoidance post-intervention and at 3 months follow-up. Measures assessed social avoidance, cognitive and emotional avoidance (IES Avoidance), as well as information seeking and treatment adherence (General Adherence Scale). Repeated-measures ANOVAs evaluated possible longitudinal changes in disgust and forward entry regression models contrasted the ability of the affective variables to predict avoidance. Although disgust did not change over time or vary between groups, greater disgust predicted greater social, cognitive, and emotional avoidance, as well as greater information seeking. Social avoidance was predicted by trait embarrassment and distress predicted non-adherence. This report represents the first investigation of disgust's ability to prospectively predict avoidance in people undergoing chemotherapy. Compared to embarrassment and distress, disgust was a more consistent predictor across avoidance domains and its predictive ability was evident across a longer period of time. Findings highlight disgust's role as an indicator of likely avoidance in this health context. Early identification of cancer patients at risk of deleterious avoidance may enable timely interventions and has important clinical implications (ACTRN12613000238774).

Detection of Survival and Proliferation of Sulfate Reducers Under Simulated Martian Atmospheric and Soil Conditions

NASA Astrophysics Data System (ADS)

Mora, Sergio Mosquera

Numerous studies have tried to determine the survivability and proliferation of microorganisms under simulated Martian conditions. Furthermore, most of them have been focused on the ability of these microbes to cope with high brines' salt (NaCl) concentrations inherent of the Martian surface. However, there are not studies related to the ability of bacteria to survive on subsurface environments that have increasing concentrations of sulfate compounds. For this research, a group of microorganisms known as sulfate-reducing bacteria or simply sulfate reducers were chosen due to their ability to use sulfate compounds as terminal electron acceptors to produce metabolic energy, their tolerance to low temperatures (psychrophilic microbes) and their anaerobic metabolism. Moreover, the principal purpose of this study was to determine the ability of sulfate reducers to carry active metabolism under conditions similar to those present on Mars subsurface (low temperature, high concentration of sulfate compounds, anoxic atmosphere-95% carbon dioxide, low nutrients availability, among others). Furthermore, we cultivated strains of Desulfotalea psychrophila, Desulfuromusa ferrireducens and Desulfotomaculum arcticum using different concentrations of minerals. The latter (CaSO 4, MgSO4, FeSO4 and Fe2(SO4) 3) are normally found as part of the Martian subsurface components and they can act as terminal electron acceptors in sulfate respiration. Moreover, PCR amplifications of the 16S rDNA gene and the dsrAB genes were performed in order to determine the growth and survivability of the three microorganisms tested. Finally, we were able to determine that they were metabolically active at the different types and mineral concentrations under study.

Analysis of the Relationships between Waste Cooking Oil Qualities and Rejuvenated Asphalt Properties

PubMed Central

Zhang, Dong; Chen, Meizhu; Wu, Shaopeng; Liu, Jingxiang; Amirkhanian, Serji

2017-01-01

Waste cooking oil (WCO), in many cases, can rejuvenate aged asphalt and restore its properties. However, the influence of WCO qualities on rejuvenation behaviors of aged asphalt has not been investigated in detail. The objective of this paper was to evaluate the effects of WCO viscosity and acid value on the basic, rheological, and chemical properties of a typical rejuvenated asphalt. Penetration, ring and ball (R and B) softening point, and ductility were tested to evaluate the influence of WCO qualities on basic properties of rejuvenated asphalts. Then, the rheological properties of rejuvenated asphalt were characterized based on rotational viscometer (RV), dynamic shear rheometer (DSR), and bending beam rheometer (BBR) test results. Further, SARA (saturates, aromatics, resins, and asphaltenes) fraction analysis and Fourier transform infrared spectroscopy (FTIR) tests were performed to investigate the effects of WCO qualities on asphalt chemical composition. Finally, grey correlation coefficients were calculated and the relationships between WCO qualities and rejuvenated asphalt properties were quantitatively evaluated. The experimental results indicated that WCO qualities influence the rejuvenation behaviors of aged asphalt significantly, and the WCO with higher qualities (low acid value and viscosity, as defined in this research) tends to achieve better rejuvenation effects. Based on the results of grey correlation analyses, the acid value is, relatively, a better indicator than viscosity in predicting the rejuvenation efficiency of WCO. The rejuvenation thresholds of WCO are varied with the categories of properties of rejuvenated asphalts, and WCO with an acid value of 0.4–0.7 mg KOH/g, or a viscosity of 140–540 mm2/s, can meet all of the performance requirements for asphalt rejuvenation used in this research. PMID:28772862

Characterizing RecA-Independent Induction of Shiga toxin2-Encoding Phages by EDTA Treatment

PubMed Central

Imamovic, Lejla; Muniesa, Maite

2012-01-01

Background The bacteriophage life cycle has an important role in Shiga toxin (Stx) expression. The induction of Shiga toxin-encoding phages (Stx phages) increases toxin production as a result of replication of the phage genome, and phage lysis of the host cell also provides a means of Stx toxin to exit the cell. Previous studies suggested that prophage induction might also occur in the absence of SOS response, independently of RecA. Methodology/Principal Findings The influence of EDTA on RecA-independent Stx2 phage induction was assessed, in laboratory lysogens and in EHEC strains carrying Stx2 phages in their genome, by Real-Time PCR. RecA-independent mechanisms described for phage λ induction (RcsA and DsrA) were not involved in Stx2 phage induction. In addition, mutations in the pathway for the stress response of the bacterial envelope to EDTA did not contribute to Stx2 phage induction. The effect of EDTA on Stx phage induction is due to its chelating properties, which was also confirmed by the use of citrate, another chelating agent. Our results indicate that EDTA affects Stx2 phage induction by disruption of the bacterial outer membrane due to chelation of Mg2+. In all the conditions evaluated, the pH value had a decisive role in Stx2 phage induction. Conclusions/Significance Chelating agents, such as EDTA and citrate, induce Stx phages, which raises concerns due to their frequent use in food and pharmaceutical products. This study contributes to our understanding of the phenomenon of induction and release of Stx phages as an important factor in the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) and in the emergence of new pathogenic strains. PMID:22393404

Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean.

PubMed

Mori, Koji; Maruyama, Akihiko; Urabe, Tetsuro; Suzuki, Ken-Ichiro; Hanada, Satoshi

2008-04-01

A novel thermophilic, strictly anaerobic archaeon, designated strain Arc51T, was isolated from a rock sample collected from a deep-sea hydrothermal field in Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Cells of the isolate were irregular cocci with single flagella and exhibited blue-green fluorescence at 436 nm. The optimum temperature, pH and NaCl concentration for growth were 70 degrees C, pH 6.5 and 3 % (w/v), respectively. Strain Arc51T could grow on thiosulfate or sulfite as an electron acceptor in the presence of hydrogen. This strain required acetate as a carbon source for its growth, suggesting that the reductive acetyl CoA pathway for CO2 fixation was incomplete. In addition, coenzyme M (2-mercaptoethanesulfonic acid), which is a known methyl carrier in methanogenesis, was also a requirement for growth of the strain. Analysis of the 16S rRNA gene sequence revealed that the isolate was similar to members of the genus Archaeoglobus, with sequence similarities of 93.6-97.2 %; the closest relative was Archaeoglobus veneficus. Phylogenetic analyses of the dsrAB and apsA genes, encoding the alpha and beta subunits of dissimilatory sulfite reductase and the alpha subunit of adenosine-5'-phosphosulfate reductase, respectively, produced results similar to those inferred from comparisons based on the 16S rRNA gene sequence. On the basis of phenotypic and phylogenetic data, strain Arc51T represents a novel species of the genus Archaeoglobus, for which the name Archaeoglobus infectus sp. nov. is proposed. The type strain is Arc51T (=NBRC 100649T=DSM 18877T).

Oxygen Minimum Zones in Miniature: Microbial Community Diversity, Activity, and Assembly Across Oxygen Gradients in Meromictic Marine Lakes, Palau

NASA Astrophysics Data System (ADS)

Beman, J. M.

