Science.gov

Sample records for simultaneous multiple species

  1. Acoustic classification of multiple simultaneous bird species: a multi-instance multi-label approach.

    PubMed

    Briggs, Forrest; Lakshminarayanan, Balaji; Neal, Lawrence; Fern, Xiaoli Z; Raich, Raviv; Hadley, Sarah J K; Hadley, Adam S; Betts, Matthew G

    2012-06-01

    Although field-collected recordings typically contain multiple simultaneously vocalizing birds of different species, acoustic species classification in this setting has received little study so far. This work formulates the problem of classifying the set of species present in an audio recording using the multi-instance multi-label (MIML) framework for machine learning, and proposes a MIML bag generator for audio, i.e., an algorithm which transforms an input audio signal into a bag-of-instances representation suitable for use with MIML classifiers. The proposed representation uses a 2D time-frequency segmentation of the audio signal, which can separate bird sounds that overlap in time. Experiments using audio data containing 13 species collected with unattended omnidirectional microphones in the H. J. Andrews Experimental Forest demonstrate that the proposed methods achieve high accuracy (96.1% true positives/negatives). Automated detection of bird species occurrence using MIML has many potential applications, particularly in long-term monitoring of remote sites, species distribution modeling, and conservation planning.

  2. Development of a bead-based multiplex PCR assay for the simultaneous detection of multiple Mycoplasma species.

    PubMed

    Righter, Daniel J; Rurangirwa, Fred R; Call, Douglas R; McElwain, Terry F

    2011-12-15

    We describe the development and analytical validation of a 7-plex polymerase chain reaction assay coupled to a bead-based liquid suspension array for detection of multiple ruminant Mycoplasma spp. The assay employs a combination of newly designed and previously validated primer-probe sets that target genetic loci specific for Mycoplasma bovis, Mycoplasma mycoides cluster, Mycoplasma mycoides subsp. mycoides SC (MmmSC) and Mycoplasma capricolum subspecies capripneumoniae (Mccp). Analytical sensitivity for the targeted Mycoplasma species ranged from 10 fg to 1 pg of purified gDNA extracted from broth cultures (approximately 8-800 MmmSC genome equivalents). In silico comparison of primers and probes, and analytical assessment with a range of near-neighbor Mycoplasma species and multiple bacterial respiratory pathogens demonstrated 100% analytical specificity of the assay. To assess assay performance and diagnostic specificity, 192 bovine respiratory samples were analyzed by incorporating a high throughput DNA extraction platform. The assay correctly classified all samples as negative for MmmSC or Mccp. All 33 field samples confirmed as positive for M. bovis by sequencing the uvrC gene were positive in the assay. The results from this study indicate that the bead-based liquid suspension array will provide a reliable, analytically sensitive and specific platform to simultaneously interrogate ruminant respiratory samples for multiple Mycoplasma species, including M. mycoides cluster organisms that are exotic to the United States. Sequential addition of primer-probe sets to the assay did not significantly impact analytical sensitivity of individual primer-probe combinations, suggesting that expanding the assay to include more Mycoplasma species will not compromise overall performance.

  3. Combined coherent anti-Stokes Raman spectroscopy and linear Raman spectroscopy for simultaneous temperature and multiple species measurements.

    PubMed

    Weikl, Markus C; Beyrau, Frank; Kiefer, Johannes; Seeger, Thomas; Leipertz, Alfred

    2006-06-15

    The simultaneous application of pure rotational coherent anti-Stokes Raman spectroscopy (CARS) and vibrational linear Raman spectroscopy (LRS) for the measurement of temperature and species concentrations in combustion systems is demonstrated. In addition to the standard rotational CARS experimental setup, only one detection system (spectrometer and intensified CCD camera) for the collection of the LRS signals was applied. The emission of the broadband dye laser used for CARS was shifted to the deep red to avoid interferences with the LRS signals located in the visible region. First experimental results from a vaporizing propane spray using an engine injection system are shown.

  4. A simultaneous multiple species acute toxicity test comparing relative sensitivities of six aquatic organisms to HgCl{sub 2}

    SciTech Connect

    McCrary, J.E.; Heagler, M.G.

    1995-12-31

    In the last few years there has been concern in the scientific community about observed declines in some amphibian species. These population declines could be reflecting a global phenomenon due to a general class sensitivity or may be part of a natural cycle. The suggestion of an overall greater sensitivity of amphibians is not supported. Studies show that amphibians, as a class, are neither more or less susceptible than fish to environmental conditions. Mercury has been found to be one of the most toxic of the heavy metals introduced into amphibian breeding waters. Six aquatic species were simultaneously exposed in a comparative acute toxicity test with mercury chloride: three amphibians, Rana catesbeiana (bullfrog), R. clamitans (green frog), and R. sphenocephala (southern leopard frog, formally classified as R. utricularia); two fish, Gambusia affinis (mosquitofish) and Notemigonus crysoleucas (golden shiner); one aquatic aligochaete, Lumbriculus variegatus (aquatic earthworm). The five test concentrations used were 1.4, 3.9, 12.0, 110.0, and 487.0 {micro}g Hg/L respectively. Ten organisms per species were randomly placed into the six test tanks (control and five concentrations), each species in a separate chamber. The resultant LC50-96hr values produced the following rank order: R. sphenocephala, 6.59 {micro}g Hg/L; R. clamitans, 14.7 {micro}g Hg/L; N. crysoleucas, 16.75 {micro}g Hg/L; L. variegatus, 43.72,ug Hg/L; G. affinis, 52.62 {micro}g Hg/L; R. catesbeiana, 63.36 {micro}g Hg/L. No general organism class sensitivity trend, for amphibians, was developed from this data, contrary to the implicit suggestions of some researchers.

  5. Reconstructing species phylogeny of the carabid beetles Ohomopterus using multiple nuclear DNA sequences: heterogeneous information content and the performance of simultaneous analyses.

    PubMed

    Sota, Teiji; Vogler, Alfried P

    2003-01-01

    We attempted a phylogenetic reconstruction for the carabid subgenus Ohomopterus (genus Carabus), a notable case of radiation with mitochondrial introgression across species. Sequence data from five nuclear single copy loci were used, including wingless (Wg), phosphoenolpyruvate carboxykinase (PepCK), cytochrome c (Cytc), elongation factor-1alpha (EF-1alpha), and an anonymous single copy locus (Carab1). Sequences of Cytc, EF-1alpha, and Carab1 included intron or intron-like parts with length variation. The analysis of individual loci resulted in low resolution of the phylogenetic relationships, and the monophyly of several morphologically recognized species for which multiple specimens were analyzed was not revealed. Several specimens were heterozygous, with non-monophyletic alleles observed in three of the five loci at which alleles in heterozygotes were separated. In a simultaneous analysis of the five loci with ambiguously aligned parts eliminated and heterozygotic sites treated as missing, the resulting tree was well resolved, but the branch support was generally weak because of conflicting phylogenetic signals from different loci. We also attempted to incorporate allelic sequence data plus the ambiguously aligned parts in the analysis, by using all possible combinations of alleles from different loci in heterozygotic individuals, but the resultant tree was not supported more strongly. Nonetheless, these simultaneous analyses provided support for the monophyly of several species and species groups, and revealed the basic evolutionary trend of OHOMOPTERUS: initial widespread groups with simpler genitalia and the origination of exaggerated genitalia in a derived clade. This study exemplifies problems inherent in the phylogenetic reconstruction of closely related organisms where low levels of variation limit the information content from each locus, while heterozygosity, different phylogenetic history of multiple loci, and alignment ambiguity further hamper

  6. Simultaneous quantification of multiple magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Rauwerdink, Adam M.; Giustini, Andrew J.; Weaver, John B.

    2010-11-01

    Distinct magnetic nanoparticle designs can have unique spectral responses to an AC magnetic field in a technique called the magnetic spectroscopy of Brownian motion (MSB). The spectra of the particles have been measured using desktop spectrometers and in vivo measurements. If multiple particle types are present in a region of interest, the unique spectral signatures allow for the simultaneous quantification of the various particles. We demonstrate such a potential experimentally with up to three particle types. This ability to concurrently detect multiple particles will enable new biomedical applications.

  7. Simultaneous use of multiple seismic arrays

    NASA Astrophysics Data System (ADS)

    Stipčević, J.; Kennett, B. L. N.; Tkalčić, H.

    2017-01-01

    Seismic arrays provide an important means of enhancing seismic signals and determining the directional properties of the wavefield by beam-forming. When multiple arrays are to be used together, the viewpoint needs to be modified from looking outwards from each array to focusing on a specific target area and so constraining the portions of the waveforms to be analysed. Beam-forming for each array is supplemented by the relative time constraints for propagation from the target to each array to provide tight spatial control. Simultaneous multiple array analysis provides a powerful tool for source characterisation, and for structural analysis of scatterers as virtual sources. The multiple array concept allows us to illuminate a specific point in the Earth from many different directions and thus map detailed patterns of heterogeneity in the Earth. Furthermore, illumination of the structure from multiple directions using data from the same event minimizes source effects to provide clearer images of heterogeneity. The analysis is based on a similar concept to the back-projection technique, where a part of the seismic wavetrain is mapped to a specific point in space by ray-tracing. In contrast to classic back-projection where the incoming energy is mapped onto a horizontal plane with limited vertical resolution, the multi-array method controls depth response by combining relative time constraints between the arrays and conventional beam-forming. We illustrate this approach with application to two earthquakes at moderate depth. The results show that the use of simultaneous multiple arrays can provide improvement both in signal quality and resolution, with the additional benefit of being able to accurately locate the source of the incoming energy and map large areas with only a limited number of such arrays.

  8. Simultaneous Assembly of Multiple Test Forms.

    ERIC Educational Resources Information Center

    van der Linden, Wim J.; Adema, Jos J.

    1998-01-01

    Proposes an algorithm for the assembly of multiple test forms in which the multiple-form problem is reduced to a series of computationally less intensive two-form problems. Illustrates how the method can be implemented using 0-1 linear programming and gives two examples. (SLD)

  9. Evaluating the Effects of Emission Reductions on Multiple Pollutants Simultaneously

    EPA Science Inventory

    Modeling studies over the Philadelphia metropolitan area have examined how emission control strategies might affect several types of air pollutants simultaneously. This study supports considering effects of multiple pollutants in determining optimum pollution control strategies. ...

  10. Multiple Shape Models for Simultaneous Object Classification and Segmentation

    DTIC Science & Technology

    2009-02-01

    MULTIPLE SHAPE MODELS FOR SIMULTANEOUS OBJECT CLASSIFICATION AND SEGMENTATION By Federico Lecumberry Álvaro Pardo and Guillermo Sapiro IMA Preprint...SIMULTANEOUS OBJECT CLASSIFICATION AND SEGMENTATION Federico Lecumberry IIE, Universidad de la República fefo@fing.edu.uy Álvaro Pardo DIE, Universidad

  11. Simultaneous detection of Legionella species and L. anisa, L. bozemanii, L. longbeachae and L. micdadei using conserved primers and multiple probes in a multiplex real-time PCR assay.

    PubMed

    Cross, Kristen E; Mercante, Jeffrey W; Benitez, Alvaro J; Brown, Ellen W; Diaz, Maureen H; Winchell, Jonas M

    2016-07-01

    Legionnaires' disease is a severe respiratory disease that is estimated to cause between 8,000 and 18,000 hospitalizations each year, though the exact burden is unknown due to under-utilization of diagnostic testing. Although Legionella pneumophila is the most common species detected in clinical cases (80-90%), other species have also been reported to cause disease. However, little is known about Legionnaires' disease caused by these non-pneumophila species. We designed a multiplex real-time PCR assay for detection of all Legionella spp. and simultaneous specific identification of four clinically-relevant Legionella species, L. anisa, L. bozemanii, L. longbeachae, and L. micdadei, using 5'-hydrolysis probe real-time PCR. The analytical sensitivity for detection of nucleic acid from each target species was ≤50fg per reaction. We demonstrated the utility of this assay in spiked human sputum specimens. This assay could serve as a tool for understanding the scope and impact of non-pneumophila Legionella species in human disease.

  12. Bayesian estimation applied to multiple species

    SciTech Connect

    Kunz, Martin; Bassett, Bruce A.; Hlozek, Renee A.

    2007-05-15

    Observed data are often contaminated by undiscovered interlopers, leading to biased parameter estimation. Here we present BEAMS (Bayesian estimation applied to multiple species) which significantly improves on the standard maximum likelihood approach in the case where the probability for each data point being ''pure'' is known. We discuss the application of BEAMS to future type-Ia supernovae (SNIa) surveys, such as LSST, which are projected to deliver over a million supernovae light curves without spectra. The multiband light curves for each candidate will provide a probability of being Ia (pure) but the full sample will be significantly contaminated with other types of supernovae and transients. Given a sample of N supernovae with mean probability,

    , of being Ia, BEAMS delivers parameter constraints equal to N

    spectroscopically confirmed SNIa. In addition BEAMS can be simultaneously used to tease apart different families of data and to recover properties of the underlying distributions of those families (e.g. the type-Ibc and II distributions). Hence BEAMS provides a unified classification and parameter estimation methodology which may be useful in a diverse range of problems such as photometric redshift estimation or, indeed, any parameter estimation problem where contamination is an issue.

  13. Simultaneous real-time monitoring of multiple cortical systems

    NASA Astrophysics Data System (ADS)

    Gupta, Disha; Hill, N. Jeremy; Brunner, Peter; Gunduz, Aysegul; Ritaccio, Anthony L.; Schalk, Gerwin

    2014-10-01

    Objective. Real-time monitoring of the brain is potentially valuable for performance monitoring, communication, training or rehabilitation. In natural situations, the brain performs a complex mix of various sensory, motor or cognitive functions. Thus, real-time brain monitoring would be most valuable if (a) it could decode information from multiple brain systems simultaneously, and (b) this decoding of each brain system were robust to variations in the activity of other (unrelated) brain systems. Previous studies showed that it is possible to decode some information from different brain systems in retrospect and/or in isolation. In our study, we set out to determine whether it is possible to simultaneously decode important information about a user from different brain systems in real time, and to evaluate the impact of concurrent activity in different brain systems on decoding performance. Approach. We study these questions using electrocorticographic signals recorded in humans. We first document procedures for generating stable decoding models given little training data, and then report their use for offline and for real-time decoding from 12 subjects (six for offline parameter optimization, six for online experimentation). The subjects engage in tasks that involve movement intention, movement execution and auditory functions, separately, and then simultaneously. Main results. Our real-time results demonstrate that our system can identify intention and movement periods in single trials with an accuracy of 80.4% and 86.8%, respectively (where 50% would be expected by chance). Simultaneously, the decoding of the power envelope of an auditory stimulus resulted in an average correlation coefficient of 0.37 between the actual and decoded power envelopes. These decoders were trained separately and executed simultaneously in real time. Significance. This study yielded the first demonstration that it is possible to decode simultaneously the functional activity of multiple

  14. Array biosensor for simultaneous detection of multiple analytes

    NASA Astrophysics Data System (ADS)

    Ligler, Frances S.; Golden, Joel P.; Rowe-Taitt, Chris A.; Dodson, James P.

    2001-05-01

    The array biosensor has been developed for simultaneous analysis of multiple samples for multiple analytes. A patterned array of capture antibodies is immobilized on the surface of a planar waveguide and a sandwich immunoassay conducted using a cocktail of fluorescent tracer antibodies. Upon excitation of the fluorescent label using a 635 nm diode laser, a CCD camera detects the pattern of fluorescent antigen:antibody complexes on the sensor surface. Image analysis software correlates the position of fluorescent signals with the identity of the analyte. The assays are fast, sensitive, and specific.

  15. Structured plant metabolomics for the simultaneous exploration of multiple factors

    PubMed Central

    Vasilev, Nikolay; Boccard, Julien; Lang, Gerhard; Grömping, Ulrike; Fischer, Rainer; Goepfert, Simon; Rudaz, Serge; Schillberg, Stefan

    2016-01-01

    Multiple factors act simultaneously on plants to establish complex interaction networks involving nutrients, elicitors and metabolites. Metabolomics offers a better understanding of complex biological systems, but evaluating the simultaneous impact of different parameters on metabolic pathways that have many components is a challenging task. We therefore developed a novel approach that combines experimental design, untargeted metabolic profiling based on multiple chromatography systems and ionization modes, and multiblock data analysis, facilitating the systematic analysis of metabolic changes in plants caused by different factors acting at the same time. Using this method, target geraniol compounds produced in transgenic tobacco cell cultures were grouped into clusters based on their response to different factors. We hypothesized that our novel approach may provide more robust data for process optimization in plant cell cultures producing any target secondary metabolite, based on the simultaneous exploration of multiple factors rather than varying one factor each time. The suitability of our approach was verified by confirming several previously reported examples of elicitor–metabolite crosstalk. However, unravelling all factor–metabolite networks remains challenging because it requires the identification of all biochemically significant metabolites in the metabolomics dataset. PMID:27853298

  16. Optically Mapping Multiple Bacterial Genomes Simultaneously in a Single Run

    DTIC Science & Technology

    2011-11-21

    sequence orientation. We have demonstrated mapping of Shigella dysenteriae and Escherichia coli simultaneously, despite their very close phylogenetic...relationship ( Shigella and Escherichia coli are generally considered to be within a single species, but are segregated at the genus level for historical...reasons [4]); two clones of Shigella would likely not map together successfully using the mixed DNA method. Similarly, based on reference maps being

  17. SIMULTANEOUS TELEPORTATION OF MULTIPLE SINGLE-PHOTON DEGREES OF FREEDOM

    SciTech Connect

    Humble, Travis S; Bennink, Ryan S; Grice, Warren P

    2011-01-01

    We report how quantum information encoded into multiple photonic degrees of freedom may be simultaneously teleported using a single, common physical process. The application of teleportation to the complete quantum state of a photon, i.e., the spectral, spatial, and polarization component states, permits the full photonic Hilbert space to be used for encoding information while simultaneously enabling subspaces to be addressed individually, e.g., for quantum information processing. We analyze the feasibility of teleporting the full quantum state through numerical analysis of the fidelity under nominal experimental conditions and for different types of input states, e.g., single-photon states that are separable and entangled in the physical degrees of freedom.

  18. Simultaneous Real-Time Monitoring of Multiple Cortical Systems

    PubMed Central

    Gupta, Disha; Hill, N. Jeremy; Brunner, Peter; Gunduz, Aysegul; Ritaccio, Anthony L.; Schalk, Gerwin

    2014-01-01

    Objective Real-time monitoring of the brain is potentially valuable for performance monitoring, communication, training or rehabilitation. In natural situations, the brain performs a complex mix of various sensory, motor, or cognitive functions. Thus, real-time brain monitoring would be most valuable if (a) it could decode information from multiple brain systems simultaneously, and (b) this decoding of each brain system were robust to variations in the activity of other (unrelated) brain systems. Previous studies showed that it is possible to decode some information from different brain systems in retrospect and/or in isolation. In our study, we set out to determine whether it is possible to simultaneously decode important information about a user from different brain systems in real time, and to evaluate the impact of concurrent activity in different brain systems on decoding performance. Approach We study these questions using electrocorticographic (ECoG) signals recorded in humans. We first document procedures for generating stable decoding models given little training data, and then report their use for offline and for real-time decoding from 12 subjects (6 for offline parameter optimization, 6 for online experimentation). The subjects engage in tasks that involve movement intention, movement execution and auditory functions, separately, and then simultaneously. Main results Our real-time results demonstrate that our system can identify intention and movement periods in single trials with an accuracy of 80.4% and 86.8%, respectively (where 50% would be expected by chance). Simultaneously, the decoding of the power envelope of an auditory stimulus resulted in an average correlation coefficient of 0.37 between the actual and decoded power envelope. These decoders were trained separately and executed simultaneously in real time. Significance This study yielded the first demonstration that it is possible to decode simultaneously the functional activity of multiple

  19. Simultaneous demultiplexing and steering of multiple orbital angular momentum modes

    PubMed Central

    Li, Shuhui; Wang, Jian

    2015-01-01

    We present a simple scheme to perform simultaneous demultiplexing and steering of multiple orbital angular momentum (OAM) modes using a single complex phase mask. By designing the phase mask, the propagation directions of demultiplexed beams can be arbitrarily steered. System experiments using orthogonal frequency-division multiplexing 32-ary quadrature amplitude modulation (OFDM-32QAM) signals over two OAM modes are carried out by using a two-mode complex phase mask. Moreover, demultiplexing of sixteen OAM modes and arbitrary demultiplexed beam steering are also demonstrated in the experiment. PMID:26503167

  20. Negotiating for more: the multiple equivalent simultaneous offer.

    PubMed

    Heller, Richard E

    2014-02-01

    Whether a doctor, professional baseball manager, or a politician, having successful negotiation skills is a critical part of being a leader. Building upon prior journal articles on negotiation strategy, the author presents the concept of the multiple equivalent simultaneous offer (MESO). The concept of a MESO is straightforward: as opposed to making a single offer, make multiple offers with several variables. Each offer alters the different variables, such that the end result of each offer is equivalent from the perspective of the party making the offer. Research has found several advantages to the use of MESOs. For example, using MESOs, an offer was more likely to be accepted, and the counterparty was more likely to be satisfied with the negotiated deal. Additional benefits have been documented as well, underscoring why a prepared radiology business leader should understand the theory and practice of MESO.

  1. Simultaneous fusion, compression, and encryption of multiple images.

    PubMed

    Alfalou, A; Brosseau, C; Abdallah, N; Jridi, M

    2011-11-21

    We report a new spectral multiple image fusion analysis based on the discrete cosine transform (DCT) and a specific spectral filtering method. In order to decrease the size of the multiplexed file, we suggest a procedure of compression which is based on an adapted spectral quantization. Each frequency is encoded with an optimized number of bits according its importance and its position in the DC domain. This fusion and compression scheme constitutes a first level of encryption. A supplementary level of encryption is realized by making use of biometric information. We consider several implementations of this analysis by experimenting with sequences of gray scale images. To quantify the performance of our method we calculate the MSE (mean squared error) and the PSNR (peak signal to noise ratio). Our results consistently improve performances compared to the well-known JPEG image compression standard and provide a viable solution for simultaneous compression and encryption of multiple images.

  2. Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

    PubMed Central

    Yang, Ziheng; Rannala, Bruce

    2014-01-01

    A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation. PMID:25274273

  3. Structural modal reanalysis for large, simultaneous and multiple type modifications

    NASA Astrophysics Data System (ADS)

    Jian-jun, He; Xiang-zi, Chen; Bin, Xu

    2015-10-01

    Eigenvalue problem is widely used to investigate the dynamic characteristics of large and complex structure. For finite element models, iterative solvers are needed to precisely calculate eigenvectors and eigenvalues. However, in cases such as large-scale reanalysis studies, or optimization design of huge structure, computational cost can quickly become too time consuming. This paper focus on the structural modal reanalysis for large and multiple modifications (including simultaneous boundary, topology and type modifications), which can greatly affect the eigen-modes of the modified structures. The proposed methods are based on the results from the modal analysis of the original structure, and the stiffness and mass matrix of the modified structures. A highly approximate eigensolution are generated by the proposed method, which is combined the newly added DOF (Degrees of Freedom) condensation, ICMO strategy (Independent and Coupling Mass Orthogonalization) with the Rayleigh-Ritz analysis. The numerical examples show that the proposed method is efficient with high precision even when large and multiple type modifications of the structural topology, boundary and type are made simultaneously.

  4. Simultaneous rapid sequencing of multiple RNA virus genomes.

    PubMed

    Neill, John D; Bayles, Darrell O; Ridpath, Julia F

    2014-06-01

    Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines. However, the difficulty, time and expense of generating full-length sequences individually from each archived sample have hampered these studies. Next generation sequencing technologies have been utilized for analysis of clinical and environmental samples to identify viral pathogens that may be present. This has led to the discovery of many new, uncharacterized viruses from a number of viral families. Use of these sequencing technologies would be advantageous in examining viral evolution. In this study, a sequencing procedure was used to sequence simultaneously and rapidly multiple archived samples using a single standard protocol. This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3'-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. This conferred sequence independence by random priming both first and second strand cDNA synthesis. Viral stocks were treated with a nuclease cocktail to reduce the presence of host nucleic acids. Viral RNA was extracted, followed by single tube random-primed double-stranded cDNA synthesis. The resultant cDNAs were amplified by primer-specific PCR, pooled, size fractionated and sequenced on the Ion Torrent PGM platform. The individual virus genomes were readily assembled by both de novo and template-assisted assembly methods. This procedure consistently resulted in near full length, if not full-length, genomic sequences and was used to sequence multiple bovine pestivirus and coronavirus isolates simultaneously.

  5. Simultaneous Identification of Multiple Causal Mutations in Rice

    PubMed Central

    Yan, Wei; Chen, Zhufeng; Lu, Jiawei; Xu, Chunjue; Xie, Gang; Li, Yiqi; Deng, Xing Wang; He, Hang; Tang, Xiaoyan

    2017-01-01

    Next-generation sequencing technologies (NGST) are being used to discover causal mutations in ethyl methanesulfonate (EMS)-mutagenized plant populations. However, the published protocols often deliver too many candidate sites and sometimes fail to find the mutant gene of interest. Accurate identification of the causal mutation from massive background polymorphisms and sequencing deficiencies remains challenging. Here we describe a NGST-based method, named SIMM, that can simultaneously identify the causal mutations in multiple independent mutants. Multiple rice mutants derived from the same parental line were back-crossed, and for each mutant, the derived F2 individuals of the recessive mutant phenotype were pooled and sequenced. The resulting sequences were aligned to the Nipponbare reference genome, and single nucleotide polymorphisms (SNPs) were subsequently compared among the mutants. Allele index (AI) and Euclidean distance (ED) were incorporated into the analysis to reduce noises caused by background polymorphisms and re-sequencing errors. Corrections of sequence bias against GC- and AT-rich sequences in the candidate region were conducted when necessary. Using this method, we successfully identified seven new mutant alleles from Huanghuazhan (HHZ), an elite indica rice cultivar in China. All mutant alleles were validated by phenotype association assay. A pipeline based on Perl scripts for SIMM is publicly available at https://sourceforge.net/projects/simm/. PMID:28144247

  6. Kidney tumor biomarkers revealed by simultaneous multiple matrix metabolomics analysis.

    PubMed

    Ganti, Sheila; Taylor, Sandra L; Abu Aboud, Omran; Yang, Joy; Evans, Christopher; Osier, Michael V; Alexander, Danny C; Kim, Kyoungmi; Weiss, Robert H

    2012-07-15

    Metabolomics is increasingly being used in cancer biology for biomarker discovery and identification of potential novel therapeutic targets. However, a systematic metabolomics study of multiple biofluids to determine their interrelationships and to describe their use as tumor proxies is lacking. Using a mouse xenograft model of kidney cancer, characterized by subcapsular implantation of Caki-1 clear cell human kidney cancer cells, we examined tissue, serum, and urine all obtained simultaneously at baseline (urine) and at, or close to, animal sacrifice (urine, tissue, and plasma). Uniform metabolomics analysis of all three "matrices" was accomplished using gas chromatography- and liquid chromatography-mass spectrometry. Of all the metabolites identified (267 in tissue, 246 in serum, and 267 in urine), 89 were detected in all 3 matrices, and the majority was altered in the same direction. Heat maps of individual metabolites showed that alterations in serum were more closely related to tissue than was urine. Two metabolites, cinnamoylglycine and nicotinamide, were concordantly and significantly (when corrected for multiple testing) altered in tissue and serum, and cysteine-glutathione disulfide showed the highest change (232.4-fold in tissue) of any metabolite. On the basis of these and other considerations, three pathways were chosen for biologic validation of the metabolomic data, resulting in potential therapeutic target identification. These data show that serum metabolomics analysis is a more accurate proxy for tissue changes than urine and that tryptophan degradation (yielding anti-inflammatory metabolites) is highly represented in renal cell carcinoma, and support the concept that PPAR-α antagonism may be a potential therapeutic approach for this disease.

  7. Doses of Nearby Nature Simultaneously Associated with Multiple Health Benefits.

    PubMed

    Cox, Daniel T C; Shanahan, Danielle F; Hudson, Hannah L; Fuller, Richard A; Anderson, Karen; Hancock, Steven; Gaston, Kevin J

    2017-02-09

    Exposure to nature provides a wide range of health benefits. A significant proportion of these are delivered close to home, because this offers an immediate and easily accessible opportunity for people to experience nature. However, there is limited information to guide recommendations on its management and appropriate use. We apply a nature dose-response framework to quantify the simultaneous association between exposure to nearby nature and multiple health benefits. We surveyed ca. 1000 respondents in Southern England, UK, to determine relationships between (a) nature dose type, that is the frequency and duration (time spent in private green space) and intensity (quantity of neighbourhood vegetation cover) of nature exposure and (b) health outcomes, including mental, physical and social health, physical behaviour and nature orientation. We then modelled dose-response relationships between dose type and self-reported depression. We demonstrate positive relationships between nature dose and mental and social health, increased physical activity and nature orientation. Dose-response analysis showed that lower levels of depression were associated with minimum thresholds of weekly nature dose. Nearby nature is associated with quantifiable health benefits, with potential for lowering the human and financial costs of ill health. Dose-response analysis has the potential to guide minimum and optimum recommendations on the management and use of nearby nature for preventative healthcare.

  8. Self-presentational persona: simultaneous management of multiple impressions.

    PubMed

    Leary, Mark R; Allen, Ashley Batts

    2011-11-01

    Most research on self-presentation has examined how people convey images of themselves on only 1 or 2 dimensions at a time. In everyday interactions, however, people often manage their impressions on several image-relevant dimensions simultaneously. By examining people's self-presentations to several targets across multiple dimensions, these 2 studies offer new insights into the nature of self-presentation and provide a novel paradigm for studying impression management. Results showed that most people rely on a relatively small number of basic self-presentational personas in which they convey particular profiles of impressions as a set and that these personas reflect both normative influences to project images that are appropriate to a particular target and distinctive influences by which people put an idiosyncratic spin on these normative images. Furthermore, although people's self-presentational profiles correlate moderately with their self-views, they tailor their public images to specific targets. The degree to which participants' self-presentations were normative and distinctive, as well as the extent to which they reflected their own self-views, were moderated by individual differences in agreeableness, self-esteem, authenticity, and Machiavellianism.

  9. Doses of Nearby Nature Simultaneously Associated with Multiple Health Benefits

    PubMed Central

    Cox, Daniel T. C.; Shanahan, Danielle F.; Hudson, Hannah L.; Fuller, Richard A.; Anderson, Karen; Hancock, Steven; Gaston, Kevin J.

    2017-01-01

    Exposure to nature provides a wide range of health benefits. A significant proportion of these are delivered close to home, because this offers an immediate and easily accessible opportunity for people to experience nature. However, there is limited information to guide recommendations on its management and appropriate use. We apply a nature dose-response framework to quantify the simultaneous association between exposure to nearby nature and multiple health benefits. We surveyed ca. 1000 respondents in Southern England, UK, to determine relationships between (a) nature dose type, that is the frequency and duration (time spent in private green space) and intensity (quantity of neighbourhood vegetation cover) of nature exposure and (b) health outcomes, including mental, physical and social health, physical behaviour and nature orientation. We then modelled dose-response relationships between dose type and self-reported depression. We demonstrate positive relationships between nature dose and mental and social health, increased physical activity and nature orientation. Dose-response analysis showed that lower levels of depression were associated with minimum thresholds of weekly nature dose. Nearby nature is associated with quantifiable health benefits, with potential for lowering the human and financial costs of ill health. Dose-response analysis has the potential to guide minimum and optimum recommendations on the management and use of nearby nature for preventative healthcare. PMID:28208789

  10. [Simultaneous screening method for Bordetella species by conventional PCR assay].

    PubMed

    Akiyama, Yumi; Saito, Etsuko; Enomoto, Miki; Tsuji, Hidetaka; Chikahira, Masatsugu; Yoshida, Masashi

    2013-11-01

    A simultaneous screening method using conventional PCR was developed for the detection and discrimination of Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii. A formulated multiprex method employing 4 kinds of paired primers on amplification of 4 corresponding different insertion sequences (IS481, IS1001, IS1002 and hIS1001) enabled rapid screening and identification. The detection limits of each DNA extracted from 3 kinds of Bordetella species were 5fg/microL for each. Obscure existences of B. pertussis and B. holmesii at low levels were confirmed with the LAMP method. This multiplex assay was applied to the clinical specimens obtained from patients with pertussis-like symptoms at sentinel clinics under the epidemiological surveillance of infectious diseases of Hyogo prefecture in FY2012. Among 42 nasopharyngeal swabs, B. pertussis was detected from 12 samples including 8 samples collected at outbreak in nursery school. The use of this method for the surveillance of infectious agents enabled us to search for 3 kinds of Bordetella species at once with low costs.

  11. Microfabricated capillary electrophoresis chip and method for simultaneously detecting multiple redox labels

    DOEpatents

    Mathies, Richard A.; Singhal, Pankaj; Xie, Jin; Glazer, Alexander N.

    2002-01-01

    This invention relates to a microfabricated capillary electrophoresis chip for detecting multiple redox-active labels simultaneously using a matrix coding scheme and to a method of selectively labeling analytes for simultaneous electrochemical detection of multiple label-analyte conjugates after electrophoretic or chromatographic separation.

  12. Quantification of multiple simultaneously occurring nitrogen flows in the euphotic ocean

    NASA Astrophysics Data System (ADS)

    Xu, Min Nina; Wu, Yanhua; Zheng, Li Wei; Zheng, Zhenzhen; Zhao, Huade; Laws, Edward A.; Kao, Shuh-Ji

    2017-03-01

    The general features of the N cycle in the sunlit region of the ocean are well known, but methodological difficulties have previously confounded simultaneous quantification of transformation rates among the many different forms of N, e.g., ammonium (NH4+), nitrite (NO2-), nitrate (NO3-), and particulate/dissolved organic nitrogen (PN/DON). However, recent advances in analytical methodology have made it possible to employ a convenient isotope labeling technique to quantify in situ fluxes among oft-measured nitrogen species within the euphotic zone. Addition of a single 15N-labeled NH4+ tracer and monitoring of the changes in the concentrations and isotopic compositions of the total dissolved nitrogen (TDN), PN, NH4+, NO2-, and NO3- pools allowed us to quantify the 15N and 14N fluxes simultaneously. Constraints expressing the balance of 15N and 14N fluxes between the different N pools were expressed in the form of simultaneous equations, the unique solution of which via matrix inversion yielded the relevant N fluxes, including rates of NH4+, NO2-, and NO3- uptake; ammonia oxidation; nitrite oxidation; DON release; and NH4+ uptake by bacteria. The matrix inversion methodology that we used was designed specifically to analyze the results of incubations under simulated in situ conditions in the euphotic zone. By taking into consideration simultaneous fluxes among multiple N pools, we minimized potential artifacts caused by non-targeted processes in traditional source-product methods. The proposed isotope matrix method facilitates post hoc analysis of data from on-deck incubation experiments and can be used to probe effects of environmental factors (e.g., pH, temperature, and light) on multiple processes under controlled conditions.

  13. Simultaneous Identification of Neutral and Anionic Species in Complex Mixtures without Separation.

    PubMed

    Zhao, Yanchuan; Chen, Lily; Swager, Timothy M

    2016-01-18

    A chemosensory system is reported that operates without the need for separation techniques and is capable of identifying anions and structurally similar bioactive molecules. In this strategy, the coordination of analytes to a metal complex with an open binding cleft generates "static structures" on the NMR timescale. Unique signals are created by strategically placing fluorine atoms in close proximity to bound analytes so that small structural differences induce distinct (19)F NMR shifts that can be used to identify each analyte. The utility of this method is illustrated by quantifying caffeine levels in coffee, by identifying ingredients in tea and energy drinks, and by discriminating between multiple biogenic amines with remote structural differences six carbon atoms away from the binding site. We further demonstrate the simultaneous identification of multiple neutral and anionic species in a complex mixture.

  14. Simultaneous Identification of Neutral and Anionic Species in Complex Mixtures without Separation

    PubMed Central

    Zhao, Yanchuan; Chen, Lily; Swager, Timothy M.

    2016-01-01

    A chemosensory system is reported that operates without the need for separation techniques and is capable of identifying anions and structurally similar bioactive molecules. In this strategy, the coordination of analytes to a metal complex with an open binding cleft generates “static structures” on the NMR time scale. Unique signals are created by strategically placing fluorine atoms in close proximity to bound analytes so that small structural differences induce distinct 19F NMR shifts that can be used to identify each analyte. The utility of this method is illustrated by quantifying caffeine levels in coffee, by identifying ingredients in tea and energy drinks, and by discriminating between multiple biogenic amines with remote structural differences 6 carbons away from the binding site. We further demonstrate the simultaneous identification of multiple neutral and anionic species in a complex mixture. PMID:26756442

  15. Simultaneous Two-Way Clustering of Multiple Correspondence Analysis

    ERIC Educational Resources Information Center

    Hwang, Heungsun; Dillon, William R.

    2010-01-01

    A 2-way clustering approach to multiple correspondence analysis is proposed to account for cluster-level heterogeneity of both respondents and variable categories in multivariate categorical data. Specifically, in the proposed method, multiple correspondence analysis is combined with k-means in a unified framework in which "k"-means is…

  16. Simultaneous registration of multiple images: similarity metrics and efficient optimization.

    PubMed

    Wachinger, Christian; Navab, Nassir

    2013-05-01

    We address the alignment of a group of images with simultaneous registration. Therefore, we provide further insights into a recently introduced framework for multivariate similarity measures, referred to as accumulated pair-wise estimates (APE), and derive efficient optimization methods for it. More specifically, we show a strict mathematical deduction of APE from a maximum-likelihood framework and establish a connection to the congealing framework. This is only possible after an extension of the congealing framework with neighborhood information. Moreover, we address the increased computational complexity of simultaneous registration by deriving efficient gradient-based optimization strategies for APE: Gauss-Newton and the efficient second-order minimization (ESM). We present next to SSD the usage of intrinsically nonsquared similarity measures in this least squares optimization framework. The fundamental assumption of ESM, the approximation of the perfectly aligned moving image through the fixed image, limits its application to monomodal registration. We therefore incorporate recently proposed structural representations of images which allow us to perform multimodal registration with ESM. Finally, we evaluate the performance of the optimization strategies with respect to the similarity measures, leading to very good results for ESM. The extension to multimodal registration is in this context very interesting because it offers further possibilities for evaluations, due to publicly available datasets with ground-truth alignment.

  17. Modeling Coordination in Multiple Simultaneous Latent Change Scores

    PubMed Central

    Butner, Jonathan E.; Berg, Cynthia A.; Baucom, Brian R.; Wiebe, Deborah J.

    2016-01-01

    Coordination is a taxonomy of how processes change together through time. It depicts the changes of two or more variables in terms of the strength and consistency of their covariation, the directionality of their covariation (i.e., do increases in one variable correspond with increases [in-phase] or decreases [anti-phase] in the other variable), and the timing of their covariation (i.e., do both variables change at the same rate or does one variable change faster than the other). Current methods are able to characterize some, but not all, of these aspects of coordination and provide incomplete information as a result. The current study addresses this limitation by demonstrating that multivariate latent change score models can be used to fully differentiate all possible coordination patterns. Furthermore, one can then expand coordination beyond the two outcome case to test arrangements of underlying coordination mechanisms or patterns. Examples using two simultaneous latent change score models and four simultaneous latent change score models illustrate this approach within the context of adolescents and parents regulating type 1 diabetes. PMID:26735358

  18. Integrative Data Analysis: The Simultaneous Analysis of Multiple Data Sets

    ERIC Educational Resources Information Center

    Curran, Patrick J.; Hussong, Andrea M.

    2009-01-01

    There are both quantitative and methodological techniques that foster the development and maintenance of a cumulative knowledge base within the psychological sciences. Most noteworthy of these techniques is meta-analysis, which allows for the synthesis of summary statistics drawn from multiple studies when the original data are not available.…

  19. Simultaneous Exposure to Multiple Air Pollutants Influences Alveolar Epithelial Cell Ion Transport

    EPA Science Inventory

    Purpose. Air pollution sources generally release multiple pollutants simultaneously and yet, research has historically focused on the source-to-health linkages of individual air pollutants. We recently showed that exposure of alveolar epithelial cells to a combination of particul...

  20. Dissolution Model of Multiple Species: Leaching of Highly Soluble Minerals

    NASA Astrophysics Data System (ADS)

    Moreno, Luis; Ordóñez, Javier I.; Cisternas, Luis A.

    2017-03-01

    Dissolution of multi-species from a solid matrix is widely extended in different processes such as leaching of minerals; however, its modeling is often focused on a single species. A model for the simultaneous dissolution of soluble species was developed, which considers different solubilities and dissolution rates and considers that particle collapses when the rapidly soluble species is depleted. The collapsed matter is formed by inert material and a fraction of the soluble species with lower dissolution rate that has not dissolved yet. The model is applied to the leaching of a water-soluble mineral (caliche) with two soluble species dissolving simultaneously with different rates. Measured outlet concentrations of nitrate and magnesium were used to validate the model. Results showed that the model reproduced adequately the leaching of species with rapid and intermediate dissolution rate. Effect of the operating and kinetic parameters on the leaching process is also shown using the actual conditions of heap leaching for caliche mineral.

  1. Simultaneous Object Classification and Segmentation with High-Order Multiple Shape Models

    DTIC Science & Technology

    2009-05-01

    SIMULTANEOUS OBJECT CLASSIFICATION AND SEGMENTATION WITH HIGH-ORDER MULTIPLE SHAPE MODELS By Federico Lecumberry Álvaro Pardo and Guillermo Sapiro...Simultaneous Object Classification and Segmentation with High-Order Multiple Shape Models Federico Lecumberry , Student Member, IEEE, Álvaro Pardo, Member...weighted linear F. Lecumberry is with the Instituto de Ingenierı́a Eléctrica, Facultad de Ingenierı́a, Universidad de la República, Montevideo

  2. A PDP model of the simultaneous perception of multiple objects

    NASA Astrophysics Data System (ADS)

    Henderson, Cynthia M.; McClelland, James L.

    2011-06-01

    Illusory conjunctions in normal and simultanagnosic subjects are two instances where the visual features of multiple objects are incorrectly 'bound' together. A connectionist model explores how multiple objects could be perceived correctly in normal subjects given sufficient time, but could give rise to illusory conjunctions with damage or time pressure. In this model, perception of two objects benefits from lateral connections between hidden layers modelling aspects of the ventral and dorsal visual pathways. As with simultanagnosia, simulations of dorsal lesions impair multi-object recognition. In contrast, a large ventral lesion has minimal effect on dorsal functioning, akin to dissociations between simple object manipulation (retained in visual form agnosia and semantic dementia) and object discrimination (impaired in these disorders) [Hodges, J.R., Bozeat, S., Lambon Ralph, M.A., Patterson, K., and Spatt, J. (2000), 'The Role of Conceptual Knowledge: Evidence from Semantic Dementia', Brain, 123, 1913-1925; Milner, A.D., and Goodale, M.A. (2006), The Visual Brain in Action (2nd ed.), New York: Oxford]. It is hoped that the functioning of this model might suggest potential processes underlying dorsal and ventral contributions to the correct perception of multiple objects.

  3. Delivering multiple independent RIB simultaneously: Technical and operational challenges

    NASA Astrophysics Data System (ADS)

    Morton, A. C.

    2016-06-01

    ISAC is an ISOL-type facility at which RIB are produced by direct reactions of 480 MeV protons from TRIUMFs main cyclotron on thick targets. Like other ISOL-type facilities, ISAC is limited to the production and delivery of a single RIB at any given time. ARIEL, the Advanced Rare-IsotopE Laboratory, will provide for the production and delivery of, ultimately, two additional RIB, the first produced by photofission on actinide targets using electrons from a new superconducting electron linac and the second by direct and indirect reactions with protons from TRIUMFs main cyclotron. This will allow for the simultaneous delivery of three independent RIB to experimental areas at ARIEL and ISAC. The shift from single-user to multi-user operation will introduce significant technical and operational challenges that RIB facilities have not yet had to address. Almost all aspects of facility operation will become more complex as the first RIB from ARIEL targets become available.

  4. Simultaneous multiple uniform spot generation with micro optics

    NASA Astrophysics Data System (ADS)

    Fruendt, J.; Jarczynski, M.; Mitra, T.

    2008-08-01

    Direct laser patterning of various materials is industrially implemented into several micro-system production lines such as inkjet printing, solar cell technology, flat-panel display production and medical engineering. In contrast to applications of single-mode sources, multi-mode lasers can provide very high power. This allows multi channel material processing and thus high operation speed if uniform light fields can be provided. Here within an illumination system is presented based on a high power multi-mode laser source that generates several uniform spots simultaneously without high stability requirements for the incoming laser source. These spots can be generated in various sizes and at various distances and can be located periodically and non-periodically. The concept consists of two beam processing steps: First the beam is homogenized by use of cylindrical micro-optic lens arrays. Secondly anamorphotic telecentric microoptic objectives split the beam into several uniform segments and image the spots onto the working plane. Because of LIMO's unique production technology the lens arrays can be optimized freely. It results in accurate dimensions and uniform intensity distributions for every single illuminated area. Field dimensions are only restricted by the diffraction limit. Applications could be direct material processing as well as mask illumination approaches.

  5. Learning multiple rules simultaneously: Affixes are more salient than reduplications.

    PubMed

    Gervain, Judit; Endress, Ansgar D

    2016-11-21

    Language learners encounter numerous opportunities to learn regularities, but need to decide which of these regularities to learn, because some are not productive in their native language. Here, we present an account of rule learning based on perceptual and memory primitives (Endress, Dehaene-Lambertz, & Mehler, Cognition, 105(3), 577-614, 2007; Endress, Nespor, & Mehler, Trends in Cognitive Sciences, 13(8), 348-353, 2009), suggesting that learners preferentially learn regularities that are more salient to them, and that the pattern of salience reflects the frequency of language features across languages. We contrast this view with previous artificial grammar learning research, which suggests that infants "choose" the regularities they learn based on rational, Bayesian criteria (Frank & Tenenbaum, Cognition, 120(3), 360-371, 2013; Gerken, Cognition, 98(3)B67-B74, 2006, Cognition, 115(2), 362-366, 2010). In our experiments, adult participants listened to syllable strings starting with a syllable reduplication and always ending with the same "affix" syllable, or to syllable strings starting with this "affix" syllable and ending with the "reduplication". Both affixation and reduplication are frequently used for morphological marking across languages. We find three crucial results. First, participants learned both regularities simultaneously. Second, affixation regularities seemed easier to learn than reduplication regularities. Third, regularities in sequence offsets were easier to learn than regularities at sequence onsets. We show that these results are inconsistent with previous Bayesian rule learning models, but mesh well with the perceptual or memory primitives view. Further, we show that the pattern of salience revealed in our experiments reflects the distribution of regularities across languages. Ease of acquisition might thus be one determinant of the frequency of regularities across languages.

  6. A combination assay for simultaneous assessment of multiple signaling pathways.

    PubMed

    Goetz, A S; Liacos, J; Yingling, J; Ignar, D M

    1999-12-01

    We have developed an assay in which modulation of two or more signaling pathways can be assessed concurrently by combining reporter gene systems with fluorescent probe technology. The validation of this method was achieved by indirect analysis of adenylyl cyclase activation with the use of a cyclic AMP response element (CRE)-luciferase reporter system in combination with the measurement of calcium mobilization by Calcium Green-1 AM fluorescence on a fluorescent imaging plate reader. To demonstrate the utility of the method in studying the pharmacology of receptors that couple to more than one G protein, Chinese hamster ovary (CHO) cells, which stably expressed both the CRE-luciferase reporter gene and the human pituitary adenylyl cyclase-activating peptide (PACAP) receptor, were treated with PACAP 1-27 and 1-38. Calcium mobilization and the induction of adenylyl cyclase activity in response to each concentration of peptide were assessed in individuals wells. This assay may also be used to screen for ligands of two or more unrelated receptors simultaneously without compromising the assessment of either signaling pathway. To illustrate this point, Rat-1 fibroblasts, which expressed human alpha1A receptors, were cocultured with CRE-luciferase CHO cells, which expressed human GLP-1 receptors. Calcium mobilization elicited by phenylephrine agonism of the alpha1A receptor was assessed in the same assay as GLP-1-induced activation of adenylyl cyclase. The pEC(50) for each agonist was similar to that observed when the cell lines were not cocultured. The number of different receptors that can be screened per well is limited only by the ability to distinguish different reporter gene signals and fluorescent indicators.

  7. Simultaneous multiple degrees of freedom (DoF) measurement system

    NASA Astrophysics Data System (ADS)

    Molnar, G.; Strube, S.; Köchert, P.; Danzebrink, H.-U.; Flügge, J.

    2016-08-01

    This paper presents a newly developed highly accurate interferometric 6° of freedom (DoF) measurement system with Ångström resolution for displacement and μrad resolution for angle measurement, respectively. The new interferometer is based on a modified homodyne Twyman-Green interferometer concept. It uses a novel signal acquisition and processing approach whereby a spatial interferogram is captured by a CMOS camera and the registered fringe pattern is transformed into its frequency spectrum [1]. The spectral representation of a movement of e.g. a positioning stage is analyzed for its major components: the phase information directly correlates with the displacement of the stage, while a possible rotational motion causes a shift in the frequency spectrum. The developed compact 6 DoF head uses multiple rays in parallel to detect x-y-z displacements and roll-pitch-yaw movements.

  8. Simultaneity, Sequentiality, and Speed: Organizational Messages about Multiple-Task Completion

    ERIC Educational Resources Information Center

    Stephens, Keri K.; Cho, Jaehee K.; Ballard, Dawna I.

    2012-01-01

    Workplace norms for task completion increasingly value speed and the ability to accomplish multiple tasks at once. This study situates this popularized issue of multitasking within the context of chronemics scholarship by addressing related issues of simultaneity, sequentiality, and speed. Ultimately, we consider 2 multiple-task completion…

  9. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.

    PubMed

    Li, Huameng; Li, Chenglong

    2010-07-30

    Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively.

  10. Multiple peaks of species abundance distributions induced by sparse interactions

    NASA Astrophysics Data System (ADS)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u , we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions.

  11. Method of analyzing multiple sample simultaneously by detecting absorption and systems for use in such a method

    DOEpatents

    Yeung, Edward S.; Gong, Xiaoyi

    2004-09-07

    The present invention provides a method of analyzing multiple samples simultaneously by absorption detection. The method comprises: (i) providing a planar array of multiple containers, each of which contains a sample comprising at least one absorbing species, (ii) irradiating the planar array of multiple containers with a light source and (iii) detecting absorption of light with a detetion means that is in line with the light source at a distance of at leaat about 10 times a cross-sectional distance of a container in the planar array of multiple containers. The absorption of light by a sample indicates the presence of an absorbing species in it. The method can further comprise: (iv) measuring the amount of absorption of light detected in (iii) indicating the amount of the absorbing species in the sample. Also provided by the present invention is a system for use in the abov metho.The system comprises; (i) a light source comrnpising or consisting essentially of at leaat one wavelength of light, the absorption of which is to be detected, (ii) a planar array of multiple containers, and (iii) a detection means that is in line with the light source and is positioned in line with and parallel to the planar array of multiple contiainers at a distance of at least about 10 times a cross-sectional distance of a container.

  12. Evidence for simultaneous syntactic processing of multiple words during reading.

    PubMed

    Snell, Joshua; Meeter, Martijn; Grainger, Jonathan

    2017-01-01

    A hotly debated issue in reading research concerns the extent to which readers process parafoveal words, and how parafoveal information might influence foveal word recognition. We investigated syntactic word processing both in sentence reading and in reading isolated foveal words when these were flanked by parafoveal words. In Experiment 1 we found a syntactic parafoveal preview benefit in sentence reading, meaning that fixation durations on target words were decreased when there was a syntactically congruent preview word at the target location (n) during the fixation on the pre-target (n-1). In Experiment 2 we used a flanker paradigm in which participants had to classify foveal target words as either noun or verb, when those targets were flanked by syntactically congruent or incongruent words (stimulus on-time 170 ms). Lower response times and error rates in the congruent condition suggested that higher-order (syntactic) information can be integrated across foveal and parafoveal words. Although higher-order parafoveal-on-foveal effects have been elusive in sentence reading, results from our flanker paradigm show that the reading system can extract higher-order information from multiple words in a single glance. We propose a model of reading to account for the present findings.

  13. Evidence for simultaneous syntactic processing of multiple words during reading

    PubMed Central

    Meeter, Martijn; Grainger, Jonathan

    2017-01-01

    A hotly debated issue in reading research concerns the extent to which readers process parafoveal words, and how parafoveal information might influence foveal word recognition. We investigated syntactic word processing both in sentence reading and in reading isolated foveal words when these were flanked by parafoveal words. In Experiment 1 we found a syntactic parafoveal preview benefit in sentence reading, meaning that fixation durations on target words were decreased when there was a syntactically congruent preview word at the target location (n) during the fixation on the pre-target (n-1). In Experiment 2 we used a flanker paradigm in which participants had to classify foveal target words as either noun or verb, when those targets were flanked by syntactically congruent or incongruent words (stimulus on-time 170 ms). Lower response times and error rates in the congruent condition suggested that higher-order (syntactic) information can be integrated across foveal and parafoveal words. Although higher-order parafoveal-on-foveal effects have been elusive in sentence reading, results from our flanker paradigm show that the reading system can extract higher-order information from multiple words in a single glance. We propose a model of reading to account for the present findings. PMID:28278305

  14. Simultaneous breakdown of multiple antibiotic resistance mechanisms in S. aureus.

    PubMed

    Kaneti, Galoz; Sarig, Hadar; Marjieh, Ibrahim; Fadia, Zaknoon; Mor, Amram

    2013-12-01

    In previous studies, the oligo-acyl-lysyl (OAK) C12(ω7)K-β12 added to cultures of gram-positive bacteria exerted a bacteriostatic activity that was associated with membrane depolarization, even at high concentrations. Here, we report that multidrug-resistant Staphylococcus aureus strains, unlike other gram-positive species, have reverted to the sensitive phenotype when exposed to subminimal inhibitory concentrations (sub-MICs) of the OAK, thereby increasing antibiotics potency by up to 3 orders of magnitude. Such chemosensitization was achieved using either cytoplasm or cell-wall targeting antibiotics. Moreover, eventual emergence of resistance to antibiotics was significantly delayed. Using the mouse peritonitis-sepsis model, we show that on single-dose administration of oxacillin and OAK combinations, death induced by a lethal staphylococcal infection was prevented in a synergistic manner, thereby supporting the likelihood for synergism to persist under in vivo conditions. Toward illuminating the molecular basis for these observations, we present data arguing that sub-MIC OAK interactions with the plasma membrane can inhibit proton-dependent signal transduction responsible for expression and export of resistance factors, as demonstrated for β-lactamase and PBP2a. Collectively, the data reveal a potentially useful approach for overcoming antibiotic resistance and for preventing resistance from emerging as readily as when bacteria are exposed to an antibiotic alone.

  15. Using Simultaneous Prompting Procedure to Promote Recall of Multiplication Facts by Middle School Students with Cognitive Impairment

    ERIC Educational Resources Information Center

    Rao, Shaila; Mallow, Lynette

    2009-01-01

    This study examined effectiveness of simultaneous prompting system in teaching students with cognitive impairment to automate recall of multiplication facts. A multiple probes design with multiple sets of math facts and replicated across multiple subjects was used to assess effectiveness of simultaneous prompting on recall of basic multiplication…

  16. SIMULTANEOUS CONSTRAINTS ON THE NUMBER AND MASS OF RELATIVISTIC SPECIES

    SciTech Connect

    Riemer-Sorensen, Signe; Parkinson, David; Davis, Tamara M.; Blake, Chris

    2013-02-15

    Recent indications from both particle physics and cosmology suggest the possible existence of more than three neutrino species. In cosmological analyses the effects of neutrino mass and number of species can in principle be disentangled for fixed cosmological parameters. However, since we do not have perfect measurements of the standard {Lambda} cold dark matter model parameters, some correlation remains between the neutrino mass and number of species, and both parameters should be included in the analysis. Combining the newest observations of several cosmological probes (cosmic microwave background, large-scale structure, expansion rate), we obtain N {sub eff} = 3.58{sup +0.15} {sub -0.16}(68% CL){sup +0.55} {sub -0.53}(95% CL) and {Sigma}m {sub {nu}} < 0.60 eV(95% CL), which are currently the strongest constraints on N {sub eff} and {Sigma}m {sub {nu}} from an analysis including both parameters. The preference for N {sub eff} >3 is at the 2{sigma} level.

  17. Optimal invasive species management under multiple uncertainties.

    PubMed

    Kotani, Koji; Kakinaka, Makoto; Matsuda, Hiroyuki

    2011-09-01

    The management programs for invasive species have been proposed and implemented in many regions of the world. However, practitioners and scientists have not reached a consensus on how to control them yet. One reason is the presence of various uncertainties associated with the management. To give some guidance on this issue, we characterize the optimal strategy by developing a dynamic model of invasive species management under uncertainties. In particular, focusing on (i) growth uncertainty and (ii) measurement uncertainty, we identify how these uncertainties affect optimal strategies and value functions. Our results suggest that a rise in growth uncertainty causes the optimal strategy to involve more restrained removals and the corresponding value function to shift up. Furthermore, we also find that a rise in measurement uncertainty affects optimal policies in a highly complex manner, but their corresponding value functions generally shift down as measurement uncertainty rises. Overall, a rise in growth uncertainty can be beneficial, while a rise in measurement uncertainty brings about an adverse effect, which implies the potential gain of precisely identifying the current stock size of invasive species.

  18. VORICONAZOLE TOXICITY IN MULTIPLE PENGUIN SPECIES.

    PubMed

    Hyatt, Michael W; Georoff, Timothy A; Nollens, Hendrik H; Wells, Rebecca L; Clauss, Tonya M; Ialeggio, Donna M; Harms, Craig A; Wack, Allison N

    2015-12-01

    Aspergillosis is a common respiratory fungal disease in penguins managed under human care. Triazole antifungal drugs, including itraconazole, are most commonly used for treatment; however, itraconazole treatment failures from drug resistance are becoming more common, requiring newer treatment options. Voriconazole, a newer triazole, is being used more often. Until recently, no voriconazole pharmacokinetic studies had been performed in penguins, leading to empiric dosing based on other avian studies. This has led to increased anecdotal reporting of apparent voriconazole toxicity in penguins. This report describes 18 probable and 6 suspected cases of voriconazole toxicity in six penguin species from nine institutions: 12 African penguins (Spheniscus demersus), 5 Humboldt penguins (Spheniscus humboldti), 3 Magellanic penguins (Spheniscus magellanicus), 2 gentoo penguins (Pygoscelis papua papua), 1 macaroni penguin (Eudyptes chrysolophus), and 1 emperor penguin (Aptenodytes forsteri). Observed clinical signs of toxicity included anorexia, lethargy, weakness, ataxia, paresis, apparent vision changes, seizure-like activity, and generalized seizures. Similar signs of toxicity have also been reported in humans, in whom voriconazole therapeutic plasma concentration for Aspergillus spp. infections is 2-6 μg/ml. Plasma voriconazole concentrations were measured in 18 samples from penguins showing clinical signs suggestive of voriconazole toxicity. The concentrations ranged from 8.12 to 64.17 μg/ml, with penguins having plasma concentrations above 30 μg/ml exhibiting moderate to severe neurologic signs, including ataxia, paresis, and seizures. These concentrations were well above those known to result in central nervous system toxicity, including encephalopathy, in humans. This case series highlights the importance of species-specific dosing of voriconazole in penguins and plasma therapeutic drug monitoring. Further investigation, including pharmacokinetic studies, is

  19. Simultaneous nano-tracking of multiple motor proteins via spectral discrimination of quantum dots

    PubMed Central

    Kakizuka, Taishi; Ikezaki, Keigo; Kaneshiro, Junichi; Fujita, Hideaki; Watanabe, Tomonobu M.; Ichimura, Taro

    2016-01-01

    Simultaneous nanometric tracking of multiple motor proteins was achieved by combining multicolor fluorescent labeling of target proteins and imaging spectroscopy, revealing dynamic behaviors of multiple motor proteins at the sub-diffraction-limit scale. Using quantum dot probes of distinct colors, we experimentally verified the localization precision to be a few nanometers at temporal resolution of 30 ms or faster. One-dimensional processive movement of two heads of a single myosin molecule and multiple myosin molecules was successfully traced. Furthermore, the system was modified for two-dimensional measurement and applied to tracking of multiple myosin molecules. Our approach is useful for investigating cooperative movement of proteins in supramolecular nanomachinery. PMID:27446684

  20. Simultaneous Excitation of Multiple-Input Multiple-Output CFD-Based Unsteady Aerodynamic Systems

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2008-01-01

    A significant improvement to the development of CFD-based unsteady aerodynamic reduced-order models (ROMs) is presented. This improvement involves the simultaneous excitation of the structural modes of the CFD-based unsteady aerodynamic system that enables the computation of the unsteady aerodynamic state-space model using a single CFD execution, independent of the number of structural modes. Four different types of inputs are presented that can be used for the simultaneous excitation of the structural modes. Results are presented for a flexible, supersonic semi-span configuration using the CFL3Dv6.4 code.

  1. Simultaneous Excitation of Multiple-Input Multiple-Output CFD-Based Unsteady Aerodynamic Systems

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2007-01-01

    A significant improvement to the development of CFD-based unsteady aerodynamic reduced-order models (ROMs) is presented. This improvement involves the simultaneous excitation of the structural modes of the CFD-based unsteady aerodynamic system that enables the computation of the unsteady aerodynamic state-space model using a single CFD execution, independent of the number of structural modes. Four different types of inputs are presented that can be used for the simultaneous excitation of the structural modes. Results are presented for a flexible, supersonic semi-span configuration using the CFL3Dv6.4 code.

  2. Electrochemical camera chip for simultaneous imaging of multiple metabolites in biofilms

    PubMed Central

    Bellin, Daniel L.; Sakhtah, Hassan; Zhang, Yihan; Price-Whelan, Alexa; Dietrich, Lars E. P.; Shepard, Kenneth L.

    2016-01-01

    Monitoring spatial distribution of metabolites in multicellular structures can enhance understanding of the biochemical processes and regulation involved in cellular community development. Here we report on an electrochemical camera chip capable of simultaneous spatial imaging of multiple redox-active phenazine metabolites produced by Pseudomonas aeruginosa PA14 colony biofilms. The chip features an 8 mm × 8 mm array of 1,824 electrodes multiplexed to 38 parallel output channels. Using this chip, we demonstrate potential-sweep-based electrochemical imaging of whole-biofilms at measurement rates in excess of 0.2 s per electrode. Analysis of mutants with various capacities for phenazine production reveals distribution of phenazine-1-carboxylic acid (PCA) throughout the colony, with 5-methylphenazine-1-carboxylic acid (5-MCA) and pyocyanin (PYO) localized to the colony edge. Anaerobic growth on nitrate confirms the O2-dependence of PYO production and indicates an effect of O2 availability on 5-MCA synthesis. This integrated-circuit-based technique promises wide applicability in detecting redox-active species from diverse biological samples. PMID:26813638

  3. A light-switchable bidirectional expression module allowing simultaneous regulation of multiple genes.

    PubMed

    Chen, Xianjun; Li, Ting; Wang, Xue; Yang, Yi

    2015-10-02

    Several light-regulated genetic circuits have been applied to spatiotemporally control transgene expression in mammalian cells. However, simultaneous regulation of multiple genes using one genetic device by light has not yet been reported. In this study, we engineered a bidirectional expression module based on LightOn system. Our data showed that both reporter genes could be regulated at defined and quantitative levels. Simultaneous regulation of four genes was further achieved in cultured cells and mice. Additionally, we successfully utilized the bidirectional expression module to monitor the expression of a suicide gene, showing potential for photodynamic gene therapy. Collectively, we provide a robust and useful tool to simultaneously control multiple genes expression by light, which will be widely used in biomedical research and biotechnology.

  4. Predicting Final GPA of Graduate School Students: Comparing Artificial Neural Networking and Simultaneous Multiple Regression

    ERIC Educational Resources Information Center

    Anderson, Joan L.

    2006-01-01

    Data from graduate student applications at a large Western university were used to determine which factors were the best predictors of success in graduate school, as defined by cumulative graduate grade point average. Two statistical models were employed and compared: artificial neural networking and simultaneous multiple regression. Both models…

  5. Complete Revascularization of Simultaneous Multiple Culprit Lesions in a Septuagenarian with ST-Elevation Myocardial Infarction

    PubMed Central

    Ifedili, Ikechukwu A.; Bob-Manuel, Tamunoinemi; Bolorunduro, Oluwaseyi; Askari, Raza; Ibebuogu, Uzoma N.

    2016-01-01

    Patient: Female, 74 Final Diagnosis: Multiple culprit lesions in ST-elevation myocardial infarction Symptoms: Chest pain • shortness of breath Medication: — Clinical Procedure: Cardiac catheterization Specialty: Cardiology Objective: Unusual clinical course Background: ST-elevation myocardial infarction (STEMI) is usually caused by rupture of unstable plaque with thrombus formation and abrupt cessation of blood flow through a single coronary artery that is deemed the culprit. The simultaneous thrombotic occlusions of multiple coronary arteries in the setting of STEMI is a rare occurrence with implications for patient management and outcome not fully addressed in the current STEMI guidelines, although more recent studies suggest a benefit of complete revascularization compared to culprit vessel-only treatment in the setting of STEMI. Case Report: A 74-year-old female presented with STEMI. Coronary angiography revealed simultaneous multiple coronary thrombotic occlusions involving the right coronary, left circumflex, and ramus intermedius arteries successfully treated with primary percutaneous revascularization at the same setting with good outcome and short hospital length of stay. Conclusions: Although the most appropriate timing to treat simultaneous multiple culprit lesions has yet to be definitively defined, multi-vessel percutaneous coronary intervention in the setting of a STEMI with multiple culprit lesions is feasible with good outcome as shown by our index case. PMID:28035135

  6. Simultaneous Multiple-Jet Impacts in Concrete-Experiments and Advanced Computational Simulations

    SciTech Connect

    Baum, D.W.; Kuklo, R.M.; Routh, J.W.; Simonson, S.C.

    1999-08-12

    The simultaneous impact of multiple shaped-charge jets on a concrete target has been observed experimentally to lead to the formation of a larger and deeper entrance crater than would be expected from the superposition of the craters of the individual jets. The problem has been modeled with the 3-D simulation code ALE3D, running on massively parallel processors. These calculations indicate that the enlarged damage area is the result of tensile stresses caused by the interactions among the pressure waves simultaneously emanating from the three impact sites. This phenomenon has the potential for enhancing the penetration of a follow-on projectile.

