Science.gov

Sample records for simultaneous multiple species

  1. Fabrication of a microfluidic device for simultaneous patterning of multiple chemical species by Dip Pen Nanolithography (DPN)

    NASA Astrophysics Data System (ADS)

    Rivas-Cordona, J. Alberto; Banerjee, Debjyoti

    2006-05-01

    This paper describes the fabrication and testing of a microfluidic ink delivery device for Dip Pen Nanolithography (DPN TM). The purpose of this microfluidic device is to maximize the number of chemical species (inks) for nanofabrication that can be simultaneously patterned by DPN. The device (called 'Centiwells') consists of a two-dimensional array of 96micro-wells micro-machined on a silicon substrate and a thermoelectric module attached to the bottom of the substrate. Microbeads of a hygroscopic material (Poly-Ethylene Glycol) are dispensed into the microwells. By reducing the temperature of the substrate to below the dew point water droplets are condensed on the PEG microbeads, dissolving the beads and creating PEG solutions. Following the formation of the PEG solutions, an AFM tip (pen) is lowered into the micro-wells for loading ink ('dipping' or 'inking' step) and subsequently nanolithography is performed.

  2. 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.

  3. Simultaneous statistical bias correction of multiple PM2.5 species from a regional photochemical grid model

    NASA Astrophysics Data System (ADS)

    Crooks, James L.; Özkaynak, Halûk

    2014-10-01

    In recent years environmental epidemiologists have begun utilizing regional-scale air quality computer models to predict ambient air pollution concentrations in health studies instead of or in addition to data from fixed-site ambient monitors. The advantages of using such models include better spatio-temporal coverage and the capability to predict concentrations of unmonitored pollutants. However, there are also drawbacks, chief among them being that these models can exhibit systematic spatial and temporal biases. In order to use these models in epidemiological investigations it is very important to bias-correct the model surfaces. We present a novel statistical method of spatio-temporal bias correction for the Community Multi-scale Air Quality (CMAQ) model that allows simultaneous bias adjustment of PM2.5 mass and its major constituent species using publically available speciated data from ambient monitors. The method uses mass conservation and the more widespread unspeciated PM2.5 mass observations to constrain the sum of the PM2.5 species' concentrations in locations without speciated monitors. We develop the model in the context of an epidemiological study investigating the association between PM2.5 species' ambient concentrations and birth outcomes throughout the state of New Jersey. Since our exposures of interest are multi-month averages we focus specifically on modeling seasonal bias trends rather than daily biases. Using a cross-validation study we find that our bias-corrected CMAQ results are more accurate than either the original CMAQ output or a spline fit without CMAQ. More interestingly, we find that our model clearly performs better when mass conservation is enforced, and furthermore that our model is competitive with Kriging in a comparison in which the latter has the advantage.

  4. Multiple spiking species-specific isotope dilution analysis by molecular mass spectrometry: simultaneous determination of inorganic mercury and methylmercury in fish tissues.

    PubMed

    Castillo, Angel; Rodríguez-González, Pablo; Centineo, Giuseppe; Roig-Navarro, Antoni Francesc; García Alonso, J Ignacio

    2010-04-01

    This work demonstrates, for the first time, the applicability of multiple spiking isotope dilution analysis to molecular mass spectrometry exemplified by the speciation analysis of mercury using GC(EI)MS instrumentation. A double spike isotope dilution approach using isotopically enriched mercury isotopes has been applied for the determination of inorganic mercury Hg(II) and methylmercury (MeHg) in fish reference materials. The method is based on the application of isotope pattern deconvolution for the simultaneous determination of degradation-corrected concentrations of methylmercury and inorganic mercury. Mass isotopomer distributions are employed instead of isotope ratios to calculate the corrected concentrations of the Hg species as well as the extent of species degradation reactions. The isotope pattern deconvolution equations developed here allow the calculation of the different molar fractions directly from the GC(EI)MS mass isotopomer distribution pattern and take into account possible impurities present in the spike solutions employed. The procedure has been successfully validated with the analysis of two different certified reference materials (BCR-464 and DOLT-4) and with the comparison of the results obtained by GC(ICP)MS. For the tuna fish matrix (BCR-464), no interconversion reactions were observed at the optimized conditions of open focused microwave extraction at 70 degrees C during 8 min. However, significant demethylation was found under the same conditions in the case of the certified dogfish liver DOLT-4. Methylation and demethylation factors were confirmed by GC(ICP)MS. Transformation reactions have been found to depend on the sample matrix and on the derivatization reagent employed. Thus, it is not possible to recommend optimum extraction conditions suitable for all types of matrices demonstrating the need to apply multiple spiking methodologies for the determination of MeHg and Hg(II) in biological samples. Double spike isotope dilution

  5. Multiple spiking species-specific isotope dilution analysis by molecular mass spectrometry: simultaneous determination of inorganic mercury and methylmercury in fish tissues.

    PubMed

    Castillo, Angel; Rodríguez-González, Pablo; Centineo, Giuseppe; Roig-Navarro, Antoni Francesc; García Alonso, J Ignacio

    2010-04-01

    This work demonstrates, for the first time, the applicability of multiple spiking isotope dilution analysis to molecular mass spectrometry exemplified by the speciation analysis of mercury using GC(EI)MS instrumentation. A double spike isotope dilution approach using isotopically enriched mercury isotopes has been applied for the determination of inorganic mercury Hg(II) and methylmercury (MeHg) in fish reference materials. The method is based on the application of isotope pattern deconvolution for the simultaneous determination of degradation-corrected concentrations of methylmercury and inorganic mercury. Mass isotopomer distributions are employed instead of isotope ratios to calculate the corrected concentrations of the Hg species as well as the extent of species degradation reactions. The isotope pattern deconvolution equations developed here allow the calculation of the different molar fractions directly from the GC(EI)MS mass isotopomer distribution pattern and take into account possible impurities present in the spike solutions employed. The procedure has been successfully validated with the analysis of two different certified reference materials (BCR-464 and DOLT-4) and with the comparison of the results obtained by GC(ICP)MS. For the tuna fish matrix (BCR-464), no interconversion reactions were observed at the optimized conditions of open focused microwave extraction at 70 degrees C during 8 min. However, significant demethylation was found under the same conditions in the case of the certified dogfish liver DOLT-4. Methylation and demethylation factors were confirmed by GC(ICP)MS. Transformation reactions have been found to depend on the sample matrix and on the derivatization reagent employed. Thus, it is not possible to recommend optimum extraction conditions suitable for all types of matrices demonstrating the need to apply multiple spiking methodologies for the determination of MeHg and Hg(II) in biological samples. Double spike isotope dilution

  6. Simultaneous alignment of short reads against multiple genomes

    PubMed Central

    Schneeberger, Korbinian; Hagmann, Jörg; Ossowski, Stephan; Warthmann, Norman; Gesing, Sandra; Kohlbacher, Oliver; Weigel, Detlef

    2009-01-01

    Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at . PMID:19761611

  7. Simultaneous Dual-Species Atom Interferometry

    NASA Astrophysics Data System (ADS)

    Bonnin, Alexis; Zahzam, Nassim; Bidel, Yannick; Bresson, Alexandre; Sensors; Micro Technologie unit Team

    2015-05-01

    In the context of testing the Weak Equivalence Principle (WEP) with matter-wave accelerometers, some projects under development aim to compare the acceleration of two different atomic species during few seconds of free fall in order to achieve highly sensitive measurements. A simultaneous interrogation of both atomic species is crucial to fully take advantage of a differential measurement. We report the realization of an atom interferometer based on Raman transitions which simultaneously interrogates both isotopes of Rubidium. The simultaneous aspect of our experiment allows the resolution of the differential accelerometer to remain lower than 7.10-9 g even with vibration levels up to 3.10-3 g thanks to common-mode vibration noise rejection. These results exhibit a rejection ratio of 90 dB. An atom based test of the WEP has been carried out leading to a differential free fall measurement between both isotopes of Δg / g =(1 . 2 +/- 3 . 2) ×10-7 .

  8. Simultaneous Multiple-Location Separation Control

    NASA Technical Reports Server (NTRS)

    Greenblatt, David (Inventor)

    2009-01-01

    A method of controlling a shear layer for a fluid dynamic body introduces first periodic disturbances into the fluid medium at a first flow separation location. Simultaneously, second periodic disturbances are introduced into the fluid medium at a second flow separation location. A phase difference between the first and second periodic disturbances is adjusted to control flow separation of the shear layer as the fluid medium moves over the fluid dynamic body.

  9. Simultaneous labeling of multiple components in a single fingermark.

    PubMed

    van Dam, Annemieke; Aalders, Maurice C G; van de Braak, Kevin; Hardy, Huub J J; van Leeuwen, Ton G; Lambrechts, Saskia A G

    2013-10-10

    A fingermark contains important forensic information of the donor, not only in its ridge pattern, but also in the chemical composition of its secretion. Detection and identification of these secretions can be done by immunolabeling. In this study, we describe for the first time a reproducible immunolabeling method that allows the simultaneous detection of multiple components of interest. This method not only reduces the manipulation of fingermarks, but also different types of information can be obtained about the donor in one labeling session. To prove the concept of this technique, we selected two general components as antigens of interest, dermcidin and the human serum albumin. Conjugation of both antibodies to two different synthetic fluorophores, followed by simultaneous incubation of both conjugated antibodies, resulted in successful multiple immunolabeling of fingermarks left on a porous nitrocellulose membrane and on a non-porous glass slide surface. In order to minimize false positives to prevent non-specific binding of antibodies to fingermarks and surface carriers, careful blocking and washing steps were found crucial. With this reproducible protocol, high quality images could be obtained from the multiple labeled fingermarks. In conclusion, simultaneous multiple immunolabeling of antibodies in fingermarks can identify specific components in the secretion of the fingermark, including components related to hygiene, diet, time of day, contacts gender and drug use. Multiple immunolabeling therefore has the potential to make a major impact in the forensic field. PMID:24053878

  10. 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.

  11. 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

  12. Simultaneous Removal of Multiple DNA Segments by Polymerase Chain Reactions.

    PubMed

    Krishnamurthy, Vishnu; Zhang, Kai

    2017-01-01

    Precise DNA manipulation is a key enabling technology for synthetic biology. Approaches based on restriction digestion are often limited by the presence of certain restriction enzyme recognition sites. Recent development of restriction-free cloning approaches has greatly enhanced the flexibility and speed of molecular cloning. Most restriction-free cloning methods focus on DNA assembly. Much less work has been dedicated towards DNA removal. Here we introduce a protocol that allows simultaneous removal of multiple DNA segments from a plasmid using polymerase chain reactions (PCR). Our approach will be beneficial to applications in multiple sites mutagenesis, DNA library construction, genetic and protein engineering, and synthetic biology. PMID:27671942

  13. 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.

  14. 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

  15. 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

  16. Interaction and coalescence of multiple simultaneous and non-simultaneous blast waves

    NASA Astrophysics Data System (ADS)

    Qiu, S.; Eliasson, V.

    2016-05-01

    Interaction of multiple blast waves can be used to direct energy toward a target while simultaneously reducing collateral damage away from the target area. In this paper, simulations of multiple point source explosives were performed and the resulting shock interaction and coalescence behavior were explored. Three to ten munitions were placed concentrically around the target, and conditions at the target area were monitored and compared to those obtained using a single munition. For each simulation, the energy summed over all munitions was kept constant, while the radial distances between target and munitions and the munition initiation times were varied. Each munition was modeled as a point source explosion. The resulting blast wave propagation and shock front coalescence were solved using the inviscid Euler equations of gas dynamics on overlapping grids employing a finite difference scheme. Results show that multiple munitions can be beneficial for creating extreme conditions at the intended target area; over 20 times higher peak pressure is obtained for ten simultaneous munitions compared to a single munition. Moreover, peak pressure at a point away from the target area is reduced by more than a factor of three.

  17. 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. PMID:24042029

  18. 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.

  19. 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.

  20. An Intravaginal Ring for the Simultaneous Delivery of Multiple Drugs

    PubMed Central

    Baum, Marc M.; Butkyavichene, Irina; Gilman, Joshua; Kennedy, Sean; Kopin, Etana; Malone, Amanda M.; Nguyen, Cali; Smith, Thomas J.; Friend, David R.; Clark, Meredith R.; Moss, John A.

    2013-01-01

    Intravaginal delivery of microbicide combinations is a promising approach for the prevention of sexually transmitted infections, but requires a method of providing simultaneous, independent release of multiple agents into the vaginal compartment. A novel intravaginal ring (IVR) platform has been developed for simultaneous delivery of the reverse-transcriptase inhibitor tenofovir (TFV) and the guanosine analogue antiviral acyclovir (ACV) with independent control of release rate for each drug. The IVR is based on a pod design, with up to 10 individual polymer-coated drug cores embedded in the ring releasing through preformed delivery channels. The release rate from each pod is controlled independently of the others by the drug properties, polymer coating, and size and number of delivery channels. Pseudo-zero-order in vitro release of TFV (144 ± 10 µg day) and ACV (120 ± 19 µg day−1) from an IVR containing both drugs was sustained for 28 days. The mechanical properties of the pod IVR were evaluated and compared with the commercially available Estring® (Pfizer, NY, NY). The pod-IVR design enables the vaginal delivery of multiple microbicides with differing physicochemical properties, and is an attractive approach for the sustained intravaginal delivery of relatively hydrophilic drugs that are difficult to deliver using conventional matrix IVR technology. PMID:22619076

  1. Unguided species delimitation using DNA sequence data from multiple Loci.

    PubMed

    Yang, Ziheng; Rannala, Bruce

    2014-12-01

    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

  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. Neural network-based multiple robot simultaneous localization and mapping.

    PubMed

    Saeedi, Sajad; Paull, Liam; Trentini, Michael; Li, Howard

    2011-12-01

    In this paper, a decentralized platform for simultaneous localization and mapping (SLAM) with multiple robots is developed. Each robot performs single robot view-based SLAM using an extended Kalman filter to fuse data from two encoders and a laser ranger. To extend this approach to multiple robot SLAM, a novel occupancy grid map fusion algorithm is proposed. Map fusion is achieved through a multistep process that includes image preprocessing, map learning (clustering) using neural networks, relative orientation extraction using norm histogram cross correlation and a Radon transform, relative translation extraction using matching norm vectors, and then verification of the results. The proposed map learning method is a process based on the self-organizing map. In the learning phase, the obstacles of the map are learned by clustering the occupied cells of the map into clusters. The learning is an unsupervised process which can be done on the fly without any need to have output training patterns. The clusters represent the spatial form of the map and make further analyses of the map easier and faster. Also, clusters can be interpreted as features extracted from the occupancy grid map so the map fusion problem becomes a task of matching features. Results of the experiments from tests performed on a real environment with multiple robots prove the effectiveness of the proposed solution.

  4. Neural network-based multiple robot simultaneous localization and mapping.

    PubMed

    Saeedi, Sajad; Paull, Liam; Trentini, Michael; Li, Howard

    2011-12-01

    In this paper, a decentralized platform for simultaneous localization and mapping (SLAM) with multiple robots is developed. Each robot performs single robot view-based SLAM using an extended Kalman filter to fuse data from two encoders and a laser ranger. To extend this approach to multiple robot SLAM, a novel occupancy grid map fusion algorithm is proposed. Map fusion is achieved through a multistep process that includes image preprocessing, map learning (clustering) using neural networks, relative orientation extraction using norm histogram cross correlation and a Radon transform, relative translation extraction using matching norm vectors, and then verification of the results. The proposed map learning method is a process based on the self-organizing map. In the learning phase, the obstacles of the map are learned by clustering the occupied cells of the map into clusters. The learning is an unsupervised process which can be done on the fly without any need to have output training patterns. The clusters represent the spatial form of the map and make further analyses of the map easier and faster. Also, clusters can be interpreted as features extracted from the occupancy grid map so the map fusion problem becomes a task of matching features. Results of the experiments from tests performed on a real environment with multiple robots prove the effectiveness of the proposed solution. PMID:22156983

  5. Multiple Cracks Propagate Simultaneously in Polymer Liquids in Tension.

    PubMed

    Huang, Qian; Alvarez, Nicolas J; Shabbir, Aamir; Hassager, Ole

    2016-08-19

    Understanding the mechanism of fracture is essential for material and process design. While the initiation of fracture in brittle solids is generally associated with the preexistence of material imperfections, the mechanism for initiation of fracture in viscoelastic fluids, e.g., polymer melts and solutions, remains an open question. We use high speed imaging to visualize crack propagation in entangled polymer liquid filaments under tension. The images reveal the simultaneous propagation of multiple cracks. The critical stress and strain for the onset of crack propagation are found to be highly reproducible functions of the stretch rate, while the position of initiation is completely random. The reproducibility of conditions for fracture points to a mechanism for crack initiation that depends on the dynamic state of the material alone, while the crack profiles reveal the mechanism of energy dissipation during crack propagation. PMID:27588883

  6. Severe laminitis in multiple zoo species.

    PubMed

    Wiedner, Ellen; Holland, Jeff; Trupkiewicz, John; Uzal, Francisco

    2014-01-01

    A 10-year record review from a zoological institution in the western USA identified four cases of severe laminitis resulting in rotation and protrusion of the third phalanx through the sole. Laminitis is reported in a Masai giraffe (Giraffa camelopardalis tippelskirchi), a Sichuan takin (Budorcas taxicolor tibetana), a greater Malayan chevrotain (Tragulus napu) and a giant eland (Taurotragus derbianus). This is the first report of severe laminitis with pedal bone rotation and protrusion in multiple species of non-domestic hoofstock, and the first report of this disease in three of these species (takin, chevrotain, and giant eland). PMID:24730432

  7. Translocation strategies for multiple species depend on interspecific interaction type.

    PubMed

    Plein, Michaela; Bode, Michael; Moir, Melinda L; Vesk, Peter A

    2016-06-01

    Conservation translocations, anthropogenic movements of species to prevent their extinction, have increased substantially over the last few decades. Although multiple species are frequently moved to the same location, current translocation guidelines consider species in isolation. This practice ignores important interspecific interactions and thereby risks translocation failure. We model three different two-species systems to illustrate the inherent complexity of multispecies translocations and to assess the influence of different interaction types (consumer-resource, mutualism, and competition) on translocation strategies. We focus on how these different interaction types influence the optimal founder population sizes for successful translocations and the order in which the species are moved (simultaneous or sequential). Further, we assess the effect of interaction strength in simultaneous translocations and the time delay between translocations when moving two species sequentially. Our results show that translocation decisions need to reflect the type of interaction. While all translocations of interacting species require a minimum founder population size, which is demarked by an extinction boundary, consumer-resource translocations also have a maximum founder population limit. Above the minimum founder size, increasing the number of translocated individuals leads to a substantial increase in the extinction boundary of competitors and consumers, but not of mutualists. Competitive and consumer-resource systems benefit from sequential translocations, but the order of translocations does not change the outcomes for mutualistic interaction partners noticeably. Interspecific interactions are important processes that shape population dynamics and should therefore be incorporated into the quantitative planning of multispecies translocations. Our findings apply whenever interacting species are moved, for example, in reintroductions, conservation introductions, biological

  8. Translocation strategies for multiple species depend on interspecific interaction type.

    PubMed

    Plein, Michaela; Bode, Michael; Moir, Melinda L; Vesk, Peter A

    2016-06-01

    Conservation translocations, anthropogenic movements of species to prevent their extinction, have increased substantially over the last few decades. Although multiple species are frequently moved to the same location, current translocation guidelines consider species in isolation. This practice ignores important interspecific interactions and thereby risks translocation failure. We model three different two-species systems to illustrate the inherent complexity of multispecies translocations and to assess the influence of different interaction types (consumer-resource, mutualism, and competition) on translocation strategies. We focus on how these different interaction types influence the optimal founder population sizes for successful translocations and the order in which the species are moved (simultaneous or sequential). Further, we assess the effect of interaction strength in simultaneous translocations and the time delay between translocations when moving two species sequentially. Our results show that translocation decisions need to reflect the type of interaction. While all translocations of interacting species require a minimum founder population size, which is demarked by an extinction boundary, consumer-resource translocations also have a maximum founder population limit. Above the minimum founder size, increasing the number of translocated individuals leads to a substantial increase in the extinction boundary of competitors and consumers, but not of mutualists. Competitive and consumer-resource systems benefit from sequential translocations, but the order of translocations does not change the outcomes for mutualistic interaction partners noticeably. Interspecific interactions are important processes that shape population dynamics and should therefore be incorporated into the quantitative planning of multispecies translocations. Our findings apply whenever interacting species are moved, for example, in reintroductions, conservation introductions, biological

  9. 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.

  10. Simultaneous measurement of multiple ear proteins with multiplex ELISA assays.

    PubMed

    Trune, Dennis R; Larrain, Barbara E; Hausman, Frances A; Kempton, J Beth; MacArthur, Carol J

    2011-05-01

    A recent advancement in enzyme-linked immunosorbent assay (ELISA) technology is the multiplex antibody array that measures multiple proteins simultaneously within a single sample. This allows reduction in sample volume, time, labor, and material costs, while increasing sensitivity over single ELISA. Current multiplex platforms include planar-based systems using microplates or slides, or bead-based suspension assay with microspheres. To determine the applicability of this technology for ear research, we used 3 different multiplex ELISA-based immunoassay arrays from 4 different companies to measure cytokine levels in mouse middle and inner ear tissue lysate extracts 24 h following transtympanic Haemophilus influenzae inoculation. Middle and inner ear tissue lysates were analyzed using testing services from Quansys Biosciences, Aushon Biosystems SearchLight (both microplate-based), MILLIPLEX MAP Sample (bead-based), and a RayBiotech, Inc (slide-based) kit. Samples were assayed in duplicate or triplicate. Results were compared to determine their relative sensitivity and reliability for measures of cytokines related to inflammation. The cytokine pg/ml amounts varied among the multiplex assays, so a comparison also was made of the mean fold increase in cytokines from untreated controls. Several cytokines and chemokines were elevated, the extent dependent upon the assay sensitivity. Those most significantly elevated were IL-1α, IL-1β, IL-6, TNFα, VEGF, and IL-8/MIP-2. The results of the multiplex systems were compared with single ELISA kits (IL-1β, IL-6) to assess sensitivity over the traditional method. Overall, the Quansys Biosciences and SearchLight arrays showed the greatest sensitivity, both employing the same multiplex methodology of a spotted array within a microplate well with chemiluminescent detection. They also were more sensitive than the traditional single ELISA performed with commercial kits and matched gene expression changes determined by quantitative

  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. Simultaneous timing of multiple intervals: implications of the scalar property.

    PubMed

    Leak, T M; Gibbon, J

    1995-01-01

    Three experiments with pigeons are reported in which the scalar property in simultaneous timing tasks was studied. According to scalar expectancy theory, the scalar property should be maintained in simultaneous timing, but the behavioral theory of timing predicts that the scalar property should be evident only in independent timing. Experiment 1 showed that the appearance of distinct peaks at reinforcement times required about a 4:1 ratio between intervals. Experiment 2 (2-interval timing task) and Experiment 3 (3-interval timing task) used an individual trial analysis technique to examine high-rate responding segments bracketing the times of reinforcement. The standard deviations of the starting and stopping times of high-rate segments were linearly related to their means and to reinforcement time, supporting the scalar property in simultaneous timing.

  13. 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 applied…

  14. Imaging of enzyme activity using bio-LSI system enables simultaneous immunosensing of different analytes in multiple specimens.

    PubMed

    Hokuto, Toshiki; Yasukawa, Tomoyuki; Kunikata, Ryota; Suda, Atsushi; Inoue, Kumi Y; Ino, Kosuke; Matsue, Tomokazu; Mizutani, Fumio

    2016-06-01

    Electrochemical imaging is an excellent technique to characterize an activity of biomaterials, such as enzymes and cells. Large scale integration-based amperometric sensor (Bio-LSI) has been developed for the simultaneous and continuous detection of the concentration distribution of redox species generated by reactions of biomolecules. In this study, the Bio-LSI system was demonstrated to be applicable for simultaneous detection of different anaytes in multiple specimens. The multiple specimens containing human immunoglobulin G (hIgG) and mouse IgG (mIgG) were introduced into each channel of the upper substrate across the antibody lines for hIgG and mIgG on the lower substrate. Hydrogen peroxide generated by the enzyme reaction of glucose oxidase captured at intersections was simultaneously detected by 400 microelectrodes of Bio-LSI chip. The oxidation current increased with increasing the concentrations of hIgG, which can be detected in the range of 0.01-1.0 µg mL(-1) . Simultaneous detection of hIgG and mIgG in multiple specimens was achieved by using line pattern of both antibodies. Therefore, the presence of different target molecules in the multiple samples would be quantitatively and simultaneously visualized as a current image by the Bio-LSI system. PMID:27150897

  15. 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. PMID:26756442

  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. 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.

  1. 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.

  2. How species respond to multiple extinction threats.

    PubMed Central

    Isaac, Nick J. B.; Cowlishaw, Guy

    2004-01-01

    It is well established that different species vary in their vulnerability to extinction risk and that species biology can underpin much of this variation. By contrast, very little is known about how the same species responds to different threat processes. The purpose of this paper is therefore twofold: to examine the extent to which a species' vulnerability to different types of threat might covary and to explore the biological traits that are associated with threat-specific responses. We use an objective and quantitative measure of local extinction risk to show that vulnerability to local population decline in primates varies substantially among species and between threat types. Our results show that a species' response to one threat type does not predict its response to others. Multivariate analyses also suggest that different mechanisms of decline are associated with each type of threat, since different biological traits are correlated with each threat-specific response. Primate species at risk from forestry tend to exhibit low ecological flexibility, while those species vulnerable to agriculture tend to live in the canopy and eat low-fruit diets; in further contrast, primates at risk from hunting tend to exhibit large body size. Our analyses therefore indicate that a species' vulnerability to local extinction can be highly variable and is likely to depend on both threat type and biology. PMID:15306363

  3. Simultaneous fast measurement of circuit dynamics at multiple sites across the mammalian brain.

    PubMed

    Kim, Christina K; Yang, Samuel J; Pichamoorthy, Nandini; Young, Noah P; Kauvar, Isaac; Jennings, Joshua H; Lerner, Talia N; Berndt, Andre; Lee, Soo Yeun; Ramakrishnan, Charu; Davidson, Thomas J; Inoue, Masatoshi; Bito, Haruhiko; Deisseroth, Karl

    2016-04-01

    Real-time activity measurements from multiple specific cell populations and projections are likely to be important for understanding the brain as a dynamical system. Here we developed frame-projected independent-fiber photometry (FIP), which we used to record fluorescence activity signals from many brain regions simultaneously in freely behaving mice. We explored the versatility of the FIP microscope by quantifying real-time activity relationships among many brain regions during social behavior, simultaneously recording activity along multiple axonal pathways during sensory experience, performing simultaneous two-color activity recording, and applying optical perturbation tuned to elicit dynamics that match naturally occurring patterns observed during behavior.

  4. 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.

  5. 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.