2016-02-01

Oxygen minimum zones (OMZs) play a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet our understanding of these changes is limited by a lack of systematic analyses of low-oxygen ecosystems. In particular, forecasting biogeochemical feedbacks to deoxygenation requires detailed knowledge of microbial community assembly and activity as oxygen declines. Marine `lakes'—isolated bodies of seawater surrounded by land—are an ideal comparative system, as they provide a pronounced oxygen gradient extending from well-mixed, holomictic lakes to stratified, meromictic lakes that vary in their extent of anoxia. We examined 13 marine lakes using pyrosequencing of 16S rRNA genes, quantitative PCR for nitrogen (N)- and sulfur (S)-cycling functional genes and groups, and N- and carbon (C)-cycling rate measurements. All lakes were inhabited by well-known marine bacteria, demonstrating the broad relevance of this study system. Microbial diversity was typically highest in the anoxic monimolimnion of meromictic lakes, with marine cyanobacteria, SAR11, and other common bacteria replaced by anoxygenic phototrophs, sulfate-reducing bacteria (SRBs), and SAR406 in the monimolimnion. Denitrifier nitrite reductase (nirS) genes were also detected alongside high abundances (>106 ml-1) of dissimilatory sulfite reductase (dsrA) genes from SRBs in the monimolimnion. Sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis=76%) and deterministic processes dominated community assembly at all depths (nearest taxon index values >4). These results indicate that oxygen is a strong, deterministic driver of microbial community assembly. We also observed enhanced N- and C-cycling rates along the transition from hypoxic to anoxic to sulfidic conditions, suggesting that microbial communities form a positive feedback loop that may accelerate deoxygenation and OMZ expansion.

Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

PubMed Central

Lee, Jackson Z.; Burow, Luke C.; Woebken, Dagmar; Everroad, R. Craig; Kubo, Mike D.; Spormann, Alfred M.; Weber, Peter K.; Pett-Ridge, Jennifer; Bebout, Brad M.; Hoehler, Tori M.

2013-01-01

Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico—permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)—were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H2 consumption. Incubation with 13C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi. PMID:24616716

The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans

PubMed Central

Beller, Harry R.; Chain, Patrick S. G.; Letain, Tracy E.; Chakicherla, Anu; Larimer, Frank W.; Richardson, Paul M.; Coleman, Matthew A.; Wood, Ann P.; Kelly, Donovan P.

2006-01-01

The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, β-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by β-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration. PMID:16452431

Activation of the Glutamic Acid-Dependent Acid Resistance System in Escherichia coli BL21(DE3) Leads to Increase of the Fatty Acid Biotransformation Activity

PubMed Central

Woo, Ji-Min; Kim, Ji-Won; Song, Ji-Won; Blank, Lars M.; Park, Jin-Byung

2016-01-01

The biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. The productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. Here, we have investigated factors that influence the tolerance of Escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. The metabolic and genomic responses of E. coli BL21(DE3) and MG1655 grown in the presence of n-heptanoic acid indicated that the GadA/B-based glutamic acid-dependent acid resistance (GDAR) system might be critical for cellular tolerance. The GDAR system, which is responsible for scavenging intracellular protons by catalyzing decarboxylation of glutamic acid, was inactive in E. coli BL21(DE3). Activation of the GDAR system in this strain by overexpressing the rcsB and dsrA genes, of which the gene products are involved in the activation of GadE and RpoS, respectively, resulted in acid tolerance not only to HCl but also to n-heptanoic acid. Furthermore, activation of the GDAR system allowed the recombinant E. coli BL21(DE3) expressing the alcohol dehydrogenase of Micrococcus luteus and the Baeyer-Villiger monooxygenase of Pseudomonas putida to reach 60% greater product concentration in the biotransformation of ricinoleic acid (i.e., 12-hydroxyoctadec-9-enoic acid (1)) into n-heptanoic acid (5) and 11-hydroxyundec-9-enoic acid (4). This study may contribute to engineering E. coli-based biocatalysts for the production of carboxylic acids from renewable biomass. PMID:27681369

Analysis of the Relationships between Waste Cooking Oil Qualities and Rejuvenated Asphalt Properties.

PubMed

Zhang, Dong; Chen, Meizhu; Wu, Shaopeng; Liu, Jingxiang; Amirkhanian, Serji

2017-05-06

Waste cooking oil (WCO), in many cases, can rejuvenate aged asphalt and restore its properties. However, the influence of WCO qualities on rejuvenation behaviors of aged asphalt has not been investigated in detail. The objective of this paper was to evaluate the effects of WCO viscosity and acid value on the basic, rheological, and chemical properties of a typical rejuvenated asphalt. Penetration, ring and ball (R and B) softening point, and ductility were tested to evaluate the influence of WCO qualities on basic properties of rejuvenated asphalts. Then, the rheological properties of rejuvenated asphalt were characterized based on rotational viscometer (RV), dynamic shear rheometer (DSR), and bending beam rheometer (BBR) test results. Further, SARA (saturates, aromatics, resins, and asphaltenes) fraction analysis and Fourier transform infrared spectroscopy (FTIR) tests were performed to investigate the effects of WCO qualities on asphalt chemical composition. Finally, grey correlation coefficients were calculated and the relationships between WCO qualities and rejuvenated asphalt properties were quantitatively evaluated. The experimental results indicated that WCO qualities influence the rejuvenation behaviors of aged asphalt significantly, and the WCO with higher qualities (low acid value and viscosity, as defined in this research) tends to achieve better rejuvenation effects. Based on the results of grey correlation analyses, the acid value is, relatively, a better indicator than viscosity in predicting the rejuvenation efficiency of WCO. The rejuvenation thresholds of WCO are varied with the categories of properties of rejuvenated asphalts, and WCO with an acid value of 0.4-0.7 mg KOH/g, or a viscosity of 140-540 mm²/s, can meet all of the performance requirements for asphalt rejuvenation used in this research.

Effect of Warm Asphalt Additive on the Creep and Recovery Behaviour of Aged Binder Containing Waste Engine Oil

NASA Astrophysics Data System (ADS)

Hassan, Norhidayah Abdul; Kamaruddin, Nurul Hidayah Mohd; Rosli Hainin, Mohd; Ezree Abdullah, Mohd

2017-08-01

The use of waste engine oil as an additive in asphalt mixture has been reported to be able to offset the stiffening effect caused by the recycled asphalt mixture. Additionally, the fumes and odor of the waste engine oil has caused an uncomfortable condition for the workers during road construction particularly at higher production temperature. Therefore, this problem was addressed by integrating chemical warm asphalt additive into the mixture which functions to reduce the mixing and compaction temperature. This study was initiated by blending the additive in the asphalt binder of bitumen penetration grade 80/100 prior to the addition of pavement mixture. The effect of chemical warm asphalt additive, Rediset WMX was investigated by modifying the aged binder containing waste engine oil with 0%, 1%, 2% and 3% by weight of the binder. The samples were then tested for determining the rutting behaviour under different loading stress levels of 3Pa (low), 10Pa (medium) and 50Pa (high) using Dynamic Shear Rheometer (DSR). A reference temperature of 60 °C was fixed to reflect the maximum temperature of the pavement. The results found that the addition of Rediset did not affect the creep and recovery behavior of the modified binder under different loading. On the other hand, 2% Rediset resulted a slight decrease in its rutting resistance as shown by the reduction of non-recoverable compliance under high load stress. However, overall, the inclusion of chemical warm asphalt additive to the modified binder did not adversely affect the rutting resistance which could be beneficial in lowering the temperature of asphalt production and simultaneously not compromising the binder properties.

Desulfomicrobium thermophilum sp. nov., a novel thermophilic sulphate-reducing bacterium isolated from a terrestrial hot spring in Colombia.