  7. Comparing Multiple Criteria for Species Identification in Two Recently Diverged Seabirds

    PubMed Central

    Militão, Teresa; Gómez-Díaz, Elena; Kaliontzopoulou, Antigoni; González-Solís, Jacob

    2014-01-01

    Correct species identification is a crucial issue in systematics with key implications for prioritising conservation effort. However, it can be particularly challenging in recently diverged species due to their strong similarity and relatedness. In such cases, species identification requires multiple and integrative approaches. In this study we used multiple criteria, namely plumage colouration, biometric measurements, geometric morphometrics, stable isotopes analysis (SIA) and genetics (mtDNA), to identify the species of 107 bycatch birds from two closely related seabird species, the Balearic (Puffinus mauretanicus) and Yelkouan (P. yelkouan) shearwaters. Biometric measurements, stable isotopes and genetic data produced two stable clusters of bycatch birds matching the two study species, as indicated by reference birds of known origin. Geometric morphometrics was excluded as a species identification criterion since the two clusters were not stable. The combination of plumage colouration, linear biometrics, stable isotope and genetic criteria was crucial to infer the species of 103 of the bycatch specimens. In the present study, particularly SIA emerged as a powerful criterion for species identification, but temporal stability of the isotopic values is critical for this purpose. Indeed, we found some variability in stable isotope values over the years within each species, but species differences explained most of the variance in the isotopic data. Yet this result pinpoints the importance of examining sources of variability in the isotopic data in a case-by-case basis prior to the cross-application of the SIA approach to other species. Our findings illustrate how the integration of several methodological approaches can help to correctly identify individuals from recently diverged species, as each criterion measures different biological phenomena and species divergence is not expressed simultaneously in all biological traits. PMID:25541978

  8. Simultaneously measuring multiple protein interactions and their correlations in a cell by Protein-interactome Footprinting

    PubMed Central

    Luo, Si-Wei; Liang, Zhi; Wu, Jia-Rui

    2017-01-01

    Quantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers. Using PiF, we quantitatively reveal dynamic patterns of PPIs and their correlation network in E. coli two-component systems. PMID:28338015

  9. Three-dimensional fluorescent microscopy via simultaneous illumination and detection at multiple planes

    PubMed Central

    Ma, Qian; Khademhosseinieh, Bahar; Huang, Eric; Qian, Haoliang; Bakowski, Malina A.; Troemel, Emily R.; Liu, Zhaowei

    2016-01-01

    The conventional optical microscope is an inherently two-dimensional (2D) imaging tool. The objective lens, eyepiece and image sensor are all designed to capture light emitted from a 2D ‘object plane’. Existing technologies, such as confocal or light sheet fluorescence microscopy have to utilize mechanical scanning, a time-multiplexing process, to capture a 3D image. In this paper, we present a 3D optical microscopy method based upon simultaneously illuminating and detecting multiple focal planes. This is implemented by adding two diffractive optical elements to modify the illumination and detection optics. We demonstrate that the image quality of this technique is comparable to conventional light sheet fluorescent microscopy with the advantage of the simultaneous imaging of multiple axial planes and reduced number of scans required to image the whole sample volume. PMID:27527813

  10. The use of cycleave PCR for the differentiation of the rejuvenating herb species Pueraria candollei (White Kwao Khruea), Butea superba (Red Kwao Khruea), and Mucuna macrocarpa (Black Kwao Khruea), and the simultaneous detection of multiple DNA targets in a DNA admixture.

    PubMed

    Wiriyakarun, Suchaya; Zhu, Shu; Komatsu, Katsuko; Sukrong, Suchada

    2014-01-01

    Kwao Khruea, the tuberous roots of Pueraria candollei Graham ex Benth. (White Kwao Khruea), Butea superba Roxb. (Red Kwao Khruea), and Mucuna macrocarpa Wall. (Black Kwao Khruea), are used as rejuvenating herbs in traditional medicine in many tropical countries. Although Kwao Khruea has attracted strong interest because of its rejuvenation properties, each species is used for specific purposes and effects. P. candollei shows estrogenic effects in females. In contrast, B. superba and M. macrocarpa show androgenic effects in males. The potential misidentification of dried tuberous roots of various Kwao Khruea species might cause problems in the drug market, especially when they are reduced into powders. A cycleave PCR, which is based on the sequence of chloroplast matK gene, was developed to differentiate P. candollei, B. superba, and M. macrocarpa. The results showed that cycleave PCR is able to identify specific Kwao Khruea species. A multiplex cycleave PCR was optimized for the simultaneous detection of two different DNA targets in a DNA admixture. The specificity of this technique was confirmed by its ability to distinguish M. macrocarpa from five related Mucuna species. Cycleave PCR can be a specific, sensitive, and rapid method for the identification of medicinal plants and crude plant samples.

  11. MULTIPLE SOLVENT EXPOSURE IN HUMANS: CROSS-SPECIES EXTRAPOLATIONS

    EPA Science Inventory

    Multiple Solvent Exposures in Humans:
    Cross-Species Extrapolations
    (Future Research Plan)

    Vernon A. Benignus1, Philip J. Bushnell2 and William K. Boyes2

    A few solvents can be safely studied in acute experiments in human subjects. Data exist in rats f...

  12. Crosstalk-insensitive method for simultaneously coupling multiple pairs of resonators

    NASA Astrophysics Data System (ADS)

    Yang, Chui-Ping; Su, Qi-Ping; Zheng, Shi-Biao; Nori, Franco

    2016-04-01

    In a circuit consisting of two or more resonators, the intercavity crosstalk is inevitable, which could create some problems, such as degrading the performance of quantum operations and the fidelity of various quantum states. The focus of this work is to propose a crosstalk-insensitive method for simultaneously coupling multiple pairs of resonators, which is important in large-scale quantum information processing and communication in a network consisting of resonators or cavities. In this work, we consider 2 N resonators of different frequencies, which are coupled to a three-level quantum system (qutrit). By applying a strong pulse to the coupler qutrit, we show that an effective Hamiltonian can be constructed for simultaneously coupling multiple pairs of resonators. The main advantage of this proposal is that the effect of inter-resonator crosstalks is greatly suppressed by using resonators of different frequencies. In addition, by employing the qutrit-resonator dispersive interaction, the intermediate higher-energy level of the qutrit is virtually excited and thus decoherence from this level is suppressed. This effective Hamiltonian can be applied to implement quantum operations with photonic qubits distributed in different resonators. As one application of this Hamiltonian, we show how to simultaneously generate multiple Einstein-Podolsky-Rosen pairs of photonic qubits distributed in 2 N resonators. Numerical simulations show that it is feasible to prepare two high-fidelity EPR photonic pairs using a setup of four one-dimensional transmission line resonators coupled to a superconducting flux qutrit with current circuit QED technology.

  13. Intracellular Microreactors as Artificial Organelles to Conduct Multiple Enzymatic Reactions Simultaneously.

    PubMed

    Godoy-Gallardo, María; Labay, Cédric; Jansman, Michelle M T; Ek, Pramod K; Hosta-Rigau, Leticia

    2017-02-01

    The creation of artificial organelles is a new paradigm in medical therapy that aims to substitute for missing cellular function by replenishing a specific cellular task. Artificial organelles tackle the challenge of mimicking metabolism, which is the set of chemical reactions that occur within a cell, mainly catalyzed by enzymes. So far, the few reported carriers able to conduct enzymatic reactions intracellularly are based on single-compartment carriers. However, cell organelles outperform by conducting multiple reactions simultaneously within confined sub-compartments. Here, the field of artificial organelles is advanced by reporting the assembly of a microreactor consisting of polymer capsules entrapping gold nanoclusters (AuNCs) and liposomes as sub-compartments. The fluorescence properties of AuNCs are employed to monitor the microreactors uptake by macrophages. Encapsulation is demonstrated and functionality of microreactors with trypsin (TRP) and horseradish peroxidase (HRP)-loaded liposomes is preserved. Multiple enzymatic reactions taking place simultaneously is demonstrated by exposing macrophages with the internalized microreactors to bis-(benzyloxycarbonyl-Ile-Pro-Arg)-Rho-110 and Amplex Red substrates, which are specific for TRP and HRP, respectively. Conversion of the substrates into the respective fluorescent products is observed. This report on the first microreactor conducting multiple enzymatic reactions simultaneously inside a cell is a considerable step in the field of artificial organelles.

  14. Spontaneous Raman scattering for simultaneous measurements of in-cylinder species

    NASA Astrophysics Data System (ADS)

    Zhao, H.; Zhang, S.

    2007-10-01

    A technique for multi-species mole fraction measurement in internal combustion engines is described. The technique is based on the spontaneous Raman scattering. It can simultaneously provide the mole fractions of several species of N2, O2, H2O, CO2 and fuel. Using the system, simultaneous measurement of air/fuel ratio and burnt residual gas are carried out during the mixture process in a Controlled Auto Ignition (CAI) combustion engine. The accuracy and consistency of the measured results were confirmed by the measured air fuel ratio using an exhaust gas analyzer and independently calculated mole fraction values. Measurement of species mole fractions during combustion process has also been demonstrated. It shows that the SRS can provide valuable data on this process in a CAI combustion engine.

  15. Simultaneous Multiple Preoperative Localizations of Small Pulmonary Lesions Using a Short Hook Wire and Suture System

    SciTech Connect

    Iguchi, Toshihiro Hiraki, Takao Gobara, Hideo Fujiwara, Hiroyasu Matsui, Yusuke; Sugimoto, Seiichiro Toyooka, Shinichi Oto, Takahiro Miyoshi, Shinichiro; Kanazawa, Susumu

    2015-08-15

    PurposeThe aim of the study was to retrospectively evaluate simultaneous multiple hook wire placement outcomes before video-assisted thoracoscopic surgery (VATS).Materials and MethodsThirty-eight procedures were performed on 35 patients (13 men and 22 women; mean age, 59.9 years) with 80 lung lesions (mean diameter 7.9 mm) who underwent simultaneous multiple hook wire placements for preoperative localizations. The primary endpoints were technical success, complications, procedure duration, and VATS outcome; secondary endpoints included comparisons between technical success rates, complication rates, and procedure durations of the 238 single-placement procedures performed. Complications were also evaluated.ResultsIn 35 procedures including 74 lesions, multiple hook wire placements were technically successful; in the remaining three procedures, the second target placement was aborted because of massive pneumothorax after the first placement. Although complications occurred in 34 procedures, no grade 3 or above adverse event was observed. The mean procedure duration was 36.4 ± 11.8 min. Three hook wires dislodged during patient transport to the surgical suite. Seventy-four successfully marked lesions were resected. Six lesions without hook wires were successfully resected after detection by palpation with an additional mini-thoracotomy or using subtle pleural changes as a guide. The complication rates and procedure durations of multiple-placement procedures were significantly higher (P = 0.04) and longer (P < 0.001) than those in the single-placement group, respectively, while the technical success rate was not significantly different (P = 0.051).ConclusionsSimultaneous multiple hook wire placements before VATS were clinically feasible, but increased the complication rate and lengthened the procedure time.

  16. Efficient expansion of global protected areas requires simultaneous planning for species and ecosystems

    PubMed Central

    Polak, Tal; Watson, James E. M.; Fuller, Richard A.; Joseph, Liana N.; Martin, Tara G.; Possingham, Hugh P.; Venter, Oscar; Carwardine, Josie

    2015-01-01

    The Convention on Biological Diversity (CBD)'s strategic plan advocates the use of environmental surrogates, such as ecosystems, as a basis for planning where new protected areas should be placed. However, the efficiency and effectiveness of this ecosystem-based planning approach to adequately capture threatened species in protected area networks is unknown. We tested the application of this approach in Australia according to the nation's CBD-inspired goals for expansion of the national protected area system. We set targets for ecosystems (10% of the extent of each ecosystem) and threatened species (variable extents based on persistence requirements for each species) and then measured the total land area required and opportunity cost of meeting those targets independently, sequentially and simultaneously. We discover that an ecosystem-based approach will not ensure the adequate representation of threatened species in protected areas. Planning simultaneously for species and ecosystem targets delivered the most efficient outcomes for both sets of targets, while planning first for ecosystems and then filling the gaps to meet species targets was the most inefficient conservation strategy. Our analysis highlights the pitfalls of pursuing goals for species and ecosystems non-cooperatively and has significant implications for nations aiming to meet their CBD mandated protected area obligations. PMID:26064645

  17. To open or to close: species-specific stomatal responses to simultaneously applied opposing environmental factors.

    PubMed

    Merilo, Ebe; Jõesaar, Indrek; Brosché, Mikael; Kollist, Hannes

    2014-04-01

    Plant stomatal responses to single environmental factors are well studied; however, responses to a change in two (or more) factors - a common situation in nature - have been less frequently addressed. We studied the stomatal responses to a simultaneous application of opposing environmental factors in six evolutionarily distant mono- and dicotyledonous herbs representing different life strategies (ruderals, competitors and stress-tolerators) to clarify whether the crosstalk between opening- and closure-inducing pathways leading to stomatal response is universal or species-specific. Custom-made gas exchange devices were used to study the stomatal responses to a simultaneous application of two opposing factors: decreased/increased CO2 concentration and light availability or reduced air humidity. The studied species responded similarly to changes in single environmental factors, but showed species-specific and nonadditive responses to two simultaneously applied opposing factors. The stomata of the ruderals Arabidopsis thaliana and Thellungiella salsuginea (previously Thellungiella halophila) always opened, whereas those of competitor-ruderals either closed in all two-factor combinations (Triticum aestivum), remained relatively unchanged (Nicotiana tabacum) or showed a response dominated by reduced air humidity (Hordeum vulgare). Our results, indicating that in changing environmental conditions species-specific stomatal responses are evident that cannot be predicted from studying one factor at a time, might be interesting for stomatal modellers, too.

  18. Quantitative Comparison of Tumor Delivery for Multiple Targeted Nanoparticles Simultaneously by Multiplex ICP-MS

    PubMed Central

    Elias, Andrew; Crayton, Samuel H.; Warden-Rothman, Robert; Tsourkas, Andrew

    2014-01-01

    Given the rapidly expanding library of disease biomarkers and targeting agents, the number of unique targeted nanoparticles is growing exponentially. The high variability and expense of animal testing often makes it unfeasible to examine this large number of nanoparticles in vivo. This often leads to the investigation of a single formulation that performed best in vitro. However, nanoparticle performance in vivo depends on many variables, many of which cannot be adequately assessed with cell-based assays. To address this issue, we developed a lanthanide-doped nanoparticle method that allows quantitative comparison of multiple targeted nanoparticles simultaneously. Specifically, superparamagnetic iron oxide (SPIO) nanoparticles with different targeting ligands were created, each with a unique lanthanide dopant. Following the simultaneous injection of the various SPIO compositions into tumor-bearing mice, inductively coupled plasma mass spectroscopy was used to quantitatively and orthogonally assess the concentration of each SPIO composition in serial blood and resected tumor samples. PMID:25068300

  19. Simultaneous dispersion measurements of multiple fiber modes using virtual reference interferometry.

    PubMed

    Galle, Michael A; Saini, Simarjeet S; Mohammed, Waleed S; Sillard, Pierre; Qian, Li

    2014-03-24

    We present the simultaneous measurement of first and second order dispersion in short length (< 1 m) few mode fibers (polarization and transverse) using virtual reference interferometry. This technique generates results equivalent to balanced spectral interferometry, without the complexity associated with physical balancing. This is achieved by simulating a virtual reference with a group delay equal to that of the physical interferometer. The amplitude modulation that results from mixing the interferograms, generated in both the unbalanced interferometer and the virtual reference, is equivalent to the first order interference that would be produced by physical balancing. The advantages of the technique include speed, simplicity, convenience and the capability for simultaneous measurement of multiple modes. The theoretical framework is first developed and then verified experimentally.

  20. Simultaneous measurement of multiple radiation-induced protein expression profiles using the Luminex(TM) system

    NASA Technical Reports Server (NTRS)

    Desai, N.; Wu, H.; George, K.; Gonda, S. R.; Cucinotta, F. A.; Cucniotta, F. A. (Principal Investigator)

    2004-01-01

    Space flight results in the exposure of astronauts to a mixed field of radiation composed of energetic particles of varying energies, and biological indicators of space radiation exposure provides a better understanding of the associated long-term health risks. Current methods of biodosimetry have employed the use of cytogenetic analysis for biodosimetry, and more recently the advent of technological progression has led to advanced research in the use of genomic and proteomic expression profiling to simultaneously assess biomarkers of radiation exposure. We describe here the technical advantages of the Luminex(TM) 100 system relative to traditional methods and its potential as a tool to simultaneously profile multiple proteins induced by ionizing radiation. The development of such a bioassay would provide more relevant post-translational dynamics of stress response and will impart important implications in the advancement of space and other radiation contact monitoring. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

  1. Quantitative Comparison of Tumor Delivery for Multiple Targeted Nanoparticles Simultaneously by Multiplex ICP-MS

    NASA Astrophysics Data System (ADS)

    Elias, Andrew; Crayton, Samuel H.; Warden-Rothman, Robert; Tsourkas, Andrew

    2014-07-01

    Given the rapidly expanding library of disease biomarkers and targeting agents, the number of unique targeted nanoparticles is growing exponentially. The high variability and expense of animal testing often makes it unfeasible to examine this large number of nanoparticles in vivo. This often leads to the investigation of a single formulation that performed best in vitro. However, nanoparticle performance in vivo depends on many variables, many of which cannot be adequately assessed with cell-based assays. To address this issue, we developed a lanthanide-doped nanoparticle method that allows quantitative comparison of multiple targeted nanoparticles simultaneously. Specifically, superparamagnetic iron oxide (SPIO) nanoparticles with different targeting ligands were created, each with a unique lanthanide dopant. Following the simultaneous injection of the various SPIO compositions into tumor-bearing mice, inductively coupled plasma mass spectroscopy was used to quantitatively and orthogonally assess the concentration of each SPIO composition in serial blood and resected tumor samples.

  2. Microfluidic Quantitative PCR for Simultaneous Quantification of Multiple Viruses in Environmental Water Samples

    PubMed Central

    Kitamura, Gaku; Segawa, Takahiro; Kobayashi, Ayano; Miura, Takayuki; Sano, Daisuke; Okabe, Satoshi

    2014-01-01

    To secure food and water safety, quantitative information on multiple pathogens is important. In this study, we developed a microfluidic quantitative PCR (MFQPCR) system to simultaneously quantify 11 major human viral pathogens, including adenovirus, Aichi virus, astrovirus, enterovirus, human norovirus, rotavirus, sapovirus, and hepatitis A and E viruses. Murine norovirus and mengovirus were also quantified in our MFQPCR system as a sample processing control and an internal amplification control, respectively. River water contaminated with effluents from a wastewater treatment plant in Sapporo, Japan, was collected and used to validate our MFQPCR system for multiple viruses. High-throughput quantitative information was obtained with a quantification limit of 2 copies/μl of cDNA/DNA. Using this MFQPCR system, we could simultaneously quantify multiple viral pathogens in environmental water samples. The viral quantities obtained using MFQPCR were similar to those determined by conventional quantitative PCR. Thus, the MFQPCR system developed in this study can provide direct and quantitative information for viral pathogens, which is essential for risk assessments. PMID:25261510

  3. Radio Frequency Identification Sensor Chips with Anticollision Algorithm for Simultaneous Detection of Multiple DNA Targets

    NASA Astrophysics Data System (ADS)

    Yazawa, Yoshiaki; Oonishi, Tadashi; Watanabe, Kazuki; Nemoto, Ryo; Shiratori, Akiko

    2010-04-01

    A newly developed DNA measurement method for multiple single nucleotide polymorphism (SNP) typing using a radio-frequency identification (RFID) sensor chip was demonstrated. The RFID sensor chip monolithically integrates a sensor, amplifier, analog-to-digital converter (ADC), and a passive wireless communication interface for receiving commands and transmitting data on a 2.5×2.5 mm2 silicon chip. For the simultaneous multitarget measurement, anticollision control and peak-power suppression are essential. To assign a unique identification number (UID) for the identification of multiple sensor chips, a reproducible random number generator circuit (RRG) was designed and installed on the chip. Peak-power consumption was reduced to 1018 µW by a clock gating of functional circuit blocks. Multiple SNP typing was carried out by simultaneously operating five RFID sensor chips (four with photosensors and one with a temperature sensor). The target DNA was captured on the sensor chips, and SNPs were detected by observing bioluminescence. Finally, the observed data were wirelessly transmitted to the reader.

  4. Widespread transmission of independent cancer lineages within multiple bivalve species

    PubMed Central

    Metzger, Michael J.; Villalba, Antonio; Carballal, María J.; Iglesias, David; Sherry, James; Reinisch, Carol; Muttray, Annette F.; Baldwin, Susan A.; Goff, Stephen P.

    2016-01-01

    Most cancers arise from oncogenic changes in the genomes of somatic cells, and while the cells may migrate by metastasis, they remain within that single individual. Natural transmission of cancer cells from one individual to another has been observed in two distinctive cases in mammals (Tasmanian devils1 and dogs2,3), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria)4 suggested that this phenomenon might be more widespread. Here we analyzed disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and found that neoplasias in all three species are attributable to independent transmissible cancer lineages. In mussels and cockles, the cancer lineages are derived from their respective host species, but unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographic area. No cases of disseminated neoplasia have thus far been found in V. corrugata from the same region. These findings show that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers were found spreading within the species of origin, cross-species transmission of cancer cells can occur. PMID:27338791

  5. Instrumentation for simultaneous kinetic imaging of multiple fluorophores in single living cells

    NASA Astrophysics Data System (ADS)

    Morris, Stephen J.; Beatty, Diane M.; Welling, Larry W.; Wiegmann, Thomas B.

    1991-05-01

    Low-light fluorescence video microscopy has established itself as an excellent method for investigations of cell dynamics. There is a growing interest in resolving multiple images of 'ratio' fluorophores like indo or BCECF or the emission from multiple dyes placed in the same cell system. For rapid kinetic studies, the problems of photodynamic damage and photobleaching on one hand and the need for good spatial and temporal resolution on the other, press the resolution of the instrumentation. Rapid resolution of multiple probes at multiple wavelengths presents a third set of problems of exciting the probes and appropriately imaging the emitted light. The authors have designed a new real-time low-light fluorescence video microscope for capturing intensified images of up to four dyes contained in the same cell system. These can be two dual-emission wavelength 'ratio' dyes or multiple dyes. The optics allow simultaneous excitation of up to four fluorophores and the real-time (30 frames/second) capture of four separate fluorescence emission images. Each emission wavelength is imaged simultaneously by one of four cameras, then digitized and appropriately combined at standard video frame rates to be stored at high resolution on tape or video disk for further off-line correction and analysis. The design has no moving parts in its optical train, which overcomes a number of technical difficulties encountered in filter wheel or mechanical shutter designs for multiple imaging. The instrument can be assembled form off-the-shelf components. Coupled to compatible image processing software utilizing PC-AT computers, it can be realized for relatively low cost. Two examples of simultaneous multi-parameter imaging are presented. Synchronous observations of calcium and pH distribution in kidney epithelial cells, loaded with both indo-1 and SNARF-1TM, show that both are altered in response to ionomycin treatment; however, the kinetics for the two changes are quite different

  6. CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

    NASA Technical Reports Server (NTRS)

    Cutler, Andrew D.; Magnotti, Gaetano

    2010-01-01

    The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

  7. Multiple species of noninteracting molecules adsorbed on a Bethe lattice.

    PubMed

    Cohen, Michael; Harris, A B

    2008-10-01

    A simple method, previously used to calculate the equilibrium concentration of dimers adsorbed on a Bethe lattice as a function of the dimer activity, is generalized to solve the problem of a Bethe lattice in contact with a reservoir containing a mixture of molecules. The molecules may have arbitrary sizes and shapes consistent with the geometry of the lattice and the molecules do not interact with one another except for the hard-core restriction that two molecules cannot touch the same site. We obtain a set of simultaneous nonlinear equations, one equation for each species of molecule, which determines the equilibrium concentration of each type of molecule as a function of the (arbitrary) activities of the various species. Surprisingly, regardless of the number of species, the equilibrium concentrations are given explicitly in terms of the solution of a single equation in one unknown which can be solved numerically, if need be. Some numerical examples show that increasing the activity of one species need not necessarily decrease the equilibrium concentration of all other species. We also calculate the adsorption isotherm of an "annealed" Bethe lattice consisting of two types of sites which differently influence the activity of an adsorbed molecule. We prove that if the reservoir contains a finite number of molecular species, regions of two different polymer densities cannot simultaneously exist on the lattice. The widely used Guggenheim theory of mixtures, which can also be construed as a theory of adsorption, assumes for simplicity that the molecules in the mixture are composed of elementary units, which occupy sites of a lattice of coordination number q . Guggenheim's analysis relies on approximate combinatorial formulas which become exact on a Bethe lattice of the same coordination number, as we show in an appendix. Our analysis involves no combinatorics and relies only on recognizing the statistical independence of certain quantities. Despite the nominal

  8. Effect of Multiple Simultaneous Vaccines on Polio Seroresponse and Associated Health Outcomes

    DTIC Science & Technology

    2015-01-01

    responses to biological warfare vaccines in human vaccinees . Clin Infect Dis 2006;43:1–7. 20] Butler D. Admission on Gulf War vaccines spurs debate on...Naval Health Research Center Effect of Multiple, Simultaneous Vaccines on Polio Seroresponse and Associated Health Outcomes Michael P...Diego, California 92106-3521 E a M C a b a A R R A A K P I S M T T 1 t c i o c i A h 0 Vaccine 33 (2015) 2842–2848 Contents lists available at

  9. A sparse matrix iterative method for efficiently computing multiple simultaneous solutions

    SciTech Connect

    Boyse, W.E.; Seidl, A.A.

    1994-12-31

    The authors consider the solution of large sparse complex symmetric indefinite systems of equations where multiple solutions are required. This type of problem occurs in calculating monostatic radar cross sections in electromagnetic scattering using the finite element method. The Quasi Minimum Residual (QMR) method, ideally suited for these matrices, is generalized using the block Lanozos algorithm to solve blocks of solutions simultaneously. The algorithm is presented and a natural convergence criterion is proposed which is shown to be as effective as the usual equation residual in monitoring convergence.

  10. Mapping habitat for multiple species in the Desert Southwest

    USGS Publications Warehouse

    Inman, Richard D.; Nussear, Kenneth E.; Esque, Todd C.; Vandergast, Amy G.; Hathaway, Stacie A.; Wood, Dustin A.; Barr, Kelly R.; Fisher, Robert N.

    2014-01-01

    Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet (http://vertnet.org/), HerpNET (http://www.herpnet.org), and MaNIS (http://manisnet.org), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.

  11. Simultaneous Determination of Arsenic and Selenium Species in Sediment Extracts Utilizing Coupled Techniques with Mass Spectrometric Detection

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Yoon, C.

    2009-12-01

    Arsenic has been recognized as one of the major problems of toxicity in several parts of the world. It is well known that the toxicity of arsenic depends on its chemical form. Selenium is one of the minor but plays an important biological role in human health. The multiple roles of selenium, deficiency and toxicity, depend on its chemical form and concentration. The multielement detection capability of ICP-MS makes it an ideal detector for multielement chromatographic separation. Most of multielement separation analyses by LC-ICP-MS are applied to standard or to water samples. Only very few reports deal with solid matrices. A procedure for the simultaneous determination of arsenic and selenium species in phosphoric acid extracts of sediment samples by liquid chromatography coupled to ICP-MS has been developing. Arsenic species, arsenite [As(III)], arsenate [As(V)], dimethylarsinic acid (DMA), monomethylarsonic acid (MMA), and selenium species, selenite [Se(IV)], selenate [Se(VI)] were separated on anion exchange column by a mobile phase of ammonium dihydrogen phosphate. The total analysis took less than 10 min with gradient elution at flow rate of 1.0 mL/min. The sonication extraction was used with dry sediment and phosphoric acid. Reaction gases such as methane and oxygen was used to remove spectral interferences on arsenic and selenium measurement. The estimated detection limits in the sediment ranged between 1 and 25 ng/g for the arsenic and selenium species. The repeatability was less than 15% (RSD) for 1 µg/L arsenic species and 5 µg/L selenium species. Accuracy of the method was assessed through the recovery of the spiked sediment. Recoveries ranged between 82 and 115 % for all the species.

  12. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

    PubMed Central

    Faria, Nuno Rodrigues; Suchard, Marc A.; Rambaut, Andrew; Streicker, Daniel G.; Lemey, Philippe

    2013-01-01

    The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes. PMID:23382420

  13. Energetics of Multiple-Ion Species Hohlraum Plasmas

    SciTech Connect

    Neumayer, P; Berger, R; Callahan, D; Divol, L; Froula, D; London, R; MacGowan, B J; Meezan, N; Michel, P; Ross, J S; Sorce, C; Widmann, K; Suter, L; Glenzer, S H

    2007-11-05

    A study of the laser-plasma interaction processes in multiple-ion species plasmas has been performed in plasmas that are created to emulate the plasma conditions in indirect drive inertial confinement fusion targets. Gas-filled hohlraums with densities of xe22/cc are heated to Te=3keV and backscattered laser light is measured by a suite of absolutely calibrated backscatter diagnostics. Ion Landau damping is increased by adding hydrogen to the CO2/CF4 gas fill. We find that the backscatter from stimulated Brillouin scattering is reduced is monotonically reduced with increasing damping, demonstrating that Landau damping is the controlling damping mechanism in ICF relevant high-electron temperature plasmas. The reduction in backscatter is accompanied by a comparable increase in both transmission of a probe beam and an increased hohlraum radiation temperature, showing that multiple-ion species plasmas improve the overall hohlraum energetics/performance. Comparison of the experimental data to linear gain calculations as well as detailed full-scale 3D laser-plasma interaction simulations show quantitative agreement. Our findings confirm the importance of Landau damping in controlling backscatter from high-electron temperature hohlraum plasmas and have lead to the inclusion of multi-ion species plasmas in the hohlraum point design for upcoming ignition campaigns at the National Ignition Facility.

  14. Simultaneous two-axis shearographic interferometer using multiple wavelengths and a color camera

    NASA Astrophysics Data System (ADS)

    Richoz, Guillaume L.; Schajer, Gary S.

    2016-02-01

    Multi-component measurements in shearography and other applications of Electronic Speckle Pattern Interferometry (ESPI) are typically achieved using multiple optical configurations that are activated sequentially to measure each desired quantity separately. A novel optical setup is introduced here where orthogonal shearography measurements are simultaneously made using a single color-camera imaging multiple monochromatic light sources of different wavelengths. The Red-Green-Blue (RGB) sensors of a conventional Bayer type camera are read separately, thereby providing three independent color signals and independent ESPI phase maps. Orthogonal axis shearography is achieved using a modified shearography interferometer where a dichroic filter is added to provide a second wavelength-dependent measurement. The availability of the two surface slopes gives the opportunity for the data to be summed numerically to give the surface displacement shape. This application is of significant practical interest because the surface displacement measurement can be made under field conditions by taking advantage of the well-known optical stability of shearography measurements. The two simultaneously measured surface slopes also offer the possibility to mathematically compensate for non-uniformity and non-orthogonality in the image shear caused by mirror non-flatness and/or mirror misalignments.

  15. Technical note: Simultaneous fully dynamic characterization of multiple input–output relationships in climate models

    SciTech Connect

    Kravitz, Ben; MacMartin, Douglas G.; Rasch, Philip J.; Wang, Hailong

    2017-01-01

    We introduce system identification techniques to climate science wherein multiple dynamic input–output relationships can be simultaneously characterized in a single simulation. This method, involving multiple small perturbations (in space and time) of an input field while monitoring output fields to quantify responses, allows for identification of different timescales of climate response to forcing without substantially pushing the climate far away from a steady state. We use this technique to determine the steady-state responses of low cloud fraction and latent heat flux to heating perturbations over 22 regions spanning Earth's oceans. We show that the response characteristics are similar to those of step-change simulations, but in this new method the responses for 22 regions can be characterized simultaneously. Furthermore, we can estimate the timescale over which the steady-state response emerges. The proposed methodology could be useful for a wide variety of purposes in climate science, including characterization of teleconnections and uncertainty quantification to identify the effects of climate model tuning parameters.

  16. Technical note: Simultaneous fully dynamic characterization of multiple input–output relationships in climate models

    DOE PAGES

    Kravitz, Ben; MacMartin, Douglas G.; Rasch, Philip J.; ...

    2017-02-17

    We introduce system identification techniques to climate science wherein multiple dynamic input–output relationships can be simultaneously characterized in a single simulation. This method, involving multiple small perturbations (in space and time) of an input field while monitoring output fields to quantify responses, allows for identification of different timescales of climate response to forcing without substantially pushing the climate far away from a steady state. We use this technique to determine the steady-state responses of low cloud fraction and latent heat flux to heating perturbations over 22 regions spanning Earth's oceans. We show that the response characteristics are similar to thosemore » of step-change simulations, but in this new method the responses for 22 regions can be characterized simultaneously. Moreover, we can estimate the timescale over which the steady-state response emerges. The proposed methodology could be useful for a wide variety of purposes in climate science, including characterization of teleconnections and uncertainty quantification to identify the effects of climate model tuning parameters.« less

  17. SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

    PubMed

    Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

    2010-07-01

    We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

  18. Technical note: Simultaneous fully dynamic characterization of multiple input-output relationships in climate models

    NASA Astrophysics Data System (ADS)

    Kravitz, Ben; MacMartin, Douglas G.; Rasch, Philip J.; Wang, Hailong

    2017-02-01

    We introduce system identification techniques to climate science wherein multiple dynamic input-output relationships can be simultaneously characterized in a single simulation. This method, involving multiple small perturbations (in space and time) of an input field while monitoring output fields to quantify responses, allows for identification of different timescales of climate response to forcing without substantially pushing the climate far away from a steady state. We use this technique to determine the steady-state responses of low cloud fraction and latent heat flux to heating perturbations over 22 regions spanning Earth's oceans. We show that the response characteristics are similar to those of step-change simulations, but in this new method the responses for 22 regions can be characterized simultaneously. Furthermore, we can estimate the timescale over which the steady-state response emerges. The proposed methodology could be useful for a wide variety of purposes in climate science, including characterization of teleconnections and uncertainty quantification to identify the effects of climate model tuning parameters.

  19. Assessing Neurocognition via Gamified Experimental Logic: A Novel Approach to Simultaneous Acquisition of Multiple ERPs

    PubMed Central

    Nair, Ajay K.; Sasidharan, Arun; John, John P.; Mehrotra, Seema; Kutty, Bindu M.

    2016-01-01

    The present study describes the development of a neurocognitive paradigm: “Assessing Neurocognition via Gamified Experimental Logic” (ANGEL), for performing the parametric evaluation of multiple neurocognitive functions simultaneously. ANGEL employs an audiovisual sensory motor design for the acquisition of multiple event related potentials (ERPs)—the C1, P50, MMN, N1, N170, P2, N2pc, LRP, P300, and ERN. The ANGEL paradigm allows assessment of 10 neurocognitive variables over the course of three “game” levels of increasing complexity ranging from simple passive observation to complex discrimination and response in the presence of multiple distractors. The paradigm allows assessment of several levels of rapid decision making: speeded up response vs. response-inhibition; responses to easy vs. difficult tasks; responses based on gestalt perception of clear vs. ambiguous stimuli; and finally, responses with set shifting during challenging tasks. The paradigm has been tested using 18 healthy participants from both sexes and the possibilities of varied data analyses have been presented in this paper. The ANGEL approach provides an ecologically valid assessment (as compared to existing tools) that quickly yields a very rich dataset and helps to assess multiple ERPs that can be studied extensively to assess cognitive functions in health and disease conditions. PMID:26858586

  20. The simultaneous occurrence of multiple myeloma and JAK2 positive myeloproliferative neoplasms - Report on two cases

    PubMed Central

    Badelita, S; Dobrea, C; Colita, A; Dogaru, M; Dragomir, M; Jardan, C; Coriu, D

    2015-01-01

    Multiple myeloma and JAK2 positive chronic myeloproliferative neoplasms are hematologic malignancies with a completely different cellular origin. Two cases of simultaneous occurrence of multiple myeloma, one with primary myelofibrosis and another one with essential thrombocythemia are reported in this article. In such cases, an accurate diagnosis requires a molecular testing, including gene sequencing and differential diagnosis of pancytosis associated with splenic amyloidosis. In general, in such cases, of two coexisting malignant hematologic diseases, the treatment of the most aggressive one is recommended. For our two cases, it was decided to start a Velcade based therapy. The main concern was the medullar toxicity, especially when a multiple myeloma was associated with a primary myelofibrosis. Abbreviations:JAK2 = Janus kinase 2 gene, PMF = primary myelofibrosis, MPNs = myeloproliferative neoplasms, ET = essential thrombocythemia, PV = polycythemia vera, MM = multiple myeloma, WBC = white blood cells, Hb = haemoglobin, Ht = haematocrit, Plt = platelets, BMB = bone marrow biopsy, CBC = blood cell count, CT = computerized tomography, LAP = leukocyte alkaline phosphatase, MGUS = monoclonal gammopathy of undetermined significance. PMID:25914740

  1. Channel selection for simultaneous and proportional myoelectric prosthesis control of multiple degrees-of-freedom

    NASA Astrophysics Data System (ADS)

    Hwang, Han-Jeong; Hahne, Janne Mathias; Müller, Klaus-Robert

    2014-10-01

    Objective. Recent studies have shown the possibility of simultaneous and proportional control of electrically powered upper-limb prostheses, but there has been little investigation on optimal channel selection. The objective of this study is to find a robust channel selection method and the channel subsets most suitable for simultaneous and proportional myoelectric prosthesis control of multiple degrees-of-freedom (DoFs). Approach. Ten able-bodied subjects and one person with congenital upper-limb deficiency took part in this study, and performed wrist movements with various combinations of two DoFs (flexion/extension and radial/ulnar deviation). During the experiment, high density electromyographic (EMG) signals and the actual wrist angles were recorded with an 8 × 24 electrode array and a motion tracking system, respectively. The wrist angles were estimated from EMG features with ridge regression using the subsets of channels chosen by three different channel selection methods: (1) least absolute shrinkage and selection operator (LASSO), (2) sequential feature selection (SFS), and (3) uniform selection (UNI). Main results. SFS generally showed higher estimation accuracy than LASSO and UNI, but LASSO always outperformed SFS in terms of robustness, such as noise addition, channel shift and training data reduction. It was also confirmed that about 95% of the original performance obtained using all channels can be retained with only 12 bipolar channels individually selected by LASSO and SFS. Significance. From the analysis results, it can be concluded that LASSO is a promising channel selection method for accurate simultaneous and proportional prosthesis control. We expect that our results will provide a useful guideline to select optimal channel subsets when developing clinical myoelectric prosthesis control systems based on continuous movements with multiple DoFs.

  2. Simultaneous π/2 rotation of two spin species of different gyromagnetic ratios

    DOE PAGES

    Chu, Ping -Han; Peng, Jen -Chieh

    2015-06-05

    Here, we examine the characteristics of the π/2 pulse for simultaneously rotating two spin species of different gyromagnetic ratios with the same sign. For a π/2 pulse using a rotating magnetic field, we derive an equation relating the frequency and strength of the pulse to the gyromagnetic ratios of the two particles and the strength of the constant holding field. For a π/2 pulse using a linear oscillatory magnetic field, we obtain the solutions numerically, and compare them with the solutions for the rotating π/2 pulse. Application of this analysis to the specific case of rotating neutrons and 3He atomsmore » simultaneously with a π/2 pulse, proposed for a neutron electric dipole moment experiment, is also presented.« less

  3. Multiple-species analysis of point count data: A more parsimonious modelling framework

    USGS Publications Warehouse

    Alldredge, M.W.; Pollock, K.H.; Simons, T.R.; Shriner, S.A.

    2007-01-01

    1. Although population surveys often provide information on multiple species, these data are rarely analysed within a multiple-species framework despite the potential for more efficient estimation of population parameters. 2. We have developed a multiple-species modelling framework that uses similarities in capture/detection processes among species to model multiple species data more parsimoniously. We present examples of this approach applied to distance, time of detection and multiple observer sampling for avian point count data. 3. Models that included species as a covariate and individual species effects were generally selected as the best models for distance sampling, but group models without species effects performed best for the time of detection and multiple observer methods. Population estimates were more precise for no-species-effect models than for species-effect models, demonstrating the benefits of exploiting species' similarities when modelling multiple species data. Partial species-effect models and additive models were also useful because they modelled similarities among species while allowing for species differences. 4. Synthesis and applications. We recommend the adoption of multiple-species modelling because of its potential for improved population estimates. This framework will be particularly beneficial for modelling count data from rare species because information on the detection process can be 'borrowed' from more common species. The multiple-species modelling framework presented here is applicable to a wide range of sampling techniques and taxa. ?? 2007 The Authors.

  4. Simultaneous infection by four feline lungworm species and implications for the diagnosis.

    PubMed

    Varcasia, A; Brianti, E; Tamponi, C; Pipia, A P; Cabras, P A; Mereu, M; Dantas-Torres, F; Scala, A; Otranto, D

    2015-01-01

    Besides Aelurostrongylus abstrusus, other parasites belonging to the superfamily Metastrongyloidea, namely Oslerus rostratus, Troglostrongylus brevior and to the family Trichuridae, i.e. Eucoleus aerophilus (syn. Capillaria aerophila), have also been reported as agents of respiratory infection in domestic cats. A case of simultaneous infection by four feline lungworm species in Sardinia is herein described. An adult female cat (Felis silvestris catus), road-killed in the southeast part of Sardinia (municipality of Villacidro, province of Cagliari), Italy, was referred to the Laboratory of Parasitology of the Veterinary Teaching Hospital in Sassari. At necropsy, the lungs were examined and dissected under a stereomicroscope for the presence of parasites, and first-stage larvae (L1) of broncho-pulmonary nematodes were searched for in a faecal sample using the Baermann method. Parasites collected in the lungs were morphologically identified as A. abstrusus, E. aerophilus, and O. rostratus. In addition to the above species, L1s of Troglostrongylus spp. were detected at coproscopy but no adult specimen was found in the lungs. The morphological identification was confirmed by the molecular amplification and sequencing of cox1 mitochondrial gene, 18S and ITS2 ribosomal DNA. This finding stands as the first simultaneous infection by four feline lungworm species in the same animal, and as the first report of O. rostratus and E. aerophilus in Sardinia.

  5. Simultaneous Segmentation of Prostatic Zones Using Active Appearance Models With Multiple Coupled Levelsets.

    PubMed

    Toth, Robert; Ribault, Justin; Gentile, John; Sperling, Dan; Madabhushi, Anant

    2013-09-01

    In this work we present an improvement to the popular Active Appearance Model (AAM) algorithm, that we call the Multiple-Levelset AAM (MLA). The MLA can simultaneously segment multiple objects, and makes use of multiple levelsets, rather than anatomical landmarks, to define the shapes. AAMs traditionally define the shape of each object using a set of anatomical landmarks. However, landmarks can be difficult to identify, and AAMs traditionally only allow for segmentation of a single object of interest. The MLA, which is a landmark independent AAM, allows for levelsets of multiple objects to be determined and allows for them to be coupled with image intensities. This gives the MLA the flexibility to simulataneously segmentation multiple objects of interest in a new image. In this work we apply the MLA to segment the prostate capsule, the prostate peripheral zone (PZ), and the prostate central gland (CG), from a set of 40 endorectal, T2-weighted MRI images. The MLA system we employ in this work leverages a hierarchical segmentation framework, so constructed as to exploit domain specific attributes, by utilizing a given prostate segmentation to help drive the segmentations of the CG and PZ, which are embedded within the prostate. Our coupled MLA scheme yielded mean Dice accuracy values of .81, .79 and .68 for the prostate, CG, and PZ, respectively using a leave-one-out cross validation scheme over 40 patient studies. When only considering the midgland of the prostate, the mean DSC values were .89, .84, and .76 for the prostate, CG, and PZ respectively.

  6. Simultaneous Segmentation of Prostatic Zones Using Active Appearance Models With Multiple Coupled Levelsets

    PubMed Central

    Toth, Robert; Ribault, Justin; Gentile, John; Sperling, Dan; Madabhushi, Anant

    2013-01-01

    In this work we present an improvement to the popular Active Appearance Model (AAM) algorithm, that we call the Multiple-Levelset AAM (MLA). The MLA can simultaneously segment multiple objects, and makes use of multiple levelsets, rather than anatomical landmarks, to define the shapes. AAMs traditionally define the shape of each object using a set of anatomical landmarks. However, landmarks can be difficult to identify, and AAMs traditionally only allow for segmentation of a single object of interest. The MLA, which is a landmark independent AAM, allows for levelsets of multiple objects to be determined and allows for them to be coupled with image intensities. This gives the MLA the flexibility to simulataneously segmentation multiple objects of interest in a new image. In this work we apply the MLA to segment the prostate capsule, the prostate peripheral zone (PZ), and the prostate central gland (CG), from a set of 40 endorectal, T2-weighted MRI images. The MLA system we employ in this work leverages a hierarchical segmentation framework, so constructed as to exploit domain specific attributes, by utilizing a given prostate segmentation to help drive the segmentations of the CG and PZ, which are embedded within the prostate. Our coupled MLA scheme yielded mean Dice accuracy values of .81, .79 and .68 for the prostate, CG, and PZ, respectively using a leave-one-out cross validation scheme over 40 patient studies. When only considering the midgland of the prostate, the mean DSC values were .89, .84, and .76 for the prostate, CG, and PZ respectively. PMID:23997571

  7. Bias correction in species distribution models: pooling survey and collection data for multiple species

    PubMed Central

    Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A.

    2016-01-01

    Summary Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence–absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence–absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model’s performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence–absence data for a given species is scarceIf we have only presence-only data and no presence–absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species’ geographic range. PMID:27840673

  8. Nanoscale NMR spectroscopy and imaging of multiple nuclear species

    NASA Astrophysics Data System (ADS)

    Devience, Stephen J.; Pham, Linh M.; Lovchinsky, Igor; Sushkov, Alexander O.; Bar-Gill, Nir; Belthangady, Chinmay; Casola, Francesco; Corbett, Madeleine; Zhang, Huiliang; Lukin, Mikhail; Park, Hongkun; Yacoby, Amir; Walsworth, Ronald L.

    2015-02-01

    Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) provide non-invasive information about multiple nuclear species in bulk matter, with wide-ranging applications from basic physics and chemistry to biomedical imaging. However, the spatial resolution of conventional NMR and MRI is limited to several micrometres even at large magnetic fields (>1 T), which is inadequate for many frontier scientific applications such as single-molecule NMR spectroscopy and in vivo MRI of individual biological cells. A promising approach for nanoscale NMR and MRI exploits optical measurements of nitrogen-vacancy (NV) colour centres in diamond, which provide a combination of magnetic field sensitivity and nanoscale spatial resolution unmatched by any existing technology, while operating under ambient conditions in a robust, solid-state system. Recently, single, shallow NV centres were used to demonstrate NMR of nanoscale ensembles of proton spins, consisting of a statistical polarization equivalent to ˜100-1,000 spins in uniform samples covering the surface of a bulk diamond chip. Here, we realize nanoscale NMR spectroscopy and MRI of multiple nuclear species (1H, 19F, 31P) in non-uniform (spatially structured) samples under ambient conditions and at moderate magnetic fields (˜20 mT) using two complementary sensor modalities.

  9. Simultaneous detection of multiple chemical residues in milk using broad-specifity antibodies in a hybrid immunosorbent assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The wide array of applications using quantum dots (QDs) for detection of multiple analytes reflects the versatility of the technology. In this study, a novel immunoassay using 2 types of sensors (QDs and an enzyme) were simultaneously used for detecting multiple structurally different low-molecular...

  10. Extracellular DNA in Single- and Multiple-Species Unsaturated Biofilms

    PubMed Central

    Steinberger, R. E.; Holden, P. A.

    2005-01-01

    The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that Pseudomonas aeruginosa unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423, 2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for P. aeruginosa biofilms. Significantly more eDNA was produced in P. aeruginosa and Pseudomonas putida biofilms than in Rhodococcus erythropolis or Variovorax paradoxus biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA. PMID:16151131

  11. Extracellular DNA in single- and multiple-species unsaturated biofilms.

    PubMed

    Steinberger, R E; Holden, P A

    2005-09-01

    The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that Pseudomonas aeruginosa unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423, 2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for P. aeruginosa biofilms. Significantly more eDNA was produced in P. aeruginosa and Pseudomonas putida biofilms than in Rhodococcus erythropolis or Variovorax paradoxus biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA.

  12. Development of a DNA macroarray for simultaneous detection of multiple foodborne pathogenic bacteria in fresh chicken meat.

    PubMed

    Kupradit, Chanida; Rodtong, Sureelak; Ketudat-Cairns, Mariena

    2013-12-01

    A DNA macroarray was developed to provide the ability to detect multiple foodborne pathogens in fresh chicken meat. Probes targeted to the 16S rRNA and genus- and species-specific genes, including fimY, ipaH, prfA, and uspA, were selected for the specific detection of Salmonella spp., Shigella spp., Listeria monocytogenes, and Escherichia coli, respectively. The combination of target gene amplification by PCR and a DNA macroarray in our system was able to distinguish all target bacteria from pure cultures with a detection sensitivity of 10⁵ c.f.u. ml⁻¹. The DNA macroarray was also applied to 10 fresh chicken meat samples. The assay validation demonstrated that by combining the enrichment steps for the target bacteria and the DNA macroarray, all 4 target bacteria could be detected simultaneously from the fresh chicken samples. The sensitivity of L. monocytogenes and Shigella boydii detection in the fresh chicken samples was at least 10 and 3 c.f.u. of the initial contamination in 25 g samples, respectively. The advantages of our developed protocol are high accuracy and time reduction when compared to conventional culture. The macroarray developed in our investigation was cost effective compared to modern oligonucleotide microarray techniques because there was no expensive equipment required for the detection of multiple foodborne pathogens.

  13. A signal processing framework for simultaneous detection of multiple environmental contaminants

    NASA Astrophysics Data System (ADS)

    Chakraborty, Subhadeep; Manahan, Michael P.; Mench, Matthew M.

    2013-11-01

    The possibility of large-scale attacks using chemical warfare agents (CWAs) has exposed the critical need for fundamental research enabling the reliable, unambiguous and early detection of trace CWAs and toxic industrial chemicals. This paper presents a unique approach for the identification and classification of simultaneously present multiple environmental contaminants by perturbing an electrochemical (EC) sensor with an oscillating potential for the extraction of statistically rich information from the current response. The dynamic response, being a function of the degree and mechanism of contamination, is then processed with a symbolic dynamic filter for the extraction of representative patterns, which are then classified using a trained neural network. The approach presented in this paper promises to extend the sensing power and sensitivity of these EC sensors by augmenting and complementing sensor technology with state-of-the-art embedded real-time signal processing capabilities.

  14. Simultaneous optical sensing of multiple fluids via spatially multiplexed surface-multiplasmonic-resonance imaging

    NASA Astrophysics Data System (ADS)

    Swiontek, Stephen E.; Lakhtakia, Akhlesh

    2016-09-01

    Multiple surface-plasmon-polariton (SPP) waves are guided by the interface of a metal and a chiral sculptured thin film (STF) at a single wavelength. Spatially multiplexed 4-quadrant chips comprising a lanthanum-fluoride chiral STF embedded with a silver-nanoparticle layer were deposited atop an aluminum-coated glass substrate, each quadrant functioning as an autonomous sensor. The void regions of the chiral STF in each quadrant were in filtrated with sucrose solutions of increasing molarity and deployed in a prism-coupled surface-multi-plasmonics-resonance- imaging (SMPRI) machine. The angular locations of the SPP-wave modes shift as the molarity of the fluid increases, thus demonstrating simultaneous sensing of fluids via SMPRI.

  15. Novel method of simultaneous multiple immunogold localization on resin sections in high resolution scanning electron microscopy.

    PubMed

    Nebesarova, Jana; Wandrol, Petr; Vancova, Marie

    2016-01-01

    We present a new method of multiple immunolabeling that is suitable for a broad spectrum of biomedical applications. The general concept is to label both sides of the ultrathin section with the thickness of 70-80 nm with different antibodies conjugated to gold nanoparticles and to distinguish the labeled side by advanced imaging methods with high resolution scanning electron microscopy, such as by correlating images acquired at different energies of primary electrons using different signals. From the Clinical Editor: The use of transmission electron microscopy has become an indispensible tool in the detection of cellular proteins. In this short but interesting article, the authors described their new method of labeling and the identification of four different proteins simultaneously, which represents another advance in imaging technique.

  16. Aptamer- and nucleic acid enzyme-based systems for simultaneous detection of multiple analytes

    DOEpatents

    Lu, Yi [Champaign, IL; Liu, Juewen [Albuquerque, NM

    2011-11-15

    The present invention provides aptamer- and nucleic acid enzyme-based systems for simultaneously determining the presence and optionally the concentration of multiple analytes in a sample. Methods of utilizing the system and kits that include the sensor components are also provided. The system includes a first reactive polynucleotide that reacts to a first analyte; a second reactive polynucleotide that reacts to a second analyte; a third polynucleotide; a fourth polynucleotide; a first particle, coupled to the third polynucleotide; a second particle, coupled to the fourth polynucleotide; and at least one quencher, for quenching emissions of the first and second quantum dots, coupled to the first and second reactive polynucleotides. The first particle includes a quantum dot having a first emission wavelength. The second particle includes a second quantum dot having a second emission wavelength different from the first emission wavelength. The third polynucleotide and the fourth polynucleotide are different.

  17. Simultaneous multiple-point velocity measurements using laser-induced iodine fluorescence

    NASA Technical Reports Server (NTRS)

    Mcdaniel, J. C.; Hiller, B.; Hanson, R. K.

    1983-01-01

    A technique is demonstrated for measuring velocity at multiple locations in a plane of a gaseous flowfield using Doppler-shifted absorption with fluorescence detection from iodine molecules, excited by a sheet of tunable single-axial-mode argon-ion laser radiation at 514.5 nm. Measurements were made simultaneously at 10,000 points in an iodine-seeded supersonic flow field with a 100 x 100 element photodiode array camera and were found to agree well with a numerical solution for the velocity field. The accuracy with which a component of velocity can be measured is limited, in the current approach, by the iodine linewidth to about 5 m/sec.

  18. Directed evolution of a cellobiose utilization pathway in Saccharomyces cerevisiae by simultaneously engineering multiple proteins

    PubMed Central

    2013-01-01

    Background The optimization of metabolic pathways is critical for efficient and economical production of biofuels and specialty chemicals. One such significant pathway is the cellobiose utilization pathway, identified as a promising route in biomass utilization. Here we describe the optimization of cellobiose consumption and ethanol productivity by simultaneously engineering both proteins of the pathway, the β-glucosidase (gh1-1) and the cellodextrin transporter (cdt-1), in an example of pathway engineering through directed evolution. Results The improved pathway was assessed based on the strain specific growth rate on cellobiose, with the final mutant exhibiting a 47% increase over the wild-type pathway. Metabolite analysis of the engineered pathway identified a 49% increase in cellobiose consumption (1.78 to 2.65 g cellobiose/(L · h)) and a 64% increase in ethanol productivity (0.611 to 1.00 g ethanol/(L · h)). Conclusions By simultaneously engineering multiple proteins in the pathway, cellobiose utilization in S. cerevisiae was improved. This optimization can be generally applied to other metabolic pathways, provided a selection/screening method is available for the desired phenotype. The improved in vivo cellobiose utilization demonstrated here could help to decrease the in vitro enzyme load in biomass pretreatment, ultimately contributing to a reduction in the high cost of biofuel production. PMID:23802545

  19. Simultaneous bioaccumulation of multiple metals from electroplating effluent using Aspergillus lentulus.

    PubMed

    Mishra, Abhishek; Malik, Anushree

    2012-10-15

    Toxic impacts of heavy metals in the environment have lead to intensive research on various methods of heavy metal remediation. However, in spite of abundant work on heavy metals removal from simple synthetic solutions, a very few studies demonstrate the potential of microbial strains for the treatment of industrial effluents containing mixtures of metals. In the present study, the efficiency of an environmental isolate (Aspergillus lentulusFJ172995), for simultaneous removal of chromium, copper and lead from a small-scale electroplating industry effluent was investigated. Initial studies with synthetic solutions infer that A. lentulus has a remarkable tolerance against Cr, Cu, Pb and Ni. During its growth, a significant bioaccumulation of individual metal was recorded. After 5 d of growth, the removal of metals from synthetic solutions followed the trend Pb(2+) (100%) > Cr(3+) (79%) > Cu(2+) (78%), > Ni(2+) (42%). When this strain was applied to the treatment of multiple metal containing electroplating effluent (after pH adjustment), the metal concentrations decreased by 71%, 56% and 100% for Cr, Cu and Pb, respectively within 11 d. Based on our results, we propose that the simultaneous removal of hazardous metals from industrial effluents can be accomplished using A. lentulus.

  20. Integrating the effects of simultaneous multiple stresses on plants using the simulation model TREGRO

    SciTech Connect

    Weinstein, D.A.; Yanai, R.D.

    1994-05-01

    TREGRO, a model of tree physiological response to environmental stress, was developed to examine the details of tree response to the interaction between ozone sum and nutrient deficiency. TREGRO was used to test the hypothesis that the nutrient deficiency would exacerbate growth reductions caused by ozone. When TREGRO was applied to a range of multiple-stress scenarios involving these two stresses, the simulated effects of the combined stresses in reducing red spruce (Rcea rubens Sarg.) tree growth were less than the sum of the effects simulated when each stress was acting alone. Red spruce, a species with a growth strategy involving low maximum potential growth rates and storage in C reserves, showed simulated patterns of allocation that minimized the added effect of ozone when Mg nutrient availability was low. In contrast, ponderosa pine (Pinus ponderosa Dougl.), a species that allocated C to the construction of new tissue preferentially, showed little ability to ameliorate ozone stress under low nutrient conditions. In neither case were the effects of ozone increased by nutrient deficiency. It is speculated that a species which maintains maximum C demand rates considerably below rates of C supply may be better able to adjust to conditions of multiple stresses. 22 refs., 12 figs., 1 tab.

  1. Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs

    PubMed Central

    Hart, Yuval; Mayo, Avraham E.; Shoval, Oren; Alon, Uri

    2013-01-01

    Sensory systems often detect multiple types of inputs. For example, a receptor in a cell-signaling system often binds multiple kinds of ligands, and sensory neurons can respond to different types of stimuli. How do sensory systems compare these different kinds of signals? Here, we consider this question in a class of sensory systems – including bacterial chemotaxis- which have a property known as fold-change detection: their output dynamics, including amplitude and response time, depends only on the relative changes in signal, rather than absolute changes, over a range of several decades of signal. We analyze how fold-change detection systems respond to multiple signals, using mathematical models. Suppose that a step of fold F1 is made in input 1, together with a step of F2 in input 2. What total response does the system provide? We show that when both input signals impact the same receptor with equal number of binding sites, the integrated response is multiplicative: the response dynamics depend only on the product of the two fold changes, F1F2. When the inputs bind the same receptor with different number of sites n1 and n2, the dynamics depend on a product of power laws, . Thus, two input signals which vary over time in an inverse way can lead to no response. When the two inputs affect two different receptors, other types of integration may be found and generally the system is not constrained to respond according to the product of the fold-change of each signal. These predictions can be readily tested experimentally, by providing cells with two simultaneously varying input signals. The present study suggests how cells can compare apples and oranges, namely by comparing each to its own background level, and then multiplying these two fold-changes. PMID:23469195

  2. Simultaneous Bayesian Estimation of Excitatory and Inhibitory Synaptic Conductances by Exploiting Multiple Recorded Trials

    PubMed Central

    Lankarany, Milad; Heiss, Jaime E.; Lampl, Ilan; Toyoizumi, Taro

    2016-01-01

    Advanced statistical methods have enabled trial-by-trial inference of the underlying excitatory and inhibitory synaptic conductances (SCs) of membrane-potential recordings. Simultaneous inference of both excitatory and inhibitory SCs sheds light on the neural circuits underlying the neural activity and advances our understanding of neural information processing. Conventional Bayesian methods can infer excitatory and inhibitory SCs based on a single trial of observed membrane potential. However, if multiple recorded trials are available, this typically leads to suboptimal estimation because they neglect common statistics (of synaptic inputs (SIs)) across trials. Here, we establish a new expectation maximization (EM) algorithm that improves such single-trial Bayesian methods by exploiting multiple recorded trials to extract common SI statistics across the trials. In this paper, the proposed EM algorithm is embedded in parallel Kalman filters or particle filters for multiple recorded trials to integrate their outputs to iteratively update the common SI statistics. These statistics are then used to infer the excitatory and inhibitory SCs of individual trials. We demonstrate the superior performance of multiple-trial Kalman filtering (MtKF) and particle filtering (MtPF) relative to that of the corresponding single-trial methods. While relative estimation error of excitatory and inhibitory SCs is known to depend on the level of current injection into a cell, our numerical simulations using MtKF show that both excitatory and inhibitory SCs are reliably inferred using an optimal level of current injection. Finally, we validate the robustness and applicability of our technique through simulation studies, and we apply MtKF to in vivo data recorded from the rat barrel cortex. PMID:27867353

  3. Mobile CARS - IRS Instrument for Simultaneous Spectroscopic Measurement of Multiple Properties in Gaseous Flows

    NASA Technical Reports Server (NTRS)

    Bivolaru, Daniel; Lee, Joseph W.; Jones, Stephen B.; Tedder, Sarah A.; Danehy, Paul M.; Weikl, M. C.; Magnotti, G.; Cutler, Andrew D.

    2007-01-01

    This paper describes a measurement system based on the dual-pump coherent anti-Stokes Raman spectroscopy (CARS) and interferometric Rayleigh scattering (IRS) methods. The IRS measurement is performed simultaneously with the CARS measurement using a common green laser beam as a narrow-band light source. The mobile CARS-IRS instrument is designed for the use both in laboratories as well as in ground-based combustion test facilities. Furthermore, it is designed to be easily transported between laboratory and test facility. It performs single-point spatially and temporally resolved simultaneous measurements of temperature, species mole fraction of N2, O2, and H2, and two-components of velocity. A mobile laser system can be placed inside or outside the test facility, while a beam receiving and monitoring system is placed near the measurement location. Measurements in a laboratory small-scale Mach 1.6 H2-air combustion-heated supersonic jet were performed to test the capability of the system. Final setup and pretests of a larger scale reacting jet are ongoing at NASA Langley Research Center s Direct Connect Supersonic Combustor Test Facility (DCSCTF).

  4. Simultaneous Retrieval of Multiple Aerosol Parameters Using a Multi-Angular Approach

    NASA Technical Reports Server (NTRS)

    Kuo, K. S.; Weger, R. C.; Welch, R. M.

    1997-01-01

    Atmospheric aerosol particles, both natural and anthropogenic, are important to the earth's radiative balance through their direct and indirect effects. They scatter the incoming solar radiation (direct effect) and modify the shortwave reflective properties of clouds by acting as cloud condensation nuclei (indirect effect). Although it has been suggested that aerosols exert a net cooling influence on climate, this effect has received less attention than the radiative forcing due to clouds and greenhouse gases. In order to understand the role that aerosols play in a changing climate, detailed and accurate observations are a prerequisite. The retrieval of aerosol optical properties by satellite remote sensing has proven to be a difficult task. The difficulty results mainly from the tenuous nature and variable composition of aerosols. To date, with single-angle satellite observations, we can only retrieve reliably against dark backgrounds, such as over oceans and dense vegetation. Even then, assumptions must be made concerning the chemical composition of aerosols. The best hope we have for aerosol retrievals over bright backgrounds are observations from multiple angles, such as those provided by the MISR and POLDER instruments. In this investigation we examine the feasibility of simultaneous retrieval of multiple aerosol optical parameters using reflectances from a typical set of twelve angles observed by the French POLDER instrument. The retrieved aerosol optical parameters consist of asymmetry factor, single scattering albedo, surface albedo, and optical thickness.

  5. Simultaneous estimation of the locations and effects of multiple disease loci in case-control studies.

    PubMed

    Chien, Li-Chu; Chiu, Yen-Feng; Liang, Kung-Yee; Chuang, Lee-Ming

    2015-04-01

    The genetic basis of complex diseases often involves multiple causative loci. Under such a disease etiology, assuming one disease locus in linkage disequilibrium mapping is likely to induce bias and lead to efficiency loss in disease locus estimation. An approach is needed for simultaneously localizing multiple functional loci within the same region. However, due to the increasing number of parameters accompanying disease loci, these estimates can be computationally infeasible. To circumvent this problem, we propose to estimate the main and two-adjacent-locus joint effects and a nuisance parameter at the disease loci separately through a linear approximation. Estimates of the genetic effects are entered into a generalized estimating equation to estimate disease loci, and the procedure is conducted iteratively until convergence. The proposed method provides estimates and confidence intervals (CIs) for the disease loci, the genetic main effects, and the joint effects of two adjacent disease loci, with the CIs for the disease loci providing useful regions for further fine-mapping. We apply the proposed approach to a data example of case-control studies. Results of the simulations and data example suggest that the developed method performs well in terms of bias, variance, and coverage probability under scenarios with up to three disease loci.

  6. DEP-On-Go for Simultaneous Sensing of Multiple Heavy Metals Pollutants in Environmental Samples.

    PubMed

    Biyani, Madhu; Biyani, Radhika; Tsuchihashi, Tomoko; Takamura, Yuzuru; Ushijima, Hiromi; Tamiya, Eiichi; Biyani, Manish

    2016-12-27

    We describe a simple and affordable "Disposable electrode printed (DEP)-On-Go" sensing platform for the rapid on-site monitoring of trace heavy metal pollutants in environmental samples for early warning by developing a mobile electrochemical device composed of palm-sized potentiostat and disposable unmodified screen-printed electrode chips. We present the analytical performance of our device for the sensitive detection of major heavy metal ions, namely, mercury, cadmium, lead, arsenic, zinc, and copper with detection limits of 1.5, 2.6, 4.0, 5.0, 14.4, and, 15.5 μg·L(-1), respectively. Importantly, the utility of this device is extended to detect multiple heavy metals simultaneously with well-defined voltammograms and similar sensitivity. Finally, "DEP-On-Go" was successfully applied to detect heavy metals in real environmental samples from groundwater, tap water, house dust, soil, and industry-processed rice and noodle foods. We evaluated the efficiency of this system with a linear correlation through inductively coupled plasma mass spectrometry, and the results suggested that this system can be reliable for on-site screening purposes. On-field applications using real samples of groundwater for drinking in the northern parts of India support the easy-to-detect, low-cost (<1 USD), rapid (within 5 min), and reliable detection limit (ppb levels) performance of our device for the on-site detection and monitoring of multiple heavy metals in resource-limited settings.

  7. Towards Omni-Tomography—Grand Fusion of Multiple Modalities for Simultaneous Interior Tomography

    PubMed Central

    Wang, Ge; Zhang, Jie; Gao, Hao; Weir, Victor; Yu, Hengyong; Cong, Wenxiang; Xu, Xiaochen; Shen, Haiou; Bennett, James; Furth, Mark; Wang, Yue; Vannier, Michael

    2012-01-01

    We recently elevated interior tomography from its origin in computed tomography (CT) to a general tomographic principle, and proved its validity for other tomographic modalities including SPECT, MRI, and others. Here we propose “omni-tomography”, a novel concept for the grand fusion of multiple tomographic modalities for simultaneous data acquisition in a region of interest (ROI). Omni-tomography can be instrumental when physiological processes under investigation are multi-dimensional, multi-scale, multi-temporal and multi-parametric. Both preclinical and clinical studies now depend on in vivo tomography, often requiring separate evaluations by different imaging modalities. Over the past decade, two approaches have been used for multimodality fusion: Software based image registration and hybrid scanners such as PET-CT, PET-MRI, and SPECT-CT among others. While there are intrinsic limitations with both approaches, the main obstacle to the seamless fusion of multiple imaging modalities has been the bulkiness of each individual imager and the conflict of their physical (especially spatial) requirements. To address this challenge, omni-tomography is now unveiled as an emerging direction for biomedical imaging and systems biomedicine. PMID:22768108

  8. Simultaneous manipulation and observation of multiple ro-vibrational eigenstates in solid para-hydrogen

    NASA Astrophysics Data System (ADS)

    Katsuki, Hiroyuki; Ohmori, Kenji

    2016-09-01

    We have experimentally performed the coherent control of delocalized ro-vibrational wave packets (RVWs) of solid para-hydrogen (p-H2) by the wave packet interferometry (WPI) combined with coherent anti-Stokes Raman scattering (CARS). RVWs of solid p-H2 are delocalized in the crystal, and the wave function with wave vector k ˜ 0 is selectively excited via the stimulated Raman process. We have excited the RVW twice by a pair of femtosecond laser pulses with delay controlled by a stabilized Michelson interferometer. Using a broad-band laser pulse, multiple ro-vibrational states can be excited simultaneously. We have observed the time-dependent Ramsey fringe spectra as a function of the inter-pulse delay by a spectrally resolved CARS technique using a narrow-band probe pulse, resolving the different intermediate states. Due to the different fringe oscillation periods among those intermediate states, we can manipulate their amplitude ratio by tuning the inter-pulse delay on the sub-femtosecond time scale. The state-selective manipulation and detection of the CARS signal combined with the WPI is a general and efficient protocol for the control of the interference of multiple quantum states in various quantum systems.