  6. 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…

  7. Novel microarrays for simultaneous serodiagnosis of multiple antiviral antibodies.

    PubMed

    Sivakumar, Ponnurengam Malliappan; Moritsugu, Nozomi; Obuse, Sei; Isoshima, Takashi; Tashiro, Hideo; Ito, Yoshihiro

    2013-01-01

    We developed an automated diagnostic system for the detection of virus-specific immunoglobulin Gs (IgGs) that was based on a microarray platform. We compared efficacies of our automated system with conventional enzyme immunoassays (EIAs). Viruses were immobilized to microarrays using a radical cross-linking reaction that was induced by photo-irradiation. A new photoreactive polymer containing perfluorophenyl azide (PFPA) and poly(ethylene glycol) methacrylate was prepared and coated on plates. Inactivated measles, rubella, mumps, Varicella-Zoster and recombinant Epstein-Barr viruse antigen were added to coated plates, and irradiated with ultraviolet light to facilitate immobilization. Virus-specific IgGs in healthy human sera were assayed using these prepared microarrays and the results obtained compared with those from conventional EIAs. We observed high correlation (0.79-0.96) in the results between the automated microarray technique and EIAs. The microarray-based assay was more rapid, involved less reagents and sample, and was easier to conduct compared with conventional EIA techniques. The automated microarray system was further improved by introducing reagent storage reservoirs inside the chamber, thereby conserving the use of expensive reagents and antibodies. We considered the microarray format to be suitable for rapid and multiple serological diagnoses of viral diseases that could be developed further for clinical applications. PMID:24367491

  8. Finite element simulations involving simultaneous multiple interface fronts in phase change problems

    NASA Technical Reports Server (NTRS)

    Ouyang, Tianhong; Tamma, Kumar K.

    1992-01-01

    The present paper describes the simulation of phase change problems involving simultaneous multiple interface fronts employing the finite element method. Much of the past investigations employing finite elements have been restricted to primarily a single phase change situation. The existence of more than one phase, that is, the presence of multiple phase fronts poses certain challenges and further complications. However, the results provide a very interesting thermal behavior for this class of problems. In this paper, attention is focused on fixed grid methods and the trapezoidal family of one-step methods using the enthalpy formulations. Illustrative examples which handle simultaneous multiple fronts in phase change problems are presented.

  9. 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.

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

    PubMed

    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. PMID:27627322

  11. 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.

  12. 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…

  13. Multi-compound polarization by DNP allows simultaneous assessment of multiple enzymatic activities in vivo

    NASA Astrophysics Data System (ADS)

    Wilson, David M.; Keshari, Kayvan R.; Larson, Peder E. Z.; Chen, Albert P.; Hu, Simon; Van Criekinge, Mark; Bok, Robert; Nelson, Sarah J.; Macdonald, Jeffrey M.; Vigneron, Daniel B.; Kurhanewicz, John

    2010-07-01

    recorded for the individual metabolites. These studies demonstrated the feasibility of simultaneously measuring in vivo pH and tumor metabolism using nontoxic, endogenous species, and the potential to extend the multi-polarization approach to include up to four hyperpolarized probes providing multiple metabolic and physiologic measures in a single MR acquisition.

  14. 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.

  15. SIMULTANEOUSLY SPARSE SOLUTIONS TO LINEAR INVERSE PROBLEMS WITH MULTIPLE SYSTEM MATRICES AND A SINGLE OBSERVATION VECTOR*

    PubMed Central

    ZELINSKI, ADAM C.; GOYAL, VIVEK K.; ADALSTEINSSON, ELFAR

    2010-01-01

    A problem that arises in slice-selective magnetic resonance imaging (MRI) radio-frequency (RF) excitation pulse design is abstracted as a novel linear inverse problem with a simultaneous sparsity constraint. Multiple unknown signal vectors are to be determined, where each passes through a different system matrix and the results are added to yield a single observation vector. Given the matrices and lone observation, the objective is to find a simultaneously sparse set of unknown vectors that approximately solves the system. We refer to this as the multiple-system single-output (MSSO) simultaneous sparse approximation problem. This manuscript contrasts the MSSO problem with other simultaneous sparsity problems and conducts an initial exploration of algorithms with which to solve it. Greedy algorithms and techniques based on convex relaxation are derived and compared empirically. Experiments involve sparsity pattern recovery in noiseless and noisy settings and MRI RF pulse design. PMID:20445814

  16. Strong neutral spatial effects shape tree species distributions across life stages at multiple scales.

    PubMed

    Hu, Yue-Hua; Lan, Guo-Yu; Sha, Li-Qing; Cao, Min; Tang, Yong; Li, Yi-De; Xu, Da-Ping

    2012-01-01

    Traditionally, ecologists use lattice (regional summary) count data to simulate tree species distributions to explore species coexistence. However, no previous study has explicitly compared the difference between using lattice count and basal area data and analyzed species distributions at both individual species and community levels while simultaneously considering the combined scenarios of life stage and scale. In this study, we hypothesized that basal area data are more closely related to environmental variables than are count data because of strong environmental filtering effects. We also address the contribution of niche and the neutral (i.e., solely dependent on distance) factors to species distributions. Specifically, we separately modeled count data and basal area data while considering life stage and scale effects at the two levels with simultaneous autoregressive models and variation partitioning. A principal coordinates of neighbor matrix (PCNM) was used to model neutral spatial effects at the community level. The explained variations of species distribution data did not differ significantly between the two types of data at either the individual species level or the community level, indicating that the two types of data can be used nearly identically to model species distributions. Neutral spatial effects represented by spatial autoregressive parameters and the PCNM eigenfunctions drove species distributions on multiple scales, different life stages and individual species and community levels in this plot. We concluded that strong neutral spatial effects are the principal mechanisms underlying the species distributions and thus shape biodiversity spatial patterns. PMID:22666497

  17. 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

  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. Device for simultaneous multiple-line mode locking of an argon-ion laser

    SciTech Connect

    Kitahara, T.

    1987-11-01

    An acousto-optic device that can simultaneously mode lock multiple lines of a laser source has been designed and demonstrated. The device is an intracavity acousto-optic modulator with an end mirror. Multiple argon-ion laser lines at 476.5, 488.0, 496.5, and 514.5 nm were simultaneously modulated by using this device. Pulse trains with pulses having a width of approximately 100 psec FWHM at a repetition of 130 MHz were obtained for each line.

  20. 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

  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. 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.

  3. 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

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

    PubMed

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

    2016-01-27

    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.

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

    PubMed

    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

  6. 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…

  7. 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.

  8. Simultaneous detection of randomly arranged multiple barcodes using time division multiplexing technique

    NASA Astrophysics Data System (ADS)

    Haider, Saad Md. Jaglul; Islam, Md. Kafiul

    2010-02-01

    A method of detecting multiple barcodes simultaneously using time division multiplexing technique has been proposed in this paper to minimize the effective time needed for handling multiple tags of barcodes and to lessen the overall workload. Available barcode detection systems can handle multiple types of barcode but a single barcode at a time. This is not so efficient and can create large queue and chaos in places like mega shopping malls or large warehouses where we need to scan huge number of barcodes daily. Our proposed system is expected to improve the real time identification of goods or products on production lines and in automated warehouses or in mega shopping malls in a much more convenient and efficient way. For identifying of multiple barcodes simultaneously, a particular arrangement and orientation of LASER scanner and reflector have been used with a special curve shaped basement where the barcodes are placed. An effective and novel algorithm is developed to extract information from multiple barcodes which introduces starting pattern and ending pattern in barcodes with bit stuffing technique for the convenience of multiple detections. CRC technique is also used for trustworthiness of detection. The overall system enhances the existing single barcode detection system by a great amount although it is easy to implement and use.

  9. 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

  10. 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

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

    PubMed

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

    2016-08-16

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

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

    PubMed

    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

  14. SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs.

    PubMed

    Chakrabarti, Saikat; Anand, A Prem; Bhardwaj, Nitin; Pugalenthi, Ganesan; Sowdhamini, R

    2005-07-01

    Establishment of similarities between proteins is very important for the study of the relationship between sequence, structure and function and for the analysis of evolutionary relationships. Motif-based search methods play a crucial role in establishing the connections between proteins that are particularly useful for distant relationships. This paper reports SCANMOT, a web-based server that searches for similarities between proteins by simultaneous matching of multiple motifs. SCANMOT searches for similar sequences in entire sequence databases using multiple conserved regions and utilizes inter-motif spacing as restraints. The SCANMOT server is available via http://www.ncbs.res.in/~faculty/mini/scanmot/scanmot.html.

  15. Effects of species evenness and dominant species identity on multiple ecosystem functions in model grassland communities.

    PubMed

    Orwin, Kate H; Ostle, Nick; Wilby, Andrew; Bardgett, Richard D

    2014-03-01

    Ecosystems provide multiple services upon which humans depend. Understanding the drivers of the ecosystem functions that support these services is therefore important. Much research has investigated how species richness influences functioning, but we lack knowledge of how other community attributes affect ecosystem functioning. Species evenness, species spatial arrangement, and the identity of dominant species are three attributes that could affect ecosystem functioning, by altering the relative abundance of functional traits and the probability of synergistic species interactions such as facilitation and complementary resource use. We tested the effect of these three community attributes and their interactions on ecosystem functions over a growing season, using model grassland communities consisting of three plant species from three functional groups: a grass (Anthoxanthum odoratum), a forb (Plantago lanceolata), and a N-fixing forb (Lotus corniculatus). We measured multiple ecosystem functions that support ecosystem services, including ecosystem gas exchange, water retention, C and N loss in leachates, and plant biomass production. Species evenness and dominant species identity strongly influenced the ecosystem functions measured, but spatial arrangement had few effects. By the end of the growing season, evenness consistently enhanced ecosystem functioning and this effect occurred regardless of dominant species identity. The identity of the dominant species under which the highest level of functioning was attained varied across the growing season. Spatial arrangement had the weakest effect on functioning, but interacted with dominant species identity to affect some functions. Our results highlight the importance of understanding the role of multiple community attributes in driving ecosystem functioning. PMID:24213721

  16. Effects of species evenness and dominant species identity on multiple ecosystem functions in model grassland communities.

    PubMed

    Orwin, Kate H; Ostle, Nick; Wilby, Andrew; Bardgett, Richard D

    2014-03-01

    Ecosystems provide multiple services upon which humans depend. Understanding the drivers of the ecosystem functions that support these services is therefore important. Much research has investigated how species richness influences functioning, but we lack knowledge of how other community attributes affect ecosystem functioning. Species evenness, species spatial arrangement, and the identity of dominant species are three attributes that could affect ecosystem functioning, by altering the relative abundance of functional traits and the probability of synergistic species interactions such as facilitation and complementary resource use. We tested the effect of these three community attributes and their interactions on ecosystem functions over a growing season, using model grassland communities consisting of three plant species from three functional groups: a grass (Anthoxanthum odoratum), a forb (Plantago lanceolata), and a N-fixing forb (Lotus corniculatus). We measured multiple ecosystem functions that support ecosystem services, including ecosystem gas exchange, water retention, C and N loss in leachates, and plant biomass production. Species evenness and dominant species identity strongly influenced the ecosystem functions measured, but spatial arrangement had few effects. By the end of the growing season, evenness consistently enhanced ecosystem functioning and this effect occurred regardless of dominant species identity. The identity of the dominant species under which the highest level of functioning was attained varied across the growing season. Spatial arrangement had the weakest effect on functioning, but interacted with dominant species identity to affect some functions. Our results highlight the importance of understanding the role of multiple community attributes in driving ecosystem functioning.

  17. 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. PMID:24660477

  18. 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.

  19. 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...

  20. Breach, Leach, and Transport-Multiple Species UNCERT

    2006-04-01

    BLTPLOT_UNCERT is a FORTRAN code developed to facilitate plotting of 2-D concentration data for the Nuclear Regulatory Commission code called Breach, Leach, and Transport - Multiple Species (BLT-MS). BLTPLOT_UNCERT is open-source code. It functions under a DOS window.

  1. Breach, Leach, and Transport-Multiple Species GRID

    2006-04-01

    BLTMS-GRID is a FORTRAN code developed to facilitate specifications of a finite-element grid for the Nuclear Regulatory Commission code called Breach, Leach, and Transport - Multiple Species (BLT-MS). BLTMS-GRID is an open-source code. It functions under a DOS window.

  2. 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.

  3. Simultaneous Multiple Footprint and Multiple Field of View LiDAR for Submerged Topographic Mapping (Invited)

    NASA Astrophysics Data System (ADS)

    Wright, C. W.

    2013-12-01

    capture backscatter from the same laser pulse, in very different ways to give a way to preserve very shallow water ( 0 to 3-5 meters) measurement capability and fidelity while simultaneously capturing highly scattered and/or refracted light which enables bottom detection at deeper depths in the presence of significantly more suspended sediment. We examine the LiDAR back scattered waveforms from both the 2mr and 18mr channels over a wide range of water depths and varying levels of turbidity.

  4. Species diversity and predation strategies in a multiple species predator-prey model

    NASA Astrophysics Data System (ADS)

    Mullan, Rory; Glass, David H.; McCartney, Mark

    2015-08-01

    A single predator, single prey ecological model, in which the behaviour of the populations relies upon two control parameters has been expanded to allow for multiple predators and prey to occupy the ecosystem. The diversity of the ecosystem that develops as the model runs is analysed by assessing how many predator or prey species survive. Predation strategies that dictate how the predators distribute their efforts across the prey are introduced in this multiple species model. The paper analyses various predation strategies and highlights their effect on the survival of the predators and prey species.

  5. Development of a multiple immunoaffinity column for simultaneous determination of multiple mycotoxins in feeds using UPLC-MS/MS.

    PubMed

    Hu, Xiaofeng; Hu, Rui; Zhang, Zhaowei; Li, Peiwu; Zhang, Qi; Wang, Min

    2016-09-01

    A sensitive and specific immunoaffinity column to clean up and isolate multiple mycotoxins was developed along with a rapid one-step sample preparation procedure for ultra-performance liquid chromatography-tandem mass spectrometry analysis. Monoclonal antibodies against aflatoxin B1, aflatoxin B2, aflatoxin G1, aflatoxin G2, zearalenone, ochratoxin A, sterigmatocystin, and T-2 toxin were coupled to microbeads for mycotoxin purification. We optimized a homogenization and extraction procedure as well as column loading and elution conditions to maximize recoveries from complex feed matrices. This method allowed rapid, simple, and simultaneous determination of mycotoxins in feeds with a single chromatographic run. Detection limits for these toxins ranged from 0.006 to 0.12 ng mL(-1), and quantitation limits ranged from 0.06 to 0.75 ng mL(-1). Concentration curves were linear from 0.12 to 40 μg kg(-1) with correlation coefficients of R (2) > 0.99. Intra-assay and inter-assay comparisons indicated excellent repeatability and reproducibility of the multiple immunoaffinity columns. As a proof of principle, 80 feed samples were tested and several contained multiple mycotoxins. This method is sensitive, rapid, and durable enough for multiple mycotoxin determinations that fulfill European Union and Chinese testing criteria. PMID:27225172

  6. 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

  7. Laboratory Studies Of Titan Haze: Simultaneous In Situ Detection Of Gas And Particle Species

    NASA Astrophysics Data System (ADS)

    Horst, Sarah; Li, R.; Yoon, H.; Hicks, R.; de Gouw, J.; Tolbert, M.

    2012-10-01

    Analyses of data obtained by multiple instruments carried by Cassini and Huygens have increased our knowledge of the composition of Titan’s atmosphere. While a wealth of new information about the aerosols in Titan’s atmosphere was obtained, their composition is still not well constrained. Laboratory experiments will therefore play a key role in furthering our understanding of the chemical processes resulting in the formation of haze in Titan’s atmosphere and its possible composition. We have obtained simultaneous in situ measurements of the gas- and particle-phase compositions produced by our Titan atmosphere simulation experiments (see e.g. [1]). The gas phase composition was measured using a Proton-Transfer Ion-Trap Mass Spectrometer (PIT-MS) and the aerosol composition was measured using a High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS). This complementary set of measurements will allow us to address the partitioning of gas- and aerosol-phase species. Knowledge of the gas phase composition in which the particles in our experiments form allows both for better comparison to the chemistry that is occurring in Titan’s atmosphere and for enabling more accurate determination of the possible pathways involved in the transition from gas phase to aerosol. We will compare the results from experiments that used two different initial gas mixtures (98% N2/2% CH4 and 98%N2/2%CH4/50 ppm CO) and two different energy sources to initiate the chemical reactions that result in particle formation (spark discharge using a Tesla coil or FUV irradiation from a deuterium lamp (115-400 nm)). [1] Trainer, M.G., et al. (2012) Astrobiology, 12, 315-326. SMH is supported by NSF Astronomy and Astrophysics Postdoctoral Fellowship AST-1102827.

  8. Asymmetric signal amplification for simultaneous SERS detection of multiple cancer markers with significantly different levels.

    PubMed

    Ye, Sujuan; Wu, Yanying; Zhai, Xiaomo; Tang, Bo

    2015-08-18

    Simultaneous detection of cancer biomarkers holds great promise for the early diagnosis of different cancers. However, in the presence of high-concentration biomarkers, the signals of lower-expression biomarkers are overlapped. Existing techniques are not suitable for simultaneously detecting multiple biomarkers at concentrations with significantly different orders of magnitude. Here, we propose an asymmetric signal amplification method for simultaneously detecting multiple biomarkers with significantly different levels. Using the bifunctional probe, a linear amplification mode responds to high-concentration markers, and quadratic amplification mode responds to low-concentration markers. With the combined biobarcode probe and hybridization chain reaction (HCR) amplification method, the detection limits of microRNA (miRNA) and ATP via surface-enhanced Raman scattering (SERS) detection are 0.15 fM and 20 nM, respectively, with a breakthrough of detection concentration difference over 11 orders of magnitude. Furthermore, successful determination of miRNA and ATP in cancer cells supports the practicability of the assay. This methodology promises to open an exciting new avenue for the detection of various types of biomolecules. PMID:26218034

  9. Cotrapping different species in ion traps using multiple radio frequencies

    NASA Astrophysics Data System (ADS)

    Trypogeorgos, Dimitris; Foot, Christopher J.

    2016-08-01

    We consider the stability of systems subjected to periodic parametric driving in the context of ions confined by oscillating electric fields. The behavior of these systems can be understood in terms of a pseudopotential approximation and resonances arising from parametric excitation. We investigate the key properties of a way of operating a linear Paul trap with two radio frequencies that simultaneously confines two species with extremely different charge-to-mass ratios. The theoretical calculations have been verified by molecular dynamics simulations and normal modes analysis.

  10. 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. PMID:24392838

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Simultaneous transfer of linear and orbital angular momentum to multiple low-index particles

    NASA Astrophysics Data System (ADS)

    Daria, Vincent Ricardo; Go, Mary Ann; Bachor, Hans-A.

    2011-04-01

    We demonstrate simultaneous transfer of linear and orbital angular momentum (OAM) to hollow glass microbeads using a dynamic array of optical vortices. Previous reports have shown that the transfer of OAM is due to light scattering which creates a tangential force on a particle and causes it to move on a circular orbit around a vortex. In this paper we describe a case with reduced frictional force, as the low-index particle is pinned to the wall of the sample cell. This results in a more efficient transfer of OAM, which sets a hollow microbead into orbital motion around the optical vortex. We show that the localized OAM carried by each vortex in the array can be independently transferred to one microbead trapped per vortex. Finally, we present novel demonstrations showing simultaneous transfer of both orbital angular and linear momentum to multiple microbeads.

  16. Simultaneous detection of multiple elastic surfaces with application to tumor segmentation in CT images

    NASA Astrophysics Data System (ADS)

    Li, Kang; Jolly, Marie-Pierre

    2008-03-01

    We present a new semi-supervised method for segmenting multiple interrelated object boundaries with spherical topology in volumetric images. The core of our method is a novel graph-theoretic algorithm that simultaneously detects multiple surfaces under smoothness, distance, and elasticity constraints. The algorithm computes the global optimum of an objective function that incorporates boundary, regional and surface elasticity information. A single straight line drawn by the user in a cross-sectional slice is the sole user input, which roughly indicates the extent of the object. We employ a multi-seeded Dijkstra-based range competition algorithm to pre-segment the object on two orthogonal multiplanar reformatted (MPR) planes that pass through the input line. Based on the 2D pre-segmentation results, we estimate the object and background intensity histograms, and employ an adaptive mean-shift mode-seeking process on the object histogram to automatically determine the number of surface layers to be segmented. The final multiple-surface segmentation is performed in an ellipsoidal coordinate frame constructed by an automated ellipsoid fitting procedure. We apply our method to the segmentation of liver lesions with necrosis or calcification, and various other tumors in CT images. For liver tumor segmentation, our method can simultaneously delineate both tumor and necrosis boundaries. This capability is unprecedented and is valuable for cancer diagnosis, treatment planning, and evaluation.

  17. Simultaneous and spatially separated detection of multiple orbital angular momentum states

    NASA Astrophysics Data System (ADS)

    Tudor, R.; Mihailescu, M.; Kusko, C.; Paun, I. A.; Nan, A. E.; Kusko, M.

    2016-06-01

    We present a method for spatially separated detection of multiple orbital angular momentum (OAM) states, simultaneous. The starting point is the generation of axially superposed Laguerre-Gauss beams, carrying multiple OAM states using a single computer generated hologram. The information contained in the OAM superposition is transferred to the first diffraction order and is detected at the receiver with a reading mask, which contains two perpendicular superposed fork-like holograms, ensuring the spatial separation of the OAM states. The dynamic of the process is studied in terms of the number of generated OAM states and the constructive parameters values. The experimental investigations use an optical arrangement based on a spatial light modulator in the transmitter unit and an amplitude mask in the receiver unit. This proof of concept experiment demonstrates the possibility of simultaneously detection of multiple OAM states in points located at different coordinates, controlled through the design of the holograms and shows the capability of our proposed method to increase the capacity of free-space optical communication channels.

  18. 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.

  19. Breach, Leach and Transport-Multiple Species WIN

    2005-12-01

    BLTMSIN-WIN is a Windows-based preprocessor for the Breach, Leach, and Transport - Multiple Species (BLT-MS) code developed by the Nuclear Regulatory Commission (NRC) for performance assessment analyses of low-level radioactive waste disposal facilities. It is based, in part, on the preprocessor that the NRC developed, BLTMSIN. The code is written in Fortran and compiled with the Lahey Fortran compiler.

  20. Simultaneous optical tracking of multiple targets in a field of view greater than 20°.

    PubMed

    Kawakami, Kotomi; Okamura, Hideki; Komurasaki, Kimiya

    2015-04-20

    A multi-target tracking system using a self-starting optical phase conjugator was developed in this study. This system generates phase conjugate light (PCL) in a Nd:YAG resonator. Accurate tracking capability with a beam wander of 120 μrad and constant PCL generation were confirmed over a field of view greater than 20°. This field of view was expanded by means of collector optics positioned in front of the phase conjugator. The developed scheme enables automatic and simultaneous optical energy transfer to multiple distant targets by utilizing the unique properties of optical phase conjugation of automatic target tracking and pointing. PMID:25969017

  1. Simultaneous optical tracking of multiple targets in a field of view greater than 20°.

    PubMed

    Kawakami, Kotomi; Okamura, Hideki; Komurasaki, Kimiya

    2015-04-20

    A multi-target tracking system using a self-starting optical phase conjugator was developed in this study. This system generates phase conjugate light (PCL) in a Nd:YAG resonator. Accurate tracking capability with a beam wander of 120 μrad and constant PCL generation were confirmed over a field of view greater than 20°. This field of view was expanded by means of collector optics positioned in front of the phase conjugator. The developed scheme enables automatic and simultaneous optical energy transfer to multiple distant targets by utilizing the unique properties of optical phase conjugation of automatic target tracking and pointing.

  2. 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.

  3. A two-species occupancy model accommodating simultaneous spatial and interspecific dependence.

    PubMed

    Rota, Christopher T; Wikle, Christopher K; Kays, Roland W; Forrester, Tavis D; McShea, William J; Parsons, Arielle W; Millspaugh, Joshua J

    2016-01-01

    Occupancy models are popular for estimating the probability a site is occupied by a species of interest when detection is imperfect. Occupancy models have been extended to account for interacting species and spatial dependence but cannot presently allow both factors to act simultaneously. We propose a two-species occupancy model that accommodates both interspecific and spatial dependence. We use a point-referenced multivariate hierarchical spatial model to account for both spatial and interspecific dependence. We model spatial random effects with predictive process models and use probit regression to improve efficiency of posterior sampling. We model occupancy probabilities of red fox (Vulpes vulpes) and coyote (Canis latrans) with camera trap data collected from six mid-Atlantic states in the eastern United States. We fit four models comprising a fully factorial combination of spatial and interspecific dependence to two-thirds of camera trapping sites and validated models with the remaining data. Red fox and coyotes each exhibited spatial dependence at distances > 0.8 and 0.4 km, respectively, and exhibited geographic variation in interspecific dependence. Consequently, predictions from the model assuming simultaneous spatial and interspecific dependence best matched test data observations. This application highlights the utility of simultaneously accounting for spatial and interspecific dependence.

  4. A two-species occupancy model accommodating simultaneous spatial and interspecific dependence.

    PubMed

    Rota, Christopher T; Wikle, Christopher K; Kays, Roland W; Forrester, Tavis D; McShea, William J; Parsons, Arielle W; Millspaugh, Joshua J

    2016-01-01

    Occupancy models are popular for estimating the probability a site is occupied by a species of interest when detection is imperfect. Occupancy models have been extended to account for interacting species and spatial dependence but cannot presently allow both factors to act simultaneously. We propose a two-species occupancy model that accommodates both interspecific and spatial dependence. We use a point-referenced multivariate hierarchical spatial model to account for both spatial and interspecific dependence. We model spatial random effects with predictive process models and use probit regression to improve efficiency of posterior sampling. We model occupancy probabilities of red fox (Vulpes vulpes) and coyote (Canis latrans) with camera trap data collected from six mid-Atlantic states in the eastern United States. We fit four models comprising a fully factorial combination of spatial and interspecific dependence to two-thirds of camera trapping sites and validated models with the remaining data. Red fox and coyotes each exhibited spatial dependence at distances > 0.8 and 0.4 km, respectively, and exhibited geographic variation in interspecific dependence. Consequently, predictions from the model assuming simultaneous spatial and interspecific dependence best matched test data observations. This application highlights the utility of simultaneously accounting for spatial and interspecific dependence. PMID:27008774

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

    PubMed

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

    2016-06-30

    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 distinct cases in mammals (Tasmanian devils and dogs), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria) suggested that this phenomenon might be more widespread. Here we analyse disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and find 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; however, unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographical 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 are found spreading within the species of origin, cross-species transmission of cancer cells can occur. PMID:27338791

  6. Scanning multiple samples simultaneously in tube-based microCT systems

    NASA Astrophysics Data System (ADS)

    Stock, S. R.; Rajamannan, N. M.; Spelsberg, T. C.; Malayannan, S.; Riaz, R.; Polavarapu, M.; Hsu, E. L.; Hsu, W., K.; Chen, Yan; Zhang, Ming

    2010-09-01

    The world-wide explosion of commercial microComputed Tomography (microCT) system emplacement has led to dayin, day-out access to laboratory scanners. Most biologically-oriented microCT facilities must characterize large numbers of samples rapidly at moderate spatial resolution (e.g., 10-20 μm isotropic volume elements, voxels). Scanning multiple specimens simultaneously is one efficient solution. Sample positioning is critical if the region of interest of each specimen is to be imaged without increasing the number of slices recorded (i.e., data acquisition and reconstruction times). Three very different, multiple sample data acquisitions are reported: mouse heart tissue calcification, rat spinal fusion and mouse tibial bone cancer models

  7. 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.