PubMed

Thevenieau, France; Fardeau, Marie-Laure; Ollivier, Bernard; Joulian, Catherine; Baena, Sandra

2007-03-01

A moderately thermophilic, sulphate-reducing bacterium, designated strain P6-2(T), was isolated from a terrestrial hot spring located at a height of 2,500 m in the Andean region, Colombia (5 degrees 43'69''N, 73 degrees 6'10''W). Cells of strain P6-2(T) were rod-shaped, stained Gram-negative and were motile by means of a single polar flagellum. The strain grew lithotrophically with H(2) as the electron donor and organotrophically on lactate, pyruvate, ethanol, malate, fumarate, n-propanol and succinate in the presence of sulphate as the terminal electron acceptor. Fumarate and pyruvate was fermented. Strain P6-2(T) grew optimally at 55 degrees C (range 37-60 degrees C), pH 6.6 (range 5.8-8.8) in the presence of 0.5% NaCl (range 0-4.5%) with lactate and sulphate and produced acetate, CO(2) and H(2)S as the major end-products. Sulphate, sulphite and thiosulphate could be used as electron acceptors but not elemental sulphur or nitrate. The G + C content of the genomic DNA was 58.7 mol%. The 16S rRNA sequence analysis indicated that strain P6-2(T) was a member of the class Deltaproteobacteria, domain Bacteria with Desulfomicrobium baculatum being the closest relative (similarity value of 94%). Phylogeny of genes encoding alpha- and beta-subunits of the dissimilatory sulphite reductase (dsrAB genes) supported its affiliation to members of the genus Desulfomicrobium. On the basis of this evidence, we propose to assign strain P6-2(T) as new species of the genus Desulfomicrobium, D. thermophilum sp. nov., with strain P6-2(T) as the type strain (= DSM 16697(T) = CCUG 49732(T)).

Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

DOE PAGES

Lee, Jackson Z.; Burow, Luke C.; Woebken, Dagmar; ...

2014-01-01

Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico$-$ permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)$-$were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H 2 production occurred under dark anoxic conditions with simultaneous production of a suitemore » of organic acids. H 2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO 2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H 2 consumption. Incubation with 13C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.« less

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer

DOE PAGES

Zhang, Ping; He, Zhili; Van Nostrand, Joy D.; ...

2017-03-16

To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H 2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, andmore » 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO 4 –2, U(VI), NO 3 –, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4–31 days, whereas Desulfobacterium became dominant at 80–140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant ( P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Lastly, our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.« less

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer

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

Zhang, Ping; He, Zhili; Van Nostrand, Joy D.

To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H 2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, andmore » 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO 4 –2, U(VI), NO 3 –, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4–31 days, whereas Desulfobacterium became dominant at 80–140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant ( P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Lastly, our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.« less

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer

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

Zhang, Ping; He, Zhili; Van Nostrand, Joy D.

To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced in this paper genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H 2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21more » ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO 4 –2, U(VI), NO 3 –, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4–31 days, whereas Desulfobacterium became dominant at 80–140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Finally, our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.« less

Molecular assessment of the sensitivity of sulfate-reducing microbial communities remediating mine drainage to aerobic stress.

PubMed

Lefèvre, Emilie; Pereyra, Luciana P; Hiibel, Sage R; Perrault, Elizabeth M; De Long, Susan K; Reardon, Kenneth F; Pruden, Amy

2013-09-15

Sulfate-reducing permeable reactive zones (SR-PRZs) are microbially-driven anaerobic systems designed for the removal of heavy metals and sulfate in mine drainage. Environmental perturbations, such as oxygen exposure, may adversely affect system stability and long-term performance. The objective of this study was to examine the effect of two successive aerobic stress events on the performance and microbial community composition of duplicate laboratory-scale lignocellulosic SR-PRZs operated using the following microbial community management strategies: biostimulation with ethanol or carboxymethylcellulose; bioaugmentation with sulfate-reducing or cellulose-degrading enrichments; inoculation with dairy manure only; and no inoculation. A functional gene-based approach employing terminal restriction fragment length polymorphism and quantitative polymerase chain reaction targeting genes of sulfate-reducing (dsrA), cellulose-degrading (cel5, cel48), fermentative (hydA), and methanogenic (mcrA) microbes was applied. In terms of performance (i.e., sulfate removal), biostimulation with ethanol was the only strategy that clearly had an effect (positive) following exposure to oxygen. In terms of microbial community composition, significant shifts were observed over the course of the experiment. Results suggest that exposure to oxygen more strongly influenced microbial community shifts than the different microbial community management strategies. Sensitivity to oxygen exposure varied among different populations and was particularly pronounced for fermentative bacteria. Although the community structure remained altered after exposure, system performance recovered, indicating that SR-PRZ microbial communities were functionally redundant. Results suggest that pre-exposure to oxygen might be a more effective strategy to improve the resilience of SR-PRZ microbial communities relative to bioaugmentation or biostimulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbial community functional structure in response to micro-aerobic conditions in sulfate-reducing sulfur-producing bioreactor.

PubMed

Yu, Hao; Chen, Chuan; Ma, Jincai; Xu, Xijun; Fan, Ronggui; Wang, Aijie

2014-05-01

Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur (S(0)) recovery, coupling sulfate reduction and sulfide oxidation. However, little is known about the impact of dissolved oxygen (DO) on the microbial functional structures in these systems. We used a high throughput tool (GeoChip) to evaluate the microbial community structures in a biological desulfurization reactor under micro-aerobic conditions (DO: 0.02-0.33 mg/L). The results indicated that the microbial community functional compositions and structures were dramatically altered with elevated DO levels. The abundances of dsrA/B genes involved in sulfate reduction processes significantly decreased (p < 0.05, LSD test) at relatively high DO concentration (DO: 0.33 mg/L). The abundances of sox and fccA/B genes involved in sulfur/sulfide oxidation processes significantly increased (p < 0.05, LSD test) in low DO concentration conditions (DO: 0.09 mg/L) and then gradually decreased with continuously elevated DO levels. Their abundances coincided with the change of sulfate removal efficiencies and elemental sulfur (S(0)) conversion efficiencies in the bioreactor. In addition, the abundance of carbon degradation genes increased with the raising of DO levels, showing that the heterotrophic microorganisms (e.g., fermentative microorganisms) were thriving under micro-aerobic condition. This study provides new insights into the impacts of micro-aerobic conditions on the microbial functional structure of sulfate-reducing sulfur-producing bioreactors, and revealed the potential linkage between functional microbial communities and reactor performance. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Metatranscriptome Analysis of Aquifer Samples Reveals Unexpected Metabolic Lifestyles Relevant to Active Biogeochemical Cycling

NASA Astrophysics Data System (ADS)

Beller, H. R.; Jewell, T. N. M.; Karaoz, U.; Banfield, J. F.; Brodie, E.; Williams, K. H.

2015-12-01

Modern molecular ecology techniques are revealing the metabolic potential of uncultivated microorganisms, but there is still much to be learned about the actual biogeochemical roles of microbes that have cultivated relatives. Here, we present metatranscriptomic and metagenomic data from a field study that provides evidence of coupled redox processes that have not been documented in cultivated relatives and, indeed, represent strains with metabolic traits that are novel with respect to closely related isolates. The data come from omics analysis of groundwater samples collected during an experiment in which nitrate (a native electron acceptor) was injected into a perennially suboxic aquifer in Rifle (CO). Transcriptional data indicated that just two groups of chemolithoautotrophic bacteria accounted for a very large portion (~80%) of overall community gene expression: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Metabolic lifestyles for Gallionellaceae strains that were novel compared to cultivated representatives included nitrate-dependent Fe(II) oxidation and S oxidation. Evidence for these metabolisms included highly correlated temporal expression in binned data of nitrate reductase (e.g., narGHI) genes (which have never been reported in Gallionellaceae genomes) and Fe(II) oxidation genes (e.g., mtoA) or S oxidation genes (e.g., dsrE, aprA). Of the two most active strains of S. denitrificans, only one showed strong expression of S oxidation genes, whereas the other was apparently using an unexpected (as-yet unidentified) primary electron donor. Transcriptional data added considerable interpretive value to this study, as (1) metagenomic data would not have highlighted these organisms, which had a disproportionately large role in community metabolism relative to their populations, and (2) co-expression of coupled pathway genes could not be predicted based solely on metagenomic data.