  9. Solid-state Hadamard NMR spectroscopy: simultaneous measurements of multiple selective homonuclear scalar couplings.

    PubMed

    Kakita, Veera Mohana Rao; Kupče, Eriks; Bharatam, Jagadeesh

    2015-02-01

    Unambiguous measurement of homonuclear scalar couplings (J) in multi-spin scalar network systems is not straightforward. Further, the direct measurement of J-couplings is obscured in solid-state samples due to the dipolar and chemical shift anisotropy (CSA)-dominated line broadening, even under the magic angle spinning (MAS). We present a new multiple frequency selective spin-echo method based on Hadamard matrix encoding, for simultaneous measurement of multiple homonuclear scalar couplings (J) in the solid-state. In contrast to the Hadamard encoded selective excitation schemes known for the solution-state, herein the selectivity is achieved during refocusing period. The Hadamard encoded refocusing scheme concurrently allows to create the spin-spin commutation property between number of spin-pairs of choice in uniformly labelled molecules, which, therefore avoids (1) the repetition of the double selective refocusing experiments for each spin-pair and (2) the synthesis of expensive selective labelled molecules. The experimental scheme is exemplified for determining (1)JCC and (3)JCC values in (13)C6l-Histidine.HCl molecule, which are found to be in excellent agreement with those measured in conventional double frequency selective refocusing mode as well as in the solution-state. This method can be simply extended to 2D/3D pulse schemes and be applied to small bio-molecular solids.

  10. Dynamic models for problems of species occurrence with multiple states

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture?recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.

  11. Modeling species occurrence dynamics with multiple states and imperfect detection

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics. ?? 2009 by the Ecological Society of America.

  12. New multiplex PCR method for the simultaneous diagnosis of the three known species of equine tapeworm.

    PubMed

    Bohórquez, G Alejandro; Luzón, Mónica; Martín-Hernández, Raquel; Meana, Aránzazu

    2015-01-15

    Although several techniques exist for the detection of equine tapeworms in serum and feces, the differential diagnosis of tapeworm infection is usually based on postmortem findings and the morphological identification of eggs in feces. In this study, a multiplex polymerase chain reaction (PCR)-based method for the simultaneuos detection of Anoplocephala magna, Anoplocephala perfoliata and Anoplocephaloides mamillana has been developed and validated. The method simultaneously amplifies hypervariable SSUrRNA gene regions in the three tapeworm species in a single reaction using three pairs of primers, which exclusively amplify the internal transcribed spacer 2 (ITS-2) in each target gene. The method was tested on three types of sample: (a) 1/10, 1/100, 1/500, 1/1000, 1/2000 and 1/5000 dilutions of 70 ng of genomic DNA of the three tapeworm species, (b) DNA extracted from negative aliquots of sediments of negative control fecal samples spiked with 500, 200, 100, 50 and 10 eggs (only for A. magna and A. perfoliata; no A. mamillana eggs available) and (c) DNA extracted from 80, 50, 40, 30, 10 and 1 egg per 2 μl of PCR reaction mix (only for A. magna and A. perfoliata; no A. mamillana eggs available). No amplification was observed against the DNA of Gasterophilus intestinalis, Parascaris equorum and Strongylus vulgaris. The multiplex PCR method emerged as specific for the three tapeworms and was able to identify as few as 50 eggs per fecal sample and as little as 0.7 ng of control genomic DNA obtained from the three species. The method proposed is able to differentiate infections caused by the two most frequent species A. magna or A. perfoliata when the eggs are present in feces and is also able to detect mixed infections by the three cestode species.

  13. Simultaneous Non-Negative Matrix Factorization for Multiple Large Scale Gene Expression Datasets in Toxicology

    PubMed Central

    Lee, Clare M.; Mudaliar, Manikhandan A. V.; Haggart, D. R.; Wolf, C. Roland; Miele, Gino; Vass, J. Keith; Higham, Desmond J.; Crowther, Daniel

    2012-01-01

    Non-negative matrix factorization is a useful tool for reducing the dimension of large datasets. This work considers simultaneous non-negative matrix factorization of multiple sources of data. In particular, we perform the first study that involves more than two datasets. We discuss the algorithmic issues required to convert the approach into a practical computational tool and apply the technique to new gene expression data quantifying the molecular changes in four tissue types due to different dosages of an experimental panPPAR agonist in mouse. This study is of interest in toxicology because, whilst PPARs form potential therapeutic targets for diabetes, it is known that they can induce serious side-effects. Our results show that the practical simultaneous non-negative matrix factorization developed here can add value to the data analysis. In particular, we find that factorizing the data as a single object allows us to distinguish between the four tissue types, but does not correctly reproduce the known dosage level groups. Applying our new approach, which treats the four tissue types as providing distinct, but related, datasets, we find that the dosage level groups are respected. The new algorithm then provides separate gene list orderings that can be studied for each tissue type, and compared with the ordering arising from the single factorization. We find that many of our conclusions can be corroborated with known biological behaviour, and others offer new insights into the toxicological effects. Overall, the algorithm shows promise for early detection of toxicity in the drug discovery process. PMID:23272042

  14. Simultaneous Analyses and Applications of Multiple Fluorobenzoate and Halide Tracers in Hydrologic Studies

    SciTech Connect

    Hu, Q; Moran, J E

    2004-01-22

    An analytical method that employs ion chromatography has been developed to more fully exploit the use of fluorobenzoic acids (FBAs) and halides as hydrologic tracers. In a single run, this reliable, sensitive, and robust method can simultaneously separate and quantify halides (fluoride, chloride, bromide, and iodide) and up to seven FBAs from other common groundwater constituents (e.g., nitrate and sulfate). The usefulness of this ion chromatographic (IC) analytical method is demonstrated in both field and laboratory tracer experiments. Field experiments in unsaturated tuff featuring fractures or a fault show that this efficient and cost-effective method helps achieve the objectives of tracer studies that use multiple FBAs and/or diffusivity tracers (simultaneous use of one or more FBA and halide). The field study examines the hydrologic response of fractures and the matrix to different flow rates and the contribution of matrix diffusion in chemical transport. Laboratory tracer experiments with eight geologic media from across the United States--mostly from Department of Energy facilities where groundwater contamination is prevalent and where subsurface characterization employing tracers has been ongoing or is in need--reveal several insights about tracer transport behavior: (1) Bromide and FBAs are not always transported conservatively. (2) The delayed transport of these anionic tracers is likely related to geologic media characteristics, such as organic matter, pH, iron oxide content, and clay mineralogy. (3) Any use of iodine as a hydrologic tracer should take into account the different sorption behaviors of iodide and iodate and the possible conversion of iodine's initial chemical form. (4) The transport behavior of potential FBA and halide tracers under relevant geochemical conditions should be evaluated before beginning ambitious, large-scale field tracer experiments.

  15. Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles.

    PubMed

    Hoch, Jeffrey Matthew; Levinton, Jeffrey S

    2012-05-01

    Sex allocation theory for simultaneous hermaphrodites predicts increases in relative allocation to male-specific function as competition for fertilizations increases. Theoretical models developed specifically for competing acorn barnacles predict that the proportional allocation to male function increases toward an asymptote of 50% as the number of competitors for fertilizations increases. Experimental manipulations were used to investigate how mate competition affected both relative and absolute allocation to the sex functions for two species of acorn barnacle: Semibalanus balanoides and Balanus glandula. The ratio of male to female allocation did not increase with the number of competitors for either species. However, both species showed increased allocation to male function (estimated as total mass of sex-specific tissues) with increased crowding. Allocation to female function seemed to be limited by other factors and did not vary with mating group size as predicted. Allocation to male and female function were both positively related to body size, but a trade-off between male and female function, a key assumption of prior models, was not observed.

  16. Simultaneous analysis of glycolipids and phospholids molecular species in avocado (Persea americana Mill) fruit.

    PubMed

    Pacetti, Deborah; Boselli, Emanuele; Lucci, Paolo; Frega, Natale G

    2007-05-25

    The molecular species of phospholipids (PLs) and glycolipids (GLs) were simultaneously characterized in the pulp and almond of the avocado fruit (Persea americana Mill) of four varieties by means of high performance liquid chromatography-electrospray ionisation ion-trap tandem mass spectrometry. In the pulp, the predominant species of monoglycosyldiglycerides (MGD) were m/z 796.6 (oleic/linolenic and linoleic/linoleic acids) and m/z 800.4 (stearic/linoleic and oleic/oleic acids). One of the main diglycosyldiglycerides (DGD) both in the pulp and almond was m/z 958.5 (oleic/linolenic); however, the pulp was also rich of m/z 962.4 (oleic/oleic), whereas in the almond, m/z 934.5 (palmitic/linoleic and palmitoleic/oleic) and m/z 960.5 (oleic/linoleic and stearic/linolenic) were more abundant. In the almond, the main PL classes (phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI)) contained always palmitic/linoleic acids. Alpha-linolenic acid was contained as MGD (linolenic/linolenic) and DGD (linolenic/linolenic), more present in the pulp than in the almond. The major molecular species of glycocerebrosides (GCer) in the pulp and almond carried hydroxy-palmitic acid (C(16h:0))/4,8-sphyngadienine (d(18:2)).

  17. Atomic species identification at the (101) anatase surface by simultaneous scanning tunnelling and atomic force microscopy

    PubMed Central

    Stetsovych, Oleksandr; Todorović, Milica; Shimizu, Tomoko K.; Moreno, César; Ryan, James William; León, Carmen Pérez; Sagisaka, Keisuke; Palomares, Emilio; Matolín, Vladimír; Fujita, Daisuke; Perez, Ruben; Custance, Oscar

    2015-01-01

    Anatase is a pivotal material in devices for energy-harvesting applications and catalysis. Methods for the accurate characterization of this reducible oxide at the atomic scale are critical in the exploration of outstanding properties for technological developments. Here we combine atomic force microscopy (AFM) and scanning tunnelling microscopy (STM), supported by first-principles calculations, for the simultaneous imaging and unambiguous identification of atomic species at the (101) anatase surface. We demonstrate that dynamic AFM-STM operation allows atomic resolution imaging within the material's band gap. Based on key distinguishing features extracted from calculations and experiments, we identify candidates for the most common surface defects. Our results pave the way for the understanding of surface processes, like adsorption of metal dopants and photoactive molecules, that are fundamental for the catalytic and photovoltaic applications of anatase, and demonstrate the potential of dynamic AFM-STM for the characterization of wide band gap materials. PMID:26118408

  18. Atomic species identification at the (101) anatase surface by simultaneous scanning tunnelling and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Stetsovych, Oleksandr; Todorović, Milica; Shimizu, Tomoko K.; Moreno, César; Ryan, James William; León, Carmen Pérez; Sagisaka, Keisuke; Palomares, Emilio; Matolín, Vladimír; Fujita, Daisuke; Perez, Ruben; Custance, Oscar

    2015-06-01

    Anatase is a pivotal material in devices for energy-harvesting applications and catalysis. Methods for the accurate characterization of this reducible oxide at the atomic scale are critical in the exploration of outstanding properties for technological developments. Here we combine atomic force microscopy (AFM) and scanning tunnelling microscopy (STM), supported by first-principles calculations, for the simultaneous imaging and unambiguous identification of atomic species at the (101) anatase surface. We demonstrate that dynamic AFM-STM operation allows atomic resolution imaging within the material's band gap. Based on key distinguishing features extracted from calculations and experiments, we identify candidates for the most common surface defects. Our results pave the way for the understanding of surface processes, like adsorption of metal dopants and photoactive molecules, that are fundamental for the catalytic and photovoltaic applications of anatase, and demonstrate the potential of dynamic AFM-STM for the characterization of wide band gap materials.

  19. DEP-On-Go for Simultaneous Sensing of Multiple Heavy Metals Pollutants in Environmental Samples

    PubMed Central

    Biyani, Madhu; Biyani, Radhika; Tsuchihashi, Tomoko; Takamura, Yuzuru; Ushijima, Hiromi; Tamiya, Eiichi; Biyani, Manish

    2016-01-01

    We describe a simple and affordable “Disposable electrode printed (DEP)-On-Go” sensing platform for the rapid on-site monitoring of trace heavy metal pollutants in environmental samples for early warning by developing a mobile electrochemical device composed of palm-sized potentiostat and disposable unmodified screen-printed electrode chips. We present the analytical performance of our device for the sensitive detection of major heavy metal ions, namely, mercury, cadmium, lead, arsenic, zinc, and copper with detection limits of 1.5, 2.6, 4.0, 5.0, 14.4, and, 15.5 μg·L−1, respectively. Importantly, the utility of this device is extended to detect multiple heavy metals simultaneously with well-defined voltammograms and similar sensitivity. Finally, “DEP-On-Go” was successfully applied to detect heavy metals in real environmental samples from groundwater, tap water, house dust, soil, and industry-processed rice and noodle foods. We evaluated the efficiency of this system with a linear correlation through inductively coupled plasma mass spectrometry, and the results suggested that this system can be reliable for on-site screening purposes. On-field applications using real samples of groundwater for drinking in the northern parts of India support the easy-to-detect, low-cost (<1 USD), rapid (within 5 min), and reliable detection limit (ppb levels) performance of our device for the on-site detection and monitoring of multiple heavy metals in resource-limited settings. PMID:28036003

  20. On the improvement of SKS splitting measurements by the Simultaneous Inversion of Multiple Waveforms (SIMW)

    NASA Astrophysics Data System (ADS)

    Roy, C.; Winter, A.; Ritter, J. R. R.; Schweitzer, J.

    2017-03-01

    The birefringence of core-refracted shear waves (e.g. SKS or SKKS) is often used to study seismic anisotropy in the Earth. However, depth resolution and multilayer anisotropy is generally poor for many regions on Earth. This is primarily due to SKS or SKKS phases that are not observable for different backazimuths either because of missing seismicity at the required distance range or because of a too low signal-to-noise ratio (SNR). We propose a new method called Simultaneous Inversion of Multiple Waveforms (SIMW), which allows the joint inversion of multiple core-refracted shear waves from different earthquakes within the same source region, observed by either the same seismic station or by a seismic network. The waveforms are concatenated into a combined signal, which is then inverted with the Silver & Chan method to determine the two splitting parameters: time delay δt, and fast polarization direction Φ. We apply our method to recordings at the large aperture Norwegian NORSAR Array and the German Gräfenberg array (GRF). Our results demonstrate that SIMW allows a stable determination of splitting results for low-amplitude or noisy SKS signals. Splitting parameter uncertainties can be reduced and reliable results are obtained for both arrays. Moreover, new backazimuth directions can be explored, enabling a more accurate derivation of two-layer anisotropy models. Our new methodology is particularly helpful for temporary station deployments with limited recording times in order to utilize as many as possible signals including such with low-amplitude and small SNR.

  1. Herbivores, tidal elevation, and species richness simultaneously mediate nitrate uptake by seaweed assemblages.

    PubMed

    Bracken, Matthew E S; Jones, Emily; Williams, Susan L

    2011-05-01

    In order for research into the consequences of biodiversity changes to be more applicable to real-world ecosystems, experiments must be conducted in the field, where a variety of factors other than diversity can affect the rates of key biogeochemical and physiological processes. Here, we experimentally evaluate the effects of two factors known to affect the diversity and composition of intertidal seaweed assemblages--tidal elevation and herbivory--on nitrate uptake by those assemblages. Based on surveys of community composition at the end of a 1.5-year press experiment, we found that both tide height and herbivores affected seaweed community structure. Not surprisingly, seaweed species richness was greater at lower tidal elevations. Herbivores did not affect richness, but they altered the types of species that were present; seaweed species characterized by higher rates of nitrate uptake were more abundant in herbivore-removal plots. Both tide height and herbivores affected nitrate uptake by seaweed assemblages. Individual seaweed species, as well as entire seaweed assemblages, living higher on the shore had greater rates of biomass-specific nitrate uptake, particularly at high ambient nitrate concentrations. Grazed seaweed assemblages exhibited reduced nitrate uptake, but only at low nitrate concentrations. We evaluated the effect of seaweed richness on nitrate uptake, both alone and after accounting for effects of tidal elevation and herbivores. When only richness was considered, we found no effect on uptake. However, when simultaneous effects of richness, tide height, and herbivores on uptake were evaluated, we found that all three had relatively large and comparable effects on nitrate uptake coefficients and that there was a negative relationship between seaweed richness and nitrate uptake. Particularly because effects of richness on uptake were not apparent unless the effects of tide height and herbivory were also considered, these results highlight the

  2. Simultaneous Retrieval of Multiple Aerosol Parameters Using a Multi-Angular Approach

    NASA Technical Reports Server (NTRS)

    Kuo, K.-S.; Weger, R. C.; Welch, R. M.

    1997-01-01

    Atmospheric aerosol particles, both natural and anthropogenic, are important to the earth's radiative balance through their direct and indirect effects. They scatter the incoming solar radiation (direct effect) and modify the shortwave reflective properties of clouds by acting as cloud condensation nuclei (indirect effect). Although it has been suggested that aerosols exert a net cooling influence on climate, this effect has received less attention than the radiative forcing due to clouds and greenhouse gases. In order to understand the role that aerosols play in a changing climate, detailed and accurate observations are a prerequisite. The retrieval of aerosol optical properties by satellite remote sensing has proven to be a difficult task. The difficulty results mainly from the tenuous nature and variable composition of aerosols. To date, with single-angle satellite observations, we can only retrieve reliably against dark backgrounds, such as over oceans and dense vegetation. Even then, assumptions must be made concerning the chemical composition of aerosols. In this investigation we examine the feasibility of simultaneous retrieval of multiple aerosol optical parameters using reflectances from a typical set of twelve angles observed by the French POLDER instrument. The retrieved aerosol optical parameters consist of asymmetry factor, single scattering albedo, surface albedo, and optical thickness.

  3. Simultaneous Multiple Response Regression and Inverse Covariance Matrix Estimation via Penalized Gaussian Maximum Likelihood.

    PubMed

    Lee, Wonyul; Liu, Yufeng

    2012-10-01

    Multivariate regression is a common statistical tool for practical problems. Many multivariate regression techniques are designed for univariate response cases. For problems with multiple response variables available, one common approach is to apply the univariate response regression technique separately on each response variable. Although it is simple and popular, the univariate response approach ignores the joint information among response variables. In this paper, we propose three new methods for utilizing joint information among response variables. All methods are in a penalized likelihood framework with weighted L(1) regularization. The proposed methods provide sparse estimators of conditional inverse co-variance matrix of response vector given explanatory variables as well as sparse estimators of regression parameters. Our first approach is to estimate the regression coefficients with plug-in estimated inverse covariance matrices, and our second approach is to estimate the inverse covariance matrix with plug-in estimated regression parameters. Our third approach is to estimate both simultaneously. Asymptotic properties of these methods are explored. Our numerical examples demonstrate that the proposed methods perform competitively in terms of prediction, variable selection, as well as inverse covariance matrix estimation.

  4. A new parameter to simultaneously assess antioxidant activity for multiple phenolic compounds present in food products.

    PubMed

    Yang, Hong; Xue, Xuejia; Li, Huan; Tay-Chan, Su Chin; Ong, Seng Poon; Tian, Edmund Feng

    2017-08-15

    In this work, we established a new methodology to simultaneously assess the relative reaction rates of multiple antioxidant compounds in one experimental set-up. This new methodology hypothesizes that the competition among antioxidant compounds towards limiting amount of free radical (in this article, DPPH) would reflect their relative reaction rates. In contrast with the conventional detection of DPPH decrease at 515nm on a spectrophotometer, depletion of antioxidant compounds treated by a series of DPPH concentrations was monitored instead using liquid chromatography coupled with quadrupole time-of-flight (LC-QTOF). A new parameter, namely relative antioxidant activity (RAA), has been proposed to rank these antioxidants according to their reaction rate constants. We have investigated the applicability of RAA using pre-mixed standard phenolic compounds, and also extended this application to two food products, i.e. red wine and green tea. It has been found that RAA correlates well with the reported k values. This new parameter, RAA, provides a new perspective in evaluating antioxidant compounds present in food and herbal matrices. It not only realistically reflects the antioxidant activity of compounds when co-existing with competitive constituents; and it could also quicken up the discovery process in the search for potent yet rare antioxidants from many herbs of food/medicinal origins.

  5. Simultaneous detection of multiple biomarkers by means of SERS on polymer nanopillar gold arrays

    NASA Astrophysics Data System (ADS)

    Morasso, Carlo; Picciolini, Silvia; Mehn, Dora; Pellacani, Paola; Frangolho, Ana; Marchesini, Gerardo; Vanna, Renzo; Gualerzi, Alice; Bedoni, Marzia; Marabelli, Franco; Gramatica, Furio

    2016-03-01

    The detection of biomarkers by means of Surface Enhanced Raman Spectroscopy (SERS) is foreseen to became a very important tool in the clinical practice because of its excellent sensitivity and potential for the simultaneous detection of multiple biomarkers. In the present paper we describe how it was possible to build a sensor for the detection of genetic biomarkers involved in acute myeloid leukemia. The assay is based on the use of a specifically designed SERS substrate made of a 2D crystal structure of polymeric pillars embedded in a gold layer. This substrate is characterized by good enhancing properties coupled with an excellent homogeneity. The SERS substrate was conjugated with DNA probes complementary to a target sequence and used in a sandwich assay with gold nanoparticles labeled with a second DNA probe and a Raman reporter. The so developed assay allowed the detection of a leukemia biomarker (WT1 gene) and an housekeeping gene with low picomolar sensitivity. At last, we optimized the assay in order to tackle one of the main limitations of SERS based assay: the loss of signal that is observed when the Raman spectra are collected in liquid. Combining a preferential functionalization on the polymeric pillars with a different height of the polymer pillars from the gold layer the assay demonstrated its effectiveness even when measured in buffer.

  6. Expanded beam deflection method for simultaneous measurement of displacement and vibrations of multiple microcantilevers.

    PubMed

    Nieradka, K; Małozięć, G; Kopiec, D; Grabiec, P; Janus, P; Sierakowski, A; Gotszalk, T

    2011-10-01

    Here we present an extension of optical beam deflection (OBD) method for measuring displacement and vibrations of an array of microcantilevers. Instead of focusing on the cantilever, the optical beam is either focused above or below the cantilever array, or focused only in the axis parallel to the cantilevers length, allowing a wide optical line to span multiple cantilevers in the array. Each cantilever reflects a part of the incident beam, which is then directed onto a photodiode array detector in a manner allowing distinguishing between individual beams. Each part of reflected beam behaves like a single beam of roughly the same divergence angle in the bending sensing axis as the incident beam. Since sensitivity of the OBD method depends on the divergence angle of deflected beam, high sensitivity is preserved in proposed expanded beam deflection (EBD) method. At the detector, each spot's position is measured at the same time, without time multiplexing of light sources. This provides real simultaneous readout of entire array, unavailable in most of competitive methods, and thus increases time resolution of the measurement. Expanded beam can also span another line of cantilevers allowing monitoring of specially designed two-dimensional arrays. In this paper, we present first results of application of EBD method to cantilever sensors. We show how thermal noise resolution can be easily achieved and combined with thermal noise based resonance frequency measurement.

  7. Expanded beam deflection method for simultaneous measurement of displacement and vibrations of multiple microcantilevers

    NASA Astrophysics Data System (ADS)

    Nieradka, K.; Małozieć, G.; Kopiec, D.; Grabiec, P.; Janus, P.; Sierakowski, A.; Gotszalk, T.

    2011-10-01

    Here we present an extension of optical beam deflection (OBD) method for measuring displacement and vibrations of an array of microcantilevers. Instead of focusing on the cantilever, the optical beam is either focused above or below the cantilever array, or focused only in the axis parallel to the cantilevers length, allowing a wide optical line to span multiple cantilevers in the array. Each cantilever reflects a part of the incident beam, which is then directed onto a photodiode array detector in a manner allowing distinguishing between individual beams. Each part of reflected beam behaves like a single beam of roughly the same divergence angle in the bending sensing axis as the incident beam. Since sensitivity of the OBD method depends on the divergence angle of deflected beam, high sensitivity is preserved in proposed expanded beam deflection (EBD) method. At the detector, each spot's position is measured at the same time, without time multiplexing of light sources. This provides real simultaneous readout of entire array, unavailable in most of competitive methods, and thus increases time resolution of the measurement. Expanded beam can also span another line of cantilevers allowing monitoring of specially designed two-dimensional arrays. In this paper, we present first results of application of EBD method to cantilever sensors. We show how thermal noise resolution can be easily achieved and combined with thermal noise based resonance frequency measurement.

  8. Simultaneous detection of multiple DNA targets based on encoding metal ions.

    PubMed

    Zheng, Lichun; Li, Xiaoyan; Liu, Panpan; Wu, Guofan; Lu, Xiaoquan; Liu, Xiuhui

    2014-02-15

    We present a novel strategy for simultaneous electrochemical detection of multiple DNA targets based on the use of different encoding metal ions as tags. The principle of this scheme is that metal ions bound to metallothionein (MT) molecules can be released down after hybridization with DNA targets and then be detected by stripping voltammetry. The novel detection probes, ssDNA/MT conjugates, covered with different metal ions were synthesized for the first time, then three encoding metal ions (Zn(2+), Cd(2+), and Pb(2+)) were used to differentiate the signals of three virus DNA due to their well-defined anodic stripping peaks at -1.13 V (Zn), -0.78 V (Cd), and -0.52 V (Pb) at BiFE, respectively. The anodic peak currents increased linearly with the concentrations of DNA targets in the range from 0.1 nM to 10nM with a detection limit of 33 pM. In addition, the one-base mismatched target was effectively discriminated from the complementary target. The described results demonstrated that this method possesses high sensitivity and selectivity for multi-target DNA assay and has great potential in applications for detection of even more targets in biological assays, particularly immunoassays.

  9. Report for simultaneous, multiple independently steered beam study for Airborne Electronically Steerable Phased Array (AESPA) program

    NASA Technical Reports Server (NTRS)

    1978-01-01

    Design concepts of an array for the formation of multiple, simultaneous, independently pointed beams for satellite communication links were investigated through tradeoffs of various approaches which were conceived as possible solutions to the problem. After the preferred approach was selected, a more detailed design was configured and is presented as a candidate system that should be given further consideration for development leading to a preliminary design. This array uses an attenuator and a phase shifter with every element. The aperture excitation necessary to form the four beams is calculated and then placed across the array using these devices. Pattern analysis was performed for two beam and four beam cases with numerous patterns being presented. Parameter evaluation shown includes pointing accuracy and beam shape, sidelobe characteristics, gain control, and beam normalization. It was demonstrated that a 4 bit phase shifter and a 6 bit, 30 dB attenuator were sufficient to achieve adequate pattern performances. The phase amplitude steered multibeam array offers the flexibility of 1 to 4 beams with an increase in gain of 6 dB if only one beam is selected.

  10. Multifunctional magnetic-optical nanoparticle probes for simultaneous detection, separation, and thermal ablation of multiple pathogens.

    PubMed

    Wang, Chungang; Irudayaraj, Joseph

    2010-01-01

    Multifunctional nanoparticles possessing magnetization and near-infrared (NIR) absorption have warranted interest due to their significant applications in magnetic resonance imaging, diagnosis, bioseparation, target delivery, and NIR photothermal ablation. Herein, the site-selective assembly of magnetic nanoparticles onto the ends or ends and sides of gold nanorods with different aspect ratios (ARs) to create multifunctional nanorods decorated with varying numbers of magnetic particles is described for the first time. The resulting hybrid nanoparticles are designated as Fe(3)O(4)-Au(rod)-Fe(3)O(4) nanodumbbells and Fe(3)O(4)-Au(rod) necklacelike constructs with tunable optical and magnetic properties, respectively. These hybrid nanomaterials can be used for multiplex detection and separation because of their tunable magnetic and plasmonic functionality. More specifically, Fe(3)O(4)-Au(rod) necklacelike probes of different ARs are utilized for simultaneous optical detection based on their plasmon properties, magnetic separation, and photokilling of multiple pathogens from a single sample at one time. The combined functionalities of the synthesized probes will open up many exciting opportunities in dual imaging for targeted delivery and photothermal therapy.

  11. Simultaneous occurrence of diabetic ketoacidosis, thyroid storm, and multiple cerebral infarctions due to Moyamoya disease.

    PubMed

    Noh, Byoungho H; Cho, Sang-Won; Ahn, Sung Yeon

    2016-02-01

    Diabetic ketoacidosis (DKA) is one of the precipitating factors that can evoke a thyroid storm. Thyroid storm may cause cerebral ischemia in Moyamoya disease, which can coexist in patients with Graves' disease. A 16-year-old girl complaining of dizziness and palpitations visited the emergency department and was diagnosed with DKA combined with hyperthyroidism. A thyroid storm occurred 6 h after the start of DKA management. Her Burch and Wartofsky score was 65 points. Right hemiplegia developed during the thyroid storm, and brain magnetic resonance (MR) diffusion-weighted images revealed multiple acute infarcts in both hemispheres. MR angiography showed stenosis of both distal internal carotid arteries and both M1 portions of the middle cerebral arteries, consistent with Moyamoya disease. After acute management for the thyroid storm with methimazole, Lugol solution and hydrocortisone, the patient's neurological symptoms completely resolved within 1 month, and free T4 level normalized within 2 months. Thyroid storm may trigger cerebral ischemia in Moyamoya disease and lead to rapid progression of cerebrovascular occlusive disease. As a simultaneous occurrence of DKA, thyroid storm and cerebrovascular accident in Moyamoya disease highly elevates morbidity and mortality, prompt recognition and management are critical to save the patient's life.

  12. Modular time division multiplexer: Efficient simultaneous characterization of fast and slow transients in multiple samples

    NASA Astrophysics Data System (ADS)

    Kim, Stephan D.; Luo, Jiajun; Buchholz, D. Bruce; Chang, R. P. H.; Grayson, M.

    2016-09-01

    A modular time division multiplexer (MTDM) device is introduced to enable parallel measurement of multiple samples with both fast and slow decay transients spanning from millisecond to month-long time scales. This is achieved by dedicating a single high-speed measurement instrument for rapid data collection at the start of a transient, and by multiplexing a second low-speed measurement instrument for slow data collection of several samples in parallel for the later transients. The MTDM is a high-level design concept that can in principle measure an arbitrary number of samples, and the low cost implementation here allows up to 16 samples to be measured in parallel over several months, reducing the total ensemble measurement duration and equipment usage by as much as an order of magnitude without sacrificing fidelity. The MTDM was successfully demonstrated by simultaneously measuring the photoconductivity of three amorphous indium-gallium-zinc-oxide thin films with 20 ms data resolution for fast transients and an uninterrupted parallel run time of over 20 days. The MTDM has potential applications in many areas of research that manifest response times spanning many orders of magnitude, such as photovoltaics, rechargeable batteries, amorphous semiconductors such as silicon and amorphous indium-gallium-zinc-oxide.

  13. Expanded beam deflection method for simultaneous measurement of displacement and vibrations of multiple microcantilevers

    SciTech Connect

    Nieradka, K.; MaloziePc, G.; Kopiec, D.; Gotszalk, T.

    2011-10-15

    Here we present an extension of optical beam deflection (OBD) method for measuring displacement and vibrations of an array of microcantilevers. Instead of focusing on the cantilever, the optical beam is either focused above or below the cantilever array, or focused only in the axis parallel to the cantilevers length, allowing a wide optical line to span multiple cantilevers in the array. Each cantilever reflects a part of the incident beam, which is then directed onto a photodiode array detector in a manner allowing distinguishing between individual beams. Each part of reflected beam behaves like a single beam of roughly the same divergence angle in the bending sensing axis as the incident beam. Since sensitivity of the OBD method depends on the divergence angle of deflected beam, high sensitivity is preserved in proposed expanded beam deflection (EBD) method. At the detector, each spot's position is measured at the same time, without time multiplexing of light sources. This provides real simultaneous readout of entire array, unavailable in most of competitive methods, and thus increases time resolution of the measurement. Expanded beam can also span another line of cantilevers allowing monitoring of specially designed two-dimensional arrays. In this paper, we present first results of application of EBD method to cantilever sensors. We show how thermal noise resolution can be easily achieved and combined with thermal noise based resonance frequency measurement.

  14. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species.

    PubMed

    Radhika, M; Saugata, Majumder; Murali, H S; Batra, H V

    2014-01-01

    Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC). The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.

  15. S4MPLE--sampler for multiple protein-ligand entities: simultaneous docking of several entities.

    PubMed

    Hoffer, Laurent; Horvath, Dragos

    2013-01-28

    S4MPLE is a conformational sampling tool, based on a hybrid genetic algorithm, simulating one (conformer enumeration) or more molecules (docking). Energy calculations are based on the AMBER force field [Cornell et al. J. Am. Chem. Soc. 1995, 117, 5179.] for biological macromolecules and its generalized version GAFF [Wang et al. J. Comput. Chem. 2004 , 25, 1157.] for ligands. This paper describes more advanced, specific applications of S4MPLE to problems more complex than classical redocking of drug-like compounds [Hoffer et al. J. Mol. Graphics Modell. 2012, submitted for publication.]. Here, simultaneous docking of multiple entities is addressed in two different important contexts. First, simultaneous docking of two fragment-like ligands was attempted, as such ternary complexes are the basis of fragment-based drug design by linkage of the independent binders. As a preliminary, the capacity of S4MPLE to dock fragment-like compounds has been assessed, since this class of small probes used in fragment-based drug design covers a different chemical space than drug-like molecules. Herein reported success rates from fragments redocking are as good as classical benchmarking results on drug-like compounds (Astex Diverse Set [Hartshorn et al. J. Med. Chem. 2007, 50, 726.]). Then, S4MPLE is successfully challenged to predict locations of fragments involved in ternary complexes by means of multientity docking. Second, the key problem of predicting water-mediated interaction is addressed by considering explicit water molecules as additional entities to be docked in the presence of the "main" ligand. Blind prediction of solvent molecule positions, reproducing relevant ligand-water-site mediated interactions, is achieved in 76% cases over saved poses. S4MPLE was also successful to predict crystallographic water displacement by a therefore tailored functional group in the optimized ligand. However, water localization is an extremely delicate issue in terms of weighing of

  16. Hierarchical pictorial structures for simultaneously localizing multiple organs in volumetric pre-scan CT

    NASA Astrophysics Data System (ADS)

    Montillo, Albert; Song, Qi; Das, Bipul; Yin, Zhye

    2015-03-01

    Parsing volumetric computed tomography (CT) into 10 or more salient organs simultaneously is a challenging task with many applications such as personalized scan planning and dose reporting. In the clinic, pre-scan data can come in the form of very low dose volumes acquired just prior to the primary scan or from an existing primary scan. To localize organs in such diverse data, we propose a new learning based framework that we call hierarchical pictorial structures (HPS) which builds multiple levels of models in a tree-like hierarchy that mirrors the natural decomposition of human anatomy from gross structures to finer structures. Each node of our hierarchical model learns (1) the local appearance and shape of structures, and (2) a generative global model that learns probabilistic, structural arrangement. Our main contribution is twofold. First we embed the pictorial structures approach in a hierarchical framework which reduces test time image interpretation and allows for the incorporation of additional geometric constraints that robustly guide model fitting in the presence of noise. Second we guide our HPS framework with the probabilistic cost maps extracted using random decision forests using volumetric 3D HOG features which makes our model fast to train and fast to apply to novel test data and posses a high degree of invariance to shape distortion and imaging artifacts. All steps require approximate 3 mins to compute and all organs are located with suitably high accuracy for our clinical applications such as personalized scan planning for radiation dose reduction. We assess our method using a database of volumetric CT scans from 81 subjects with widely varying age and pathology and with simulated ultra-low dose cadaver pre-scan data.

  17. Simultaneous Evaluation of Multiple Rotationally Excited States of Floppy Molecules Using Diffusion Monte Carlo

    NASA Astrophysics Data System (ADS)

    McCoy, Anne B.; Ford, Jason E.; Marlett, Melanie L.; Petit, Andrew S.

    2014-06-01

    In this work, an extension to diffusion Monte Carlo (DMC) is proposed, allowing for the simultaneous calculation of the energy and wave function of multiple rotationally excited states of floppy molecules. The total wave function is expanded into a set of Dirac δ-functions called walkers, while the rotational portion of the wave function is expanded in a symmetric top basis set. Each walker is given a rotational state vector containing coefficients for all states of interest. The positions of the atoms and the coefficients in the state vector evolve according to the split operator approximation of the quantum propagator. The method was benchmarked by comparing calculated rotation-vibration energies for H_3^+, H_2D^+, and H_3O^+ to experimental values. For low to moderate values of J, the resulting energies are within the statistical uncertainty of the calculation. Rotation-vibration coupling is captured through flexibility introduced in the form of the vibrational wave function. This coupling is found to increase with increasing J-values. Based on the success achieved through these systems, the method was applied to CH_5^+ and its deuterated isotopologues for v = 0, J ≥ 10. Based on these calculations, the energy level structure of CH_5^+ is found to resemble that for a of a spherical top, and excitations up to J = 10 displayed insignificant rotation-vibration coupling. Extensions of this approach that explicitly account for vibrations will also be discussed. ` A. S. Petit, J. E. Ford and A. B. McCoy, J. Phys. Chem. A, in press, K. D. Jordan Festschrift, DOI: 10.1021/jp408821a

  18. Suppression of Stimulated Brillouin Scattering in multiple-ion species inertial confinemen fusion Hohlraum Plasmas

    SciTech Connect

    Neumayer, P

    2007-05-14

    A long-standing problem in the field of laser-plasma interactions is to successfully employ multiple-ion species plasmas to reduce stimulated Brillouin scattering (SBS) in inertial confinement fusion (ICF) hohlraum conditions. Multiple-ion species increase significantly the linear Landau damping for acoustic waves. Consequently, recent hohlraum designs for indirect-drive ignition on the National Ignition Facility investigate wall liner material options so that the liner gain for parametric instabilities will be below threshold for the onset SBS. Although the effect of two-ion species plasmas on Landau damping has been directly observed with Thomson scattering, early experiments on SBS in these plasmas have suffered from competing non-linear effects or laser beam filamentation. In this study, a reduction of SBS scattering to below the percent level has been observed in hohlraums at Omega that emulate the plasma conditions in an indirect drive ICF experiments. These experiments have measured the laser-plasma interaction processes in ignition-relevant high-electron temperature regime demonstrating Landau damping as a controlling process for SBS. The hohlraums have been filled with various fractions of CO{sub 2} and C{sub 3}H{sub 8} varying the ratio of the light (H) to heavy (C and O) ion density from 0 to 2.6. They have been heated by 14.5 kJ of 351-nm light, thus increasing progressively Landau damping by an order of magnitude at constant electron density and temperature. A delayed 351-nm interaction beam, spatially smoothed to produce a 200-{micro}m laser spot at best focus, has propagated along the axis of the hohlraum. The backscattered light, both into the lens and outside, the transmitted light through the hohlraum plasma and the radiation temperature of the hohlraum has been measured. For ignition relevant laser intensities (3-9 10{sup 14} Wcm{sup -2}), we find that the SBS reflectivity scales as predicted with Landau damping from >30% to <1%. Simultaneously

  19. Characteristics of 263K Scrapie Agent in Multiple Hamster Species

    PubMed Central

    Barbian, Kent D.; Race, Brent; Favara, Cynthia; Gardner, Don; Taubner, Lara; Porcella, Stephen; Race, Richard

    2009-01-01

    Transmissible spongiform encephalopathy (TSE) diseases are known to cross species barriers, but the pathologic and biochemical changes that occur during transmission are not well understood. To better understand these changes, we infected 6 hamster species with 263K hamster scrapie strain and, after each of 3 successive passages in the new species, analyzed abnormal proteinase K (PK)–resistant prion protein (PrPres) glycoform ratios, PrPres PK sensitivity, incubation periods, and lesion profiles. Unique 263K molecular and biochemical profiles evolved in each of the infected hamster species. Characteristics of 263K in the new hamster species seemed to correlate best with host factors rather than agent strain. Furthermore, 2 polymorphic regions of the prion protein amino acid sequence correlated with profile differences in these TSE-infected hamster species. PMID:19193264

  20. Simultaneous Bioreduction of Multiple Oxidized Contaminants Using a Membrane Biofilm Reactor.

    PubMed

    Li, Haixiang; Lin, Hua; Xu, Xiaoyin; Jiang, Minmin; Chang, Chein-Chi; Xia, Siqing

    2017-02-01

      This study tests a hydrogen-based membrane biofilm reactor (MBfR) to investigate simultaneous bioreduction of selected oxidized contaminants, including nitrate (-N), sulfate (), bromate (), chromate (Cr(VI)) and para-chloronitrobenzene (p-CNB). The experiments demonstrate that MBfR can achieve high performance for contaminants bioreduction to harmless or immobile forms in 240 days, with a maximum reduction fluxes of 0.901 g -N/m2·d, 1.573 g /m2·d, 0.009 g /m2·d, 0.022 g Cr(VI)/m2·d, and 0.043 g p-CNB/m2·d. Increasing H2 pressure and decreasing influent surface loading enhanced removal efficiency of the reactor. Flux analysis indicates that nitrate and sulfate reductions competed more strongly than , Cr(VI) and p-CNB reduction. The average H2 utilization rate, H2 flux, and H2 utilization efficiency of the reactor were 0.026 to 0.052 mg H2/cm3·d, 0.024 to 0.046 mg H2/cm2·d, and 97.5% to 99.3% (nearly 100%). Results show the hydrogen-based MBfR may be suitable for removing multiple oxidized contaminants in drinking water or groundwater.

  1. Simultaneous thrombosis of multiple coronary arteries in a patient with rheumatoid arthritis

    PubMed Central

    Kalayci, Arzu; Arslan, Erol; Bakar, Salih Murat; Guneri, Mahmut; Dizman, Rafet; Kivanc, Eylem; Karabay, Can Yucel

    2016-01-01

    We present a case of simultaneous coronary thrombosis of the left main, the left anterior descending artery and the right coronary artery in a patient, recently diagnosed with rheumatoid arthritis. PMID:27489603

  2. STATISTICAL METHODOLOGY FOR THE SIMULTANEOUS ANALYSIS OF MULTIPLE TYPES OF OUTCOMES IN NONLINEAR THRESHOLD MODELS.

    EPA Science Inventory

    Multiple outcomes are often measured on each experimental unit in toxicology experiments. These multiple observations typically imply the existence of correlation between endpoints, and a statistical analysis that incorporates it may result in improved inference. When both disc...

  3. Multibeam long-path differential optical absorption spectroscopy instrument: a device for simultaneous measurements along multiple light paths.

    PubMed

    Pundt, Irene; Mettendorf, Kai Uwe

    2005-08-10

    A novel long-path differential optical absorption spectroscopy (DOAS) apparatus for measuring tropospheric trace gases and the first results from its use are presented: We call it the multibeam instrument. It is the first active DOAS device that emits several light beams simultaneously through only one telescope and with only one lamp as a light source, allowing simultaneous measurement along multiple light paths. In contrast to conventional DOAS instruments, several small mirrors are positioned near the lamp, creating multiple virtual light sources that emit one light beam each in one specific direction. The possibility of error due to scattering between the light beams is negligible. The trace-gas detection limits of NO2, SO2, O3, and H2CO are similar to those of the traditional long-path DOAS instrument.

  4. Simultaneous imaging of multiple focal planes for three-dimensional microscopy using ultra-high-speed adaptive optics.

    PubMed

    Duocastella, Martí; Sun, Bo; Arnold, Craig B

    2012-05-01

    Traditional white-light and fluorescent imaging techniques provide powerful methods to extract high-resolution information from two-dimensional (2-D) sections, but to retrieve information from a three-dimensional (3-D) volume they require relatively slow scanning methods that result in increased acquisition time. Using an ultra-high speed liquid lens, we circumvent this problem by simultaneously acquiring images from multiple focal planes. We demonstrate this method by imaging microparticles and cells flowing in 3-D microfluidic channels.

  5. A novel GMO biosensor for rapid ultrasensitive and simultaneous detection of multiple DNA components in GMO products.

    PubMed

    Huang, Lin; Zheng, Lei; Chen, Yinji; Xue, Feng; Cheng, Lin; Adeloju, Samuel B; Chen, Wei

    2015-04-15

    Since the introduction of genetically modified organisms (GMOs), there has been on-going and continuous concern and debates on the commercialization of products derived from GMOs. There is an urgent need for development of highly efficient analytical methods for rapid and high throughput screening of GMOs components, as required for appropriate labeling of GMO-derived foods, as well as for on-site inspection and import/export quarantine. In this study, we describe, for the first time, a multi-labeling based electrochemical biosensor for simultaneous detection of multiple DNA components of GMO products on the same sensing interface. Two-round signal amplification was applied by using both an exonuclease enzyme catalytic reaction and gold nanoparticle-based bio-barcode related strategies, respectively. Simultaneous multiple detections of different DNA components of GMOs were successfully achieved with satisfied sensitivity using this electrochemical biosensor. Furthermore, the robustness and effectiveness of the proposed approach was successfully demonstrated by application to various GMO products, including locally obtained and confirmed commercial GMO seeds and transgenetic plants. The proposed electrochemical biosensor demonstrated unique merits that promise to gain more interest in its use for rapid and on-site simultaneous multiple screening of different components of GMO products.

  6. The ultrasound brain helmet: early human feasibility study of multiple simultaneous 3D scans of cerebral vasculature

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.; Ivancevich, Nikolas M.; Whitman, John; Light, Edward; Fronheiser, Matthew; Nicoletto, Heather A.; Laskowitz, Daniel T.; Smith, Stephen W.

    2009-02-01

    We describe early stage experiments to test the feasibility of an ultrasound brain helmet to produce multiple simultaneous real-time 3D scans of the cerebral vasculature from temporal and suboccipital acoustic windows of the skull. The transducer hardware and software of the Volumetrics Medical Imaging real-time 3D scanner were modified to support dual 2.5 MHz matrix arrays of 256 transmit elements and 128 receive elements which produce two simultaneous 64° pyramidal scans. The real-time display format consists of two coronal B-mode images merged into a 128° sector, two simultaneous parasagittal images merged into a 128° × 64° C-mode plane, and a simultaneous 64° axial image. Real-time 3D color Doppler images acquired in initial clinical studies after contrast injection demonstrate flow in several representative blood vessels. An offline Doppler rendering of data from two transducers simultaneously scanning via the temporal windows provides an early visualization of the flow in vessels on both sides of the brain. The long-term goal is to produce real-time 3D ultrasound images of the cerebral vasculature from a portable unit capable of internet transmission, thus enabling interactive 3D imaging, remote diagnosis and earlier therapeutic intervention. We are motivated by the urgency for rapid diagnosis of stroke due to the short time window of effective therapeutic intervention.

  7. PCR-Based Multiple Species Cell Counting for In Vitro Mixed Culture.

    PubMed

    Huang, Ruijie; Zhang, Junjie; Yang, X Frank; Gregory, Richard L

    2015-01-01

    Changes of bacterial profiles in microbial communities are strongly associated with human health. There is an increasing need for multiple species research in vitro. To avoid high cost or measurement of a limited number of species, PCR-based multiple species cell counting (PCR-MSCC) has been conceived. Species-specific sequence is defined as a unique sequence of one species in a multiple species mixed culture. This sequence is identified by comparing a random 1000 bp genomic sequence of one species with the whole genome sequences of the other species in the same artificial mixed culture. If absent in the other genomes, it is the species-specific sequence. Species-specific primers were designed based on the species-specific sequences. In the present study, ten different oral bacterial species were mixed and grown in Brain Heart Infusion Yeast Extract with 1% sucrose for 24 hours. Biofilm was harvested and processed for DNA extraction and q-PCR amplification with the species-specific primers. By comparing the q-PCR data of each species in the unknown culture with reference cultures, in which the cell number of each species was determined by colony forming units on agar plate, the cell number of that strain in the unknown mixed culture was calculated. This technique is reliable to count microorganism numbers that are less than 100,000 fold different from other species within the same culture. Theoretically, it can be used in detecting a species in a mixed culture of over 200 species. Currently PCR-MSCC is one of the most economic methods for quantifying single species cell numbers, especially for the low abundant species, in a multiple artificial mixed culture in vitro.

  8. Genetically engineered Mengo virus vaccination of multiple captive wildlife species.

    PubMed

    Backues, K A; Hill, M; Palmenberg, A C; Miller, C; Soike, K F; Aguilar, R

    1999-04-01

    Encephalomyocarditis virus (EMCV), has caused the deaths of many species of animals in zoological parks and research institutions. The Audubon Park Zoo, (New Orleans, Louisiana, USA) attempted vaccination of several species with a killed EMCV vaccine with mixed results. This paper reports an attempt at vaccination against EMCV using a genetically engineered, live attenuated Mengo virus (vMC0) at the Audubon Park Zoo and Miami Metro Zoo, (Miami, Florida, USA) from December 1996 to June 1997. Several species of animals were vaccinated with vMC0, which is serologically indistinguishable from the field strain of EMCV. Serum samples were taken at the time of vaccination and again 21 days later, then submitted for serum neutralization titers against EMCV. The vaccinate species included red capped mangebey (Cercocebus torquatus), colobus (Colobus guereza), angolan colobus (Colobus angolensis), ruffed lemur (Lemur variegatus ruber and Lemur variegatus variegatus), back lemur (Lemur macaco), ring-tailed lemur (Lemur catta), siamang (Hylobates syndactylus), diana guenon (Cercopithicus diana), spider monkey (Ateles geoffroyi), common marmoset (Callithrix jacchus), talapoin monkey (Cercopithecus talapoin), Brazilian tapir (Tapirus terrestris), Baird's tapir (Tapirus bairdii), Malayan tapir (Tapirus indicus), dromedary camel (Camelus dromedarius), bactrian camel (Camelus bactrianus), gerenuk (Litocranius walleri), guanaco (Lama glama guanicoe), black duiker (Cephalophus niger), Vietnamese potbellied pig (Sus scrofa), babirusa (Babyrousa babyrussa), collard peccary (Tayass tajacu), and African crested porcupine (Hystrix africaeaustralis). The vaccine response was variable, with high virus neutralizing antibody titer responses in some primate species and mixed to poor responses for other species. No ill effects were seen with vaccination.

  9. Simultaneous field measurements of terpene and isoprene emissions from two dominant mediterranean oak species in relation to a North American species

    NASA Astrophysics Data System (ADS)

    Kesselmeier, J.; Bode, K.; Schäfer, L.; Schebeske, G.; Wolf, A.; Brancaleoni, E.; Cecinato, A.; Ciccioli, P.; Frattoni, M.; Dutaur, L.; Fugit, J. L.; Simon, V.; Torres, L.

    We investigated the emission of monoterpenes and isoprene from tree species growing at a site near Montpellier (South France). We compared the emission pattern and behaviour of two important oak species representative of the Mediterranean ecosystem, namely, Quercus ilex (Holm oak), a strong monoterpene emitter, and Quercus pubescens (White oak), a strong isoprene emitter by measuring the two species growing side by side simultaneously. Additionally, we included a Californian oak species Quercus agrifolia (Coast Live Oak), which is anatomically and morphologically comparable with Quercus ilex. The data show that Live Oak and Holm oak though they appear identical, differ as far as the emission of terpenoids is concerned, emitting isoprene or terpenes, respectively. The isoprene emitting White oak and the monoterpene emitting Holm oak react identically to the same environmental conditions, fluctuating light and temperature, indicating that close metabolic pathways are involved in the actual emission of the C5 and C10 compounds from these two species, as seen under field conditions.

  10. Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus cichla) using multi-locus data

    PubMed Central

    2012-01-01

    Background Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). Results We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. Conclusions Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient

  11. GroEL-GroES assisted folding of multiple recombinant proteins simultaneously over-expressed in Escherichia coli.

    PubMed

    Goyal, Megha; Chaudhuri, Tapan K

    2015-07-01

    Folding of aggregation prone recombinant proteins through co-expression of chaperonin GroEL and GroES has been a popular practice in the effort to optimize preparation of functional protein in Escherichia coli. Considering the demand for functional recombinant protein products, it is desirable to apply the chaperone assisted protein folding strategy for enhancing the yield of properly folded protein. Toward the same direction, it is also worth attempting folding of multiple recombinant proteins simultaneously over-expressed in E. coli through the assistance of co-expressed GroEL-ES. The genesis of this thinking was originated from the fact that cellular GroEL and GroES assist in the folding of several endogenous proteins expressed in the bacterial cell. Here we present the experimental findings from our study on co-expressed GroEL-GroES assisted folding of simultaneously over-expressed proteins maltodextrin glucosidase (MalZ) and yeast mitochondrial aconitase (mAco). Both proteins mentioned here are relatively larger and aggregation prone, mostly form inclusion bodies, and undergo GroEL-ES assisted folding in E. coli cells during over-expression. It has been reported that the relative yield of properly folded functional forms of MalZ and mAco with the exogenous GroEL-ES assistance were comparable with the results when these proteins were overexpressed alone. This observation is quite promising and highlights the fact that GroEL and GroES can assist in the folding of multiple substrate proteins simultaneously when over-expressed in E. coli. This method might be a potential tool for enhanced production of multiple functional recombinant proteins simultaneously in E. coli.

  12. Detection of alpha and betacoronaviruses in multiple Iberian bat species.

    PubMed

    Falcón, Ana; Vázquez-Morón, Sonia; Casas, Inmaculada; Aznar, Carolina; Ruiz, Guillermo; Pozo, Francisco; Perez-Breña, Pilar; Juste, Javier; Ibáñez, Carlos; Garin, Inazio; Aihartza, Joxerra; Echevarría, Juan E

    2011-10-01

    Bat coronaviruses (CoV) are putative precursors of the severe acute respiratory syndrome (SARS) CoV and other CoV that crossed the species barrier from zoonotic reservoirs into the human population. To determine the presence and distribution of CoV in Iberian bats, 576 individuals of 26 different bat species were captured in 13 locations in Spain. We report for the first time the presence of 14 coronaviruses in 9 Iberian bat species. Phylogenetic analysis of a conserved CoV genome region (RdRp gene) shows a wide diversity and distribution of alpha and betacoronavirus in Spain. Interestingly, although some of these viruses are related to other European BatCoV, or to Asian CoV, some of the viruses found in Spain cluster in new groups of α and β CoV.

  13. Predicting Gene-Disease Associations Using Multiple Species Data

    DTIC Science & Technology

    2011-10-20

    regulatory networks from only positive and unlabeled data. BMC Bioinformatics, 11, 2010. [4] Ernesto Estrada and Desmond J. Higham. Network properties revealed...David Warde-Farley, Chris Grouios, and Quaid Morris . GeneMANIA: a real-time multiple association network integration algorithm for predicting gene

  14. Phylogenetic analysis reveals multiple introductions of Cynodon species in Australia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The distinction between native and introduced flora in Australia presents some unique challenges given its geological and colonization history. While it is believed that seven species of Cynodon are present in Australia, no genetic analyses, to date, have investigated the origin, diversity and phylo...

  15. Multiple-level defect species evaluation from average carrier decay

    NASA Astrophysics Data System (ADS)

    Debuf, Didier

    2003-10-01

    An expression for the average decay is determined by solving the the carrier continuity equations, which include terms for multiple defect recombination. This expression is the decay measured by techniques such as the contactless photoconductance decay method, which determines the average or volume integrated decay. Implicit in the above is the requirement for good surface passivation such that only bulk properties are observed. A proposed experimental configuration is given to achieve the intended goal of an assessment of the type of defect in an n-type Czochralski-grown silicon semiconductor with an unusually high relative lifetime. The high lifetime is explained in terms of a ground excited state multiple-level defect system. Also, minority carrier trapping is investigated.

  16. Optimal design of compact and connected nature reserves for multiple species.

    PubMed

    Wang, Yicheng; Önal, Hayri

    2016-04-01

    When designing a conservation reserve system for multiple species, spatial attributes of the reserves must be taken into account at species level. The existing optimal reserve design literature considers either one spatial attribute or when multiple attributes are considered the analysis is restricted only to one species. We built a linear integer programing model that incorporates compactness and connectivity of the landscape reserved for multiple species. The model identifies multiple reserves that each serve a subset of target species with a specified coverage probability threshold to ensure the species' long-term survival in the reserve, and each target species is covered (protected) with another probability threshold at the reserve system level. We modeled compactness by minimizing the total distance between selected sites and central sites, and we modeled connectivity of a selected site to its designated central site by selecting at least one of its adjacent sites that has a nearer distance to the central site. We considered structural distance and functional distances that incorporated site quality between sites. We tested the model using randomly generated data on 2 species, one ground species that required structural connectivity and the other an avian species that required functional connectivity. We applied the model to 10 bird species listed as endangered by the state of Illinois (U.S.A.). Spatial coherence and selection cost of the reserves differed substantially depending on the weights assigned to these 2 criteria. The model can be used to design a reserve system for multiple species, especially species whose habitats are far apart in which case multiple disjunct but compact and connected reserves are advantageous. The model can be modified to increase or decrease the distance between reserves to reduce or promote population connectivity.

  17. Spatially controlled simultaneous patterning of multiple growth factors in three-dimensional hydrogels

    NASA Astrophysics Data System (ADS)

    Wylie, Ryan G.; Ahsan, Shoeb; Aizawa, Yukie; Maxwell, Karen L.; Morshead, Cindi M.; Shoichet, Molly S.

    2011-10-01

    Three-dimensional (3D) protein-patterned scaffolds provide a more biomimetic environment for cell culture than traditional two-dimensional surfaces, but simultaneous 3D protein patterning has proved difficult. We developed a method to spatially control the immobilization of different growth factors in distinct volumes in 3D hydrogels, and to specifically guide differentiation of stem/progenitor cells therein. Stem-cell differentiation factors sonic hedgehog (SHH) and ciliary neurotrophic factor (CNTF) were simultaneously immobilized using orthogonal physical binding pairs, barnase-barstar and streptavidin-biotin, respectively. Barnase and streptavidin were sequentially immobilized using two-photon chemistry for subsequent concurrent complexation with fusion proteins barstar-SHH and biotin-CNTF, resulting in bioactive 3D patterned hydrogels. The technique should be broadly applicable to the patterning of a wide range of proteins.

  18. Calculation of Multiple Burst Interactions for Six Simultaneous Explosions of 120 Ton ANFO Charges

    DTIC Science & Technology

    1979-12-15

    rivll, spheric ity , etc. would gene iratly be t’XpeLcted toLVI) ld Lo iow’~t tile illt!Lerct ionl Over- p rca no rca . A iiyd iocude aCUIIciaL Ion...detonations. The MISERS BLUFF II--2 test consisted of the simultaneous detonation of six 120-ton ANFO charges placed in a hexa - gonal array with 100-ft

  19. Simultaneous initiation and growth of multiple radial hydraulic fractures from a horizontal wellbore

    NASA Astrophysics Data System (ADS)

    Lecampion, Brice; Desroches, Jean

    2015-09-01

    Multi-stage fracturing is the current preferred method of completion of horizontal wells in unconventional hydrocarbon reservoirs. Its core component consists in simultaneously initiating and propagating an array of hydraulic fractures. We develop a numerical model for the initiation and growth of an array of parallel radial hydraulic fractures. The solution accounts for fracture growth, coupling between elastic deformation and fluid flow in the fractures, elastic stress interactions between fractures and fluid flow in the wellbore. We also take into account the presence of a local pressure drop (function of the entering flow rate) at the connection between the well and the fracture, i.e., a choke-like effect due to current well completion practices, also referred to as entry friction. The partitioning of the fluid into the different fractures at any given time is part of the solution and is a critical indicator of simultaneous (balanced fluid partitioning) versus preferential growth. We validate our numerical model against reference solutions and a laboratory experiment for the initiation and growth of a single radial hydraulic fracture. We then investigate the impact of stress interaction on preferential growth of a subset of fractures in the array. Our results show that a sufficiently large local entry friction provides a strong feedback in the system and thus can counteract elastic stress interaction between fractures, thereby ensuring simultaneous growth. We propose a dimensionless number capturing the competition between stress interaction and local entry friction. This dimensionless number is a function of rock properties, fracture spacing and injection parameters. We verify that it captures the transition from the case of simultaneous growth (entry friction larger than interaction stress) to the case of preferential growth of some fractures (interaction stress larger than entry friction). We also discuss the implication of these results for multi

  20. Simultaneous Treatment of Missing Data and Measurement Error in HIV Research using Multiple Overimputation

    PubMed Central

    Schomaker, Michael; Hogger, Sara; Johnson, Leigh F.; Hoffmann, Christopher J.; Bärnighausen, Till; Heumann, Christian

    2015-01-01

    Background Both CD4 count and viral load in HIV infected persons are measured with error. There is no clear guidance on how to deal with this measurement error in the presence of missing data. Methods We used multiple overimputation, a method recently developed in the political sciences, to account for both measurement error and missing data in CD4 count and viral load measurements from four South African cohorts of a Southern African HIV cohort collaboration. Our knowledge about the measurement error of lnCD4 and log10 viral load is part of an imputation model that imputes both missing and mismeasured data. In an illustrative example we estimate the association of CD4 count and viral load with the hazard of death among patients on highly active antiretroviral therapy by means of a Cox model. Simulation studies evaluate the extent to which multiple overimputation is able to reduce bias in survival analyses. Results Multiple overimputation emphasizes more strongly the influence of having a high baseline CD4 counts compared to a complete case analysis and multiple imputation (hazard ratio for >200 cells/mm3 vs. <25 cells/mm3: 0.21 [95%CI: 0.18;0.24] vs. 0.38 [0.29;0.48] and 0.29 [0.25;0.34] respectively). Similar results are obtained when varying assumptions about the measurement error, when using p-splines, and when evaluating time-updated CD4 count in a longitudinal analysis. The estimates of the association with viral load are slightly more attenuated when using multiple imputation instead of multiple overimputation. Our simulation studies suggest that multiple overimputation is able to reduce bias and mean squared error in survival analyses. Conclusions Multiple overimputation, which can be used with existing software, offers a convenient approach to account for both missing and mismeasured data in HIV research. PMID:26214336

  1. Reverse Transcription Polymerase Chain Reaction-based System for Simultaneous Detection of Multiple Lily-infecting Viruses

    PubMed Central

    Kwon, Ji Yeon; Ryu, Ki Hyun; Choi, Sun Hee

    2013-01-01

    A detection system based on a multiplex reverse transcription (RT) polymerase chain reaction (PCR) was developed to simultaneously identify multiple viruses in the lily plant. The most common viruses infecting lily plants are the cucumber mosaic virus (CMV), lily mottle virus (LMoV), lily symptomless virus (LSV). Leaf samples were collected at lily-cultivation facilities located in the Kangwon province of Korea and used to evaluate the detection system. Simplex and multiplex RT-PCR were performed using virus-specific primers to detect single-or mixed viral infections in lily plants. Our results demonstrate the selective detection of 3 different viruses (CMV, LMoV and LSV) by using specific primers as well as the potential of simultaneously detecting 2 or 3 different viruses in lily plants with mixed infections. Three sets of primers for each target virus, and one set of internal control primers were used to evaluate the detection system for efficiency, reliability, and reproducibility. PMID:25288961

  2. Untangling the Diverse Interior and Multiple Exterior Guest Interactions of a Supramolecular Host by the Simultaneous Analysis of Complementary Observables.

    PubMed

    Sgarlata, Carmelo; Raymond, Kenneth N

    2016-07-05

    The entropic and enthalpic driving forces for encapsulation versus sequential exterior guest binding to the [Ga4L6](12-) supramolecular host in solution are very different, which significantly complicates the determination of these thermodynamic parameters. The simultaneous use of complementary techniques, such as NMR, UV-vis, and isothermal titration calorimetry, enables the disentanglement of such multiple host-guest interactions. Indeed, data collected by each technique measure different components of the host-guest equilibria and together provide a complete picture of the solution thermodynamics. Unfortunately, commercially available programs do not allow for global analysis of different physical observables. We thus resorted to a novel procedure for the simultaneous refinement of multiple parameters (ΔG°, ΔH°, and ΔS°) by treating different observables through a weighted nonlinear least-squares analysis of a constrained model. The refinement procedure is discussed for the multiple binding of the Et4N(+) guest, but it is broadly applicable to the deconvolution of other intricate host-guest equilibria.

  3. A convenient method for simultaneous quantification of multiple phytohormones and metabolites: application in study of rice-bacterium interaction

    PubMed Central

    2012-01-01

    Background Simultaneous analysis of multiple functional-related phytohormones and their metabolites will improve our understanding of interactions among different hormones in the same biologic process. Results A method was developed for simultaneous quantification of multiple phytohormones, abscisic acid, indole-3-acetic acid (IAA), jasmonic acid (JA), and salicylic acid, hormone conjugates, IAA-aspartic acid, JA-isoleucine, and methyl JA, and phytoalexins, momilactone A, naringenin, and sakuranetin. This method combines a convenient procedure for preparing filtrated crude extracted samples and a sensitive quantification assay using ultra fast liquid chromatography-electrospray ionization tandem mass spectrometry (UFLC-ESI-MS). With this method, we determined the dynamic profiles of defense-related phytohormones, hormone metabolites, and phytoalexins in the interaction of rice with Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight, one of the most devastating diseases of rice worldwide. Conclusion This UFLC-ESI-MS method is convenient, sensitive, reliable, and inexpensive for quantification of multiple phytohormones and metabolites compared to current methods. The results obtained by application of this method in studying rice-bacterial interaction provide a basis for understanding the molecular mechanisms of rice defense responses. PMID:22243810

  4. Gateway Vectors for Simultaneous Detection of Multiple Protein−Protein Interactions in Plant Cells Using Bimolecular Fluorescence Complementation

    PubMed Central

    Hikino, Kazumi; Goto-Yamada, Shino; Nishimura, Mikio; Nakagawa, Tsuyoshi; Mano, Shoji

    2016-01-01

    Bimolecular fluorescence complementation (BiFC) is widely used to detect protein—protein interactions, because it is technically simple, convenient, and can be adapted for use with conventional fluorescence microscopy. We previously constructed enhanced yellow fluorescent protein (EYFP)-based Gateway cloning technology-compatible vectors. In the current study, we generated new Gateway cloning technology-compatible vectors to detect BiFC-based multiple protein—protein interactions using N- and C-terminal fragments of enhanced cyan fluorescent protein (ECFP), enhanced green fluorescent protein (EGFP), and monomeric red fluorescent protein (mRFP1). Using a combination of N- and C-terminal fragments from ECFP, EGFP and EYFP, we observed a shift in the emission wavelength, enabling the simultaneous detection of multiple protein—protein interactions. Moreover, we developed these vectors as binary vectors for use in Agrobacterium infiltration and for the generate transgenic plants. We verified that the binary vectors functioned well in tobacco cells. The results demonstrate that the BiFC vectors facilitate the design of various constructions and are convenient for the detection of multiple protein—protein interactions simultaneously in plant cells. PMID:27490375

  5. Simultaneous determination of structurally diverse compounds in different Fangchi species by UHPLC-DAD and UHPLC-ESI-MS/MS.