  8. 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/.

  9. 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

  10. 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

  11. 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.

  12. Recurrent habitat disturbance and species diversity in a multiple-competitive species system.

    PubMed

    Ohsawa, Kyoko; Kawasaki, Kohkichi; Takasu, Fugo; Shigesada, Nanako

    2002-05-21

    To address how species interactions, dispersal and environmental disturbances interplay to affect the spatial distribution and diversity of species, we present a compartment model in which multiple species undergo competitive interaction of Lotka-Volterra type in a patchy environment arranged in a square lattice. Dispersal of species occurs between adjacent patches. Disturbances are periodically imposed on a central part of the environment in a belt-like block or an island-like block of various sizes where each species is killed for a certain time interval and then allowed to recover for the rest of a disturbance cycle. We deal with a case in which the local population dynamics within each patch is analytically determinable and has multiple locally stable equilibrium states in the absence of environmental disturbance. We further assume a trade-off between the reproductive rate of species and its dispersal ability. With these settings, we numerically examine how the spatio-temporal distributions of species are affected by changes in the pattern, size and duration of disturbances. The results demonstrate that: (1) in the undisturbed area, environmental disturbances could generate spatially segregated distributions of species; (2) in the disturbed area, species with higher dispersal abilities quickly invade and preferentially recover their population during the post-disturbance period, being temporarily relieved of competition from other species. These mechanisms collectively lead to increased species diversity in the whole habitat, functioning best when both the size and duration of disturbances are intermediate. In particular, the belt-like disturbance is more effective than the island-like disturbance in sustaining spatial heterogeneity for a wider range of duration of disturbance. PMID:12079366

  13. 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.

  14. 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.

  15. 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.

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

    DOE PAGESBeta

    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

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

    NASA Astrophysics Data System (ADS)

    Chu, Ping-Han; Peng, Jen-Chieh

    2015-09-01

    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 atoms simultaneously with a π / 2 pulse, proposed for a neutron electric dipole moment experiment, is also presented.

  18. A Multi-RNAi Microsponge Platform for Simultaneous Controlled Delivery of Multiple Small Interfering RNAs.

    PubMed

    Roh, Young Hoon; Deng, Jason Z; Dreaden, Erik C; Park, Jae Hyon; Yun, Dong Soo; Shopsowitz, Kevin E; Hammond, Paula T

    2016-03-01

    Packaging multiple small interfering RNA (siRNA) molecules into nanostructures at precisely defined ratios is a powerful delivery strategy for effective RNA interference (RNAi) therapy. We present a novel RNA nanotechnology based approach to produce multiple components of polymerized siRNA molecules that are simultaneously self-assembled and densely packaged into composite sponge-like porous microstructures (Multi-RNAi-MSs) by rolling circle transcription. The Multi-RNAi-MSs were designed to contain a combination of multiple polymeric siRNA molecules with precisely controlled stoichiometry within a singular microstructure by manipulating the types and ratios of the circular DNA templates. The Multi-RNAi-MSs were converted into nanosized complexes by polyelectrolyte condensation to manipulate their physicochemical properties (size, shape, and surface charge) for favorable delivery, while maintaining the multifunctional properties of the siRNAs for combined therapeutic effects. These Multi-RNAi-MS systems have great potential in RNAi-mediated biomedical applications, for example, for the treatment of cancer, genetic disorders, and viral infections. PMID:26695874

  19. Multiple simultaneous detection of Harmful Algal Blooms (HABs) through a high throughput bead array technology, with potential use in phytoplankton community analysis.

    PubMed

    Scorzetti, G; Brand, L E; Hitchcock, G L; Rein, K S; Sinigalliano, C D; Fell, J W

    2009-01-01

    As an alternative to traditional, morphology-based methods, molecular techniques can provide detection of multiple species within the HAB community and, more widely, the phytoplankton community in a rapid, accurate and simultaneous qualitative analysis. These methods require detailed knowledge of the molecular diversity within taxa in order to design efficient specific primers and specific probes able to avoid cross-reaction with non-target sequences. Isolates from Florida coastal communities were sequence-analyzed and compared with the GenBank database. Almost 44% of the genotypes obtained did not match any sequence in GenBank, showing the existence of a large and still unexplored biodiversity among taxa. Based on these results and on the GenBank database, we designed 14 species-specific probes and 4 sets of specific primers. Multiple simultaneous detection was achieved with a bead array method based on the use of a flow cytometer and color-coded microspheres, which are conjugated to the developed probes. Following a parallel double PCR amplification, which employed universal primers in a singleplex reaction and a set of species-specific primers in multiplex, detection was performed in a cost effective and highly specific analysis. This multi-format assay, which required less than 4 h to complete from sample collection, can be expanded according to need. Up to 100 different species can be identified simultaneously in a single sample, which allows for additional use of this method in community analyses extended to all phytoplankton species. Our initial field trials, which were based on the 14 species-specific probes, showed the co-existence and dominance of two or more species of Karenia during toxic blooms in Florida waters.

  20. Multiple simultaneous detection of Harmful Algal Blooms (HABs) through a high throughput bead array technology, with potential use in phytoplankton community analysis.

    PubMed

    Scorzetti, G; Brand, L E; Hitchcock, G L; Rein, K S; Sinigalliano, C D; Fell, J W

    2009-01-01

    As an alternative to traditional, morphology-based methods, molecular techniques can provide detection of multiple species within the HAB community and, more widely, the phytoplankton community in a rapid, accurate and simultaneous qualitative analysis. These methods require detailed knowledge of the molecular diversity within taxa in order to design efficient specific primers and specific probes able to avoid cross-reaction with non-target sequences. Isolates from Florida coastal communities were sequence-analyzed and compared with the GenBank database. Almost 44% of the genotypes obtained did not match any sequence in GenBank, showing the existence of a large and still unexplored biodiversity among taxa. Based on these results and on the GenBank database, we designed 14 species-specific probes and 4 sets of specific primers. Multiple simultaneous detection was achieved with a bead array method based on the use of a flow cytometer and color-coded microspheres, which are conjugated to the developed probes. Following a parallel double PCR amplification, which employed universal primers in a singleplex reaction and a set of species-specific primers in multiplex, detection was performed in a cost effective and highly specific analysis. This multi-format assay, which required less than 4 h to complete from sample collection, can be expanded according to need. Up to 100 different species can be identified simultaneously in a single sample, which allows for additional use of this method in community analyses extended to all phytoplankton species. Our initial field trials, which were based on the 14 species-specific probes, showed the co-existence and dominance of two or more species of Karenia during toxic blooms in Florida waters. PMID:20046212

  1. 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.

  2. 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...

  3. 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.

  4. Simultaneous measurements of multiple flow parameters for scramjet characterization using tunable diode-laser sensors.

    PubMed

    Li, Fei; Yu, Xilong; Gu, Hongbin; Li, Zhi; Zhao, Yan; Ma, Lin; Chen, Lihong; Chang, Xinyu

    2011-12-20

    This paper reports the simultaneous measurements of multiple flow parameters in a scramjet facility operating at a nominal Mach number of 2.5 using a sensing system based on tunable diode-laser absorption spectroscopy (TDLAS). The TDLAS system measures velocity, temperature, and water vapor partial pressure at three different locations of the scramjet: the inlet, the combustion region near the flame stabilization cavity, and the exit of the combustor. These measurements enable the determination of the variation of the Mach number and the combustion mode in the scramjet engine, which are critical for evaluating the combustion efficiency and optimizing engine performance. The results obtained in this work clearly demonstrated the applicability of TDLAS sensors in harsh and high-speed environments. The TDLAS system, due to its unique virtues, is expected to play an important role in the development of scramjet engines.

  5. Simultaneous detection of multiple biomarkers with over three orders of concentration difference using phase change nanoparticles.

    PubMed

    Wang, Chaoming; Sun, Zhaoyong; Ma, Liyuan; Su, Ming

    2011-03-15

    A big challenge for multiplexed detection of cancer biomarkers is that biomarker concentrations in body fluid differs several orders of magnitude. Existing techniques are not suitable to detect low- and high-concentration biomarkers (protein and DNA) at the same time, and liquid chromatography or electrophoresis is used to separate or purify target biomarkers before analysis. This paper describes a new broad-range biomarker assay using solid to liquid phase change nanoparticles, where a panel of metallic nanoparticles (i.e., metals and eutectic alloys) are modified with a panel of ligands to establish a one-to-one correspondence and attached onto ligand-modified substrates by forming sandwiched complexes. The melting peak and fusion enthalpy of phase change nanoparticles during thermal analysis reflect the type and concentration of biomarkers, respectively. The thermal readout condition can be adjusted in such a way that multiple biomarkers with concentration difference over 3 orders of magnitude have been simultaneously detected under the same condition.

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

    DOEpatents

    Lu, Yi; Liu, Juewen

    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.

  7. 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.

  8. Multiple Simultaneous Gastrointestinal Parasitic Infections in a Patient with Human Immunodeficiency Virus.

    PubMed

    Del Pilar-Morales, Esteban A; Cardona-Rodríguez, Zaydalee; Bertrán-Pasarell, Jorge; Soto-Malave, Ruth; De León-Borras, Rafeal

    2016-06-01

    Patients with the human immunodeficiency virus (HIV) infection are at high risk for gastrointestinal infections causing diarrhea, particularly when those infections are parasitic in nature. This propensity is more pronounced in AIDS, where opportunistic parasitic infections may cause severe diarrhea, marked absorptive dysfunction, and significant risk of mortality. There are scant data regarding parasitic infections among HIV patients in the developed world; most studies and research come from povertystricken areas of South Africa, India, Iran, and the South Pacific. Although multiple infections with the same or different parasites have been reported, simultaneous infections are rare. We present the case of a 35-year-old man who developed a co-infection with Giardia, Cryptosporidium, and Strongyloides, simultaneously, the diagnosis being made after the judicious evaluation of a stool sample. Given the associated morbidity, prompt diagnosis and treatment are needed to avoid further complications in patients with HIV. To our knowledge this is the first reported case of triple parasitic infection in a patient with HIV.

  9. 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

  10. Reduced Response to Multiple Vaccines Sharing Common Protein Epitopes That Are Administered Simultaneously to Infants

    PubMed Central

    Dagan, Ron; Eskola, Juhani; Leclerc, Claude; Leroy, Odile

    1998-01-01

    The plethora of newly discovered vaccines implies that, in the future, many vaccines will have to be administered simultaneously to infants. We examined the potential interference with the immune response of several coadministered vaccines containing the same protein component, namely, tetanus toxoid (TT). Infants simultaneously receiving a tetravalent pneumococcal vaccine conjugated to TT (PncT) and a diphtheria-tetanus-pertussis–poliovirus–Haemophilus influenzae type b-tetanus conjugate vaccine showed significantly lower anti-H. influenzae type b polysaccharide (polyribosylribitol phosphate [PRP]) antibody concentrations than those receiving either a tetravalent pneumococcal vaccine conjugated to diphtheria toxoid or placebo. A dose range study showed that anti-PRP antibody concentrations were inversely related to the TT content of the PncT vaccines administered in infancy. Postimmunization antitetanus antibody concentrations were also affected adversely as the TT content of the coadministered vaccines was increased. This phenomenon, which we believe derives from interference by a common protein carrier, should be taken into account when the introduction of an immunization program including multiple conjugate vaccines is considered. PMID:9573094

  11. Nanoscale NMR spectroscopy and imaging of multiple nuclear species.

    PubMed

    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 ((1)H, (19)F, (31)P) in non-uniform (spatially structured) samples under ambient conditions and at moderate magnetic fields (∼20 mT) using two complementary sensor modalities. PMID:25559712

  12. Polarimetric scattering from layered media with multiple species of scatterers

    NASA Technical Reports Server (NTRS)

    Nghiem, S. V.; Kwok, R.; Yueh, S. H.; Kong, J. A.; Hsu, C. C.; Tassoudji, M. A.; Shin, R. T.

    1995-01-01

    Geophysical media are usually heterogeneous and contain multiple species of scatterers. In this paper a model is presented to calculate effective permittivities and polarimetric backscattering coefficients of multispecies-layered media. The same physical description is consistently used in the derivation of both permittivities and scattering coefficients. The strong permittivity fluctuation theory is extended to account for the multiple species of scatterers with a general ellipsoidal shape whose orientations are randomly distributed. Under the distorted Born approximation, polarimetric scattering coefficients are obtained. These calculations are applicable to the special cases of spheroidal and spherical scatterers. The model is used to study effects of scatterer shapes and multispecies mixtures on polarimetric signatures of heterogeneous media. The multispecies model accounts for moisture content in scattering media such as snowpack in an ice sheet. The results indicate a high sensitivity of backscatter to moisture with a stronger dependence for drier snow and ice grain size is important to the backscatter. For frost-covered saline ice, model results for bare ice are compared with measured data at C band and then the frost flower formation is simulated with a layer of fanlike ice crystals including brine infiltration over a rough interface. The results with the frost cover suggest a significant increase in scattering coefficients and a polarimetric signature closer to isotropic characteristics compared to the thin saline ice case.

  13. 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).

  14. Simultaneous Identification of Spectral Properties and Sizes of Multiple Particles in Solution with Subnanometer Resolution.

    PubMed

    Karabudak, Engin; Brookes, Emre; Lesnyak, Vladimir; Gaponik, Nikolai; Eychmüller, Alexander; Walter, Johannes; Segets, Doris; Peukert, Wolfgang; Wohlleben, Wendel; Demeler, Borries; Cölfen, Helmut

    2016-09-19

    We report an unsurpassed solution characterization technique based on analytical ultracentrifugation, which demonstrates exceptional potential for resolving particle sizes in solution with sub-nm resolution. We achieve this improvement in resolution by simultaneously measuring UV/Vis spectra while hydrodynamically separating individual components in the mixture. By equipping an analytical ultracentrifuge with a novel multi-wavelength detector, we are adding a new spectral discovery dimension to traditional hydrodynamic characterization, and amplify the information obtained by orders of magnitude. We demonstrate the power of this technique by characterizing unpurified CdTe nanoparticle samples, avoiding tedious and often impossible purification and fractionation of nanoparticles into apparently monodisperse fractions. With this approach, we have for the first time identified the pure spectral properties and band-gap positions of discrete species present in the CdTe mixture. PMID:27461742

  15. Simultaneous Determination of Multiple microRNA Levels Utilizing Biotinylated Dideoxynucleotides and Mass Spectrometry.

    PubMed

    Kim, Sobin; Park, Jungyun; Na, Jeongkyeong; Jung, Gyoo Yeol; Hwang, Jungwook

    2016-01-01

    MicroRNAs (miRNAs) are important regulators of gene translation and have been suggested as potent biomarkers in various disease states. In this study, we established an efficient method for simultaneous determination of multiple miRNA levels, employing the previously developed SPC-SBE (solid phase capture-single base extension) approach and MALDI-TOF mass spectrometry (MS). In this approach, we first perform reverse transcription of miRNAs extracted using stem-loop primers. Then the cDNA is co-amplified with competitors, synthetic oligonucleotides whose sequences precisely match cDNA except for one base, and the amplicons serve as templates for a multiplexed SBE reaction. Extension products are isolated using SPC and quantitatively analyzed with MALDI-TOF MS to determine multiple miRNA levels. Here we demonstrated concurrent analysis of four miRNA levels utilizing the approach. Furthermore, we showed the presented method significantly facilitated MS analysis of peak area ratio owing to SPC. The SPC process allowed effective removal of irrelevant reaction components prior to MS and promoted MS sample purification. Data obtained in this study was verified with RT-qPCR and agreement was shown on one order of magnitude scale, suggesting the SPC-SBE and MS approach has strong potential as a viable tool for high throughput miRNA analysis. PMID:27380276

  16. Simultaneous Determination of Multiple microRNA Levels Utilizing Biotinylated Dideoxynucleotides and Mass Spectrometry

    PubMed Central

    Kim, Sobin; Park, Jungyun; Na, Jeongkyeong; Jung, Gyoo Yeol; Hwang, Jungwook

    2016-01-01

    MicroRNAs (miRNAs) are important regulators of gene translation and have been suggested as potent biomarkers in various disease states. In this study, we established an efficient method for simultaneous determination of multiple miRNA levels, employing the previously developed SPC-SBE (solid phase capture-single base extension) approach and MALDI-TOF mass spectrometry (MS). In this approach, we first perform reverse transcription of miRNAs extracted using stem-loop primers. Then the cDNA is co-amplified with competitors, synthetic oligonucleotides whose sequences precisely match cDNA except for one base, and the amplicons serve as templates for a multiplexed SBE reaction. Extension products are isolated using SPC and quantitatively analyzed with MALDI-TOF MS to determine multiple miRNA levels. Here we demonstrated concurrent analysis of four miRNA levels utilizing the approach. Furthermore, we showed the presented method significantly facilitated MS analysis of peak area ratio owing to SPC. The SPC process allowed effective removal of irrelevant reaction components prior to MS and promoted MS sample purification. Data obtained in this study was verified with RT-qPCR and agreement was shown on one order of magnitude scale, suggesting the SPC-SBE and MS approach has strong potential as a viable tool for high throughput miRNA analysis. PMID:27380276

  17. 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.

  18. Laboratory evaluation of a unified theory for simultaneous multiple axis artificial arm control.

    PubMed

    Jerard, R B; Jacobsen, S C

    1980-08-01

    This paper reports on the application of a "postulate-based" control method for multi-axis artificial arm control. This method uses shoulder muscle EMG's as control sites, but, unlike previous techniques, the theory is the first that can be rigorously defined in terms of musculoskeletal anatomy, EMG muscle-force relationships, EMG transmission characteristics, muscle recruitment, limb dynamics and normal motion constraints. The control theory results in a deterministic, mathematically expressible set of controller equations, which use the vector of natural limb torques estimated by shoulder EMG signals and a "constraint" for input. The output of the controller equations is a vector of prosthetic torques to be applied to the artificial limb. We report on the implementation of the theory up to the point of laboratory feasibility trials of actual simultaneous above-elbow amputee control of elbow flexion and humeral rotation. Implementation of the theory required: 1) deviation of the controller equations from Newton's dynamic equations of motion into controller form in conformity with the postulate theory; 2) development of a methodology for estimating natural musculoskeletal torques from EMG signals; 3) hardware and software for experimental testing with actual closed loop amputee control of the prosthesis; and 4) a methodology for evaluating the performance of the prosthesis relative to both alternative prosthetic systems and the natural arm. These tasks were completed and simultaneous multiple-axis control of a prosthetic arm was accomplished by both amputee and nonamputee subjects. Key questions of control compatibility, naturalness, stability, and performance evaluation relative to other prostheses and the natural arm were addressed. Various problems are discussed with the conclusion that this method, despite some difficulties, holds great promise as a practical rehabilitation tool.

  19. 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

  20. 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.

  1. 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.

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

    PubMed

    MacKenzie, Darryl I; Nichols, James D; Seamans, Mark E; Gutiérrez, R J

    2009-03-01

    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. PMID:19341151

  3. Microchip fluorescence-enhanced immunoaasay for simultaneous quantification of multiple tumor markers.

    PubMed

    Shi, Ming; Zhao, Shulin; Huang, Yong; Liu, Yi-Ming; Ye, Fanggui

    2011-09-15

    A microchip fluorescence-enhanced immunoassay method was developed for simultaneous detection of carcinoma antigen 125 (CA125) and carbohydrate antigen 15-3 (CA15-3). In this method, CA125 and CA15-3 react with excess amount of fluorescein isothiocyanate (FITC)-labeled monoclonal antibodies (Ab(*)) of CA125 and CA15-3 to form CA125-Ab(125)(*) and CA15-3-Ab(15-3)(*) complexes. Microchip electrophoresis (MCE) separation of free Ab(125)(*), Ab(15-3)(*), and CA125-Ab(125)(*), CA15-3-Ab(15-3)(*) complexes were then performed. The separated species were sensitively detected by laser-induced fluorescence detection (LIF). CA125 and CA15-3 were quantified simultaneously by measuring the fluorescence intensity of CA125-Ab(125)(*) and CA15-3-Ab(15-3)(*) complexes, respectively. Under the optimum conditions, the limits of detection were 0.23 U/mL for CA125 and 0.09 U/mL for CA15-3. The present MCE-LIF method was applied to the determination of CA125 and CA15-3 in serum from healthy subjects and cancer patients. The levels of CA125 and CA15-3 in these sera samples were found to be in the ranges of 15.6-36.1 U/mL and 13.8-28.4 U/mL for healthy subjects, and 192.5-368.3 U/mL and 63.3-198.4 U/mL for cancer patients.

  4. 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.

  5. 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

  6. 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.

  7. Moyamoya disease manifested as multiple simultaneous intracerebral hemorrhages: A case report and literature review

    PubMed Central

    Yu, Jinlu; Yuan, Yongjie; Li, Wei; Xu, Kan

    2016-01-01

    Multiple simultaneous intracerebral hemorrhages (MSIH) caused by Moyamoya disease (MMD) is extremely rare. To date, the clinical manifestations, imaging characteristics and mechanism of MMD-induced MSIH have not yet been elucidated. In order to improve the understanding on such cases, the present study described a rare case of MSIH caused by MMD. A 40-year-old female patient with no history of hypertension or diabetes mellitus experienced a sudden headache followed by coma. Cranial computed tomography (CT) examination revealed MSIH in the left frontal area, temporal lobe and basal ganglia. CT angiography and digital subtraction angiography examinations revealed typical characteristics of MMD. Subsequent to excluding disorders of the blood system and blood coagulation, we concluded that the present case of MSIH was caused by MMD. Hematoma evacuation and decompressive craniectomy were performed with satisfactory results. In addition, after reviewing previous MSIH cases in the literature, potential mechanisms of MMD-mediated MSIH were considered. In conclusion, MMD should be considered as a possible cause of MSIH during diagnosis and treatment. MMD can lead to pathological changes in the fragility of small arteries; therefore, rupture and hemorrhage at one site may induce a transient increase in blood pressure, causing the rupture of small arteries at other sites, and thus leading to MSIH. Hematoma evacuation and decompression should be conducted in selective cases of MMD-induced MSIH in order to achieve a good prognosis. PMID:27588064

  8. 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.

  9. Simultaneous multiple view high resolution surface geometry acquisition using structured light and mirrors.

    PubMed

    Basevi, Hector R A; Guggenheim, James A; Dehghani, Hamid; Styles, Iain B

    2013-03-25

    Knowledge of the surface geometry of an imaging subject is important in many applications. This information can be obtained via a number of different techniques, including time of flight imaging, photogrammetry, and fringe projection profilometry. Existing systems may have restrictions on instrument geometry, require expensive optics, or require moving parts in order to image the full surface of the subject. An inexpensive generalised fringe projection profilometry system is proposed that can account for arbitrarily placed components and use mirrors to expand the field of view. It simultaneously acquires multiple views of an imaging subject, producing a cloud of points that lie on its surface, which can then be processed to form a three dimensional model. A prototype of this system was integrated into an existing Diffuse Optical Tomography and Bioluminescence Tomography small animal imaging system and used to image objects including a mouse-shaped plastic phantom, a mouse cadaver, and a coin. A surface mesh generated from surface capture data of the mouse-shaped plastic phantom was compared with ideal surface points provided by the phantom manufacturer, and 50% of points were found to lie within 0.1mm of the surface mesh, 82% of points were found to lie within 0.2mm of the surface mesh, and 96% of points were found to lie within 0.4mm of the surface mesh. PMID:23546107

  10. Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

    PubMed Central

    Tuncbag, Nurcan; Braunstein, Alfredo; Pagnani, Andrea; Huang, Shao-Shan Carol; Chayes, Jennifer; Borgs, Christian; Zecchina, Riccardo

    2013-01-01

    Abstract Signaling and regulatory networks are essential for cells to control processes such as growth, differentiation, and response to stimuli. Although many “omic” data sources are available to probe signaling pathways, these data are typically sparse and noisy. Thus, it has been difficult to use these data to discover the cause of the diseases and to propose new therapeutic strategies. We overcome these problems and use “omic” data to reconstruct simultaneously multiple pathways that are altered in a particular condition by solving the prize-collecting Steiner forest problem. To evaluate this approach, we use the well-characterized yeast pheromone response. We then apply the method to human glioblastoma data, searching for a forest of trees, each of which is rooted in a different cell-surface receptor. This approach discovers both overlapping and independent signaling pathways that are enriched in functionally and clinically relevant proteins, which could provide the basis for new therapeutic strategies. Although the algorithm was not provided with any information about the phosphorylation status of receptors, it identifies a small set of clinically relevant receptors among hundreds present in the interactome. PMID:23383998

  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. 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.

  13. 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.

  14. All set, indeed! N2pc components reveal simultaneous attentional control settings for multiple target colors.

    PubMed

    Grubert, Anna; Eimer, Martin

    2016-08-01

    To study whether top-down attentional control processes can be set simultaneously for different visual features, we employed a spatial cueing procedure to measure behavioral and electrophysiological markers of task-set contingent attentional capture during search for targets defined by 1 or 2 possible colors (one-color and two-color tasks). Search arrays were preceded by spatially nonpredictive color singleton cues. Behavioral spatial cueing effects indicative of attentional capture were elicited only by target-matching but not by distractor-color cues. However, when search displays contained 1 target-color and 1 distractor-color object among gray nontargets, N2pc components were triggered not only by target-color but also by distractor-color cues both in the one-color and two-color task, demonstrating that task-set nonmatching items attracted attention. When search displays contained 6 items in 6 different colors, so that participants had to adopt a fully feature-specific task set, the N2pc to distractor-color cues was eliminated in both tasks, indicating that nonmatching items were now successfully excluded from attentional processing. These results demonstrate that when observers adopt a feature-specific search mode, attentional task sets can be configured flexibly for multiple features within the same dimension, resulting in the rapid allocation of attention to task-set matching objects only. (PsycINFO Database Record

  15. Multiparameter Analysis-Based Electrochemiluminescent Assay for Simultaneous Detection of Multiple Biomarker Proteins on a Single Interface.

    PubMed

    Liang, Wenbin; Fan, Chenchen; Zhuo, Ying; Zheng, Yingning; Xiong, Chengyi; Chai, Yaqin; Yuan, Ruo

    2016-05-01

    Electrochemiluminescent (ECL) assay with high sensitivity has been considered as one of the potential strategies to simultaneously detect multiple biomarker proteins. However, it was essential, but full of challenges, to overcome the limitation caused by cross reactions among different ECL indicators. Herein, the multiparameter analysis of ECL-potential signals demonstrated by multivariate linear algebraic equations was first employed in the simultaneous ECL assay to realize multiple detection of biomarker proteins on a single interface. Additionally, owing to the exponential amplification of self-synthesized nucleotide dendrimer by hybridization chain reaction (HCR) and rolling circle amplification (RCA), the developed simultaneous ECL assay showed improved sensitivity and satisfactory accuracy for the detection of N-terminal of the prohormone brain natriuretic peptide (BNPT) and cardiac troponin I (cTnI). Furthermore, a self-designed magnetic beads-based flow system was also employed to improve the feasibility and analysis speed of the simultaneous ECL assay. Importantly, the proposed strategy enabled simultaneous detection of multiple biomarker proteins simply, which could be readily expanded for the multiplexed estimation of various kinds of proteins and nucleotide sequence also, revealing a new avenue for early disease diagnosis with higher efficiency. PMID:27064937

  16. Improving the efficiency of lepidopteran pest detection and surveillance: constraints and opportunities for multiple-species trapping.