Effect of Crumb Rubber and Warm Mix Additives on Asphalt Aging, Rheological, and Failure Properties

NASA Astrophysics Data System (ADS)

Agrawal, Prashant

Asphalt-rubber mixtures have been shown to have useful properties with respect to distresses observed in asphalt concrete pavements. The most notable change in properties is a large increase in viscosity and improved low-temperature cracking resistance. Warm mix additives can lower production and compaction temperatures. Lower temperatures reduce harmful emissions and lower energy consumption, and thus provide environmental benefits and cut costs. In this study, the effects of crumb rubber modification on various asphalts such as California Valley, Boscan, Alaska North Slope, Laguna and Cold Lake were also studied. The materials used for warm mix modification were obtained from various commercial sources. The RAF binder was produced by Imperial Oil in their Nanticoke, Ontario, refinery on Lake Erie. A second commercial PG 52-34 (hereafter denoted as NER) was obtained/sampled during the construction of a northern Ontario MTO contract. Some regular tests such as Dynamic Shear Rheometer (DSR) and Bending Beam Rheometer (BBR), Multiple Stress Creep Recovery (MSCR) and some modified new protocols such as the extended BBR test (LS-308) and the Double-Edge Notched Tension (DENT) test (LS-299) are used to study, the effect of warm mix and a host of other additives on rheological, aging and failure properties. A comparison in the properties of RAF and NER asphalts has also been made as RAF is good quality asphalt and NER is bad quality asphalt. From the studies the effect of additives on chemical and physical hardening tendencies was found to be significant. The asphalt samples tested in this study showed a range of tendencies for chemical and physical hardening.

Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

PubMed Central

Holman, Hoi-Ying N.; DeSantis, Todd Z.; Wanner, Gerhard; Andersen, Gary L.; Perras, Alexandra K.; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A.; Wirth, Reinhard; Moissl-Eichinger, Christine

2014-01-01

Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. PMID:24971452

Race-dependent association of sulfidogenic bacteria with colorectal cancer.

PubMed

Yazici, Cemal; Wolf, Patricia G; Kim, Hajwa; Cross, Tzu-Wen L; Vermillion, Karin; Carroll, Timothy; Augustus, Gaius J; Mutlu, Ece; Tussing-Humphreys, Lisa; Braunschweig, Carol; Xicola, Rosa M; Jung, Barbara; Llor, Xavier; Ellis, Nathan A; Gaskins, H Rex

2017-11-01

Colorectal cancer (CRC) incidence is higher in African Americans (AAs) compared with non-Hispanic whites (NHWs). A diet high in animal protein and fat is an environmental risk factor for CRC development. The intestinal microbiota is postulated to modulate the effects of diet in promoting or preventing CRC. Hydrogen sulfide, produced by autochthonous sulfidogenic bacteria, triggers proinflammatory pathways and hyperproliferation, and is genotoxic. We hypothesised that sulfidogenic bacterial abundance in colonic mucosa may be an environmental CRC risk factor that distinguishes AA and NHW. Colonic biopsies from uninvolved or healthy mucosa from CRC cases and tumour-free controls were collected prospectively from five medical centres in Chicago for association studies. Sulfidogenic bacterial abundance in uninvolved colonic mucosa of AA and NHW CRC cases was compared with normal mucosa of AA and NHW controls. In addition, 16S rDNA sequencing was performed in AA cases and controls. Correlations were examined among bacterial targets, race, disease status and dietary intake. AAs harboured a greater abundance of sulfidogenic bacteria compared with NHWs regardless of disease status. Bilophila wadsworthia -specific dsrA was more abundant in AA cases than controls. Linear discriminant analysis of 16S rRNA gene sequences revealed five sulfidogenic genera that were more abundant in AA cases. Fat and protein intake and daily servings of meat were significantly higher in AAs compared with NHWs, and multiple dietary components correlated with a higher abundance of sulfidogenic bacteria. These results implicate sulfidogenic bacteria as a potential environmental risk factor contributing to CRC development in AAs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

PubMed

Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

What domains of clinical function should be assessed after sport-related concussion? A systematic review.

PubMed

Feddermann-Demont, Nina; Echemendia, Ruben J; Schneider, Kathryn J; Solomon, Gary S; Hayden, K Alix; Turner, Michael; Dvořák, Jiří; Straumann, Dominik; Tarnutzer, Alexander A

2017-06-01

Sport-related concussion (SRC) is a clinical diagnosis made after a sport-related head trauma. Inconsistency exists regarding appropriate methods for assessing SRC, which focus largely on symptom-scores, neurocognitive functioning and postural stability. Systematic literature review. MEDLINE, EMBASE, PsycINFO, Cochrane-DSR, Cochrane CRCT, CINAHL, SPORTDiscus (accessed July 9, 2016). Original (prospective) studies reporting on postinjury assessment in a clinical setting and evaluation of diagnostic tools within 2 weeks after an SRC. Forty-six studies covering 3284 athletes were included out of 2170 articles. Only the prospective studies were considered for final analysis (n=33; 2416 athletes). Concussion diagnosis was typically made on the sideline by an (certified) athletic trainer (55.0%), mainly on the basis of results from a symptom-based questionnaire. Clinical domains affected included cognitive, vestibular and headache/migraine. Headache, fatigue, difficulty concentrating and dizziness were the symptoms most frequently reported. Neurocognitive testing was used in 30/33 studies (90.9%), whereas balance was assessed in 9/33 studies (27.3%). The overall quality of the studies was considered low. The absence of an objective, gold standard criterion makes the accurate diagnosis of SRC challenging. Current approaches tend to emphasise cognition, symptom assessment and postural stability with less of a focus on other domains of functioning. We propose that the clinical assessment of SRC should be symptom based and interdisciplinary. Whenever possible, the SRC assessment should incorporate neurological, vestibular, ocular motor, visual, neurocognitive, psychological and cervical aspects. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

PubMed Central

Pester, Michael; Bittner, Norbert; Deevong, Pinsurang; Wagner, Michael; Loy, Alexander

2015-01-01

Methane emission from peatlands contributes substantially to global warming but is significantly reduced by sulfate reduction, which is fuelled by globally increasing aerial sulfur pollution. However, the biology behind sulfate reduction in terrestrial ecosystems is not well understood and the key players for this process as well as their abundance remained unidentified. Comparative 16S rRNA gene stable isotope probing in the presence and absence of sulfate indicated that a Desulfosporosinus species, which constitutes only 0.006% of the total microbial community 16S rRNA genes, is an important sulfate reducer in a long-term experimental peatland field site. Parallel stable isotope probing using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] identified no additional sulfate reducers under the conditions tested. For the identified Desulfosporosinus species a high cell-specific sulfate reduction rate of up to 341 fmol SO42− cell−1 day−1 was estimated. Thus, the small Desulfosporosinus population has the potential to reduce sulfate in situ at a rate of 4.0–36.8 nmol (g soil w. wt.)−1 day−1, sufficient to account for a considerable part of sulfate reduction in the peat soil. Modeling of sulfate diffusion to such highly active cells identified no limitation in sulfate supply even at bulk concentrations as low as 10 μM. Collectively, these data show that the identified Desulfosporosinus species, despite being a member of the ‘rare biosphere’, contributes to an important biogeochemical process that diverts the carbon flow in peatlands from methane to CO2 and, thus, alters their contribution to global warming. PMID:20535221

Trace element partitioning in fluvial tufa reveals variable portions of biologically influenced calcite precipitation

NASA Astrophysics Data System (ADS)

Ritter, Simon M.; Isenbeck-Schröter, Margot; Schröder-Ritzrau, Andrea; Scholz, Christian; Rheinberger, Stefan; Höfle, Bernhard; Frank, Norbert

2018-03-01

The formation of tufa is essentially influenced by biological processes and, in order to infer environmental information from tufa deposits, it has to be determined how the geochemistry of biologically influenced tufa deviates from equilibrium conditions between water and calcite precipitate. We investigated the evolution of the water and tufa geochemistry of consecutive tufa barrages in a small tufa-depositing creek in Southern Germany. High incorporation of divalent cations into tufa is ubiquitous, which is probably promoted by an influence of biofilms in the tufa element partitioning. The distribution coefficients for the incorporation of Mg, Sr and Ba into tufa at the Kaisinger creek D(Mg), D(Sr) and D(Ba) are 0.020-0.031, 0.13-0.18 and 0.26-0.43, respectively. This agrees with previous research suggesting that biofilm influenced tufa will be enriched in divalent cations over equilibrium values in the order of Mg < Sr < Ba. Furthermore, the incorporation of Mg, Sr and Ba into tufa of the Kaisinger creek decreases downstream, which can be attributed to changes of the relative portions of bio-influenced tufa formation with likely higher distribution coefficients and inorganically-driven tufa formation with likely lower distribution coefficients. Additionally, the distribution coefficients of metals in tufa of the Kaisinger creek D(Cd), D(Zn), D(Co) and D(Mn) show values of 11-22, 2.2-12, 0.7-4.9 and 30-57, respectively. These metals are highly enriched in upstream tufa deposits and their contents in tufa strongly decrease downstream. Such highly compatible elements could therefore be used to distinguish easily between different lateral sections in fluvial barrage-dam tufa depositional systems and could serve as a useful geochemical tool in studying ancient barrage-dam tufa depositional systems.