    PubMed

    Sim, Hee-Jung; Kim, Ji Hee; Lee, Kang Ro; Hong, Jongki

    2013-05-07

    Two bisbenzylisoquinoline alkaloids, two morphine alkaloids, one aporphine alkaloid, syringaresinol and aristolochic acid І were selected as marker compounds and simultaneously analyzed using an ultra-high pressure liquid chromatography-diode array detection (UHPLC-DAD) method. These marker compounds were used for the quality control of Fangchi species of different origins, including Sinomenium acutum, Stephania tetrandra, Cocculus trilobus and Aristolochia fangchi. A reversed-phase UHPLC-DAD method was developed and validated for the simultaneous quantification of structurally diverse markers in different Fangchi species. In addition, an UHPLC-electrospray ionization tandem mass spectrometry (ESI-MS/MS) method was used for marker identification in Fangchi species, which provided diagnostic MS/MS spectral patterns that were dependent upon the marker structures. The UHPLC-MS/MS data were used to confirm and complement the UHPLC-DAD quality evaluation results. Additionally, magnoflorine and syringaresinol were observed for the first time in S. tetrandra and C. trilobus, respectively. Twenty different Fangchi species samples were analyzed for aristolochic acid I, syringaresinol and the alkaloids using the UHPLC-DAD and MS/MS method. Based on the levels of markers and principal component analysis (PCA), this method allowed for the clear classification of the samples into four different groups representing samples originating from the four species.

  6. Simultaneous quantification of adrenergic amines and flavonoids in C. aurantium, various Citrus species, and dietary supplements by liquid chromatography.

    PubMed

    Avula, Bharathi; Upparapalli, Sampath Kumar; Navarrete, Andres; Khan, Ikhlas A

    2005-01-01

    An analytical method was developed for the simultaneous quantitative analysis of 6 amines and 20 flavonoids in fruits and extracts of 30 Citrus species, including C. aurantium, near-Citrus relatives, and dietary supplements by liquid chromatography with photodiode array detection. The separation was achieved with a Phenomenex Synergi Hydro reversed-phase column using gradient mobile phase of sodium acetate buffer (pH 5.5) and acetonitrile. Elution was run at a flow rate of 1.0 mL/min and UV at 254, 280, and 330 nm. Among the amines analyzed, synephrine, the main component, was present in the levels from 0.11 to 2.0 mg/g dry weight in 21 Citrus species and 0.07 to 18.62% in dietary supplements claiming to contain C. aurantium. The flavanones and flavones were analyzed in the same Citrus samples and were species-specific. The levels of flavones were very low compared with those of flavanones. The method facilitated the simultaneous quantification of 6 amines and 20 flavonoids in various Citrus species, the distinction between the different Citrus species, and the analysis of dietary supplements containing C. aurantium.

  7. Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

    PubMed

    Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

    2016-08-01

    Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species.

  8. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    PubMed

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity.

  9. Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species

    PubMed Central

    Guo, Wen-Ping; Tian, Jun-Hua; Lin, Xian-Dan; Ni, Xue-Bing; Chen, Xiao-Ping; Liao, Yong; Yang, Si-Yuan; Dumler, J. Stephen; Holmes, Edward C.; Zhang, Yong-Zhen

    2016-01-01

    Rickettsiales are important zoonotic pathogens, causing severe disease in humans globally. Although mosquitoes are an important vector for diverse pathogens, with the exception of members of the genus Wolbachia little is known about their role in the transmission of Rickettsiales. Herein, Rickettsiales were identified by PCR in five species of mosquitoes (Anopheles sinensis, Armigeres subalbatus, Aedes albopictus, Culex quinquefasciatus and Cu. tritaeniorhynchus) collected from three Chinese provinces during 2014–2015. Subsequent phylogenetic analyses of the rrs, groEL and gltA genes revealed the presence of Anaplasma, Ehrlichia, Candidatus Neoehrlichia, and Rickettsia bacteria in mosquitoes, comprising nine documented and five tentative species bacteria, as well as three symbionts/endosybionts. In addition, bacteria were identified in mosquito eggs, larvae, and pupae sampled from aquatic environments. Hence, these data suggest that Rickettsiales circulate widely in mosquitoes in nature. Also of note was that Ehrlichia and Rickettsia bacteria were detected in each life stage of laboratory cultured mosquitoes, suggesting that Rickettsiales may be maintained in mosquitoes through both transstadial and transovarial transmission. In sum, these data indicate that mosquitoes may have played an important role in the transmission and evolution of Rickettsiales in nature. PMID:27934910

  10. A planning study of simultaneous integrated boost with forward IMRT for multiple brain metastases

    SciTech Connect

    Liang, Xiaodong; Ni, Lingqin; Hu, Wei; Chen, Weijun; Ying, Shenpeng; Gong, Qiangjun; Liu, Yanmei

    2013-07-01

    The objective of this study was to evaluate the dose conformity and feasibility of whole-brain radiotherapy with a simultaneous integrated boost by forward intensity-modulated radiation therapy in patients with 1 to 3 brain metastases. Forward intensity-modulated radiation therapy plans were generated for 10 patients with 1 to 3 brain metastases on Pinnacle 6.2 Treatment Planning System. The prescribed dose was 30 Gy to the whole brain (planning target volume [PTV]{sub wbrt}) and 40 Gy to individual brain metastases (PTV{sub boost}) simultaneously, and both doses were given in 10 fractions. The maximum diameters of individual brain metastases ranged from 1.6 to 6 cm, and the summated PTVs per patient ranged from 1.62 to 69.81 cm{sup 3}. Conformity and feasibility were evaluated regarding conformation number and treatment delivery time. One hundred percent volume of the PTV{sub boost} received at least 95% of the prescribed dose in all cases. The maximum doses were less than 110% of the prescribed dose to the PTV{sub boost}, and all of the hot spots were within the PTV{sub boost}. The volume of the PTV{sub wbrt} that received at least 95% of the prescribed dose ranged from 99.2% to 100%. The mean values of conformation number were 0.682. The mean treatment delivery time was 2.79 minutes. Ten beams were used on an average in these plans. Whole-brain radiotherapy with a simultaneous integrated boost by forward intensity-modulated radiation therapy in 1 to 3 brain metastases is feasible, and treatment delivery time is short.

  11. Holographic 3D display observable for multiple simultaneous viewers from all horizontal directions by using a time division method.

    PubMed

    Sando, Yusuke; Barada, Daisuke; Yatagai, Toyohiko

    2014-10-01

    A holographic three-dimensional display system with a viewing angle of 360°, by using a high-speed digital micromirror device (DMD), has been proposed. The wavefront modulated by the DMD enters a rotating mirror tilted vertically downward. The synchronization of the rotating mirror and holograms displayed on the DMD allows for the reconstruction of a wavefront propagating in all horizontal directions. An optical experiment has been demonstrated in order to verify our proposed system. Binocular vision is realized from anywhere within the horizontal plane. Our display system enables simultaneous observation by multiple viewers at an extremely close range.

  12. Ca analysis: an Excel based program for the analysis of intracellular calcium transients including multiple, simultaneous regression analysis.

    PubMed

    Greensmith, David J

    2014-01-01

    Here I present an Excel based program for the analysis of intracellular Ca transients recorded using fluorescent indicators. The program can perform all the necessary steps which convert recorded raw voltage changes into meaningful physiological information. The program performs two fundamental processes. (1) It can prepare the raw signal by several methods. (2) It can then be used to analyze the prepared data to provide information such as absolute intracellular Ca levels. Also, the rates of change of Ca can be measured using multiple, simultaneous regression analysis. I demonstrate that this program performs equally well as commercially available software, but has numerous advantages, namely creating a simplified, self-contained analysis workflow.

  13. Detection of multiple Bartonella species in digestive and reproductive tissues of fleas collected from sympatric mammals.

    PubMed

    Brinkerhoff, R Jory; Kabeya, Hidenori; Inoue, Kai; Bai, Ying; Maruyama, Soichi

    2010-07-01

    At least 12 species in the genus Bartonella are zoonotic pathogens that may be transmitted among mammalian hosts by fleas or other arthropods. Apparent host specificity by some Bartonella species to mammalian hosts has been observed, and the detection of multiple Bartonella species in mammalian fleas suggests that fleas take bloodmeals from a variety of host species. However, many flea species are observed to parasitize a narrow host range. Therefore, we suspect that fleas may acquire Bartonella by a mechanism other than ingesting infectious blood. We found that detection of multiple Bartonella genotypes and species is apparently common in fleas and that the majority of fleas tested (5/9) carried Bartonella species atypical of their hosts. We also detected Bartonella DNA in flea reproductive tissues, suggesting that vertical transmission of this organism in vectors is possible, potentially leading to the accumulation of Bartonella diversity over time within fleas.

  14. A highly tunable system for the simultaneous expression of multiple enzymes in Saccharomyces cerevisiae.

    PubMed

    Ito, Yoichiro; Yamanishi, Mamoru; Ikeuchi, Akinori; Matsuyama, Takashi

    2015-01-16

    Control of the expression levels of multiple enzymes in transgenic yeasts is essential for the effective production of complex molecules through fermentation. Here, we propose a tunable strategy for the control of expression levels based on the design of terminator regions and other gene-expression control elements in Saccharomyces cerevisiae. Our genome-integrated system, which is capable of producing high expression levels over a wide dynamic range, will broadly enable metabolic engineering and synthetic biology. We demonstrated that the activities of multiple cellulases and the production of ethanol were doubled in a transgenic yeast constructed with our system compared with those achieved with a standard expression system.

  15. Simultaneous object classification and segmentation with high-order multiple shape models.

    PubMed

    Lecumberry, Federico; Pardo, Alvaro; Sapiro, Guillermo

    2010-03-01

    Shape models (SMs), capturing the common features of a set of training shapes, represent a new incoming object based on its projection onto the corresponding model. Given a set of learned SMs representing different objects classes, and an image with a new shape, this work introduces a joint classification-segmentation framework with a twofold goal. First, to automatically select the SM that best represents the object, and second, to accurately segment the image taking into account both the image information and the features and variations learned from the online selected model. A new energy functional is introduced that simultaneously accomplishes both goals. Model selection is performed based on a shape similarity measure, online determining which model to use at each iteration of the steepest descent minimization, allowing for model switching and adaptation to the data. High-order SMs are used in order to deal with very similar object classes and natural variability within them. Position and transformation invariance is included as part of the modeling as well. The presentation of the framework is complemented with examples for the difficult task of simultaneously classifying and segmenting closely related shapes, such as stages of human activities, in images with severe occlusions.

  16. ALDH2 Mediates 5-Nitrofuran Activity in Multiple Species

    PubMed Central

    Zhou, Linna; Ishizaki, Hironori; Spitzer, Michaela; Taylor, Kerrie L.; Temperley, Nicholas D.; Johnson, Stephen L.; Brear, Paul; Gautier, Philippe; Zeng, Zhiqiang; Mitchell, Amy; Narayan, Vikram; McNeil, Ewan M.; Melton, David W.; Smith, Terry K.; Tyers, Mike; Westwood, Nicholas J.; Patton, E. Elizabeth

    2012-01-01

    Summary Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of prodrugs widely used to treat bacterial and trypanosome infections, but despite relative specificity, 5-nitrofurans often cause serious toxic side effects in people. Here, we use yeast and zebrafish, as well as human in vitro systems, to assess the biological activity of 5-nitrofurans, and we identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome prodrug, is dependent on zebrafish Aldh2 and is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5-nitrofuran treatment. PMID:22840776

  17. Molecular and morphologic data reveal multiple species in Peromyscus pectoralis

    PubMed Central

    Bradley, Robert D.; Schmidly, David J.; Amman, Brian R.; Platt, Roy N.; Neumann, Kathy M.; Huynh, Howard M.; Muñiz-Martínez, Raúl; López-González, Celia; Ordóñez-Garza, Nicté

    2015-01-01

    DNA sequence and morphometric data were used to re-evaluate the taxonomy and systematics of Peromyscus pectoralis. Phylogenetic analyses (maximum likelihood and Bayesian inference) of DNA sequences from the mitochondrial cytochrome-b gene in 44 samples of P. pectoralis indicated 2 well-supported monophyletic clades. The 1st clade contained specimens from Texas historically assigned to P. p. laceianus; the 2nd was comprised of specimens previously referable to P. p. collinus, P. p. laceianus, and P. p. pectoralis obtained from northern and eastern Mexico. Levels of genetic variation (~7%) between these 2 clades indicated that the genetic divergence typically exceeded that reported for other species of Peromyscus. Samples of P. p. laceianus north and south of the Río Grande were not monophyletic. In addition, samples representing P. p. collinus and P. p. pectoralis formed 2 clades that differed genetically by 7.14%. Multivariate analyses of external and cranial measurements from 63 populations of P. pectoralis revealed 4 morpho-groups consistent with clades in the DNA sequence analysis: 1 from Texas and New Mexico assignable to P. p. laceianus; a 2nd from western and southern Mexico assignable to P. p. pectoralis; a 3rd from northern and central Mexico previously assigned to P. p. pectoralis but herein shown to represent an undescribed taxon; and a 4th from southeastern Mexico assignable to P. p. collinus. Based on the concordance of these results, populations from the United States are referred to as P. laceianus, whereas populations from Mexico are referred to as P. pectoralis (including some samples historically assigned to P. p. collinus, P. p. laceianus, and P. p. pectoralis). A new subspecies is described to represent populations south of the Río Grande in northern and central Mexico. Additional research is needed to discern if P. p. collinus warrants species recognition. PMID:26937045

  18. All Set! Evidence of Simultaneous Attentional Control Settings for Multiple Target Colors

    ERIC Educational Resources Information Center

    Irons, Jessica L.; Folk, Charles L.; Remington, Roger W.

    2012-01-01

    Although models of visual search have often assumed that attention can only be set for a single feature or property at a time, recent studies have suggested that it may be possible to maintain more than one attentional control setting. The aim of the present study was to investigate whether spatial attention could be guided by multiple attentional…

  19. Simultaneous determination of multiple (fluoro)quinolone antibiotics in food samples by a one-step fluorescence polarization immunoassay.

    PubMed

    Mi, Tiejun; Wang, Zhanhui; Eremin, Sergei A; Shen, Jianzhong; Zhang, Suxia

    2013-10-02

    This paper describes a rapid one-step fluorescence polarization immunoassay (FPIA) for the simultaneous determination of multiple (fluoro)quinolone antibiotics (FQs) in food samples. Several fluorescent tracers were synthesized and evaluated in the FPIA method based on a broad-specificity of monoclonal antibodies toward FQs. The heterogeneous tracer, SAR-5-FAM, was considered as the optimal choice to prepare the immunocomplex single reagent, which allows a rapid and sensitive displacement reaction by addition of analytes. Optimized single-reagent FPIA exhibited broad cross-reactivities in the range of 7.8-172.2% with 16 FQs tested and was capable of determining most FQs at the level of maximum residue limits. Recoveries for spiked milk and chicken muscle samples were from 77.8 to 116%, with relative standard deviation lower than 17.4%. Therefore, this method could be applicable in routine screening analysis of multiple FQ residues in food samples.

  20. Simultaneous inhibition of multiple oncogenic miRNAs by a multi-potent microRNA sponge.

    PubMed

    Jung, Jaeyun; Yeom, Chanjoo; Choi, Yeon-Sook; Kim, Sinae; Lee, EunJi; Park, Min Ji; Kang, Sang Wook; Kim, Sung Bae; Chang, Suhwan

    2015-08-21

    The roles of oncogenic miRNAs are widely recognized in many cancers. Inhibition of single miRNA using antagomiR can efficiently knock-down a specific miRNA. However, the effect is transient and often results in subtle phenotype, as there are other miRNAs contribute to tumorigenesis. Here we report a multi-potent miRNA sponge inhibiting multiple miRNAs simultaneously. As a model system, we targeted miR-21, miR-155 and miR-221/222, known as oncogenic miRNAs in multiple tumors including breast and pancreatic cancers. To achieve efficient knockdown, we generated perfect and bulged-matched miRNA binding sites (MBS) and introduced multiple copies of MBS, ranging from one to five, in the multi-potent miRNA sponge. Luciferase reporter assay showed the multi-potent miRNA sponge efficiently inhibited 4 miRNAs in breast and pancreatic cancer cells. Furthermore, a stable and inducible version of the multi-potent miRNA sponge cell line showed the miRNA sponge efficiently reduces the level of 4 target miRNAs and increase target protein level of these oncogenic miRNAs. Finally, we showed the miRNA sponge sensitize cells to cancer drug and attenuate cell migratory activity. Altogether, our study demonstrates the multi-potent miRNA sponge is a useful tool to examine the functional impact of simultaneous inhibition of multiple miRNAs and proposes a therapeutic potential.

  1. Simultaneous planning of the project scheduling and material procurement problem under the presence of multiple suppliers

    NASA Astrophysics Data System (ADS)

    Tabrizi, Babak H.; Farid Ghaderi, Seyed

    2016-09-01

    Simultaneous planning of project scheduling and material procurement can improve the project execution costs. Hence, the issue has been addressed here by a mixed-integer programming model. The proposed model facilitates the procurement decisions by accounting for a number of suppliers offering a distinctive discount formula from which to purchase the required materials. It is aimed at developing schedules with the best net present value regarding the obtained benefit and costs of the project execution. A genetic algorithm is applied to deal with the problem, in addition to a modified version equipped with a variable neighbourhood search. The underlying factors of the solution methods are calibrated by the Taguchi method to obtain robust solutions. The performance of the aforementioned methods is compared for different problem sizes, in which the utilized local search proved efficient. Finally, a sensitivity analysis is carried out to check the effect of inflation on the objective function value.

  2. Implementation of Multiple Spectroscopic Techniques to Simultaneously Observe Native and Mutated Protein Unfolding

    NASA Astrophysics Data System (ADS)

    Cull, Brennan; Ben, Kelty; Link, Justin

    A protein's natural, correctly folded structure can determine the protein's ability to carry out its function. If the unfolding process of proteins can be observed, then the relative stability can be better understood between native and mutated proteins. A global picture of the unfolding process may be completed through the studies of strategically mutated proteins using tryptophan as a probe. Horse heart cytochrome c, a thoroughly studied, model protein was used in our investigation to explore this idea. Various spectroscopic techniques such as circular dichroism (CD), absorbance, and fluorescence were simultaneously applied while slowly unfolding our protein by increasing the concentration of a chemical denaturant, guanidine hydrochloride. This provided us information about the thermodynamic properties of the protein and several mutants which can then be interpreted to gain relative stability information among mutations. Efforts to utilize these techniques on native and mutated proteins in comparison to current scientific unfolding theories will be presented in this session.

  3. In-situ determination of dispersion and resolving power in simultaneous multiple-angle XUV spectroscopy

    NASA Astrophysics Data System (ADS)

    Zastrau, U.; Hilbert, V.; Brown, C.; Döppner, T.; Dziarzhytski, S.; Förster, E.; Glenzer, S. H.; Göde, S.; Gregori, G.; Harmand, M.; Hochhaus, D.; Laarmann, T.; Lee, H. J.; Meiwes-Broer, K.-H.; Neumayer, P.; Przystawik, A.; Radcliffe, P.; Schulz, M.; Skruszewicz, S.; Tavella, F.; Tiggesbäumker, J.; Toleikis, S.; White, T.

    2011-10-01

    We report on the simultaneous determination of non-linear dispersion functions and resolving power of three flat-field XUV grating spectrometers. A moderate-intense short-pulse infrared laser is focused onto technical aluminum which is commonly present as part of the experimental setup. In the XUV wavelength range of 10-19 nm, the spectrometers are calibrated using Al-Mg plasma emission lines. This cross-calibration is performed in-situ in the very same setup as the actual main experiment. The results are in excellent agreement with ray-tracing simulations. We show that our method allows for precise relative and absolute calibration of three different XUV spectrometers.

  4. Double random phase encryption scheme to multiplex and simultaneous encode multiple images.

    PubMed

    Alfalou, Ayman; Mansour, Ali

    2009-11-01

    Here we present a new approach of multiplexing and simultaneous encoding of target images. Our approach can enhance the encryption level of a classical double random phase (DRP) encryption system by adding a supplementary security layer. The new approach can be divided into two security layers. The first layer is called the multiplexing level, which consists in using iterative Fourier transformations along with several encryption key images. These latter can be a set of biometric images. At the second layer, we use a classical DRP system. The two layers enable us to encode several target images (multi-encryption) and to reduce, at the same time, the requested decoded information (transmitted or storage information).

  5. Miniature stereo radio transmitter for simultaneous recording of multiple single-neuron signals from behaving owls.

    PubMed

    Nieder, A

    2000-09-15

    Wireless radiotelemetric transmission of neuronal activity is an elegant technique to study brain-behavior interaction in unrestrained animals. In the current study, a miniature FM-stereo radio transmitter is described that permitted simultaneous recordings from two microelectrodes in behaving barn owls. Input from two independent channels is multiplexed to form a stereo composite signal that modulates a radio frequency carrier. The high quality of broadcasted extracellular signals enabled separation of single units based on differences in spike waveforms. Recording several single cells from different electrodes allows the possibility of investigating correlations between small, distributed neuronal ensembles. Multi-channel radiotelemetry that meets the demands of modern electrophysiology might open a new perspective for combined behavioral/neurophysiological approaches in freely-behaving animals.

  6. Simultaneous and rapid determination of multiple component concentrations in a Kraft liquor process stream

    DOEpatents

    Li, Jian; Chai, Xin Sheng; Zhu, Junyoung

    2008-06-24

    The present invention is a rapid method of determining the concentration of the major components in a chemical stream. The present invention is also a simple, low cost, device of determining the in-situ concentration of the major components in a chemical stream. In particular, the present invention provides a useful method for simultaneously determining the concentrations of sodium hydroxide, sodium sulfide and sodium carbonate in aqueous kraft pulping liquors through use of an attenuated total reflectance (ATR) tunnel flow cell or optical probe capable of producing a ultraviolet absorbency spectrum over a wavelength of 190 to 300 nm. In addition, the present invention eliminates the need for manual sampling and dilution previously required to generate analyzable samples. The inventive method can be used in Kraft pulping operations to control white liquor causticizing efficiency, sulfate reduction efficiency in green liquor, oxidation efficiency for oxidized white liquor and the active and effective alkali charge to kraft pulping operations.

  7. Simultaneous SU(2) rotations on multiple quantum dot exciton qubits using a single shaped pulse

    NASA Astrophysics Data System (ADS)

    Mathew, Reuble; Yang, Hong Yi Shi; Hall, Kimberley C.

    2015-10-01

    Recent experimental demonstration of a parallel (π ,2 π ) single qubit rotation on excitons in two distant quantum dots [Nano Lett. 13, 4666 (2013), 10.1021/nl4018176] is extended in numerical simulations to the design of pulses for more general quantum state control, demonstrating the feasibility of full SU(2) rotations of each exciton qubit. Our results show that simultaneous high-fidelity quantum control is achievable within the experimentally accessible parameter space for commercial Fourier-domain pulse shaping systems. The identification of a threshold of distinguishability for the two quantum dots (QDs) for achieving high-fidelity parallel rotations, corresponding to a difference in transition energies of ˜0.25 meV , points to the possibility of controlling more than 10 QDs with a single shaped optical pulse.

  8. Large Roads Reduce Bat Activity across Multiple Species

    PubMed Central

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations. PMID:24823689

  9. Large roads reduce bat activity across multiple species.

    PubMed

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.

  10. Online evaluation of novel choices by simultaneous representation of multiple memories

    PubMed Central

    Barron, Helen C; Dolan, Raymond J; Behrens, Timothy E J

    2014-01-01

    Prior experience plays a critical role in decision making. It enables explicit representation of potential outcomes and provides training to valuation mechanisms. However, we can also make choices in the absence of prior experience, by merely imagining the consequences of a new experience. Here, using fMRI repetition suppression in humans, we show how neuronal representations of novel rewards can be constructed and evaluated. A likely novel experience is constructed by invoking multiple independent memories within hippocampus and medial prefrontal cortex. This construction persists for only a short time period, during which new associations are observed between the memories for component items. Together these findings suggest that in the absence of direct experience, co-activation of multiple relevant memories can provide a training signal to the valuation system which allows the consequences of new experiences to be imagined and acted upon. PMID:24013592

  11. Space-time delta-sigma modulation for reception of multiple simultaneous independent RF beams

    NASA Astrophysics Data System (ADS)

    Rong, Guoguang; Black, Bruce A.; Siahmakoun, Azad Z.

    2005-09-01

    In this paper we introduce and analyze a multiple-RF-beam beamformer in receive mode utilizing the principle of space-time delta-sigma modulation. This principle is based on sampling input signals in both time and space and converting the sampled signals into a digital format by delta-sigma conversion. Noise shaping is achieved in 2D frequency domain. We show that the modulator can receive signals of narrow and wide bandwidths with steering capability, can receive multiple beams, and establish tradeoffs between sampling in time and in space. The ability of the modulator to trade off between time and space provides an effective way to sample high frequency RF signals without down conversion. In addition, a space-time delta-sigma modulator has better performance than a solely temporal delta-sigma modulator (for the same filter order), as is typically used in communication systems to digitize the down-converted analog signals.

  12. A Bose-condensed, simultaneous dual-species Mach-Zehnder atom interferometer

    NASA Astrophysics Data System (ADS)

    Kuhn, C. C. N.; McDonald, G. D.; Hardman, K. S.; Bennetts, S.; Everitt, P. J.; Altin, P. A.; Debs, J. E.; Close, J. D.; Robins, N. P.

    2014-07-01

    This paper presents the first realization of a simultaneous 87Rb-85Rb Mach-Zehnder atom interferometer with Bose-condensed atoms. A number of ambitious proposals for precise terrestrial and space based tests of the weak equivalence principle rely on such a system. This implementation utilizes hybrid magnetic-optical trapping to produce spatially overlapped condensates with a repetition rate of 20 s. A horizontal optical waveguide with co-linear Bragg beamsplitters and mirrors is used to simultaneously address both isotopes in the interferometer. We observe a non-linear phase shift on a non-interacting 85Rb interferometer as a function of interferometer time, T, which we show arises from inter-isotope scattering with the co-incident 85Rb interferometer. A discussion of implications for future experiments is given.

  13. Complete inhibition of tobamovirus multiplication by simultaneous mutations in two homologous host genes.

    PubMed

    Yamanaka, Takuya; Imai, Takahiro; Satoh, Rena; Kawashima, Arata; Takahashi, Miki; Tomita, Kayo; Kubota, Kenji; Meshi, Tetsuo; Naito, Satoshi; Ishikawa, Masayuki

    2002-03-01

    The TOM1 gene of Arabidopsis thaliana encodes a putative multipass transmembrane protein which is necessary for the efficient multiplication of tobamoviruses. We have previously shown that mutations severely destructive to the TOM1 gene reduce tobamovirus multiplication to low levels but do not impair it completely. In this report, we subjected one of the tom1 mutants (tom1-1) to another round of mutagenesis and isolated a new mutant which did not permit a detectable level of tobamovirus multiplication. In addition to tom1-1, this mutant carried a mutation referred to as tom3-1. Positional cloning showed that TOM3 was one of two TOM1-like genes in Arabidopsis. Based on the similarity between the amino acid sequences of TOM1 and TOM3, together with the results of a Sos recruitment assay suggesting that both TOM1 and TOM3 bind tobamovirus-encoded replication proteins, we propose that TOM1 and TOM3 play parallel and essential roles in the replication of tobamoviruses.

  14. Multiple Developmental Dental Anomalies in a Non-Syndromic Patient: Report of a Rare Simultaneous Occurrence

    PubMed Central

    Ghasempour, Maryam; Hemmati, Samane; Mooudi, Ehsan

    2015-01-01

    A case of multiple pulp stones, a supernumerary tooth and a congenitally missing tooth accompanied by several developmental dental anomalies concurrently affecting the upper and lower anterior teeth in an Iranian healthy girl is reported. Developmental tooth abnormalities are usually found in conjunction with certain diseases or conditions. In the present case, although the patient had consanguineous parents and the role of genetics should be considered particularly for autosomal recessive traits, based on the child’s family and medical history, no correlation could be established between dental findings and systemic or metabolic diseases. PMID:26877734

  15. Simultaneous Detection of Multiple Fish Pathogens Using a Naked-Eye Readable DNA Microarray

    PubMed Central

    Chang, Chin-I; Hung, Pei-Hsin; Wu, Chia-Che; Cheng, Ta Chih; Tsai, Jyh-Ming; Lin, King-Jung; Lin, Chung-Yen

    2012-01-01

    We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum) commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer) complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3′-indolylphosphate, p-toluidine salt (NBT/BCIP), resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 103 CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens. PMID:22736973

  16. Simultaneous analysis of multiple neurotransmitters by hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry.

    PubMed

    Tufi, Sara; Lamoree, Marja; de Boer, Jacob; Leonards, Pim

    2015-05-22

    Neurotransmitters are endogenous metabolites that allow the signal transmission across neuronal synapses. Their biological role is crucial for many physiological functions and their levels can be changed by several diseases. Because of their high polarity, hydrophilic interaction liquid chromatography (HILIC) is a promising tool for neurotransmitter analysis. Due to the large number of HILIC stationary phases available, an evaluation of the column performances and retention behaviors has been performed on five different commercial HILIC packing materials (silica, amino, amide and two zwitterionic stationary phases). Several parameters like the linear correlation between retention and the distribution coefficient (logD), the separation factor k and the column resolution Rs have been investigated and the column performances have been visualized with a heat map and hierarchical clustering analysis. An optimized and validated HILIC-MS/MS method based on the ZIC-cHILIC column is proposed for the simultaneous detection and quantification of twenty compounds consisting of neurotransmitters, precursors and metabolites: 3-methoxytyramine (3-MT), 5-hydroxyindoleacetic acid (5-HIAA), 5-hydroxy-L-tripthophan, acetylcholine, choline, L-3,4-dihydroxyphenylalanine (L-DOPA), dopamine, epinephrine, γ-aminobutyric acid (GABA), glutamate, glutamine, histamine, histidine, L-tryptophan, L-tyrosine, norepinephrine, normetanephrine, phenylalanine, serotonin and tyramine. The method was applied to neuronal metabolite profiling of the central nervous system of the freshwater snail Lymnaea stagnalis. This method is suitable to explore neuronal metabolism and its alteration in different biological matrices.

  17. Frequency scanning interferometry in ATLAS: remote, multiple, simultaneous and precise distance measurements in a hostile environment

    NASA Astrophysics Data System (ADS)

    Coe, P. A.; Howell, D. F.; Nickerson, R. B.

    2004-11-01

    ATLAS is the largest particle detector under construction at CERN Geneva. Frequency scanning interferometry (FSI), also known as absolute distance interferometry, will be used to monitor shape changes of the SCT (semiconductor tracker), a particle tracker in the inaccessible, high radiation environment at the centre of ATLAS. Geodetic grids with several hundred fibre-coupled interferometers (30 mm to 1.5 m long) will be measured simultaneously. These lengths will be measured by tuning two lasers and comparing the resulting phase shifts in grid line interferometers (GLIs) with phase shifts in a reference interferometer. The novel inexpensive GLI design uses diverging beams to reduce sensitivity to misalignment, albeit with weaker signals. One micrometre precision length measurements of grid lines will allow 10 µm precision tracker shape corrections to be fed into ATLAS particle tracking analysis. The technique was demonstrated by measuring a 400 mm interferometer to better than 400 nm and a 1195 mm interferometer to better than 250 nm. Precise measurements were possible, even with poor quality signals, using numerical analysis of thousands of intensity samples. Errors due to drifts in interferometer length were substantially reduced using two lasers tuned in opposite directions and the precision was further improved by linking measurements made at widely separated laser frequencies.

  18. Simultaneous analysis of multiple serum proteins adhering to the surface of medical grade polydimethylsiloxane elastomers.

    PubMed

    Backovic, Aleksandar; Wolfram, Dolores; Del-Frari, Barbara; Piza, Hildegunde; Huber, Lukas A; Wick, Georg

    2007-12-01

    Although polydimethylsiloxane (PDMS, silicone) elastomers are presumed to be chemically inert and of negligible toxicity, they induce a prompt acute inflammatory response with subsequent fibrotic reactions. Since local inflammatory and fibrotic side effects are associated with the proteinaceous film on the surface of silicone implants, the process of protein adherence to silicone is of practical medical relevance, and interesting from theoretical, clinical and biotechnological perspectives. It is hypothesized that the systemic side effects resembling rheumatoid and other connective tissue diseases may be triggered by local immunological changes, but this functional relationship has yet to be defined. Because the proteinaceous film on the surface of silicone has been identified as a key player in the activation of host defense mechanisms, we propose a test system based on a proteomics screen to simultaneously identify proteins adsorbed from serum to the surface of silicone. Herein, we describe protein adsorption kinetics on the surface of silicone implants, correlate the adhesion properties of serum proteins with the occurrence of adverse reactions to silicone, and successfully discriminate their signature on the silicone surface in a blinded study of patients suffering from fibrotic reactions (as determined by Baker scale) to silicone implants.

  19. All set! Evidence of simultaneous attentional control settings for multiple target colors.

    PubMed

    Irons, Jessica L; Folk, Charles L; Remington, Roger W

    2012-06-01

    Although models of visual search have often assumed that attention can only be set for a single feature or property at a time, recent studies have suggested that it may be possible to maintain more than one attentional control setting. The aim of the present study was to investigate whether spatial attention could be guided by multiple attentional control settings for color. In a standard spatial cueing task, participants searched for either of two colored targets accompanied by an irrelevantly colored distractor. Across five experiments, results consistently showed that nonpredictive cues matching either target color produced a significant spatial cueing effect, while irrelevantly colored cues did not. This was the case even when the target colors could not be linearly separated from irrelevantly cue colors in color space, suggesting that participants were not simply adopting one general color set that included both target colors. The results could not be explained by intertrial priming by previous targets, nor could they be explained by a single inhibitory set for the distractor color. Overall, the results are most consistent with the maintenance of multiple attentional control settings.

  20. Simultaneous multiple-excitation multiphoton microscopy yields increased imaging sensitivity and specificity

    PubMed Central

    2011-01-01

    Background Multiphoton microscopy (MPM) offers many advantages over conventional wide-field and confocal laser scanning microscopy (CLSM) for imaging biological samples such as 3D resolution of excitation, reduced phototoxicity, and deeper tissue imaging. However, adapting MPM for critical multi-color measurements presents a challenge because of the largely overlapping two-photon absorption (TPA) peaks of common biological fluorophores. Currently, most multi-color MPM relies on the absorbance at one intermediate wavelength of multiple dyes, which introduces problems such as decreased and unequal excitation efficiency across the set of dyes. Results Here we describe an MPM system incorporating two, independently controlled sources of two-photon excitation whose wavelengths are adjusted to maximally excite one dye while minimally exciting the other. We report increased signal-to-noise ratios and decreased false positive emission bleed-through using this novel multiple-excitation MPM (ME-MPM) compared to conventional single-excitation MPM (SE-MPM) in a variety of multi-color imaging applications. Conclusions Similar to the tremendous gain in popularity of CLSM after the introduction of multi-color imaging, we anticipate that the ME-MPM system will further increase the popularity of MPM. In addition, ME-MPM provides an excellent tool to more rapidly design and optimize pairs of fluorescence probes for multi-color two-photon imaging, such as CFP/YFP or GFP/DsRed for CLSM. PMID:21366923

  1. Journey to Flexible, Reliable, Laboratory Platform for Simultaneous Control of Multiple Reactive Power Producing Devices

    SciTech Connect

    Foster, Jason; Rizy, D Tom; Kueck, John D

    2007-01-01

    Herein is discussed the instrumentation and control requirements for achieving the goal of operating multiple Distributed Energy (DE) devices in parallel to regulate local voltage. The process for establishing the flexible laboratory control and data acquisition system that allows for the integration of multiple Distributed Energy (DE) devices in XXXX Laboratory's Distributed Energy - Communications and Controls Laboratory (DECC) is discussed. The DE devices control local distribution system voltage through dynamic reactive power production. Although original efforts were made to control the reactive power (RP) output using information from commercially available meters specifically designed for monitoring and analyzing electric power values, these "intelligent" meters did not provide the flexibility needed. A very flexible and capable real-time monitoring and control system was selected after the evaluation of various methods of data acquisition (DAQ) and control. The purpose of this paper is to describe the DAQ and controls system development. The chosen controller is a commercially available real-time controller from dSPACE. This controller has many excellent features including a very easy programming platform through Simulink and Matlab's Real Time Workshop. The dSPACE system proved to provide both the flexibility and expandability needed to integrate and control the RP producing devices under consideration. The desire was to develop controls with this flexible laboratory instrumentation and controls setup that could be eventually be included in an embedded controller on a DE device. Some experimental results are included that clearly show that some functional control strategies are currently being tested.

  2. Development of a standardized sequential extraction protocol for simultaneous extraction of multiple actinide elements

    DOE PAGES

    Faye, Sherry A.; Richards, Jason M.; Gallardo, Athena M.; ...

    2017-02-07

    Sequential extraction is a useful technique for assessing the potential to leach actinides from soils; however, current literature lacks uniformity in experimental details, making direct comparison of results impossible. This work continued development toward a standardized five-step sequential extraction protocol by analyzing extraction behaviors of 232Th, 238U, 239,240Pu and 241Am from lake and ocean sediment reference materials. Results produced a standardized procedure after creating more defined reaction conditions to improve method repeatability. A NaOH fusion procedure is recommended following sequential leaching for the complete dissolution of insoluble species.

  3. Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction.

    PubMed

    Soon, Villu; Saarma, Urmas

    2011-07-01

    The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute

  4. A dynamic factor modeling framework for analyzing multiple groundwater head series simultaneously

    NASA Astrophysics Data System (ADS)

    Berendrecht, W. L.; van Geer, F. C.

    2016-05-01

    In this paper we present an approach in which we combine a dynamic factor model (DFM) and predefined response functions to analyze a set of groundwater head series simultaneously. Each groundwater head series is decomposed into: (a) one or more deterministic components as a response to known driving forces, (b) one or more common dynamic factors, representing spatial patterns not related to any of the input series and (c) one specific dynamic factor for each groundwater head series, describing unique variation for that series. The approach reduces the degrees of freedom for each response function, enables the application to irregular observed data, and exploits the correlation between residual series of a set of groundwater head series. The common dynamic factors may be interpreted as spatial patterns due to e.g. limitations in the model specification or concept, spatially correlated errors in input variables, or driving forces which have not been included in the model. In the latter case the model can be applied in the context of an alarming system, e.g. to monitor regional trends. The specific dynamic factor depicts the variation of a particular groundwater head series that cannot be related to any other time series of the set nor to any input series. Therefore the specific dynamic factor is suitable for analyzing local variations and detecting incidental measurement errors, for example in a quality control procedure. The DFM framework is illustrated with a set of 8 groundwater head series and applied for filling gaps in time series, reconstructing high-frequency data, and detecting outliers.

  5. A technology platform to assess multiple cancer agents simultaneously within a patient's tumor

    PubMed Central

    Klinghoffer, Richard A.; Frazier, Jason P.; Moreno-Gonzalez, Alicia; Strand, Andrew D.; Kerwin, William S.; Casalini, Joseph R.; Thirstrup, Derek J.; You, Sheng; Morris, Shelli M.; Watts, Korashon L.; Veiseh, Mandana; Grenley, Marc O.; Tretyak, Ilona; Dey, Joyoti; Carleton, Michael; Beirne, Emily; Pedro, Kyle D.; Ditzler, Sally H.; Girard, Emily J.; Deckwerth, Thomas L.; Bertout, Jessica A.; Meleo, Karri A.; Filvaroff, Ellen H.; Chopra, Rajesh; Press, Oliver W.; Olson, James M.

    2016-01-01

    A fundamental problem in cancer drug development is that antitumor efficacy in preclinical cancer models does not translate faithfully to patient outcomes. Much of early cancer drug discovery is performed under in vitro conditions in cell-based models that poorly represent actual malignancies. To address this inconsistency, we have developed a technology platform called CIVO, which enables simultaneous assessment of up to eight drugs or drug combinations within a single solid tumor in vivo. The platform is currently designed for use in animal models of cancer and patients with superficial tumors but can be modified for investigation of deeper-seated malignancies. In xenograft lymphoma models, CIVO microinjection of well-characterized anticancer agents (vincristine, doxorubicin, mafosfamide, and prednisolone) induced spatially defined cellular changes around sites of drug exposure, specific to the known mechanisms of action of each drug. The observed localized responses predicted responses to systemically delivered drugs in animals. In pair-matched lymphoma models, CIVO correctly demonstrated tumor resistance to doxorubicin and vincristine and an unexpected enhanced sensitivity to mafosfamide in multidrug-resistant lymphomas compared with chemotherapy-naïve lymphomas. A CIVO-enabled in vivo screen of 97 approved oncology agents revealed a novel mTOR (mammalian target of rapamycin) pathway inhibitor that exhibits significantly increased tumor-killing activity in the drug-resistant setting compared with chemotherapy-naïve tumors. Finally, feasibility studies to assess the use of CIVO in human and canine patients demonstrated that microinjection of drugs is toxicity-sparing while inducing robust, easily tracked, drug-specific responses in autochthonous tumors, setting the stage for further application of this technology in clinical trials. PMID:25904742

  6. Simultaneous and rapid detection of multiple pesticide and veterinary drug residues by suspension array technology.

    PubMed

    Liu, Nan; Gao, Zhixian; Ma, Hongwei; Su, Pu; Ma, Xinhua; Li, Xiaoli; Ou, Guorong

    2013-03-15

    Suspension array technology is proposed for the simultaneous quantitative determination of seven kinds of pesticide and veterinary drug residues, namely, atrazine, chloramphenicol, carbaryl, clenbuterol, 17-β-estradiol, imidacloprid, and tylosin. The assay is simple and can be accomplished within 2h without repeated pumping and washing steps unlike conventional suspension arrays. The hapten-protein conjugate-coated beads bind to their complementary biotinylated antibodies using a competitive immunoassay format. The coefficients of determination R(2) for six targets were greater than 0.992, whereas that for atrazine was 0.961, which indicate good logistic correlations. The dynamic ranges for the seven targets in the 7-plex assay ranged from 2 log units to 4 log units(1.60×10(0)-1.64×10(3), 5.12×10(-2)-1.60×10(2), 1.00×10(0)-3.13×10(3), 4.00×10(-1)-4.10×10(2), 4.00×10(-1)-4.10×10(2), 5.12×10(-2)-1.60×10(2), and 2.00×10(0)-4.00×10(2)ngmL(-1)). The minimum detection concentrations of chloramphenicol, carbaryl, clenbuterol and 17-β-estradiol in the suspension array (0.05, 1.00, 0.40 and 0.40 ng mL(-1)) were lower than the corresponding limits of detection (0.25, 6.60, 24.23 and 13.96 ng mL(-1)) of using an indirect competitive enzyme-linked immunosorbent assay. Environmental scanning electron microscope was employed to characterize the bead surface, which directly confirmed the reactions on the beads. The suspension array is more flexible and feasible than ELISA for the fast quantitative analysis of pesticide and veterinary drug residues.

  7. Trade-off between multiple constraints enables simultaneous formation of modules and hubs in neural systems.

    PubMed

    Chen, Yuhan; Wang, Shengjun; Hilgetag, Claus C; Zhou, Changsong

    2013-01-01

    The formation of the complex network architecture of neural systems is subject to multiple structural and functional constraints. Two obvious but apparently contradictory constraints are low wiring cost and high processing efficiency, characterized by short overall wiring length and a small average number of processing steps, respectively. Growing evidence shows that neural networks are results from a trade-off between physical cost and functional value of the topology. However, the relationship between these competing constraints and complex topology is not well understood quantitatively. We explored this relationship systematically by reconstructing two known neural networks, Macaque cortical connectivity and C. elegans neuronal connections, from combinatory optimization of wiring cost and processing efficiency constraints, using a control parameter α, and comparing the reconstructed networks to the real networks. We found that in both neural systems, the reconstructed networks derived from the two constraints can reveal some important relations between the spatial layout of nodes and the topological connectivity, and match several properties of the real networks. The reconstructed and real networks had a similar modular organization in a broad range of α, resulting from spatial clustering of network nodes. Hubs emerged due to the competition of the two constraints, and their positions were close to, and partly coincided, with the real hubs in a range of α values. The degree of nodes was correlated with the density of nodes in their spatial neighborhood in both reconstructed and real networks. Generally, the rebuilt network matched a significant portion of real links, especially short-distant ones. These findings provide clear evidence to support the hypothesis of trade-off between multiple constraints on brain networks. The two constraints of wiring cost and processing efficiency, however, cannot explain all salient features in the real networks. The

  8. Simultaneous imaging of multiple neurotransmitters and neuroactive substances in the brain by desorption electrospray ionization mass spectrometry.

    PubMed

    Shariatgorji, Mohammadreza; Strittmatter, Nicole; Nilsson, Anna; Källback, Patrik; Alvarsson, Alexandra; Zhang, Xiaoqun; Vallianatou, Theodosia; Svenningsson, Per; Goodwin, Richard J A; Andren, Per E

    2016-08-01

    With neurological processes involving multiple neurotransmitters and neuromodulators, it is important to have the ability to directly map and quantify multiple signaling molecules simultaneously in a single analysis. By utilizing a molecular-specific approach, namely desorption electrospray ionization mass spectrometry imaging (DESI-MSI), we demonstrated that the technique can be used to image multiple neurotransmitters and their metabolites (dopamine, dihydroxyphenylacetic acid, 3-methoxytyramine, serotonin, glutamate, glutamine, aspartate, γ-aminobutyric acid, adenosine) as well as neuroactive drugs (amphetamine, sibutramine, fluvoxamine) and drug metabolites in situ directly in brain tissue sections. The use of both positive and negative ionization modes increased the number of identified molecular targets. Chemical derivatization by charge-tagging the primary amines of molecules significantly increased the sensitivity, enabling the detection of low abundant neurotransmitters and other neuroactive substances previously undetectable by MSI. The sensitivity of the imaging approach of neurochemicals has a great potential in many diverse applications in fields such as neuroscience, pharmacology, drug discovery, neurochemistry, and medicine.

  9. Chemical species separation with simultaneous estimation of field map and T2* using a k-space formulation.

    PubMed

    Honorato, Jose Luis; Parot, Vicente; Tejos, Cristian; Uribe, Sergio; Irarrazaval, Pablo

    2012-08-01

    Chemical species separation techniques in image space are prone to incorporate several distortions. Some of these are signal accentuation in borders and geometrical warping from field inhomogeneity. These errors come from neglecting intraecho time variations. In this work, we present a new approach for chemical species separation in MRI with simultaneous estimation of field map and T2* decay, formulated entirely in k-space. In this approach, the time map is used to model the phase accrual from off-resonance precession and also the amplitude decay due to T2*. Our technique fits the signal model directly in k-space with the acquired data minimizing the l(2)-norm with an interior-point algorithm. Standard two dimensional gradient echo sequences in the thighs and head were used for demonstrating the technique. With this approach, we were able to obtain excellent estimation for the species, the field inhomogeneity, and T2* decay images. The results do not suffer from geometric distortions derived from the chemical shift or the field inhomogeneity. Importantly, as the T2* map is well positioned, the species signal in borders is correctly estimated. Considering intraecho time variations in a complete signal model in k-space for separating species yields superior estimation of the variables of interest when compared to existing methods.

  10. True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex

    PubMed Central

    2013-01-01

    Background Species are the fundamental units in evolutionary biology. However, defining them as evolutionary independent lineages requires integration of several independent sources of information in order to develop robust hypotheses for taxonomic classification. Here, we exemplarily propose an integrative framework for species delimitation in the “brown lemur complex” (BLC) of Madagascar, which consists of seven allopatric populations of the genus Eulemur (Primates: Lemuridae), which were sampled extensively across northern, eastern and western Madagascar to collect fecal samples for DNA extraction as well as recordings of vocalizations. Our data base was extended by including museum specimens with reliable identification and locality information for skull shape and pelage color analysis. Results Between-group analyses of principal components revealed significant heterogeneity in skull shape, pelage color variation and loud calls across all seven populations. Furthermore, post-hoc statistical tests between pairs of populations revealed considerable discordance among different data sets for different dyads. Despite a high degree of incomplete lineage sorting among nuclear loci, significant exclusive ancestry was found for all populations, except for E. cinereiceps, based on one mitochondrial and three nuclear genetic loci. Conclusions Using several independent lines of evidence, our results confirm the species status of the members of the BLC under the general lineage concept of species. More generally, the present analyses demonstrate the importance and value of integrating different kinds of data in delimiting recently evolved radiations. PMID:24159931

  11. Simultaneous Identification of Four "Legal High" Plant Species in a Multiplex PCR High-Resolution Melt Assay().

    PubMed

    Elkins, Kelly M; Perez, Anjelica C U; Quinn, Alicia A

    2016-12-13

    The international prevalence of "legal high" drugs necessitates the development of a method for their detection and identification. Herein, we describe the development and validation of a tetraplex multiplex real-time polymerase chain reaction (PCR) assay used to simultaneously identify morning glory, jimson weed, Hawaiian woodrose, and marijuana detected by high-resolution melt using LCGreen Plus(®) . The PCR assay was evaluated based on the following: (i) specificity and selectivity-primers were tested on DNA extracted from 30 species and simulated forensic samples, (ii) sensitivity-serial dilutions of the target DNA were prepared, and (iii) reproducibility and reliability-sample replicates were tested and remelted on different days. The assay is ideal for cases in which inexpensive assays are needed to quickly detect and identify trace biological material present on drug paraphernalia that is too compromised for botanical microscopic identification and for which analysts are unfamiliar with the morphology of the emerging "legal high" species.

  12. A method for rapid and simultaneous mapping of genetic loci and introgression sizes in nematode species.

    PubMed

    Yan, Cheung; Bi, Yu; Yin, Da; Zhao, Zhongying

    2012-01-01

    Caenorhabditis briggsae is emerging as an attractive model organism not only in studying comparative biology against C. elegans, but also in developing novel experimentation avenues. In particular, recent identification of a new Caenorhabditis species, C. sp.9 with which it can mate and produce viable progeny provides an opportunity for studying the genetics of hybrid incompatibilities (HI) between the two. Mapping of a specific HI locus demands repeated backcrossing to get hold of the specific genomic region underlying an observed phenotype. To facilitate mapping of HI loci between C. briggsae and C. sp.9, an efficient mapping method and a genetic map ideally consisting of dominant markers are required for systematic introgression of genomic fragments between the two species. We developed a fast and cost-effective method for high throughput mapping of dominant loci with resolution up to 1 million bps in C. briggsae. The method takes advantage of the introgression between C. briggsae and C. sp.9 followed by PCR genotyping using C. briggsae specific primers. Importantly, the mapping results can not only serve as an effective way for estimating the chromosomal position of a genetic locus in C. briggsae, but also provides size information for the introgression fragment in an otherwise C. sp.9 background. In addition, it also helps generate introgression line as a side-product that is invaluable for the subsequent mapping of HI loci. The method will greatly facilitate the construction of a genetic map consisting of dominant markers and pave the way for systematic isolation of HI loci between C. briggsae and C. sp.9 which has so far not been attempted between nematode species. The method is designed for mapping of a dominant allele, but can be easily adapted for mapping of any other type of alleles in any other species if introgression between a sister species pair is feasible.

  13. Portable simultaneous multiple analyte whole-blood analyzer for point-of-care testing.

    PubMed

    Schembri, C T; Ostoich, V; Lingane, P J; Burd, T L; Buhl, S N

    1992-09-01

    We describe a portable clinical chemistry analyzer for point-of-care measurements of multiple analytes in less than 10 min from approximately 40 microL of whole blood (fingerstick or venous). Whole blood is applied directly to a 7.9-cm-diameter, single-use plastic rotor containing liquid diluent and greater than or equal to 4-12 tests in the form of 1- to 2-mm-diameter dry reagent beads. The reagent/rotor is immediately placed in a portable instrument along with a ticket/label results card. As the instrument spins the rotor, capillary and rotational forces process the blood into diluted plasma, distribute the patient's diluted sample to cuvettes containing the reagent beads, and mix the diluted sample with the reagents. The instrument monitors the chemical reactions optically at nine wavelengths; sample volume and temperature are also measured optically. The calibration data for each reagent are read from a bar code on the periphery of each rotor. The instrument processes all the measurements to calculate, store, print, and communicate the results. Each reagent/rotor contains an enzymatic control that must be within a defined range before the results from that analysis are reported.

  14. Microfluidic assay for simultaneous culture of multiple cell types on surfaces or within hydrogels

    PubMed Central

    Shin, Yoojin; Han, Sewoon; Jeon, Jessie S.; Yamamoto, Kyoko; Zervantonakis, Ioannis K.; Sudo, Ryo; Kamm, Roger D.; Chung, Seok

    2014-01-01

    This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel incorporating chambers between surface-accessible microchannels. Using this platform, well-defined biochemical and biophysical stimuli can be applied to multiple cell types interacting over distances of <1mm, thereby replicating many aspects of the in vivo microenvironment. Capabilities exist for time-dependent manipulation of flows and concentration gradients as well as high-resolution real-time imaging for observing spatial-temporal single cell behavior, cell-cell communication, cell-matrix interactions and cell population dynamics. These heterotypic cell type assays can be used to study cell survival, proliferation, migration, morphogenesis and differentiation under controlled conditions. Applications include the study of previously unexplored cellular interactions, and have already provided new insights into how biochemical and biophysical factors regulate interactions between populations of different cell types. It takes 3 days to fabricate the system and experiments can run for up to several weeks. PMID:22678430

  15. ESCRT-0 assembles as a heterotetrameric complex on membranes and binds multiple ubiquitinylated cargoes simultaneously.

    PubMed

    Mayers, Jonathan R; Fyfe, Ian; Schuh, Amber L; Chapman, Edwin R; Edwardson, J Michael; Audhya, Anjon

    2011-03-18

    The ESCRT machinery consists of multiple protein complexes that collectively participate in the biogenesis of multivesicular endosomes (MVEs). The ESCRT-0 complex is composed of two subunits, Hrs and STAM, both of which can engage ubiquitinylated substrates destined for lysosomal degradation. Here, we conduct a comprehensive analysis of ESCRT-0:ubiquitin interactions using isothermal titration calorimetry and define the affinity of each ubiquitin-binding domain (UBD) within the intact ESCRT-0 complex. Our data demonstrate that ubiquitin binding is non-cooperative between the ESCRT-0 UBDs. Additionally, our findings show that the affinity of the Hrs double ubiquitin interacting motif (DUIM) for ubiquitin is more than 2-fold greater than that of UBDs found in STAM, suggesting that Hrs functions as the major ubiquitin-binding protein in ESCRT-0. In vivo, Hrs and STAM localize to endosomal membranes. To study recombinant ESCRT-0 assembly on lipid bilayers, we used atomic force microscopy. Our data show that ESCRT-0 forms mostly heterodimers and heterotetramers of Hrs and STAM when analyzed in the presence of membranes. Consistent with these findings, hydrodynamic analysis of endogenous ESCRT-0 indicates that it exists largely as a heterotetrameric complex of its two subunits. Based on these data, we present a revised model for ESCRT-0 function in cargo recruitment and concentration at the endosome.

  16. Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling

    PubMed Central

    Sillanpää, M J; Pikkuhookana, P; Abrahamsson, S; Knürr, T; Fries, A; Lerceteau, E; Waldmann, P; García-Gil, M R

    2012-01-01

    A novel hierarchical quantitative trait locus (QTL) mapping method using a polynomial growth function and a multiple-QTL model (with no dependence in time) in a multitrait framework is presented. The method considers a population-based sample where individuals have been phenotyped (over time) with respect to some dynamic trait and genotyped at a given set of loci. A specific feature of the proposed approach is that, instead of an average functional curve, each individual has its own functional curve. Moreover, each QTL can modify the dynamic characteristics of the trait value of an individual through its influence on one or more growth curve parameters. Apparent advantages of the approach include: (1) assumption of time-independent QTL and environmental effects, (2) alleviating the necessity for an autoregressive covariance structure for residuals and (3) the flexibility to use variable selection methods. As a by-product of the method, heritabilities and genetic correlations can also be estimated for individual growth curve parameters, which are considered as latent traits. For selecting trait-associated loci in the model, we use a modified version of the well-known Bayesian adaptive shrinkage technique. We illustrate our approach by analysing a sub sample of 500 individuals from the simulated QTLMAS 2009 data set, as well as simulation replicates and a real Scots pine (Pinus sylvestris) data set, using temporal measurements of height as dynamic trait of interest. PMID:21792229

  17. A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia

    PubMed Central

    Wang, Le; Zhao, Mengchuan; Shi, Zhongren; Feng, Zhishan; Guo, Weiwei; Yang, Shuo; Liu, Lanping; Li, Guixia

    2016-01-01

    The GeXP-based assay has recently been developed for simultaneous detection of multiple pathogens. So far, the application of the GeXP assay to test larger clinical samples has hardly been reported. Community-acquired pneumonia (CAP) is the leading cause of death in children worldwide and a substantial proportion of childhood CAP is caused by viruses. Rapid and accurate diagnosis of virus infection is important for the clinical management of CAP. In this study, we explored the GeXP assay for simultaneous detection of 20 types/subtypes of viruses in hospitalized children with CAP. A total of 1699 nasopharyngeal swabs were prospectively collected and viral nucleic acid was extracted and assayed. Using viral genomic DNA or RNA as template, we showed that at the concentration of 104 copies of DNA or RNA of each virus/μl, all 20 target viruses were simultaneously identified by the GeXP assay. Fifteen control microorganisms, in contrast, failed to be amplified by the assay. About 65% of cases tested in this study had viral infection, with patients aged <3 years having a 70% positive rate, significantly higher than that in patients aged > 3 years (40%). The most frequently detected virus was RSV followed by PIV3, HRV, ADV and HBoV. Seasonal distribution analysis revealed that RSV was the most predominant in autumn and winter, while in spring and summer PIV3 and RSV were the most frequently identified with similar positive percentages. One hundred twenty randomly-chosen samples tested by the GeXP assay were re-evaluated by mono-RT-PCR, the results showed 97.5% diagnosis agreement between these 2 methods. Our findings suggest that the GeXP assay could be a valuable diagnostic tool for virus infection in pediatric patients with CAP. PMID:27627439

  18. A system for recording neural activity chronically and simultaneously from multiple cortical and subcortical regions in nonhuman primates

    PubMed Central

    Feingold, Joseph; Desrochers, Theresa M.; Fujii, Naotaka; Harlan, Ray; Tierney, Patrick L.; Shimazu, Hideki; Amemori, Ken-ichi

    2012-01-01

    A major goal of neuroscience is to understand the functions of networks of neurons in cognition and behavior. Recent work has focused on implanting arrays of ∼100 immovable electrodes or smaller numbers of individually adjustable electrodes, designed to target a few cortical areas. We have developed a recording system that allows the independent movement of hundreds of electrodes chronically implanted in several cortical and subcortical structures. We have tested this system in macaque monkeys, recording simultaneously from up to 127 electrodes in 14 brain regions for up to one year at a time. A key advantage of the system is that it can be used to sample different combinations of sites over prolonged periods, generating multiple snapshots of network activity from a single implant. Used in conjunction with microstimulation and injection methods, this versatile system represents a powerful tool for studying neural network activity in the primate brain. PMID:22170970

  19. Simultaneous quantification of Myelin Basic Protein and Tau proteins in cerebrospinal fluid and serum of Multiple Sclerosis patients using nanoimmunosensor.

    PubMed

    Derkus, Burak; Acar Bozkurt, Pinar; Tulu, Metin; Emregul, Kaan C; Yucesan, Canan; Emregul, Emel

    2017-03-15

    This study was aimed at the development of an immunosensor for the simultaneous quantification of Myelin Basic Protein (MBP) and Tau proteins in cerebrospinal fluid (CSF) and serum, obtained from Multiple Sclerosis (MS) patients. The newly developed GO/pPG/anti-MBP/anti-Tau nanoimmunosensor has been established by immobilization of MBP and Tau antibodies. The newly developed nanoimmunosensor was tested, optimized and characterized using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The developed nanoimmunosensor was seen to have detection limits of 0.30nM for MBP and 0.15nM for Tau proteins which were sufficient for the levels to be analysed in neuro-clinic. The clinical study performed using CSF and serum of MS patients showed that the designed nanoimmunosensor was capable of detecting the proteins properly, that were essentially proven by ELISA.

  20. Ca analysis: An Excel based program for the analysis of intracellular calcium transients including multiple, simultaneous regression analysis☆

    PubMed Central

    Greensmith, David J.

    2014-01-01

    Here I present an Excel based program for the analysis of intracellular Ca transients recorded using fluorescent indicators. The program can perform all the necessary steps which convert recorded raw voltage changes into meaningful physiological information. The program performs two fundamental processes. (1) It can prepare the raw signal by several methods. (2) It can then be used to analyze the prepared data to provide information such as absolute intracellular Ca levels. Also, the rates of change of Ca can be measured using multiple, simultaneous regression analysis. I demonstrate that this program performs equally well as commercially available software, but has numerous advantages, namely creating a simplified, self-contained analysis workflow. PMID:24125908

  1. Multiple defocused coherent diffraction imaging: method for simultaneously reconstructing objects and probe using X-ray free-electron lasers.

    PubMed

    Hirose, Makoto; Shimomura, Kei; Suzuki, Akihiro; Burdet, Nicolas; Takahashi, Yukio

    2016-05-30

    The sample size must be less than the diffraction-limited focal spot size of the incident beam in single-shot coherent X-ray diffraction imaging (CXDI) based on a diffract-before-destruction scheme using X-ray free electron lasers (XFELs). This is currently a major limitation preventing its wider applications. We here propose multiple defocused CXDI, in which isolated objects are sequentially illuminated with a divergent beam larger than the objects and the coherent diffraction pattern of each object is recorded. This method can simultaneously reconstruct both objects and a probe from the coherent X-ray diffraction patterns without any a priori knowledge. We performed a computer simulation of the prposed method and then successfully demonstrated it in a proof-of-principle experiment at SPring-8. The prposed method allows us to not only observe broad samples but also characterize focused XFEL beams.

  2. A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model

    PubMed Central

    Stojowska, Karolina; Krawczyk, Beata

    2014-01-01

    We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s), while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR), whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR). The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal “band-based” results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb) complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3′ recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5′ rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided. PMID:25522278

  3. Cocktail-Dosing Microdialysis Study to Simultaneously Assess Delivery of Multiple Organic-Cationic Drugs to the Brain.

    PubMed

    Kitamura, Atsushi; Okura, Takashi; Higuchi, Kei; Deguchi, Yoshiharu

    2016-02-01

    Brain microdialysis is a powerful tool to estimate brain-to-plasma unbound concentration ratio at the steady state (Kp,uu) of compounds by direct measurement of the unbound concentration in brain interstitial fluid. Here, we evaluated a method to estimate Kp,uu values of multiple organic-cationic drugs simultaneously, by means of brain microdialysis combined with cocktail dosing. Five cationic drugs (diphenhydramine, memantine, oxycodone, pyrilamine, and tramadol), substrates of the proton-coupled organic cation antiport system, were selected as model drugs, and compared under single-dosing and cocktail-dosing conditions. We selected doses of the drugs at which no significant drug-drug interaction occurs at the proton-coupled organic cation antiport system in the blood-brain barrier (BBB). This was confirmed by uptake studies in hCMEC/D3 cells, an in vitro BBB model. The Kp,uu values after cocktail administration were in the range of 1.8-5.2, and were in good agreement with those after single administration. These results suggest that the microdialysis method with cocktail dosing is suitable to estimate Kp,uu values of several cationic drugs simultaneously, if there is no drug-drug interaction during BBB transport. The method could be useful for evaluating drug candidates with high Kp,uu values at an early stage in the development of central nervous system-acting drugs.

  4. A method for simultaneously delineating multiple targets in 3D-FISH using limited channels, lasers, and fluorochromes.

    PubMed

    Zhao, F Y; Yang, X; Chen, D Y; Ma, W Y; Zheng, J G; Zhang, X M

    2014-01-01

    Many studies have suggested a link between the spatial organization of genomes and fundamental biological processes such as genome reprogramming, gene expression, and differentiation. Multicolor fluorescence in situ hybridization on three-dimensionally preserved nuclei (3D-FISH), in combination with confocal microscopy, has become an effective technique for analyzing 3D genome structure and spatial patterns of defined nucleus targets including entire chromosome territories and single gene loci. This technique usually requires the simultaneous visualization of numerous targets labeled with different colored fluorochromes. Thus, the number of channels and lasers must be sufficient for the commonly used labeling scheme of 3D-FISH, "one probe-one target". However, these channels and lasers are usually restricted by a given microscope system. This paper presents a method for simultaneously delineating multiple targets in 3D-FISH using limited channels, lasers, and fluorochromes. In contrast to other labeling schemes, this method is convenient and simple for multicolor 3D-FISH studies, which may result in widespread adoption of the technique. Lastly, as an application of the method, the nucleus locations of chromosome territory 18/21 and centromere 18/21/13 in normal human lymphocytes were analyzed, which might present evidence of a radial higher order chromatin arrangement.

  5. Simultaneous determination of free and total glycerol in biodiesel by capillary electrophoresis using multiple short-end injection.

    PubMed

    Spudeit, Daniel Alfonso; Piovezan, Marcel; Dolzan, Maressa D; Vistuba, Jacqueline Pereira; Azevedo, Mônia Stremel; Vitali, Luciano; Leal Oliveira, Marcone Augusto; Oliveira Costa, Ana Carolina; Micke, Gustavo Amadeu

    2013-12-01

    A rapid method for the simultaneous determination of free glycerol (FG) and total glycerol (TG) in biodiesel by CE using a short-end multiple injection (SE/MI) configuration system is described. The sample preparation for FG involves the extraction of glycerol with water and for TG a saponification reaction is carried out followed by extraction as in the case of FG. The glycerol extracted in both cases is submitted to periodate oxidation and the iodate ions formed are measured on a CE-SE/MI system. The relevance of this study lies in the fact that no analytical procedure has been previously reported for the determination of TG (or of FG and TG simultaneously) by CE. The optimum conditions for the saponification/extraction process were 1.25% KOH and 25°C, with a time of only 5 min, and biodiesel mass in the range of 50.0-200.0 mg can be used. Multiple injections were performed hydrodynamically with negative pressure as follows: 50 mbar/3s (FG sample); 50 mbar/6s (electrolyte spacer); 50 mbar/3s (TG sample). The linear range obtained was 1.55-46.5 mg/L with R(2) > 0.99. The LOD and LOQ were 0.16 mg/L and 0.47 mg/L, respectively for TG. The method provides acceptable throughput for application in quality control and monitoring biodiesel synthesis process. In addition, it offers simple sample preparation (saponification process), it can be applied to a variety biodiesel samples (soybean, castor, and waste cooking oils) and it can be used for the determination of two key parameters related to the biodiesel quality with a fast separation (less than 30 s) using an optimized CE-SE/MI system.