    PubMed

    Brockerhoff, Eckehard G; Suckling, D Maxwell; Roques, Alain; Jactel, Hervé; Branco, Manuela; Twidle, Andrew M; Mastro, Victor C; Kimberley, Mark O

    2013-01-01

    Surveillance using attractants for invasive species can allow early detection of new incursions and provide decision support to response programs. Simultaneous trapping for multiple species, by baiting traps with several lures, is expected to increase the number of species that can be targeted in surveillance programs and improve the cost-effectiveness without affecting surveillance coverage. We tested this hypothesis by choosing four potential forest and urban lepidopteran pest species that are present in Europe but not yet in New Zealand and many other countries. We deployed traps in central and southern Europe with single lures or all possible species combinations (up to four lures per trap). There was only limited interference, apparently due to trap saturation, but no evidence for interspecific repellency among lures for gypsy moth, Lymantria dispar, fall webworm, Hyphantria cunea, pine processionary moth, Thaumetopoea pityocampa, and pine shoot moth, Rhyacionia buoliana. To assess what factors may be important in species compatibility/suitability for multiple-species trapping, we combined our results with those of previous studies conducted by the United States Department of Agriculture. For 75 combinations of pheromones, tested singly or in combination, 19 % showed no effect on trap catch for any of the species tested. In the other cases, either one or both species showed a reduction in trap catch. However, few lure combinations caused complete or nearly complete suppression. For most combinations, catches were still sufficiently high for detection purposes. Species from the same superfamily exhibited more interference than more distantly related species. Together, these results suggest that there are opportunities to improve the range of exotic pests under surveillance, at little additional cost, by multiple-species trapping for which compatibility has been demonstrated. PMID:23254379

  17. Simultaneous multiple-depths en-face optical coherence tomography using multiple signal excitation of acousto-optic deflectors.

    PubMed

    Zurauskas, Mantas; Rogers, John; Podoleanu, Adrian Gh

    2013-01-28

    We present a novel low-coherence interferometer configuration, equipped with acousto-optic deflectors that can be used to simultaneously acquire up to eight time domain optical coherence tomography en-face images. The capabilities of the configuration are evaluated in terms of depth resolution, signal to noise ratio and crosstalk. Then the configuration is employed to demonstrate simultaneous en-face optical coherence tomography imaging at five different depths in a specimen of armadillidium vulgare. PMID:23389175

  18. A case of fungal keratitis and onychomycosis simultaneously infected by Trichophyton species

    PubMed Central

    2014-01-01

    Background Fungal keratitis is difficult to treat that can result in corneal blindness requiring penetrating keratoplasty and in fungal endothalmitis. We report a case of fungal keratitis and onychomycosis simultaneously infected by Trichophyton. Case presentation A 77-year old male presented with ocular pain, conjunctival injection, and severe loss of vision in his left eye. His best corrected visual acuity was hand movements in the left eye, and slit-lamp examination showed a corneal ulcer with feathery margin and hypopyon. Bacterial and fungal smear/culture showed no organism, and there was no improvement in spite of treatment with topical fortified 5% cefazolin and 2% tobramycin. Trichophyton species was identified by repeated cultures. We found onychomycosis on the patient’s foot, where the same fungal species were identified. Regimen was changed to topical itraconazole and systemic intravenous itraconazole. No clinical improvement was observed, so therapeutic penetrating keratoplasty and cryotherapy was done with continuation of antifungal therapy. The graft was clear at postoperative 1 month and no evidence of recurrence was found. Conclusion It is important to identify the pathogen of keratitis because early identification of pathogen causing keratitis provides the appropriate treatment in early phase of keratitis. It is necessary to search for other fungal skin infections such as onychomycosis and athelete’s foot considering the fungal keratitis following skin infection. In addition, fungal skin infection including onychomycosis should be treated for prevention of fungal keratitis as soon as possible. PMID:25015110

  19. DictyBase 2013: integrating multiple Dictyostelid species.

    PubMed

    Basu, Siddhartha; Fey, Petra; Pandit, Yogesh; Dodson, Robert; Kibbe, Warren A; Chisholm, Rex L

    2013-01-01

    dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past 3 years, dictyBase has taken significant strides toward becoming a genome portal for the whole Amoebozoa clade. In its latest release, dictyBase has scaled up to host multiple Dictyostelids, including Dictyostelium purpureum [Sucgang, Kuo, Tian, Salerno, Parikh, Feasley, Dalin, Tu, Huang, Barry et al.(2011) (Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol., 12, R20)], Dictyostelium fasciculatum and Polysphondylium pallidum [Heidel, Lawal, Felder, Schilde, Helps, Tunggal, Rivero, John, Schleicher, Eichinger et al. (2011) (Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res., 21, 1882-1891)]. The new release includes a new Genome Browser with RNAseq expression, interspecies Basic Local Alignment Search Tool alignments and a unified Basic Local Alignment Search Tool search for cross-species comparisons.

  20. 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

  1. A Platform for Rapid, Quantitative Assessment of Multiple Drug Combinations Simultaneously in Solid Tumors In Vivo

    PubMed Central

    Grenley, Marc O.; Casalini, Joseph R.; Tretyak, Ilona; Ditzler, Sally H.; Thirstrup, Derek J.; Frazier, Jason P.; Pierce, Daniel W.; Carleton, Michael; Klinghoffer, Richard A.

    2016-01-01

    While advances in high-throughput screening have resulted in increased ability to identify synergistic anti-cancer drug combinations, validation of drug synergy in the in vivo setting and prioritization of combinations for clinical development remain low-throughput and resource intensive. Furthermore, there is currently no viable method for prospectively assessing drug synergy directly in human patients in order to potentially tailor therapies. To address these issues we have employed the previously described CIVO platform and developed a quantitative approach for investigating multiple combination hypotheses simultaneously in single living tumors. This platform provides a rapid, quantitative and cost effective approach to compare and prioritize drug combinations based on evidence of synergistic tumor cell killing in the live tumor context. Using a gemcitabine resistant model of pancreatic cancer, we efficiently investigated nine rationally selected Abraxane-based combinations employing only 19 xenografted mice. Among the drugs tested, the BCL2/BCLxL inhibitor ABT-263 was identified as the one agent that synergized with Abraxane® to enhance acute induction of localized apoptosis in this model of human pancreatic cancer. Importantly, results obtained with CIVO accurately predicted the outcome of systemic dosing studies in the same model where superior tumor regression induced by the Abraxane/ABT-263 combination was observed compared to that induced by either single agent. This supports expanded use of CIVO as an in vivo platform for expedited in vivo drug combination validation and sets the stage for performing toxicity-sparing drug combination studies directly in cancer patients with solid malignancies. PMID:27359113

  2. Multi-color femtosecond source for simultaneous excitation of multiple fluorescent proteins in two-photon fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Liu, Tzu-Ming; Wu, Juwell; Horton, Nicholas G.; Lin, Charles P.; Xu, Chris

    2013-02-01

    Simultaneous imaging of cells expressing multiple fluorescent proteins (FPs) is of particular interest in applications such as mapping neural circuits, tracking multiple immune cell populations, etc. To visualize both in vivo and ex vivo tissue morphology and physiology at a cellular level deep within scattering tissues, two-photon fluorescence microscopy (2PM) is a powerful tool that has found wide applications. However, simultaneous imaging of multiple FPs with 2PM is greatly hampered by the lack of proper ultrafast lasers offering multi-color femtosecond pulses, each targeting the two-photon absorption peak of a different FP. Here we demonstrate simultaneous two-photon fluorescence excitation of RFP, YFP, and CFP in human melanoma cells engineered to express a "rainbow" pallet of colors, using a novel fiber-based source with energetic, three-color femtosecond pulses. The three-color pulses, centered at 775 nm, 864 nm and 950 nm, are obtained through second harmonic generation of the 1550 nm pump laser and SHG of the solitons at 1728 nm and 1900 nm generated through soliton self-frequency shift (SSFS) of the pump laser in a large-mode-area (LMA) fiber. The resulting wavelengths are well matched to the two-photon absorption peaks of the three FPs for efficient excitation. Our results demonstrate that multi-color femtosecond pulse generation using SSFS and a turn-key, fiber-based femtosecond laser can fulfill the requirements for simultaneous imaging of multiple FPs in 2PM, opening new opportunities for a wide range of biological applications where non-invasive, high-resolution imaging of multiple fluorescent indicators is required.

  3. Non-intrusive, on-line, simultaneous multi-species impurity monitoring in hydrogen using LIBS

    NASA Astrophysics Data System (ADS)

    Eseller, K. E.; Yueh, F.-Y.; Singh, J. P.

    2011-03-01

    Laser-induced breakdown spectroscopy (LIBS) has been evaluated for on-line, simultaneous multi-species impurity monitoring in hydrogen. A miniature spectrometer with spectral coverage of 620-800 nm and a gated detection system with spectral coverage of 40 nm were both used to record LIBS spectra from the spark produced in sample gas by a frequency-doubled Nd YAG laser. The effect of pressure on detecting the impurity (e.g., nitrogen, argon, and oxygen) in hydrogen was studied. LIBS spectra with different impurity levels of nitrogen, argon, and oxygen were recorded, and the intensity of the spectral lines of Ar, O, N, and H observed were used to form calibration plots for impurity measurement. The limits of detection (LODs) for oxygen, argon, and nitrogen in hydrogen were estimated from the calibration obtained with both the gated and ungated detection. The hydrogen impurity measurements based on the ungated miniature system show reliable and reproductive results. But the LODs with this system are about four times higher than the LODs obtained with a gated detection system in this work.

  4. 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

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

    PubMed

    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

  6. 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...

  7. 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

  8. Performance of a demonstration system for simultaneous laser beacon tracking and low data rate optical communications with multiple platforms

    NASA Astrophysics Data System (ADS)

    Short, R. C.; Cosgrove, M.; Clark, D. L.; Oleski, P.

    1991-06-01

    The ability of a system based on a high-speed area array detector to simultaneously track and receive data from multiple low-power optical communication beacons is demonstrated. Specifically, the MOCTR POC system has achieved tracking precision of order 0.1 pixel with 2.7 picowatts, the minimum beacon power for the assumed system architecture; a data rate of 1 kbps with BER of order 1 to 10 x 10 exp -5, readily correctable with forward error correction; tracking and communication with simulated maximum earth background in the detector FOV; and simultaneous tracking of asynchronously modulated beacons. Areas needed to be addressed before an operational system can be implemented include reduction in size, weight and power, the demonstration of independent acquisition of multiple beacons, and the implementation of a full tracking algorithm in firmware.

  9. 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. PMID:16114540

  10. CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae.

    PubMed

    Mans, Robert; van Rossum, Harmen M; Wijsman, Melanie; Backx, Antoon; Kuijpers, Niels G A; van den Broek, Marcel; Daran-Lapujade, Pascale; Pronk, Jack T; van Maris, Antonius J A; Daran, Jean-Marc G

    2015-03-01

    A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast strain construction in yeast and explores their potential for simultaneous introduction of multiple genetic modifications. An open-source tool (http://yeastriction.tnw.tudelft.nl) is presented for identification of suitable Cas9 target sites in S. cerevisiae strains. A transformation strategy, using in vivo assembly of a guideRNA plasmid and subsequent genetic modification, was successfully implemented with high accuracies. An alternative strategy, using in vitro assembled plasmids containing two gRNAs, was used to simultaneously introduce up to six genetic modifications in a single transformation step with high efficiencies. Where previous studies mainly focused on the use of CRISPR/Cas9 for gene inactivation, we demonstrate the versatility of CRISPR/Cas9-based engineering of yeast by achieving simultaneous integration of a multigene construct combined with gene deletion and the simultaneous introduction of two single-nucleotide mutations at different loci. Sets of standardized plasmids, as well as the web-based Yeastriction target-sequence identifier and primer-design tool, are made available to the yeast research community to facilitate fast, standardized and efficient application of the CRISPR/Cas9 system.

  11. CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae

    PubMed Central

    Mans, Robert; van Rossum, Harmen M.; Wijsman, Melanie; Backx, Antoon; Kuijpers, Niels G.A.; van den Broek, Marcel; Daran-Lapujade, Pascale; Pronk, Jack T.; van Maris, Antonius J.A.; Daran, Jean-Marc G.

    2015-01-01

    A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast strain construction in yeast and explores their potential for simultaneous introduction of multiple genetic modifications. An open-source tool (http://yeastriction.tnw.tudelft.nl) is presented for identification of suitable Cas9 target sites in S. cerevisiae strains. A transformation strategy, using in vivo assembly of a guideRNA plasmid and subsequent genetic modification, was successfully implemented with high accuracies. An alternative strategy, using in vitro assembled plasmids containing two gRNAs, was used to simultaneously introduce up to six genetic modifications in a single transformation step with high efficiencies. Where previous studies mainly focused on the use of CRISPR/Cas9 for gene inactivation, we demonstrate the versatility of CRISPR/Cas9-based engineering of yeast by achieving simultaneous integration of a multigene construct combined with gene deletion and the simultaneous introduction of two single-nucleotide mutations at different loci. Sets of standardized plasmids, as well as the web-based Yeastriction target-sequence identifier and primer-design tool, are made available to the yeast research community to facilitate fast, standardized and efficient application of the CRISPR/Cas9 system. PMID:25743786

  12. 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. PMID:25497983

  13. 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.

  14. Simultaneous use of electrochemistry and chemiluminescence to detect reactive oxygen species produced by human neutrophils.

    PubMed

    Shleev, Sergey; Wetterö, Jonas; Magnusson, Karl-Eric; Ruzgas, Tautgirdas

    2008-12-01

    A novel approach for the simultaneous optical and electrochemical detection of biologically produced reactive oxygen species has been developed and applied. The set-up consists of a luminol-dependent chemiluminescence assay combined with two amperometric biosensors sensitive to superoxide anion radicals (O(2)(-)) and hydrogen peroxide (H(2)O(2)), respectively. The method permits direct, real-time in vitro determination of both extra- and intracellular O(2)(-) and H(2)O(2) produced by human neutrophil granulocytes. The rate of O(2)(-) production by stimulated neutrophils was calculated to about 10(-17)mol s(-1) per single cell. With inhibited NADPH oxidase, a distinct extracellular release of H(2)O(2) instead of O(2)(-) was obtained from stimulated neutrophils with the rate of about 3 x 10(-18)mol s(-1) per single cell. When the H(2)O(2) release was discontinued, fast H(2)O(2) utilisation was observed. Direct interaction with and possibly attachment of neutrophils to redox protein-modified gold electrodes, resulted in a spontaneous respiratory burst in the population of cells closely associated to the electrode surface. Hence, further stimulation of human neutrophils with a potent receptor agonist (fMLF) did not significantly increase the O(2)(-) sensitive amperometric response. By contrast, the H(2)O(2) sensitive biosensor, based on an HRP-modified graphite electrode, was able to reflect the bulk concentration of H(2)O(2), produced by stimulated neutrophils and would be very useful in modestly equipped biomedical research laboratories. In summary, the system would also be appropriate for assessment of several other metabolites in different cell types, and tissues of varying complexity, with only minor electrode modifications.

  15. Do siblings always form and evolve simultaneously? Testing the coevality of multiple protostellar systems through SEDs

    NASA Astrophysics Data System (ADS)

    Murillo, N. M.; van Dishoeck, E. F.; Tobin, J. J.; Fedele, D.

    2016-07-01

    Context. Multiplicity is common in field stars and among protostellar systems. Models suggest two paths of formation: turbulent fragmentation and protostellar disk fragmentation. Aims: We attempt to find whether or not the coevality frequency of multiple protostellar systems can help to better understand their formation mechanism. The coevality frequency is determined by constraining the relative evolutionary stages of the components in a multiple system. Methods: Spectral energy distributions (SEDs) for known multiple protostars in Perseus were constructed from literature data. Herschel PACS photometric maps were used to sample the peak of the SED for systems with separations ≥7″, a crucial aspect in determining the evolutionary stage of a protostellar system. Inclination effects and the surrounding envelope and outflows were considered to decouple source geometry from evolution. This together with the shape and derived properties from the SED was used to determine each system's coevality as accurately as possible. SED models were used to examine the frequency of non-coevality that is due to geometry. Results: We find a non-coevality frequency of 33 ± 10% from the comparison of SED shapes of resolved multiple systems. Other source parameters suggest a somewhat lower frequency of non-coevality. The frequency of apparent non-coevality that is due to random inclination angle pairings of model SEDs is 17 ± 0.5%. Observations of the outflow of resolved multiple systems do not suggest significant misalignments within multiple systems. Effects of unresolved multiples on the SED shape are also investigated. Conclusions: We find that one-third of the multiple protostellar systems sampled here are non-coeval, which is more than expected from random geometric orientations. The other two-thirds are found to be coeval. Higher order multiples show a tendency to be non-coeval. The frequency of non-coevality found here is most likely due to formation and enhanced by

  16. Tunable diode laser sensor for multiple species monitoring in harsh atmospheres

    NASA Astrophysics Data System (ADS)

    Von Drasek, William A.; Wehe, Shawn; Allen, Mark

    2004-03-01

    Energy intensive industries such as steel, aluminum, and glass require combustion processes that are characteristically at high temperature with high levels of particulate matter. Monitoring and control of these processes for improved efficiency, pollutant reduction, and product quality requires a sensor adaptable for such harsh environments. Traditional industrial monitoring relies on extractive sampling that requires frequent maintenance due to probe plugging or corrosion and routine calibration. In addition, capturing the temporal behavior of the process can be problematic with extractive sampling systems because of the slow response time associated with the sampling line lengths and slow response analyzers. To meet the demands of these harsh combustion processes the ideal sensor would perform in-situ process monitoring, require little or no maintenance and provide real-time process information The use of tunable diode lasers based on absorption monitoring overcomes many of the problems associated with conventional extractive sampling. However, the majority of industrial combustion processes will undergo temperature variations along with changes in the atmosphere oxidation or reducing state during normal operation. Therefore, temperature monitoring along with key combustion species monitoring that describes the atmosphere e.g., O2 and CO, is often necessary for optimal process control. The temperature is not only a useful parameter describing the state of the process, but is needed to accurately determine the species concentration since the absorption measured is dependent on temperature. To monitor both reducing and oxidizing combustion atmospheres in addition to gas temperature requires a diode laser system capable of multiple species monitoring. Here we describe an industrial prototype system operating in the near-infrared for simultaneous monitoring of O2 (.76 μm), CO (1.5 μm), H2O (1.5 μm) and gas temperature. The prototype system addresses the issues of

  17. 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

  18. Benign Paroxysmal Positional Vertigo with Simultaneous Involvement of Multiple Semicircular Canals

    PubMed Central

    Shim, Dae Bo; Song, Chang Eun; Jung, Eun Jung; Ko, Kyung Min; Park, Jin Woo

    2014-01-01

    Background and Objectives Benign paroxysmal positional vertigo (BPPV) generally involves a single semicircular canal (single canal BPPV) but it has been reported that more than one semicircular canal on either the same or the opposite side can be involved in 6.8-20% of the cases (multiple canal BPPV). In this study, the clinical characteristics of multiple canal BPPV were analyzed and compared to those of single canal BPPV. Materials and Methods Retrospective analysis was performed on 1054 consecutive patients diagnosed with BPPV. Multiple canal BPPV was diagnosed when the combination of typical nystagmus was provoked by the Dix-Hallpike and supine head roll tests. Canalith repositioning maneuver was performed sequentially starting with the semicircular canal causing more severe nystagmus or symptoms. Clinical characteristics and the treatment course were statistically compared between single canal BPPV and multiple canal BPPV. Results Among the 1054 patients, single canal BPPV was diagnosed in 1005 patients (95.4%) while multiple canal BPPV was diagnosed in 49 patients (4.6%). BPPV involving semicircular canals on the same side was more common (79.6%) than BPPV with bilateral involvement. The most common combination of the involved canals was ipsilateral posterior and horizontal semicircular canals (63.3%). Multiple canal BPPV was significantly more associated with underlying otologic diseases, especially labyrinthitis. Multiple canal BPPV required more treatment sessions and longer duration of treatment to achieve resolution of nystagmus and symptoms. Conclusions As all cases of multiple canal BPPV were treated successfully although a longer duration of treatment and more treatment sessions were required compared to single canal BPPV, the results of our study could aid in making an accurate diagnosis and providing appropriate treatment of multiple canal BPPV. PMID:25558406

  19. Intraguild predation reduces redundancy of predator species in multiple predator assemblage.

    PubMed

    Griffen, Blaine D; Byers, James E

    2006-07-01

    1. Interference between predator species frequently decreases predation rates, lowering the risk of predation for shared prey. However, such interference can also occur between conspecific predators. 2. Therefore, to understand the importance of predator biodiversity and the degree that predator species can be considered functionally interchangeable, we determined the degree of additivity and redundancy of predators in multiple- and single-species combinations. 3. We show that interference between two invasive species of predatory crabs, Carcinus maenas and Hemigrapsus sanguineus, reduced the risk of predation for shared amphipod prey, and had redundant per capita effects in most multiple- and single-species predator combinations. 4. However, when predator combinations with the potential for intraguild predation were examined, predator interference increased and predator redundancy decreased. 5. Our study indicates that trophic structure is important in determining how the effects of predator species combine and demonstrates the utility of determining the redundancy, as well as the additivity, of multiple predator species.

  20. Intraguild predation reduces redundancy of predator species in multiple predator assemblage.

    PubMed

    Griffen, Blaine D; Byers, James E

    2006-07-01

    1. Interference between predator species frequently decreases predation rates, lowering the risk of predation for shared prey. However, such interference can also occur between conspecific predators. 2. Therefore, to understand the importance of predator biodiversity and the degree that predator species can be considered functionally interchangeable, we determined the degree of additivity and redundancy of predators in multiple- and single-species combinations. 3. We show that interference between two invasive species of predatory crabs, Carcinus maenas and Hemigrapsus sanguineus, reduced the risk of predation for shared amphipod prey, and had redundant per capita effects in most multiple- and single-species predator combinations. 4. However, when predator combinations with the potential for intraguild predation were examined, predator interference increased and predator redundancy decreased. 5. Our study indicates that trophic structure is important in determining how the effects of predator species combine and demonstrates the utility of determining the redundancy, as well as the additivity, of multiple predator species. PMID:17009759

  1. 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. PMID:10231768

  2. 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.

  3. Simultaneous imaging of multiple focal planes using a two-photon scanning microscope

    NASA Astrophysics Data System (ADS)

    Amir, W.; Carriles, R.; Hoover, E. E.; Planchon, T. A.; Durfee, C. G.; Squier, J. A.

    2007-06-01

    Despite all the advances in nonlinear microscopy, all existing instruments are constrained to obtain images of one focal plane at a time. In this Letter we demonstrate a two-photon absorption fluorescence scanning microscope capable of imaging two focal planes simultaneously. This is accomplished by temporally demultiplexing the signal coming from two focal volumes at different sample depths. The scheme can be extended to three or more focal planes.

  4. A new multiple-stage electrocoagulation process on anaerobic digestion effluent to simultaneously reclaim water and clean up biogas.

    PubMed

    Liu, Zhiguo; Stromberg, David; Liu, Xuming; Liao, Wei; Liu, Yan

    2015-03-21

    A new multiple-stage treatment process was developed via integrating electrocoagulation with biogas pumping to simultaneously reclaim anaerobic digestion effluent and clean up biogas. The 1st stage of electrocoagulation treatment under the preferred reaction condition led to removal efficiencies of 30%, 81%, 37% and >99.9% for total solids, chemical oxygen demand, total nitrogen and total phosphorus, respectively. Raw biogas was then used as a reactant and pumped into the effluent to simultaneously neutralize pH of the effluent and remove H2S in the biogas. The 2nd stage of electrocoagulation treatment on the neutralized effluent showed that under the selected reaction condition, additional 60% and 10% of turbidity and chemical oxygen demand were further removed. The study concluded a dual-purpose approach for the first time to synergistically combine biogas purification and water reclamation for anaerobic digestion system, which well addresses the downstream challenges of anaerobic digestion technology.

  5. A new multiple-stage electrocoagulation process on anaerobic digestion effluent to simultaneously reclaim water and clean up biogas.

    PubMed

    Liu, Zhiguo; Stromberg, David; Liu, Xuming; Liao, Wei; Liu, Yan

    2015-03-21

    A new multiple-stage treatment process was developed via integrating electrocoagulation with biogas pumping to simultaneously reclaim anaerobic digestion effluent and clean up biogas. The 1st stage of electrocoagulation treatment under the preferred reaction condition led to removal efficiencies of 30%, 81%, 37% and >99.9% for total solids, chemical oxygen demand, total nitrogen and total phosphorus, respectively. Raw biogas was then used as a reactant and pumped into the effluent to simultaneously neutralize pH of the effluent and remove H2S in the biogas. The 2nd stage of electrocoagulation treatment on the neutralized effluent showed that under the selected reaction condition, additional 60% and 10% of turbidity and chemical oxygen demand were further removed. The study concluded a dual-purpose approach for the first time to synergistically combine biogas purification and water reclamation for anaerobic digestion system, which well addresses the downstream challenges of anaerobic digestion technology. PMID:25540943

  6. 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

    2016-07-01

    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. PMID:27244346

  7. 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

  8. Generating multiple wavelengths, simultaneously, in a Ti:sapphire ring laser with a ramp-hold-fire seeding technique

    NASA Astrophysics Data System (ADS)

    Moore, Thomas Z.; Anderson, F. Scott

    2012-03-01

    The ability to simultaneously produce pulsed laser output over multiple discrete wavelengths can mitigate many of the timing and jitter issues associated with the use of multiple laser systems. In addition, Fourier-transform limited laser output on every pulse is required for many applications such as with pump-probe detection, non-linear frequency mixing, differential absorption lidar (DIAL), and resonance ionization. As a matter of practice, such lasers need to be capable of operating within uncontrolled or noisy environments. We report on a novel Ti:sapphire ring laser that has been developed to produce Fourier-transform limited 20-ns laser pulses at multiple discrete wavelengths, simultaneously, utilizing a Ramp-Hold-Fire (RHF) seeding technique. Resonance of the seed light is achieved by using a KD*P crystal to modify the phase of the light circulating within the slave oscillator cavity where the fast response of the crystal results in a seeding technique that is immune to noise throughout the acoustic regime.

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

    PubMed

    Kamigaki, Akane; Nito, Kazumasa; 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

  10. 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

    2016-07-01

    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.

  11. Simultaneous quantitative detection of multiple tumor markers with a rapid and sensitive multicolor quantum dots based immunochromatographic test strip.