Controls of precipitation δ18O on the northwestern Tibetan Plateau: A case study at Ngari station

NASA Astrophysics Data System (ADS)

Guo, Xiaoyu; Tian, Lide; Wen, Rong; Yu, Wusheng; Qu, Dongmei

2017-06-01

The shifting atmospheric circulation between the Indian monsoon and the westerlies on the northwestern Tibetan Plateau (TP) influences precipitation as well as precipitation isotopes. Isotopic records will therefore show historical fluctuations. To understand better the factors controlling present day precipitation δ18O values on the northwestern TP, we made continuous observations of precipitation isotopes at Ngari station from 2010 to 2013. The drivers of precipitation δ18O were investigated using analyses of their statistical relations with temperature, precipitation amount, relative humidity, and convective activities based on outgoing longwave radiation (OLR) data from NOAA satellites, and downward shortwave radiation (DSR) data collected at the Ngari automatic weather station. Atmospheric circulation patterns from NCAR reanalysis, and moisture transport paths of individual events derived from the HYSPLIT model using NCEP data, were also used to trace moisture sources. The results of our study include: (1) The slope and intercept of the Local Meteoric Water Line (LMWL) at Ngari (δD = 8.51 δ18O + 11.57 (R2 = 0.97, p < 0.01)) were higher than for the Global Meteoric Water Line (GMWL), indicating drier local climatic conditions; (2) Precipitation δ18O values showed a weak ;temperature effect; and a weak ;precipitation amount effect; at Ngari; and (3) Convection (or temperature patterns) integrated over several days (0-20) preceding each event were determined to be the main driver of precipitation isotopic values in monsoon (or non-monsoon) season. The longer (shorter) periods of τm days when correlation coefficients between precipitation δ18O and OLR were at their maxima (minima) indicate deep convective activities (shorter moisture transportation pathways) in August (June, July, and September).

Quantification of Microbial Communities in Subsurface Marine Sediments of the Black Sea and off Namibia.

PubMed

Schippers, Axel; Kock, Dagmar; Höft, Carmen; Köweker, Gerrit; Siegert, Michael

2012-01-01

Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition - fluorescence in situ hybridization (CARD-FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 10(9) to 10(10) cells/mL at the sediment surface to 10(7)-10(9) cells/mL below one meter depth. Based on CARD-FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

Table grape consumption reduces adiposity and markers of hepatic lipogenesis and alters gut microbiota in butter fat-fed mice

PubMed Central

Baldwin, Jessie; Collins, Brian; Wolf, Patricia G.; Martinez, Kristina; Shen, Wan; Chuang, Chia-Chi; Zhong, Wei; Cooney, Paula; Cockrell, Chase; Chang, Eugene; Gaskins, H. Rex; McIntosh, Michael K.

2016-01-01

Our objective was to determine if consuming table grapes reduces adiposity and its metabolic consequences and alters gut microbiota in mice fed a high fat (HF), butter-rich diet. C57BL/6J mice were fed a low fat (LF) diet or HF diet with 3% or 5% grapes for 11 weeks. Total body and inguinal fat were moderately, but significantly reduced in mice fed both levels of grapes compared to their controls. Mice fed 5% grapes had lower liver weights and triglyceride levels, and decreased expression of glycerol-3-phosphate acyltransferase (Gpat1) compared to the 5% controls. Mice fed 3% grapes had lower hepatic mRNA levels of peroxisome proliferator-activated receptor gamma 2, sterol-CoA desaturase 1, fatty-acid binding protein 4, and Gpat1 compared to the 3% controls. Although grape feeding had only a minor impact on markers of inflammation or lipogenesis in adipose tissue or intestine, 3% grapes decreased the intestinal abundance of sulfidogenic Desulfobacter spp., and the Bilophila wadsworthia-specific dissimilatory sulfite reductase gene (dsrA-Bw), and tended to increase the abundance of the beneficial bacterium Akkermansia muciniphila compared to controls. Additionally, Bifidobacterium, Lactobacillus, Allobaculum, and several other genera correlated negatively with adiposity. Allobaculum in particular was increased in the LF and 3% grapes groups compared to the HF-fed controls. Notably, grape feeding attenuated the HF-induced impairment in epithelial localization of the intestinal tight junction protein zonula occludens. Collectively, these data indicate that some of the adverse health consequences of consuming a HF diet rich in saturated fat can be attenuated by table grape consumption. PMID:26423887

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.

PubMed

Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U; Schramm, Andreas

2016-07-01

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species. Copyright © 2016 The Author(s). Published by Elsevier GmbH.. All rights reserved.

Population-specific demographic estimates provide insights into declines of Lark Buntings (Calamospiza melanocorys)

USGS Publications Warehouse

Yackel Adams, A.A.; Skagen, S.K.; Savidge, J.A.

2007-01-01

Many North American prairie bird populations have recently declined, and the causes of these declines remain largely unknown. To determine whether population limitation occurs during breeding, we evaluated the stability of a population of prairie birds using population-specific values for fecundity and postfledging survival. During 2001-2003, we radiomarked 67 female Lark Buntings (Calamospiza melanocorys) to determine annual fecundity and evaluate contributing factors such as nest survival and breeding response (number of breeding attempts and dispersal). Collectively, 67 females built 112 nests (1.67 ± 0.07 nests female−1 season−1; range: 1–3); 34 were second nests and 11 were third nests. Daily nest survival estimates were similar for initial and later nests with overall nest survival (DSR19) of 30.7% and 31.7%, respectively. Nest predation was the most common cause of failure (92%). Capture and radiomarking of females did not affect nest survival. Lark Bunting dispersal probabilities increased among females that fledged young from initial nests and females that lost their original nests late in the season. Conservative and liberal estimates of mean annual fecundity were 0.96 ±0.11 and 1.24 ± 0.09 female offspring per female, respectively. Given the fecundity and juvenile-survival estimates for this population, annual adult survival values of 71–77% are necessary to achieve a stable population. Because adult survival of prairie passerines ranges between 55% and 65%, this study area may not be capable of sustaining a stable population in the absence of immigration. We contrast our population assessment with one that assumes indirect values of fecundity and juvenile survival. To elucidate limiting factors, estimation of population-specific demographic parameters is desirable. We present an approach for selecting species and areas for evaluation of population stability.

Design and implementation of spatial knowledge grid for integrated spatial analysis

NASA Astrophysics Data System (ADS)

Liu, Xiangnan; Guan, Li; Wang, Ping

2006-10-01

Supported by spatial information grid(SIG), the spatial knowledge grid (SKG) for integrated spatial analysis utilizes the middleware technology in constructing the spatial information grid computation environment and spatial information service system, develops spatial entity oriented spatial data organization technology, carries out the profound computation of the spatial structure and spatial process pattern on the basis of Grid GIS infrastructure, spatial data grid and spatial information grid (specialized definition). At the same time, it realizes the complex spatial pattern expression and the spatial function process simulation by taking the spatial intelligent agent as the core to establish space initiative computation. Moreover through the establishment of virtual geographical environment with man-machine interactivity and blending, complex spatial modeling, network cooperation work and spatial community decision knowledge driven are achieved. The framework of SKG is discussed systematically in this paper. Its implement flow and the key technology with examples of overlay analysis are proposed as well.