  6. Uniformity of simultaneous deposition of powder in multiple dies: Measurements and modeling

    NASA Astrophysics Data System (ADS)

    Xie, Xinsheng

    This research aimed at testing, evaluating, analyzing, and modeling the deposition process and uniformity of powder fill in multiple dies. The second generation pressure deposition tester (PDT-II) was developed to investigate the effects of some factors (die geometry and size, die configuration and location of the die, powder characteristics, and feed shoe speed) on the deposition process and final pressure distribution. A battery powder mixture and an alumina powder were used to fill three parallel-oriented dies. Cylindrical, toroidal, and E-shaped dies were investigated. For the cylindrical and toroidal dies, feed shoe speeds of 20, 100, 200 (for the alumina powder), and 500 mm/s (for the battery powder mixture) were tested For the E-shaped dies, 20 mm/s was used. A computed tomography (CT) scanner was employed to obtain fill density distribution for the cylindrical and toroidal dies filled with the two powders. PDT-II satisfactorily generates a real-time pressure profile of the process and final pressures at multiple locations. For the cylindrical dies filled with the battery powder mixture: (1) at 20 and 100 mm/s feed shoe speeds, the half circle close to the leeward end had higher final pressures; (2) at 500 mm/s, the final pressure distribution was more uniform; (3) the final pressure distribution was not always symmetrical about the center line. Final pressure decreased with increasing radial distance for low feed shoe speeds. The distribution was not always regular for high speed; (4) the three parallel dies did not always have similar pressure distributions; (5) the 500 mm/s feed shoe speed resulted in higher (P < 0.05) final pressures (774.5 to 1424.5 Pa) than at lower speeds (235.2 to 1136.0 Pa) at most locations; (6) at 20 and 100 mm/s feed shoe speeds, the right die tended to have higher (P < 0.05) final pressures (393.8 to 1136.0 Pa) than the center die (235.2 to 726.0 Pa). At 500 mm/s, the quantitative differences between the center (774.5 to 1246

  7. Method development for simultaneous analyses of multiple legacy and emerging organic chemicals in sediments.

    PubMed

    Guo, Jiehong; Li, Zhuona; Sandy, Andy L; Li, An

    2014-11-28

    The objective of this work was to investigate the feasibility of using a single pretreatment procedure for the analyses of multiple groups of organics, which have a wide range of chemical structures and physicochemical properties, in sediment samples. Nine groups of 162 individual compounds (including 11 surrogates) were investigated, including polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), polychlorinated diphenyl ethers (PCDEs), polychlorinated naphthalenes (PCNs), organochlorine pesticides (OCPs), polybrominated diphenyl ethers (PBDEs), novel halogenated flame retardants (nXFRs), musk fragrances (MFs) and organophosphate flame retardants (OPFRs). The individual and grouped recoveries of spiked analytes from adsorption chromatographic columns using either only fully activated, neutral silica gel (SG) or the combinations of silica gel and alumina (Si/Al) sorbents were compared. The results showed a generally stronger adsorption and more effective fractionation on the Si/Al column than on the SG column. The dependence of fractionation on halogen substitution, molecular planarity, and polar functional groups was discussed. The effects of adding sulfuric acid with two different methods were investigated, and the recoveries of a number of MFs, OCPs, nXFRs and OPFRs were recovered less than 60%. Sodium hydroxide treatment of silica gel had minor effects on some OPFRs. Copper used to remove elemental sulfur did not affect the recoveries of all target analytes except chloroneb. The finalized method was validated by spiking the target analysts into the sediment samples and comparing the analytical results of this work on two standard reference materials for sediment (SRMs 1941b and 1944) with the certified or reference values.

  8. A multiplex PCR assay for the simultaneous identification of three mealybug species (Hemiptera: Pseudococcidae).

    PubMed

    Saccaggi, D L; Krüger, K; Pietersen, G

    2008-02-01

    Molecular species identification is becoming more wide-spread in diagnostics and ecological studies, particularly with regard to insects for which morphological identification is difficult or time-consuming. In this study, we describe the development and application of a single-step multiplex PCR for the identification of three mealybug species (Hemiptera: Pseudococcidae) associated with grapevine in South Africa: Planococcus ficus (vine mealybug), Planococcus citri (citrus mealybug) and Pseudococcus longispinus (longtailed mealybug). Mealybugs are pests on many commercial crops, including grapevine, in which they transmit viral diseases. Morphological identification of mealybug species is usually time-consuming, requires a high level of taxonomic expertise and usually only adult females can be identified. The single-step multiplex PCR developed here, based on the mitochondrial cytochrome c oxidase subunit 1 (CO I) gene, is rapid, reliable, sensitive, accurate and simple. The entire identification protocol (including DNA extraction, PCR and electrophoresis) can be completed in approximately four hours. Successful DNA extraction from laboratory and unparasitized field-collected individuals stored in absolute ethanol was 97%. Specimens from which DNA could be extracted were always correctly identified (100% accuracy). The technique developed is simple enough to be implemented in any molecular laboratory. The principles described here can be extended to any organism for which rapid, reliable identification is needed.

  9. Simultaneous colour visualizations of multiple ALS point cloud attributes for land cover and vegetation analysis

    NASA Astrophysics Data System (ADS)

    Zlinszky, András; Schroiff, Anke; Otepka, Johannes; Mandlburger, Gottfried; Pfeifer, Norbert

    2014-05-01

    LIDAR point clouds hold valuable information for land cover and vegetation analysis, not only in the spatial distribution of the points but also in their various attributes. However, LIDAR point clouds are rarely used for visual interpretation, since for most users, the point cloud is difficult to interpret compared to passive optical imagery. Meanwhile, point cloud viewing software is available allowing interactive 3D interpretation, but typically only one attribute at a time. This results in a large number of points with the same colour, crowding the scene and often obscuring detail. We developed a scheme for mapping information from multiple LIDAR point attributes to the Red, Green, and Blue channels of a widely used LIDAR data format, which are otherwise mostly used to add information from imagery to create "photorealistic" point clouds. The possible combinations of parameters are therefore represented in a wide range of colours, but relative differences in individual parameter values of points can be well understood. The visualization was implemented in OPALS software, using a simple and robust batch script, and is viewer independent since the information is stored in the point cloud data file itself. In our case, the following colour channel assignment delivered best results: Echo amplitude in the Red, echo width in the Green and normalized height above a Digital Terrain Model in the Blue channel. With correct parameter scaling (but completely without point classification), points belonging to asphalt and bare soil are dark red, low grassland and crop vegetation are bright red to yellow, shrubs and low trees are green and high trees are blue. Depending on roof material and DTM quality, buildings are shown from red through purple to dark blue. Erroneously high or low points, or points with incorrect amplitude or echo width usually have colours contrasting from terrain or vegetation. This allows efficient visual interpretation of the point cloud in planar

  10. Simultaneous gene quantitation of multiple genes in individual bovine nuclear transfer blastocysts.

    PubMed

    Smith, Craig; Berg, Debbie; Beaumont, Sue; Standley, Neil T; Wells, David N; Pfeffer, Peter L

    2007-01-01

    During somatic cell nuclear transfer (NT), the transcriptional status of the donor cell has to be reprogrammed to reflect that of an embryo. We analysed the accuracy of this process by comparing transcript levels of four developmentally important genes (Oct4, Otx2, Ifitm3, GATA6), a gene involved in epigenetic regulation (Dnmt3a) and three housekeeping genes (beta-actin, beta-tubulin and GAPDH) in 21 NT blastocysts with that in genetically half-identical in vitro produced (IVP, n=19) and in vivo (n=15) bovine embryos. We have optimised an RNA-isolation and SYBR-green-based real-time RT-PCR procedure allowing the reproducible absolute quantification of multiple genes from a single blastocyst. Our data indicated that transcript levels did not differ significantly between stage and grade-matched zona-free NT and IVP embryos except for Ifitm3/Fragilis, which was expressed at twofold higher levels in NT blastocysts. Ifitm3 expression is confined to the inner cell mass at day 7 blastocysts and to the epiblast in day 14 embryos. No ectopic expression in the trophectoderm was seen in NT embryos. Gene expression in NT and IVP embryos increased between two- and threefold for all eight genes from early to late blastocyst stages. This increase exceeded the increase in cell number over this time period indicating an increase in transcript number per cell. Embryo quality (morphological grading) was correlated to cell number for NT and IVP embryos with grade 3 blastocysts containing 30% fewer cells. However, only NT embryos displayed a significant reduction in gene expression (50%) with loss of quality. Variability in gene expression levels was not significantly different in NT, IVP or in vivo embryos but differed among genes, suggesting that the stringency of regulation is intrinsic to a gene and not affected by culture or nuclear transfer. Oct4 levels exhibited the lowest variability. Analysing the total variability of all eight genes for individual embryos revealed that in

  11. Simultaneous determination of most prescribed antibiotics in multiple urban wastewater by SPE-LC-MS/MS.

    PubMed

    Rossmann, Julia; Schubert, Sara; Gurke, Robert; Oertel, Reinhard; Kirch, Wilhelm

    2014-10-15

    A rapid analytical method was developed for the application of a long-term monitoring (>one year) of the most prescribed and often in hospitals used antibiotics in diverse wastewaters of an urban sewage treatment plant (STP). Additionally to the selected multi-class antibiotics amoxicillin, penicillin V and piperacillin (penicillins), cefotaxime and cefuroxime (cephalosporins), azithromycin, clarithromycin and roxithromycin (macrolids), ciprofloxacin and levofloxacin-ofloxacin (fluoroquinolones), clindamycin (lincosamide), doxycycline (tetracycline), sulfamethoxazole (sulfonamide) and trimethoprim (dihydrofolate reductase inhibitor), the bioactive metabolite clindamycin-sulfoxide, the reserve antibiotic vancomycin (glycopeptide) and as tracer of the STP the anticonvulsant carbamazepine and the antifungal fluconazole were involved. The analytical method combines a low-sample-volume solid phase extraction (SPE), followed by a chromatographic separation using a reversed phase (RP) and hydrophilic interaction liquid chromatography (HILIC) technique, respectively, coupled to a triple quadrupole mass spectrometer. Detection was performed with multiple reaction monitoring (MRM) measured with positive electrospray ionization (ESI+). The extraction efficiency of different SPE cartridges and optimized pH-values of the preparation procedure were tested. Finally, the extraction of antibiotics was realized with the Oasis HLB cartridge and a pH adjustment at 3.5. An external calibration curve in diluted blank urine was used for quality control of the sample set of daily composite samples of the STP for the duration of one year monitoring. The squared coefficient of determination (r(2)) in the concentration range (20-20,000ng/L or 100-100,000ng/L) of the calibration curves for the method was higher than 0.99 for all determined substances. The limit of quantification (LoQ) ranged between 0.8ng/L (azithromycin) and 245.1ng/L (vancomycin). Furthermore, a standard addition was used

  12. Hydrodynamic description of an unmagnetized plasma with multiple ion species. II. Two and three ion species plasmas

    SciTech Connect

    Simakov, Andrei Nikolaevich; Molvig, Kim

    2016-03-17

    Paper I [A. N. Simakov and K. Molvig, Phys. Plasmas23, 032115 (2016)] obtained a fluid description for an unmagnetized collisional plasma with multiple ion species. To evaluate collisional plasmatransport fluxes, required for such a description, two linear systems of equations need to be solved to obtain corresponding transport coefficients. In general, this should be done numerically. Herein, the general formalism is used to obtain analytical expressions for such fluxes for several specific cases of interest: a deuterium-tritium plasma; a plasma containing two ion species with strongly disparate masses, which agrees with previously obtained results; and a three ion species plasma made of deuterium, tritium, and gold. We find that these results can be used for understanding the behavior of the aforementioned plasmas, or for verifying a code implementation of the general multi-ion formalism.

  13. Hydrodynamic description of an unmagnetized plasma with multiple ion species. II. Two and three ion species plasmas

    DOE PAGES

    Simakov, Andrei Nikolaevich; Molvig, Kim

    2016-03-17

    Paper I [A. N. Simakov and K. Molvig, Phys. Plasmas23, 032115 (2016)] obtained a fluid description for an unmagnetized collisional plasma with multiple ion species. To evaluate collisional plasmatransport fluxes, required for such a description, two linear systems of equations need to be solved to obtain corresponding transport coefficients. In general, this should be done numerically. Herein, the general formalism is used to obtain analytical expressions for such fluxes for several specific cases of interest: a deuterium-tritium plasma; a plasma containing two ion species with strongly disparate masses, which agrees with previously obtained results; and a three ion species plasmamore » made of deuterium, tritium, and gold. We find that these results can be used for understanding the behavior of the aforementioned plasmas, or for verifying a code implementation of the general multi-ion formalism.« less

  14. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)

    PubMed Central

    2012-01-01

    Background Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages. Results Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups. Conclusions Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation. PMID:22353848

  15. Amplitude of Sensorimotor Mu Rhythm Is Correlated with BOLD from Multiple Brain Regions: A Simultaneous EEG-fMRI Study

    PubMed Central

    Yin, Siyang; Liu, Yuelu; Ding, Mingzhou

    2016-01-01

    The mu rhythm is a field oscillation in the ∼10Hz range over the sensorimotor cortex. For decades, the suppression of mu (event-related desynchronization) has been used to index movement planning, execution, and imagery. Recent work reports that non-motor processes, such as spatial attention and movement observation, also desynchronize mu, raising the possibility that the mu rhythm is associated with the activity of multiple brain regions and systems. In this study, we tested this hypothesis by recording simultaneous resting-state EEG-fMRI from healthy subjects. Independent component analysis (ICA) was applied to extract the mu components. The amplitude (power) fluctuations of mu were estimated as a time series using a moving-window approach, which, after convolving with a canonical hemodynamic response function (HRF), was correlated with blood-oxygen-level-dependent (BOLD) signals from the entire brain. Two main results were found. First, mu power was negatively correlated with BOLD from areas of the sensorimotor network, the attention control network, the putative mirror neuron system, and the network thought to support theory of mind. Second, mu power was positively correlated with BOLD from areas of the salience network, including anterior cingulate cortex and anterior insula. These results are consistent with the hypothesis that sensorimotor mu rhythm is associated with multiple brain regions and systems. They also suggest that caution should be exercised when attempting to interpret mu modulation in terms of a single brain network. PMID:27499736

  16. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae.

    PubMed

    Maury, Jérôme; Germann, Susanne M; Baallal Jacobsen, Simo Abdessamad; Jensen, Niels B; Kildegaard, Kanchana R; Herrgård, Markus J; Schneider, Konstantin; Koza, Anna; Forster, Jochen; Nielsen, Jens; Borodina, Irina

    2016-01-01

    Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci and a range of expression levels were obtained, as assessed with the green fluorescent protein (GFP) reporter system. The EasyCloneMulti vector set was applied to balance the expression of the rate-controlling step in the β-alanine pathway for biosynthesis of 3-hydroxypropionic acid (3HP). The best 3HP producing clone, with 5.45 g.L(-1) of 3HP, produced 11 times more 3HP than the lowest producing clone, which demonstrates the capability of EasyCloneMulti vectors to impact metabolic pathway enzyme activity.

  17. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae

    PubMed Central

    Baallal Jacobsen, Simo Abdessamad; Jensen, Niels B.; Kildegaard, Kanchana R.; Herrgård, Markus J.; Schneider, Konstantin; Koza, Anna; Forster, Jochen; Nielsen, Jens; Borodina, Irina

    2016-01-01

    Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci and a range of expression levels were obtained, as assessed with the green fluorescent protein (GFP) reporter system. The EasyCloneMulti vector set was applied to balance the expression of the rate-controlling step in the β-alanine pathway for biosynthesis of 3-hydroxypropionic acid (3HP). The best 3HP producing clone, with 5.45 g.L-1 of 3HP, produced 11 times more 3HP than the lowest producing clone, which demonstrates the capability of EasyCloneMulti vectors to impact metabolic pathway enzyme activity. PMID:26934490

  18. Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO.

    PubMed

    Raghavendra, S; Aditya Rao, S J; Kumar, Vadlapudi; Ramesh, C K

    2015-12-01

    Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the protein Polyphenoloxidase (PPO). The protein was isolated from Mucuna pruriens and confirmed as tyrosinases involved in L-DOPA production. The activity was measured using different inhibitors at different concentrations taking catechol as substrate. A high-throughput binding study was conducted to compare the binding orientations of individual ligands and multiple ligands employing Autodock 4.2. The results of single substrate docking showed a better binding of urea with the binding energy of -3.48 kJ mol(-1) and inter molecular energy of -3.48 kJ mol(-1) while the results of MLSD revealed that ascorbic acid combined with the substrate showed better inhibition with a decreased binding energy of -2.37 kJ mol(-1).

  19. Amplitude of Sensorimotor Mu Rhythm Is Correlated with BOLD from Multiple Brain Regions: A Simultaneous EEG-fMRI Study.

    PubMed

    Yin, Siyang; Liu, Yuelu; Ding, Mingzhou

    2016-01-01

    The mu rhythm is a field oscillation in the ∼10Hz range over the sensorimotor cortex. For decades, the suppression of mu (event-related desynchronization) has been used to index movement planning, execution, and imagery. Recent work reports that non-motor processes, such as spatial attention and movement observation, also desynchronize mu, raising the possibility that the mu rhythm is associated with the activity of multiple brain regions and systems. In this study, we tested this hypothesis by recording simultaneous resting-state EEG-fMRI from healthy subjects. Independent component analysis (ICA) was applied to extract the mu components. The amplitude (power) fluctuations of mu were estimated as a time series using a moving-window approach, which, after convolving with a canonical hemodynamic response function (HRF), was correlated with blood-oxygen-level-dependent (BOLD) signals from the entire brain. Two main results were found. First, mu power was negatively correlated with BOLD from areas of the sensorimotor network, the attention control network, the putative mirror neuron system, and the network thought to support theory of mind. Second, mu power was positively correlated with BOLD from areas of the salience network, including anterior cingulate cortex and anterior insula. These results are consistent with the hypothesis that sensorimotor mu rhythm is associated with multiple brain regions and systems. They also suggest that caution should be exercised when attempting to interpret mu modulation in terms of a single brain network.

  20. Instability-Enhanced Collisional Friction Determines the Bohm Criterion in Multiple-Ion-Species Plasmas

    NASA Astrophysics Data System (ADS)

    Baalrud, S. D.; Hegna, C. C.; Callen, J. D.

    2009-11-01

    Ion-ion streaming instabilities are excited in the presheath region of plasmas with multiple ion species if the ions are much colder than the electrons. Streaming instabilities onset when the relative fluid flow between ion species exceeds a critical speed, δVc, of order the ion thermal speeds. Using a generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses [1], one is able to show the instabilities rapidly enhance the collisional friction between ion species far beyond the contribution from Coulomb collisions alone. This strong frictional force determines the relative fluid speed between species. When this condition is combined with the Bohm criterion generalized for multiple ion species, the fluid speed of each ion species is determined at the sheath edge. For each species, this speed differs from the common ``system'' sound speed by a factor that depends on the species concentrations, masses and δVc.[4pt] [1] S.D. Baalrud, J.D. Callen, and C.C. Hegna, Phys. Plasmas 15, 092111 (2008).

  1. A massive and simultaneous sex event of two Pseudo-nitzschia species

    NASA Astrophysics Data System (ADS)

    Sarno, Diana; Zingone, Adriana; Montresor, Marina

    2010-02-01

    Sex is an obligatory event in the life cycle of many diatoms, being the means of restoration of maximum cell size that counteracts the progressive miniaturization induced by asexual divisions. Nonetheless, sexual stages and evidence for sexual reproduction in diatoms have rarely been directly reported from the marine environment. On September 20, 2006, different stages of the sexual cycle of two species, Pseudo-nitzschia cf. delicatissima and P. cf. calliantha, were detected in surface waters of the Gulf of Naples, at the Long Term Ecological Research Station MareChiara. The sampling date corresponded with a seasonal peak of abundance of the two species, which reached maximum concentrations of 9.1×10 6 and 7.0×10 5 cells L -1, respectively. Gametangia, auxospores of different size, and initial cells within and outside the perizonium were observed. Up to 9.2% of P. cf. delicatissima and 14.3% of P. cf. calliantha cells were undergoing sexual reproduction. The sexual event was mainly concentrated in surface waters and no sexual stages were observed a week before or after the date. The low percentage of sexual stages and the short duration of such events are probably the reasons for the scarcity of sexual stage observations in nature.

  2. Assessing the performance of a method of simultaneous compression and encryption of multiple images and its resistance against various attacks.

    PubMed

    Alfalou, A; Brosseau, C; Abdallah, N; Jridi, M

    2013-04-08

    We introduce a double optimization procedure for spectrally multiplexing multiple images. This technique is adapted from a recently proposed optical setup implementing the discrete cosine transformation (DCT). The new analysis technique is a combination of spectral fusion based on the properties of DCT, specific spectral filtering, and quantization of the remaining encoded frequencies using an optimal number of bits. Spectrally multiplexing multiple images defines a first level of encryption. A second level of encryption based on a real key image is used to reinforce encryption. A set of numerical simulations and a comparison with the well known JPEG (Joint Photographic Experts Group) image compression standard have been carried out to demonstrate the improved performances of this method. The focus here will differ from the method of simultaneous fusion, compression, and encryption of multiple images (SFCE) [Opt. Express 19, 24023 (2011)] in the following ways. Firstly, we shall be concerned with optimizing the compression rate by adapting the size of the spectral block to each target image and decreasing the number of bits required to encode each block. This size adaptation is achieved by means of the root-mean-square (RMS) time-frequency criterion. We found that this size adaptation provides a good tradeoff between bandwidth of spectral plane and number of reconstructed output images. Secondly, the encryption rate is improved by using a real biometric key and randomly changing the rotation angle of each block before spectral fusion. By using a real-valued key image we have been able to increase the compression rate of 50% over the original SFCE method. We provide numerical examples of the effects for size, rotation, and shifting of DCT-blocks which play noteworthy roles in the optimization of the bandwidth of the spectral plane. Inspection of the results for different types of attack demonstrates the robustness of our procedure.

  3. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    PubMed Central

    2012-01-01

    Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution. PMID:22214193

  4. Integrated optic chemical sensor for the simultaneous detection and quantification of multiple ions. Final report, March--September 1995

    SciTech Connect

    Mendoza, E.

    1995-09-01

    This final report summarizes the work performed by Physical Optics Corporation (POC) on the DOE contract entitled {open_quotes}Integrated Optic Chemical Sensor for the Simultaneous Detection and Quantification of Multiple Metal Ions{close_quotes}. This project successfully demonstrated a multi-element integrated optic chemical sensor (IOCS) system capable of simultaneous detection and quantification of metal ions in a water flow stream. POC`s innovative integrated optic chemical sensor technology uses an array of chemically active optical waveguides integrated in parallel in a single small IOCS chip. The IOCS technique uses commonly available materials and straightforward processing to produce channel waveguides in porous glass, each channel treated with a chemical indicator that responds optically to heavy metal ions in a water flow stream. The porosity of the glass allows metal ions present in the water to diffuse into the glass and interact with the immobilized indicators, producing a measurable optical chance. For the {open_quotes}proof-of-concept{close_quotes} demonstration, POC designed and fabricated two types of IOCS chips. Type I uses an array of four straight channel waveguides, three of which are doped with a metal sensitive indicator, an ionophore. The undoped fourth channel is used as the reference channel. Type II uses a 1 x 4 star coupler structure with three sensing channels and a reference channel. Successful implementation of the IOCS technology is expected to have a broad impact on water quality control as well as in the commercial environmental monitoring market. Because of the self-referenced, multidetection capability of the IOCS technique, POC`s water quality sensors are expected to find markets in environmental monitoring and protection, ground water monitoring, and in-line process control. Specific applications include monitoring of chromium, copper, and iron ions in water discharged by the metal plating industry.

  5. Simultaneous Observation of an Intraband Transition and Distinct Transient Species in the Infrared Region for Perovskite Solar Cells.

    PubMed

    Narra, Sudhakar; Chung, Chih-Chun; Diau, Eric Wei-Guang; Shigeto, Shinsuke

    2016-07-07

    Solar cells based on organometal-halide perovskites such as CH3NH3PbI3 have emerged as a promising next-generation photovoltaic system, but the underlying photophysics and photochemistry remain to be established because of the limited availability of methods to implement the simultaneous and direct measurement of various charge carriers and ions that play a crucial role in the operating device. We used nanosecond time-resolved infrared (IR) spectroscopy to investigate, with high molecular specificity, distinct transient species that are formed in perovskite solar cells after photoexcitation. In CH3NH3PbI3 planar-heterojuction solar cells, we simultaneously observed infrared spectral signatures that are associated with an intraband transition of conduction-band electrons, Fano resonance, and the spiro-OMeTAD cation having an exceptionally short lifetime of 1.0 μs (at ∼1485 cm(-1)). The present results show that the time-resolved IR method offers a unique capability to elucidate these important transients in perovskite solar cells and their dynamic interplay in a comprehensive manner.

  6. A single-tube duplex and multiplex PCR for simultaneous detection of four cassava mosaic begomovirus species in cassava plants.

    PubMed

    Aloyce, R C; Tairo, F; Sseruwagi, P; Rey, M E C; Ndunguru, J

    2013-04-01

    A single-tube duplex and multiplex PCR was developed for the simultaneous detection of African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Malawi virus (EACMMV) and East African cassava mosaic Zanzibar virus (EACMZV), four cassava mosaic begomoviruses (CMBs) affecting cassava in sub-Saharan Africa. Co-occurrence of the CMBs in cassava synergistically enhances disease symptoms and complicates their detection and diagnostics. Four primer pairs were designed to target DNA-A component sequences of cassava begomoviruses in a single tube PCR amplification using DNA extracted from dry-stored cassava leaves. Duplex and multiplex PCR enabled the simultaneous detection and differentiation of the four CMBs, namely ACMV (940bp), EACMCV (435bp), EACMMV (504bp) and EACMZV (260bp) in single and mixed infections, and sequencing results confirmed virus identities according to the respective published sequences of begomovirus species. In addition, we report here a modified Dellapotra et al. (1983) protocol, which was used to extract DNA from dry and fresh cassava leaves with comparable results. Using the duplex and multiplex techniques, time was saved and amount of reagents used were reduced, which translated into reduced cost of the diagnostics. This tool can be used by cassava breeders screening for disease resistance; scientists doing virus diagnostic studies; phytosanitary officers checking movement of diseased planting materials, and seed certification and multipliers for virus indexing.

  7. Finding all multiple stable fixpoints of n-species Lotka-Volterra competition models.

    PubMed

    Lischke, Heike; Löffler, Thomas

    2017-02-22

    One way to explore assembly of extant and novel communities from species pools, and by that biodiversity and species ranges, is to study the equilibrium behavior of dynamic competition models such as the Lotka-Volterra competition (LVC) model. We present a novel method (COMMUSTIX) to determine all stable fixpoints of the general LVC model with abundances x from a given pool of n species. To that purpose, we split the species in potentially surviving species (xi>0) and in others going extinct (xi=0). We derived criteria for the stability of xi=0 and for the equilibrium of xi>0 to determine possible combinations of extinct and surviving species by iteratively applying a mixed binary linear optimization algorithm. We tested this new method against (a) the numerical solution at equilibrium of the LVC ordinary differential equations (ODEs) and (b) the fixpoints of all combinations of surviving and extinct species (possible only for small n), tested for stability and non-negativity. The tests revealed that COMMUSTIX is reliable, it detects all multiple stable fixpoints (SFPs), which is not guaranteed by solving the ODEs, and more efficient than the combinations method. With COMMUSTIX, we studied the dependence of the fixpoint behavior on the competition strengths relative to the intra-specific competition. If inter-specific competition was considerably lower than intra-specific competition, only globally SFPs occurred. In contrast, if all inter-specific was higher than intra-specific competition, multiple SFPs consisting of only one species occurred. If competition strengths in the species pool ranged from below to above the intra-specific competition, either global or multiple SFPs strongly differing in species composition occurred. The species richness over all SFPs was high for pools of species with similar, either weak or strong competition, and lower for species with dissimilar or close to intra-specific competition strengths. The new approach is a reliable and

  8. Effects of multiple predator species on green treefrog (Hyla cinerea) tadpoles

    USGS Publications Warehouse

    Gunzburger, M.S.; Travis, J.

    2005-01-01

    Prey species that occur across a range of habitats may be exposed to variable communities of multiple predator species across habitats. Predicting the combined effects of multiple predators can be complex. Many experiments evaluating the effects of multiple predators on prey confound either variation in predator density with predator identity or variation in relative predator frequency with overall predation rates. We develop a new experimental design of factorial predator combinations that maintains a constant expected predation rate, under the null hypothesis of additive predator effects. We implement this design to evaluate the combined effects of three predator species (bass, aeshnid and libellulid odonate naiads) on mortality rate of a prey species, Hyla cinerea (Schneider, 1799) tadpoles, that occurs across a range of aquatic habitats. Two predator treatments (libellulid and aeshnid + libellulid) resulted in lower tadpole mortality than any of the other predator treatments. Variation in tadpole mortality across treatments was not related to coarse variation in microhabitat use, but was likely due to intraguild predation, which occurred in all predator treatments. Hyla cinerea tadpoles have constant, low survival values when exposed to many different combinations of predator species, and predation rate probably increases linearly with predator density.

  9. Multiple cryptic species in the blue-spotted maskray (Myliobatoidei: Dasyatidae: Neotrygon spp.): An update.

    PubMed

    Borsa, Philippe; Shen, Kang-Ning; Arlyza, Irma S; Hoareau, Thierry B

    2016-01-01

    Previous investigations have uncovered divergent mitochondrial clades within the blue-spotted maskray, previously Neotrygon kuhlii (Müller and Henle). The hypothesis that the blue-spotted maskray may consist of a complex of multiple cryptic species has been proposed, and four species have been recently described or resurrected. To test the multiple cryptic species hypothesis, we investigated the phylogenetic relationships and coalescence patterns of mitochondrial sequences in a sample of 127 new individuals from the Indian Ocean and the Coral Triangle region, sequenced at both the CO1 and cytochrome b loci. The maximum-likelihood (ML) tree of concatenated CO1+cytochrome b gene sequences, rooted by the New Caledonian maskray N. trigonoides, yielded 9 strongly supported, main clades. Puillandre's ABGD algorithm detected gaps in nucleotide distance consistent with the ML phylogeny. The general mixed Yule-coalescent algorithm partitioned the dataset into putative species generally consistent with the ML phylogeny. Nuclear markers generally confirmed that distinct mitochondrial clades correspond to genetically isolated lineages. The nine main lineages identified by ML analysis were geographically distributed in a parapatric fashion, indicating reproductive isolation. The hypothesis of multiple cryptic species is thus validated.

  10. Simultaneous Single Molecule Fluorescence and Conductivity Studies Reveal Distinct Classes of Aβ Species on Lipid Bilayers

    PubMed Central

    Schauerte, Joseph A.; Wong, Pamela T.; Wisser, Kathleen C.; Ding, Hao; Steel, Duncan G.; Gafni, Ari

    2010-01-01

    The extracellular senile plaques prevalent in brain tissue in Alzheimer's disease (AD) are composed of amyloid fibrils formed by the Aβ peptide. These fibrils have been traditionally believed to feature in neurotoxicity; however, numerous recent studies provide evidence that cytotoxicity in AD may be associated with low molecular weight oligomers of Aβ that associate with neuronal membranes and may lead to membrane permeabilization and disruption of the ion balance in the cell. The underlying mechanism leading to disruption of the membrane is the subject of many recent studies. Here we report the application of single molecule optical detection, using fluorescently labeled human Aβ40, combined with membrane conductivity measurements, to monitor the interaction of single oligomeric peptide structures with model planar black lipid membranes (BLM). In a qualitative study, we show that the binding of Aβ to the membrane can be described by three distinctly different behaviors, depending on the Aβ monomer concentration. For concentrations much below 10 nM, there is uniform binding of monomers over the surface of the membrane with no evidence of oligomer formation or membrane permeabilization. Between 10 nM and a few 100 nM, the uniform monomer binding is accompanied by the presence of peptide species ranging from dimers to small oligomers. The dimers are not found to permeabilize the membrane but the larger oligomers lead to permeabilization with individual oligomers producing ion conductances of less than 10 pS/pore. At higher concentration, perhaps beyond physiologically relevant concentrations, larger extended and dynamic structures are found with large conductance (100's of pS) suggesting major disruption of the membrane. PMID:20201586

  11. LC-MS method for the simultaneous quantitation of the anti-inflammatory constituents in oregano (Origanum species).

    PubMed

    Shen, Diandian; Pan, Min-Hsiung; Wu, Qing-Li; Park, Chung-Heon; Juliani, H Rodolfo; Ho, Chi-Tang; Simon, James E

    2010-06-23

    Oregano (Origanum spp.), a popular herb in western and Middle Eastern cuisine, was reported to show anti-inflammatory activities in vitro and in vivo but without any information as to the compounds responsible, whether the plants were authenticated or only contained true Origanum spp. Using a wide range of botanically authenticated oregano, we were able to show that oregano had anti-inflammatory activity and then using biodirected-guided fractionation, identified the anti-inflammatory agents in oregano as rosmarinic acid, oleanolic acid, and ursolic acid. In this study, we successfully developed an LC-MS (SIM mode) method to achieve coquantitation of these three organic acids with the application of a unique tandem column system. The detection of rosmarinic acid was optimal under negative ion mode of SIM, whereas oleanolic acid and ursolic acid were sensitive to positive ion mode. The simultaneous quantitation was attained by setting two time segments in one run to facilitate the ESI polarity switch. For the investigated analytes romarinic acid, oleanolic acid, and ursolic acid, good linearities (r(2) > 0.999) were obtained for each calibration curve. Validation for this method showed a precision (relative standard deviation) ranging from 4.84 to 6.41%, and the recoveries varied from 92.2 to 100.8% for the three analytes. A quantitative survey of these anti-inflammatory constituents in different oregano species (O. vulgare ssp. hirtum, O. vulgare, and O. syriacum) and chemotypes within the species varied significantly in their accumulation of rosmarinic, oleanolic, and ursolic acids. Significant variation in chemical composition between species and within a species was found.

  12. Distribution of baboon endogenous virus among species of African monkeys suggests multiple ancient cross-species transmissions in shared habitats.

    PubMed Central

    van der Kuyl, A C; Dekker, J T; Goudsmit, J

    1995-01-01

    PCR amplification of baboon endogenous virus (BaEV) long terminal repeat, reverse transcriptase gene, and env fragments from 24 different species of African monkeys indicates that BaEV is less widespread than was formerly thought. Instead of being present in every species of African primates, BaEV can be found only in baboons, geladas, and mangabeys (all belonging to the Papionini tribe) and in African green monkey (Cercopithecus aethiops)subspecies. BaEV, which can be activated from baboon and gelada tissues, was most likely introduced in the germ line only recently (less than a few million years ago) and has not been inherited from a common ancestor of all extant African monkeys. Neighbor-joining and maximum-likelihood analyses of the sequences obtained showed that two distinct virus clusters can be distinguished: the first containing baboon, gelada, and African green monkey BaEV sequences and the second consisting of mandrill and mangabey BaEV sequences. This viral evolutionary tree does not follow host phylogeny, indicating the cross-species transmissions and multiple germ line fixations of the virus must have occurred in the past. BaEV sequences are found in monkeys inhabiting savannas (baboons, geladas, and African green monkeys) as well as forests (managabeys and mandrills) and cluster according to the habitats of their hosts, providing evidence for cross-species transmission in shared habitats. PMID:7494300

  13. Whole-Brain Radiotherapy With Simultaneous Integrated Boost to Multiple Brain Metastases Using Volumetric Modulated Arc Therapy

    SciTech Connect

    Lagerwaard, Frank J. Hoorn, Elles A.P. van der; Verbakel, Wilko; Haasbeek, Cornelis J.A.; Slotman, Ben J.; Senan, Suresh

    2009-09-01

    Purpose: Volumetric modulated arc therapy (RapidArc [RA]; Varian Medical Systems, Palo Alto, CA) allows for the generation of intensity-modulated dose distributions by use of a single gantry rotation. We used RA to plan and deliver whole-brain radiotherapy (WBRT) with a simultaneous integrated boost in patients with multiple brain metastases. Methods and Materials: Composite RA plans were generated for 8 patients, consisting of WBRT (20 Gy in 5 fractions) with an integrated boost, also 20 Gy in 5 fractions, to Brain metastases, and clinically delivered in 3 patients. Summated gross tumor volumes were 1.0 to 37.5 cm{sup 3}. RA plans were measured in a solid water phantom by use of Gafchromic films (International Specialty Products, Wayne, NJ). Results: Composite RA plans could be generated within 1 hour. Two arcs were needed to deliver the mean of 1,600 monitor units with a mean 'beam-on' time of 180 seconds. RA plans showed excellent coverage of planning target volume for WBRT and planning target volume for the boost, with mean volumes receiving at least 95% of the prescribed dose of 100% and 99.8%, respectively. The mean conformity index was 1.36. Composite plans showed much steeper dose gradients outside Brain metastases than plans with a conventional summation of WBRT and radiosurgery. Comparison of calculated and measured doses showed a mean gamma for double-arc plans of 0.30, and the area with a gamma larger than 1 was 2%. In-room times for clinical RA sessions were approximately 20 minutes for each patient. Conclusions: RA treatment planning and delivery of integrated plans of WBRT and boosts to multiple brain metastases is a rapid and accurate technique that has a higher conformity index than conventional summation of WBRT and radiosurgery boost.

  14. [Microchip electrophoresis coupled with multiplex allele-specific am-plification for typing multiple single nucleotide polymorphisms (SNPs) simultaneously].

    PubMed

    Wang, Wei-Peng; Zhou, Guo-Hua

    2009-02-01

    A new method of DNA adapter ligation-mediated allele-specific amplification (ALM-ASA) was developed for typing multiple single nucleotide polymorphisms (SNPs) on the platform of microchip electrophoresis. Using seven SNPs of 794C>T, 1274C>T, 2143T>C, 2766T>del, 3298G>A, 5200G>A, and 5277C>T in the interleukin 1B (IL1B) gene as a target object, a long DNA fragment containing the seven SNPs of interest was pre-amplified to enhance the specificity. The pre-amplified DNA fragment was digested by a restriction endonuclease to form sticky ends; and then the adapter was ligated to either end of the digested fragment. Using the adapter-ligated fragments as templates, a 7-plex allele-specific amplification was performed by 7 allele-specific primers and a universal primer in one tube. The allele-specific products amplified were separated by chip electrophoresis and the types of SNPs were easily discriminated by the product sizes. The seven SNPs in IL1B gene in 48 healthy Chinese were successfully typed by microchip electrophoresis and the results coincided with those by PCR-restriction fragment length polymorphism and sequencing method. The method established was accurate and can be used to type multiple SNPs simultaneously. In combination with microchip electrophoresis for readout, ALM-ASA assay can be used for fast SNP detection with a small amount of sample. Using self-prepared gel matrix and reused chips for analysis, the SNP can be typed at an ultra low cost.

  15. High throughput LC-MS/MS method for the simultaneous analysis of multiple vitamin D analytes in serum

    PubMed Central

    Jenkinson, Carl; Adams, John S.; Stewart, Paul M.; Hewison, Martin; Keevil, Brian G.

    2016-01-01

    Recent studies suggest that vitamin D-deficiency is linked to increased risk of common human health problems. To define vitamin D ‘status’ most routine analytical methods quantify one particular vitamin D metabolite, 25-hydroxyvitamin D3 (25OHD3). However, vitamin D is characterized by complex metabolic pathways, and simultaneous measurement of multiple vitamin D metabolites may provide a more accurate interpretation of vitamin D status. To address this we developed a high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to analyse multiple vitamin D analytes, with particular emphasis on the separation of epimer metabolites. A supportive liquid-liquid extraction (SLE) and LC-MS/MS method was developed to quantify 10 vitamin D metabolites as well as separation of an interfering 7α-hydroxy-4-cholesten-3-one (7αC4) isobar (precursor of bile acid), and validated by analysis of human serum samples. In a cohort of 116 healthy subjects, circulating concentrations of 25-hydroxyvitamin D3 (25OHD3), 3-epi-25-hydroxyvitamin D3 (3-epi-25OHD3), 24,25-dihydroxyvitamin D3 (24R,25(OH)2D3), 1,25-dihydroxyvitamin D3 (1α,25(OH)2D3), and 25-hydroxyvitamin D2 (25OHD2) were quantifiable using 220 μl of serum, with 25OHD3 and 24R,25(OH)2D3 showing significant seasonal variations. This high-throughput LC-MS/MS method provides a novel strategy for assessing the impact of vitamin D on human health and disease. PMID:26874878

  16. High throughput LC-MS/MS method for the simultaneous analysis of multiple vitamin D analytes in serum.

    PubMed

    Jenkinson, Carl; Taylor, Angela E; Hassan-Smith, Zaki K; Adams, John S; Stewart, Paul M; Hewison, Martin; Keevil, Brian G

    2016-03-01

    Recent studies suggest that vitamin D-deficiency is linked to increased risk of common human health problems. To define vitamin D 'status' most routine analytical methods quantify one particular vitamin D metabolite, 25-hydroxyvitamin D3 (25OHD3). However, vitamin D is characterized by complex metabolic pathways, and simultaneous measurement of multiple vitamin D metabolites may provide a more accurate interpretation of vitamin D status. To address this we developed a high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to analyse multiple vitamin D analytes, with particular emphasis on the separation of epimer metabolites. A supportive liquid-liquid extraction (SLE) and LC-MS/MS method was developed to quantify 10 vitamin D metabolites as well as separation of an interfering 7α-hydroxy-4-cholesten-3-one (7αC4) isobar (precursor of bile acid), and validated by analysis of human serum samples. In a cohort of 116 healthy subjects, circulating concentrations of 25-hydroxyvitamin D3 (25OHD3), 3-epi-25-hydroxyvitamin D3 (3-epi-25OHD3), 24,25-dihydroxyvitamin D3 (24R,25(OH)2D3), 1,25-dihydroxyvitamin D3 (1α,25(OH)2D3), and 25-hydroxyvitamin D2 (25OHD2) were quantifiable using 220μL of serum, with 25OHD3 and 24R,25(OH)2D3 showing significant seasonal variations. This high-throughput LC-MS/MS method provides a novel strategy for assessing the impact of vitamin D on human health and disease.

  17. Polymer nanopillar-gold arrays as surface-enhanced Raman spectroscopy substrate for the simultaneous detection of multiple genes.

    PubMed

    Picciolini, Silvia; Mehn, Dora; Morasso, Carlo; Vanna, Renzo; Bedoni, Marzia; Pellacani, Paola; Marchesini, Gerardo; Valsesia, Andrea; Prosperi, Davide; Tresoldi, Cristina; Ciceri, Fabio; Gramatica, Furio

    2014-10-28

    In our study, 2D nanopillar arrays with plasmonic crystal properties are optimized for surface-enhanced Raman spectroscopy (SERS) application and tested in a biochemical assay for the simultaneous detection of multiple genetic leukemia biomarkers. The special fabrication process combining soft lithography and plasma deposition techniques allows tailoring of the structural and chemical parameters of the crystal surfaces. In this way, it has been possible to tune the plasmonic resonance spectral position close to the excitation wavelength of the monochromatic laser light source in order to maximize the enhancing properties of the substrate. Samples are characterized by scanning electron microscopy and reflectance measurements and tested for SERS activity using malachite green. Besides, as the developed substrate had been prepared on a simple glass slide, SERS detection from the support side is also demonstrated. The optimized substrate is functionalized with thiol-modified capture oligonucleotides, and concentration-dependent signal of the target nucleotide is detected in a sandwich assay with labeled gold nanoparticles. Gold nanoparticles functionalized with different DNA and various Raman reporters are applied in a microarray-based assay recognizing a disease biomarker (Wilms tumor gene) and housekeeping gene expressions in the same time on spatially separated microspots. The multiplexing performance of the SERS-based bioassay is illustrated by distinguishing Raman dyes based on their complex spectral fingerprints.

  18. Simultaneous screening of multiple mutations by invader assay improves molecular diagnosis of hereditary hearing loss: a multicenter study.

    PubMed

    Usami, Shin-ichi; Nishio, Shin-ya; Nagano, Makoto; Abe, Satoko; Yamaguchi, Toshikazu

    2012-01-01

    Although etiological studies have shown genetic disorders to be a common cause of congenital/early-onset sensorineural hearing loss, there have been no detailed multicenter studies based on genetic testing. In the present report, 264 Japanese patients with bilateral sensorineural hearing loss from 33 ENT departments nationwide participated. For these patients, we first applied the Invader assay for screening 47 known mutations of 13 known deafness genes, followed by direct sequencing as necessary. A total of 78 (29.5%) subjects had at least one deafness gene mutation. Mutations were more frequently found in the patients with congenital or early-onset hearing loss, i.e., in those with an awareness age of 0-6 years, mutations were significantly higher (41.8%) than in patients with an older age of awareness (16.0%). Among the 13 genes, mutations in GJB2 and SLC26A4 were mainly found in congenital or early-onset patients, in contrast with mitochondrial mutations (12S rRNA m.1555A>G, tRNA(Leu(UUR)) m.3243A>G), which were predominantly found in older-onset patients. The present method of simultaneous screening of multiple deafness mutations by Invader assay followed by direct sequencing will enable us to detect deafness mutations in an efficient and practical manner for clinical use.

  19. Simultaneous acute shoulder arthritis and multiple mononeuropathy in a newly diagnosed type 2 diabetes patient - First case report.

    PubMed

    Kotlęga, Dariusz; Gołąb-Janowska, Monika; Zaborowski, Grzegorz; Ciećwież, Sylwester; Nowacki, Przemysław

    Diabetes is a common disorder that leads to the musculoskeletal symptoms such as the shoulder arthritis. The involvement of peripheral nervous system is one of the troublesome for the patients as it provokes chronic sensory symptoms, lower motor neuron involvement and autonomic symptoms. In the course of the disease there has been several types of neuropathies described. A 41-year-old male patient was admitted to the internal medicine department because of the general weakness, malaise, polydypsia and polyuria since several days. The initial blood glucose level was 780mg/dl. During the first day the continuous insulin infusion was administered. On the next day when he woke up, the severe pain in the right shoulder with limited movement, right upper extremity weakness and burning pain in the radial aspect of this extremity appeared. On examination right shoulder joint movement limitation was found with the muscle weakness and sensory symptoms in the upper limbs. The clinical picture indicated on the right shoulder arthritis and the peripheral nervous system symptoms such as the right musculocutaneous, supraspinatus, right radial nerve and left radial nerve damage. We present a first case report of simultaneous, acute involvement of the shoulder joint and multiple neuropathy in a patient with newly diagnosed type 2 diabetes, presumably in the state of ketoacidosis.

  20. Simultaneous analysis of multiple lipid oxidation products in vivo by liquid chromatographic-mass spectrometry (LC-MS).

    PubMed

    Yin, Huiyong; Davis, Todd; Porter, Ned A

    2010-01-01

    Free radical-induced oxidation of polyunsaturated fatty acid (PUFAs) has been linked to a number of human diseases including atherosclerosis and neurodegenerative disorders. Oxidation of PUFAs generates hydroperoxides and cyclic peroxides that are reduced to lipid alcohol, such as hydroxyeicosatetraenoic acid (HETEs), and isoprostanes (IsoPs) respectively. The IsoPs are isomers of prostaglandins that are generated from autoxidation of arachidonic acid (C20:4). Quantification of F(2)-IsoPs has been regarded as the "gold standard" to assess oxidative stress status in various human diseases. We herein report the protocol of analyzing HETEs and F(2)-IsoPs using a triple quadrupole mass spectrometer coupled to reverse phase liquid chromatography. The selected reaction monitoring (SRM) mode selects the parent ion of interest in the first Quad (m/z 319 for HETE and m/z 353 for F(2)-IsoPs) and fragments it in the second while an ion characteristic of the analyte of interest is monitored in the third Quad. This highly selective technique permits the simultaneous analysis of multiple oxidation products such as the HETEs and F(2)-IsoPs. This LC-MS technique can be applied to study the free radical oxidation mechanism in vitro and assess the oxidative stress status in biological tissues and fluids.

  1. Structure of North American mantle constrained by simultaneous inversion of multiple-frequency SH, SS, and Love waves

    NASA Astrophysics Data System (ADS)

    Tian, Yue; Zhou, Ying; Sigloch, Karin; Nolet, Guust; Laske, Gabi

    2011-02-01

    We simultaneously invert for the velocity and attenuation structure of the North American mantle from a mixed data set: SH wave traveltime and amplitude anomalies, SS wave differential traveltime anomalies, and Love wave fundamental mode phase delays. All data are measured for multiple frequency bands, and finite frequency sensitivity kernels are used to explain the observations. In the resulting SH velocity model, a lower mantle plume is observed to originate at about 1500 km depth beneath the Yellowstone area, tilting about 40° from vertical. The plume rises up through a gap in the subducting Farallon slab. The SH velocity model confirms high-level segmentation of the Farallon slab, which was observed in the recent P velocity model. Attenuation structure is resolvable in the upper mantle and transition zone; in estimating it, we correct for focusing. High-correlation coefficients between δlnVS and δlnQS under the central and eastern United States suggest one main physical source, most likely temperature. The smaller correlation coefficients and larger slopes of the δlnQS - δlnVS relationship under the western United States suggest an influence of nonthermal factors such as the existence of water and partial melt. Finally, we analyze the influence of the different components of our data set. The addition of Love wave phase delays helps to improve the resolution of both velocity and attenuation, and the effect is noticeable even in the lower mantle.

  2. Native Australian species are effective in extracting multiple heavy metals from biosolids.

    PubMed

    Mok, Hoi-Fei; Majumder, Ramaprasad; Laidlaw, W Scott; Gregory, David; Baker, Alan J M; Arndt, Stefan K

    2013-01-01

    Selecting native plant species with characteristics suitable for extraction of heavy metals may have multiple advantages over non-native plants. Six Australian perennial woody plant species and one willow were grown in a pot trial in heavy metal-contaminated biosolids and a potting mix. The plants were harvested after fourteen months and above-ground parts were analysed for heavy metal concentrations and total metal contents. All native species were capable of growing in biosolids and extracted heavy metals to varying degrees. No single species was able to accumulate heavy metals at particularly high levels and metal extraction depended upon the bioavailability of the metal in the substrate. Metal extraction efficiency was driven by biomass accumulation, with the species extracting the most metals also having the greatest biomass yield. The study demonstrated that Grevillea robusta, Acacia mearnsii, Eucalyptus polybractea, and E. cladocalyx have the greatest potential as phytoextractor species in the remediation of heavy metal-contaminated biosolids. Species survival and growth were the main determinants of metal extraction efficiency and these traits will be important for future screening of native species.

  3. Integrated airborne lidar and multiple endmember spectral mixture analysis (MESMA) for plant species mapping across multiple functional groups

    NASA Astrophysics Data System (ADS)

    Dahlin, K.; Asner, G. P.

    2010-12-01

    The ability to map plant species distributions has long been one of the key goals of terrestrial remote sensing. Achieving this goal has been challenging, however, due to technical constraints and the difficulty in relating remote observations to ground measurements. Advances in both the types of data that can be collected remotely and in available analytical tools like multiple endmember spectral mixture analysis (MESMA) are allowing for rapid improvements in this field. In 2007 the Carnegie Airborne Observatory (CAO) acquired high resolution lidar and hyperspectral imagery of Jasper Ridge Biological Preserve (Woodside, California). The site contains a mosaic of vegetation types, from grassland to chaparral to evergreen forest. To build a spectral library, 415 GPS points were collected in the field, made up of 44 plant species, six plant categories (for nonphotosynthetic vegetation), and four substrate types. Using the lidar data to select the most illuminated pixels as seen from the aircraft (based on canopy shape and viewing angle), we then reduced the spectral library to only the most fully lit pixels. To identify individual plant species in the imagery, first the hyperspectral data was used to calculate the normalized difference vegetation index (NDVI), and then pixels with an NDVI less than 0.15 were removed from further analysis. The remaining image was stratified into five classes based on vegetation height derived from the lidar data. For each class, a suite of possible endmembers was identified and then three endmember selection procedures (endmember average RMS, minimum average spectral angle, and count based endmember selection) were employed to select the most representative endmembers from each species in each class. Two and three endmember models were then applied and each pixel was assigned a species or plant category based on the highest endmember fraction. To validate the approach, an independent set of 200 points was collected throughout the

  4. Self-similar flow channel designs for parallel multiscale transport of multiple fluid species

    NASA Astrophysics Data System (ADS)

    Lee, Kenneth; Savas, Omer

    2011-11-01

    The need for multiscale fluid transport arises in a number of engineering applications involving fluid delivery or collection over a range of different lengthscales. A ``tree-shaped'' system of flow channels has been an efficient transport solution commonly practiced by biomimetics. There has been much work in optimizing these dendritic flow systems, primarily for cooling applications. However, most designs can be costly to manufacture and limited in scalability. Moreover, most systems are restricted to the transport of a single fluid species. This work explores the feasibility of self-similar flow channel designs to provide parallel multiscale transport of multiple fluid species. The self-similar characteristic of these designs simplifies manufacturing and allows for flexible scalability. Prototypes for the parallel transport of one and two independent fluid species are supported with analytical theory and experimental work. Designs for three and four species are presented as well. Supported by Joint Center for Artificial Photosynthesis (JCAP)

  5. The Sri Lankan torrent toads (Bufonidae: Adenominae: Adenomus): species boundaries assessed using multiple criteria.

    PubMed

    Meegaskumbura, Madhava; Senevirathne, Gayani; Wijayathilaka, Nayana; Jayawardena, Beneeta; Bandara, Champika; Manamendra-Arachchi, Kelum; Pethiyagoda, Rohan

    2015-01-19

    The bufonid genus Adenomus, an endemic of the montane and lowland rainforests of central and south-western Sri Lanka, has been considered to comprise of three species, viz. A. kelaartii, A. dasi and A. kandianus, the last of which has been recently highlighted as "the world's rarest toad". We conducted a survey across the known range of Adenomus and used multiple criteria to delineate species boundaries within the genus. These include: a molecular phylogeny based on a 16S ribosomal RNA gene fragment; an examination of the external morphology of adults and larvae, and the skeletal morphology of adults; a bioacoustic analysis; and ecological niche modelling. We show that Adenomus is monophyletic and that it comprises only two species: A. kelaartii and A. kandianus, with A. dasi being a junior synonym of the latter. For the two valid species of Adenomus, we provide detailed osteological descriptions; clarify the distribution patterns; and provide genetic data to facilitate their scientific conservation management. 

  6. Assessing multiple paternity in three commercially exploited shark species: Mustelus mustelus, Carcharhinus obscurus and Sphyrna lewini.

    PubMed

    Rossouw, C; Wintner, S P; Bester-Van Der Merwe, A E

    2016-08-01

    In this study, multiple paternity (MP) was investigated in three commercially important shark species, common smoothhound Mustelus mustelus, dusky shark Carcharhinus obscurus and scalloped hammerhead Sphyrna lewini occurring in southern Africa. Reduced marker panels of between five and six microsatellite loci were constructed for each species and used to genotype and assess the presence of MP in a total of 60 M. mustelus individuals from six litters, 90 C. obscurus individuals from 14 litters and 54 S. lewini individuals from 13 litters. Analysis in GERUD and COLONY revealed the presence of MP in all three species. Multiple paternities were observed in 67, 35 and 46% of the litters of M. mustelus, C. obscurus and S. lewini, with corresponding average sire size of 1·6, 1·4 and 2·0, respectively. The variation in the rate of MP among the three species is in accordance with previous studies whilst the comparatively high frequency of MP observed for M. mustelus, matches what has previously been reported for shark species demonstrating aggregation behaviour.

  7. Liquid metal ion source and alloy for ion emission of multiple ionic species

    DOEpatents

    Clark, Jr., William M.; Utlaut, Mark W.; Wysocki, Joseph A.; Storms, Edmund K.; Szklarz, Eugene G.; Behrens, Robert G.; Swanson, Lynwood W.; Bell, Anthony E.

    1987-06-02

    A liquid metal ion source and alloy for the simultaneous ion evaporation of arsenic and boron, arsenic and phosphorus, or arsenic, boron and phosphorus. The ionic species to be evaporated are contained in palladium-arsenic-boron and palladium-arsenic-boron-phosphorus alloys. The ion source, including an emitter means such as a needle emitter and a source means such as U-shaped heater element, is preferably constructed of rhenium and tungsten, both of which are readily fabricated. The ion sources emit continuous beams of ions having sufficiently high currents of the desired species to be useful in ion implantation of semiconductor wafers for preparing integrated circuit devices. The sources are stable in operation, experience little corrosion during operation, and have long operating lifetimes.

  8. Using multiple gears to assess acoustic detectability and biomass of fish species in lake superior

    USGS Publications Warehouse

    Yule, D.L.; Adams, J.V.; Stockwell, J.D.; Gorman, O.T.

    2007-01-01

    Recent predator demand and prey supply studies suggest that an annual daytime bottom trawl survey of Lake Superior underestimates prey fish biomass. A multiple-gear (acoustics, bottom trawl, and midwater trawl) nighttime survey has been recommended, but before abandoning a long-term daytime survey the effectiveness of night sampling of important prey species must be verified. We sampled three bottom depths (30, 60, and 120 m) at a Lake Superior site where the fish community included all commercially and ecologically important species. Day and night samples were collected within 48 h at all depths during eight different periods (one new and one full moon period during both early summer and late summer to early fall over 2 years). Biomass of demersal and benthic species was higher in night bottom trawl samples than in day bottom trawl samples. Night acoustic collections showed that pelagic fish typically occupied water cooler than 15°C and light levels less than 0.001 lx. Using biomass in night bottom trawls and acoustic biomass above the bottom trawl path, we calculated an index of acoustic detectability for each species. Ciscoes Coregonus artedi, kiyis C. kiyi, and rainbow smeltOsmerus mordax left the bottom at night, whereas bloaters C. hoyi stayed nearer the bottom. We compared the biomass of important prey species estimated with two survey types: day bottom trawls and night estimates of the entire water column (bottom trawl biomass plus acoustic biomass). The biomass of large ciscoes (>200 mm) was significantly greater when measured at night than when measured during daylight, but the differences for other sizes of important species did not vary significantly by survey type. Nighttime of late summer is a period when conditions for biomass estimation are largely invariant, and all important prey species can be sampled using a multiple-gear approach.

  9. Functional responses of cougars (Puma concolor) in a multiple prey-species system.

    PubMed

    Soria-Díaz, Leroy; Fowler, Mike S; Monroy-Vilchis, Octavio; Oro, Daniel

    2017-03-06

    The study of predator-prey interactions is commonly analyzed using functional responses to gain an understanding of predation patterns and the impact they have on prey populations. Despite this, little is known about predator-prey systems with multiple prey species in sites near the equator. Here we studied the functional response of cougars (Puma concolor) in Sierra Nanchititla Natural Reserve (Mexico), in relation to their main prey, armadillo (Dasypus novemcinctus), coati (Nasua narica) and white-tailed deer (Odocoileus virginianus). Between 2004 and 2010, cougar scats were collected along five transects to estimate the consumption of different prey species. A relative abundance index (RAI) was calculated for each prey species and cougar using 18 camera traps. We compared Holling type I, II and III functional response models to determine patterns in prey consumption based on the relative abundance and biomass of each prey species consumed. The three main prey species comprised 55% (armadillo), 17% (coati) and 8% (white-tailed deer) of the diet. Type I and II functional responses described consumption of the two most common prey species armadillos and coati similarly well, while a type I response best characterized consumption of white-tailed deer. A negative correlation between the proportions of armadillo versus coati and white-tailed deer biomass in cougar scats suggests switching to consume alternative prey, confirming high foraging plasticity of this carnivore. This work represents one of the few studies to compare functional responses across multiple prey species, combined with evidence for prey-switching at low densities of preferred prey. This article is protected by copyright. All rights reserved.

  10. Simultaneous measurement at multiple depths of in situ rates of denitrification in the bed of a groundwater-fed river

    NASA Astrophysics Data System (ADS)

    Lansdown, Katrina; Trimmer, Mark; Heppell, Kate

    2010-05-01

    Typically characterised by steep chemical gradients and variable redox conditions, the hyporheic zone is considered a 'hotpot' or site of enhanced biogeochemical activity in the aquatic environment. As such the importance of the hyporheic zone for the attenuation of nutrients such as nitrate in a fluvial network has long been recognised. Controls on nitrogen transformations, however, especially at depths greater than 10cm below the sediment-water interface, remain comparatively less understood. Most work aimed at quantifying denitrification in the hyporheic zone has involved laboratory incubation of recovered sediments which is likely to affect the estimate of the true in situ rate. Results of such studies are usually cited as 'potential' rates of denitrification and have undoubtedly improved the understanding of nitrogen cycling in the aquatic environment. There is, however, a need for in situ measurement to improve our knowledge of nitrogen cycling in the river bed. Here, rates of denitrification in the hyporheic zone have been measured at multiple depths, simultaneously using 'push-pull' methodology (e.g. Snodgrass and Kitanidis 1998). The 'push-pull' technique involves injection of a solution containing reactant(s) (e.g. nitrate) and a conservative tracer (e.g. chloride) into the sediment and extraction of pore water samples over time. Recovered samples are screened for the removal of reactant(s) and/or the accumulation of products(s). Temporal changes in the conservative tracer are used to correct the concentration of the reactant(s) and product(s) for dispersion and advection. The disadvantage of the 'traditional' 'push-pull' methodology is that rates of nitrate removal are measured rather than rates of denitrification. In this research, comparison of measured and 'corrected' nitrate concentrations allowed the rate of nitrate removal (or production) to be quantified. In order to determine in situ rates of denitrification we used 15N-enriched nitrate as the

  11. Multiple approaches for enhancing all-organic electronics photoluminescent sensors: simultaneous oxygen and pH monitoring.

    PubMed

    Liu, Rui; Xiao, Teng; Cui, Weipan; Shinar, Joseph; Shinar, Ruth

    2013-05-17

    Key issues in using organic light emitting diodes (OLEDs) as excitation sources in structurally integrated photoluminescence (PL)-based sensors are the low forward light outcoupling, the OLEDs' broad electroluminescence (EL) bands, and the long-lived remnant EL that follows an EL pulse. The outcoupling issue limits the detection sensitivity (S) as only ~20% of the light generated within standard OLEDs can be forward outcoupled and used for sensor probe excitation. The EL broad band interferes with the analyte-sensitive PL, leading to a background that reduces S and dynamic range. In particular, these issues hinder designing compact sensors, potentially miniaturizable, that are devoid of optical filters and couplers. We address these shortcomings by introducing easy-to-employ multiple approaches for outcoupling improvement, PL enhancement, and background EL reduction leading to novel, compact all-organic device architectures demonstrated for simultaneous monitoring of oxygen and pH. The sensor comprises simply-fabricated, directionally-emitting, narrower-band, multicolor microcavity OLED excitation and small molecule- and polymer-based organic photodetectors (OPDs) with a more selective spectral response. Additionally, S and PL intensity for oxygen are enhanced by using polystyrene (PS):polyethylene glycol (PEG) blends as the sensing film matrix. By utilizing higher molecular weight PS, the ratio τ0/τ100 (PL decay time τ at 0% O2/τ at 100% O2) that is often used to express S increases ×1.9 to 20.7 relative to the lower molecular weight PS, where this ratio is 11.0. This increase reduces to ×1.7 when the PEG is added (τ0/τ100=18.2), but the latter results in an increase ×2.7 in the PL intensity. The sensor's response time is <10s in all cases. The microporous structure of these blended films, with PEG decorating PS pores, serves a dual purpose. It results in light scattering that reduces the EL that is waveguided in the substrate of the OLEDs and

  12. A multiplex nanoparticle-based bio-barcoded DNA sensor for the simultaneous detection of multiple pathogens.

    PubMed

    Zhang, Deng; Huarng, Michael C; Alocilja, Evangelyn C

    2010-12-15

    A highly amplified, nanoparticle-based, bio-barcoded electrochemical biosensor for the simultaneous multiple detection of the protective antigen A (pagA) gene (accession number, M22589) of Bacillus anthracis and the insertion element (Iel) gene (accession number, Z83734) of Salmonella enteritidis is reported in this paper. The biosensor system is mainly composed of three nanoparticles: gold nanoparticles (AuNPs), magnetic nanoparticles (MNPs), and nanoparticle tracers (NTs, such as PbS and CdS). The AuNPs are coated with the first target-specific DNA probe (1pDNA), which can recognize one end of the target DNA sequence (tDNA), and many NT-terminated bio-barcode ssDNA (bDNA-NT), which act as signal reporter and amplifier. The MNPs are coated with the second target-specific DNA probe (2pDNA) that can recognize the other end of the target gene. After binding the nanoparticles with the target DNA, the following sandwich structure is formed: MNP-2pDNA/tDNA/1pDNA-AuNP-bDNA-NTs. A magnetic field is applied to separate the sandwich structure from the unreacted materials. Because the AuNPs have a large number of nanoparticle tracers per DNA probe binding event, there is substantial amplification. After the nanoparticle tracer is dissolved in 1M nitric acid, the NT(2+) ions are detected by square wave anodic stripping voltammetry (SWASV) on screen-printed carbon electrode (SPCE) chips. The results show that the detection limit of this multiplex bio-barcoded DNA sensor are 0.5 ng/mL of the insertion element (Iel) gene of S. enteritidis using CdS, and 50 pg/mL of the pagA gene of B. anthracis using PbS NTs. The nanoparticle-based bio-barcoded DNA sensor has potential application in rapid detection of multiple pathogenic agents in the same sample.

  13. Simultaneous determination of multiple phthalate metabolites and bisphenol-A in human urine by liquid chromatography-tandem mass spectrometry

    PubMed Central

    Chen, Mei; Tao, Lin; Collins, Erin M.; Austin, Christine; Lu, Chensheng

    2013-01-01

    Phthalates and bisphenol A are environmental endocrine-disrupting chemicals used widely in common consumer products. There is increasing concern about human exposure to phthalates and bisphenol A due to the potential adverse effects related to the anti-androgenic activity of phthalates and estrogenic activity of bisphenol A. In assessing environmental exposure to phthalates and bisphenol A, it is essential to have a validated analytical method that can quantify trace concentrations of phthalate metabolites and bisphenol A in humans. In this study, we developed and validated an accurate, sensitive, and robust LC-MS/MS method to simultaneously quantify 5 phthalate monoester metabolites, including mono-methyl phthalate, mono-ethyl phthalate, mono-butyl phthalate, mono-benzyl phthalate, mono-2-ethylhexyl phthalate, and bisphenol A in human urine. In this method, the phthalate metabolites and bisphenol A, along with their isotope labeled internal standards, were extracted from 200 μl of human urine using automated off-line solid phase extraction. The analytes were quantitatively determined using LC-MS/MS operated in negative electrospray ionization multiple reaction-monitoring mode. The limit of quantification was 0.3 ng/ml for mono-methyl phthalate, mono-ethyl phthalate, mono-benzyl phthalate and bisphenol A, and 1 ng/ml for mono-butyl phthalate and mono-2-ethylhexyl phthalate. The precision and accuracy were well within the acceptable 15% range. This validated method has been used successfully in assessing exposure to phthalates and bisphenol A in humans. PMID:22884473

  14. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

    PubMed Central

    Felicori, Liza; Jameson, Katie H.; Roblin, Pierre; Fogg, Mark J.; Garcia-Garcia, Transito; Ventroux, Magali; Cherrier, Mickaël V.; Bazin, Alexandre; Noirot, Philippe; Wilkinson, Anthony J.; Molina, Franck; Terradot, Laurent; Noirot-Gros, Marie-Françoise

    2016-01-01

    YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell. PMID:26615189

  15. Peptide-MHC Cellular Microarray with Innovative Data Analysis System for Simultaneously Detecting Multiple CD4 T-Cell Responses

    PubMed Central

    Ge, Xinhui; Gebe, John A.; Bollyky, Paul L.; James, Eddie A.; Yang, Junbao; Stern, Lawrence J.; Kwok, William W.