    PubMed

    Wang, Chunying; Hou, Fei; Ma, Yicai

    2015-06-15

    A novel multicolor quantum dots (QDs) based immunochromatographic test strip (ICTS) was developed for simultaneous quantitative detection of multiple tumor markers, by utilizing alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) as models. The immunosensor could realize simultaneous quantitative detection of tumor markers with only one test line and one control line on the nitrocellulose membrane (NC membrane) due to the introduction of multicolor QDs. In this method, a mixture of mouse anti-AFP McAb and mouse anti-CEA McAb was coated on NC membrane as test line and goat anti-mouse IgG antibody was coated as control line. Anti-AFP McAb-QDs546 conjugates and anti-CEA McAb-QDs620 conjugates were mixed and applied to the conjugate pad. Simultaneous quantitative detection of multiple tumor markers was achieved by detecting the fluorescence intensity of captured QDs labels on test line and control line using a test strip reader. Under the optimum conditions, AFP and CEA could be detected as low as 3 ng/mL and 2 ng/mL in 15 min with a sample volume of 80 μL, and no obvious cross-reactivity was observed. The immunosensor was validated with 130 clinical samples and in which it exhibited high sensitivity (93% for AFP and 87% for CEA) and specificity (94% for AFP and 97% for CEA). The immunosensor also demonstrated high recoveries (87.5-113% for AFP and 90-97.3% for CEA) and low relative standard deviations (RSDs) (2.8-6.2% for AFP and 4.9-9.6% for CEA) when testing spiked human serum. This novel multicolor QDs based ICTS provides an easy and rapid, simultaneous quantitative detecting strategy for point-of-care testing of tumor markers. PMID:25562743

  12. Multi-color quantum dot-based fluorescence immunoassay array for simultaneous visual detection of multiple antibiotic residues in milk.

    PubMed

    Song, Erqun; Yu, Mengqun; Wang, Yunyun; Hu, Weihua; Cheng, Dan; Swihart, Mark T; Song, Yang

    2015-10-15

    Antibiotic residues, which are among the most common contaminants in animal-based food products such as milk, have become a significant public health concern. Here, we combine a multicolor quantum dot (QD)-based immunofluorescence assay and an array analysis method to achieve simultaneous, sensitive and visual detection of streptomycin (SM), tetracycline (TC), and penicillin G (PC-G) in milk. Antibodies (Abs) for SM, TC and PC-G were conjugated to QDs with different emission wavelengths (QD 520 nm, QD 565 nm and QD 610 nm) to serve as detection probes (QD-Ab). Then a direct competitive fluorescent immunoassay was performed in antigen-coated microtiter plate wells for simultaneous qualitative and quantitative detection of SM, TC, and PC-G residues, based on fluorescence of the QD-Ab probes. The linear ranges for SM, TC and PC-G were 0.01-25 ng/mL, 0.01-25 ng/mL and 0.01-10 ng/mL, respectively, with detection limit of 5 pg/mL for each of them. Based on fluorescence of the QD-Ab probes, residues of the three antibiotics were determined visually and simultaneously. Compared with a commercial enzyme-linked immunosorbent assay kit, our method could achieve simultaneous analysis of multiple target antibiotics in multiple samples in a single run (high-throughput analysis) and improved accuracy and sensitivity for analysis of residues of the three antibiotics in authentic milk samples. This new analytical tool can play an important role in ameliorating the negative impact of the residual antibiotics on human health and the ecosystem. PMID:26002016

  13. 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. PMID:26365329

  14. 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.

  15. Propylation technique for the simultaneous determination of tetraalkyllead and ionic alkyllead species by gas chromatography/atomic absorption spectrometry

    SciTech Connect

    Radojevic, M.; Allen, A.; Rapsomanikis, S.; Harrison, R.M.

    1986-03-01

    The only technique capable of simultaneous determination of R/sub 4/Pb and ionic alkyllead compounds involves extraction into an organic solvent in the presence of sodium diethyldithiocarbamate (NaDDTC) and derivatizations of ionic species to R/sub 4/Pb forms using a butylating Grignard reagent (n-butylmagnesium chloride) followed by GC/AAS analysis. This technique has been applied to many environmental samples with some degree of success, although for many less polluted samples even greater sensitivity is required. In this communication the authors present an improved and novel derivatization technique of the simultaneous determination R/sub 4/Pb and ionic alkyllead species involving extraction into n-hexane and propylation to the tetraalkyllead form using propylmagnesium chloride with GC/electrothermal AAS analysis. The technique is compared to the previously reported butylation method, and procedures of extract concentration are investigated. 11 references, 2 figures, 1 table.

  16. Simultaneous observation of VHF radio wave transmission anomaly propagated beyond line of site prior to earthquakes in multiple sites

    NASA Astrophysics Data System (ADS)

    Yamashita, H.; Mogi, T.; Moriya, T.; Takada, M.; Morisada, M.

    2010-12-01

    The VHF radio wave transmission anomalies propagated beyond line of site prior to earthquakes (M>4), (hereafter termed EQ-echo) have been observed more than 20 times from 2004 at the Erimo observatory (ERM) in Hokkaido, Northern Japan. A statistical relationship between magnitude of preceding earthquake and total duration time of the EQ-echo has been proposed (Moriya et al.2009). To confirm a region where the EQ-echo simultaneously observed for each earthquake, we installed another 3 observatory with approximately 5 km spacing in the surroundings of ERM. The EQ-echoes have been observed simultaneously at two observatories prior to four earthquakes since 2008. The initial time and duration of each EQ echo were same time in several cases but different at some minutes each other in other cases. The wave forms of the EQ-echoes were similar in both records. In the Fuyushima observatory (FYS, 10km away from ERM) , three-way antennas were installed at every 120 degree to detect an arrival direction of EQ-echoes. Simultaneous observations of EQ-echoes at ERM and FYS for the preceding EQ (M=4.7) that occurred in the Hidaka mountains revealed that this EQ-echo came from direction of the epicenter based on the FYS observation and this direction was consistent with that of EQ-echo observed simultaneously in ERM. Although some of simultaneous observed EQ-echoes were observed in same time completely at both observatories, but some of them were with time rag of duration of each EQ-echo between multiple observed sites. We discussed what these time rags mean by considering possibilities of moving of scattering objects, generation of a radio duct, and so on, as in response to this fact.

  17. 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.

  18. Research of robot simultaneous localization and mapping in multiple mobile robot system

    NASA Astrophysics Data System (ADS)

    Huang, Yanbiao; Yang, Yimin; He, Qicheng; Zhang, Xuexi

    2007-11-01

    It needs an exact global map when the multiple mobile robot system making decisions in the task allocation and action control, but each robot can only obtain the information which surrounds him nearby and often lose the information at long bowls, in other words, the robot can not build a comprehensive global map of whole field. Aimed at these problems, a multi-sensor data fusion subsystem was designed and added into the multiple mobile robot system. The experiment shows the whole system's fault-tolerance capability and identifying capability are both enhanced evidently.

  19. Frequency Modulation Multiplexing for Simultaneous Detection of Multiple Gases by use of Wavelength Modulation Spectroscopy with Diode Lasers.

    PubMed

    Oh, D B; Paige, M E; Bomse, D S

    1998-04-20

    Modulation frequency multiplexing provides a straightforward method, analogous to television or radio broadcasting, for performing simultaneous detection of multiple gases by use of wavelength modulation spectroscopy with diode lasers. When fiber-optic coupled lasers are used, our approach guarantees that all beams transit the same optical path and impinge on the same detector. Each laser is modulated at a different frequency and the detector output is processed by a set of lock-in amplifiers, one for each laser, to measure the absorbance encountered by each laser. PMID:18273185

  20. 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.

  1. Simultaneous determination of multiple androgens in mice organs with liquid chromatography tandem mass spectrometry.

    PubMed

    Soh, Shu Fang; Yin, Xiaoxing; Sun, Jiaquan; Li, Jun; Yong, Eu Leong; Wei, Qunli; Gong, Yinhan

    2015-11-10

    Prostate cancer (PCa) is the most commonly diagnosed cancer in men worldwide. It is essentially dependent on potent androgens, such as testosterone (T) and dihydrotestosterone (DHT). The precursors of T and DHT, which includes androstenedione (A4) and dihydroepiandrosterone (DHEA), and also the metabolites of DHT, 5α-androstane-3α,17β-diol (3α-Diol) and 5α-androstane-3β,17β-diol (3β-Diol) are able to affect the development of PCa. Therefore, it is important to simultaneously determine all these key androgens. This study aims to develop and validate an LC-MS/MS quantification method to simultaneously detect and quantify the six related androgens, including T, DHT, A4, DHEA, 3α-Diol, and 3β-Diol in limited sample volume. The sample preparation involved liquid extraction with methyl tert-butyl ether (MTBE), following by chemical derivatisation with hydroxylamine. The limits of quantitation for T, DHT, A4, and DHEA were 0.05nM and 3α-Diol and 3β-Diol were 0.5nM with S/N ratio of at least 5:1 by using 100μL samples.

  2. 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.

  3. 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…

  4. 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.

  5. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26284487

  7. Simultaneous Analysis of Multiple Promoters: An Application of the PC-GW Binary Vector Series.

    PubMed

    Dalal, Jyoti

    2016-01-01

    With the advances in the field of synthetic biology, there is an increasing demand for multi-gene cloning technologies. Molecular cloning to generate multi-gene constructs can be performed by restriction digestion, or by recombination-based cloning strategies such as Gateway(®). This chapter details cloning, transformation, and selection procedures involved in generation of multi-gene expressing transgenic plants. Methods are described for cloning five distinct promoter-reporter fusion constructs into the PC-GW-BAR vector (from the PC-GW vector series) using Gateway(®) technology and meganuclease sites. Further, transformation and selection methods are described for the biofuel crop Camelina sativa from the Brassicaceae family. These methods would be constructive toward generating multi-gene expressing plants for simultaneous expression analysis of five promoters in a short time period. PMID:27557769

  8. Simultaneous determination of multiple constituents in real beer samples of different origins by capillary zone electrophoresis.

    PubMed

    Cortacero-Ramírez, Sonia; Segura-Carretero, Antonio; Cruces-Blanco, Carmen; Romero-Romero, Maria Luisa; Fernández-Gutiérrez, Alberto

    2004-11-01

    Simultaneous determination of alcohols, amines, amino acids, flavonoids, and purine and pyrimidine bases in bottled beer samples directly without any pre-treatment was carried out by capillary zone electrophoresis with diode-array detection. Electrolyte conditions such as pH, composition and concentration of the buffer, working voltage and type and time of injection were checked. The best separation of the cited analytes was achieved in 70 mM sodium borate solution and pH 10.25. The detection limits were from 2.1 to 5.6 mg L(-1) for the 18 compounds studied. The developed method is rapid, sensitive and quantitative and has been applied to seven types of international bottled beers of different origins bought locally. PMID:15490130

  9. 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.

  10. 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.

  11. Characterisation of a cryostat using simultaneous, single-beam multiple-surface laser vibrometry

    NASA Astrophysics Data System (ADS)

    Kissinger, Thomas; Charrett, Thomas O. H.; James, Stephen W.; Adams, Alvin; Twin, Andrew; Tatam, Ralph P.

    2016-06-01

    A novel range-resolved interferometric signal processing technique that uses sinusoidal optical frequency modulation is applied to multi-surface vibrometry, demonstrating simultaneous optical measurements of vibrations on two surfaces using a single, collimated laser beam, with a minimum permissible distance of 3.5 cm between surfaces. The current system, using a cost-effective laser diode and a fibre-coupled, downlead insensitive setup, allows an interferometric fringe rate of up to 180 kHz to be resolved with typical displacement noise levels of 8 pm . Hz-0 5. In this paper, the system is applied to vibrometry measurements of a table-top cryostat, with concurrent measurements of the optical widow and the sample holder target inside. This allows the separation of common-mode vibrations of the whole cryostat from differential vibrations between the window and the target, allowing any resonances to be identified.

  12. Simultaneous photoacoustic detection of multiple compounds based on orthogonal functions stimulation

    NASA Astrophysics Data System (ADS)

    Starecki, T.

    2008-01-01

    The paper presents a concept of photoacoustic measurements based on use of two different light wavelengths which intensities are modulated with sine waves of the same frequency but with phase difference of 90 degrees. Resultant photoacoustic signal is of the same frequency, but its amplitude and phase depends on the absorption at both wavelengths. Taking into consideration that sine and cosine are orthogonal functions, and having measured amplitude of the photoacoustic signal and its phase referred to the phase of the stimulating light modulation, it is possible to retrieve both components corresponding to sine and cosine modulation. As a result, the method can be applied to simultaneous detection of two compounds. An important advantage of the method is that it can be comfortably used with high Q-factor cells.

  13. A semiconductor metasurface with multiple functionalities: A polarizing beam splitter with simultaneous focusing ability

    SciTech Connect

    Lee, Jun Hyung; Jin Jung, Myoung; Ho Song, Seok; Woong Yoon, Jae; Magnusson, Robert; Kyun Hong, Jong

    2014-06-09

    We propose a semiconductor metasurface that simultaneously performs two independent functions: focusing and polarization filtering. The wavefronts of the reflected and transmitted light distributions are precisely manipulated by spatial parametric variation of a subwavelength thin-film Si grating, which inherently possesses polarization filtering properties. We design a 12-μm-wide metasurface containing only nineteen Si grating ridges. Under a 10-μm-wide unpolarized Gaussian beam incidence at wavelength of 1.55 μm, the resulting device shows promising theoretical performance with high power efficiency exceeding 80% and polarization extinction ratio of ∼10 dB with focal spot diameters near 1–2 μm.

  14. 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.

  15. Simultaneous HPLC determination of multiple components in a commercial cosmetic cream.

    PubMed

    Sottofattori, E; Anzaldi, M; Balbi, A; Tonello, G

    1998-10-01

    A high-performance liquid chromatographic method for the simultaneous determination of magnesium ascorbyl phosphate (I), imidazolidinylurea (II), a mixture of methyl-(III), ethyl-(IV), propyl-(V), butyl-(VI) parabens dissolved in phenoxyethanol, and ascorbyl palmitate (VII), was studied by using a cyano-propyl column and a methanol gradient at 220 and 240 nm. Calibration curves were found to be linear in the 0.05-5 mg ml(-1) range (compounds I, II, VII) and 0.9-160 mg ml(-1) (compounds III-VI). Linear regression analysis of the data demonstrates the efficacy of the method in terms of precision and accuracy. An extraction method is developed and validated in order to apply this chromatographic method to a commercial cosmetic cream. The precision of this method, calculated as the relative standard deviation (RSD) of the recoveries (1.57-2.21%) was excellent for all compounds I-VII.

  16. 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.

  17. 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

  18. 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

  19. Rapid Screening for Flavone C-Glycosides in the Leaves of Different Species of Bamboo and Simultaneous Quantitation of Four Marker Compounds by HPLC-UV/DAD

    PubMed Central

    Wang, Jin; Yue, Yong-de; Jiang, Hao; Tang, Feng

    2012-01-01

    A strategy for analyzing flavone C-glucosides in the leaves of different species of bamboo was developed. Firstly, the flavone C-glycosides were extracted from the bamboo leaves (51 species in 17 genera) with methanol and chromatographed on silica gel 60 plates in automatic developing chamber (ADC2), and a qualitative survey using simple derivatization steps with the NP reagent was carried out. The flavone C-glycosides were found in 40 of 51 species of bamboo examined. Secondly, an HPLC method with photodiode array and multiple wavelength detector was optimized and validated for the simultaneous determination of flavone C-glycosides, including isoorientin, isovitexin, orientin, and vitexin in the leaves of three species of bamboo and the flavone C-glycosides were confirmed by LC/MS. The optimized HPLC method proved to be linear in the concentration range tested (0.2–100 μg/mL, r2 ≥ 0.9997), precise (RSD ≤ 1.56%), and accurate (88–106%). The concentration ranges of isoorientin, isovitexin, orientin, and vitexin in three bamboo leaves samples were 1.00–2.78, 0–0.31, 0–0.07, and 0.20–0.68 mg/g, respectively. The proposed method was validated to be simple and reliable and can be a tool for quality control of bamboo leaf extract or its commercial products. PMID:22654910

  20. Multiple routes to asexuality in an aphid species.

    PubMed

    Delmotte, F; Leterme, N; Bonhomme, J; Rispe, C; Simon, J C

    2001-11-22

    Cyclical parthenogens, including aphids, are important models for studying the evolution of sex. However, little is known about transitions to asexuality in aphids, although the mode of origin of asexual lineages has important consequences for their level of genetic diversity, ecological adaptability and the outcome of competition with their sexual relatives. Thus, we surveyed nuclear, mitochondrial and biological data obtained on cyclical and obligate parthenogens of the bird cherry-oat aphid, Rhopalosiphum padi (L), to investigate the frequency of transitions from sexuality to permanent asexuality. Many instances of asexual lineages retaining the ability to produce males are known in aphids, so particular attention was paid to the existence of occasional matings between females from sexual lineages and males produced by asexual lineages, which have the potential to produce new asexual lineages. Phylogenetic inference based on microsatellite and mitochondrial data indicates at least three independent origins of asexuality in R. padi, yielding the strongest evidence to date for multiple origins of asexuality in an aphid. Moreover, several lines of evidence demonstrate that transitions to asexuality result from two mechanisms: a complete spontaneous loss of sex and repeated gene flow from essentially asexual lineages into sexual ones.

  1. 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

  2. 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

  3. 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

  4. Simultaneous occurrence of Hodgkin's lymphoma and multiple myeloma: A case report and review of the literature

    PubMed Central

    HUANG, CHEN; ZHAO, GUIMIN; WANG, LIANJING; ZHANG, HUICHAO; WU, XIAOLIN; ZHANG, MINGZENG; MA, RUIJUAN; WANG, LING; LIU, YUEPING; LIU, LIHONG

    2016-01-01

    Hodgkin's lymphoma (HL) is a type of hematological neoplasm that generally appears alone, with a low incidence. The majority of cases histopathologically present as B-cell lymphoma. Multiple myeloma (MM) is defined as the neoplastic proliferation of a single clone of plasma cells producing a monoclonal immunoglobulin (Ig). The coexistence of HL and MM is rare, however, the present study reports such a case. On May 31, 2012, a 45-year-old man was diagnosed with HL, stage III, 31 months ago. At the same time, computed tomography and magnetic resonance imaging showed osteolytic lesions, a significant increase in IgA λ chains, and multiple myeloma cells on bone marrow aspiration. Following 8 cycles of chemotherapy, the patient received maintenance treatment with thalidomide and dexamethasone. During 2 years of follow-up, the patient has maintained a complete response for HL and a stable disease state for MM. The coexistence of HL and MM is rare. Further study of such cases may explain the associations between these two tumors and aid the production of effective treatment options. PMID:27313755

  5. 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.

  6. 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

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

    PubMed

    Klinghoffer, Richard A; Bahrami, S Bahram; Hatton, Beryl 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

    2015-04-22

    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

  8. Generation of Benzyne Species from Diphenylphosphoryl Derivatives: Simultaneous Exchange of Three Functional Groups.

    PubMed

    Gorobets, Evgueni; Parvez, Masood; Derksen, Darren J; Keay, Brian A

    2016-06-13

    Interaction of (2-diphenylphosphoryl-3-iodo-4-methoxy-phenyl) methanol with NaH in DMF at ambient temperature results in the generation of benzyne intermediates that can be trapped by furan or DMF. Trapping with DMF forms 3-(dimethylaminomethyl)-2-hydroxy-6-methoxybenzaldehyde demonstrating the simultaneous exchange of three functionalities in a single step. The presence of the alkoxy substituent adjacent to iodine is critical for high regioselectivity addition of DMF. The corresponding bromide or triflate can be used in place of the iodide with equal efficiency. This methodology was used to synthesize the reported structure of gigasol and leading to a structural reassignment of this biscoumarin natural product.

  9. DNA-based Simultaneous Identification of Three Terminalia Species Targeting Adulteration

    PubMed Central

    Sharma, Sonal; Shrivastava, Neeta

    2016-01-01

    Background: Various parts of three Terminalia species, namely, Terminalia arjuna (stem bark), Terminalia bellirica (fruit), and Terminalia chebula (fruit) are widely known for their therapeutic principles and other commercial values. However, stem bark of T. bellirica and T. chebula along with Terminalia tomentosa are reported as adulterants of T. arjuna. Correct botanical identification is very critical for safe and effective herbal drugs. DNA-based identification approaches are advancing the conventional methods and sometime proved more beneficial. Objective: The purpose of the study was to develop polymerase chain reaction (PCR) method using internal transcribed spacer (ITS) region to ascertain the identity of T. arjuna herbal material as well as detection of mixing of other three Terminalia species. Materials and Methods: DNA from stem barks samples were isolated and subjected to ITS region amplification and sequencing. Sequences were compared for polymorphic nucleotides determination to develop species-specific primers. Final primers were selected on the basis of in silico analysis and experimentally validated. PCR assays for botanical identification of Terminalia species were developed. Sensitivity testing and assay validation were also performed. Results: The PCR assays developed for Terminalia species were resulted in definite amplicons of the corresponding species. No cross-reactivity of the primers was detected. Sensitivity was found enough to amplify as low as 2 ng of DNA. Mixing of DNA in various concentrations for validation also proved the sensitivity of assay to detect original botanicals in the mixture. The developed methods proved very specific and sensitive to authenticate Arjuna bark to develop evidence-based herbal medicines. SUMMARY Internal transcribed spacer-based species-specific polymerase chain reaction.(PCR) assays were developed to authenticate Terminalia arjuna stem bark and to identify substitution/adulteration of Terminalia bellirica

  10. Simultaneous saccharification and fermentation of hemicellulose to butanol by a non-sporulating Clostridium species.

    PubMed

    Li, Tinggang; He, Jianzhong

    2016-11-01

    Production of lignocellulosic butanol has drawn increasing attention. However, currently few microorganisms can produce biofuels, particularly butanol, from lignocellulosic biomass via simultaneous saccharification and fermentation. Here we report discovery of a wild-type, mesophilic Clostridium sp. strain MF28 that ferments xylan to produce butanol (up to 3.2g/L) without the addition of saccharolytic enzymes and without any chemical pretreatments. Application of selective pressure from 2-deoxy-d-glucose facilitated isolation of strain MF28, which exhibits inactivation of genes (gid and ccp genes) responsible for carbon catabolite repression, thus allowing strain MF28 to simultaneously ferment a combination of glucose (30g/L), xylose (15g/L), and arabinose (15g/L) to produce 11.9g/L of butanol. Strain MF28 possesses several unique features: (i) non-sporulating, (ii) no acetone/ethanol, (iii) complete hemicellulose-binding enzymatic domain, and (iv) absence of carbon catabolite repression. These unique characteristics demonstrate the industrial potential of strain MF28 for cost-effective biofuel generation from lignocellulosic biomass. PMID:27513648

  11. Simultaneous saccharification and fermentation of hemicellulose to butanol by a non-sporulating Clostridium species.

    PubMed

    Li, Tinggang; He, Jianzhong

    2016-11-01

    Production of lignocellulosic butanol has drawn increasing attention. However, currently few microorganisms can produce biofuels, particularly butanol, from lignocellulosic biomass via simultaneous saccharification and fermentation. Here we report discovery of a wild-type, mesophilic Clostridium sp. strain MF28 that ferments xylan to produce butanol (up to 3.2g/L) without the addition of saccharolytic enzymes and without any chemical pretreatments. Application of selective pressure from 2-deoxy-d-glucose facilitated isolation of strain MF28, which exhibits inactivation of genes (gid and ccp genes) responsible for carbon catabolite repression, thus allowing strain MF28 to simultaneously ferment a combination of glucose (30g/L), xylose (15g/L), and arabinose (15g/L) to produce 11.9g/L of butanol. Strain MF28 possesses several unique features: (i) non-sporulating, (ii) no acetone/ethanol, (iii) complete hemicellulose-binding enzymatic domain, and (iv) absence of carbon catabolite repression. These unique characteristics demonstrate the industrial potential of strain MF28 for cost-effective biofuel generation from lignocellulosic biomass.

  12. ESCRT-0 Assembles as a Heterotetrameric Complex on Membranes and Binds Multiple Ubiquitinylated Cargoes Simultaneously*

    PubMed Central

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

    2011-01-01

    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. PMID:21193406

  13. Does multiple hosts mean multiple parasites? Population genetic structure of Schistosoma japonicum between definitive host species.

    PubMed

    Wang, T P; Shrivastava, J; Johansen, M V; Zhang, S Q; Wang, F F; Webster, J P

    2006-10-01

    Multi-host parasites, those capable of infecting more than one species of host, are responsible for the majority of all zoonotic, emerging or persistent human and animal diseases and are considered one of the major challenges for the biomedical sciences in the 21st century. We characterized the population structure of the multi-host parasite Schistosoma japonicum in relation to its definitive host species by genotyping miracidia collected from humans and domestic animals across five villages around the Yangtze River in Anhui Province, mainland China, using microsatellite markers. High levels of polymorphisms were observed and two main genetic clusters were identified which separated water buffalo, cattle and humans from goats, pigs, dogs and cats. We thereby believe that we present the first evidence of definitive host-based genetic variation in Schistosoma japonicum which has important epidemiological, evolutionary, medical and veterinary implications.

  14. First molecular evidence of the simultaneous human infection with two species of Echinococcus granulosus sensu lato: Echinococcus granulosus sensu stricto and Echinococcus canadensis.

    PubMed

    Oudni-M'rad, Myriam; M'rad, Selim; Ksia, Amine; Lamiri, Rachida; Mekki, Mongi; Nouri, Abdellatif; Mezhoud, Habib; Babba, Hamouda

    2016-03-01

    Cystic echinococcosis is a widespread zoonotic parasitic disease especially in Tunisia which is one of the most endemic countries in the Mediterranean area. The etiological agent, Echinococcus granulosus sensu lato, implies dogs and other canids as definitive hosts and different herbivore species as intermediate hosts. Human contamination occurs during the consumption of parasite eggs passed in the environment through canid feces. Hydatid cysts coming from a child operated for multiple echinococcosis were collected and analyzed in order to genotype and to obtain some epidemiological molecular information. Three targets, ribosomal DNA ITS1 fragment, NADH dehydrogenase subunit 1 (nad1), and mitochondrial cytochrome c oxydase subunit 1 (CO1) genes, were amplified and analyzed by RFLP and sequencing approach. This study presents the first worldwide report in human of a simultaneous infection with Echinococcus granulosus sensu stricto (genotype G1) and Echinococcus canadensis (genotype G6) species. This is also the first report of the presence of E. canadensis in the Tunisian population which argues in favor of a greater importance of this species in human infestation in Tunisia than previously believed.

  15. 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

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

    PubMed

    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

  17. 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. PMID:25454124

  18. 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.

  19. Simultaneous and spectroscopic redox molecular imaging of multiple free radical intermediates using dynamic nuclear polarization-magnetic resonance imaging.