Rainfall Control of Karst Solution and the Inter/Intra Annual Hydrogeochemical Evolution of Cave Dripwater: A Long-term, Site-specific Study, Soreq Cave, Israel

NASA Astrophysics Data System (ADS)

Burstyn, Yuval; Bar-Matthews, Miryam; Ayalon, Avner; Matthews, Alan

2016-04-01

Speleothem laminae preserve climate information transferred to the cave via dripwater. High spatial resolution methods allow in situ measurement of geochemical and isotopic proxies at seasonal resolution. Existing hydrogeochemical calibration models suggest that high rainfall inhibits karst water chemical evolution, resulting in low δ 18O values, and low Mg/Ca and Sr/Ca ratios that are not necessarily correlated. Drought periods display opposite chemical behaviour owing to lower infiltration rates and increased Prior Calcite Precipitation (PCP). This study aims to provide a site-specific, high-resolution hydrogeochemical calibration for the Soreq Cave. We examine four sites that were continuously sampled since 1990. Four main rainfall conditions are characterized: very wet years, average, drought and very dry years. Two sites are fed by 'fast drips', which only become active after ˜ 250mm rainfall has accumulated since the beginning of the winter season. Two sites, located deeper in the cave, are fed by 'slow drips' that are active all year round. Drip rate measurements identify two main reservoirs - fissure and matrix - that mainly differ in residence time. The δ 18O of fissure water is closer to that of mean annual rainfall (˜ -6 ‰VSMOW), while matrix values are higher (˜ -3.5 ‰VSMOW). Two main Sr and Mg sources are identified - dolomitic bedrock (Mg/Ca ˜ 700 mM/M, Sr/Ca ˜ 0.4 mM/M) and soil leachate (Mg/Ca ˜ 300 mM/M, Sr/Ca ˜ 1.1 mM/M). Most cave dripwater evolves from ˜ 1:1 soil-bedrock solution. PCP effect on dripwater solution at each site is estimated by comparing the ln(Mg/Ca) vs ln(Sr/Ca) linear slope to the PCP slope calculated using cave specific D(Mg) and D(Sr). Soreq Cave PCP slope is similar to the global slope of 0.88± 0.13. The composition and chemical evolution of each reservoir and its contribution to water influx at each site is primarily governed by annual effective infiltration. Higher seasonal amplitude in δ 18O, Mg/Ca and Sr/Ca in all sites is positively correlated to increase in rainfall. For the deeper site, with rock cover of >40 m, the `classic' wet-dry model can be applied - more soil input and less PCP in the wetter years and vice-versa. Conversely, in the shallower sites, high PCP is observed in wetter years. Results from this study are compared with high-resolution δ 18O and trace element records of modern speleothems (age ˜ 20y). The speleothem from the deeper site shows a good match with the hydrogeochemical data, thus supporting the applicability of the model to palaeoclimate studies. However, the speleothem from the shallow site shows a strong winter bias, which may be due to complete secession of summer drip during dry years (micro-hiatuses), or during wetter years, considerable winter calcite precipitation resulting in minimal summer imprint on each seasonal lamina. We plan to analyse a fast growing modern sample from the shallow site to resolve this seasonal bias. Therefore, contemporaneous speleothem records from different sites can be utilized to estimate past changes in annual and decadal effective infiltration, allowing evaluation of water availability in the region during periods of rapid climate change. [1] Orland, I.J. et al. 2014. Chemical Geology, v. 363, p. 322-333.

A Big Spatial Data Processing Framework Applying to National Geographic Conditions Monitoring

NASA Astrophysics Data System (ADS)

Xiao, F.

2018-04-01

In this paper, a novel framework for spatial data processing is proposed, which apply to National Geographic Conditions Monitoring project of China. It includes 4 layers: spatial data storage, spatial RDDs, spatial operations, and spatial query language. The spatial data storage layer uses HDFS to store large size of spatial vector/raster data in the distributed cluster. The spatial RDDs are the abstract logical dataset of spatial data types, and can be transferred to the spark cluster to conduct spark transformations and actions. The spatial operations layer is a series of processing on spatial RDDs, such as range query, k nearest neighbor and spatial join. The spatial query language is a user-friendly interface which provide people not familiar with Spark with a comfortable way to operation the spatial operation. Compared with other spatial frameworks, it is highlighted that comprehensive technologies are referred for big spatial data processing. Extensive experiments on real datasets show that the framework achieves better performance than traditional process methods.

Disgust and fear: common emotions between eating and phobic disorders.

PubMed

Bou Khalil, Rami; Bou-Orm, Ibrahim R; Tabet, Yara; Souaiby, Lama; Azouri, Hayat

2018-05-15

Eating disorders (ED) are prevalent mental illnesses composed mainly of anorexia nervosa, bulimia nervosa and binge eating disorders. Anxiety disorders are another set of mental illnesses, with phobic disorder (PD) being the most prevalent disorder. ED and PD are highly comorbid. The aim of this study is to assess, in 131 individuals attending an outpatient clinic for different health issues, the level of fear related to situations generating avoidance such as in social anxiety and specific phobias according to the fear questionnaire (FQ), the level of disgust according to the disgust scale (DS-R) and the vulnerability towards ED according to the SCOFF scale to demonstrate that high levels of both fear and disgust increase the vulnerability towards ED. The study demonstrated that the level of disgust increased when fear increases (r = 0.377, p < 0.001 for the first part of the FQ; r = 0.225, p = 0.01 for the second part of the FQ). Moreover, individuals with vulnerability towards having an ED presented a higher level of disgust than individuals without this vulnerability (p = 0.009). Furthermore, individuals with vulnerability towards ED have a higher level of anxiety related to PD subtypes (p = 0.008 for agoraphobia; p = 0.001 for injection/blood phobia) as well as to social anxiety (p = 0.01), independently from having a depressive or another anxiety disorder. In the multivariate analysis, a history of psychiatric consultation has been the only significantly different parameter between individuals with or without vulnerability towards ED (p = 0.0439). Accordingly, fear and disgust are negative emotions that seem to be clinically associated which better explains the comorbidity of ED with PD. Level III. Evidence obtained from well-designed cohort or case-control analytic studies, preferably from more than one center or research group.

Contrasting nest survival patterns for ducks and songbirds in northern mixed-grass prairie

USGS Publications Warehouse

Grant, Todd; Shaffer, Terry L.; Madden, Elizabeth M.; Nenneman, Melvin P.

2017-01-01

Management actions intended to protect or improve habitat for ducks may benefit grassland-nesting passerines, but scant information is available to explore this assumption. During 1998–2003, we examined nest survival of ducks and songbirds to determine whether effects of prescribed fire and other habitat features (e.g., shrub cover and distance to habitat edges) were similar for ducks and passerines breeding in North Dakota. We used the logistic-exposure method to estimate survival of duck and songbird nests (n = 3,171). We used an information-theoretic approach to identify factors that most influenced nest survival. Patterns of nest survival were markedly different between taxonomic groups. For ducks, nest survival was greater during the first postfire nesting season (daily survival rate [DSR] = 0.957, 85% CI = 0.951–0.963), relative to later postfire nesting seasons (DSR = 0.946, 85% CI = 0.942–0.950). Furthermore duck nest survival and nest densities were inversely related. Duck nest survival also was greater as shrub cover decreased and as distance from cropland and wetland edges increased. Passerines had lower nest survival during the first postfire nesting season (DSR = 0.934, 85% CI = 0.924–0.944), when densities also were low compared to subsequent postfire nesting seasons (DSR = 0.947, 85% CI = 0.944–0.950). Parasitism by brown-headed cowbirds (Molothrus ater) reduced passerine nest survival and this effect was more pronounced during the first postfire nesting season compared to subsequent nesting seasons. Passerine nest survival was greater as shrub cover decreased and perhaps for more concealed nests. Duck and songbird nest survival rates were not correlated during this study and for associated studies that examined additional variables using the same dataset, suggesting that different mechanisms influenced their survival. Based on our results, ducks should not be considered direct surrogates for passerines when predicting effects of prescribed fire, shrub cover, and habitat edges on nest survival.