    2010-01-01

    Background Peptide:MHC cellular microarrays have been proposed to simultaneously characterize multiple Ag-specific populations of T cells. The practice of studying immune responses to complicated pathogens with this tool demands extensive knowledge of T cell epitopes and the availability of peptide:MHC complexes for array fabrication as well as a specialized data analysis approach for result interpretation. Methodology/Principal Findings We co-immobilized peptide:DR0401 complexes, anti-CD28, anti-CD11a and cytokine capture antibodies on the surface of chamber slides to generate a functional array that was able to detect rare Ag-specific T cell populations from previously primed in vitro T cell cultures. A novel statistical methodology was also developed to facilitate batch processing of raw array-like data into standardized endpoint scores, which linearly correlated with total Ag-specific T cell inputs. Applying these methods to analyze Influenza A viral antigen-specific T cell responses, we not only revealed the most prominent viral epitopes, but also demonstrated the heterogeneity of anti-viral cellular responses in healthy individuals. Applying these methods to examine the insulin producing beta-cell autoantigen specific T cell responses, we observed little difference between autoimmune diabetic patients and healthy individuals, suggesting a more subtle association between diabetes status and peripheral autoreactive T cells. Conclusions/Significance The data analysis system is reliable for T cell specificity and functional testing. Peptide:MHC cellular microarrays can be used to obtain multi-parametric results using limited blood samples in a variety of translational settings. PMID:20634998

  16. Simultaneous multiplicative column-normalized method (SMART) for 3-D ionosphere tomography in comparison to other algebraic methods

    NASA Astrophysics Data System (ADS)

    Gerzen, T.; Minkwitz, D.

    2016-01-01

    The accuracy and availability of satellite-based applications like GNSS positioning and remote sensing crucially depends on the knowledge of the ionospheric electron density distribution. The tomography of the ionosphere is one of the major tools to provide link specific ionospheric corrections as well as to study and monitor physical processes in the ionosphere. In this paper, we introduce a simultaneous multiplicative column-normalized method (SMART) for electron density reconstruction. Further, SMART+ is developed by combining SMART with a successive correction method. In this way, a balancing between the measurements of intersected and not intersected voxels is realised. The methods are compared with the well-known algebraic reconstruction techniques ART and SART. All the four methods are applied to reconstruct the 3-D electron density distribution by ingestion of ground-based GNSS TEC data into the NeQuick model. The comparative case study is implemented over Europe during two periods of the year 2011 covering quiet to disturbed ionospheric conditions. In particular, the performance of the methods is compared in terms of the convergence behaviour and the capability to reproduce sTEC and electron density profiles. For this purpose, independent sTEC data of four IGS stations and electron density profiles of four ionosonde stations are taken as reference. The results indicate that SMART significantly reduces the number of iterations necessary to achieve a predefined accuracy level. Further, SMART+ decreases the median of the absolute sTEC error up to 15, 22, 46 and 67 % compared to SMART, SART, ART and NeQuick respectively.

  17. Simultaneous Measurements of Temperature and Major Species Concentration in a Hydrocarbon-Fueled Dual Mode Scramjet Using WIDECARS

    NASA Astrophysics Data System (ADS)

    Gallo, Emanuela Carolina Angela

    Width increased dual-pump enhanced coherent anti-Stokes Raman spectroscopy (WIDECARS) measurements were conducted in a McKenna air-ethylene premixed burner, at nominal equivalence ratio range between 0.55 and 2.50 to provide quantitative measurements of six major combustion species (C2H 4, N2, O2, H2, CO, CO2) concentration and temperature simultaneously. The purpose of this test was to investigate the uncertainties in the experimental and spectral modeling methods in preparation for an subsequent scramjet C2H4/air combustion test at the University of Virginia-Aerospace Research Laboratory. A broadband Pyrromethene (PM) PM597 and PM650 dye laser mixture and optical cavity were studied and optimized to excite the Raman shift of all the target species. Two hundred single shot recorded spectra were processed, theoretically fitted and then compared to computational models, to verify where chemical equilibrium or adiabatic condition occurred, providing experimental flame location and formation, species concentrations, temperature, and heat losses inputs to computational kinetic models. The Stark effect, temperature, and concentration errors are discussed. Subsequently, WIDECARS measurements of a premixed air-ethylene flame were successfully acquired in a direct connect small-scale dual-mode scramjet combustor, at University of Virginia Supersonic Combustion Facility (UVaSCF). A nominal Mach 5 flight condition was simulated (stagnation pressure p0 = 300 kPa, temperature T0 = 1200 K, equivalence ratio range ER = 0.3 -- 0.4). The purpose of this test was to provide quantitative measurements of the six major combustion species concentration and temperature. Point-wise measurements were taken by mapping four two-dimensional orthogonal planes (before, within, and two planes after the cavity flame holder) with respect to the combustor freestream direction. Two hundred single shot recorded spectra were processed and theoretically fitted. Mean flow and standard deviation are

  18. Trinuclear nickel complexes with triplesalen ligands: simultaneous occurrence of mixed valence and valence tautomerism in the oxidized species.

    PubMed

    Glaser, Thorsten; Heidemeier, Maik; Fröhlich, Roland; Hildebrandt, Peter; Bothe, Eberhart; Bill, Eckhard

    2005-07-25

    forms exhibit the phenomena of valence tautomerism and mixed valence simultaneously. The extent of delocalization of the radical species and of the Ni(III) species is discussed.

  19. Identification and characterization of multiple emissive species in aggregated minor antenna complexes.

    PubMed

    Wahadoszamen, Md; Belgio, Erica; Rahman, Md Ashiqur; Ara, Anjue Mane; Ruban, Alexander V; van Grondelle, Rienk

    2016-12-01

    Aggregation induced conformational change of light harvesting antenna complexes is believed to constitute one of the pathways through which photosynthetic organisms can safely dissipate the surplus of energy while exposed to saturating light. In this study, Stark fluorescence (SF) spectroscopy is applied to minor antenna complexes (CP24, CP26 and CP29) both in their light-harvesting and energy-dissipating states to trace and characterize different species generated upon energy dissipation through aggregation (in-vitro) induced conformational change. SF spectroscopy could identify three spectral species in the dissipative state of CP24, two in CP26 and only one in CP29. The comprehensive analysis of the SF spectra yielded different sets of molecular parameters for the multiple spectral species identified in CP24 or CP26, indicating the involvement of different pigments in their formation. Interestingly, a species giving emission around the 730nm spectral region is found to form in both CP24 and CP26 following transition to the energy dissipative state, but not in CP29. The SF analyses revealed that the far red species has exceptionally large charge transfer (CT) character in the excited state. Moreover, the far red species was found to be formed invariably in both Zeaxanthin (Z)- and Violaxathin (V)-enriched CP24 and CP26 antennas with identical CT character but with larger emission yield in Z-enriched ones. This suggests that the carotenoid Z is not directly involved but only confers an allosteric effect on the formation of the far red species. Similar far red species with remarkably large CT character were also observed in the dissipative state of the major light harvesting antenna (LHCII) of plants [Wahadoszamen et al. PCCP, 2012], the fucoxanthin-chlorophyll protein (FCP) of brown algae [Wahadoszamen et al. BBA, 2014] and cyanobacterial IsiA [Wahadoszamen et al. BBA, 2015], thus pointing to identical sites and pigments active in the formation of the far red

  20. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    PubMed

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras.

  1. Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species.

    PubMed

    Fitzpatrick, David A

    2009-02-01

    Phenazines are secondary metabolites with broad-spectrum antibiotic activity against bacteria, fungi, and eukaryotes. In pseudomonad species, a conserved seven-gene phenazine operon (phzABCDEFG) is required for the conversion of chorismic acid to the broad-spectrum antibiotic phenazine-1-carboxylate. Previous analyses of genes involved in phenazine production from nonpseudomonad species uncovered a high degree of sequence similarity to pseudomonad homologues. The analyses undertaken in this study wished to eluciadate the evolutionary history of genes involved in the production of phenazines. Furthermore, I wanted to determine if the phenazine operon has been transferred through horizontal gene transfer. Analyses of GC content, codon usage patterns, frequency of 3:1 dinucleotides, sequence similarities, and phylogenetic reconstructions were undertaken to map the evolutionary history of phenazine genes from multiple bacterial species. Patchy phyletic distribution, high sequence similarities, and phylogenetic evidence infer that pseudomonad, Streptomyces cinnamonensis, Pantoea agglomerans, Burkholderia cepacia, Pectobacterium atrosepticum, Brevibacterium linens, and Mycobacterium abscessus species all contain a phenazine operon which has most likely been transferred among these species through horizontal gene transfer. The acquisition of an antibiotic-associated operon is significant, as it may increase the relative fitness of the recipient species.

  2. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    PubMed

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear.

  3. Seroepidemiological Prevalence of Multiple Species of Filoviruses in Fruit Bats (Eidolon helvum) Migrating in Africa.

    PubMed

    Ogawa, Hirohito; Miyamoto, Hiroko; Nakayama, Eri; Yoshida, Reiko; Nakamura, Ichiro; Sawa, Hirofumi; Ishii, Akihiro; Thomas, Yuka; Nakagawa, Emiko; Matsuno, Keita; Kajihara, Masahiro; Maruyama, Junki; Nao, Naganori; Muramatsu, Mieko; Kuroda, Makoto; Simulundu, Edgar; Changula, Katendi; Hang'ombe, Bernard; Namangala, Boniface; Nambota, Andrew; Katampi, Jackson; Igarashi, Manabu; Ito, Kimihito; Feldmann, Heinz; Sugimoto, Chihiro; Moonga, Ladslav; Mweene, Aaron; Takada, Ayato

    2015-10-01

    Fruit bats are suspected to be a natural reservoir of filoviruses, including Ebola and Marburg viruses. Using an enzyme-linked immunosorbent assay based on the viral glycoprotein antigens, we detected filovirus-specific immunoglobulin G antibodies in 71 of 748 serum samples collected from migratory fruit bats (Eidolon helvum) in Zambia during 2006-2013. Although antibodies to African filoviruses (eg, Zaire ebolavirus) were most prevalent, some serum samples showed distinct specificity for Reston ebolavirus, which that has thus far been found only in Asia. Interestingly, the transition of filovirus species causing outbreaks in Central and West Africa during 2005-2014 seemed to be synchronized with the change of the serologically dominant virus species in these bats. These data suggest the introduction of multiple species of filoviruses in the migratory bat population and point to the need for continued surveillance of filovirus infection of wild animals in sub-Saharan Africa, including hitherto nonendemic countries.

  4. Multiple species of scuttle flies (Diptera: Phoridae) as contaminants in forensic entomology laboratory insect colony.

    PubMed

    Zuha, R M; Jenarthanan, L X Q; Disney, R H L; Omar, B

    2015-09-01

    In forensic entomology, larval rearing usually includes the presence of biological contaminants including scuttle flies (Diptera: Phoridae). Scuttle flies are recognized as forensically important insects and have been reported causing nuisance and contamination in laboratory environments. This paper reports for the first time the finding of multiple scuttle fly species affecting colonies of third instar larvae of the Oriental latrine blowfly, Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae), reared indoors at the Forensic Science Simulation Site, Universiti Kebangsaan Malaysia. Adult scuttle flies were discovered inside a rearing container after the emergence of adult C. megacephala., The scuttle fly species are Megaselia scalaris (Loew), M. spiracularis Schmitz and Puliciphora borinquenensis (Wheeler). Notes on the life history and biology of these species are discussed herein.

  5. Total soft-tissue reconstruction of the middle and lower face with multiple simultaneous free flaps in a pediatric patient.

    PubMed

    Burt, J D; Burns, A J; Muzaffar, A R; Byrd, H S; Hobar, P C; Beran, S J; Adams, W P; Kenkel, J M

    2000-06-01

    A 2-year-old boy sustained a massive facial soft-tissue wound secondary to a dog attack. Essentially all the soft tissues of the face were absent, including innervation and intraoral lining. We describe the reconstruction of this defect with five simultaneous free tissue transfers. To our knowledge, this is the first report of five simultaneous free flaps in any patient.

  6. Multiplication of different Legionella species in Mono Mac 6 cells and in Acanthamoeba castellanii.

    PubMed Central

    Neumeister, B; Schöniger, S; Faigle, M; Eichner, M; Dietz, K

    1997-01-01

    Survival and distribution of legionellae in the environment are assumed to be associated with their multiplication in amoebae, whereas the ability to multiply in macrophages is usually regarded to correspond to pathogenicity. Since most investigations focused on Legionella pneumophila serogroup 1, we examined the intracellular multiplication of different Legionella species in Mono Mac 6 cells, which express phenotypic and functional features of mature monocytes, and in Acanthamoeba castellanii, an environmental host of Legionella spp. According to the bacterial doubling time in Mono Mac 6 cells and in A. castellanii, seven clusters of legionellae could be defined which could be split further with regard to finer differences. L. longbeachae serogroup 1, L. jordanis, and L. anisa were not able to multiply in either A. castellanii or Mono Mac 6 cells and are members of the first cluster. L. dumoffi did not multiply in Mono Mac 6 cells but showed a delayed multiplication in A. castellanii 72 h after infection and is the only member of the second cluster. L. steigerwaltii, L. gormanii, L. pneumophila serogroup 6 ATCC 33215, L. bozemanii, and L. micdadei showed a stable bacterial count in Mono Mac 6 cells after infection but a decreasing count in amoebae. They can be regarded as members of the third cluster. As the only member of the fourth cluster, L. oakridgensis was able to multiply slight in Mono Mac 6 cells but was killed within amoebae. A strain of L. pneumophila serogroup 1 Philadelphia obtained after 30 passages on SMH agar and a strain of L. pneumophila serogroup 1 Philadelphia obtained after intraperitoneal growth in guinea pigs are members of the fifth cluster, which showed multiplication in Mono Mac 6 cells but a decrease of bacterial counts in A. castellanii. The sixth cluster is characterized by intracellular multiplication in both host cell systems and consists of several strains of L. pneumophila serogroup 1 Philadelphia, a strain of L. pneumophila

  7. Hydrodynamic description of an unmagnetized plasma with multiple ion species. I. General formulation

    SciTech Connect

    Simakov, Andrei Nikolaevich; Molvig, Kim

    2016-03-17

    A generalization of the Braginskii ion fluid description [S. I. Braginskii, Sov. Phys. JETP 6, 358 (1958)] to the case of an unmagnetized collisional plasma with multiple ion species is presented. An asymptotic expansion in the ion Knudsen number is used to derive the individual ion species continuity, as well as the total ion mass density, momentum, and energy evolution equations accurate through the second order. Expressions for the individual ion species drift velocities with respect to the center of mass reference frame, as well as for the total ion heat flux and viscosity, which are required to close the fluid equations, are evaluated in terms of the first-order corrections to the lowest order Maxwellian ion velocity distribution functions. A variational formulation for evaluating such corrections and its relation to the plasma entropy are presented. Employing trial functions for the corrections, written in terms of expansions in generalized Laguerre polynomials, and maximizing the resulting functionals produces two systems of linear equations (for “vector” and “tensor” portions of the corrections) for the expansion coefficients. A general matrix formulation of the linear systems as well as expressions for the resulting transport fluxes are presented in forms convenient for numerical implementation. The general formulation is employed in the companion paper [A. N. Simakov and K. Molvig, Hydrodynamic description of an unmagnetized plasma with multiple ion species. II. Two and three ion species plasmas, submitted to Phys. Plasmas (2015)] to evaluate the individual ion drift velocities and the total ion heat flux and viscosity for specific cases of two and three ion species plasmas.

  8. Hydrodynamic description of an unmagnetized plasma with multiple ion species. I. General formulation

    DOE PAGES

    Simakov, Andrei Nikolaevich; Molvig, Kim

    2016-03-17

    A generalization of the Braginskii ion fluid description [S. I. Braginskii, Sov. Phys. JETP 6, 358 (1958)] to the case of an unmagnetized collisional plasma with multiple ion species is presented. An asymptotic expansion in the ion Knudsen number is used to derive the individual ion species continuity, as well as the total ion mass density, momentum, and energy evolution equations accurate through the second order. Expressions for the individual ion species drift velocities with respect to the center of mass reference frame, as well as for the total ion heat flux and viscosity, which are required to close themore » fluid equations, are evaluated in terms of the first-order corrections to the lowest order Maxwellian ion velocity distribution functions. A variational formulation for evaluating such corrections and its relation to the plasma entropy are presented. Employing trial functions for the corrections, written in terms of expansions in generalized Laguerre polynomials, and maximizing the resulting functionals produces two systems of linear equations (for “vector” and “tensor” portions of the corrections) for the expansion coefficients. A general matrix formulation of the linear systems as well as expressions for the resulting transport fluxes are presented in forms convenient for numerical implementation. The general formulation is employed in the companion paper [A. N. Simakov and K. Molvig, Hydrodynamic description of an unmagnetized plasma with multiple ion species. II. Two and three ion species plasmas, submitted to Phys. Plasmas (2015)] to evaluate the individual ion drift velocities and the total ion heat flux and viscosity for specific cases of two and three ion species plasmas.« less

  9. Simultaneous Separation of Negatively and Positively Charged Species in Dynamic Field Gradient Focusing Using a Dual Polarity Electric Field

    PubMed Central

    Burke, Jeffrey M.; Huang, Zheng; Ivory, Cornelius F.

    2011-01-01

    Dynamic field gradient focusing (DFGF) utilizes an electric field gradient established by a computer-controlled electrode array to separate and concentrate charged analytes at unique axial positions. Traditionally, DFGF has been restricted to the analysis of negatively charged species due to limitations in the software of our voltage controller. This paper introduces a new voltage controller capable of operating under normal polarity (positive potentials applied to the electrode array) and reversed polarity (negative potentials applied to the electrode array) for the separation of negatively and positively charged analytes, respectively. The experiments conducted under normal polarity and reversed polarity illustrate the utility of the new controller to perform reproducible DFGF separations (elution times showing less than 1% run-to-run variation) over a wide pH range (3.08 to 8.5) regardless of the protein charge. A dual polarity experiment is then shown in which the separation channel has been divided into normal polarity and reversed polarity regions. This simultaneous separation of negatively charged R-phycoerythrin (R-PE) and positively charged cytochrome c (CYTC) within the same DFGF apparatus is shown. PMID:19722517

  10. Simultaneous separation of negatively and positively charged species in dynamic field gradient focusing using a dual polarity electric field.

    PubMed

    Burke, Jeffrey M; Huang, Zheng; Ivory, Cornelius F

    2009-10-01

    Dynamic field gradient focusing (DFGF) utilizes an electric field gradient established by a computer-controlled electrode array to separate and concentrate charged analytes at unique axial positions. Traditionally, DFGF has been restricted to the analysis of negatively charged species due to limitations in the software of our voltage controller. This paper introduces a new voltage controller capable of operating under normal polarity (positive potentials applied to the electrode array) and reversed polarity (negative potentials applied to the electrode array) for the separation of negatively and positively charged analytes, respectively. The experiments conducted under normal polarity and reversed polarity illustrate the utility of the new controller to perform reproducible DFGF separations (elution times showing less than 1% run-to-run variation) over a wide pH range (3.08 to 8.5) regardless of the protein charge. A dual polarity experiment is then shown in which the separation channel has been divided into normal polarity and reversed polarity regions. This simultaneous separation of negatively charged R-phycoerythrin (R-PE) and positively charged cytochrome c (CYTC) within the same DFGF apparatus is shown.

  11. Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

    PubMed Central

    Hammel, Stephen; Higgins, Desmond G.; Bagagli, Eduardo

    2016-01-01

    Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi. PMID:27806045

  12. Simultaneous determination of alkaloids and flavonoids from aerial parts of Passiflora species and dietary supplements using UPLC-UV-MS and HPTLC

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A rapid UPLC method was developed for the simultaneous analysis of five indole alkaloids (harmalol, harmol, harmane, harmaline and harmine) and four flavonoids (orientin, isoorientin, vitexin, and isovitexin) from the aerial parts of Passiflora incarnata L. (Passifloracea), different species of Pass...

  13. Polarization-modulation infrared reflection-absorption spectroscopy affording time-resolved simultaneous detection of surface and liquid phase species at catalytic solid-liquid interfaces.

    PubMed

    Meier, Daniel M; Urakawa, Atsushi; Baiker, Alfons

    2009-09-01

    Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) combined with concentration modulation allows simultaneous monitoring of dynamic evolutions of surface and liquid phase species during reactions at catalytic interfaces as demonstrated for the Pt-catalysed oxidation of CO by O2 in cyclohexane.

  14. Multiple vs. single phytoplankton species alter stoichiometry of trophic interaction with zooplankton.

    PubMed

    Plum, Christoph; Hüsener, Matthias; Hillebrand, Helmut

    2015-11-01

    Despite the progress made in explaining trophic interactions through the stoichiometric interplay between consumers and resources, it remains unclear how the number of species in a trophic group influences the effects of elemental imbalances in food webs. Therefore, we conducted a laboratory experiment to test the hypothesis that multispecies producer assemblages alter the nutrient dynamics in a pelagic community. Four algal species were reared in mono- and polycultures under a 2 x 2 factorial combination of light and nutrient supply, thereby contrasting the stoichiometry of trophic interactions involving single vs. multiple producer species. After 9 d, these cultures were fed to the calanoid copepod Acartia tonsa, and we monitored biomass, resource use, and C:N:P stoichiometry in both phyto- and zooplankton. According to our expectations, light and N supply resulted in gradients of phytoplankton biomass and nutrient composition (C:N:P). Significant net diversity effects for algal biomass and C:N:P ratios reflected the greater responsiveness of the phytoplankton polyculture to altered resource supply compared to monocultures. These alterations of elemental ratios were common, and were partly triggered by changes in species frequency in the mixtures and partly by diversity-related changes in resource use. Copepod individual biomass increased under high light (HL) and N-reduced (-N) conditions, when food was high in C:N but low in C:P and N:P, whereas copepod growth was obviously P limited, and copepod stoichiometry was not affected by phytoplankton elemental composition. Correspondingly, copepod individual biomass reflected significant net diversity effects: compared to expectations- derived from monocultures, copepod individuals feeding on algal polycultures remained smaller than predicted under HL and N-sufficient (+N) conditions but grew larger than predicted under HL, -N and low light +N conditions. In conclusion, multiple producer species altered the

  15. High prevalence of multiple paternity in the invasive crayfish species, Procambarus clarkii.

    PubMed

    Yue, Gen Hua; Li, Jia Le; Wang, Chun Ming; Xia, Jun Hong; Wang, Gen Lin; Feng, Jian Bing

    2010-02-17

    Reproductive strategy is a central feature of the ecology of invasive species as it determines the potential for population increase and range expansion. The red swamp crayfish, Procambarus clarkii, has invaded many countries and caused serious problems in freshwater ecosystems. However, little is known about the effects of environmental conditions on crayfish paternity and offspring traits in the wild. We studied these reproductive characteristics of P. clarkii in wild populations from two different habitats (ponds and ditches) in three locations with different environmental conditions in China. Genotyping of 1,436 offspring and 30 mothers of 30 broods was conducted by using four microsatellites. An analysis of genotyping results revealed that gravid females were the exclusive mother of the progeny they tended. Twenty-nine of 30 mothers had mated with multiple (2-4) males, each of which contributed differently to the number of offspring in a brood. The average number of fathers per brood and the number of offspring per brood were similar (P>0.05) among six sampling sites, indicating that in P. clarkii multiple paternity and offspring number per brood are independent of environmental conditions studied. Indirect benefits from increasing the genetic diversity of broods, male and sperm competition, and cryptic female choice are a possible explanation for the high level multiple paternity and different contribution of fathers to offspring in this species.

  16. Simultaneous detection of Anaplasma and Ehrlichia species in ruminants and detection of Ehrlichia ruminantium in Amblyomma variegatum ticks by reverse line blot hybridization.

    PubMed

    Bekker, Cornelis P J; de Vos, Sander; Taoufik, Amar; Sparagano, Olivier A E; Jongejan, Frans

    2002-10-22

    The detection of Anaplasma and Ehrlichia species is usually based on species-specific PCR assays, since no assay is yet available which can detect and identify these species simultaneously. To this end, we developed a reverse line blot (RLB) assay for simultaneous detection and identification of Anaplasma and Ehrlichia species in domestic ruminants and ticks. In a PCR the hypervariable V1 region of the 16S ribosomal RNA (rRNA) gene was amplified with a set of primers unique for members of the genera Anaplasma and Ehrlichia [Int. J. Syst. Evol. Microbiol. 51 (2001) 2145]. Amplified PCR products from blood of domestic ruminants or Amblyomma variegatum tick samples were hybridized onto a membrane to which eight species-specific oligonucleotide probes and one Ehrlichia and Anaplasma catch-all oligonucleotide probe were covalently linked. No DNA was amplified from uninfected blood, nor from other hemoparasites such as Theileria annulata, or Babesia bigemina. The species-specific probes did not cross-react with DNA amplified from other species. E. ruminantium, A. ovis and another Ehrlichia were identified by RLB in blood samples collected from small ruminants in Mozambique. Finally, A. variegatum ticks were tested after feeding on E. ruminantium infected sheep. E. ruminantium could be detected in adult ticks even if feeding of nymphs was carried out 3.5 years post-infection. In conclusion, the developed species-specific oligonucleotide probes used in an RLB assay can simultaneously detect and identify several Ehrlichia and Anaplasma species. However, as no quantitative data for the detection limit are available yet, only positive results are interpretable at this stage.

  17. Multiple paternity and sporophytic inbreeding depression in a dioicous moss species.

    PubMed

    Szövényi, P; Ricca, M; Shaw, A J

    2009-11-01

    Multiple paternity (polyandry) frequently occurs in flowering plants and animals and is assumed to have an important function in the evolution of reproductive traits. Polyandry in bryophytes may occur among multiple sporophytes of a female gametophyte; however, its occurrence and extent is unknown. In this study we investigate the occurrence and extent of multiple paternity, spatial genetic structure, and sporophytic inbreeding depression in natural populations of a dioicous bryophyte species, Sphagnum lescurii, using microsatellite markers. Multiple paternity is prevalent among sporophytes of a female gametophyte and male genotypes exhibit significant skew in paternity. Despite significant spatial genetic structure in the population, suggesting frequent inbreeding, the number of inbred and outbred sporophytes was balanced, resulting in an average fixation coefficient and population level selfing rate of zero. In line with the prediction of sporophytic inbreeding depression sporophyte size was significantly correlated with the level of heterozygosity. Furthermore, female gametophytes preferentially supported sporophytes with higher heterozygosity. These results indicate that polyandry provides the opportunity for postfertilization selection in bryophytes having short fertilization distances and spatially structured populations facilitating inbreeding. Preferential maternal support of the more heterozygous sporophytes suggests active inbreeding avoidance that may have significant implications for mating system evolution in bryophytes.

  18. A Patchy Growth via Successive and Simultaneous Cambia: Key to Success of the Most Widespread Mangrove Species Avicennia marina?

    PubMed Central

    Schmitz, Nele; Robert, Elisabeth M. R.; Verheyden, Anouk; Kairo, James Gitundu; Beeckman, Hans; Koedam, Nico

    2008-01-01

    Background and Aims Secondary growth via successive cambia has been intriguing researchers for decades. Insight into the mechanism of growth layer formation is, however, limited to the cellular level. The present study aims to clarify secondary growth via successive cambia in the mangrove species Avicennia marina on a macroscopic level, addressing the formation of the growth layer network as a whole. In addition, previously suggested effects of salinity on growth layer formation were reconsidered. Methods A 1-year cambial marking experiment was performed on 80 trees from eight sites in two mangrove forests in Kenya. Environmental (soil water salinity and nutrients, soil texture, inundation frequency) and tree characteristics (diameter, height, leaf area index) were recorded for each site. Both groups of variables were analysed in relation to annual number of growth layers, annual radial increment and average growth layer width of stem discs. Key Results Between trees of the same site, the number of growth layers formed during the 1-year study period varied from only part of a growth layer up to four growth layers, and was highly correlated to the corresponding radial increment (0–5 mm year–1), even along the different sides of asymmetric stem discs. The radial increment was unrelated to salinity, but the growth layer width decreased with increasing salinity and decreasing tree height. Conclusions A patchy growth mechanism was proposed, with an optimal growth at distinct moments in time at different positions around the stem circumference. This strategy creates the opportunity to form several growth layers simultaneously, as observed in 14 % of the studied trees, which may optimize tree growth under favourable conditions. Strong evidence was provided for a mainly endogenous trigger controlling cambium differentiation, with an additional influence of current environmental conditions in a trade-off between hydraulic efficiency and mechanical stability. PMID

  19. Simultaneous reductions in emissions of black carbon and co-emitted species will weaken the aerosol net cooling effect

    NASA Astrophysics Data System (ADS)

    Wang, Z. L.; Zhang, H.; Zhang, X. Y.

    2015-04-01

    Black carbon (BC), a distinct type of carbonaceous material formed from the incomplete combustion of fossil and biomass based fuels under certain conditions, can interact with solar radiation and clouds through its strong light-absorption ability, thereby warming the Earth's climate system. Some studies have even suggested that global warming could be slowed down in the short term by eliminating BC emission due to its short lifetime. In this study, we estimate the influence of removing some sources of BC and other co-emitted species on the aerosol radiative effect by using an aerosol-climate atmosphere-only model BCC_AGCM2.0.1_CUACE/Aero with prescribed sea surface temperature and sea ice cover, in combination with the aerosol emissions from the Representative Concentration Pathways (RCPs) scenarios. We find that the global annual mean aerosol net cooling effect at the top of the atmosphere (TOA) will be enhanced by 0.12 W m-2 compared with recent past year 2000 levels if the emissions of only BC are reduced to the level projected for 2100 based on the RCP2.6 scenario. This will be beneficial~for the mitigation of global warming. However, both aerosol negative direct and indirect radiative effects are weakened when BC and its co-emitted species (sulfur dioxide and organic carbon) are simultaneously reduced. Relative to year 2000 levels, the global annual mean aerosol net cooling effect at the TOA will be weakened by 1.7-2.0 W m-2 if the emissions of all these aerosols are decreased to the levels projected for 2100 in different ways based on the RCP2.6, RCP4.5, and RCP8.5 scenarios. Because there are no effective ways to remove the BC exclusively without influencing the other co-emitted components, our results therefore indicate that a reduction in BC emission can lead to an unexpected warming on the Earth's climate system in the future.

  20. Multiple species production systems: reversing underdevelopment and nonsustainability in Latin America.

    PubMed

    Uhart, Marcela; Milano, Fernando

    2002-10-01

    Latin America (LA) is suffering the environmental consequences of worldwide increased productivity and agricultural expansion as well as strong economic restrictions. To survive, LA landowners must turn to higher income products and/or increase productivity. Alternatives are few. But while intensification relies on unaffordable and nonsustainable subsidies, diversification is solely dependent on improved management of available resources. Diversified, multiple-species production systems (MSPS) add wildlife use to traditional production systems, promoting economic and ecological stability. We present examples of MSPS in Latin America. Although results are technically encouraging, their future sustainability is threatened by: i) local subvaluation of wildlife and ii) restricted international markets.

  1. Modeling reaction and transport of multiple species in water distribution systems.

    PubMed

    Shang, Feng; Uber, James G; Rossman, Lewis A

    2008-02-01

    A general framework for modeling the reaction and transport of multiple, interacting chemical species in drinking water distribution systems is developed. It accommodates reactions between constituents in both the bulk flow (through pipes and storage tanks) and those attached to pipe walls. The framework has been implemented as an extension to the well-known EPANET programmer's toolkit (a library of functions that simulates hydraulic behavior and water quality transport in pipe networks). The implementation allows modelers to define the particular species of interest and their chemical equilibrium and reaction rate equations in a natural fashion using standard functional notation. It also employs several different numerical methods, including a stiff differential equation solver, to solve the reaction/equilibrium system throughout the pipe network using the standard EPANET transport algorithm. The flexibility and power of the framework is demonstrated with two examples that model water quality dynamics governed by different reaction/equilibrium systems.

  2. Extension of the Viscous Collision Limiting Direct Simulation Monte Carlo Technique to Multiple Species

    NASA Technical Reports Server (NTRS)

    Liechty, Derek S.; Burt, Jonathan M.

    2016-01-01

    There are many flows fields that span a wide range of length scales where regions of both rarefied and continuum flow exist and neither direct simulation Monte Carlo (DSMC) nor computational fluid dynamics (CFD) provide the appropriate solution everywhere. Recently, a new viscous collision limited (VCL) DSMC technique was proposed to incorporate effects of physical diffusion into collision limiter calculations to make the low Knudsen number regime normally limited to CFD more tractable for an all-particle technique. This original work had been derived for a single species gas. The current work extends the VCL-DSMC technique to gases with multiple species. Similar derivations were performed to equate numerical and physical transport coefficients. However, a more rigorous treatment of determining the mixture viscosity is applied. In the original work, consideration was given to internal energy non-equilibrium, and this is also extended in the current work to chemical non-equilibrium.

  3. Adaptation of a stage-projection model for species with multiple year reproductive cycles

    USGS Publications Warehouse

    Gilbert, James R.; Udevitz, Mark S.

    1997-01-01

    We apply stage projection matrices to multiple age and reproductive categories, deriving the stable age - reproductive category distribution for populations with multi-year reproductive cycles and identifying conditions for the existence of a dominant latent root. Given the stable distribution of age and reproductive category and the number of female young for each reproductive category, the age specific fecundity rates can be calculated. For species with multi-year reproductive cycles, the fecundity rate associated with the stable age distribution is often not a smooth function of age, but fluctuates as a larger or smaller fraction of females becomes available to breed. We suggest that fecundity rates for species with multi-year reproductive cycles be defined in terms of litter size and probabilities of conception and successful gestation rather than average fecundity.

  4. Extension of the viscous collision limiting direct simulation Monte Carlo technique to multiple species

    NASA Astrophysics Data System (ADS)

    Liechty, Derek S.; Burt, Jonathan M.

    2016-11-01

    There are many flows fields that span a wide range of length scales where regions of both rarefied and continuum flow exist and neither direct simulation Monte Carlo (DSMC) nor computational fluid dynamics (CFD) provide the appropriate solution everywhere. Recently, a new viscous collision limited (VCL) DSMC technique was proposed to incorporate effects of physical diffusion into collision limiter calculations to make the low Knudsen number regime normally limited to CFD more tractable for an all-particle technique. This original work had been derived for a single-species gas. The current work extends the VCL-DSMC technique to gases with multiple species. Similar derivations were performed to equate numerical and physical transport coefficients. However, a more rigorous treatment of determining the mixture viscosity is applied. In the original work, consideration was given to internal energy non-equilibrium, and this is also extended in the current work to chemical non-equilibrium.

  5. Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis.

    PubMed

    de Vienne, Damien M; Ollier, Sébastien; Aguileta, Gabriela

    2012-06-01

    Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and are thus likely to share the same evolutionary history. On the other hand, it is also essential to identify which genes and species produce discordant topologies and therefore evolve in a different way or represent noise in the data. The latter are outlier genes or species and they can provide a wealth of information on potentially interesting biological processes, such as incomplete lineage sorting, hybridization, and horizontal gene transfers. Here, we propose a new method to explore the genomic tree space and detect outlier genes and species based on multiple co-inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced by individual genes. Our method allows the rapid identification of outlier genes and species by extracting the similarities and discrepancies, in terms of the pairwise distances, between all the species in all the trees, simultaneously. This is achieved by using MCOA, which finds successive decomposition axes from individual ordinations (i.e., derived from distance matrices) that maximize a covariance function. The method is freely available as a set of R functions. The source code and tutorial can be found online at http://phylomcoa.cgenomics.org.

  6. Cockles, barnacles and ascidians compose a subtidal facilitation cascade with multiple hierarchical levels of foundation species.

    PubMed

    Yakovis, Eugeniy; Artemieva, Anna

    2017-03-22

    Facilitation cascades occur when multiple foundation species in a community are involved in a hierarchy of positive interactions, and consist of a primary facilitator which positively affects secondary facilitators, each supporting a suit of dependent species. There is no theoretical limit to the number of levels in a facilitation cascade, yet the existence of more than two has rarely been examined. We manipulated biogenic substrate produced by a primary facilitator (cockle shells) and a secondary facilitator (barnacles and their empty tests) in a space-limited subtidal community to test the hypothesis that solitary ascidians would be the third-level facilitator. In the field, most ascidians were found on barnacles, and most barnacles occupied cockle shells. To produce this pattern, barnacles could nurse ascidians (a longer 'facilitation chain') or outcompete them from cockle shells (a shorter chain). Experimental results clearly supported the nursing hypothesis providing evidence for a facilitation cascade with three hierarchical levels of foundation species. Our findings confirm that like predation and competition, positive interspecific interactions nest into multi-tier hierarchies with numerous levels. While the number of foundation species should increase community stability and resilience as it increases diversity and reduces environmental stress, facilitation chain length may have the opposite effect.

  7. Forelimb preferences in human beings and other species: multiple models for testing hypotheses on lateralization.

    PubMed

    Versace, Elisabetta; Vallortigara, Giorgio

    2015-01-01

    Functional preferences in the use of right/left forelimbs are not exclusively present in humans but have been widely documented in a variety of vertebrate and invertebrate species. A matter of debate is whether non-human species exhibit a degree and consistency of functional forelimb asymmetries comparable to human handedness. The comparison is made difficult by the variability in hand use in humans and the few comparable studies conducted on other species. In spite of this, interesting continuities appear in functions such as feeding, object manipulation and communicative gestures. Studies on invertebrates show how widespread forelimb preferences are among animals, and the importance of experience for the development of forelimb asymmetries. Vertebrate species have been extensively investigated to clarify the origins of forelimb functional asymmetries: comparative evidence shows that selective pressures for different functions have likely driven the evolution of human handedness. Evidence of a complex genetic architecture of human handedness is in line with the idea of multiple evolutionary origins of this trait.

  8. Hydrodynamic description of an unmagnetized plasma with multiple ion species. I. General formulation

    NASA Astrophysics Data System (ADS)

    Simakov, Andrei N.; Molvig, Kim

    2016-03-01

    A generalization of the Braginskii ion fluid description [S. I. Braginskii, Sov. Phys. - JETP 6, 358 (1958)] to the case of an unmagnetized collisional plasma with multiple ion species is presented. An asymptotic expansion in the ion Knudsen number is used to derive the individual ion species continuity, as well as the total ion mass density, momentum, and energy evolution equations accurate through the second order. Expressions for the individual ion species drift velocities with respect to the center of mass reference frame, as well as for the total ion heat flux and viscosity, which are required to close the fluid equations, are evaluated in terms of the first-order corrections to the lowest order Maxwellian ion velocity distribution functions. A variational formulation for evaluating such corrections and its relation to the plasma entropy are presented. Employing trial functions for the corrections, written in terms of expansions in generalized Laguerre polynomials, and maximizing the resulting functionals produce two systems of linear equations (for "vector" and "tensor" portions of the corrections) for the expansion coefficients. A general matrix formulation of the linear systems as well as expressions for the resulting transport fluxes are presented in forms convenient for numerical implementation. The general formulation is employed in Paper II [A. N. Simakov and K. Molvig, Phys. Plasmas 23, 032116 (2016)] to evaluate the individual ion drift velocities and the total ion heat flux and viscosity for specific cases of two and three ion species plasmas.

  9. Molecular Diversity Within Melanomys caliginosus (Rodentia: Oryzomyini): Evidence for Multiple Species

    PubMed Central

    Hanson, J. Delton; Bradley, Robert D.

    2010-01-01

    Nucleotide sequences from the mitochondrial DNA cytochrome-b gene were used to infer phylogenetic relationships and estimate genetic distances from 10 individuals of Melanomys caliginosus and to explore the hypothesis that this taxon is comprised of multiple species. Individuals of four geographic populations of M. caliginosus from Central America (Nicaragua and Costa Rica), Panama, Venezuela, and Ecuador, respectively, were included in this analysis. Topologies obtained from maximum parsimony and Bayesian inference analyses were identical and produced clades referable to each of the geographic populations. Genetic distances between any pair-wise comparisons of the four groups (except between Panamanian and Venezuelan samples) were comparable to values estimated from comparisons of sister species in the closely related genus Nectomys. Distances between samples from Panama and Venezuela were greater than those of samples within the Ecuadorian and Central American clades, but less than that between species of Nectomys. Based on results from the sequence data, it appears that all four of the populations should be elevated to species level; however, additional data are needed to resolve the nomenclature of the Panamanian and Venezuelan populations. PMID:21614136

  10. Forelimb preferences in human beings and other species: multiple models for testing hypotheses on lateralization

    PubMed Central

    Versace, Elisabetta; Vallortigara, Giorgio

    2015-01-01

    Functional preferences in the use of right/left forelimbs are not exclusively present in humans but have been widely documented in a variety of vertebrate and invertebrate species. A matter of debate is whether non-human species exhibit a degree and consistency of functional forelimb asymmetries comparable to human handedness. The comparison is made difficult by the variability in hand use in humans and the few comparable studies conducted on other species. In spite of this, interesting continuities appear in functions such as feeding, object manipulation and communicative gestures. Studies on invertebrates show how widespread forelimb preferences are among animals, and the importance of experience for the development of forelimb asymmetries. Vertebrate species have been extensively investigated to clarify the origins of forelimb functional asymmetries: comparative evidence shows that selective pressures for different functions have likely driven the evolution of human handedness. Evidence of a complex genetic architecture of human handedness is in line with the idea of multiple evolutionary origins of this trait. PMID:25798121

  11. Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source

    PubMed Central

    Benazzo, A; Ghirotto, S; Vilaça, S T; Hoban, S

    2015-01-01

    The introduction of invasive species to new locations (that is, biological invasions) can have major impact on biodiversity, agriculture and public health. As such, determining the routes and modality of introductions with genetic data has become a fundamental goal in molecular ecology. To assist with this goal, new statistical methods and frameworks have been developed, such as approximate Bayesian computation (ABC) for inferring invasion history. Here, we present a model of invasion accounting for multiple introductions from a single source (MISS), a heretofore largely unexplored model. We simulate microsatellite data to evaluate the power of ABC to distinguish between single and multiple introductions from the same source, under a range of demographic parameters. We also apply ABC to microsatellite data from three invasions of bumblebee in New Zealand. In addition, we assess the performance of several methods of summary statistics selection. Our simulated results suggested good ability to distinguish between one- and two-wave models over much but not all of the parameter space tested, independent of summary statistics used. Globally, parameter estimation was good except for bottleneck timing. For one of the bumblebee species, we clearly rejected the MISS model, while for the other two we found inconclusive results. Since a second wave may provide genetic reinforcement to initial colonists, help relieve inbreeding among founders, or increase the hazard of the invasion, its detection may be crucial for managing invasions; we suggest that the MISS model could be considered as a potential model in future theoretical and empirical studies of invasions. PMID:25920671

  12. The Coachella Valley Multiple Species Habitat Conservation Plan: a decade of delays.

    PubMed

    Alagona, Peter S; Pincetl, Stephanie

    2008-01-01

    This article describes the history of the Coachella Valley Multiple Species Habitat Conservation Plan (CVMSHCP), in the Riverside County region of Southern California. When this collaborative biodiversity conservation planning process began, in 1994, local participants and supporters had numerous factors working in their favor. Yet, as of April 2007, nearly 13 years had passed without an approved plan. This is a common problem. Many multiple species habitat conservation plans now take more than a decade to complete, and the long duration of these processes often results in negative consequences. The CVMSHCP process became bogged down-despite strong scientific input and many political advantages-due to problematic relationships between the Plan's local supporters, its municipal signatory parties, and officials from the state and federal wildlife agencies, particularly the regional office of the US Fish and Wildlife Service. This case study demonstrates the crucial importance of institutional structures and relationships, process management, and timeliness in habitat conservation planning. We conclude by offering several related recommendations for future HCP processes.

  13. Optimising the Application of Multiple-Capture Traps for Invasive Species Management Using Spatial Simulation

    PubMed Central

    Warburton, Bruce; Gormley, Andrew M.

    2015-01-01

    Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes) it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single

  14. Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

    PubMed

    Warburton, Bruce; Gormley, Andrew M

    2015-01-01

    Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes) it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single

  15. Connexin36 Expression in the Mammalian Retina: A Multiple-Species Comparison

    PubMed Central

    Kovács-Öller, Tamás; Debertin, Gábor; Balogh, Márton; Ganczer, Alma; Orbán, József; Nyitrai, Miklós; Balogh, Lajos; Kántor, Orsolya; Völgyi, Béla

    2017-01-01

    Much knowledge about interconnection of human retinal neurons is inferred from results on animal models. Likewise, there is a lack of information on human retinal electrical synapses/gap junctions (GJ). Connexin36 (Cx36) forms GJs in both the inner and outer plexiform layers (IPL and OPL) in most species including humans. However, a comparison of Cx36 GJ distribution in retinas of humans and popular animal models has not been presented. To this end a multiple-species comparison was performed in retinas of 12 mammals including humans to survey the Cx36 distribution. Areas of retinal specializations were avoided (e.g., fovea, visual streak, area centralis), thus observed Cx36 distribution differences were not attributed to these species-specific architecture of central retinal areas. Cx36 was expressed in both synaptic layers in all examined retinas. Cx36 plaques displayed an inhomogenous IPL distribution favoring the ON sublamina, however, this feature was more pronounced in the human, swine and guinea pig while it was less obvious in the rabbit, squirrel monkey, and ferret retinas. In contrast to the relative conservative Cx36 distribution in the IPL, the labels in the OPL varied considerably among mammals. In general, OPL plaques were rare and rather small in rod dominant carnivores and rodents, whereas the human and the cone rich guinea pig retinas displayed robust Cx36 labels. This survey presented that the human retina displayed two characteristic features, a pronounced ON dominance of Cx36 plaques in the IPL and prevalent Cx36 plaque conglomerates in the OPL. While many species showed either of these features, only the guinea pig retina shared both. The observed similarities and subtle differences in Cx36 plaque distribution across mammals do not correspond to evolutionary distances but may reflect accomodation to lifestyles of examined species. PMID:28337128

  16. Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions

    PubMed Central

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.; Stensvold, Christen Rune; Nejsum, Peter

    2015-01-01

    Background The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found in primates. Methods and Findings We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes of Trichuris recovered from a human and a porcine host in China and from a françois’ leaf-monkey (China) were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from Trichuris from françois’ leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related. Conclusion and Significance Our results indicate that Trichuris species infecting humans and pigs are phylogenetically distinct across geographical regions, which might have important implications for the implementation of suitable and effective control strategies in different regions. Moreover, we provide support for the hypothesis that Trichuris infecting primates represents a complex of cryptic species with some species being able to infect both humans and non-human primates

  17. Interactions among invaders: community and ecosystem effects of multiple invasive species in an experimental aquatic system.

    PubMed

    Johnson, Pieter T J; Olden, Julian D; Solomon, Christopher T; Vander Zanden, M Jake

    2009-02-01

    With ecosystems increasingly supporting multiple invasive species, interactions among invaders could magnify or ameliorate the undesired consequences for native communities and ecosystems. We evaluated the individual and combined effects of rusty crayfish (Orconectes rusticus) and Chinese mystery snails [Bellamya (=Cipangopaludina) chinensis] on native snail communities (Physa, Helisoma and Lymnaea sp.) and ecosystem attributes (algal chlorophyll a and nutrient concentrations). Both invaders are widespread in the USA and commonly co-occur within northern temperate lakes, underscoring the importance of understanding their singular and joint effects. An outdoor mesocosm experiment revealed that while the two invaders had only weakly negative effects upon one another, both negatively affected the abundance and biomass of native snails, and their combined presence drove one native species to extinction and reduced a second by >95%. Owing to its larger size and thicker shell, adult Bellamya were protected from crayfish attack relative to native species (especially Physa and Lymnaea), suggesting the co-occurrence of these invaders in nature could have elevated consequences for native communities. The per capita impacts of Orconectes (a snail predator) on native snails were substantially greater than those of Bellamya (a snail competitor). Crayfish predation also had a cascading effect by reducing native snail biomass, leading to increased periphyton growth. Bellamya, in contrast, reduced periphyton biomass, likely causing a reduction in growth by native lymnaeid snails. Bellamya also increased water column N:P ratio, possibly because of a low P excretion rate relative to native snail species. Together, these findings highlight the importance of understanding interactions among invasive species, which can have significant community- and ecosystem-level effects.

  18. Recombination in liquid filled ionisation chambers with multiple charge carrier species: Theoretical and numerical results

    NASA Astrophysics Data System (ADS)

    Aguiar, P.; González-Castaño, D. M.; Gómez, F.; Pardo-Montero, J.

    2014-10-01

    Liquid-filled ionisation chambers (LICs) are used in radiotherapy for dosimetry and quality assurance. Volume recombination can be quite important in LICs for moderate dose rates, causing non-linearities in the dose rate response of these detectors, and needs to be corrected for. This effect is usually described with Greening and Boag models for continuous and pulsed radiation respectively. Such models assume that the charge is carried by two different species, positive and negative ions, each of those species with a given mobility. However, LICs operating in non-ultrapure mode can contain different types of electronegative impurities with different mobilities, thus increasing the number of different charge carriers. If this is the case, Greening and Boag models can be no longer valid and need to be reformulated. In this work we present a theoretical and numerical study of volume recombination in parallel-plate LICs with multiple charge carrier species, extending Boag and Greening models. Results from a recent publication that reported three different mobilities in an isooctane-filled LIC have been used to study the effect of extra carrier species on recombination. We have found that in pulsed beams the inclusion of extra mobilities does not affect volume recombination much, a behaviour that was expected because Boag formula for charge collection efficiency does not depend on the mobilities of the charge carriers if the Debye relationship between mobilities and recombination constant holds. This is not the case in continuous radiation, where the presence of extra charge carrier species significantly affects the amount of volume recombination.

  19. SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species

    PubMed Central

    Veltri, Daniel; Wight, Martha Malapi; Crouch, Jo Anne

    2016-01-01

    Defining syntenic relationships among orthologous gene clusters is a frequent undertaking of biologists studying organismal evolution through comparative genomic approaches. With the increasing availability of genome data made possible through next-generation sequencing technology, there is a growing need for user-friendly tools capable of assessing synteny. Here we present SimpleSynteny, a new web-based platform capable of directly interrogating collinearity of local genomic neighbors across multiple species in a targeted manner. SimpleSynteny provides a pipeline for evaluating the synteny of a preselected set of gene targets across multiple organismal genomes. An emphasis has been placed on ease-of-use, and users are only required to submit FASTA files for their genomes and genes of interest. SimpleSynteny then guides the user through an iterative process of exploring and customizing genomes individually before combining them into a final high-resolution figure. Because the process is iterative, it allows the user to customize the organization of multiple contigs and incorporate knowledge from additional sources, rather than forcing complete dependence on the computational predictions. Additional tools are provided to help the user identify which contigs in a genome assembly contain gene targets and to optimize analyses of circular genomes. SimpleSynteny is freely available at: http://www.SimpleSynteny.com. PMID:27141960

  20. Simultaneous micro-electromembrane extractions of anions and cations using multiple free liquid membranes and acceptor solutions.

    PubMed

    Kubáň, Pavel; Boček, Petr

    2016-02-18

    Micro-electromembrane extractions (μ-EMEs) across free liquid membranes (FLMs) were applied to simultaneous extractions of anions and cations. A transparent narrow-bore polymeric tubing was filled with adjacent plugs of μL volumes of aqueous and organic solutions, which formed a stable five-phase μ-EME system. For the simultaneous μ-EMEs of anions and cations, aqueous donor solution was the central phase, which was sandwiched between two organic FLMs and two aqueous acceptor solutions. On application of electric potential, anions and cations in the donor solution migrated across the two FLMs and into the two peripheral acceptor solutions in the direction of anode and cathode, respectively. Visual monitoring of anionic (tartrazine) and cationic (phenosafranine) dye confirmed their simultaneous μ-EMEs and their rapid (in less than 5 min) transfers into anolyte and catholyte, respectively. The concept of simultaneous μ-EMEs was further examined with selected model analytes; KClO4 was used for μ-EMEs of inorganic anions and cations and ibuprofen and procaine for μ-EMEs of acidic and basic drugs. Quantitative analyses of the resulting acceptor solutions were carried out by capillary electrophoresis with capacitively coupled contactless conductivity detection (CE-C(4)D). Good extraction recoveries (91-94%) and repeatability of peak areas (≤6.3%) were achieved for 5 min μ-EMEs of K(+) and ClO4(-). Extraction recoveries and repeatability of peak areas for 5 min μ-EMEs of ibuprofen and procaine were also satisfactory and ranged from 35 to 63% and 7.6 to 11.3%, respectively. Suitability of the presented micro-extraction procedure was further demonstrated on simultaneous μ-EMEs with subsequent CE-C(4)D of ibuprofen and procaine from undiluted human urine samples.

  1. Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.

    PubMed

    Ren, Da Wei; Chen, Wen Feng; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2011-03-01

    A group of rhizobial strains isolated from nodules of multiple legume species grown in different geographical regions of China had identical 16S rRNA genes. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the novel strains formed a subclade in the genus Rhizobium together with Rhizobium galegae, Rhizobium huautlense and Rhizobium alkalisoli, with 99.8  % gene sequence similarity between the strains. The DNA-DNA relatedness values between the representative strain CCBAU 05176(T) and R. galegae ATCC 43677(T), R. huautlense S02(T) and R. alkalisoli CCBAU 01393(T) were 22.6  %, 8.9  % and 15.9  %, respectively. The novel strains were distinguished from recognized species of the genus Rhizobium by using a polyphasic approach, including PCR-based restriction fragment length polymorphism analysis (RFLP) of the 16S-23S intergenic spacer (IGS), phenotypic and physiological tests, sequence comparisons of housekeeping genes and cellular fatty acid profiles. Therefore, it is suggested that this group of strains represents a novel species for which the name Rhizobium vignae sp. nov. is proposed. The type strain is CCBAU 05176(T) (=HAMBI 3039(T)=LMG 25447(T)).

  2. Predicting multiple ecotoxicological profiles in agrochemical fungicides: a multi-species chemoinformatic approach.

    PubMed

    Speck-Planche, Alejandro; Kleandrova, Valeria V; Luan, Feng; Cordeiro, M Natália D S

    2012-06-01

    Agriculture is needed to deal with crop losses caused by biotic stresses like pests. The use of pesticides has played a vital role, contributing to improve crop production and harvest productivity, providing a better crop quality and supply, and consequently contributing with the improvement of the human health. An important group of these pesticides is fungicides. However, the use of these agrochemical fungicides is an important source of contamination, damaging the ecosystems. Several studies have been realized for the assessment of the toxicity in agrochemical fungicides, but the principal limitation is the use of structurally related compounds against usually one indicator species. In order to overcome this problem, we explore the quantitative structure-toxicity relationships (QSTR) in agrochemical fungicides. Here, we developed the first multi-species (ms) chemoinformatic approach for the prediction multiple ecotoxicological profiles of fungicides against 20 indicators species and their classifications in toxic or nontoxic. The ms-QSTR discriminant model was based on substructural descriptors and a heterogeneous database of compounds. The percentages of correct classification were higher than 90% for both, training and prediction series. Also, substructural alerts responsible for the toxicity/no toxicity in fungicides respect all ecotoxicological profiles, were extracted and analyzed.

  3. Multiple dispersal vectors drive range expansion in an invasive marine species.

    PubMed

    Richardson, Mark F; Sherman, Craig D H; Lee, Randall S; Bott, Nathan J; Hirst, Alastair J

    2016-10-01

    The establishment and subsequent spread of invasive species is widely recognized as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, environmental DNA (eDNA) plankton sampling and hydrodynamic modelling, we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow, a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast, hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems.

  4. Multiple Species Habitat Conservation Planning: Goals and Strategies of Local Governments.

    PubMed

    LOEW

    2000-07-01

    Drawing from experiences gained from the development and implementation of four approved habitat conservation plans (HCPs), I describe the goals and strategies used by the nine local government members of the Riverside County Habitat Conservation Agency (RCHCA) to reconcile conflicts among a rapidly growing population and the need to conserve the habitat of a number of declining wildlife species in western Riverside County, California. Several important goals have been pursued by RCHCA member governments in their sponsorship of multiple-species habitat conservation plans (MSHCPs), including (1) establishing certainty and control over future uses of land; (2) eliminating project-by-project negotiations with federal and state wildlife agencies; (3) coordinating mitigation obligations under the Endangered Species Act, Clean Water Act, California Environmental Quality Act, and other federal and state laws; (4) reducing conflict and litigation resulting from land development activities; and (5) ensuring that wildlife conservation activities are conducted in a manner that permits local governments to perform those functions necessary to maintain public health, safety, and welfare. I also describe the emergence of strategies by local governments to achieve MSHCP goals, including (1) use of an inclusive planning process that seeks to build consensus among affected interests; (2) extensive involvement of federal and state wildlife agencies in the preparation of MSHCP documents; (3) management of public lands to support MSHCP conservation objectives; (4) encouragement of voluntary conservation by private property owners through incentive programs; and (5) active solicitation of federal and state funding for MSHCP implementation activities.

  5. Predicting probability of occurrence and factors affecting distribution and abundance of three Ozark endemic crayfish species at multiple spatial scales

    USGS Publications Warehouse

    Nolen, Matthew S.; Magoulick, Daniel D.; DiStefano, Robert J.; Imhoff, Emily M.; Wagner, Brian K.

    2014-01-01

    We found that a range of environmental variables were important in predicting crayfish distribution and abundance at multiple spatial scales and their importance was species-, response variable- and scale dependent. We would encourage others to examine the influence of spatial scale on species distribution and abundance patterns.

  6. Simultaneously removal of inorganic arsenic species from stored rainwater in arsenic endemic area by leaves of Tecomella undulata: a multivariate study.

    PubMed

    Brahman, Kapil Dev; Kazi, Tasneem Gul; Afridi, Hassan Imran; Baig, Jameel Ahmed; Abro, Muhammad Ishaque; Arain, Sadaf Sadia; Ali, Jamshed; Khan, Sumaira

    2016-08-01

    In the present study, an indigenous biosorbent (leaves of Tecomella undulata) was used for the simultaneous removal of inorganic arsenic species (As(III) and As(V)) from the stored rainwater in Tharparkar, Pakistan. The Plackett-Burman experimental design was used as a multivariate strategy for the evaluation of the effects of six factors/variables on the biosorption of inorganic arsenic species, simultaneously. Central composite design (CCD) was used to found the optimum values of significant factors for the removal of As(III) and As(V). Initial concentrations of both inorganic As species, pH, biosorbent dose, and contact time were selected as independent factors in CCD, while the adsorption capacity (q e) was considered as a response function. The separation of inorganic As species in water samples before and after biosorption was carried out by cloud point and solid-phase extraction methods. Theoretical values of pH, concentration of analytes, biosorbent dose, and contact time were calculated by quadratic equation for 100 % biosorption of both inorganic As species in aqueous media. Experimental data were modeled by Langmuir and Freundlich isotherms. Thermodynamic and kinetic study indicated that the biosorption of As(III) and As(V) was followed by pseudo second order. It was concluded that the indigenous biosorbent material efficiently and simultaneously removed both As species in the range of 70.8 to 98.5 % of total contents in studied ground water samples. Graphical abstract Optimizing the significant varable by central 2(3) + star orthogonal composite design.

  7. Simultaneous PET-MRI reveals brain function in activated and resting state on metabolic, hemodynamic and multiple temporal scales.

    PubMed

    Wehrl, Hans F; Hossain, Mosaddek; Lankes, Konrad; Liu, Chih-Chieh; Bezrukov, Ilja; Martirosian, Petros; Schick, Fritz; Reischl, Gerald; Pichler, Bernd J

    2013-09-01

    Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) is a new tool to study functional processes in the brain. Here we study brain function in response to a barrel-field stimulus simultaneously using PET, which traces changes in glucose metabolism on a slow time scale, and functional MRI (fMRI), which assesses fast vascular and oxygenation changes during activation. We found spatial and quantitative discrepancies between the PET and the fMRI activation data. The functional connectivity of the rat brain was assessed by both modalities: the fMRI approach determined a total of nine known neural networks, whereas the PET method identified seven glucose metabolism-related networks. These results demonstrate the feasibility of combined PET-MRI for the simultaneous study of the brain at activation and rest, revealing comprehensive and complementary information to further decode brain function and brain networks.

  8. Decision analysis for designing marine protected areas for multiple species with uncertain fishery status.

    PubMed

    White, J Wilson; Botsford, Louis W; Moffitt, Elizabeth A; Fischer, Douglas T

    2010-09-01

    Marine protected areas (MPAs) are growing in popularity as a conservation tool, and there are increasing calls for additional MPAs. Meta-analyses indicate that most MPAs successfully meet the minimal goal of increasing biomass inside the MPA, while some do not, leaving open the important question of what makes MPAs successful. An often-overlooked aspect of this problem is that the success of fishery management outside MPA boundaries (i.e., whether a population is overfished) affects how well MPAs meet both conservation goals (e.g., increased biomass) and economic goals (e.g., minimal negative effects on fishery yield). Using a simple example of a system with homogeneous habitat and periodically spaced MPAs, we show that, as area in MPAs increases, (1) conservation value (biomass) may initially be zero, implying no benefit, then at some point increases monotonically; and (2) fishery yield may be zero, then increases monotonically to a maximum beyond which further increase in MPA area causes yield to decline. Importantly, the points at which these changes in slope occur vary among species and depend on management outside MPAs. Decision makers considering the effects of a potential system of MPAs on multiple species are confronted by a number of such cost-benefit curves, and it is usually impossible to maximize benefits and minimize costs for all species. Moreover, the precise shape of each curve is unknown due to uncertainty regarding the fishery status of each species. Here we describe a decision-analytic approach that incorporates existing information on fishery stock status to present decision makers with the range of likely outcomes of MPA implementation. To summarize results from many species whose overfishing status is uncertain, our decision-analysis approach involves weighted averages over both overfishing uncertainty and species. In an example from an MPA decision process in California, USA, an optimistic projection of future fishery management success led

  9. Reconstructing Water Column Hydrography Using Individual Shell Stable Isotope Data From Multiple Planktic Foraminifera Species

    NASA Astrophysics Data System (ADS)

    Spero, H. J.; Fehrenbacher, J. S.; Davis, K. V.; Griffin, J. M.; Grimm, B. L.; Kercher, P.; Kostlan, M.; Menicucci, A. J.; Santare, L.; Starnes, J.; Vetter, L.; Wilbanks, E.; Wildgoose, M.

    2012-12-01

    Oxygen and carbon isotope data from planktic foraminifera play an important role in reconstructing past ocean temperatures, salinity and nutrient content since they first appeared in a publication by Cesare Emiliani in 1955. For most of the next 5 decades, research focused on analyses of foraminifera shells from a few mixed layer and thermocline species. Such analyses have typically been conducted on multiple shell samples from an assemblage of foraminifera, pooled into a single analysis. It has long been recognized that significant depth-specific and seasonal information is contained within populations of shells and that analyses of single specimens and some underutilized species could provide novel information about water column processes and hydrography. Nevertheless, it has only been in the past decade that researchers have begun to explore this individual-shell multispecies paleoenvironmental archive for paleoceanographic applications. As a result of experiments with living foraminifera, our understanding of the mechanisms that contribute to the vital effect black box that governs inter- and intraspecific geochemical variability in foraminifera has attained a level of maturity that now allows us to reconcile foraminifera biology and ecology with the geochemical signals obtained from marine sediments. Within this context, we present individual shell carbon and oxygen isotope data from 11 species of planktonic foraminifera (G. ruber (pink & white var.), G. sacculifer, O. universa, G. siphonifera, S. dehiscens, G. conglobatus, G. menardii, N. dutertrei, P. obliquiloculata, G. truncatulinoides and G. tumida). We use these data to reconstruct late Holocene water column hydrography from cores in the Caribbean (ODP 999A; 12°45'N, 78°25'W; 2,827 m) and eastern equatorial Pacific (TR163-19; 2°16'N, 90°57'W, 2348 m). We show that interpretation of such complex data sets requires consideration of biological and environmental controls such as symbiont photosynthesis

  10. Welding fumes from stainless steel gas metal arc processes contain multiple manganese chemical species.

    PubMed

    Keane, Michael; Stone, Samuel; Chen, Bean

    2010-05-01

    Fumes from a group of gas metal arc welding (GMAW) processes used on stainless steel were generated using three different metal transfer modes and four different shield gases. The objective was to identify and measure manganese (Mn) species in the fumes, and identify processes that are minimal generators of Mn species. The robotic welding system was operated in short-circuit (SC) mode (Ar/CO2 and He/Ar), axial spray (AXS) mode (Ar/O2 and Ar/CO2), and pulsed axial-spray (PAXS) mode (Ar/O2). The fumes were analyzed for Mn by a sequential extraction process followed by inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analysis, and by X-ray diffraction (XRD). Total elemental Mn, iron (Fe), chromium (Cr) and nickel (Ni) were separately measured after aqua regia digestion and ICP-AES analysis. Soluble Mn2+, Fe2+, Fe3+, and Ni2+ in a simple biological buffer (phosphate-buffered saline) were determined at pH 7.2 and 5.0 after 2 h incubation at 37 C by ion chromatography. Results indicate that Mn was present in soluble form, acid-soluble form, and acid-soluble form after reduction by hydroxylamine, which represents soluble Mn0 and Mn2+ compounds, other Mn2+ compounds, and (Mn3+ and Mn4+) compounds, respectively. The dominant fraction was the acid-soluble Mn2+ fraction, but results varied with the process and shield gas. Soluble Mn mass percent in the fume ranged from 0.2 to 0.9%, acid-soluble Mn2+ compounds ranged from 2.6 to 9.3%, and acid plus reducing agent-soluble (Mn3+ and Mn4+) compounds ranged from 0.6 to 5.1%. Total Mn composition ranged from 7 to 15%. XRD results showed fumes had a crystalline content of 90-99% Fe3O4, and showed evidence of multiple Mn oxides, but overlaps and weak signals limited identification. Small amounts of the Mn2+ in the fume (<0.01 to ≈ 1% or <0.1 to ≈ 10 microg ml(-1)) and Ni2+ (<0.01 to ≈ 0.2% or <0.1 to ≈ 2 mg ml(-1)) ions were found in biological buffer media, but amounts were highly dependent on pH and the

  11. Simultaneous determination of monomethylmercury, monobutyltin, dibutyltin and tributyltin in environmental samples by multi-elemental-species-specific isotope dilution analysis using electron ionisation GC-MS.