    PubMed

    Hyodo, Fuminori; Ito, Shinji; Yasukawa, Keiji; Kobayashi, Ryoma; Utsumi, Hideo

    2014-08-01

    Redox reactions that generate free radical intermediates are essential to metabolic processes. However, their intermediates can produce reactive oxygen species, which may promote diseases related to oxidative stress. We report here the use of dynamic nuclear polarization-magnetic resonance imaging (DNP-MRI) to conduct redox molecular imaging. Using DNP-MRI, we obtained simultaneous images of free radical intermediates generated from the coenzyme Q10 (CoQ10), flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) involved in the mitochondrial electron transport chain as well as the radicals derived from vitamins E and K1. Each of these free radicals was imaged in real time in a phantom comprising a mixture of free radicals localized in either lipophilic or aqueous environments. Changing the frequency of electron spin resonance (ESR) irradiation also allowed each of the radical species to be distinguished in the spectroscopic images. This study is the first to report the spectroscopic DNP-MRI imaging of free radical intermediates that are derived from endogenous species involved in metabolic processes.

  20. A multiple RT-PCR assay for simultaneous detection and differentiation of latent viruses and apscarviroids in apple trees.

    PubMed

    Hao, Lu; Xie, Jipeng; Chen, Shanyi; Wang, Shaojie; Gong, Zhuoqun; Ling, Kai-Shu; Guo, Liyun; Fan, Zaifeng; Zhou, Tao

    2016-08-01

    Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), and Apple stem pitting virus (ASPV) are three latent viruses frequently occurring in apple trees worldwide. In field orchards, these viruses are frequently found in a mixed infection with viroids in the genus Apscarviroid, including Apple scar skin viroid, and Apple dimple fruit viroid. Together these viruses and viroids could cause serious damage to apple fruit production worldwide. Rapid and efficient detection methods are pivotal to identify and select the virus-free propagation material for healthy apple orchard management. In this study a multiplex Reverse Transcription-PCR (RT-PCR) was developed and optimized for simultaneous detection and differentiation of the three latent viruses and apscarviroids. With newly designed specific primers for ACLSV, ASGV, APSV, and EF-1α (as an internal control), and a pair of degenerate primers for apscarviroids, optimized parameters for multiplex RT-PCR were determined. The resulting PCR products from each target virus and viroid could be easily identified because their product sizes differ by at least a 100bp. The multiplex RT-PCR method is expected to detect different variants of the viruses as the test results showed that a variety of isolates from different regions in China gave positive results. To the best of our knowledge, this multiplex RT-PCR assay is the first to simultaneously detect multiple viruses and viroids infecting apple trees in a single reaction tube. This assay, therefore, offers a useful tool for routine certification and quarantine programs. PMID:27054889

  1. 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.

  2. A multiple RT-PCR assay for simultaneous detection and differentiation of latent viruses and apscarviroids in apple trees.

    PubMed

    Hao, Lu; Xie, Jipeng; Chen, Shanyi; Wang, Shaojie; Gong, Zhuoqun; Ling, Kai-Shu; Guo, Liyun; Fan, Zaifeng; Zhou, Tao

    2016-08-01

    Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), and Apple stem pitting virus (ASPV) are three latent viruses frequently occurring in apple trees worldwide. In field orchards, these viruses are frequently found in a mixed infection with viroids in the genus Apscarviroid, including Apple scar skin viroid, and Apple dimple fruit viroid. Together these viruses and viroids could cause serious damage to apple fruit production worldwide. Rapid and efficient detection methods are pivotal to identify and select the virus-free propagation material for healthy apple orchard management. In this study a multiplex Reverse Transcription-PCR (RT-PCR) was developed and optimized for simultaneous detection and differentiation of the three latent viruses and apscarviroids. With newly designed specific primers for ACLSV, ASGV, APSV, and EF-1α (as an internal control), and a pair of degenerate primers for apscarviroids, optimized parameters for multiplex RT-PCR were determined. The resulting PCR products from each target virus and viroid could be easily identified because their product sizes differ by at least a 100bp. The multiplex RT-PCR method is expected to detect different variants of the viruses as the test results showed that a variety of isolates from different regions in China gave positive results. To the best of our knowledge, this multiplex RT-PCR assay is the first to simultaneously detect multiple viruses and viroids infecting apple trees in a single reaction tube. This assay, therefore, offers a useful tool for routine certification and quarantine programs.

  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. 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.

  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. PMID:24310857

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Genomic resources for multiple species in the Drosophila ananassae species group.

    PubMed

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa. PMID:23639891

  11. Genomic resources for multiple species in the Drosophila ananassae species group

    PubMed Central

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa. PMID:23639891

  12. 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. PMID:27499736

  13. 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).

  14. 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

  15. Acute simultaneous multiple lacunar infarcts as the initial presentation of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy.

    PubMed

    Hsiao, Cheng-Tsung; Chen, Yun-Chung; Liu, Yo-Tsen; Soong, Bing-Wen; Lee, Yi-Chung

    2015-07-01

    Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an adult-onset, dominantly inherited small-vessel disease of the brain caused by NOTCH3 mutations and characterized by recurrent subcortical infarctions, dementia, migraine with aura, and mood disturbance. We report a patient with unusual presentation of CADASIL with acute simultaneous multiple subcortical lacunar infarcts as the first manifestation. A 69-year-old man developed confusion, drowsiness, right hemiparesis, and slurred speech following orthopedic surgeries. Brain magnetic resonance imaging revealed diffuse leukoencephalopathy and multiple acute subcortical lacunar infarcts. Brain magnetic resonance angiography, echocardiography and 24-hour electrocardiography were unremarkable. The symptoms improved quickly after treatment with fluid hydration and antiplatelet agent, and his consciousness and mentality totally recovered within 3 days. The NOTCH3 genetic testing showed a heterozygous missense mutation, c.1630C>T (p. Arg544Cys). The experience in this case suggests that brain imaging is important in managing postoperative confusion, and any patient with diffuse leukoencephalopathy of unknown etiology may need to be tested for NOTCH3 mutations. Surgery is an important factor of encephalopathy and acute infarction in individuals with NOTCH3 mutations. Comprehensive presurgical evaluations and proactive perioperative precautions to avoid dehydration and anemia are necessary for patients with CADASIL who are about to receive anesthesia and surgery. PMID:25959358

  16. 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

  17. 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). PMID:26414950

  18. Simultaneous species concentration and temperature measurements using laser induced breakdown spectroscopy with direct spectrum matching

    NASA Astrophysics Data System (ADS)

    McGann, Brendan J.

    Laser induced breakdown spectroscopy (LIBS) is used to simultaneously measure hydrocarbon fuel concentration and temperature in high temperature, high speed, compressible, and reacting flows, a regime in which LIBS has not been done previously. Emission spectra from the plasma produced from a focused laser pulse is correlated in the combustion region of a model scramjet operating in supersonic wind tunnel. A 532 nm Nd:YAG laser operating at 10 Hz is used to induce break-down. The emissions are captured during a 10 ns gate time approximately 75 ns after the first arrival of photons at the measurement location in order to minimize the measurement uncertainty in the turbulent, compressible, high-speed, and reacting environment. Three methods of emission detection are used and a new backward scattering direction method is developed that is beneficial in reducing the amount of optical access needed to perform LIBS measurements. Measurements are taken in the model supersonic combustion and the ignition process is shown to be highly dependent on fuel concentration and gas density as well as combustion surface temperature, concentration gradient, and flow field. Direct spectrum matching method is developed and used for quantitative measurements. In addition, a comprehensive database of spectra covering the fuel concentrations and gas densities found in the wind tunnel of Research Cell 19 at Wright Patterson Air Force Base is created which can be used for further work.

  19. A PCR-RFLP method for the simultaneous differentiation of three Entamoeba species.

    PubMed

    Fontecha, Gustavo A; García, Kimberly; Rueda, María Mercedes; Sosa-Ochoa, Wilfredo; Sánchez, Ana Lourdes; Leiva, Byron

    2015-01-01

    Amoebiasis caused by Entamoeba histolytica continues to be one of the most common parasitic diseases in the developing world. Despite its relevance, due to the lack of accurate diagnostic methods, the true clinical and public health importance of this parasite remains uncertain. The aim of this study was to develop a new diagnostic tool to differentiate E.histolytica from the morphologically undistinguishable E.dispar and E.moshkovskii. We developed a specific, fast and simple PCR-RFLP method that was able to accurately differentiate experimentally-obtained restriction patterns from the three Entamoeba species. This new method could prove useful for clinical and epidemiological purposes.

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

    DOE PAGESBeta

    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

  1. 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

    2013-04-01

    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.

  2. 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.

  3. Simultaneous positive and negative density-dependent dispersal in a colonial bird species.

    PubMed

    Kim, Sin-Yeon; Torres, Roxana; Drummond, Hugh

    2009-01-01

    Contradictory patterns of density-dependent animal dispersal can potentially be reconciled by integrating the conspecific attraction hypothesis with the traditional competition hypothesis. We propose a hypothesis that predicts a U-shaped relationship between density and both natal and breeding dispersal distance. Using 10 years of observations on a breeding colony of the Blue-footed Booby (Sula nebouxii), the hypothesis was confirmed by documenting simultaneous positive and negative density-dependent dispersal distances in natal and breeding dispersal of males and breeding dispersal of females within the colony. Point-pattern analyses demonstrated that the breeding sites of Blue-footed Boobies were highly aggregated in all years within a large study area, and aggregation presumably resulted in heterogeneity in patch density throughout the colony. As predicted, at moderate to high densities, dispersal distances showed positive density dependence, with individuals moving to lower density patches. In contrast, at low to moderate densities, dispersal distances showed negative density dependence, with individuals moving to higher density patches. In both sexes of the 1994 cohort, the higher the mean density in patches used by an individual over the long term (up to age 11 years), the fewer fledglings it produced. A positive effect of density on long-term reproductive success was not detected, possibly because birds that failed during pair formation or incubation were not sampled. Density of conspecifics may be an important influence on habitat selection of breeders, and dispersal may tend to carry individuals to patches where pair formation opportunities are better and negative effects of competition on reproductive success are reduced.

  4. Simultaneous positive and negative density-dependent dispersal in a colonial bird species.

    PubMed

    Kim, Sin-Yeon; Torres, Roxana; Drummond, Hugh

    2009-01-01

    Contradictory patterns of density-dependent animal dispersal can potentially be reconciled by integrating the conspecific attraction hypothesis with the traditional competition hypothesis. We propose a hypothesis that predicts a U-shaped relationship between density and both natal and breeding dispersal distance. Using 10 years of observations on a breeding colony of the Blue-footed Booby (Sula nebouxii), the hypothesis was confirmed by documenting simultaneous positive and negative density-dependent dispersal distances in natal and breeding dispersal of males and breeding dispersal of females within the colony. Point-pattern analyses demonstrated that the breeding sites of Blue-footed Boobies were highly aggregated in all years within a large study area, and aggregation presumably resulted in heterogeneity in patch density throughout the colony. As predicted, at moderate to high densities, dispersal distances showed positive density dependence, with individuals moving to lower density patches. In contrast, at low to moderate densities, dispersal distances showed negative density dependence, with individuals moving to higher density patches. In both sexes of the 1994 cohort, the higher the mean density in patches used by an individual over the long term (up to age 11 years), the fewer fledglings it produced. A positive effect of density on long-term reproductive success was not detected, possibly because birds that failed during pair formation or incubation were not sampled. Density of conspecifics may be an important influence on habitat selection of breeders, and dispersal may tend to carry individuals to patches where pair formation opportunities are better and negative effects of competition on reproductive success are reduced. PMID:19294928

  5. A Nonparametric Lower Bound for the Number of Species Shared by Multiple Communities

    PubMed Central

    Pan, H.-Y.; Chao, Anne; Foissner, Wilhelm

    2010-01-01

    In biological and ecological statistical inference, it is practically useful to provide a lower bound for species richness in a community. Chao (1984, 1989) derived a nonparametric lower bound for species richness in a single community. However, there have been no lower bounds proposed in the literature for the number of species shared by multiple communities. Based on sample species abundance or replicated incidence records from each of the N communities, we derive in this article a nonparametric approach to constructing a lower bound for the number of species shared by N (N ≥ 2) communities. The approach is valid for all types of species abundance distributions (for abundance data) or species detection probabilities (for replicated incidence data). Variance estimators for the proposed lower bounds are obtained by using typical asymptotic theory. Simulation results are reported to examine the performance of the lower bounds. Replicated incidence data of ciliate species collected in three areas from Namibia, southwest Africa, are used for illustration. We also briefly discuss the application of the proposed method to estimate the size of a shared population (i.e., the number of individuals in the intersection of multiple populations) based on capture-recapture data from each population. PMID:20622922

  6. 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.

  7. Molecular Evidence for High Frequency of Multiple Paternity in a Freshwater Shrimp Species Caridina ensifera

    PubMed Central

    Yue, Gen Hua; Chang, Alex

    2010-01-01

    Background Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve. Methodology/Principal Findings In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers. Conclusions/Significance Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species. PMID:20856862

  8. Simultaneous determination of multiple sesquiterpenes in Curcuma wenyujin herbal medicines and related products with one single reference standard.

    PubMed

    Zhu, Jing-Jing; An, Yue-Wei; Hu, Guang; Yin, Guo-Ping; Zhang, Qi-Wei; Wang, Zhi-Min

    2013-02-06

    Some Curcuma species are widely used as herbal medicines. Sesquiterpenes are their important bioactive compounds and their quantitative analysis is generally accomplished by gas chromatography (GC) or high performance liquid chromatography (HPLC), but the instability and high cost of some sesquiterpene reference standards have limited their application. It is necessary to find a practicable means to control the quality of herbal medicines. Using one stable component contained in Curcuma species to determine multiple analogues should be a practical option. In this study, a simple HPLC method for determination of sesquiterpenes using relative response factors (RRFs) has been developed. The easily available and stable active component curdione was selected as the reference compound for calculating the RRFs of the other eight sesquiterpenes, including zedoarondiol (Zedo), isozedoarondiol (Isoz), aerugidiol (Aeru), (4S,5S)-(+)-germacrone-4,5-epoxide (Epox), curcumenone (Curc), neocurdione (Neoc), germacrone (Germ) and furanodiene (Fura). Their RRFs against curdione were between 0.131-1.301, with a good reproducibility. By using the RRFs, the quantification of sesquiterpenes in Curcuma wenyujin herbal medicines and related products was carried out. The method is especially useful for the determination of (4S,5S)-(+)-germacrone-4,5-epoxide, curcumenone, germacrone and furanodiene, which often are regarded as the principle components in Curcuma species, but unstable when were purified. It is an ideal means to analyze the components for which reference standards are not readily available.

  9. Influence of predator density on nonindependent effects of multiple predator species.

    PubMed

    Griffen, Blaine D; Williamson, Tucker

    2008-02-01

    Interactions between multiple predator species are frequent in natural communities and can have important implications for shared prey survival. Predator density may be an important component of these interactions between predator species, as the frequency of interactions between species is largely determined by species density. Here we experimentally examine the importance of predator density for interactions between predator species and subsequent impacts on prey. We show that aggressive interactions between the predatory shore crabs Carcinus maenas and Hemigrapsus sanguineus increased with predator density, yet did not increase as fast as negative interactions between conspecifics. At low density, interactions between conspecific and heterospecific predators had similar inhibitory impacts on predator function, whereas conspecific interference was greater than interference from heterospecifics at high predator density. Thus the impact of conspecific interference at high predator density was sufficient in itself that interactions with a second predator species had no additional impact on per capita predation. Spatial and temporal variability in predator density is a ubiquitous characteristic of natural systems that should be considered in studies of multiple predator species.

  10. Transport of a multiple-ion species plasma in a collisionless regime in a bumpy torus

    SciTech Connect

    Hastings, D.E.

    1984-04-01

    The ion neoclassical transport coefficient in a multiple ion species plasma in a bumpy torus are calculated in the low-collisionality regime. The poloidal electric field is calculated self-consistently with collisional electrons. Both pitch angle and energy scattering are included in the collision operator.

  11. 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.

  12. 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

    2016-07-01

    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.

  13. 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

    2016-07-01

    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. PMID:27302315

  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. 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.

  16. 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. PMID:27543138

  17. 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.

  18. Development of multiplexed bead arrays for the simultaneous detection of nucleic acid from multiple viruses in bat samples.

    PubMed

    Boyd, Victoria; Smith, Ina; Crameri, Gary; Burroughs, Amy L; Durr, Peter A; White, John; Cowled, Christopher; Marsh, Glenn A; Wang, Lin-Fa

    2015-10-01

    Virus surveillance of wildlife populations is important for identifying, monitoring, and predicting the emergence of pathogens that pose a potential threat to animal and human health. Bats are identified as important wildlife hosts of many viruses capable of causing fatal human disease, including members of the henipaviruses, coronaviruses, rhabdoviruses and filoviruses. As global warming and habitat change are thought to impact upon pathogen transmission dynamics and increase the risk of spillover, virus surveillance in bat populations remains a significant component of efforts to improve the prediction and control of potential future disease outbreaks caused by bat-borne viruses. In this study we have developed two fluid bead array assays containing customized panels that target multiple bat-borne viruses. These assays detect up to 11 viral RNA's simultaneously in urine samples collected from wild bat populations in Australia and Bangladesh. The assays developed show high specificity for the target viruses and the analytical sensitivity compares favorably to qRT-PCR. These assays enhance the ability to monitor multi-pathogen dynamics and identify patterns of virus shedding from bat populations, thus informing key approaches to outbreak response and control.

  19. Three-dimensional reconstruction of tumor microvasculature: simultaneous visualization of multiple components in paraffin-embedded tissue.

    PubMed

    Gijtenbeek, J M M; Wesseling, P; Maass, C; Burgers, L; van der Laak, J A W M

    2005-01-01

    Three-dimensional (3D) visualization of microscopic structures may provide useful information about the exact 3D configuration, and offers a useful tool to examine the spatial relationship between different components in tissues. A promising field for 3D investigation is the microvascular architecture in normal and pathological tissue, especially because pathological angiogenesis plays a key role in tumor growth and metastasis formation. This paper describes an improved method for 3D reconstruction of microvessels and other microscopic structures in transmitted light microscopy. Serial tissue sections were stained for the endothelial marker CD34 to highlight microvessels and corresponding images were selected and aligned. Alignment of stored images was further improved by automated non-rigid image registration, and automated segmentation of microvessels was performed. Using this technique, 3D reconstructions were produced of the vasculature of the normal brain. Also, to illustrate the complexity of tumor vasculature, 3D reconstructions of two brain tumors were performed: a hemangioblastoma and a glioblastoma multiforme. The possibility of multiple component visualization was shown in a 3D reconstruction of endothelium and pericytes of normal cerebellar cortex and a hemangioblastoma using alternate staining for CD34 and alpha-smooth muscle actin in serial sections, and of a GBM using immunohistochemical double staining. In conclusion, the described 3D reconstruction procedure provides a promising tool for simultaneous visualization of microscopic structures. PMID:16328157

  20. 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.

  1. Simultaneous Screening of Multiple Mutations by Invader Assay Improves Molecular Diagnosis of Hereditary Hearing Loss: A Multicenter Study

    PubMed Central

    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. PMID:22384008

  2. Comparative performance evaluation of multi-metal resistant fungal strains for simultaneous removal of multiple hazardous metals.

    PubMed

    Dey, Priyadarshini; Gola, Deepak; Mishra, Abhishek; Malik, Anushree; Kumar, Peeyush; Singh, Dileep Kumar; Patel, Neelam; von Bergen, Martin; Jehmlich, Nico

    2016-11-15

    In the present study, five fungal strains viz., Aspergillus terreus AML02, Paecilomyces fumosoroseus 4099, Beauveria bassiana 4580, Aspergillus terreus PD-17, Aspergillus fumigatus PD-18, were screened for simultaneous multimetal removal. Highest metal tolerance index for each individual metal viz., Cd, Cr, Cu, Ni, Pb and Zn (500mg/L) was recorded for A. fumigatus for the metals (Cd, 0.72; Cu, 0.72; Pb, 1.02; Zn, 0.94) followed by B. bassiana for the metals (Cd, 0.56; Cu, 0.14; Ni, 0.29; Zn, 0.85). Next, the strains were exposed to multiple metal mixture (Cd, Cr, Cu, Ni, Pb and Zn) of various concentrations (6, 12, 18, 30mg/L). Compared to other strains, B. bassiana and A. fumigatus had higher cube root growth (k) constants indicating their better adaptability to multi metal stress. After 72h, multimetal accumulation potential of B. bassiana (26.94±0.07mg/L) and A. fumigatus (27.59±0.09mg/L) were higher than the other strains at initial multimetal concentration of 30mg/L. However, considering the post treatment concentrations of individual metals in multimetal mixture (at all the tested concentrations), A. fumigatus demonstrated exceptional performance and could bring down the concentrations of Cd, Cu, Ni, Pb and Zn below the threshold level for irrigation prescribed by Food and Agriculture Organization (FAO).

  3. A Multiple Degree of Freedom Lower Extremity Isometric Device to Simultaneously Quantify Hip, Knee, and Ankle Torques.

    PubMed

    Sánchez, Natalia; Acosta, Ana Maria; Stienen, Arno H A; Dewald, Julius P A

    2015-09-01

    Characterization of the joint torque coupling strategies used in the lower extremity to generate maximal and submaximal levels of torque at either the hip, knee, or ankle is lacking. Currently, there are no available isometric devices that quantify all concurrent joint torques in the hip, knee, and ankle of a single leg during maximum voluntary torque generation. Thus, joint-torque coupling strategies in the hip, knee, and concurrent torques at ankle and/or coupling patterns at the hip and knee driven by the ankle have yet to be quantified. This manuscript describes the design, implementation, and validation of a multiple degree of freedom, lower extremity isometric device (the MultiLEIT) that accurately quantifies simultaneous torques at the hip, knee, and ankle. The system was mechanically validated and then implemented with two healthy control individuals and two post-stroke individuals to test usability and patient acceptance. Data indicated different joint torque coupling strategies used by both healthy individuals. In contrast, data showed the same torque coupling patterns in both post-stroke individuals, comparable to those described in the clinic. Successful implementation of the MultiLEIT can contribute to the understanding of the underlying mechanisms responsible for abnormal movement patterns and aid in the design of therapeutic interventions.

  4. Comparative performance evaluation of multi-metal resistant fungal strains for simultaneous removal of multiple hazardous metals.

    PubMed

    Dey, Priyadarshini; Gola, Deepak; Mishra, Abhishek; Malik, Anushree; Kumar, Peeyush; Singh, Dileep Kumar; Patel, Neelam; von Bergen, Martin; Jehmlich, Nico

    2016-11-15

    In the present study, five fungal strains viz., Aspergillus terreus AML02, Paecilomyces fumosoroseus 4099, Beauveria bassiana 4580, Aspergillus terreus PD-17, Aspergillus fumigatus PD-18, were screened for simultaneous multimetal removal. Highest metal tolerance index for each individual metal viz., Cd, Cr, Cu, Ni, Pb and Zn (500mg/L) was recorded for A. fumigatus for the metals (Cd, 0.72; Cu, 0.72; Pb, 1.02; Zn, 0.94) followed by B. bassiana for the metals (Cd, 0.56; Cu, 0.14; Ni, 0.29; Zn, 0.85). Next, the strains were exposed to multiple metal mixture (Cd, Cr, Cu, Ni, Pb and Zn) of various concentrations (6, 12, 18, 30mg/L). Compared to other strains, B. bassiana and A. fumigatus had higher cube root growth (k) constants indicating their better adaptability to multi metal stress. After 72h, multimetal accumulation potential of B. bassiana (26.94±0.07mg/L) and A. fumigatus (27.59±0.09mg/L) were higher than the other strains at initial multimetal concentration of 30mg/L. However, considering the post treatment concentrations of individual metals in multimetal mixture (at all the tested concentrations), A. fumigatus demonstrated exceptional performance and could bring down the concentrations of Cd, Cu, Ni, Pb and Zn below the threshold level for irrigation prescribed by Food and Agriculture Organization (FAO). PMID:27497228

  5. Development of multiplexed bead arrays for the simultaneous detection of nucleic acid from multiple viruses in bat samples.

    PubMed

    Boyd, Victoria; Smith, Ina; Crameri, Gary; Burroughs, Amy L; Durr, Peter A; White, John; Cowled, Christopher; Marsh, Glenn A; Wang, Lin-Fa

    2015-10-01

    Virus surveillance of wildlife populations is important for identifying, monitoring, and predicting the emergence of pathogens that pose a potential threat to animal and human health. Bats are identified as important wildlife hosts of many viruses capable of causing fatal human disease, including members of the henipaviruses, coronaviruses, rhabdoviruses and filoviruses. As global warming and habitat change are thought to impact upon pathogen transmission dynamics and increase the risk of spillover, virus surveillance in bat populations remains a significant component of efforts to improve the prediction and control of potential future disease outbreaks caused by bat-borne viruses. In this study we have developed two fluid bead array assays containing customized panels that target multiple bat-borne viruses. These assays detect up to 11 viral RNA's simultaneously in urine samples collected from wild bat populations in Australia and Bangladesh. The assays developed show high specificity for the target viruses and the analytical sensitivity compares favorably to qRT-PCR. These assays enhance the ability to monitor multi-pathogen dynamics and identify patterns of virus shedding from bat populations, thus informing key approaches to outbreak response and control. PMID:26190638

  6. A Multiple Degree of Freedom Lower Extremity Isometric Device to Simultaneously Quantify Hip, Knee and Ankle Torques

    PubMed Central

    Sánchez, Natalia; Acosta, Ana Maria; Stienen, Arno H.A.

    2015-01-01

    Characterization of the joint torque coupling strategies used in the lower extremity to generate maximal and submaximal levels of torque at either the hip, knee or ankle is lacking. Currently, there are no available isometric devices that quantify all concurrent joint torques in the hip, knee and ankle of a single leg during maximum voluntary torque generation. Thus, joint-torque coupling strategies in the hip, knee and concurrent torques at ankle and/or coupling patterns at the hip and knee driven by the ankle have yet to be quantified. This manuscript describes the design, implementation and validation of a multiple degree of freedom, lower extremity isometric device (the MultiLEIT) that accurately quantifies simultaneous torques at the hip, knee and ankle. The system was mechanically validated and then implemented with two healthy control individuals and two post-stroke individuals to test usability and patient acceptance. Data indicated different joint torque coupling strategies used by both healthy individuals. In contrast, data showed the same torque coupling patterns in both post-stroke individuals, comparable to those described in the clinic. Successful implementation of the MultiLEIT can contribute to the understanding of the underlying mechanisms responsible for abnormal movement patterns and aid in the design of therapeutic interventions. PMID:25163064

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

    PubMed

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

    2012-09-01

    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.

  8. Computational tool for risk assessment of nanomaterials: novel QSTR-perturbation model for simultaneous prediction of ecotoxicity and cytotoxicity of uncoated and coated nanoparticles under multiple experimental conditions.