Sandhill crane abundance and nesting ecology at Grays Lake, Idaho

USGS Publications Warehouse

Austin, J.E.; Henry, A.R.; Ball, I.J.

2007-01-01

We examined population size and factors influencing nest survival of greater sandhill cranes (Grus canadensis tabida) at Grays Lake National Wildlife Refuge, Idaho, USA, during 1997-2000. Average local population of cranes from late April to early May, 1998-2000, was 735 cranes, 34% higher than that reported for May 1970-1971. We estimated 228 (SE = 30) nests in the basin core (excluding renests), 14% higher than a 1971 estimate. Apparent nest success in our study (x?? = 60%, n = 519 nests) was lower than reported for Grays Lake 30-50 years earlier. Daily survival rates (DSRs) of all nests averaged 0.9707 (41.2%). The best model explaining nest survival included year and water depth and their interaction. Nest survival was highest (DSR = 0.9827) in 1998 compared with other years (0.9698-0.9707). Nest survival changed little relative to water depth in 1998, when flooding was extensive and alternative prey (microtines) irrupted, but declined markedly with lower water levels in 2000, the driest year studied. Hypotheses relating nest survival to vegetation height, land use (idle, summer grazing, fall grazing), and date were not supported. In a before-after-control-impact design using 12 experimental fields, nest survival differed among years but not among management treatments (idle, fall graze, fall burn, and summer-graze-idle rotation), nor was there an interaction between year and treatments. However, DSRs in fall-burn fields declined from 0.9781 in 1997-1998 to 0.9503 in 1999-2000 (posttreatment). Changes in the predator community have likely contributed to declines in nest success since the 1950s and 1970s. Our results did not support earlier concerns about effects of habitat management practices on crane productivity. Nest survival could best be enhanced by managing spring water levels. Managers should continue censuses during late April to evaluate long-term relationships to habitat conditions and management.

Euphausiid distribution along the Western Antarctic Peninsula—Part A: Development of robust multi-frequency acoustic techniques to identify euphausiid aggregations and quantify euphausiid size, abundance, and biomass

NASA Astrophysics Data System (ADS)

Lawson, Gareth L.; Wiebe, Peter H.; Stanton, Timothy K.; Ashjian, Carin J.

2008-02-01

Methods were refined and tested for identifying the aggregations of Antarctic euphausiids ( Euphausia spp.) and then estimating euphausiid size, abundance, and biomass, based on multi-frequency acoustic survey data. A threshold level of volume backscattering strength for distinguishing euphausiid aggregations from other zooplankton was derived on the basis of published measurements of euphausiid visual acuity and estimates of the minimum density of animals over which an individual can maintain visual contact with its nearest neighbor. Differences in mean volume backscattering strength at 120 and 43 kHz further served to distinguish euphausiids from other sources of scattering. An inversion method was then developed to estimate simultaneously the mean length and density of euphausiids in these acoustically identified aggregations based on measurements of mean volume backscattering strength at four frequencies (43, 120, 200, and 420 kHz). The methods were tested at certain locations within an acoustically surveyed continental shelf region in and around Marguerite Bay, west of the Antarctic Peninsula, where independent evidence was also available from net and video systems. Inversion results at these test sites were similar to net samples for estimated length, but acoustic estimates of euphausiid density exceeded those from nets by one to two orders of magnitude, likely due primarily to avoidance and to a lesser extent to differences in the volumes sampled by the two systems. In a companion study, these methods were applied to the full acoustic survey data in order to examine the distribution of euphausiids in relation to aspects of the physical and biological environment [Lawson, G.L., Wiebe, P.H., Ashjian, C.J., Stanton, T.K., 2008. Euphausiid distribution along the Western Antarctic Peninsula—Part B: Distribution of euphausiid aggregations and biomass, and associations with environmental features. Deep-Sea Research II, this issue [doi:10.1016/j.dsr2.2007.11.014

Performance evaluation of reactive and proactive routing protocol in IEEE 802.11 ad hoc network

NASA Astrophysics Data System (ADS)

Hamma, Salima; Cizeron, Eddy; Issaka, Hafiz; Guédon, Jean-Pierre

2006-10-01

Wireless technology based on the IEEE 802.11 standard is widely deployed. This technology is used to support multiple types of communication services (data, voice, image) with different QoS requirements. MANET (Mobile Adhoc NETwork) does not require a fixed infrastructure. Mobile nodes communicate through multihop paths. The wireless communication medium has variable and unpredictable characteristics. Furthermore, node mobility creates a continuously changing communication topology in which paths break and new one form dynamically. The routing table of each router in an adhoc network must be kept up-to-date. MANET uses Distance Vector or Link State algorithms which insure that the route to every host is always known. However, this approach must take into account the adhoc networks specific characteristics: dynamic topologies, limited bandwidth, energy constraints, limited physical security, ... Two main routing protocols categories are studied in this paper: proactive protocols (e.g. Optimised Link State Routing - OLSR) and reactive protocols (e.g. Ad hoc On Demand Distance Vector - AODV, Dynamic Source Routing - DSR). The proactive protocols are based on periodic exchanges that update the routing tables to all possible destinations, even if no traffic goes through. The reactive protocols are based on on-demand route discoveries that update routing tables only for the destination that has traffic going through. The present paper focuses on study and performance evaluation of these categories using NS2 simulations. We have considered qualitative and quantitative criteria. The first one concerns distributed operation, loop-freedom, security, sleep period operation. The second are used to assess performance of different routing protocols presented in this paper. We can list end-to-end data delay, jitter, packet delivery ratio, routing load, activity distribution. Comparative study will be presented with number of networking context consideration and the results show the appropriate routing protocol for two kinds of communication services (data and voice).

Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)

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

Rodriguez-Martinex, Enid M.; Perez, Ernie; Schadt, Christopher Warren

2006-01-01

Hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. Our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. Under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic retention time. Over 25 different cultures were isolated from the treatment unit (96% which utilized diesel constituents as sole carbon source). Approximately 20% of the isolates were also capable ofmore » complete denitrification to nitrogen gas. Sequence analysis of 16S rDNA demonstrated ample diversity with most belonging to the {infinity}, {beta} and {gamma} subdivision of the Proteobacteria, Bacilli, and Actinobacteria groups. Moreover, the genetic constitution of the microbial community was examined at multiple time points with a Functional Gene Array (FGA) containing over 12,000 probes for genes involved in organic degradation and major biogeochemical cycles. Total community DNA was extracted and amplified using an isothermal {phi}29 polymerase-based technique, labeled with Cy5 dye, and hybridized to the arrays in 50% formimide overnight at 50 C. Cluster analysis revealed comparable profiles over the course of treatment suggesting the early selection of a very stable microbial community. A total of 270 genes for organic contaminant degradation (including naphthalene, toluene [aerobic and anaerobic], octane, biphenyl, pyrene, xylene, phenanthrene, and benzene); and 333 genes involved in metabolic activities (nitrite and nitrous oxide reductases [nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB], potential metal reducing C-type cytochromes, and methane monooxygenase [pmoA]) were repeatedly detected. Genes for degradation of MTBE, nitroaromatics and chlorinated compounds were also present, indicating a broad catabolic potential of the treatment unit. FGA's demonstrated the early establishment of a diverse community with concurrent aerobic and anaerobic processes contributing to the bioremediation process.« less

Microbial Diversity and Bioremediation of aHydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)

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

Rodriguez-Martinez, E.M.; Perez, Ernie X.; Schadt, ChristopherW.