    PubMed

    Moreno, Maria Jimenez; Pacheco-Arjona, Jaime; Rodríguez-González, Pablo; Preud'Homme, Hugues; Amouroux, David; Donard, Olivier F X

    2006-11-01

    In this work, the simultaneous determination of four organometallic species (monomethylmercury, monobutyltin, dibutyltin and tributyltin) in environmental samples by using a GC-MS system with electron ionisation has been established. The measurement of isotope ratios in each species was accomplished by selecting the most adequate molecular cluster, and simple mathematical equations were applied to correct the contributions of 13C from the organic groups attached to the tin and mercury atoms. The influence of different parameters such as dwell time on the precision and accuracy of the measured isotope ratios in each target species has also been studied. The determination and the sample preparation procedures presented in this work were first individually validated by analysing several certified reference materials for butyltin compounds (mussel tissue CRM-477 and marine sediment SOPH-1) and for monomethylmercury (tuna fish CRM-464) using an innovative focused microwave technology for the extraction of the species from the solid samples. Additionally, the simultaneous determination of the four species was successfully validated by obtaining quantitative recoveries in spiked natural waters and by analysing the certified reference material BCR-710 (certified in tributyltin and monomethylmercury). The values obtained in such certified tissue were fully in agreement not only with the certified mass fractions but also with the proposed indicative values for mono- and dibutyltin.

  12. Simultaneous analysis of mercury and selenium species including chiral forms of selenomethionine in human urine and serum by HPLC column-switching coupled to ICP-MS.

    PubMed

    Moreno, F; García-Barrera, T; Gómez-Ariza, J L

    2010-10-01

    The simultaneous speciation of elements is of great concern, especially in the study of the interactions of species in living organisms. Here we report a method based on the coupling of HPLC-ICP-MS that is capable of separating and analyzing different selenium and mercury species (Se-methylselenocysteine, selenite, selenate, L-selenomethionine, D-selenomethionine, methylmercury and inorganic mercury). The proposed method uses two different mobile phases that are suitable for selenium and mercury speciation and leads to a successful determination of all the species in less than 27 min with good efficiency and resolution. The method was efficiently applied for simultaneous speciation of mercury and selenium in urine and in serum, the latter from umbilical cord samples. Selenocystine has been successfully identified in the former sample. Detection limits obtained were between 0.30 and 2.46 ng. Recovery studies of samples spiked with all species were performed to check the reliability of the method, and satisfactory recoveries (93-110%) were obtained in all cases. The relative standard deviations (RSDs) for species with ten replicate determinations of 80 μg L(-1) were between 4.5 and 9.2%. The proposed method offers a deeper insight into selenium and mercury interactions in the human body.

  13. Mutacins from Streptococcus mutans UA159 Are Active against Multiple Streptococcal Species

    PubMed Central

    Hossain, Mohammad Shahnoor; Biswas, Indranil

    2011-01-01

    Streptococcus mutans UA159, whose genome is completely sequenced, produces two nonlantibiotic mutacins, mutacin IV (encoded by nlmAB) and mutacin V (encoded by nlmC). In this study, we investigated the contribution of nlmA and nlmB to mutacin IV activity and demonstrated by performing genetic studies as well as by using semipurified molecules that, in contrast to a previous report, both of these genes are required for optimum mutacin IV activity. We also showed that mutacin IV is active against multiple Streptococcus species. In contrast, mutacin V displayed a narrower inhibitory range than mutacin IV. Our results suggest that mutacin IV and mutacin V may act synergistically to inhibit various organisms. PMID:21296932

  14. Development of an Immunochromatography Assay (QuickNavi-Ebola) to Detect Multiple Species of Ebolaviruses.

    PubMed

    Yoshida, Reiko; Muramatsu, Shino; Akita, Hiroshi; Saito, Yuji; Kuwahara, Miwa; Kato, Daisuke; Changula, Katendi; Miyamoto, Hiroko; Kajihara, Masahiro; Manzoor, Rashid; Furuyama, Wakako; Marzi, Andrea; Feldmann, Heinz; Mweene, Aaron; Masumu, Justin; Kapeteshi, Jimmy; Muyembe-Tamfum, Jean-Jacques; Takada, Ayato

    2016-10-15

    The latest outbreak of Ebola virus disease (EVD) in West Africa has highlighted the urgent need for the development of rapid and reliable diagnostic assays. We used monoclonal antibodies specific to the ebolavirus nucleoprotein to develop an immunochromatography (IC) assay (QuickNavi-Ebola) for rapid diagnosis of EVD. The IC assay was first evaluated with tissue culture supernatants of infected Vero E6 cells and found to be capable of detecting 10(3)-10(4) focus-forming units/mL of ebolaviruses. Using serum samples from experimentally infected nonhuman primates, we confirmed that the assay could detect the viral antigen shortly after disease onset. It was also noted that multiple species of ebolaviruses could be detected by the IC assay. Owing to the simplicity of the assay procedure and absence of requirements for special equipment and training, QuickNavi-Ebola is expected to be a useful tool for rapid diagnosis of EVD.

  15. A Distributed Agent Implementation of Multiple Species Flocking Model for Document Partitioning Clustering

    SciTech Connect

    Cui, Xiaohui; Potok, Thomas E

    2006-01-01

    The Flocking model, first proposed by Craig Reynolds, is one of the first bio-inspired computational collective behavior models that has many popular applications, such as animation. Our early research has resulted in a flock clustering algorithm that can achieve better performance than the Kmeans or the Ant clustering algorithms for data clustering. This algorithm generates a clustering of a given set of data through the embedding of the highdimensional data items on a two-dimensional grid for efficient clustering result retrieval and visualization. In this paper, we propose a bio-inspired clustering model, the Multiple Species Flocking clustering model (MSF), and present a distributed multi-agent MSF approach for document clustering.

  16. Species limits and relationships within Otidea inferred from multiple gene phylogenies.

    PubMed

    Hansen, K; Olariaga, I

    2015-12-01

    The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high species diversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multi-gene analyses it formed a highly supported monophyletic group. Species delimitation within Otidea is controversial and much confusion has prevailed in the naming of taxa. To provide a phylogenetic hypothesis of Otidea, elucidate species diversity and limits we compiled a four-gene dataset including the nuclear LSU rDNA and three nuclear protein-coding genes (RPB1, RPB2 and EF-1α) for 89 specimens (total 4 877 nucleotides). These were selected from a larger sample of material studied using morphology and 146 ITS (ITS1-5.8S-ITS2) and 168 LSU rDNA sequences to represent the full genetic diversity. Using genealogical concordance phylogenetic species recognition (GCPSR), Bayesian and maximum likelihood analyses of the individual datasets resolved 25 species of Otidea. An additional eight singletons are considered to be distinct species, because they were genetically divergent from their sisters. Sequences of multiple genes were included from 13 holotypes, one neotype and three epitypes. Otidea angusta, O. myosotis and O. papillata f. pallidefurfuracea are nested within O. nannfeldtii, O. leporina and O. tuomikoskii, respectively and are considered synonyms. Otidea cantharella var. minor is shown to be a distinct species. Five new species were discovered: O. oregonensis and O. pseudoleporina for North America; and O. borealis, O. brunneoparva and O. subformicarum for Europe. The analyses of the individual four gene datasets yielded phylogenies that were highly concordant topologically, except for the RPB1 that showed supported conflict for some nodes in Bayesian analysis. Excluding the RPB1 from the combined analyses produced an identical topology to the four-gene phylogeny, but with higher support for several basal nodes and lower support for several shallow

  17. Invasive species information networks: Collaboration at multiple scales for prevention, early detection, and rapid response to invasive alien species

    USGS Publications Warehouse

    Simpson, Annie; Jarnevich, Catherine S.; Madsen, John; Westbrooks, Randy G.; Fournier, Christine; Mehrhoff, Les; Browne, Michael; Graham, Jim; Sellers, Elizabeth A.

    2009-01-01

    Accurate analysis of present distributions and effective modeling of future distributions of invasive alien species (IAS) are both highly dependent on the availability and accessibility of occurrence data and natural history information about the species. Invasive alien species monitoring and detection networks (such as the Invasive Plant Atlas of New England and the Invasive Plant Atlas of the MidSouth) generate occurrence data at local and regional levels within the United States, which are shared through the US National Institute of Invasive Species Science. The Inter-American Biodiversity Information Network's Invasives Information Network (I3N), facilitates cooperation on sharing invasive species occurrence data throughout the Western Hemisphere. The I3N and other national and regional networks expose their data globally via the Global Invasive Species Information Network (GISIN). International and interdisciplinary cooperation on data sharing strengthens cooperation on strategies and responses to invasions. However, limitations to effective collaboration among invasive species networks leading to successful early detection and rapid response to invasive species include: lack of interoperability; data accessibility; funding; and technical expertise. This paper proposes various solutions to these obstacles at different geographic levels and briefly describes success stories from the invasive species information networks mentioned above. Using biological informatics to facilitate global information sharing is especially critical in invasive species science, as research has shown that one of the best indicators of the invasiveness of a species is whether it has been invasive elsewhere. Data must also be shared across disciplines because natural history information (e.g. diet, predators, habitat requirements, etc.) about a species in its native range is vital for effective prevention, detection, and rapid response to an invasion. Finally, it has been our

  18. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    SciTech Connect

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  19. Low-frequency guided waves in a fluid-filled borehole: Simultaneous effects of generation and scattering due to multiple fractures

    NASA Astrophysics Data System (ADS)

    Minato, Shohei; Ghose, Ranajit

    2017-03-01

    Low-frequency, axially-symmetric guided waves which propagate along a fluid-filled borehole (tube waves) are studied in order to characterize the hydraulic fractures intersecting the borehole. We formulate a new equation for the total tube wavefield, which includes simultaneous effects of (1) tube-wave scattering (reflection and transmission) due to wave propagation across hydraulic fractures, and (2) tube-wave generation due to incident plane P waves. The fracture is represented by the nonwelded interface boundary conditions. We use an appropriate form of the representation theorem in order to correctly handle the multiple scattering due to nonwelded interfaces. Our approach can implement any model that has so far been developed. We consider a recent model which includes simultaneous effects of fluid viscosity, dynamic fluid flow, and fracture compliance. The derived equation offers a number of important insights. We recognize that the effective generation amplitude contains the simultaneous effect of both tube-wave generation and scattering. This leads to a new physical understanding indicating that the tube waves are scattered immediately after generation. We show that this scattering is nonlinear with respect to interface compliance. This physical mechanism can be implicitly accounted for by considering more realistic boundary conditions. We also illustrate the application of the new equation in order to predict the complex signature of the total tube wavefield, including generation and scattering at multiple hydraulic fractures. A new formulation for focusing analyses is also derived in order to image and characterize the hydraulic fractures. The obtained results and discussions are important for interpretation, modeling, and imaging using low-frequency guided waves, in the presence of multiple fractures along a cylindrical inclusion.

  20. Overview of Nucleotide Sugar Transporter Gene Family Functions Across Multiple Species.

    PubMed

    Orellana, Ariel; Moraga, Carol; Araya, Macarena; Moreno, Adrian

    2016-08-14

    Glycoproteins and glycolipids are crucial in a number of cellular processes, such as growth, development, and responses to external cues, among others. Polysaccharides, another class of sugar-containing molecules, also play important structural and signaling roles in the extracellular matrix. The additions of glycans to proteins and lipids, as well as polysaccharide synthesis, are processes that primarily occur in the Golgi apparatus, and the substrates used in this biosynthetic process are nucleotide sugars. These proteins, lipids, and polysaccharides are also modified by the addition of sulfate groups in the Golgi apparatus in a series of reactions where nucleotide sulfate is needed. The required nucleotide sugar substrates are mainly synthesized in the cytosol and transported into the Golgi apparatus by nucleotide sugar transporters (NSTs), which can additionally transport nucleotide sulfate. Due to the critical role of NSTs in eukaryotic organisms, any malfunction of these could change glycan and polysaccharide structures, thus affecting function and altering organism physiology. For example, mutations or deletion on NST genes lead to pathological conditions in humans or alter cell walls in plants. In recent years, many NSTs have been identified and functionally characterized, but several remain unanalyzed. This study examined existing information on functionally characterized NSTs and conducted a phylogenetic analysis of 257 NSTs predicted from nine animal and plant model species, as well as from protists and fungi. From this analysis, relationships between substrate specificity and the primary NST structure can be inferred, thereby advancing understandings of nucleotide sugar gene family functions across multiple species.

  1. Au-ionic liquid functionalized reduced graphene oxide immunosensing platform for simultaneous electrochemical detection of multiple analytes.

    PubMed

    Liu, Na; Ma, Zhanfang

    2014-01-15

    In this work, an Au-ionic liquid functionalized reduced graphene oxide nanocomposite (IL-rGO-Au) was fabricated via the self-assembly of ionic liquid functionalized reduced graphene oxide (IL-rGO) and gold nanoparticles (AuNPs) by electrostatic interaction. The IL-rGO can be synthesized and stabilized by introducing the cations of the amine-terminated ionic liquids (IL-NH2) into the graphene oxide (GO). With the assistance of IL-NH2, AuNPs were uniformly and densely absorbed on the surfaces of the IL-rGO. The proposed IL-rGO-Au nanocomposite can be used as an immunosensing platform because it can not only facilitate the electrons transfer of the electrode surface but also provide a large accessible surface area for the immobilization of abundant antibody. To assess the performance of the IL-rGO-Au nanocomposite, a sandwich-type electrochemical immunosensor was designed for simultaneous multianalyte detection (carcinoembryonic antigen (CEA) and alpha-fetoprotein (AFP) as model analytes). The chitosan (CS) coated prussian blue nanoparticles (PBNPs) or cadmium hexacyanoferrate nanoparticles (CdNPs) and loaded with AuNPs were used as distinguishable signal tags. The resulting immunosensor exhibited high selectivity and sensitivity in simultaneous determination of CEA and AFP in a single run. The linear ranges were from 0.01 to 100 ng mL(-1) for both CEA and AFP. The detection limits reached 0.01 ng mL(-1) for CEA and 0.006 ng mL(-1) for AFP, respectively. No obvious nonspecific adsorption and cross-talk was observed during a series of analyses to detect target analytes. In addition, for the detection of clinical serum samples, it is well consistent with the data determined by the ELISA, indicating that the immunosensor provides a possible application for the simultaneous multianalyte determination of CEA and AFP in clinical diagnostics.

  2. Simultaneous translational temperature measurements of different atomic species in plasma flows using scanning Fabry-Perot interferometry

    SciTech Connect

    Loehle, Stefan; Lein, Sebastian

    2012-05-15

    A revised scientific instrument to measure simultaneously kinetic temperatures of different atoms from their optical emission profile is reported. Emission lines are simultaneously detected using one single scanning Fabry-Perot-interferometer (FPI) for a combined spectroscopic setup to acquire different emission lines simultaneously. The setup consists in a commercial Czerny-Turner spectrometer configuration which is combined with a scanning Fabry-Perot interferometer. The fast image acquisition mode of an intensified charge coupled device camera allows the detection of a wavelength interval of interest continuously while acquiring the highly resolved line during the scan of the FPI ramp. Results using this new setup are presented for the simultaneous detection of atomic nitrogen and oxygen in a high enthalpy air plasma flow as used for atmospheric re-entry research and their respective kinetic temperatures derived from the measured line profiles. The paper presents the experimental setup, the calibration procedure, and an exemplary result. The determined temperatures are different, a finding that has been published so far as due to a drawback of the experimental setup of sequential measurements, and which has now to be investigated in more detail.

  3. Predicting aquatic toxicities of chemical pesticides in multiple test species using nonlinear QSTR modeling approaches.

    PubMed

    Basant, Nikita; Gupta, Shikha; Singh, Kunwar P

    2015-11-01

    In this study, we established nonlinear quantitative-structure toxicity relationship (QSTR) models for predicting the toxicities of chemical pesticides in multiple aquatic test species following the OECD (Organization for Economic Cooperation and Development) guidelines. The decision tree forest (DTF) and decision tree boost (DTB) based QSTR models were constructed using a pesticides toxicity dataset in Selenastrum capricornutum and a set of six descriptors. Other six toxicity data sets were used for external validation of the constructed QSTRs. Global QSTR models were also constructed using the combined dataset of all the seven species. The diversity in chemical structures and nonlinearity in the data were evaluated. Model validation was performed deriving several statistical coefficients for the test data and the prediction and generalization abilities of the QSTRs were evaluated. Both the QSTR models identified WPSA1 (weighted charged partial positive surface area) as the most influential descriptor. The DTF and DTB QSTRs performed relatively better than the single decision tree (SDT) and support vector machines (SVM) models used as a benchmark here and yielded R(2) of 0.886 and 0.964 between the measured and predicted toxicity values in the complete dataset (S. capricornutum). The QSTR models applied to six other aquatic species toxicity data yielded R(2) of >0.92 (DTF) and >0.97 (DTB), respectively. The prediction accuracies of the global models were comparable with those of the S. capricornutum models. The results suggest for the appropriateness of the developed QSTR models to reliably predict the aquatic toxicity of chemicals and can be used for regulatory purpose.

  4. Substitution Structures of Multiple Silicon-Containing Species by Chirped Pulse Ftmw Spectroscopy

    NASA Astrophysics Data System (ADS)

    Seifert, Nathan A.; Lobsiger, Simon; Pate, Brooks H.; Guirgis, Gamil A.; Overby, Jason S.; Durig, James R.

    2013-06-01

    The structures of CH_{3}SiHF-NCO, 1-X-silacyclopropane (X = cyano, isocyanato), 1,1,3,3-tetrafluoro-1,3-disilacyclopentane and its hydrogen analogue (1,3-disilacyclopentane), and 1-isocyanato-silacyclohexane have been studied by chirped pulse FTMW spectroscopy in the 6-18 GHz band. Multiple conformers for some of the species were also detected: anti and gauche for both silacyclopropyl species, and axial and equatorial for the silacyclohexane. Heavy atom substitution structures were determined, with all possible single ^{13}C, ^{29}Si/^{30}Si and most ^{15}N isotopologues assigned in natural abundance. Nitrogen hyperfine and distortion parameters for all species have been determined, and the barrier for methyl internal rotation for CH_{3}SiHF-NCO has been determined as 481(20) cm^{-1}, close to the B3LYP/6-311++g(d,p) barrier of 450 cm^{-1}. A summary of the microwave and structural results for the aforementioned molecules will be presented. In addition, emphasis will be placed on the use of previously discussed automated fitting techniques as a means of efficient and fast assignment of isotopologues in spectra with increasingly large line densities. A. L. Steber, J. L. Neill, M. T. Muckle, B. H. Pate, D. F. Plusquellic, V. Lattanzi, S. Spezzano, M. C. McCarthy. 65th OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2010, TC10. E. B. Kent, M. N. McCabe, M. A. Phillips, B. P. Gordon, S. T. Shipman. 66th OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2011, RH01.

  5. Reference genes for quantitative gene expression studies in multiple avian species.

    PubMed

    Olias, Philipp; Adam, Iris; Meyer, Anne; Scharff, Constance; Gruber, Achim D

    2014-01-01

    Quantitative real-time PCR (qPCR) rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ) on different tissues of the mallard (Anas platyrhynchos), domestic chicken (Gallus gallus domesticus), common crane (Grus grus), white-tailed eagle (Haliaeetus albicilla), domestic turkey (Meleagris gallopavo f. domestica), cockatiel (Nymphicus hollandicus), Humboldt penguin (Sphenicus humboldti), ostrich (Struthio camelus) and zebra finch (Taeniopygia guttata), spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ) that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.

  6. Prevalence of avian haemosporidian parasites is positively related to the abundance of host species at multiple sites within a region.

    PubMed

    Ellis, Vincenzo A; Medeiros, Matthew C I; Collins, Michael D; Sari, Eloisa H R; Coffey, Elyse D; Dickerson, Rebecca C; Lugarini, Camile; Stratford, Jeffrey A; Henry, Donata R; Merrill, Loren; Matthews, Alix E; Hanson, Alison A; Roberts, Jackson R; Joyce, Michael; Kunkel, Melanie R; Ricklefs, Robert E

    2017-01-01

    Parasite prevalence is thought to be positively related to host population density owing to enhanced contagion. However, the relationship between prevalence and local abundance of multiple host species is underexplored. We surveyed birds and their haemosporidian parasites (genera Plasmodium and Haemoproteus) at multiple sites across eastern North America to test whether the prevalence of these parasites in a host species at a particular site is related to that host's local abundance. Prevalence was positively related to host abundance within most sites, although the effect was stronger and more consistent for Plasmodium than for Haemoproteus. In contrast, prevalence was not related to variation in the abundance of most individual host species among sites across the region. These results suggest that parasite prevalence partly reflects the relative abundances of host species in local assemblages. However, three nonnative host species had low prevalence despite being relatively abundant at one site, as predicted by the enemy release hypothesis.

  7. A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

    PubMed Central

    Matsushita, Tadashi; Arakawa, Etsuo; Voegeli, Wolfgang; Yano, Yohko F.

    2013-01-01

    An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed. PMID:23254659

  8. Simultaneous determination of arsenic and mercury species in rice by ion-pairing reversed phase chromatography with inductively coupled plasma mass spectrometry.

    PubMed

    Fang, Yong; Pan, Yushi; Li, Peng; Xue, Mei; Pei, Fei; Yang, Wenjian; Ma, Ning; Hu, Qiuhui

    2016-12-15

    An analytical method using reversed phase chromatography-inductively coupled plasma mass spectrometry for arsenic and mercury speciation analysis was described. The effect of ion-pairing reagent on simultaneous separation of four arsenic (arsenite, arsenate, monomethlyarsonate and dimethylarsinate) and three mercury species (inorganic mercury (Hg(II)), methylmecury and ethylmercury) was investigated. Parameters including concentrations and pH of the mobile phase were optimized. The separation and re-equilibration time was attained within 20min. Meanwhile, a sequential extraction method for arsenic and mercury in rice was tested. Subsequently, 1% HNO3 microwave-assisted extraction was chosen. Calibration curves based on peak area measurements were linear with correlation coefficient greater than 0.9958 for each species in the range studied. The detection limits of the species were in the range of 0.84-2.41μg/L for arsenic and 0.01-0.04μg/L for mercury, respectively. The proposed method was then successfully applied for the simultaneous determination of arsenic and mercury species in rice flour standard material and two kinds of rice from local markets.

  9. A Physiologically Based Pharmacokinetic (PB/PK) Model for Multiple Exposure Routes of Soman in Multiple Species

    DTIC Science & Technology

    2006-01-01

    levels of soman greater than 0.85 for 95% of the intravenous and sub- challenge in three species (rat, guinea pig, marmoset ). cutaneous datasets and 25...more than a single formula was available for male guinea pigs (500 g), and male marmosets estimating a particular parameter, the model averaged the...used for whole blood. Values for rat and diaphragm was used for the richly perfused compart- marmoset plasma and for liver of the three species were

  10. Simultaneous Burst Imaging of Dual Species Using Planar Laser-Induced Fluorescence at 50 kHz in Turbulent Premixed Flames.

    PubMed

    Li, Zheming; Rosell, Joakim; Aldén, Marcus; Richter, Mattias

    2016-11-18

    Spatially and temporally resolved measurements are of great importance in turbulent premixed flame studies, especially when investigating rapid processes such as when flame local extinction, re-ignition, or flashback occur in a reacting flow. Here, an experimental approach for simultaneously probing two different species at high frame rates (50 kHz) is presented by employing a multi-YAG laser system. The laser radiation at 355 nm generated by a multi-YAG laser system was split into two beam paths: one beam for exciting formaldehyde and the other for pumping an optical parametric oscillator (OPO). To be able to capture the resulting fluorescence at such a high frame rate without significant loss in spatial resolution, two framing cameras, containing a total of 16 intensified charge-coupled devices (CCDs), were employed. In principle, the proposed setup provides the possibility of probing formaldehyde and simultaneously accessing the distribution of one other relevant species at this high frame rate. In this demonstration, the laser wavelength was tuned to 283 nm and, in conjunction with the 355 nm beam path, simultaneously high speed two-dimensional (2D) visualization of OH-radicals and formaldehyde was achieved. A modified flat flame, McKenna-type burner was used to provide a turbulent premixed jet-flame supported by a surrounding pilot flame. Local flame extinction and re-ignition processes were recorded for fuel/air jet speeds of 120 m/s.

  11. Single parameter optimization for simultaneous automatic compensation of multiple orders of dispersion for a 1.28 Tbaud signal.

    PubMed

    Paquot, Yvan; Schröder, Jochen; Van Erps, Jürgen; Vo, Trung D; Pelusi, Mark D; Madden, Steve; Luther-Davies, Barry; Eggleton, Benjamin J

    2011-12-05

    We report the demonstration of automatic higher-order dispersion compensation for the transmission of 275 fs pulses associated with a Tbaud Optical Time Division Multiplexed (OTDM) signal. Our approach achieves simultaneous automatic compensation for 2nd, 3rd and 4th order dispersion using an LCOS spectral pulse shaper (SPS) as a tunable dispersion compensator and a dispersion monitor made of a photonic-chip-based all-optical RF-spectrum analyzer. The monitoring approach uses a single parameter measurement extracted from the RF-spectrum to drive a multidimensional optimization algorithm. Because these pulses are highly sensitive to fluctuations in the GVD and higher orders of chromatic dispersion, this work represents a key result towards practical transmission of ultrashort optical pulses. The dispersion can be adapted on-the-fly for a 1.28 Tbaud signal at any place in the transmission line using a black box approach.

  12. DND-CAT;s new triple area detector system for simultaneous data collection at multiple length scales

    SciTech Connect

    Weigand, Steven J.; Keane, Denis T.

    2011-11-17

    The DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) built and currently manages sector 5 at the Advanced Photon Source (APS), Argonne National Laboratory. One of the principal techniques supported by DND-CAT is Small and Wide-Angle X-ray Scattering (SAXS/WAXS), with an emphasis on simultaneous data collection over a wide azimuthal and reciprocal space range using a custom SAXS/WAXS detector system. A new triple detector system is now in development, and we describe the key parameters and characteristics of the new instrument, which will be faster, more flexible, more robust, and will improve q-space resolution in a critical reciprocal space regime between the traditional WAXS and SAXS ranges.

  13. Design of a communications system for multiple telemetry data channels operating simultaneously with a coherent turn-around ranging channel

    NASA Technical Reports Server (NTRS)

    Nguyen, Tien M.; Hinedi, Sami M.; Gevargiz, John M.

    1991-01-01

    This paper presents a simple technique to design a phase-modulated residual carrier communications link for optimum performance. The emphasis is on two data channels which are operated simultaneously with a ranging signal. The data channels employ PCM/PM and PCM/PSK/PM modulation schemes for high and low data rate channels, respectively. The technique proposed here selects the optimum (1) subcarrier frequency to minimize the interference between the two data channels, and (2) modulation indices for optimum balance of power between the two telemetry data channels and the coherent turn around ranging channel. The selected set of optimum modulation indices will allow for the specified bit error rate (BER) degradations in the two data channels. Although this technique is proposed to optimize the performance degradation for two data channels, generalizations can be made for more than two data channels.

  14. Simultaneous statistical bias correction of multiplePM2.5 species from a regional photochemical grid model

    EPA Science Inventory

    In recent years environmental epidemiologists have begun utilizing regionalscale air quality computer models to predict ambient air pollution concentrations in health studies instead of or in addition to monitoring data from central sites. The advantages of using such models i...

  15. Simultaneous, Bilateral Ophthalmoplegia as the Presenting Sign of Paediatric Multiple Sclerosis: Case Report and Discussion of the Differential Diagnosis

    PubMed Central

    Adam, Murtaza K.; Krespan, Kelly; Moster, Mark L.; Sergott, Robert C.

    2014-01-01

    Abstract An 11-year-old female developed bilateral oculomotor nerve palsies without pupillary involvement and bilateral optic neuropathy as the presenting signs of paediatric multiple sclerosis (MS). Although ocular mono-neuropathies have been reported, this is the first bilateral mono-neuropathy reported in a paediatric patient due to MS. The differential diagnosis and evaluation for bilateral ophthalmoplegia are discussed in detail. PMID:27928305

  16. Simultaneous Suppression of Multiple Genes by Single Transgenes. Down-Regulation of Three Unrelated Lignin Biosynthetic Genes in Tobacco1

    PubMed Central

    Abbott, James C.; Barakate, Abdellah; Pinçon, Gaelle; Legrand, Michel; Lapierre, Catherine; Mila, Isabelle; Schuch, Wolfgang; Halpin, Claire

    2002-01-01

    Many reports now describe the manipulation of plant metabolism by suppressing the expression of single genes. The potential of such work could be greatly expanded if multiple genes could be coordinately suppressed. In the work presented here, we test a novel method for achieving this by using single chimeric constructs incorporating partial sense sequences for multiple genes to target suppression of two or three lignin biosynthetic enzymes. We compare this method with a more conventional approach to achieving the same end by crossing plants harboring different antisense transgenes. Our results indicate that crossing antisense plants is less straightforward and predictable in outcome than anticipated. Most progeny had higher levels of target enzyme activity than predicted and had lost the expected modifications to lignin structure. In comparison, plants transformed with the chimeric partial sense constructs had more consistent high level suppression of target enzymes and had significant changes to lignin content, structure, and composition. It was possible to suppress three target genes coordinately using a single chimeric construct. Our results indicate that chimeric silencing constructs offer great potential for the rapid and coordinate suppression of multiple genes on diverse biochemical pathways and that the technique therefore deserves to be adopted by other researchers. PMID:11891241

  17. A low-cost, high-performance, digital signal processor-based lock-in amplifier capable of measuring multiple frequency sweeps simultaneously

    SciTech Connect

    Sonnaillon, Maximiliano Osvaldo; Bonetto, Fabian Jose

    2005-02-01

    A high-performance digital lock-in amplifier implemented in a low-cost digital signal processor (DSP) board is described. This lock in is capable of measuring simultaneously multiple frequencies that change in time as frequency sweeps (chirps). The used 32-bit DSP has enough computing power to generate N=3 simultaneous reference signals and accurately measure the N=3 responses, operating as three lock ins connected in parallel to a linear system. The lock in stores the measured values in memory until they are downloaded to the a personal computer (PC). The lock in works in stand-alone mode and can be programmed and configured through the PC serial port. Downsampling and multiple filter stages were used in order to obtain a sharp roll off and a long time constant in the filters. This makes measurements possible in presence of high-noise levels. Before each measurement, the lock in performs an autocalibration that measures the frequency response of analog output and input circuitry in order to compensate for the departure from ideal operation. Improvements from previous lock-in implementations allow measuring the frequency response of a system in a short time. Furthermore, the proposed implementation can measure how the frequency response changes with time, a characteristic that is very important in our biotechnological application. The number of simultaneous components that the lock in can generate and measure can be extended, without reprogramming, by only using other DSPs of the same family that are code compatible and work at higher clock frequencies.

  18. A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini).

    PubMed

    Hendrich, Lars; Balke, Michael

    2011-02-03

    Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species' taxonomy and biology. The diving beetle Neobidessodes darwiniensissp. n. (Coleoptera: Dytiscidae, Bidessini) is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea.

  19. Phytoplankton IF-FISH: Species-specific labeling of cellular proteins by immunofluorescence (IF) with simultaneous species identification by fluorescence immunohybridization (FISH).

    PubMed

    Meek, Megan E; Van Dolah, Frances M

    2016-05-01

    Phytoplankton rarely occur as unialgal populations. Therefore, to study species-specific protein expression, indicative of physiological status in natural populations, methods are needed that will both assay for a protein of interest and identify the species expressing it. Here we describe a protocol for IF-FISH, a dual labeling procedure using immunofluorescence (IF) labeling of a protein of interest followed by fluorescence in situ hybridization (FISH) to identify the species expressing that protein. The protocol was developed to monitor expression of the cell cycle marker proliferating cell nuclear antigen (PCNA) in the red tide dinoflagellate, Karenia brevis, using a large subunit (LSU) rRNA probe to identify K. brevis in a mixed population of morphologically similar Karenia species. We present this protocol as proof of concept that IF-FISH can be successfully applied to phytoplankton cells. This method is widely applicable for the analysis of single-cell protein expression of any protein of interest within phytoplankton communities.

  20. Optimization of Micellar Electrokinetic Chromatography Method for the Simultaneous Determination of Seven Hydrophilic and Four Lipophilic Bioactive Components in Three Salvia Species.

    PubMed

    Cao, Jiliang; Hu, Ji; Wei, Jinchao; Li, Baocai; Zhang, Mi; Xiang, Cheng; Li, Peng

    2015-08-21

    A micellar electrokinetic chromatography (MEKC) method was developed for the simultaneous determination of seven hydrophilic phenolic acids and four lipophilic tanshinones in three Salvia species. In normal MEKC mode using SDS as surfactant, the investigated 11 compounds could not be well separated. Therefore, several buffer modifiers including β-cyclodextrins (β-CD), ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]BF4) and organic solvents have been added to the buffer solution to improve the separation selectivity. Under the optimized conditions (BGE, 15 mM sodium tetraborate with 10 mM SDS, 5 mM β-CD, 10 mM [bmim]BF4 and 15% ACN (v/v) as additives; buffer pH, 9.8; voltage, 20 kV; temperature, 25 °C), the 11 investigated analytes could achieve baseline separation in 34 min. The proposed MEKC was additionally validated by evaluating the linearity (R(2) ≥ 0.9965), LODs (0.27-1.39 μg·mL(-1)), and recovery (94.26%-105.17%), demonstrating this method was reproducible, accurate and reliable. Moreover, the contents of the 11 compounds in three Salvia species, including S. miltiorrhiza, S. przewalskii and S. castanea were analyzed. The result showed that the established MEKC method was simple and practical for the simultaneous determination of the hydrophilic and lipophilic bioactive components in Salvia species, which could be used to effectively evaluate the quality of these valued medicinal plants.

  1. Collisonal Friction Enhanced by Two-Stream Instabilities Determines the Bohm Criterion in Plasmas With Multiple Ion Species

    NASA Astrophysics Data System (ADS)

    Baalrud, S. D.; Hegna, C. C.; Callen, J. D.

    2009-10-01

    Ion-ion streaming instabilities are excited in the presheath region of plasmas with multiple ion species if the ions are much colder than the electrons. Streaming instabilities onset when the relative fluid flow between ion species exceeds a critical speed, δVc, of order the ion thermal speeds. Using a generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses [1], one is able to show the instabilities rapidly (within a few Debye lengths) enhance the collisional friction between ion species far beyond the contribution from Coulomb collisions alone. This strong frictional force determines the relative fluid speed between species. When this condition is combined with the Bohm criterion generalized for multiple ion species, the fluid speed of each ion species is determined at the sheath edge. For each species, this speed differs from the common ``system'' sound speed by a factor that depends on the species concentration and δVc.[4pt] [1] S.D. Baalrud, J.D. Callen, and C.C. Hegna, Phys. Plasmas 15, 092111 (2008).

  2. ENDEAVOUR update: a web resource for gene prioritization in multiple species.

    PubMed

    Tranchevent, Léon-Charles; Barriot, Roland; Yu, Shi; Van Vooren, Steven; Van Loo, Peter; Coessens, Bert; De Moor, Bart; Aerts, Stein; Moreau, Yves

    2008-07-01

    Endeavour (http://www.esat.kuleuven.be/endeavourweb; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes. Using a training set of genes known to be involved in a biological process of interest, our approach consists of (i) inferring several models (based on various genomic data sources), (ii) applying each model to the candidate genes to rank those candidates against the profile of the known genes and (iii) merging the several rankings into a global ranking of the candidate genes. In the present article, we describe the latest developments of Endeavour. First, we provide a web-based user interface, besides our Java client, to make Endeavour more universally accessible. Second, we support multiple species: in addition to Homo sapiens, we now provide gene prioritization for three major model organisms: Mus musculus, Rattus norvegicus and Caenorhabditis elegans. Third, Endeavour makes use of additional data sources and is now including numerous databases: ontologies and annotations, protein-protein interactions, cis-regulatory information, gene expression data sets, sequence information and text-mining data. We tested the novel version of Endeavour on 32 recent disease gene associations from the literature. Additionally, we describe a number of recent independent studies that made use of Endeavour to prioritize candidate genes for obesity and Type II diabetes, cleft lip and cleft palate, and pulmonary fibrosis.

  3. Semiparametric bivariate zero-inflated Poisson models with application to studies of abundance for multiple species

    USGS Publications Warehouse

    Arab, Ali; Holan, Scott H.; Wikle, Christopher K.; Wildhaber, Mark L.

    2012-01-01

    Ecological studies involving counts of abundance, presence–absence or occupancy rates often produce data having a substantial proportion of zeros. Furthermore, these types of processes are typically multivariate and only adequately described by complex nonlinear relationships involving externally measured covariates. Ignoring these aspects of the data and implementing standard approaches can lead to models that fail to provide adequate scientific understanding of the underlying ecological processes, possibly resulting in a loss of inferential power. One method of dealing with data having excess zeros is to consider the class of univariate zero-inflated generalized linear models. However, this class of models fails to address the multivariate and nonlinear aspects associated with the data usually encountered in practice. Therefore, we propose a semiparametric bivariate zero-inflated Poisson model that takes into account both of these data attributes. The general modeling framework is hierarchical Bayes and is suitable for a broad range of applications. We demonstrate the effectiveness of our model through a motivating example on modeling catch per unit area for multiple species using data from the Missouri River Benthic Fishes Study, implemented by the United States Geological Survey.

  4. A study of the undisturbed mid-latitude ionosphere using simultaneous multiple site ionosonde measurements during the Sundial-86 campaign

    SciTech Connect

    Sica, R.J. ); Schunk, R.W. ); Willkinson, P.J. )

    1990-06-01

    The Sundial-86 campaign obtained simultaneous ionosonde measurements of N{sub m}F2 from 41 mid-latitude sites geographically dispersed around the world from September 21 to October 5, 1986. A three-dimensional, time-dependent model of Earth's ionoshpere has been used to fit the variations in N{sub m}F2 obtained from these sites. The model successfully reproduced the measurements in both the northern and southern hemispheres using the vertical plasma drift as a free parameter. During geomagnetically quiet conditions this drift is primarily due to the meridional neutral wind. The vertical plasma drift required to fit the data is consistent from location to location and the deduced meridional neutral wind is also consistent with previous neutral wind measurements and models. However, it is shown that a lack of knowledge of the variation of the O{sup +} flux at the top of the atmosphere introduces a large uncertainty in the deduced thermospheric winds.

  5. Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

    PubMed

    Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

    2008-09-01

    In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

  6. A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

    PubMed

    Chen, Jing; Xu, Huimin; He, Ping-An; Dai, Qi; Yao, Yuhua

    2016-01-01

    Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based. The original and consensus sequences were combined with physicochemical properties. And elements information of different rows and columns in position-specific scoring matrix were taken into consideration simultaneously for more core and essence information. Computational methods based on gene ontology (GO) have been demonstrated to be superior to methods based on other features. Then principal component analysis (PCA) is applied for feature selection and reduced vectors are input to a support vector machine (SVM) to predict protein subcellular localization. The proposed method can achieve a prediction accuracy of 98.28% and 97.87% on a stringent Gram-positive (Gpos) and Gram-negative (Gneg) dataset with Jackknife test, respectively. At last, we calculate "absolute true overall accuracy (ATOA)", which is stricter than overall accuracy. The ATOA obtained from the proposed method is also up to 97.32% and 93.06% for Gpos and Gneg. From both the rationality of testing procedure and the success rates of test results, the current method can improve the prediction quality of protein subcellular localization.

  7. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly

    PubMed Central

    Lasker, Keren; Topf, Maya; Sali, Andrej; Wolfson, Haim J.

    2009-01-01

    Summary Models of macromolecular assemblies are essential for a mechanistic description of cellular processes. Such models are increasingly obtained by fitting atomic-resolution structures of components into a density map of the whole assembly. Yet, current density-fitting techniques are frequently insufficient for an unambiguous determination of the positions and orientations of all components. Here, we describe MultiFit, a method for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25 Å. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, as well as the shape complementarity between pairs of components. The scoring function is optimized by our exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space. MultiFit was benchmarked on 7 assemblies of known structure, consisting of up to 7 proteins each. The input atomic structures of the components were obtained from the Protein Data Bank as well as by comparative modeling based on 16 – 99% sequence identity to a template structure. A near-native configuration was usually found as the top-scoring model. Therefore, MultiFit can provide initial configurations for further refinement of many multi-component assembly structures described by electron microscopy. PMID:19233204

  8. Development and primary application of a fluorescent liquid bead array for the simultaneous identification of multiple genetically modified maize.

    PubMed

    Han, Xueqing; Wang, Huiyu; Chen, Hongjun; Mei, Lin; Wu, Shaoqiang; Jia, Guangle; Cheng, Tao; Zhu, Shuifang; Lin, Xiangmei

    2013-11-15

    An integration event-specific fluorescent liquid bead array was developed for the simultaneous identification of 10 genetically modified (GM) maize, including Bt176, Bt11, MON810, NK603, GA21, MON88017, MON89034, MIR604, T25 and MIR162, as well as one non-GM maize. The system comprised 11 specific oligonucleotide probes labeled with an amino group and coupled to fluorescence-encoded microspheres. To enable fluorescence detection, 11 pairs of primers labeled with biotin at the 5' ends were used. The hybridization signal of biotinylated PCR product to the probe-coupled microspheres was then detected. The limit of detection of this assay was 0.1% for GM maize, which is lower than the current labeling threshold levels enforced in the EU (0.9%). The results of the positive and negative controls were consistent with their expected situation, which showed that the method was highly specific. We detected GM maize in 20 of the 1370 commercial food samples tested, which were labeled as containing maize. The overall sensitivity, specificity, rapidity and high throughput capacity of this liquid chip system suggest that it could provide a significant improvement over current methods, and potentially offer an improved platform for further research into the detection of other GM plants.

  9. Wireless and simultaneous detections of multiple bio-molecules in a single sensor using Love wave biosensor.

    PubMed

    Oh, Haekwan; Fu, Chen; Kim, Kunnyun; Lee, Keekeun

    2014-11-17

    A Love wave-based biosensor with a 440 MHz center frequency was developed for the simultaneous detection of two different analytes of Cartilage Oligomeric Matrix Protein (COMP) and rabbit immunoglobulin G (IgG) in a single sensor. The developed biosensor consists of one-port surface acoustic wave (SAW) reflective delay lines on a 41° YX LiNbO3 piezoelectric substrate, a poly(methyl methacrylate) (PMMA) waveguide layer, and two different sensitive films. The Love wave biosensor was wirelessly characterized using two antennas and a network analyzer. The binding of the analytes to the sensitive layers induced a large change in the time positions of the original reflection peaks mainly due to the mass loading effect. The assessed time shifts in the reflection peaks were matched well with the predicted values from coupling of mode (COM) modeling. The sensitivities evaluated from the sensitive films were ~15 deg/µg/mL for the rabbit IgG and ~1.8 deg/ng/mL for COMP.

  10. A heuristic optimization approach for Air Quality Monitoring Network design with the simultaneous consideration of multiple pollutants.

    PubMed

    Elkamel, A; Fatehifar, E; Taheri, M; Al-Rashidi, M S; Lohi, A

    2008-08-01

    An interactive optimization methodology for allocating the number and configuration of an Air Quality Monitoring Network (AQMN) in a vast area to identify the impact of multiple pollutants is described. A mathematical model based on the multiple cell approach (MCA) was used to create monthly spatial distributions for the concentrations of the pollutants emitted from different emission sources. These spatial temporal patterns were subject to a heuristic optimization algorithm to identify the optimal configuration of a monitoring network. The objective of the optimization is to provide maximum information about multi-pollutants (i.e., CO, NO(x) and SO(2)) emitted from each source within a given area. The model was applied to a network of existing refinery stacks and the results indicate that three stations can provide a total coverage of more than 70%. In addition, the effect of the spatial correlation coefficient (R(C)) on total area coverage was analyzed. The modeling results show that as the cutoff correlation coefficient R(C) is increased from 0.75 to 0.95, the number of monitoring stations required for total coverage is increased. A high R(C) based network may not necessarily cover the entire region, but the covered region will be well represented. A low R(C) based network, on the other hand, would offer more coverage of the region, but the covered region may not be satisfactorily represented.

  11. Simultaneous speciation of arsenic, selenium, and chromium: species, stability, sample preservation, and analysis of ash and soil leachates

    USGS Publications Warehouse

    Wolf, Ruth E.; Morman, Suzette A.; Hageman, Philip L.; Hoefen, Todd M.; Plumlee, Geoffrey S.

    2011-01-01

    An analytical method using high-performance liquid chromatography separation with inductively coupled plasma mass spectrometry (ICP-MS) detection previously developed for the determination of Cr(III) and Cr(VI) has been adapted to allow the determination of As(III), As(V), Se(IV), Se(VI), Cr(III), and Cr(VI) under the same chromatographic conditions. Using this method, all six inorganic species can be determined in less than 3 min. A dynamic reaction cell (DRC)-ICP-MS system was used to detect the species eluted from the chromatographic column in order to reduce interferences. A variety of reaction cell gases and conditions may be utilized with the DRC-ICP-MS, and final selection of conditions is determined by data quality objectives. Results indicated all starting standards, reagents, and sample vials should be thoroughly tested for contamination. Tests on species stability indicated that refrigeration at 10° C was preferential to freezing for most species, particularly when all species were present, and that sample solutions and extracts should be analyzed as soon as possible to eliminate species instability and interconversion effects. A variety of environmental and geological samples, including waters and deionized water [leachates] and simulated biological leachates from soils and wildfire ashes have been analyzed using this method. Analytical spikes performed on each sample were used to evaluate data quality. Speciation analyses were conducted on deionized water leachates and simulated lung fluid leachates of ash and soils impacted by wildfires. These results show that, for leachates containing high levels of total Cr, the majority of the chromium was present in the hexavalent Cr(VI) form. In general, total and hexavalent chromium levels for samples taken from burned residential areas were higher than those obtained from non-residential forested areas. Arsenic, when found, was generally in the more oxidized As(V) form. Selenium (IV) and (VI) were present

  12. Simultaneous speciation of arsenic, selenium, and chromium: Species stability, sample preservation, and analysis of ash and soil leachates

    USGS Publications Warehouse

    Wolf, R.E.; Morman, S.A.; Hageman, P.L.; Hoefen, T.M.; Plumlee, G.S.

    2011-01-01

    An analytical method using high-performance liquid chromatography separation with inductively coupled plasma mass spectrometry (ICP-MS) detection previously developed for the determination of Cr(III) and Cr(VI) has been adapted to allow the determination of As(III), As(V), Se(IV), Se(VI), Cr(III), and Cr(VI) under the same chromatographic conditions. Using this method, all six inorganic species can be determined in less than 3 min. A dynamic reaction cell (DRC)-ICP-MS system was used to detect the species eluted from the chromatographic column in order to reduce interferences. A variety of reaction cell gases and conditions may be utilized with the DRC-ICP-MS, and final selection of conditions is determined by data quality objectives. Results indicated all starting standards, reagents, and sample vials should be thoroughly tested for contamination. Tests on species stability indicated that refrigeration at 10 ??C was preferential to freezing for most species, particularly when all species were present, and that sample solutions and extracts should be analyzed as soon as possible to eliminate species instability and interconversion effects. A variety of environmental and geological samples, including waters and deionized water [leachates] and simulated biological leachates from soils and wildfire ashes have been analyzed using this method. Analytical spikes performed on each sample were used to evaluate data quality. Speciation analyses were conducted on deionized water leachates and simulated lung fluid leachates of ash and soils impacted by wildfires. These results show that, for leachates containing high levels of total Cr, the majority of the chromium was present in the hexavalent Cr(VI) form. In general, total and hexavalent chromium levels for samples taken from burned residential areas were higher than those obtained from non-residential forested areas. Arsenic, when found, was generally in the more oxidized As(V) form. Selenium (IV) and (VI) were present

  13. Simultaneous extraction of arsenic and selenium species from rice products by microwave-assisted enzymatic extraction and analysis by ion chromatography-inductively coupled plasma-mass spectrometry.

    PubMed

    Mar, Jorge L Guzmán; Reyes, Laura Hinojosa; Rahman, G M Mizanur; Kingston, H M Skip

    2009-04-22

    A microwave-assisted enzymatic extraction (MAEE) method was developed for the simultaneous extraction of arsenic (As) and selenium (Se) species in rice products. The total arsenic and selenium content in the enzymatic extracts were determined by inductively coupled plasma mass spectrometry (ICP-MS), while the speciation analysis was performed by ion chromatography coupled to inductively coupled plasma-mass spectrometry (IC-ICP-MS). The main factors affecting the enzymatic extraction process were evaluated in NIST SRM-1568a rice flour. The optimum extraction conditions were 500 mg of sample, 50 mg of protease XIV, and 25 mg of alpha-amylase in aqueous medium during 40 min at 37 degrees C. The extraction recoveries of total As and Se reached 100 +/- 3 and 80 +/- 4%, respectively. The species stability study during the MAEE process did not show transformation of the target species in rice products. The results of As speciation obtained for SRM-1568a were in agreement with previous studies of As speciation performed on the same reference material. The proposed method was applied to the determination of As and Se species in rice and rice-based cereals. Arsenite [As(III)], arsenate [As(V)], dimethylarsinic acid (DMA), and selenomethionine (SeMet) were the predominant species identified in rice products.

  14. Simultaneous and intercontinental tests show synchronism between the local gravimetric tide and the ultra-weak photon emission in seedlings of different plant species.

    PubMed

    Gallep, Cristiano M; Barlow, Peter W; Burgos, Rosilene C R; van Wijk, Eduard P A

    2017-01-01

    In order to corroborate the hypothesis that variations in the rate of spontaneous ultra-weak photon emission (UPE) from germinating seedlings are related to local variations of the lunisolar tidal force, a series of simultaneous tests was performed using the time courses of UPE collected from three plant species-corn, wheat and sunflower-and also from wheat samples whose grains were transported between continents, from Brazil to The Netherlands and vice versa. All tests which were run in parallel showed coincident inflections within the UPE time courses not only between seedlings of the same species but also between the different species. In most cases, the UPE inflections were synchronised with the turning points in the local gravimetric tidal variation. Statistical tests using the local Pearson correlation verified these coincidences in the two time series. The results therefore support the hypothesis of a relationship between UPE emissions and, in the oscillations, the local gravimetric tide. This applies to both the emissions from seedlings of different species and to the seedlings raised from transported grain samples of the same species.

  15. Simultaneous Assimilation of Multiple Data into a Conceptual Rainfall-Runoff Model using Variational Methods for Hydrological Forecasting Applications

    NASA Astrophysics Data System (ADS)

    Schwanenberg, D.; Alvarado Montero, R.; Sensoy Sorman, A.; Krahe, P.

    2015-12-01

    Data assimilation methods applied to hydrological applications have primarily focused on assimilating streamflow and, more recently, soil moisture observations. Few cases actually assimilate both observations, and even fewer incorporate additional observations into the assimilation procedure. This is despite extensive developments in remote sensing information. Most research on data assimilation has focused on the implementation of sequential assimilation using Kalman filters. We present an alternative approach using variational methods based on Moving Horizon Estimation (MHE) to simultaneously assimilate streamflow data and remote sensing information obtained from the Satellite Application Facility on Support to Operational Hydrology and Water Management (H-SAF) community, namely snow-covered area, snow water equivalent and soil moisture. This approach enables a highly flexible formulation of distance metrics for the introduction of noise into the model and the agreement between simulated and observed variables. The application of MHE on data assimilation is tested at two data-dense test sites in Germany and one data-sparse environment in Turkey. The assessment of results is based on the lead time performance of state variables of the conceptual rainfall-runoff model, i.e. not limited to the performance of streamflow forecast but also applicable to snow and soil moisture forecast skills. Results show a potential improvement on the performance of the forecasted streamflow when using a perfect time series of state variables generated through the simulation of the conceptual rainfall-runoff model HBV. The assimilation of H-SAF data, in combination with streamflow, reduces the performance of the forecasted streamflow compared to the assimilation using only streamflow data. However, other forecasted quantities such as the snow water equivalent or soil moisture are improved. Recommendations based on the test cases are given following the length of the assimilation

  16. Simultaneous Imaging of Radiation-Induced Cerebral Microbleeds, Arteries and Veins, Using a Multiple Gradient Echo Sequence at 7 Tesla

    PubMed Central

    Bian, Wei; Banerjee, Suchandrima; Kelly, Douglas A.C.; Hess, Christopher P.; Larson, Peder E.Z.; Chang, Susan M.; Nelson, Sarah J.; Lupo, Janine M.

    2016-01-01

    Background The purpose of this study was to implement and evaluate the utility of a multi-echo sequence at 7 Tesla (T) for simultaneous time-of-flight (TOF) MR-angiography (MRA) and susceptibility-weighted imaging (SWI) of radiation-induced cerebral microbleeds (CMBs), intracranial arteries, and veins. Methods A four-echo gradient-echo sequence was implemented on a 7T scanner. The first echo was used to create TOF-MRA images, while the remaining echoes were combined to visualize CMBs and veins on SWI images. The sequence was evaluated on eight brain tumor patients with known radiation-induced CMBs. Single-echo images were also acquired to visually and quantitatively compare the contrast-to-noise ratio (CNR) of small- and intermediate-vessels between acquisitions. The number of CMBs detected with each acquisition was also quantified. Statistical significance was determined using a Wilcoxon signed-rank test. Results Compared with the single-echo sequences, the CNR of small and intermediate arteries increased 7.6% (P < 0.03) and 9.5% (P = 0.06), respectively, while the CNR of small and intermediate veins were not statistically different between sequences (P = 0.95 and P = 0.46, respectively). However, these differences were not discernible by visual inspection. Also the multi-echo sequence detected 18.3% more CMBs (P < 0.008) due to higher slice resolution. Conclusion The proposed 7T multi-echo sequence depicts arteries, veins, and CMBs on a single image to facilitate quantitative evaluation of radiation-induced vascular injury. PMID:25471321

  17. Tolerable Levels of Nonclinical Vehicles and Formulations Used in Studies by Multiple Routes in Multiple Species With Notes on Methods to Improve Utility.

    PubMed

    Gad, Shayne Cox; Spainhour, Charles B; Shoemake, Catherine; Pallman, Danielle R Stackhouse; Stricker-Krongrad, Alain; Downing, Philip A; Seals, Richard E; Eagle, Leslie Anne; Polhamus, Kara; Daly, Jennifer

    2016-01-01

    Formulation of nonclinical evaluations is a challenge, with the fundamental need to achieve multiples of the clinical exposure complicated by differences in species and routes of administration-specific tolerances, depending on concentrations, volumes, dosing regimen, duration of each administration, and study duration. Current practice to approach these differences is based on individual experience and scattered literature with no comprehensive data source (the most notable exception being our 2006 publication on this same subject). Lack of formulation tolerance data results in excessive animal use, unplanned delays in the evaluation and development of drugs, and vehicle-dependent results. A consulting firm, a chemical company, and 4 contract research organizations conducted a rigorous data mining operation of vehicle data from studies dating from 1991 to 2015, enhancing the data from this author's 2006 publication (3 of the six 2015 contributors were also 2006 contributors). Additional data were found in the published literature. The results identified 108 single-component vehicles (and 305 combination formulations) used in more than 1,040 studies across multiple species (dog, primate, rat, mouse, rabbit, guinea pig, minipig, pig, chick embryo, and cat) by multiple routes for a wide range of study durations. The tabulated data include maximum tolerated use levels by species, route, duration of study, dose-limiting toxicity where reported, review of the available literature on each vehicle, guidance on syringe selection, volume and pH limits by route with basic guidance on nonclinical formulation development, and guidance on factors to be considered in nonclinical route selection.

  18. Aerial audiograms of several California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) measured using single and multiple simultaneous auditory steady-state response methods.

    PubMed

    Mulsow, Jason; Reichmuth, Colleen; Gulland, Frances; Rosen, David A S; Finneran, James J

    2011-04-01

    Measurements of the electrophysiological auditory steady-state response (ASSR) have proven to be efficient for evaluating hearing sensitivity in odontocete cetaceans. In an effort to expand these methods to pinnipeds, ASSRs elicited by single and multiple simultaneous tones were used to measure aerial hearing thresholds in several California sea lions (Zalophus californianus) and Steller sea lions (Eumetopias jubatus). There were no significant differences between thresholds measured using the single and multiple ASSR methods, despite the more rapid nature of data collection using the multiple ASSR method. There was a high degree of variability in ASSR thresholds among subjects; thresholds covered a range of ∼40 dB at each tested frequency. As expected, ASSR thresholds were elevated relative to previously reported psychophysical thresholds for California and Steller sea lions. The features of high-frequency hearing limit and relative sensitivity of most ASSR audiograms were, however, similar to those of psychophysical audiograms, suggesting that ASSR methods can be used to improve understanding of hearing demographics in sea lions, especially with respect to high-frequency hearing. Thresholds for one Steller sea lion were substantially elevated relative to all other subjects, demonstrating that ASSR methods can be used to detect hearing loss in sea lions.

  19. San Diego Multiple Species Conservation Program (MSCP) Rare Plant Monitoring Review and Revision

    USGS Publications Warehouse

    McEachern, Kathryn; Pavlik, Bruce M.; Rebman, Jon; Sutter, Rob

    2007-01-01

    Introduction The San Diego Multiple Species Conservation Program (MSCP) was developed for the conservation of plants and animals in the south part of San Diego County, under the California Natural Community Conservation Planning Act of 1991 (California Department of Fish and Game) and the Federal Endangered Species Act of 1973, as amended (16 U.S. Code 1531-1544.) The Program is on the leading edge of conservation, as it seeks to both guide development and conserve at-risk species with the oversight of both State and Federal agencies. Lands were identified for inclusion in the MSCP based on their value as habitat for at-risk plants or plant communities (Natural Community Conservation Planning, 2005). Since its inception in the mid-1990s the Program has protected over 100,000 acres, involving 15 jurisdictions and the U.S. Fish and Wildlife Service (USFWS) and California Department of Fish and Game (CDFG) in the conservation of 87 taxa. Surveys for covered species have been conducted, and management and monitoring have been implemented at some high priority sites. Each jurisdiction or agency manages and monitors their conservation areas independently, while collaborating regionally for long-term protection. The San Diego MSCP is on the forefront of conservation, in one of the most rapidly growing urban areas of the country. The planning effort that developed the MSCP was state-of-the-art, using expert knowledge, spatial habitat modeling, and principles of preserve design to identify and prioritize areas for protection. Land acquisition and protection are ahead of schedule for most jurisdictions. Surveys have verified the locations of many rare plant populations known from earlier collections, and they provide general information on population size and health useful for further conservation planning. Management plans have been written or are in development for most MSCP parcels under jurisdictional control. Several agencies are developing databases for implementation

  20. Comprehensive method for determination of aquatic butyltin and butylmethyltin species at ultratrace levels using simultaneous hydridization/extraction with gas chromatography-flame photometric detection

    SciTech Connect

    Matthias, C.L.; Bellama, J.M.; Olson, G.J.; Brinckman, F.E.

    1986-06-01

    An ultratrace method for the analysis of aquatic anthropogenic butyltin and mixed methylbutyltin species using simultaneous hydridization with sodium borohydride and extraction into dichloromethane is described. The detection limits for a 100-mL sample are 7 ng of Sn/L for tetrabutyltin, 7 ng of Sn/L for tributyltin, 3 ng of Sn/L for dibutyltin, and 22 ng of Sn/L for monobutyltin. Detection limits of approximately 1-2 ng of Sn/L for tri- and tetrabutyltin and less than 1 ng of Sn/L for dibutyltin species were achieved with 800-mL samples. The presence of tetrabutyltin in harbor waters is reported. 39 references, 9 figures, 2 tables.

  1. Development and validation of a duplex real-time PCR assay for the simultaneous detection of three mustard species (Sinapis alba, Brassica nigra and Brassica juncea) in food.

    PubMed

    Palle-Reisch, Monika; Cichna-Markl, Margit; Hochegger, Rupert

    2014-06-15

    The paper presents a duplex real-time PCR assay for the simultaneous detection of three potentially allergenic mustard species commonly used in food: white mustard (Sinapis alba), black mustard (Brassica nigra) and brown mustard (Brassica juncea). White mustard is detected in the "green" and black/brown mustard in the "yellow" channel. The duplex real-time PCR assay does not show cross-reactivity with other Brassicaceae species including broccoli, cauliflower, radish and rapeseed. Low cross-reactivities (difference in the Ct value ⩾ 11.91 compared with the positive control) were obtained with cumin, fenugreek, ginger, rye and turmeric. When applying 500 ng DNA per PCR tube, the duplex real-time PCR assay allowed the detection of white, black and brown mustard in brewed model sausages down to a concentration of 5mg/kg in 10 out of 10 replicates. The duplex real-time PCR assay was applied to verify correct labelling of commercial foodstuffs.

  2. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  3. Spatial heterogeneity in aboveground net primary production and species richness at multiple scales in the Chihuahuan Desert

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We analyzed patterns in spatial heterogeneity and the processes driving these patterns in two ecosystem properties, aboveground net primary production (ANPP) and species richness, at multiple scales in the Chihuahuan Desert. We used long-term data (1990-2009) to examine the importance of a suite of...

  4. Multiplex polymerase chain reaction-capillary gel electrophoresis: a promising tool for GMO screening--assay for simultaneous detection of five genetically modified cotton events and species.

    PubMed

    Nadal, Anna; Esteve, Teresa; Pla, Maria

    2009-01-01

    A multiplex polymerase chain reaction assay coupled to capillary gel electrophoresis for amplicon identification by size and color (multiplex PCR-CGE-SC) was developed for simultaneous detection of cotton species and 5 events of genetically modified (GM) cotton. Validated real-time-PCR reactions targeting Bollgard, Bollgard II, Roundup Ready, 3006-210-23, and 281-24-236 junction sequences, and the cotton reference gene acp1 were adapted to detect more than half of the European Union-approved individual or stacked GM cotton events in one reaction. The assay was fully specific (<1.7% of false classification rate), with limit of detection values of 0.1% for each event, which were also achieved with simulated mixtures at different relative percentages of targets. The assay was further combined with a second multiplex PCR-CGE-SC assay to allow simultaneous detection of 6 cotton and 5 maize targets (two endogenous genes and 9 GM events) in two multiplex PCRs and a single CGE, making the approach more economic. Besides allowing simultaneous detection of many targets with adequate specificity and sensitivity, the multiplex PCR-CGE-SC approach has high throughput and automation capabilities, while keeping a very simple protocol, e.g., amplification and labeling in one step. Thus, it is an easy and inexpensive tool for initial screening, to be complemented with quantitative assays if necessary.

  5. Volatiles Emitted from Maize Ears Simultaneously Infected with Two Fusarium Species Mirror the Most Competitive Fungal Pathogen

    PubMed Central

    Sherif, Mohammed; Becker, Eva-Maria; Herrfurth, Cornelia; Feussner, Ivo; Karlovsky, Petr; Splivallo, Richard

    2016-01-01

    Along with barley and rice, maize provides staple food for more than half of the world population. Maize ears are regularly infected with fungal pathogens of the Fusarium genus, which, besides reducing yield, also taint grains with toxic metabolites. In an earlier work, we have shown that maize ears infection with single Fusarium strains was detectable through volatile sensing. In nature, infection most commonly occurs with more than a single fungal strain; hence we tested how the interactions of two strains would modulate volatile emission from infected ears. For this purpose, ears of a hybrid and a dwarf maize variety were simultaneously infected with different strains of Fusarium graminearum and F. verticillioides and, the resulting volatile profiles were compared to the ones of ears infected with single strains. Disease severity, fungal biomass, and the concentration of the oxylipin 9-hydroxy octadecadienoic acid, a signaling molecule involved in plant defense, were monitored and correlated to volatile profiles. Our results demonstrate that in simultaneous infections of hybrid and dwarf maize, the most competitive fungal strains had the largest influence on the volatile profile of infected ears. In both concurrent and single inoculations, volatile profiles reflected disease severity. Additionally, the data further indicate that dwarf maize and hybrid maize might emit common (i.e., sesquiterpenoids) and specific markers upon fungal infection. Overall this suggests that volatile profiles might be a good proxy for disease severity regardless of the fungal competition taking place in maize ears. With the appropriate sensitivity and reliability, volatile sensing thus appears as a promising tool for detecting fungal infection of maize ears under field conditions. PMID:27729923

  6. Amplified Rate Acceleration by Simultaneous Up-Regulation of Multiple Active Sites in an Endo-Functionalized Porous Capsule.

    PubMed

    Kopilevich, Sivil; Müller, Achim; Weinstock, Ira A

    2015-10-14

    Using the hydrolysis of epoxides in water as a model reaction, the effect of multiple active sites on Michaelis-Menten compliant rate accelerations in a porous capsule is demonstrated. The capsule is a water-soluble Ih-symmetry Keplerate-type complex of the form, [{Mo(VI)6O21(H2O)6}12{Mo(V)2O4(L)}30](42-), in which 12 pentagonal "ligands," {(Mo(VI))Mo(VI)5O21(H2O)6}(6-), are coordinated to 30 dimolybdenum sites, {Mo(V)2O4L}(1+) (L = an endohedrally coordinated η(2)-bound carboxylate anion), resulting in 20 Mo9O9 pores. When "up-regulated" by removal of ca. one-third of the blocking ligands, L, an equal number of dimolybdenum sites are activated, and the newly freed-up space allows for encapsulation of nearly twice as many substrate guests, leading to a larger effective molarity (amplification), and an increase in the rate acceleration (k(cat)/k(uncat)) from 16,000 to an enzyme-like value of 182,800.

  7. A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH heterogeneous stock

    PubMed Central

    Johannesson, Martina; Lopez-Aumatell, Regina; Stridh, Pernilla; Diez, Margarita; Tuncel, Jonatan; Blázquez, Gloria; Martinez-Membrives, Esther; Cañete, Toni; Vicens-Costa, Elia; Graham, Delyth; Copley, Richard R.; Hernandez-Pliego, Polinka; Beyeen, Amennai D.; Öckinger, Johan; Fernández-Santamaría, Cristina; Gulko, Percio S.; Brenner, Max; Tobeña, Adolf; Guitart-Masip, Marc; Giménez-Llort, Lydia; Dominiczak, Anna; Holmdahl, Rikard; Gauguier, Dominique; Olsson, Tomas; Mott, Richard; Valdar, William; Redei, Eva E.; Fernández-Teruel, Alberto; Flint, Jonathan

    2009-01-01

    The laboratory rat (Rattus norvegicus) is a key tool for the study of medicine and pharmacology for human health. A large database of phenotypes for integrated fields such as cardiovascular, neuroscience, and exercise physiology exists in the literature. However, the molecular characterization of the genetic loci that give rise to variation in these traits has proven to be difficult. Here we show how one obstacle to progress, the fine-mapping of quantitative trait loci (QTL), can be overcome by using an outbred population of rats. By use of a genetically heterogeneous stock of rats, we map a locus contributing to variation in a fear-related measure (two-way active avoidance in the shuttle box) to a region on chromosome 5 containing nine genes. By establishing a protocol measuring multiple phenotypes including immunology, neuroinflammation, and hematology, as well as cardiovascular, metabolic, and behavioral traits, we establish the rat HS as a new resource for the fine-mapping of QTLs contributing to variation in complex traits of biomedical relevance. PMID:18971309

  8. Metabolite profiling of the multiple tyrosine kinase inhibitor lenvatinib: a cross-species comparison.

    PubMed

    Dubbelman, Anne-Charlotte; Nijenhuis, Cynthia M; Jansen, Robert S; Rosing, Hilde; Mizuo, Hitoshi; Kawaguchi, Shinki; Critchley, David; Shumaker, Robert; Schellens, Jan H M; Beijnen, Jos H

    2016-06-01

    Lenvatinib is an oral, multiple receptor tyrosine kinase inhibitor. Preclinical drug metabolism studies showed unique metabolic pathways for lenvatinib in monkeys and rats. A human mass balance study demonstrated that lenvatinib related material is mainly excreted via feces with a small fraction as unchanged parent drug, but little is reported about its metabolic fate. The objective of the current study was to further elucidate the metabolic pathways of lenvatinib in humans and to compare these results to the metabolism in rats and monkeys. To this end, we used plasma, urine and feces collected in a human mass balance study after a single 24 mg (100 μCi) oral dose of (14)C-lenvatinib. Metabolites of (14)C-lenvatinib were identified using liquid chromatography (high resolution) mass spectrometry with off-line radioactivity detection. Close to 50 lenvatinib-related compounds were detected. In humans, unchanged lenvatinib accounted for 97 % of the radioactivity in plasma, and comprised 0.38 and 2.5 % of the administered dose excreted in urine and feces, respectively. The primary biotransformation pathways of lenvatinib were hydrolysis, oxidation and hydroxylation, N-oxidation, dealkylation and glucuronidation. Various combinations of these conversions with modifications, including hydrolysis, gluthathione/cysteine conjugation, intramolecular rearrangement and dimerization, were observed. Some metabolites seem to be unique to the investigated species (human, rat, monkey). Because all lenvatinib metabolites in human plasma were at very low levels compared to lenvatinib, only lenvatinib is expected to contribute to the pharmacological effects in humans.