    PubMed

    Kleandrova, Valeria V; Luan, Feng; González-Díaz, Humberto; Ruso, Juan M; Speck-Planche, Alejandro; Cordeiro, M Natália D S

    2014-12-16

    Nanomaterials have revolutionized modern science and technology due to their multiple applications in engineering, physics, chemistry, and biomedicine. Nevertheless, the use and manipulation of nanoparticles (NPs) can bring serious damages to living organisms and their ecosystems. For this reason, ecotoxicity and cytotoxicity assays are of special interest in order to determine the potential harmful effects of NPs. Processes based on ecotoxicity and cytotoxicity tests can significantly consume time and financial resources. In this sense, alternative approaches such as quantitative structure-activity/toxicity relationships (QSAR/QSTR) modeling have provided important insights for the better understanding of the biological behavior of NPs that may be responsible for causing toxicity. Until now, QSAR/QSTR models have predicted ecotoxicity or cytotoxicity separately against only one organism (bioindicator species or cell line) and have not reported information regarding the quantitative influence of characteristics other than composition or size. In this work, we developed a unified QSTR-perturbation model to simultaneously probe ecotoxicity and cytotoxicity of NPs under different experimental conditions, including diverse measures of toxicities, multiple biological targets, compositions, sizes and conditions to measure those sizes, shapes, times during which the biological targets were exposed to NPs, and coating agents. The model was created from 36488 cases (NP-NP pairs) and exhibited accuracies higher than 98% in both training and prediction sets. The model was used to predict toxicities of several NPs that were not included in the original data set. The results of the predictions suggest that the present QSTR-perturbation model can be employed as a highly promising tool for the fast and efficient assessment of ecotoxicity and cytotoxicity of NPs.

  9. Mapping species across multiple dates of hyperspectral imagery using Iterative Endmember Selection and Multiple Endmember Spectral Mixture Analysis

    NASA Astrophysics Data System (ADS)

    Dudley, Kenneth L.

    Vegetation phenology results in seasonal changes in spectral reflectance. Phenology is often underutilized in hyperspectral vegetation mapping due to a lack of repeat imagery of the same region over time. Vegetation classification at the species level could benefit from introducing phenological information to spectral libraries. New missions, such as the proposed Hysperspectral Infrared Imager (HyspIRI) mission, could potentially provide easy access to multi-temporal datasets. The availability of these data will require new approaches to building spectral libraries for species classification. This paper explores the use of Iterative Endmember Selection (IES), an automated method for selecting endmembers from an image-derived spectral library, to create single-date and multi-temporal endmember libraries. Multiple Endmember Spectral Mixture Analysis (MESMA) was used to classify vegetation species and land cover, applying single-date and multi-temporal libraries to Airborne Visible Infrared Imaging Spectrometer (AVIRIS) data acquired on five dates in the same year. Three applications of endmember libraries were tested for their ability to classify single date AVIRIS images: 1) single-date libraries that matched the image date (same-date libraries), 2) single-date libraries that were not matched to the image date (mismatched-date libraries), and 3) a combined multi-temporal library containing spectra from all dates applied to all image dates. Results indicate that multi-temporal, seasonally-mixed spectral libraries achieved similar overall classification accuracy compared to single-date libraries, and in some cases, resulted in improved classification accuracy. Several species had increased Producer's or User accuracy using a multi-temporal library, while others had reduced accuracy compared to same-date classifications. The image dates of selected endmembers from the multi-temporal library were examined to determine if this information could improve our understanding

  10. 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

  11. 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. PMID:23819263

  12. 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. 

  13. 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. PMID:27237109

  14. Simultaneous fat suppression and band reduction with large-angle multiple-acquisition balanced steady-state free precession.

    PubMed

    Quist, Brady; Hargreaves, Brian A; Cukur, Tolga; Morrell, Glen R; Gold, Garry E; Bangerter, Neal K

    2012-04-01

    Balanced steady-state free precession (bSSFP) MRI is a rapid and signal-to-noise ratio-efficient imaging method, but suffers from characteristic bands of signal loss in regions of large field inhomogeneity. Several methods have been developed to reduce the severity of these banding artifacts, typically involving the acquisition of multiple bSSFP datasets (and the accompanying increase in scan time). Fat suppression with bSSFP is also challenging; most existing methods require an additional increase in scan time, and some are incompatible with bSSFP band-reduction techniques. This work was motivated by the need for both robust fat suppression and band reduction in the presence of field inhomogeneity when using bSSFP for flow-independent peripheral angiography. The large flip angles used in this application to improve vessel conspicuity and contrast lead to specific absorption rate considerations, longer repetition times, and increased severity of banding artifacts. In this work, a novel method that simultaneously suppresses fat and reduces bSSFP banding artifact with the acquisition of only two phase-cycled bSSFP datasets is presented. A weighted sum of the two bSSFP acquisitions is taken on a voxel-by-voxel basis, effectively synthesizing an off-resonance profile at each voxel that puts fat in the stop band while keeping water in the pass band. The technique exploits the near-sinusoidal shape of the bSSFP off-resonance spectrum for many tissues at large (>50°) flip angles.

  15. Simultaneous determination of multiple angiotensin type 1 receptor antagonists and its application to high-throughput pharmacokinetic study

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaoyan; Sun, Jianguo; Hao, Haiping; Wang, Guangji; Hu, Xiaoling; Lv, Hua; Gu, Shenghua; Wu, Xiaoming; Xu, Jinyi

    2008-05-01

    A rapid and sensitive high performance liquid chromatography-electrospray tandem mass spectrometry (HPLC-ESI-MS/MS) detection was developed for the simultaneous determination of multiple angiotensin type 1 receptor antagonists (AT1RAs) WX472, WX581, 1b and telmisartan in rat plasma for the purpose of high-throughout pharmacokinetic screening. The method was operated under selected reaction monitoring (SRM) mode in the positive ion mode. The analytes and the internal standard (pitavastatin) were extracted from 100 [mu]L rat plasma under acidic conditions by liquid-liquid extraction with ethyl acetate. The analytes and internal standard were baseline separated on a Gemini analytical column (3 [mu]m, 150 mm × 2.0 mm) with the adoption of a gradient elution using acetonitrile and 0.05% aqueous formic acid. The standard curves were linear in the concentration ranges of 4.5-900 ng/mL for WX472, 5-1000 ng/mL for WX581 and 0.5-100 ng/mL for 1b and telmisartan. Intra- and inter-batch precisions (R.S.D.%) were all within 15% and the method assessed a quite good accuracy (R.E.%). Recoveries were found to be >65% for all the compounds and no obvious matrix effects were found. This method has been successfully applied to the high-throughput pharmacokinetic screening study for both cassette dosing and cassette analysis of four compounds to rats. Significant drug-drug interactions were observed after cassette dosing. The study suggested that cassette analysis of pooled samples would be a better choice for the high-throughput pharmacokinetic screening of angiotensin type 1 receptor antagonists.

  16. 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

  17. 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

  18. Novel evidence for within-species leaf economics spectrum at multiple spatial scales

    PubMed Central

    Hu, Yu-Kun; Pan, Xu; Liu, Guo-Fang; Li, Wen-Bing; Dai, Wen-Hong; Tang, Shuang-Li; Zhang, Ya-Lin; Xiao, Tao; Chen, Ling-Yun; Xiong, Wei; Zhou, Meng-Yao; Song, Yao-Bin; Dong, Ming

    2015-01-01

    Leaf economics spectrum (LES), characterizing covariation among a suite of leaf traits relevant to carbon and nutrient economics, has been examined largely among species but hardly within species. In addition, very little attempt has been made to examine whether the existence of LES depends on spatial scales. To address these questions, we quantified the variation and covariation of four leaf economic traits (specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus contents) in a cosmopolitan wetland species (Phragmites australis) at three spatial (inter-regional, regional, and site) scales across most of the species range in China. The species expressed large intraspecific variation in the leaf economic traits at all of the three spatial scales. It also showed strong covariation among the four leaf economic traits across the species range. The coordination among leaf economic traits resulted in LES at all three scales and the environmental variables determining variation in leaf economic traits were different among the spatial scales. Our results provide novel evidence for within-species LES at multiple spatial scales, indicating that resource trade-off could also constrain intraspecific trait variation mainly driven by climatic and/or edaphic differences. PMID:26579151

  19. Novel evidence for within-species leaf economics spectrum at multiple spatial scales.

    PubMed

    Hu, Yu-Kun; Pan, Xu; Liu, Guo-Fang; Li, Wen-Bing; Dai, Wen-Hong; Tang, Shuang-Li; Zhang, Ya-Lin; Xiao, Tao; Chen, Ling-Yun; Xiong, Wei; Zhou, Meng-Yao; Song, Yao-Bin; Dong, Ming

    2015-01-01

    Leaf economics spectrum (LES), characterizing covariation among a suite of leaf traits relevant to carbon and nutrient economics, has been examined largely among species but hardly within species. In addition, very little attempt has been made to examine whether the existence of LES depends on spatial scales. To address these questions, we quantified the variation and covariation of four leaf economic traits (specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus contents) in a cosmopolitan wetland species (Phragmites australis) at three spatial (inter-regional, regional, and site) scales across most of the species range in China. The species expressed large intraspecific variation in the leaf economic traits at all of the three spatial scales. It also showed strong covariation among the four leaf economic traits across the species range. The coordination among leaf economic traits resulted in LES at all three scales and the environmental variables determining variation in leaf economic traits were different among the spatial scales. Our results provide novel evidence for within-species LES at multiple spatial scales, indicating that resource trade-off could also constrain intraspecific trait variation mainly driven by climatic and/or edaphic differences.

  20. 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.

  1. Influence of multiple ion species on low-frequency electromagnetic wave instabilities. [in solar wind

    NASA Technical Reports Server (NTRS)

    Brinca, Armando L.; Tsurutani, Bruce T.

    1989-01-01

    The effect of multiple (singly ionized) coexisting newborn ion species on the stability of low-frequency electromagnetic waves was investigated using a plasma model in which solar wind magnetoplasma is made up of isotropic Maxwellian electron and proton populations with a common number density of 4.95/cu cm and temperatures equal to 17.2 eV and 6.9 eV, respectively. It is shown that the effect of multiple ions on wave growth, for given background magnetoplasma conditions and relative densities, depends not only on their mass but also on the physical nature of the wave modes. If the ion masses are disparate, each one of the coexisting ion beams tends to stimulate instabilities without undue influence from the other species. If the masses of newborn ions are similar, they can strongly catalyze wave growth of fluidlike nonresonant modes, but bring about weak growth enhancements in cyclotron resonant instabilities.

  2. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

    PubMed

    Pavan, Ana Carolina; Marroig, Gabriel

    2016-10-01

    A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on

  3. 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.

  4. 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

  5. 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.

  6. 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. PMID:27241629

  7. 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.

  8. 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. PMID:16103373

  9. 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.

  10. 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.

  11. Valid flow combinations for stable sheath in a magnetized multiple ion species plasma

    SciTech Connect

    Sharma, Devendra; Kaw, Predhiman K.

    2012-11-15

    Theoretical study is done of the entry criterion for the plasma flow into the electrostatic boundary layer, or sheath, forming in a magnetized multiple ion species plasma. Finding valid entry velocity combinations in a magnetized set up requires a magnetized equivalent of the generalized Bohm criterion. A magnetized generalized entry criterion is obtained with the scale length distribution in a region of validity for the stable solutions. The analysis finds that the valid entry flow velocity combinations with distinct values of individual ion species can correspond to a unique system phase velocity. Magnetization effects govern the region of validity whose boundaries collapse to the unmagnetized sheath criterion in the limit of normal incidence, independent of the strength of the magnetic field. Considerably smaller entry velocities, in comparison to the unmagnetized system sound velocity, are recovered for the species in appropriate regime of magnetization in the cases of oblique incidences.

  12. Toroidal rotation of multiple species of ions in tokamak plasma driven by lower-hybrid-waves

    NASA Astrophysics Data System (ADS)

    Zuo, Yang; Wang, Shaojie; Pan, Chengkang

    2012-10-01

    A numerical simulation is carried out to investigate the toroidal rotation of multiple species of ions and the radial electric field in a tokamak plasma driven by the lower-hybrid-wave (LHW). The theoretical model is based on the neoclassical transport theory associated with the anomalous transport model. Three species of ions (primary ion and two species of impurity ions) are taken into consideration. The predicted toroidal velocity of the trace impurities during the LHW injection agrees reasonably well with the experimental observation. It is shown that the toroidal rotation velocities of the trace impurity ions and the primary ions are close, therefore the trace impurity ions are representative of the primary ions in the toroidal rotation driven by the LHW.

  13. Toroidal rotation of multiple species of ions in tokamak plasma driven by lower-hybrid-waves

    SciTech Connect

    Zuo Yang; Wang Shaojie; Pan Chengkang

    2012-10-15

    A numerical simulation is carried out to investigate the toroidal rotation of multiple species of ions and the radial electric field in a tokamak plasma driven by the lower-hybrid-wave (LHW). The theoretical model is based on the neoclassical transport theory associated with the anomalous transport model. Three species of ions (primary ion and two species of impurity ions) are taken into consideration. The predicted toroidal velocity of the trace impurities during the LHW injection agrees reasonably well with the experimental observation. It is shown that the toroidal rotation velocities of the trace impurity ions and the primary ions are close, therefore the trace impurity ions are representative of the primary ions in the toroidal rotation driven by the LHW.

  14. An N-Acetyl Cysteine Ruthenium Tricarbonyl Conjugate Enables Simultaneous Release of CO and Ablation of Reactive Oxygen Species

    PubMed Central

    Seixas, João D; Chaves-Ferreira, Miguel; Montes-Grajales, Diana; Gonçalves, Ana M; Marques, Ana R; Saraiva, Lígia M; Olivero-Verbel, Jesus; Romão, Carlos C; Bernardes, Gonçalo J L

    2015-01-01

    We have designed and synthesised a [Ru(CO)3Cl2(NAC)] pro-drug that features an N-acetyl cysteine (NAC) ligand. This NAC carbon monoxide releasing molecule (CORM) conjugate is able to simultaneously release biologically active CO and to ablate the concurrent formation of reactive oxygen species (ROS). Complexes of the general formulae [Ru(CO)3(L)3]2+, including [Ru(CO)3Cl(glycinate)] (CORM-3), have been shown to produce ROS through a water–gas shift reaction, which contributes significantly, for example, to their antibacterial activity. In contrast, NAC-CORM conjugates do not produce ROS or possess antibacterial activity. In addition, we demonstrate the synergistic effect of CO and NAC both for the inhibition of nitric oxide (formation) and in the expression of tumour-necrosis factor (TNF)-α. This work highlights the advantages of combining a CO-releasing scaffold with the anti-oxidant and anti-inflammatory drug NAC in a unique pro-drug. PMID:26316066

  15. 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

  16. Hydrodynamic description of an unmagnetized plasma with multiple ion species. I. General formulation

    DOE PAGESBeta

    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

  17. Multiple cryptic species of sympatric generalists within the avian blood parasite Haemoproteus majoris.

    PubMed

    Nilsson, E; Taubert, H; Hellgren, O; Huang, X; Palinauskas, V; Markovets, M Y; Valkiūnas, G; Bensch, S

    2016-09-01

    The avian haemosporidian parasite Haemoproteus majoris has been reported to infect a wide range of passerine birds throughout the Holarctic ecozone. Five cytochrome b (cyt b) lineages have been described as belonging to the morphological species H. majoris, and these form a tight phylogenetic cluster together with 13 undescribed lineages that differ from each other by < 1.2% in sequence divergence. Records in a database (MalAvi) that contains global findings of haemosporidian lineages generated by universal primers suggest that these lineages vary substantially in host distribution. We confirm this pattern in a data set collected at Lake Kvismaren, Sweden, where three of the generalist lineages have local transmission. However, whether these lineages represent intraspecific mitochondrial diversity or clusters of cryptic species has previously not been examined. In this study, we developed novel molecular markers to amplify the partial segments of four nuclear genes to determine the level of genetic diversity and gene phylogenies among the five morphologically described cyt b lineages of H. majoris. All five cyt b lineages were strongly associated with unique nuclear alleles at all four nuclear loci, indicating that each mitochondrial lineage represents a distinct biological species. Within lineages, there was no apparent association between nuclear alleles and host species, indicating that they form genetically unstructured populations across multiple host species. PMID:27262030

  18. 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...

  19. 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

  20. 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

  1. Immunoglobulin D Multiple Myeloma, Plasma Cell Leukemia and Chronic Myelogenous Leukemia in a Single Patient Treated Simultaneously with Lenalidomide, Bortezomib, Dexamethasone and Imatinib

    PubMed Central

    Pickens, Peter V.; Auerbach, Herbert E.

    2016-01-01

    Multiple myeloma (MM) is a neoplastic lymphoproliferative disorder characterized by uncontrolled monoclonal plasma cell proliferation. Among different isotypes of MM, immunoglobulin D (IgD) MM is very rare, representing only 1 to 2% of all isotypes. Chronic myelogenous leukemia (CML) is a neoplastic myeloproliferative disorder of pluripotent hematopoietic stem cell, which is characterized by the uncontrolled proliferation of myeloid cells. An 88-year-old male was diagnosed simultaneously with IgD kappa MM and CML. A distinctive feature in this patient was the progression to plasma cell leukemia without any symptomatic myeloma stage. He was treated simultaneously with lenalidomide, bortezomib and imatinib. Synchronous occurrence of these rare hematological malignancies in a single patient is an exceedingly rare event. Multiple hypotheses to explain co-occurrence of CML and MM have been proposed; however, the exact etiological molecular pathophysiology remains elusive. PMID:27103978

  2. New highland distribution records of multiple Anopheles species in the Ecuadorian Andes

    PubMed Central

    2011-01-01

    Background Several recent climate change reviews have stressed the possibility of some malaria vectors occupying regions of higher altitudes than previously recorded. Indeed, highland malaria has been observed in several African nations, possibly attributable to changes in land use, vector control and local climate. This study attempts to expand the current knowledge of the distribution of common Anopheles species in Ecuador, with particular attention to highland regions (> 500 m) of the Andes. Methods Extensive field collections of larvae were undertaken in 2008, 2009 and 2010 throughout all regions of Ecuador (except the lower-altitude Amazonian plain) and compared to historical distribution maps reproduced from the 1940s. Larvae were identified using both a morphological key and sequencing of the 800 bp region of the CO1 mitochondrial gene. In addition, spatial statistics (Getis-Ord Hotspot Analysis: Gi*) were used to determine high and low-density clusters of each species in Ecuador. Results Distributions have been updated for five species of Anopheles in Ecuador: Anopheles albimanus, Anopheles pseudopunctipennis, Anopheles punctimacula, Anopheles eiseni and Anopheles oswaldoi s.l.. Historical maps indicate that An. pseudopunctipennis used to be widespread in highland Andean valleys, while other species were completely restricted to lowland areas. By comparison, updated maps for the other four collected species show higher maximum elevations and/or more widespread distributions in highland regions than previously recorded. Gi* analysis determined some highland hot spots for An. albimanus, but only cold spots for all other species. Conclusions This study documents the establishment of multiple anopheline species in high altitude regions of Ecuador, often in areas where malaria eradication programs are not focused. PMID:21835004

  3. A New Method for Simultaneous Measurement of the Integrated Reflectivity of Crystals at Multiple Orders of Reflection and Comparison with New Theoretical Calculations

    SciTech Connect

    S.G. Lee; J.G. Bak; Y.S. Jung; M. Bitter; K.W. Hill; G. Hoelzer; O. Wehrhan; E. Foerster

    2003-04-09

    This paper describes a new method for the simultaneous measurement of the integrated reflectivity of a crystal for multiple orders of reflection at a predefined Bragg angle. The technique is demonstrated with a mica crystal for Bragg angles of 43{sup o}, 47{sup o}, and 50{sup o}. The measured integrated reflectivity for Bragg reflections up to the 24th order is compared with new theoretical predictions, which are also presented in this paper.

  4. Dendroclimatic Reconstructions from Multiple Co-Occurring Species from Old-Growth Deciduous Forests in Indiana, USA

    NASA Astrophysics Data System (ADS)

    Maxwell, J. T.; Harley, G. L.; Pendergrass, K.; Matheus, T.

    2014-12-01

    Tree-ring based climate reconstructions are typically derived from either (1) a single species from one or multiple locations, or (2) multiple species from multiple locations. Here, we investigate the ability of using multiple co-occurring canopy-dominant species for climate reconstructions based in the eastern United States (US). Using a variety of techniques, we first compare the climate signals of canopy-dominant species at three old-growth forests in southern Indiana. We then determine if a composite time series of these co-occurring species increases or decreases the reconstruction model skill. In all cases, climate-growth correlation analyses of the species reveal strong relationships with summer (June-August) Palmer Drought Severity Index during the period 1895-2013 CE. We first use a split-sample reconstruction technique to compare the performance of species reconstruction models. We then use a nested technique to build a composite chronology for each site against which to compare the individual species chronologies. The composite chronologies consistently outperformed each individual species model, indicating that using multiple co-occurring species increases reconstruction skill. Furthermore, the stability of the climate signal increases with the inclusion of more species, even those that are rarely used in dendroclimatic work (i.e. Juglans nigra). These results indicate that sampling co-occurring species captures greater drought variance and more accurately explains how drought is experienced within a forest. Further, sampling co-occurring species at multiple sites in the Eastern US can improve broader scale regional drought reconstructions over the Common Era.

  5. 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

  6. 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.

  7. Accurate multi-source forest species mapping using the multiple spectral-spatial classification approach

    NASA Astrophysics Data System (ADS)

    Stavrakoudis, Dimitris; Gitas, Ioannis; Karydas, Christos; Kolokoussis, Polychronis; Karathanassi, Vassilia

    2015-10-01

    This paper proposes an efficient methodology for combining multiple remotely sensed imagery, in order to increase the classification accuracy in complex forest species mapping tasks. The proposed scheme follows a decision fusion approach, whereby each image is first classified separately by means of a pixel-wise Fuzzy-Output Support Vector Machine (FO-SVM) classifier. Subsequently, the multiple results are fused according to the so-called multiple spectral- spatial classifier using the minimum spanning forest (MSSC-MSF) approach, which constitutes an effective post-regularization procedure for enhancing the result of a single pixel-based classification. For this purpose, the original MSSC-MSF has been extended in order to handle multiple classifications. In particular, the fuzzy outputs of the pixel-based classifiers are stacked and used to grow the MSF, whereas the markers are also determined considering both classifications. The proposed methodology has been tested on a challenging forest species mapping task in northern Greece, considering a multispectral (GeoEye) and a hyper-spectral (CASI) image. The pixel-wise classifications resulted in overall accuracies (OA) of 68.71% for the GeoEye and 77.95% for the CASI images, respectively. Both of them are characterized by high levels of speckle noise. Applying the proposed multi-source MSSC-MSF fusion, the OA climbs to 90.86%, which is attributed both to the ability of MSSC-MSF to tackle the salt-and-pepper effect, as well as the fact that the fusion approach exploits the relative advantages of both information sources.

  8. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

    PubMed

    Pavan, Ana Carolina; Marroig, Gabriel

    2016-10-01

    A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on

  9. Computational designing of a poly-epitope fecundity vaccine for multiple species of livestock.

    PubMed

    Ganguly, Bhaskar; Rastogi, Sunil Kumar; Prasad, Shiv

    2013-12-17

    Inhibin and follistatin are known to reduce fecundity by inhibiting the actions of activin and FSH. Thus, the immunoneutralization of these hormones is a rational proposal for augmenting reproductive performance. The present study describes a comprehensive computational methodology comprising of a consensus approach of several B- and Th-cell epitope prediction tools for the identification of epitopic regions within the structure of these hormones that can be incorporated into a poly-epitope fecundity vaccine. The proposed peptide (RGD-WSPAALRLLQRPPEEPA-KK-YSFPISSILE) should be effective in multiple animal species, generating good immunological memory.

  10. Influence of multiple ion species on low-frequency electromagnetic wave instabilities

    SciTech Connect

    Brinca, A.L.; Tsurutani, B.T. )

    1989-10-01

    Analysis of the stability of low-frequency electromagnetic modes excited by coexisting newborn ion species shows that the effect to multiple (singly ionized) ions on wave growth, for given background magnetoplasma conditions and relative densities, depends not only on their mass but also on the physical nature of the wave modes. Whereas each one of the coexisting ion beams tends to stimulate instabilities without undue influence from the other species, if ion masses are disparate, newborn ions of similar masses can strongly catalyze wave growth of fluidlike, nonresonant modes, but only bring about weak growth enhancements in cyclotron resonant instabilities. The authors contrast wave characteristics due to the coexistence of hydronium, water vapor, and oxygen newborn ions with previous results involving cometary hydrogen and oxygen ions and provide a physical interpretation of the results.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Influence of Multiple Bacterial Populations on Phenanthrene Degradation, Bacterial Cell Elution, and Species Distribution

    NASA Astrophysics Data System (ADS)

    Patterson, B. M.; Brusseau, M. L.; Maier, R. M.; Frye, R.

    2001-05-01

    A single set of degradation coefficients is typically used when representing biodegradation in contaminant transport models. Implicit to this approach is the assumption that only a single degrading isolate exists, or that the entire community of degraders more typically present in natural systems has a uniform, constant growth rate and affinity for the contaminant. This assumption was evaluated through a miscible displacement experiment conducted using a column packed with a soil containing an indigenous microbial community comprised of 24 identified phenanthrene-degrading isolates. Results produced oscillating phenanthrene concentrations in the column effluent, indicating potential competitive interactions among the isolates. A second series of experiments, conducted in a simplified system comprised of sand and 1,2, or 3 indigenous isolates, examined the effects of species interactions on phenanthrene degradation and bacterial cell elution. Bacterial growth rates, density of cells within the column, and bacterial distribution were also evaluated. Results show single bacterial species produced relatively stable cell elution and phenanthrene concentrations in the effluent. Conversely, the behavior in the multiple species systems indicated synergistic and antagonistic interactions occurred among the species. These results illustrate that the dynamics of heterogeneous microbial communities should be considered when evaluating contaminant biodegradation and transport in subsurface systems.

  16. 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.

  17. An outbreak of Sarcocystis calchasi encephalitis in multiple psittacine species within an enclosed zoological aviary.

    PubMed

    Rimoldi, Guillermo; Speer, Brian; Wellehan, James F X; Bradway, Daniel S; Wright, Lewis; Reavill, Drury; Barr, Bradd C; Childress, April; Shivaprasad, H L; Chin, Richard P

    2013-11-01

    A total of 5 psittacine birds in an enclosed zoological exhibit, including 2 princess parrots and 3 cockatoos of 2 different species, developed severe central nervous system clinical signs over a 2-3-month period and died or were euthanized. Histologically, all birds had a lymphoplasmacytic and histiocytic encephalitis with intralesional protozoa consistent with a Sarcocystis species in addition to intramuscular tissue sarcocysts. By immunohistochemical staining, merozoites in brain and tissue cysts in muscle did not react with polyclonal antisera against Sarcocystis falcatula, Sarcocystis neurona, Toxoplasma gondii, and Neospora caninum, or with a monoclonal antibody to S. neurona. Transmission electron microscopy on sarcocyst tissue cyst walls from 2 birds was morphologically consistent with Sarcocystis calchasi. Polymerase chain reaction (PCR) amplification and sequencing of partial 18S ribosomal RNA from muscle tissue cysts and brain schizonts from 3 birds was consistent with a clade containing S. calchasi and Sarcocystis columbae but could not distinguish these closely related Sarcocystis species. However, PCR amplification and sequencing of the internal transcribed spacer 1 RNA segment in the brain from 2 birds and muscle from 2 birds specifically identified the isolates as S. calchasi. The current report documents that multiple psittacine species are susceptible intermediate hosts of S. calchasi, and that infection can cause encephalitis resulting in significant morbidity and mortality in psittacine aviaries.