2006-09-30

Hydrocarbon contamination of groundwater resources hasbecome a major environmental and human health concern in many parts ofthe world. Our objectives were to employ both culture andculture-independent techniques to characterize the dynamics of microbialcommunity structure within a fluidized bed reactor used to bioremediate adiesel-contaminated groundwater in a tropical environment. Under normaloperating conditions, 97 to 99 percent of total hydrocarbons were removedwith only 14 min hydraulic retention time. Over 25 different cultureswere isolated from the treatment unit (96 percent which utilized dieselconstituents as sole carbon source). Approximately 20 percent of theisolates were also capable of complete denitrification to nitrogen gas.Sequence analysis ofmore » 16S rDNA demonstrated ample diversity with mostbelonging to the infinity, beta and gamma subdivision of theProteobacteria, Bacilli, and Actinobacteria groups. Moreover, the geneticconstitution of the microbial community was examined at multiple timepoints with a Functional Gene Array (FGA) containing over 12,000 probesfor genes involved in organic degradation and major biogeochemicalcycles. Total community DNA was extracted and amplified using anisothermal phi29 polymerase-based technique, labeled with Cy5 dye, andhybridized to the arrays in 50 percent formimide overnight at 50 degreesC. Cluster analysis revealed comparable profiles over the course oftreatment suggesting the early selection of a very stable microbialcommunity. A total of 270 genes for organic contaminant degradation(including naphthalene, toluene [aerobic and anaerobic], octane,biphenyl, pyrene, xylene, phenanthrene, and benzene); and 333 genesinvolved in metabolic activities (nitrite and nitrous oxide reductases[nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB],potential metal reducing C-type cytochromes, and methane monooxygenase[pmoA]) were repeatedly detected. Genes for degradation of MTBE,nitroaromatics and chlorinated compounds werealso present, indicating abroad catabolic potential of the treatment unit. FGA's demonstrated theearly establishment of a diverse community with concurrent aerobic andanaerobic processes contributing to the bioremediationprocess.« less

[caCORE: core architecture of bioinformation on cancer research in America].

PubMed

Gao, Qin; Zhang, Yan-lei; Xie, Zhi-yun; Zhang, Qi-peng; Hu, Zhang-zhi

2006-04-18

A critical factor in the advancement of biomedical research is the ease with which data can be integrated, redistributed and analyzed both within and across domains. This paper summarizes the Biomedical Information Core Infrastructure built by National Cancer Institute Center for Bioinformatics in America (NCICB). The main product from the Core Infrastructure is caCORE--cancer Common Ontologic Reference Environment, which is the infrastructure backbone supporting data management and application development at NCICB. The paper explains the structure and function of caCORE: (1) Enterprise Vocabulary Services (EVS). They provide controlled vocabulary, dictionary and thesaurus services, and EVS produces the NCI Thesaurus and the NCI Metathesaurus; (2) The Cancer Data Standards Repository (caDSR). It provides a metadata registry for common data elements. (3) Cancer Bioinformatics Infrastructure Objects (caBIO). They provide Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. The vision for caCORE is to provide a common data management framework that will support the consistency, clarity, and comparability of biomedical research data and information. In addition to providing facilities for data management and redistribution, caCORE helps solve problems of data integration. All NCICB-developed caCORE components are distributed under open-source licenses that support unrestricted usage by both non-profit and commercial entities, and caCORE has laid the foundation for a number of scientific and clinical applications. Based on it, the paper expounds caCORE-base applications simply in several NCI projects, of which one is CMAP (Cancer Molecular Analysis Project), and the other is caBIG (Cancer Biomedical Informatics Grid). In the end, the paper also gives good prospects of caCORE, and while caCORE was born out of the needs of the cancer research community, it is intended to serve as a general resource. Cancer research has historically contributed to many areas beyond tumor biology. At the same time, the paper makes some suggestions about the study at the present time on biomedical informatics in China.

New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.

PubMed

Imhoff, Johannes F

2016-05-24

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

PubMed

Roux, Simon; Brum, Jennifer R; Dutilh, Bas E; Sunagawa, Shinichi; Duhaime, Melissa B; Loy, Alexander; Poulos, Bonnie T; Solonenko, Natalie; Lara, Elena; Poulain, Julie; Pesant, Stéphane; Kandels-Lewis, Stefanie; Dimier, Céline; Picheral, Marc; Searson, Sarah; Cruaud, Corinne; Alberti, Adriana; Duarte, Carlos M; Gasol, Josep M; Vaqué, Dolors; Bork, Peer; Acinas, Silvia G; Wincker, Patrick; Sullivan, Matthew B

2016-09-29

Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass.

PubMed

Wright, Katherine E; Williamson, Charles; Grasby, Stephen E; Spear, John R; Templeton, Alexis S

2013-01-01

We combined free enenergy calculations and metagenomic analyses of an elemental sulfur (S(0)) deposit on the surface of Borup Fiord Pass Glacier in the Canadian High Arctic to investigate whether the energy available from different redox reactions in an environment predicts microbial metabolism. Many S, C, Fe, As, Mn, and [Formula: see text] oxidation reactions were predicted to be energetically feasible in the deposit, and aerobic oxidation of S(0) was the most abundant chemical energy source. Small subunit ribosomal RNA (SSU rRNA) gene sequence data showed that the dominant phylotypes were Sulfurovum and Sulfuricurvum, both Epsilonproteobacteria known to be capable of sulfur lithotrophy. Sulfur redox genes were abundant in the metagenome, but sox genes were significantly more abundant than reverse dsr (dissimilatory sulfite reductase)genes. Interestingly, there appeared to be habitable niches that were unoccupied at the depth of genome coverage obtained. Photosynthesis and [Formula: see text] oxidation should both be energetically favorable, but we found few or no functional genes for oxygenic or anoxygenic photosynthesis, or for [Formula: see text] oxidation by either oxygen (nitrification) or nitrite (anammox). The free energy, SSU rRNA gene and quantitative functional gene data are all consistent with the hypothesis that sulfur-based chemolithoautotrophy by Epsilonproteobacteria (Sulfurovum and Sulfuricurvum) is the main form of primary productivity at this site, instead of photosynthesis. This is despite the presence of 24-h sunlight, and the fact that photosynthesis is not known to be inhibited by any of the environmental conditions present. This is the first time that Sulfurovum and Sulfuricurvum have been shown to dominate a sub-aerial environment, rather than anoxic or sulfidic settings. We also found that Flavobacteria dominate the surface of the sulfur deposits. We hypothesize that this aerobic heterotroph uses enough oxygen to create a microoxic environment in the sulfur below, where the Epsilonproteobacteria can flourish.

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle

PubMed Central

Zapata-Peñasco, Icoquih; Poot-Hernandez, Augusto Cesar; Eguiarte, Luis E

2017-01-01

Abstract The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large “omic” datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H΄), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa. PMID:29069412

Structure-function relationships of bacterial and enzymatically produced reuterans and dextran in sourdough bread baking application.

PubMed

Chen, Xiao Yan; Levy, Clemens; Gänzle, Michael G

2016-12-19

Exopolysaccharides from lactic acid bacteria may improve texture and shelf life of bread. The effect of exopolysaccharides on bread quality, however, depends on properties of the EPS and the EPS producing strain. This study investigated structure-function relationships of EPS in baking application. The dextransucrase DsrM and the reuteransucrase GtfA were cloned from Weissella cibaria 10M and Lactobacillus reuteri TMW1.656, respectively, and heterologously expressed in Escherichia coli. Site-directed mutagenesis of GtfA was generates reuterans with different glycosidic bonds. NMR spectrum indicated reuteranPI, reuteranNS and reuteranPINS produced by GtfA-V1024P:V1027I, GtfA-S1135N:A1137S and GtfA-V1024P:V1027I:S1135N:A1137S, respectively, had a higher proportion of α-(1→4) linkages when compared to reuteran. ReuteranNS has the lowest molecular weight as measured by asymmetric flow-field-flow fractionation. The reuteransucrase negative mutant L. reuteri TMW1.656ΔgtfA was generated as EPS-negative derivative of L. reuteri TMW1.656. Cell counts, pH, and organic acid levels of sourdough fermented with L. reuteri TMW1.656 and TMW1.656ΔgtfA were comparable. Reuteran produced by L. reuteri TMW1.656 during growth in sourdough and reuteran produced ex situ by GtfA-ΔN had comparable effects on bread volume and crumb hardness. Enzymatically produced dextran improved volume and texture of wheat bread, and of bread containing 20% rye flour. ReuteranNS but not reuteranPI or reuteran was as efficient as dextran in enhancing wheat bread volume and texture. Overall, reuteran linkage type and molecular weight are determinants of EPS effects on bread quality. This study established a valuable method to elucidate structure-function relationships of glucans in baking applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

NASA Astrophysics Data System (ADS)

2016-09-01

Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.