  9. Ultra-Performance Liquid Chromatography for the Simultaneous Quantification of Rutin and Chlorogenic Acid in Leaves of Ribes L. Species by Conventional and Chemometric Calibration Approaches.

    PubMed

    Kendir, Gülsen; Dinç, Erdal; Güvenç, Ayşegül Köroǧlu

    2015-10-01

    A new ultra-performance liquid chromatography (UPLC) using conventional and chemometric calibrations was improved for the simultaneous estimation of chlorogenic acid (CA) and rutin (RUT) in leaves of Ribes L. species (R. rubrum, R. biebersteinii, R. nigrum, R. uva-crispa, R. alpinum, R. orientale, R. multiflorum and R. anatolica). The UPLC separation for CA and RUT in samples were performed on a Waters UPLC BEH phenyl column (100 mm × 1.0 mm i.d., 1.7 μm) and mobile phase consisting of acetonitrile and 0.1 M formic acid buffer, pH = 3.77 (15:85, v/v) containing 1.0 mL triethylamine in 1,000 mL mobile phase. Multi-wavelength UPLC chromatograms of CA and RUT in calibration and plant samples were obtained by the photodiode array (PDA) detection at the wavelength set from 290 to 360 nm with the interval of Δλ = 10 nm. Conventional UPLC-single and chemometric calibrations were subjected to the analysis of the related compounds. By using UPLC data, conventional and chemometric calibrations in the linear concentration range between 2.5 and 40.0 μg/mL for all compounds were applied for the simultaneous quantitative analysis of CA and RUT in plant samples of seven different Ribes species.

  10. Simultaneous light emission and detection of InGaN/GaN multiple quantum well diodes for in-plane visible light communication

    NASA Astrophysics Data System (ADS)

    Wang, Yongjin; Xu, Yin; Yang, Yongchao; Gao, Xumin; Zhu, Bingcheng; Cai, Wei; Yuan, Jialei; Zhang, Rong; Zhu, Hongbo

    2017-03-01

    This paper presents the design, fabrication, and experimental characterization of monolithically integrated p-n junction InGaN/GaN multiple quantum well diodes (MQWDs) and suspended waveguides. Suspended MQWDs can be used as transmitters and receivers simultaneously, and suspended waveguides are used for light coupling to create an in-plane visible light communication system. Compared to the waveguide with separation trench, the calculated total light efficiency is increased from 18% to 22% for the continuous waveguide. The MQWDs are characterized by their typical current-voltage performance, and the pulse excitation measurements confirm that the InGaN/GaN MQWDs can achieve the light emission and photodetection at the same time. The photocurrent measurements indicate that the photocurrent is modulated by a bias voltage and that the photons are being supplied from another transmitter. An experimental demonstration is presented showing that the proposed device works well for in-plane full-duplex communication using visible light.

  11. Rotational cars application to simultaneous and multiple-point temperature and concentration determination in a turbulent flow

    NASA Technical Reports Server (NTRS)

    Snow, J. B.; Murphy, D. V.; Chang, R. K.

    1984-01-01

    Coherent Anti-stokes Raman Scattering (CARS) from the pure rotational Raman lines of N2 is employed to measure the instantaneous rotational temperature of N2 gas at room temperature and below with good spatial resolution. A broad-bandwidth dye laser is used to obtain the entire rotational spectrum from a signal laser pulse; the CARS signal is then dispersed by a spectrograph and recorded on an optical multichannel analyzer. A best-fit temperature is found in several seconds with the aid of a computer for each experimental spectrum by a least squares comparison with calculated spectra. The model used to calculate the theoretical spectra incorporates the temperature and pressure dependence of the pressure-broadened rotational Raman lines, includes the nonresonant background susceptibility, and assumes that the pump laser has a finite linewidth. Temperatures are fit to experimental spectra recorded over the temperature range of 135 to 296K, and over the pressure range of 0.13 to 15.3 atm. In addition to the spatially resolved single point work, we have used multipoint CARS to obtain information from many spatially resolved volume elements along a cylindrical line (0.1 x 0.1 x 2.0 mm). We also obtained qualitative information on the instantaneous species concentration and temperature at 20 spatially resolved volume elements (0.1 x 0.1 x 0.1 mm) along a line.

  12. Simultaneous use of camera and probe diagnostics to unambiguously identify and study the dynamics of multiple underlying instabilities during the route to plasma turbulence

    SciTech Connect

    Thakur, S. C. Tynan, G. R.; Brandt, C.; Cui, L.; Gosselin, J. J.; Light, A.

    2014-11-15

    We use multiple-tip Langmuir probes and fast imaging to unambiguously identify and study the dynamics of underlying instabilities during the controlled route to fully-developed plasma turbulence in a linear magnetized helicon plasma device. Langmuir probes measure radial profiles of electron temperature, plasma density and potential; from which we compute linear growth rates of instabilities, cross-phase between density and potential fluctuations, Reynold's stress, particle flux, vorticity, time-delay estimated velocity, etc. Fast imaging complements the 1D probe measurements by providing temporally and spatially resolved 2D details of plasma structures associated with the instabilities. We find that three radially separated plasma instabilities exist simultaneously. Density gradient driven resistive drift waves propagating in the electron diamagnetic drift direction separate the plasma into an edge region dominated by strong, velocity shear driven Kelvin-Helmholtz instabilities and a central core region which shows coherent Rayleigh-Taylor modes propagating in the ion diamagnetic drift direction. The simultaneous, complementary use of both probes and camera was crucial to identify the instabilities and understand the details of the very rich plasma dynamics.

  13. Mathematical models for quantifying eruption velocity in degassing pipes based on exsolution of a single gas and simultaneous exsolution of multiple gases

    NASA Astrophysics Data System (ADS)

    Leon, Arturo S.

    2016-09-01

    After the limnic eruptions at Nyos and Monoun in the 1980s, degassing pipes were installed to reduce the continuous increase of CO2 at the bottom of these lakes. The degassing system consists of a vertical pipe from the lake bottom to the surface and a small pump located near the top of the pipe, which raises water in the pipe up to a level where it becomes saturated with gas, which in turn leads to volume expansion and eruption. This paper describes two new mathematical models for predicting eruption velocity in degassing pipes based on exsolution of a single gas and the simultaneous exsolution of multiple gases. The models were applied to the degassing system of lakes Nyos and Monoun, which contain two main gases, namely CO2 and CH4. Because the volume proportion of CH4 is significant only in Lake Monoun, the Lake Nyos test case considered the CO2 gas only, while as the Lake Monoun test case considered the simultaneous exsolution of CO2 and CH4. Good agreement between the results of the models and observed data is found for both test cases. The results for the eruption in Lake Monoun considering the two main gases measured in this lake (CO2 and CH4) were found to have a better agreement with the measurements compared to the model results obtained considering the main gas only (CO2).

  14. Successful Simultaneous Liver-Kidney Transplantation in the Presence of Multiple High-Titered Class I and II Antidonor HLA Antibodies

    PubMed Central

    Paterno, Flavio; Girnita, Alin; Brailey, Paul; Witte, David; Wang, Jiang; Cuffy, Madison C.; Diwan, Tayyab; Tremblay, Simon; Revollo, Jane Y.; Alloway, Rita R.; Schoech, Michael R.; Anwar, Nadim; Shah, Shimul A.; Woodle, Steve E.

    2016-01-01

    Abstract The results of simultaneous liver-kidney transplants in highly sensitized recipients have been controversial in terms of antibody-mediated rejection and kidney allograft outcomes. This case report provides a detailed and sophisticated documentation of histocompatibility and pathologic data in a simultaneous liver-kidney transplant performed in a recipient with multiple high-titered class I and II antidonor HLA antibodies and a strongly positive cytotoxic crossmatch. Patient received induction with steroids, rituximab, and eculizumab without lymphocyte depleting agents. The kidney transplant was delayed by 6 hours after the liver transplant to allow more time to the liver allograft to “absorb” donor-specific antibodies (DSA). Interestingly, the liver allograft did not prevent immediate antibody-mediated injury to the kidney allograft in this highly sensitized recipient. Anti-HLA single antigen bead analysis of liver and kidney allograft biopsy eluates revealed deposition of both class I and II DSA in both liver and kidney transplants during the first 2 weeks after transplant. Afterward, both liver and kidney allograft functions improved and remained normal after a year with progressive reduction in serum DSA values. PMID:27990486

  15. Simultaneous detection of multiple debris via a cascade of numerical evaluations and a voting scheme for lines in an image sequence

    NASA Astrophysics Data System (ADS)

    Fujita, Koki; Ichimura, Naoyuki; Hanada, Toshiya

    2017-04-01

    This paper presents a novel method to simultaneously detect multiple trajectories of space debris in an observation image sequence to establish a reliable model for space debris environment in Geosynchronous Earth Orbit (GEO). The debris in GEO often appear faintly in image sequences due to the high altitude. A simple but steady way to detect such faint debris is to decrease a threshold value of binarization applied to an image sequence during preprocessing. However, a low threshold value of binarization leads to extracting a large number of objects other than debris that become obstacles to detect debris trajectories. In order to detect debris from binarized image frames with massive obstacles, this work proposes a method that utilizes a cascade of numerical evaluations and a voting scheme to evaluate characteristics of the line segments obtained by connecting two image objects in different image frames, which are the candidates of debris trajectories. In the proposed method, the line segments corresponding to objects other than debris are filtered out using three types of characteristics, namely displacement, direction, and continuity. First, the displacement and direction of debris motion are evaluated to remove irrelevant trajectories. Then, the continuity of the remaining line segments is checked to find debris by counting the number of image objects appearing on or close to the line segments. Since checking the continuity can be regarded as a voting scheme, the proposed cascade algorithm can take advantage of the properties of voting method such as the Hough transform, i.e., the robustness against heavy noises and clutters, and ability of detecting multiple trajectories simultaneously. The experimental tests using real image sequences obtained in a past observation campaign demonstrate the effectiveness of the proposed method.

  16. Manipulation of orthogonal neural systems together in electrophysiological recordings: the MONSTER approach to simultaneous assessment of multiple neurocognitive dimensions.

    PubMed

    Kappenman, Emily S; Luck, Steven J

    2012-01-01

    Event-related potentials (ERPs) are a powerful tool in understanding and evaluating cognitive, affective, motor, and sensory processing in both healthy and pathological samples. A typical ERP recording session takes considerable time but is designed to isolate only 1-2 components. Although this is appropriate for most basic science purposes, it is an inefficient approach for measuring the broad set of neurocognitive functions that may be disrupted in a neurological or psychiatric disease. The present study provides a framework for more efficiently evaluating multiple neural processes in a single experimental paradigm through the manipulation of functionally orthogonal dimensions. We describe the general MONSTER (Manipulation of Orthogonal Neural Systems Together in Electrophysiological Recordings) approach and explain how it can be adapted to investigate a variety of neurocognitive domains, ERP components, and neural processes of interest. We also demonstrate how this approach can be used to assess group differences by providing data from an implementation of the MONSTER approach in younger (18-30 y of age) and older (65-85 y of age) adult samples. This specific implementation of the MONSTER framework assesses 4 separate neural processes in the visual domain: (1) early sensory processing, using the C1 wave; (2) shifts of covert attention, with the N2pc component; (3) categorization, with the P3 component; and (4) self-monitoring, with the error-related negativity. Although the MONSTER approach is primarily described in the context of ERP experiments, it could also be adapted easily for use with functional magnetic resonance imaging.

  17. Characterization of blue mold Penicillium species isolated from stored fruits using multiple highly conserved loci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locatio...

  18. Simultaneous determination of bioactive compounds in Piper nigrum L. and a species comparison study using HPLC-PDA.

    PubMed

    Rao, Vidadala Rama Subba; Raju, Sagi Satyanarayana; Sarma, Vanka Umamaheswara; Sabine, Fouriner; Babu, Kothapalli Hari; Babu, Katragadda Suresh; Rao, Janaswamy Madhusudana

    2011-08-01

    Piper nigrum L. is a traditional medicine widely used in India for illnesses such as constipation, diarrhoea, earache, gangrene, heart disease, hernia, hoarseness, indigestion, insect bites, insomnia, joint pain, liver problems, lung disease, oral abscesses, sunburn, tooth decay and toothaches. In this study, six bioactive compounds, namely piperine (1), pellitorine (2), guineensine (3), pipnoohine (4), trichostachine (5) and piperonal (6) were quantified in different extracts of P. nigrum L. and compared with those of P. longum L. and P. chaba Hunter. To evaluate the quality of P. nigrum, a simple, accurate and precise HPLC-PDA method was developed for the simultaneous determination of the above-mentioned six compounds. The separation was achieved by Phenomenex Luna RP C(18) column (150 × 4.6 mm, 5 µm, Phenomenex Inc, CA, USA) with a binary gradient solvent system of water-acetonitrile, at a flow rate of 1.0 mL min(-1) and detected at 210, 232, 262 and 343 nm. All six calibration curves showed good linearity (R (2) > 0.9966). The method was reproducible with intra- and inter-day variations of less than 2% and 5%, respectively. The results demonstrated that this method is simple, reliable and suitable for the quality control of these plants.

  19. Decontamination of heavy metal laden sewage sludge with simultaneous solids reduction using thermophilic sulfur and ferrous oxidizing species.

    PubMed

    Mehrotra, A; Kundu, K; Sreekrishnan, T R

    2016-02-01

    A possibility of using simultaneous sewage sludge digestion and metal leaching (SSDML) process at the thermophilic temperature to remove heavy metals and suspended solids from sewage sludge is explored in this study. Though thermophilic sludge digestion efficiently produces a stable sludge, its inability to remove heavy metals requires it to be used in tandem with another process like bioleaching for metal reduction. Previously, different temperature optima were known for the heterotrophs (thermophilic) responsible for the sludge digestion and the autotrophs involved in bioleaching (mesophilic), because of which the metal concentration was brought down separately in a different reactor. In our study, SSDML process was carried out at 50 °C (thermophilic) by using ferrous sulfate (batch-1) and sulfur (batch-2) as the energy source in two reactors. The concentration of volatile suspended solids reduced by >40% in both batches, while that of heavy metals zinc, copper, chromium, cadmium and nickel decreased by >50% in both batch-1 and batch-2. Lead got leached out only in batch-1. Using 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis analysis, Alicyclobacillus tolerans was found to be the microorganism responsible for lowering the pH in both the reactors at thermophilic temperature. The indicator organism count was also below the maximum permissible limit making sludge suitable for agricultural use. Our results indicate that SSDML at thermophilic temperature can be effectively used for reduction of heavy metals and suspended solids from sewage sludge.

  20. A novel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis.

    PubMed

    Gurtler, Volker; Grando, Danilla; Mayall, Barrie C; Wang, Jenny; Ghaly-Derias, Shahbano

    2012-09-01

    In order to develop a typing and identification method for van gene containing Enterococcus faecium, two multiplex PCR reactions were developed for use in HRM-PCR (High Resolution Melt-PCR): (i) vanA, vanB, vanC, vanC23 to detect van genes from different Enterococcus species; (ii) ISR (intergenic spacer region between the 16S and 23S rRNA genes) to detect all Enterococcus species and obtain species and isolate specific HRM curves. To test and validate the method three groups of isolates were tested: (i) 1672 Enterococcus species isolates from January 2009 to December 2009; (ii) 71 isolates previously identified and typed by PFGE (pulsed-field gel electrophoresis) and MLST (multi-locus sequence typing); and (iii) 18 of the isolates from (i) for which ISR sequencing was done. As well as successfully identifying 2 common genotypes by HRM from the Austin Hospital clinical isolates, this study analysed the sequences of all the vanB genes deposited in GenBank and developed a numerical classification scheme for the standardised naming of these vanB genotypes. The identification of Enterococcus faecalis from E. faecium was reliable and stable using ISR PCR. The typing of E. faecium by ISR PCR: (i) detected two variable peaks corresponding to different copy numbers of insertion sequences I and II corresponding to peak I and II respectively; (ii) produced 7 melt profiles for E. faecium with variable copy numbers of sequences I and II; (iii) demonstrated stability and instability of peak heights with equal frequency within the patient sample (36.4±4.5 days and 38.6±5.8 days respectively for 192 patients); (iv) detected ISR-HRM types with as much discrimination as PFGE and more than MLST; and (v) detected ISR-HRM types that differentiated some isolates that were identical by PFGE and MLST. In conjunction with the rapid and accurate van genotyping method described here, this ISR-HRM typing and identification method can be used as a stable identification and typing method with

  1. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    PubMed

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  2. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    PubMed Central

    Dayan, Franck E.; Owens, Daniel K.; Watson, Susan B.; Asolkar, Ratnakar N.; Boddy, Louis G.

    2015-01-01

    Sarmentine, 1-(1-pyrrolidinyl)-(2E,4E)-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in response between plants treated with sarmentine and herbicidal soaps such as pelargonic acid (nonanoic acid). However, little was known about the mechanism of action leading to the rapid desiccation of foliage treated by sarmentine. In cucumber cotyledon disc-assays, sarmentine induced rapid light-independent loss of membrane integrity at 100 μM or higher concentration, whereas 3 mM pelargonic acid was required for a similar effect. Sarmentine was between 10 and 30 times more active than pelargonic acid on wild mustard, velvetleaf, redroot pigweed and crabgrass. Additionally, the potency of 30 μM sarmentine was greatly stimulated by light, suggesting that this natural product may also interfere with photosynthetic processes. This was confirmed by observing a complete inhibition of photosynthetic electron transport at that concentration. Sarmentine also acted as an inhibitor of photosystem II (PSII) on isolated thylakoid membranes by competing for the binding site of plastoquinone. This can be attributed in part to structural similarities between herbicides like sarmentine and diuron. While this mechanism of action accounts for the light stimulation of the activity of sarmentine, it does not account for its ability to destabilize membranes in darkness. In this respect, sarmentine has some structural similarity to crotonoyl-CoA, the substrate of enoyl-ACP reductase, a key enzyme in the early steps of fatty acid synthesis. Inhibitors of this enzyme, such as triclosan, cause rapid loss of membrane integrity in the dark. Sarmentine inhibited the activity of enoyl-ACP reductase, with an I50app of 18.3 μM. Therefore, the herbicidal activity of sarmentine appears to be a

  3. Contrasting effects of plant species traits and moisture on the decomposition of multiple litter fractions.

    PubMed

    Riggs, Charlotte E; Hobbie, Sarah E; Cavender-Bares, Jeannine; Savage, Jessica A; Wei, Xiaojing

    2015-10-01

    Environmental variation in moisture directly influences plant litter decomposition through effects on microbial activity, and indirectly via plant species traits. Whether the effects of moisture and plant species traits are mutually reinforcing or counteracting during decomposition are unknown. To disentangle the effects of moisture from the effects of species traits that vary with moisture, we decomposed leaf litter from 12 plant species in the willow family (Salicaceae) with different native habitat moisture preferences in paired mesic and wetland plots. We fit litter mass loss data to an exponential decomposition model and estimated the decay rate of the rapidly cycling litter fraction and size of the remaining fraction that decays at a rate approaching zero. Litter traits that covaried with moisture in the species' native habitat significantly influenced the decomposition rate of the rapidly cycling litter fraction, but moisture in the decomposition environment did not. In contrast, for the slowly cycling litter fraction, litter traits that did not covary with moisture in the species' native habitat and moisture in the decomposition environment were significant. Overall, the effects of moisture and plant species traits on litter decomposition were somewhat reinforcing along a hydrologic gradient that spanned mesic upland to wetland (but not permanently surface-saturated) plots. In this system, plant trait and moisture effects may lead to greater in situ decomposition rates of wetland species compared to upland species; however, plant traits that do not covary with moisture will also influence decomposition of the slowest cycling litter fraction.

  4. No inbreeding depression for low temperature developmental acclimation across multiple Drosophila species.

    PubMed

    Kristensen, Torsten N; Loeschcke, Volker; Bilde, Trine; Hoffmann, Ary A; Sgró, Carla; Noreikienė, Kristina; Ondrésik, Marti; Bechsgaard, Jesper S

    2011-11-01

    Populations are from time to time exposed to stressful temperatures. Their thermal resistance levels are determined by inherent and plastic mechanisms, which are both likely to be under selection in natural populations. Previous studies on Drosophila species have shown that inherent resistance is highly species specific, and differs among ecotypes (e.g., tropical and widespread species). Apart from being exposed to thermal stress many small and fragmented populations face genetic challenges due to, for example, inbreeding. Inbreeding has been shown to reduce inherent resistance levels toward stressful temperatures, but whether adaptation to thermal stress through plastic responses also is affected by inbreeding is so far not clear. In this study, we test inherent cold resistance and the ability to respond plastically to temperature changes through developmental cold acclimation in inbred and outbred lines of five tropical and five widespread Drosophila species. Our results confirm that tropical species have lower cold resistance compared to widespread species, and show that (1) inbreeding reduces inherent cold resistance in both tropical and widespread species, (2) inbreeding does not affect the ability to respond adaptively to temperature acclimation, and (3) tropical species with low basal resistance show stronger adaptive plastic responses to developmental acclimation compared to widespread species.

  5. Development of PCR primers and a DNA macroarray for the simultaneous detection of major Staphylococcus species using groESL gene.

    PubMed

    Chiang, Yu-Cheng; Lu, Hsi-Chi; Li, Sheng-Chih; Chang, Yu-Hsin; Chen, Hsin-Yen; Lin, Chia-Wei; Tsen, Hau-Yang

    2012-03-01

    Staphylococcus spp., including S. aureus, S. intermedius, S. hyicus, S. epidermidis, S. saprophyticus, S. haemolyticus, S. xylosus, and S. carnosus, are major bacterial species associated with food poisoning, and human and veterinary clinics. Traditional methods for the identification of these staphylococci are time-consuming, laborious, or inaccurate. Therefore, rapid and accurate diagnostic methods are needed. In this study, we designed the DNA probes and polymerase chain reaction (PCR) primers for the detection of the aforementioned Staphylococcus species. These primers were proved to be specific for the detection of their corresponding target strains. Furthermore, by using a consensus primer pair, we were able to co-amplify the intergenic region of groES-groEL for these staphylococci. Followed by a chromogenic macroarray system with the specific probes on the plastic chips, these staphylococci in milk products or clinical samples could be simultaneously detected. When the system was used for the inspection of milk or urine samples containing N × 10⁰ target cells per milliliter of the sample, all these staphylococcal species could be identified after an 8-h pre-enrichment step. This system also allowed the adequate diagnosis of bacteremia, since N × 10⁰ target cells per milliliter of the blood samples could be detected after a 12-h pre-enrichment. Compared to the multiplex PCR method, this approach has the additional advantage that it allowed the discrimination of more bacterial strains-even some bacterial strains that may generate PCR products with the same molecular sizes.

  6. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species

    PubMed Central

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, William K.; Prinzing, Andreas; Dong, Ming; Cornelissen, Johannes H.C.

    2015-01-01

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such contribution varies among plant species at given irradiance regime, (2) whether interspecific variation in such contribution correlates with interspecific variation in the decomposition rate under shade; and (3) whether this correlation can be explained by leaf traits. We conducted a factorial experiment to determine the effects of solar radiation and environmental moisture for the mass loss and the decomposition constant k-values of 13 species litters collected in Northern China. The contribution of solar radiation to leaf litter decomposition varied significantly among species. Solar radiation accelerated decomposition in particular in the species that already decompose quickly under shade. Functional traits, notably specific leaf area, might predict the interspecific variation in that contribution. Our results provide the first empirical evidence for how the effect of solar radiation on decomposition varies among multiple species. Thus, the effect of solar radiation on the carbon flux between biosphere and atmosphere may depend on the species composition of the vegetation. PMID:26282711

  7. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species.

    PubMed

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, William K; Prinzing, Andreas; Dong, Ming; Cornelissen, Johannes H C

    2015-08-18

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such contribution varies among plant species at given irradiance regime, (2) whether interspecific variation in such contribution correlates with interspecific variation in the decomposition rate under shade; and (3) whether this correlation can be explained by leaf traits. We conducted a factorial experiment to determine the effects of solar radiation and environmental moisture for the mass loss and the decomposition constant k-values of 13 species litters collected in Northern China. The contribution of solar radiation to leaf litter decomposition varied significantly among species. Solar radiation accelerated decomposition in particular in the species that already decompose quickly under shade. Functional traits, notably specific leaf area, might predict the interspecific variation in that contribution. Our results provide the first empirical evidence for how the effect of solar radiation on decomposition varies among multiple species. Thus, the effect of solar radiation on the carbon flux between biosphere and atmosphere may depend on the species composition of the vegetation.

  8. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including S. bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, ...

  9. Quantifying the dispersal potential of seagrass vegetative fragments: A comparison of multiple subtropical species

    NASA Astrophysics Data System (ADS)

    Weatherall, E. J.; Jackson, E. L.; Hendry, R. A.; Campbell, M. L.

    2016-02-01

    Seagrass meadows are threatened by anthropogenic and natural disturbances on both a local and global scale. Understanding the potential for seagrasses to disperse, connecting populations separated by unsuitable habitat is important to assess the resilience of regional populations. This study investigated the relative dispersal potential of vegetative fragments of seagrass from five subtropical species (Zostera muelleri, Halodule uninervis, Halophila ovalis, Halophila spinulosa, Halophila decipiens). Five questions were examined: 1) do vegetative fragments of different species settle at different velocities; 2) does a species morphometric variables influence settling velocities; 3) is a species settling velocity related to the species local distribution; 4) does temperature stress affect settling velocity; and 5) what is the composition and potential viability of seagrass fragments floating in the bay. A proportional distribution index for each species was determined using data from a habitat prediction model. It was found that H. spinulosa settled significantly faster than the remaining species and Z. muelleri settled the slowest. Variables influencing settling velocity included rhizome length, weight and surface area. In both Z. muelleri and H. ovalis settling velocities were significantly greater at higher temperatures (although there was no significant difference between approximately 5 and 10 °C above ambient temperature). H. uninervis was not significantly influenced by temperature. There was a significant negative correlation between species settling velocities and their distribution.

  10. mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species.

    PubMed

    Brzostowicz, Patricia C; Walters, Dana M; Thomas, Stuart M; Nagarajan, Vasantha; Rouvière, Pierre E

    2003-01-01

    mRNA differential display has been used to identify cyclohexanone oxidation genes in a mixed microbial community derived from a wastewater bioreactor. Thirteen DNA fragments randomly amplified from the total RNA of an enrichment subculture exposed to cyclohexanone corresponded to genes predicted to be involved in the degradation of cyclohexanone. Nine of these DNA fragments are part of genes encoding three distinct Baeyer-Villiger cyclohexanone monooxygenases from three different bacterial species present in the enrichment culture. In Arthrobacter sp. strain BP2 and Rhodococcus sp. strain Phi2, the monooxygenase is part of a gene cluster that includes all the genes required for the degradation of cyclohexanone, while in Rhodococcus sp. strain Phi1 the genes surrounding the monooxygenase are not predicted to be involved in this degradation pathway but rather seem to belong to a biosynthetic pathway. Furthermore, in the case of Arthrobacter strain BP2, three other genes flanking the monooxygenase were identified by differential display, demonstrating that the repeated sampling of bacterial operons shown earlier for a pure culture (D. M. Walters, R. Russ, H. Knackmuss, and P. E. Rouvière, Gene 273:305-315, 2001) is also possible for microbial communities. The activity of the three cyclohexanone monooxygenases was confirmed and characterized following their expression in Escherichia coli.

  11. Salinomycin simultaneously induces apoptosis and autophagy through generation of reactive oxygen species in osteosarcoma U2OS cells.

    PubMed

    Kim, Sang-Hun; Choi, Young-Jun; Kim, Kwang-Youn; Yu, Sun-Nyoung; Seo, Young-Kyo; Chun, Sung-Sik; Noh, Kyung-Tae; Suh, Jeung-Tak; Ahn, Soon-Cheol

    2016-04-29

    Salinomycin, a polyether antibiotic, acts as a highly selective potassium ionophore. It was reported to anticancer activity on various cancer cell lines. In this study, salinomycin was examined on apoptosis and autophagy through generation of reactive oxygen species (ROS) in osteosarcoma U2OS cells. Apoptosis, autophagy, mitochondrial membrane potential (MMP) and ROS were analyzed using flow cytometry. Also, expressions of apoptosis- and autophagy-related proteins were determined by western blotting. As a result, salinomycin triggered apoptosis of U2OS cells, which was accompanied by change of MMP and cleavage of caspases-3 and poly (ADP-ribose) polymerase. And salinomycin increased the expression of autophagy-related protein and accumulation of acidic vesicular organelles (AVO). Salinomycin-induced ROS production promotes both apoptosis and autophagy, as evidenced by the result that treatment of N-acetyl-l-cysteine (NAC), a ROS scavenger, attenuated both apoptosis and autophagy. In addition, inhibition of autophagy by 3-methyladenine (3 MA) enhanced the salinoymcin-induced apoptosis. Taken together, these results suggested that salinomycin-induced autophagy, as a survival mechanism, might be a potential strategy through ROS regulation in cancer therapy.

  12. Development of an automated sampling-analysis system for simultaneous measurement of reactive oxygen species (ROS) in gas and particle phases: GAC-ROS

    NASA Astrophysics Data System (ADS)

    Huang, Wei; Zhang, Yuanxun; Zhang, Yang; Zeng, Limin; Dong, Huabin; Huo, Peng; Fang, Dongqing; Schauer, James J.

    2016-06-01

    A novel online system, GAC-ROS, for simultaneous measurement of reactive oxygen species (ROS) in both gas and particle phases was developed based on 2‧,7‧-dichlorofluorescin (DCFH) assay to provide fast sampling and analysis of atmospheric ROS. The GAC-ROS, composed of a Gas and Aerosol Collector (GAC), a series of reaction and transportation systems, and a fluorescence detector, was tested for instrumental performance in laboratory. Results showed good performance with a favorable R2 value for the calibration curve (above 0.998), high penetration efficiencies of ROS (above 99.5%), and low detection limits (gas-phase ROS: 0.16 nmol H2O2 m-3; particle-phase ROS: 0.12 nmol H2O2 m-3). Laboratorial comparison between online and offline methods for particle-bound ROS showed significant loss of ROS due to the relatively long time off-line treatment. Field observations in Beijing found that concentrations of ROS in winter time were significantly higher than those observed in spring. Only a few weak positive correlations were found between ROS and some air pollutants, which reflects the complexities of ROS generation and transformation in atmosphere. This study was the first to simultaneously obtain concentrations of gas and particle-phase ROS using an online method. Consequently, it provides a powerful tool to characterize the oxidizing capacity of the atmosphere and the sources of the oxidizing capacity.

  13. Development and validation of a triplex real-time PCR assay for the simultaneous detection of three mustard species and three celery varieties in food.

    PubMed

    Palle-Reisch, Monika; Hochegger, Rupert; Cichna-Markl, Margit

    2015-10-01

    The paper presents a triplex real-time PCR assay allowing the simultaneous detection of three mustard species (white, black and brown mustard) and three celery varieties (celery roots, celery stalks and leaf celery) in foodstuffs. The triplex assay does not show cross-reactivity with other Brassicaceae. Low cross-reactivities were observed with fenugreek, cumin, ginger, caraway, turmeric, lovage and rye, the ΔCt values were, however, ⩾ 12 compared to positive controls. The triplex assay allows the detection of traces of DNA of the allergenic components in spite of an excess of the other DNA templates. Analysis of extracts from model sausages containing defined concentrations of mustard and celery showed that the triplex assay is applicable to both raw and processed foods. It was found to allow the detection of 1 ppm black/brown mustard and 50 ppm white mustard and celery in raw and brewed sausages with a probability ⩾ 95%.

  14. Simultaneous recovery of metals and degradation of organic species: copper and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T).

    PubMed

    Chaudhary, Abdul J; Hassan, Mukhtar-ul; Grimes, Susan M

    2009-06-15

    In mixed wastewater streams, the presence of metal ions can retard the destruction of organic contaminants and the efficiency of recovery of the metal is reduced by the presence of organic species. The reduction in the efficiency of these methods is due to the formation of complexes between the organic species and the metal ions in solution. Results are presented for copper-2,4,5-T system in which both effects occur. A photolytic cell alone can achieve the complete degradation of 2,4,5-T, in the presence of TiO(2) or H(2)O(2), at pH 3.5. The addition of Cu(II) ions, however, retard the degradation of 2,4,5-T and complete mineralisation of 2,4,5-T was not achieved and the system also leaves Cu(II) ions in solution. An electrolytic cell alone can be used to recover copper in pH range 1.5-4.5 but is not capable of achieving complete disappearance of 2,4,5-T by anodic oxidation. A combined photolytic-electrolytic system is capable of achieving simultaneous destruction of 2,4,5-T and recovery of copper from mixed wastewater streams at pH 3.5. The percentage destruction of 2,4,5-T and the recovery of copper can be increased further by using a combined photolytic and an activated carbon concentrator cell system. This system can achieve the simultaneous recovery of copper and the degradation of 2,4,5-T without the use of an additional oxidants or catalysts.

  15. Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota

    PubMed Central

    Telleria, Erich L.; Echodu, Richard; Wu, Yineng; Okedi, Loyce M.; Weiss, Brian L.; Aksoy, Serap; Caccone, Adalgisa

    2014-01-01

    The invertebrate microbiome contributes to multiple aspects of host physiology, including nutrient supplementation and immune maturation processes. We identified and compared gut microbial abundance and diversity in natural tsetse flies from Uganda using five genetically distinct populations of Glossina fuscipes fuscipes and multiple tsetse species (Glossina morsitans morsitans, G. f. fuscipes, and Glossina pallidipes) that occur in sympatry in one location. We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals. Our results show extremely limited diversity in field flies of different tsetse species. The obligate endosymbiont Wigglesworthia dominated all samples (>99%), but we also observed wide prevalence of low-density Sodalis (tsetse's commensal endosymbiont) infections (<0.05%). There were also several individuals (22%) with high Sodalis density, which also carried coinfections with Serratia. Albeit in low density, we noted differences in microbiota composition among the genetically distinct G. f. fuscipes flies and between different sympatric species. Interestingly, Wigglesworthia density varied in different species (104 to 106 normalized genomes), with G. f. fuscipes having the highest levels. We describe the factors that may be responsible for the reduced diversity of tsetse's gut microbiota compared to those of other insects. Additionally, we discuss the implications of Wigglesworthia and Sodalis density variations as they relate to trypanosome transmission dynamics and vector competence variations associated with different tsetse species. PMID:24814785

  16. Bird and mammal species composition in distinct geographic regions and their relationships with environmental factors across multiple spatial scales.

    PubMed

    Kent, Rafi; Bar-Massada, Avi; Carmel, Yohay

    2014-05-01

    Global patters of species distributions and their underlying mechanisms are a major question in ecology, and the need for multi-scale analyses has been recognized. Previous studies recognized climate, topography, habitat heterogeneity and disturbance as important variables affecting such patterns. Here we report on analyses of species composition - environment relationships among different taxonomic groups in two continents, and the components of such relationships, in the contiguous USA and Australia. We used partial Canonical Correspondence Analysis of occurrence records of mammals and breeding birds from the Global Biodiversity Information Facility, to quantify relationships between species composition and environmental variables in remote geographic regions at multiple spatial scales, with extents ranging from 10(5) to 10(7) km(2) and sampling grids from 10 to 10,000 km(2). We evaluated the concept that two elements contribute to the impact of environmental variables on composition: the strength of species' affinity to an environmental variable, and the amount of variance in the variable. To disentangle these two elements, we analyzed correlations between resulting trends and the amount of variance contained in different environmental variables to isolate the mechanisms behind the observed relationships. We found that climate and land use-land cover are responsible for most explained variance in species composition, regardless of scale, taxonomic group and geographic region. However, the amount of variance in species composition attributed to land use / land cover (LULC) was closely related to the amount of intrinsic variability in LULC in the USA, but not in Australia, while the effect of climate on species composition was negatively correlated to the variability found in the climatic variables. The low variance in climate, compared to LULC, suggests that species in both taxonomic groups have strong affinity to climate, thus it has a strong effect on species

  17. Development of a thermostabilized, one-step, nested, tetraplex PCR assay for simultaneous identification and differentiation of Entamoeba species, Entamoeba histolytica and Entamoeba dispar from stool samples.

    PubMed

    Foo, Phiaw Chong; Chan, Yean Yean; See Too, Wei Cun; Tan, Zi Ning; Wong, Weng Kin; Lalitha, Pattabhiraman; Lim, Boon Huat

    2012-09-01

    Entamoeba histolytica is the only Entamoeba species that causes amoebiasis in humans. Approximately 50 million people are infected, with 100, 000 deaths annually in endemic countries. Molecular diagnosis of Entamoeba histolytica is important to differentiate it from the morphologically identical Entamoeba dispar to avoid unnecessary medication. Conventional molecular diagnostic tests require trained personnel, cold-chain transportation and/or are storage-dependent, which make them user-unfriendly. The aim of this study was to develop a thermostabilized, one-step, nested, tetraplex PCR assay for the detection of Entamoeba histolytica, Entamoeba dispar and Entamoeba species in cold-chain-free and ready-to-use form. The PCR test was designed based on the Entamoeba small subunit rRNA (SSU-rRNA) gene, which detects the presence of any Entamoeba species, and simultaneously can be used to differentiate Entamoeba histolytica from Entamoeba dispar. In addition, a pair of primers was designed to serve as an internal amplification control to help identify inhibitors in the samples. All PCR reagents together with the designed primers were thermostabilized by lyophilization and were stable at 24 °C for at least 6 months. The limit of detection of the tetraplex PCR was found to be 39 pg DNA or 1000 cells for Entamoeba histolytica and 78 pg DNA or 1000 cells for Entamoeba dispar, and the specificity was 100 %. In conclusion, this cold-chain-free, thermostabilized, one-step, nested, multiplex PCR assay was found to be efficacious in differentiating Entamoeba histolytica from other non-pathogenic Entamoeba species.

  18. Multiple pro-apoptotic targets of abietane diterpenoids from Salvia species.

    PubMed

    Akaberi, M; Mehri, S; Iranshahi, M

    2015-01-01

    The genus Salvia contains a large number of biologically active diterpenoids with various skeletons including abietanes, labdanes, clerodanes, pimaranes and icetexanes. Diterpenes of Salvia species showed various biological activities, particularly cytotoxic and anti-proliferative properties. In recent years many studies have been focused on the molecular mechanisms of these diterpenes in cancer cells. It should be noted, however, that anticancer studies on diterpenoids from Salvia species were dominated by tanshinones (a class of abietanes) over the past decades. A large number of targets of diterpenes have been identified in cancer cells including NF-κB, STAT3, Bcl-xL, β-catenin, cytochrome C and caspases. These studies give us deeper insights into the mechanisms of actions and cell signaling pathways of anticancer diterpenoids from Salvia species. This paper reviews protein targets of diterpenoids from Salvia species and highlights the gaps in our knowledge deserving future research.

  19. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many Phytophthora species are destructive plant pathogens imposing severe threats to both natural and agricultural vegetation. Effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of such diseases. DNA array hybridization technique is ...

  20. Multiple phenological responses to climate change among 42 plant species in Xi'an, China

    NASA Astrophysics Data System (ADS)

    Dai, Junhu; Wang, Huanjiong; Ge, Quansheng

    2013-09-01

    Phenological data of 42 woody plants in a temperate deciduous forest from the Chinese Phenological Observation Network (CPON) and the corresponding meteorological data from 1963 to 2011 in Xi'an, Shaanxi Province, China were collected and analyzed. The first leaf date (FLD), leaf coloring date (LCD) and first flower date (FFD) are revealed as strong biological signals of climatic change. The FLD, LCD and FFD of most species are sensitive to average temperature during a certain period before phenophase onset. Regional precipitation also has a significant impact on phenophases of about half of the species investigated. Affected by climate change, the FLD and FFD of these species have advanced by 5.54 days and 10.20 days on average during 2003-2011 compared with the period 1963-1996, respectively. Meanwhile, the LCD has delayed by 10.59 days, and growing season length has extended 16.13 days. Diverse responses of phenology commonly exist among different species and functional groups during the study period. Especially for FFD, the deviations between the above two periods ranged from -20.68 to -2.79 days; biotic pollination species showed a significantly greater advance than abiotic pollination species. These results were conducive to the understanding of possible changes in both the structure of plant communities and interspecific relationships in the context of climate change.

  1. SU-E-T-799: Verification of a Simultaneous Treatment of Multiple Brain Metastases Using VMAT Technique by a Composite Alanine-Gel Dosimeter Phantom

    SciTech Connect

    Pavoni, J; Silveira, M; Filho, O Baffa; Neves, W; Ramos, P; Haddad, C

    2015-06-15

    Purpose: This work presents an end-to-end test using a Gel-Alanine phantom to validate the three-dimensional (3D) dose distribution (DD) delivered by a single isocenter VMAT technique on the simultaneous treatment of multiple brain metastases. Methods: Three cylindrical phantons containing MAGIC-f gel dosimeter were used to measure the 3D DD of a VMAT treatment, the first two were filled with the gel dosimeter (Gel 1 and 2) and the third one was filled with gel and 12 alanine dosimeters distributed along it (Gel 3). Gels 1 and 3 were irradiated and gel 2 was used to map the magnetic resonance image (MRI) scanner field inomogeneities. A CT scan of gel 3 was used for the VMAT treatment planning and 5 alanine pellets were chosen as lesions, around them a PTV was grown and different dose prescriptions were assigned for each one, varying from 5 to 9Gy. Before treatment, the plan was approved in a QA based on an ionization chamber absolute dose measurement, a radiochromic film planar dose measurement and a portal dosimetry per field verification; and also the phantons positioning were verified by ExacTrac 6D correction and OBI kV Cone Beam CT. The gels were irradiated, the MRIs were acquired 24 hours after irradiation and finally, the alanine dosimeters were analysed in a X-band Electron Spin Resonance spectrometer. Results: The association of the two detectors enabled the 3D dose evaluation by gel and punctually inside target volumes by alanine. In the gamma analyses (3%/3mm) comparing the 5 PTVs’ central images DD with TPS expected DD more than 95% of the points were approved. The alanine absolute dose measurements were in agreement with TPS by less than 5%. Conclusion: The gel-alanine phantom enabled the dosimetric validation of multiple brain metastases treatment using VMAT, being an almost ideal tool for this application. This work is partially supported by FAPESP.

  2. Higher-efficiency photoelectrochemical electrodes of titanium dioxide-based nanoarrays sensitized simultaneously with plasmonic silver nanoparticles and multiple metal sulfides photosensitizers

    NASA Astrophysics Data System (ADS)

    Guo, Keying; Liu, Zhifeng; Han, Jianhua; Zhang, Xueqi; Li, Yajun; Hong, Tiantian; Zhou, Cailou

    2015-07-01

    This paper describes a novel design of high-efficiency photoelectrochemical water splitting electrode, i.e., ordered TiO2 nanorod arrays (NRs) sensitized simultaneously with noble metal (Ag), binary metal sulfides (Ag2S) and ternary metal sulfides (Ag3CuS2) multiple photosensitizers for the first time. The TiO2/Ag/Ag2S/Ag3CuS2 NRs heterostructure is successfully synthesized through successive ion layer adsorption and reaction (SILAR) and a simple ion-exchange process based on ionic reaction mechanism. On the basis of an optimal quantity of Ag, Ag2S and Ag3CuS2 nanoparticles, such TiO2/Ag/Ag2S/Ag3CuS2 NRs exhibit a higher photoelectrochemical activity ever reported for TiO2-based nanoarrays in PEC water splitting, the photocurrent density is up to 9.82 mA cm-2 at 0.47 V versus Ag/AgCl, respectively. This novel architecture is able to increase electron collection efficiency and suppress carrier recombination via (i) a higher efficiency of light-harvesting through these multiple photosensitizers (Ag, Ag2S and Ag3CuS2); (ii) the efficient separation of photo-induced electrons and holes due to the direct electrical pathways; (iii) the surface plasmon resonance (SPR) effect of Ag nanoparticles, which enhances the efficient charge separation and high carrier mobility. This work is useful to explore feasible routes to further enhance the performance of oxide semiconductors for PEC water splitting to produce clean H2 energy.

  3. Statistical framework for the utilization of simultaneous pupil plane and focal plane telemetry for exoplanet imaging. I. Accounting for aberrations in multiple planes.

    PubMed

    Frazin, Richard A

    2016-04-01

    A new generation of telescopes with mirror diameters of 20 m or more, called extremely large telescopes (ELTs), has the potential to provide unprecedented imaging and spectroscopy of exoplanetary systems, if the difficulties in achieving the extremely high dynamic range required to differentiate the planetary signal from the star can be overcome to a sufficient degree. Fully utilizing the potential of ELTs for exoplanet imaging will likely require simultaneous and self-consistent determination of both the planetary image and the unknown aberrations in multiple planes of the optical system, using statistical inference based on the wavefront sensor and science camera data streams. This approach promises to overcome the most important systematic errors inherent in the various schemes based on differential imaging, such as angular differential imaging and spectral differential imaging. This paper is the first in a series on this subject, in which a formalism is established for the exoplanet imaging problem, setting the stage for the statistical inference methods to follow in the future. Every effort has been made to be rigorous and complete, so that validity of approximations to be made later can be assessed. Here, the polarimetric image is expressed in terms of aberrations in the various planes of a polarizing telescope with an adaptive optics system. Further, it is shown that current methods that utilize focal plane sensing to correct the speckle field, e.g., electric field conjugation, rely on the tacit assumption that aberrations on multiple optical surfaces can be represented as aberration on a single optical surface, ultimately limiting their potential effectiveness for ground-based astronomy.

  4. SU-E-T-52: A New Device for Quality Assurance of a Single Isocenter Technique for the Simultaneous Treatment of Multiple Brain Metastases

    SciTech Connect

    Maurer, J; Sintay, B; Varchena, V

    2015-06-15

    Purpose: Comprehensive quality assurance (QA) of a single isocenter technique for the simultaneous treatment of multiple brain metastases is presently impractical due to the time consuming nature of measuring each lesion’s dose on film or with a micro-chamber. Three dimensional diode array and full field film measurements are sometimes used to evaluate these plans, but gamma analysis may not reveal local errors that have significant effects on one or a few of several targets. This work aimed to design, build and test a phantom to simplify comprehensive measurement and evaluation. Methods: A phantom was designed with 28 stackable slabs. The top and bottom slabs are 1.5 centimeters (cm) in thickness, and central 26 slabs are 0.5 cm thick. When assembled with radiochromic film in all 27 gaps, the phantom measures 16.5 x 15 x 19 cm. Etchings were designed to aide in identification of specific film planes on computed tomography (CT) images and correlation of individual PTVs with closest bisecting planes. Patient verification plans with a total of 16 PTVs were calculated on the phantom CT, and test deliveries both with and without couch kicks were performed to test the ability to identify correct film placements and subsequent PTV specific dose distributions on the films. Results: Bisecting planes corresponding to PTV locations were easily identified, and PTV specific dose distributions were clear for all 16 targets. For deliveries with couch kicks, the phantom PTV dose distributions closely approximated those calculated on the patient’s CT. For deliveries without couch kicks, PTV specific dosimetry was also possible, although the distributions had ‘ghosts’ equaling the number of couch kicks, with distance between ghosts increasing with distance from the isocenter. Conclusion: A new phantom facilitates fast comprehensive commissioning validation and PTV specific dosimetry for a single isocenter technique for treating multiple brain metastases. This work was

  5. Strength in numbers? Effects of multiple natural enemy species on plant performance

    PubMed Central

    Stephens, Andrea E. A.; Srivastava, Diane S.; Myers, Judith H.

    2013-01-01

    While plants are invariably attacked by numerous insects and pathogens, the consequences of multiple enemies for plant performance are poorly understood. In particular, a predictive framework is lacking for when to expect enemies to have independent versus non-independent effects on their host plant. This is problematic for weed biological control programmes where multiple enemies are frequently released with the possibility of antagonistic interactions that may reduce control. Here, we conduct an analysis of 74 unique plant–enemy–enemy combinations from 51 studies to determine the frequency of non-independent effects of natural enemies on host plant performance, and test a number of a priori predictions for determinants of independent and antagonistic effects of multiple enemies. For three-quarters of plant response measurements, enemies had independent effects on plant performance. In most of the remainder, multiple enemies led to less reduction in performance than that predicted from each enemy alone. Antagonistic effects occurred when enemies attacked the same plant part concurrently or attacked plant reproductive structures. These two predictors explained why antagonistic effects were particularly prevalent for weeds, plants in the family Asteraceae and enemies in the order Diptera. Our results suggest that a few simple rules about avoiding particular combinations of multiple enemies could improve biological control success. PMID:23595265

  6. Multiple ant species tending lac insect Kerria yunnanensis (Hemiptera: Kerriidae) provide asymmetric protection against parasitoids.

    PubMed

    Chen, Youqing; Lu, Zhixing; Li, Qiao; Hoffmann, Benjamin D; Zhang, Wei

    2014-01-01

    This study investigated the effects of ant attendance on the parasitoid community and parasitism of lac insect Kerria yunnanensis aggregations in Yunnan province, China. We manipulated ant attendance to establish three treatments: (1) ant exclusion; (2) low ant attendance by several ant species; and (3) high ant attendance by Crematogaster macaoensis. Five parasitoid species were collected, with two species contributing 82.7 and 13.2% of total abundance respectively. Total parasitoid abundance was lowest in the February sample when K. yunnanensis was in its younger life stage, being significantly lower in the ant exclusion treatment. In April, all three treatments had significantly different parasitoid abundances, being highest in the ant exclusion treatment and the lowest in the high ant attendance treatment. When ants were present, there were strong negative relationships between total parasitoid abundance and ant abundance, with the relationships being dependent upon the ant species composition and abundance. The patterns of total parasitoid abundance were driven by the two most abundant parasitoid species. Parasitoid species richness did not differ among treatments or between sample times, however, multivariate analysis confirmed that overall parasitoid community structure differed significantly among treatments and between sample times, with the high ant attendance treatment differing most from the other two treatments. Interestingly the absence of ants did not result in increased parasitism from four of the five parasitoids. Ants in lac insect farming systems have a clear role for agricultural pest management. A full understanding of the asymmetric abilities of ants to influence parasitoid communities, and affect parasitism of hosts will require further experimental manipulation to assess the relative roles of 1) the abundance of each individual ant species on parasitoid access to hosts, 2) competition among parasitoids, and 3) the interaction between the

  7. Growth of the eye lens: I. Weight accumulation in multiple species

    PubMed Central

    2014-01-01

    Purpose To examine the accumulation of wet and/or dry weight in the ocular lens as a function of age in different species. Methods Wet weights and/or fixed dry weights were obtained from measurements in the author’s laboratory and from the literature for over 14,000 lenses of known-ages, representing 130 different species. Various algorithms were tested to determine the most suitable for describing the relationship between lens weight and age. Results For 126 of the species examined, lens growth is continuous throughout life but asymptotic and can be reasonably described with a single logistic equation, W=Wm e-(k/A), where W is lens wet or dry weight; Wm is the maximum asymptotic weight, k is the logistic growth constant and A is the time from conception. For humans, elephants, hippopotami, minks, wild goats and woodchucks, lens growth appears to be biphasic. No gender differences could be detected in the lens weights for 70 species but male lenses are reportedly 10% larger than those of females in northern fur seals and pheasants. Dry weight accumulation is faster than that for wet weight in all species except birds and reptiles where the rates are the same. Low lens growth rates are associated with small animals with short gestation periods and short life spans. Conclusions Lens growth is continuous throughout life and, for most species, is independent of gender. For most, growth takes place through a monophasic asymptotic mode and is unaffected by events such as hibernation. This makes lens weight measurement a reliable tool for age determination of species culled in the wild. Compaction of the growing lens generates different properties, appropriate to an animal's lifestyle. How these events are controlled remains to be established. PMID:24715758

  8. A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

    PubMed Central

    Meyer, Miriah; Wunderlich, Zeba; Simirenko, Lisa; Luengo Hendriks, Cris L.; Keränen, Soile V. E.; Henriquez, Clara; Knowles, David W.; Biggin, Mark D.; Eisen, Michael B.; DePace, Angela H.

    2011-01-01

    Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3–4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of

  9. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

    PubMed

    Fowlkes, Charless C; Eckenrode, Kelly B; Bragdon, Meghan D; Meyer, Miriah; Wunderlich, Zeba; Simirenko, Lisa; Luengo Hendriks, Cris L; Keränen, Soile V E; Henriquez, Clara; Knowles, David W; Biggin, Mark D; Eisen, Michael B; DePace, Angela H

    2011-10-01

    Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of

  10. Simultaneous analysis of carotenoids and tocopherols in botanical species using one step solid-liquid extraction followed by high performance liquid chromatography.

    PubMed

    Valdivielso, Izaskun; Bustamante, María Ángeles; Ruiz de Gordoa, Juan Carlos; Nájera, Ana Isabel; de Renobales, Mertxe; Barron, Luis Javier R

    2015-04-15

    Carotenoids and tocopherols from botanical species abundant in Atlantic mountain grasslands were simultaneously extracted using one-step solid-liquid phase. A single n-hexane/2-propanol extract containing both types of compounds was injected twice under two different sets of HPLC conditions to separate the tocopherols by normal-phase chromatography and carotenoids by reverse-phase mode. The method allowed reproducible quantification in plant samples of very low amounts of α-, β-, γ- and δ-tocopherols (LOD from 0.0379 to 0.0720 μg g(-1) DM) and over 15 different xanthophylls and carotene isomers. The simplified one-step extraction without saponification significantly increased the recovery of tocopherols and carotenoids, thereby enabling the determination of α-tocopherol acetate in plant samples. The two different sets of chromatographic analysis provided near baseline separation of individual compounds without interference from other lipid compounds extracted from plants, and a very sensitive and accurate detection of tocopherols and carotenoids. The detection of minor individual components in botanical species from grasslands is nowadays of high interest in searching for biomarkers for foods derived from grazing animals.

  11. A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex

    PubMed Central

    Zhang, Hao; Brankovics, Balázs; van der Lee, Theo A.J.; Waalwijk, Cees; van Diepeningen, Anne A.D.; Xu, Jin; Xu, Jingsheng

    2016-01-01

    The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type. PMID:27812414

  12. Simultaneous species-specific PCR detection and viability testing of poly(vinyl alcohol) cryogel-entrapped Rhodococcus spp. after their exposure to petroleum hydrocarbons.

    PubMed

    Kuyukina, Maria S; Ivshina, Irena B; Serebrennikova, Marina K; Rubtsova, Ekaterina V; Krivoruchko, Anastasiya V

    2013-08-01

    A method of simultaneous species-specific PCR detection and viability testing of poly(vinyl alcohol) cryogel-entrapped Rhodococcus spp. was developed that allowed the estimation of immobilized Rhodococcus opacus and Rhodococcus ruber survival after their exposure to petroleum hydrocarbon mixture. Spectrophotometric INT assay revealed high tolerance of gel-immobilized rhodococci to petroleum hydrocarbons, while among two Rhodococcus strains studied, R. ruber tolerated better to hydrocarbons compared to R. opacus. These findings were confirmed by respirometry results that showed increased respiratory activity of gel-immobilized Rhodococcus strains after 10-day incubation with 3% (v/v) petroleum hydrocarbon mixture. Moreover, jointly incubated rhodococcal strains demonstrated higher oxidative activities toward petroleum hydrocarbons than individual strains. Both Rhodococcus species were recovered successfully in cryogel granules using 16S rDNA-targeted PCR, even though the granules were previously stained with INT and extracted with ethanol. The method developed can be used for rapid detection and monitoring of gel-immobilized bacterial inocula in bioreactors or contaminated soil systems.

  13. Studies on fission with ALADIN. Precise and simultaneous measurement of fission yields, total kinetic energy and total prompt neutron multiplicity at GSI

    NASA Astrophysics Data System (ADS)

    Martin, Julie-Fiona; Taieb, Julien; Chatillon, Audrey; Bélier, Gilbert; Boutoux, Guillaume; Ebran, Adeline; Gorbinet, Thomas; Grente, Lucie; Laurent, Benoit; Pellereau, Eric; Alvarez-Pol, Héctor; Audouin, Laurent; Aumann, Thomas; Ayyad, Yassid; Benlliure, Jose; Casarejos, Enrique; Cortina Gil, Dolores; Caamaño, Manuel; Farget, Fanny; Fernández Domínguez, Beatriz; Heinz, Andreas; Jurado, Beatriz; Kelić-Heil, Aleksandra; Kurz, Nikolaus; Nociforo, Chiara; Paradela, Carlos; Pietri, Stéphane; Ramos, Diego; Rodríguez-Sànchez, Jose-Luis; Rodríguez-Tajes, Carme; Rossi, Dominic; Schmidt, Karl-Heinz; Simon, Haik; Tassan-Got, Laurent; Vargas, Jossitt; Voss, Bernd; Weick, Helmut

    2015-12-01

    A novel technique for fission studies, based on the inverse kinematics approach, is presented. Following pioneering work in the nineties, the SOFIA Collaboration has designed and built an experimental set-up dedicated to the simultaneous measurement of isotopic yields, total kinetic energies and total prompt neutron multiplicities, by fully identifying both fission fragments in coincidence, for the very first time. This experiment, performed at GSI, permits to study the fission of a wide variety of fissioning systems, ranging from mercury to neptunium, possibly far from the valley of stability. A first experiment, performed in 2012, has provided a large array of unprecedented data regarding the nuclear fission process. An excerpt of the results is presented. With this solid starter, further improvements of the experimental set-up are considered, which are consistent with the expected developments at the GSI facility, in order to measure more fission observables in coincidence. The completeness reached in the SOFIA data, permits to scrutinize the correlations between the interesting features of fission, offering a very detailed insight in this still unraveled mechanism.

  14. High-performance ion-pair chromatography method for simultaneous analysis of alliin, deoxyalliin, allicin and dipeptide precursors in garlic products using multiple mass spectrometry and UV detection.

    PubMed

    Arnault, I; Christidès, J P; Mandon, N; Haffner, T; Kahane, R; Auger, J

    2003-03-28

    The quality of garlic and garlic products is usually related to their alliin content and allicin release potential. Until now no analytical method was able to quantify simultaneously allicin, its direct precursor alliin (S-allyl-L-cysteine sulfoxide), SAC (S-allyl-L-cysteine) as well as various dipeptides that apparently serve as storage compounds in garlic. It is well known that all these intermediates are involved in the allicin biosynthetic pathway. A simple and rapid HPLC method suitable for routine analysis was developed using eluents containing an ion-pairing reagent. Particularly, heptanesulfonate as ion-pairing reagent guarantees a sufficient separation between alliin and the more retained dipeptides at very low pH. Allicin was eluted after 18 min on a 150 x 3 mm column. Synthetic reference compounds were characterized by the same chromatographic method using a diode-array UV detector and an ion trap mass spectrometer (electrospray ionization) in the multiple MS mode. In routine analysis of garlic bulbs, powders and other products, the diode-array detector is sufficient for a relevant quantification. Our method has been used in studies to improve the quality of garlic and its derived products.

  15. Synergizing the multiple plasmon resonance coupling and quantum effects to obtain enhanced SERS and PEC performance simultaneously on a noble metal-semiconductor substrate.

    PubMed

    Yang, Tao; Liu, Wenna; Li, Lidong; Chen, Junhong; Hou, Xinmei; Chou, Kuo-Chih

    2017-02-09

    Aiming to achieve the synergistic enhancement of the surface-enhanced Raman scattering (SERS) and photoelectrocatalytic (PEC) performance on a noble metal-semiconductor, such as Au nanoparticles (NPs)-TiO2 nanotube arrays (TiO2 NTAs@hybrid Au NPs), theoretical calculation and experiments are performed. Theoretical calculation indicates that both the SERS and PEC performance can be enhanced by coupling different sized Au NPs on TiO2 NTAs based on synergizing the multiple plasmon resonance coupling and quantum effects. To further verify this mechanism, TiO2 NTAs@hybrid Au NPs are assembled via synthesis of TiO2 NTAs through the anodic oxidation process, followed by the deposition of different sized Au NPs onto the TiO2 surface simultaneously using physical vapor deposition (PVD) in this work. Such substrates exhibit excellent detection sensitivity towards organic dyes including Rhodamine B (RhB), the organic herbicide dichlorophenoxyacetic acid (2,4-D) and the organophosphate pesticide methyl-parathion (MP) with high reproducibility, stability and reusability. Meanwhile the PEC performance based on this substrate remains efficient compared with the reported results in the literature. The efficient PEC performance mainly originates from both the quantum effect of Au nanoparticles and the formation of a metal-semiconductor heterojunction. It is proposed that other noble metal-semiconductor complex nanomaterials can also obtain both enhanced SERS and PEC performance based on the above mechanism.

  16. Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan.

    PubMed

    Kakoi, H; Tozaki, T; Nagata, S; Gawahara, H; Kijima-Suda, I

    2009-12-01

    In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot(TM) technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.

  17. Avoidance Behavior against Positive Allergens Detected with a Multiple Allergen Simultaneous Test Immunoblot Assay in Patients with Urticaria: Factors Associated with Avoidance Success/Failure

    PubMed Central

    Lee, Min Kyung; Kwon, In Ho; Kim, Han Su; Kim, Heung Yeol; Cho, Eun Byul; Park, Gyeong Hun; Park, Eun Joo; Kim, Kwang Ho; Kim, Kwang Joong

    2016-01-01

    Background Avoidance behavior against positive allergens detected by using multiple allergen simultaneous test (MAST)-immunoblot assay in patients with urticaria has been rarely reported. Objective We aimed to assess the avoidance behavior of patients with urticaria against positive allergens detected with a MAST. Methods One hundred and one urticaria patients who showed positivity to at least one allergen on a MAST completed a questionnaire regarding their test results. The avoidance behavior of the patients was evaluated, and relevant determining factors of avoidance success/failure were statistically assessed. Results We detected 144 different data (n=51, food allergens; n=17, pollen allergens; and n=76, aeroallergens) from 101 patients with urticaria. The avoidance failure rates were 33.3% for food allergens, 70.6% for pollen allergens, and 30.3% for aeroallergens. The pollen group showed a significantly higher avoidance failure rate than the food and aeroallergen groups (p<0.05). The patients with higher educational levels or more severe urticaria tended to successfully avoid allergens (p<0.05). The monthly household income level and patients' reliability to the test showed borderline correlations (p=0.057 and p=0.075, respectively). Conclusion We believe that the results of this study could be helpful in predicting avoidance success or failure against allergens in patients with urticaria when clinicians conduct allergen-specific immunoglobulin E tests. PMID:26848222

  18. Simultaneous assessment of loss of heterozygosity at multiple microsatellite loci using semi-automated fluorescence-based detection: subregional mapping of chromosome 4 in cervical carcinoma.

    PubMed Central

    Hampton, G M; Larson, A A; Baergen, R N; Sommers, R L; Kern, S; Cavenee, W K

    1996-01-01

    Detection of loss of heterozygosity (LOH) by comparison of normal and tumor genotypes using PCR-based microsatellite loci provides considerable advantages over traditional Southern blotting-based approaches. However, current methodologies are limited by several factors, including the numbers of loci that can be evaluated for LOH in a single experiment, the discrimination of true alleles versus "stutter bands," and the use of radionucleotides in detecting PCR products. Here we describe methods for high throughput simultaneous assessment of LOH at multiple loci in human tumors; these methods rely on the detection of amplified microsatellite loci by fluorescence-based DNA sequencing technology. Data generated by this approach are processed by several computer software programs that enable the automated linear quantitation and calculation of allelic ratios, allowing rapid ascertainment of LOH. As a test of this approach, genotypes at a series of loci on chromosome 4 were determined for 58 carcinomas of the uterine cervix. The results underscore the efficacy, sensitivity, and remarkable reproducibility of this approach to LOH detection and provide subchromosomal localization of two regions of chromosome 4 commonly altered in cervical tumors. Images Fig. 2 Fig. 3 PMID:8692882

  19. Preparation of a dual-enzyme co-immobilized capillary microreactor and simultaneous screening of multiple enzyme inhibitors by capillary electrophoresis.

    PubMed

    Lin, Pingtan; Zhao, Shulin; Lu, Xin; Ye, Fanggui; Wang, Hengshan

    2013-08-01

    A CE method based on a dual-enzyme co-immobilized capillary microreactor was developed for the simultaneous screening of multiple enzyme inhibitors. The capillary microreactor was prepared by co-immobilizing adenosine deaminase and xanthine oxidase on the inner wall at the inlet end of the separation capillary. The enzymes were first immobilized on gold nanoparticles, and the functionalized gold nanoparticles were then assembled on the inner wall at the inlet end of the separation capillary treated with polyethyleneimine. With the developed CE method, the substrates and products were baseline separated within 3 min. The activity of the immobilized enzyme can be directly detected by measuring the peak height of the products. A statistical parameter Z' factor was recommended for evaluation of the accuracy of a drug screening system. In the present study, it was calculated to be larger than 0.5, implying a good accuracy. Finally, screening a small compound library containing two known enzyme inhibitors and 20 natural extracts by the proposed method was demonstrated. The known inhibitors were identified, and some natural extracts were found to be positive for two-enzyme inhibition by the present method.

  20. One health, multiple challenges: The inter-species transmission of influenza A virus

    PubMed Central

    Short, Kirsty R.; Richard, Mathilde; Verhagen, Josanne H.; van Riel, Debby; Schrauwen, Eefje J. A.; van den Brand, Judith M. A.; Mänz, Benjamin; Bodewes, Rogier

    2015-01-01

    Influenza A viruses are amongst the most challenging viruses that threaten both human and animal health. Influenza A viruses are unique in many ways. Firstly, they are unique in the diversity of host species that they infect. This includes waterfowl (the original reservoir), terrestrial and aquatic poultry, swine, humans, horses, dog, cats, whales, seals and several other mammalian species. Secondly, they are unique in their capacity to evolve and adapt, following crossing the species barrier, in order to replicate and spread to other individuals within the new species. Finally, they are unique in the frequency of inter-species transmission events that occur. Indeed, the consequences of novel influenza virus strain in an immunologically naïve population can be devastating. The problems that influenza A viruses present for human and animal health are numerous. For example, influenza A viruses in humans represent a major economic and disease burden, whilst the poultry industry has suffered colossal damage due to repeated outbreaks of highly pathogenic avian influenza viruses. This review aims to provide a comprehensive overview of influenza A viruses by shedding light on interspecies virus transmission and summarising the current knowledge regarding how influenza viruses can adapt to a new host. PMID:26309905