  18. Bioavailability of sediment-associated benzo(a)pyrene within single- versus multiple-species systems.

    PubMed

    Schuler, L J; Heagler, M G; Lydy, M J

    2002-02-01

    A series of experiments were conducted with benzo(a)pyrene (B(a)P) spiked sediments to determine if bioavailability of sediment-associated contaminants is affected by multiple species interactions. Three benthic invertebrates, Hyalella azteca, Chironomus tentans, and Lumbriculus variegatus, were exposed to sediments spiked with radiolabeled B(a)P that was aged for 60 days. Organisms were introduced into the spiked sediments in single, binary, and ternary combinations. Changes in bioavailability were then determined for each species by estimating uptake clearance coefficients (ks) and bioaccumulation factors (BAFs) during 7-day exposures. In general, there was a trend toward lower ks values in binary and ternary exposures compared to the single-species systems. In contrast, BAF estimates were more variable with fewer significant differences noted among treatments. BAF estimates were highest for L. variegatus followed by C. tentans and H. azetca and appear to be dependent on specific feeding and habitat requirements as well as the relative biotransformation/elimination potential of each species. Overall, these results suggest that animal-animal interactions may be important to consider when estimating bioavailability of sediment-bound chemicals. PMID:11815811

  19. 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.

  20. [Complete response to CPT-11 and UFT/LV combination therapy in a case with simultaneous multiple lung metastases from colon cancer].

    PubMed

    Ishida, Hideyuki; Akita, Hirofumi; Watanabe, Yasunori; Nakaguchi, Kazunori; Kabuto, Toshiyuki

    2006-06-01

    We report the complete response for one year of a patient with simultaneous multiple lung metastases from colon cancer who was treated using a combination of irinotecan (CPT-11) and uracil/tegafur (UFT)/Leucovorin (LV) using a schedule reported overseas. A 61-year-old woman was admitted to our hospital and diagnosed with ascending colon cancer and simultaneous multiple lung metastases. The patient underwent a right hemicolectomy and was treated with CPT-11 (150 mg/m(2)) on day 1 and oral UFT and oral LV on days 1-14. This treatment cycle was repeated every 3 weeks. A CT examination after 4 cycles of chemotherapy revealed a partial response of multiple lung metastases, and the next examination after 6 cycles revealed a complete response. The adverse effects observed during this chemotherapy regimen were leucopenia (grade 1), neutropenia (grade 2), vomiting (grade 2) and hair loss (grade 1). The patient is now receiving her 22nd cycle of chemotherapy, and her multiple metastases have shown a complete response for one year. The CPT-11 and UFT/LV combination therapy was well tolerated and was covered by the national health insurance system in Japan. This treatment may enable prolonged survival and improve quality of life in patients with metastatic colorectal cancer.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species.

    PubMed

    Veltri, Daniel; Wight, Martha Malapi; Crouch, Jo Anne

    2016-07-01

    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.

  8. A microfluidic device integrating dual CMOS polysilicon nanowire sensors for on-chip whole blood processing and simultaneous detection of multiple analytes.

    PubMed

    Kuan, Da-Han; Wang, I-Shun; Lin, Jiun-Rue; Yang, Chao-Han; Huang, Chi-Hsien; Lin, Yen-Hung; Lin, Chih-Ting; Huang, Nien-Tsu

    2016-08-01

    The hemoglobin-A1c test, measuring the ratio of glycated hemoglobin (HbA1c) to hemoglobin (Hb) levels, has been a standard assay in diabetes diagnosis that removes the day-to-day glucose level variation. Currently, the HbA1c test is restricted to hospitals and central laboratories due to the laborious, time-consuming whole blood processing and bulky instruments. In this paper, we have developed a microfluidic device integrating dual CMOS polysilicon nanowire sensors (MINS) for on-chip whole blood processing and simultaneous detection of multiple analytes. The micromachined polymethylmethacrylate (PMMA) microfluidic device consisted of a serpentine microchannel with multiple dam structures designed for non-lysed cells or debris trapping, uniform plasma/buffer mixing and dilution. The CMOS-fabricated polysilicon nanowire sensors integrated with the microfluidic device were designed for the simultaneous, label-free electrical detection of multiple analytes. Our study first measured the Hb and HbA1c levels in 11 clinical samples via these nanowire sensors. The results were compared with those of standard Hb and HbA1c measurement methods (Hb: the sodium lauryl sulfate hemoglobin detection method; HbA1c: cation-exchange high-performance liquid chromatography) and showed comparable outcomes. Finally, we successfully demonstrated the efficacy of the MINS device's on-chip whole blood processing followed by simultaneous Hb and HbA1c measurement in a clinical sample. Compared to current Hb and HbA1c sensing instruments, the MINS platform is compact and can simultaneously detect two analytes with only 5 μL of whole blood, which corresponds to a 300-fold blood volume reduction. The total assay time, including the in situ sample processing and analyte detection, was just 30 minutes. Based on its on-chip whole blood processing and simultaneous multiple analyte detection functionalities with a lower sample volume requirement and shorter process time, the MINS device can be

  9. Multicolor Fluorescence Detection-Based Microfluidic Device for Single-Cell Metabolomics: Simultaneous Quantitation of Multiple Small Molecules in Primary Liver Cells.

    PubMed

    Li, Qingling; Chen, Peilin; Fan, Yuanyuan; Wang, Xu; Xu, Kehua; Li, Lu; Tang, Bo

    2016-09-01

    Single-cell metabolomics can be used to study cell diversity and how cells respond to environment. There is an urgent need to develop effective detection methods for single-cell metabolomics. Microchip electrophoresis with laser-induced fluorescence detection (MCE-LIFD) is a powerful tool to detect metabolites at the single-cell level. However, the existing one-laser excitation and one-color fluorescence collection in MCE-LIFD is not sufficient for the simultaneous detection of multiple small molecules with wide variations in their fluorescence excitation and emission spectra. In this manuscript, we describe a multicolor fluorescence detection-based microfluidic device (MFD-MD) for single-cell metabolomics research. We selected primary liver cells from acute ethanol-stimulated mice as the model cells and hydrogen peroxide (H2O2), glutathione (GSH), and cysteine (Cys) as representative small-molecule metabolites for single-cell analysis. The microfluidic chip enabled accurate single-cell manipulation and effective electrophoresis separation. The new multicolor fluorescence detection permitted simultaneous analysis of H2O2, GSH, and Cys. Ethanol exposure induced an increase in H2O2 and a decrease in GSH and Cys. Obvious cell heterogeneity was observed. These results provide insights regarding the intracellular oxidative/antioxidative molecular mechanism in response to external stimuli. The MFD-MD provides a new opportunity for simultaneous single-cell analysis of multiple metabolites. PMID:27503398

  10. Multiple simultaneous venous and arterial thromboses in a patient with factor V Leiden disorder: Detection by multislice computed tomography

    PubMed Central

    Sayin, Bige; Durakoğlugil, Tuğba; Akmangit, İlkay; Vural, Murat; Elverici, Eda

    2015-01-01

    Arterial thrombosis is extremely rare in patients with factor V Leiden (FVL) mutation. Recent advances in multislice computed tomography (MSCT) technology facilitated diagnosis of thromboembolic events accurately without delay. We report a patient with FVL mutation and acute bilateral lower extremity deep venous thromboses, pulmonary thromboembolism, and acute left anterior descending artery thrombosis, all diagnosed by MSCT. MSCT has been utilized for prompt diagnosis of the concomitant thrombotic pathologies simultaneously. PMID:25838926

  11. Simultaneous spectrophotometric determination of synthetic dyes in food samples after cloud point extraction using multiple response optimizations.

    PubMed

    Heidarizadi, Elham; Tabaraki, Reza

    2016-01-01

    A sensitive cloud point extraction method for simultaneous determination of trace amounts of sunset yellow (SY), allura red (AR) and brilliant blue (BB) by spectrophotometry was developed. Experimental parameters such as Triton X-100 concentration, KCl concentration and initial pH on extraction efficiency of dyes were optimized using response surface methodology (RSM) with a Doehlert design. Experimental data were evaluated by applying RSM integrating a desirability function approach. The optimum condition for extraction efficiency of SY, AR and BB simultaneously were: Triton X-100 concentration 0.0635 mol L(-1), KCl concentration 0.11 mol L(-1) and pH 4 with maximum overall desirability D of 0.95. Correspondingly, the maximum extraction efficiency of SY, AR and BB were 100%, 92.23% and 95.69%, respectively. At optimal conditions, extraction efficiencies were 99.8%, 92.48% and 95.96% for SY, AR and BB, respectively. These values were only 0.2%, 0.25% and 0.27% different from the predicted values, suggesting that the desirability function approach with RSM was a useful technique for simultaneously dye extraction. Linear calibration curves were obtained in the range of 0.02-4 for SY, 0.025-2.5 for AR and 0.02-4 μg mL(-1) for BB under optimum condition. Detection limit based on three times the standard deviation of the blank (3Sb) was 0.009, 0.01 and 0.007 μg mL(-1) (n=10) for SY, AR and BB, respectively. The method was successfully used for the simultaneous determination of the dyes in different food samples. PMID:26653445

  12. Simultaneous spectrophotometric determination of synthetic dyes in food samples after cloud point extraction using multiple response optimizations.

    PubMed

    Heidarizadi, Elham; Tabaraki, Reza

    2016-01-01

    A sensitive cloud point extraction method for simultaneous determination of trace amounts of sunset yellow (SY), allura red (AR) and brilliant blue (BB) by spectrophotometry was developed. Experimental parameters such as Triton X-100 concentration, KCl concentration and initial pH on extraction efficiency of dyes were optimized using response surface methodology (RSM) with a Doehlert design. Experimental data were evaluated by applying RSM integrating a desirability function approach. The optimum condition for extraction efficiency of SY, AR and BB simultaneously were: Triton X-100 concentration 0.0635 mol L(-1), KCl concentration 0.11 mol L(-1) and pH 4 with maximum overall desirability D of 0.95. Correspondingly, the maximum extraction efficiency of SY, AR and BB were 100%, 92.23% and 95.69%, respectively. At optimal conditions, extraction efficiencies were 99.8%, 92.48% and 95.96% for SY, AR and BB, respectively. These values were only 0.2%, 0.25% and 0.27% different from the predicted values, suggesting that the desirability function approach with RSM was a useful technique for simultaneously dye extraction. Linear calibration curves were obtained in the range of 0.02-4 for SY, 0.025-2.5 for AR and 0.02-4 μg mL(-1) for BB under optimum condition. Detection limit based on three times the standard deviation of the blank (3Sb) was 0.009, 0.01 and 0.007 μg mL(-1) (n=10) for SY, AR and BB, respectively. The method was successfully used for the simultaneous determination of the dyes in different food samples.

  13. An optogenetics- and imaging-assisted simultaneous multiple patch-clamp recording system for decoding complex neural circuits.

    PubMed

    Wang, Guangfu; Wyskiel, Daniel R; Yang, Weiguo; Wang, Yiqing; Milbern, Lana C; Lalanne, Txomin; Jiang, Xiaolong; Shen, Ying; Sun, Qian-Quan; Zhu, J Julius

    2015-03-01

    Deciphering neuronal circuitry is central to understanding brain function and dysfunction, yet it remains a daunting task. To facilitate the dissection of neuronal circuits, a process requiring functional analysis of synaptic connections and morphological identification of interconnected neurons, we present here a method for stable simultaneous octuple patch-clamp recordings. This method allows physiological analysis of synaptic interconnections among 4-8 simultaneously recorded neurons and/or 10-30 sequentially recorded neurons, and it allows anatomical identification of >85% of recorded interneurons and >99% of recorded principal neurons. We describe how to apply the method to rodent tissue slices; however, it can be used on other model organisms. We also describe the latest refinements and optimizations of mechanics, electronics, optics and software programs that are central to the realization of a combined single- and two-photon microscopy-based, optogenetics- and imaging-assisted, stable, simultaneous quadruple-viguple patch-clamp recording system. Setting up the system, from the beginning of instrument assembly and software installation to full operation, can be completed in 3-4 d. PMID:25654757

  14. An optogenetics- and imaging-assisted simultaneous multiple patch-clamp recording system for decoding complex neural circuits

    PubMed Central

    Wang, Guangfu; Wyskiel, Daniel R; Yang, Weiguo; Wang, Yiqing; Milbern, Lana C; Lalanne, Txomin; Jiang, Xiaolong; Shen, Ying; Sun, Qian-Quan; Zhu, J Julius

    2015-01-01

    Deciphering neuronal circuitry is central to understanding brain function and dysfunction, yet it remains a daunting task. To facilitate the dissection of neuronal circuits, a process requiring functional analysis of synaptic connections and morphological identification of interconnected neurons, we present here a method for stable simultaneous octuple patch-clamp recordings. This method allows physiological analysis of synaptic interconnections among 4–8 simultaneously recorded neurons and/or 10–30 sequentially recorded neurons, and it allows anatomical identification of >85% of recorded interneurons and >99% of recorded principal neurons. We describe how to apply the method to rodent tissue slices; however, it can be used on other model organisms. We also describe the latest refinements and optimizations of mechanics, electronics, optics and software programs that are central to the realization of a combined single- and two-photon microscopy–based, optogenetics- and imaging-assisted, stable, simultaneous quadruple–viguple patch-clamp recording system. Setting up the system, from the beginning of instrument assembly and software installation to full operation, can be completed in 3–4 d. PMID:25654757

  15. An optogenetics- and imaging-assisted simultaneous multiple patch-clamp recording system for decoding complex neural circuits.

    PubMed

    Wang, Guangfu; Wyskiel, Daniel R; Yang, Weiguo; Wang, Yiqing; Milbern, Lana C; Lalanne, Txomin; Jiang, Xiaolong; Shen, Ying; Sun, Qian-Quan; Zhu, J Julius

    2015-03-01

    Deciphering neuronal circuitry is central to understanding brain function and dysfunction, yet it remains a daunting task. To facilitate the dissection of neuronal circuits, a process requiring functional analysis of synaptic connections and morphological identification of interconnected neurons, we present here a method for stable simultaneous octuple patch-clamp recordings. This method allows physiological analysis of synaptic interconnections among 4-8 simultaneously recorded neurons and/or 10-30 sequentially recorded neurons, and it allows anatomical identification of >85% of recorded interneurons and >99% of recorded principal neurons. We describe how to apply the method to rodent tissue slices; however, it can be used on other model organisms. We also describe the latest refinements and optimizations of mechanics, electronics, optics and software programs that are central to the realization of a combined single- and two-photon microscopy-based, optogenetics- and imaging-assisted, stable, simultaneous quadruple-viguple patch-clamp recording system. Setting up the system, from the beginning of instrument assembly and software installation to full operation, can be completed in 3-4 d.

  16. Simultaneous translocations of FGFR3/MMSET and CCND1 into two different IGH alleles in multiple myeloma: lack of concurrent activation of both proto-oncogenes.

    PubMed

    Sáez, Borja; Martín-Subero, José I; Lahortiga, Idoya; Largo, Cristina; Larrayoz, María J; Odero, María D; Prosper, Felipe; Cigudosa, Juan C; Siebert, Reiner; Calasanz, María J

    2007-05-01

    The simultaneous occurrence of two different translocations affecting both alleles of the IGH gene has rarely been reported in multiple myeloma. In such a case, two different oncogenes might become transcriptionally deregulated. To investigate this hypothesis, we have characterized the plasma cell leukemia cell line SK-MM2 and a primary myeloma both carrying simultaneous IGH-FGFR3/MMSET and IGH-CCND1 fusions as shown by multicolor fluorescence in situ hybridization. Remarkably, quantitative real-time polymerase chain reaction demonstrated that only one of the oncogene loci was transcriptionally upregulated in both instances. Moreover, the upregulated oncogenes differed between both samples. Thus, biallelic IGH translocations might exert different pathogenetic effects in plasma cell disorders.

  17. 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.

  18. 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. PMID:27094273

  19. Molecular genotyping of human Ureaplasma species based on multiple-banded antigen (MBA) gene sequences.

    PubMed

    Kong, F; Ma, Z; James, G; Gordon, S; Gilbert, G L

    2000-09-01

    Ureaplasma urealyticum has been divided into 14 serovars. Recently, subdivision of U. urealyticum into two species has been proposed: U. parvum (previously U. urealyticum parvo biovar), comprising four serovars (1, 3, 6, 14) and U. urealyticum (previously U. urealyticum T-960 biovar), 10 serovars (2, 4, 5, 7-13). The multiple-banded antigen (MBA) genes of these species contain both species and serovar/subtype specific sequences. Based on whole sequences of the 5'-ends of MBA genes of U. parvum serovars and partial sequences of the 5'-ends of MBA genes of U. urealyticum serovars, we previously divided each of these species into three MBA genotypes. To further elucidate the relationships between serovars, we sequenced the whole 5'-ends of MBA genes of all 10 U. urealyticum serovars and partial repetitive regions of these genes from all serovars of U. parvum and U. urealyticum. For the first time, all four serovars of U. parvum were clearly differentiated from each other. In addition, the 10 serovars of U. urealyticum were divided into five MBA genotypes, as follows: MBA genotype A comprises serovars 2, 5, 8; MBA genotype B, serovar 10 only; MBA genotype C, serovars 4, 12, 13; MBA genotype D, serovar 9 only; and MBA genotype E comprises serovars 7 and 11. There were no sequence differences between members within each MBA genotype. Further work is required to identify other genes or other regions of the MBA genes that may be used to differentiate U. urealyticum serovars within MBA genotypes A, C and E. A better understanding of the molecular basis of serotype differentiation will help to improve subtyping methods for use in studies of the pathogenesis and epidemiology of these organisms.

  20. 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

  1. 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

  2. Multiple mating and its relationship to alternative modes of gestation in male-pregnant versus female-pregnant fish species

    PubMed Central

    Avise, John C.; Liu, Jin-Xian

    2010-01-01

    We construct a verbal and graphical theory (the “fecundity-limitation hypothesis”) about how constraints on the brooding space for embryos probably truncate individual fecundity in male-pregnant and female-pregnant species in ways that should differentially influence selection pressures for multiple mating by males or by females. We then review the empirical literature on genetically deduced rates of multiple mating by the embryo-brooding parent in various fish species with three alternative categories of pregnancy: internal gestation by males, internal gestation by females, and external gestation (in nests) by males. Multiple mating by the brooding gender was common in all three forms of pregnancy. However, rates of multiple mating as well as mate numbers for the pregnant parent averaged higher in species with external as compared with internal male pregnancy, and also for dams in female-pregnant species versus sires in male-pregnant species. These outcomes are all consistent with the theory that different types of pregnancy have predictable consequences for a parent's brood space, its effective fecundity, its opportunities and rewards for producing half-sib clutches, and thereby its exposure to selection pressures for seeking multiple mates. Overall, we try to fit these fecundity-limitation phenomena into a broader conceptual framework for mating-system evolution that also includes anisogamy, sexual-selection gradients, parental investment, and other selective factors that can influence the relative proclivities of males versus females to seek multiple sexual partners. PMID:20956296

  3. 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.

  4. A putative role for Toxocara species in the aetiology of multiple sclerosis.

    PubMed

    Söndergaard, Hans Peter; Theorell, Töres

    2004-01-01

    Multiple sclerosis (MS) is a disease of unknown aetiology. The finding of monoclonal antibodies in MS has been attributed to various infectious agents. Nematodes, such as Toxocara species have not been explored as possible aetiologic agents of MS. Some epidemiological studies have found an association between exposure to stress and household pets prior to the diagnosis of MS. In a case known to the authors, slight malaise and eosinophilia in peripheral blood preceded the diagnosis of MS by one year in a middle-aged man who lived in rural surroundings with cats in the household. The ubiquitary parasite Toxocara catis or canis is prevalent and serum antibodies are found regularly in populations examined. It is able to develop into the larval stage in human beings. The hypothesis presented here is that MS could be initiated by such infections in previously unexposed subjects under conditions of long-term stress. PMID:15193348

  5. Extension of the Si:C Stressor Thickness by Using Multiple ClusterCarbon Species

    SciTech Connect

    Sekar, Karuppanan; Krull, Wade

    2011-01-07

    ClusterCarbon implantation is now well established as an attractive alternative for producing stress in advanced NMOS devices. ClusterCarbon has the advantage over monomer carbon implant in it's self-amorphization feature, eliminating the need for PAI implantation while producing highly substitutional carbon incorporation. To date, the limitation of this approach has been the high energy limit, due to the extraction limit of the available production tools for the preferred carbon species, which has been the C7Hx molecule. It is noted that the C7 species is produced by the breakup of the parent C14H14 molecule in the ion source. It is further noted that the preferred method of producing the Si:C stress layer is a multiple implant sequence with ClusterCarbon implants at various energies and doses designed to produce a carbon profile which is constant in-depth. The stressor thickness limit using C7 is known to be about 40 nm, which is less than the stressor thickness used in the conventional SiGe process for PMOS. In this work, it is shown that utilizing the C5 molecule which is also available from the breakup of C14H14 enables the stressor layer thickness to be extended to at least 60 nm, which is consistent with the conventional SiGe process. It will be shown that one additional C5 implant, performed after a standard C7 multiple implant sequence, can produce the extension of the stressor thickness while maintaining the flat depth profile. A detailed process characterization will be shown for this new process sequence.

  6. 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.

  7. Invasive species information networks: Collaboration at multiple scales for prevention, early detection, and rapid response to invasive alien species

    USGS Publications Warehouse

    Simpson, A.; Jarnevich, C.; Madsen, J.; Westbrooks, R.; Fournier, C.; Mehrhoff, L.; Browne, M.; Graham, J.; Sellers, E.

    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

  8. The formation of electronically excited species in the human multiple myeloma cell suspension

    PubMed Central

    Rác, Marek; Sedlářová, Michaela; Pospíšil, Pavel

    2015-01-01

    In this study, evidence is provided on the formation of electronically excited species in human multiple myeloma cells U266 in the growth medium exposed to hydrogen peroxide (H2O2). Two-dimensional imaging of ultra-weak photon emission using highly sensitive charge coupled device camera revealed that the addition of H2O2 to cell suspension caused the formation of triplet excited carbonyls 3(R = O)*. The kinetics of 3(R = O)* formation in the real time, as measured by one-dimensional ultra-weak photon emission using low-noise photomultiplier, showed immediate enhancement followed by a slow decay. In parallel to the formation of 3(R = O)*, the formation of singlet oxygen (1O2) in U266 cells caused by the addition of H2O2 was visualized by the imaging of 1O2 using the green fluorescence of singlet oxygen sensor green detected by confocal laser scanning microscopy. Additionally, the formation of 1O2 after the addition of H2O2 to cell suspension was detected by electron paramagnetic resonance spin-trapping spectroscopy using 2,2,6,6-tetramethyl-4-piperidone. Presented results indicate that the addition of H2O2 to cell suspension results in the formation of 3(R = O)* and 1O2 in U266 cell suspension. The contribution of the cell-free medium to the formation of electronically excited species was discussed. PMID:25744165

  9. 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.

  10. 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. PMID:27261257

  11. Enhancement of Innate and Adaptive Immune Functions by Multiple Echinacea Species

    PubMed Central

    Zhai, Zili; Liu, Yi; Wu, Lankun; Senchina, David S.; Wurtele, Eve S.; Murphy, Patricia A.; Kohut, Marian L.; Cunnick, Joan E.

    2008-01-01

    Echinacea preparations are commonly used as nonspecific immunomodulatory agents. Alcohol extracts from three widely used Echinacea species, Echinacea angustifolia, Echinacea pallida, and Echinacea purpurea, were investigated for immunomodulating properties. The three Echinacea species demonstrated a broad difference in concentrations of individual lipophilic amides and hydrophilic caffeic acid derivatives. Mice were gavaged once a day (for 7 days) with one of the Echinacea extracts (130 mg/kg) or vehicle and immunized with sheep red blood cells (sRBC) 4 days prior to collection of immune cells for multiple immunological assays. The three herb extracts induced similar, but differential, changes in the percentage of immune cell populations and their biological functions, including increased percentages of CD49+ and CD19+ lymphocytes in spleen and natural killer cell cytotoxicity. Antibody response to sRBC was significantly increased equally by extracts of all three Echinacea species. Concanavalin A-stimulated splenocytes from E. angustifolia- and E. pallida-treated mice demonstrated significantly higher T cell proliferation. In addition, the Echinacea treatment significantly altered the cytokine production by mitogen-stimulated splenic cells. The three herbal extracts significantly increased interferon-γ production, but inhibited the release of tumor necrosis factor-α and interleukin (IL)-1β. Only E. angustifolia- and E. pallida-treated mice demonstrated significantly higher production of IL-4 and increased IL-10 production. Taken together, these findings demonstrated that Echinacea is a wide-spectrum immunomodulator that modulates both innate and adaptive immune responses. In particular, E. angustifolia or E. pallida may have more anti-inflammatory potential. PMID:17887935

  12. 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.

  13. 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.

  14. 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. PMID:26142614

  15. 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. PMID:24926893

  16. Multiple effects of host-species diversity on coexisting host-specific and host-opportunistic microbes.

    PubMed

    Kedem, Hadar; Cohen, Carmit; Messika, Irit; Einav, Monica; Pilosof, Shai; Hawlena, Hadas

    2014-05-01

    While host-species diversity often influences microbial prevalence, there may be multiple mechanisms causing such effects that may also depend on the foraging strategy of the microbes. We employed a natural gradient of rodent-species richness to examine competing hypotheses describing possible mechanisms mediating the relationship between host-species richness and the prevalence of the most dominant microbes, along with microbe specificity to the different rodent host species. We sampled blood from three gerbil species in plots differing in terms of the proportion of the different species and screened for the most dominant bacteria. Two dominant bacterial lineages were detected: host-specific bacteria and host-opportunistic bacteria. Using a model selection approach, we detected evidence for both direct and indirect effects of host-species richness on the prevalence of these bacteria. Infection probability of the host-specific lineage was lower in richer host communities, most likely due to increased frequency and density of the least suitable host species. In contrast, field observations suggest that the effect of host-species richness on infection probability of the opportunistic lineage was both direct and indirect, mostly mediated by changes in flea densities on the host and by the presence of the host-specific lineage. Our results thus suggest that host-species richness has multiple effects on microbial prevalence, depending on the degree of host-specificity of the microbe in question. PMID:25000749

  17. Field cryofocussing hydride generation applied to the simultaneous multi-elemental determination of alkyl-metal(loid) species in natural waters using ICP-MS detection.

    PubMed

    Tseng, C M; Amouroux, D; Brindle, I D; Donard, O F

    2000-12-01

    Two hydride generation manifold systems, utilizing flow injection and cryotrapping techniques for alkyl-metal(loid) speciation analysis in natural waters, are described in this paper. They provide shipboard capacity for simultaneous derivatization of analytes with NaBH4 and cryotrapping of the generated products in a field packed column at -196 degrees C. The first system is a large-volume hydride generator, using a reagent-injection flow technique as a flow batch type, that has been fully optimized and applied to the simultaneous detection of alkylated species in estuarine waters. The technique permits the analysis of a large volume sample (0.5-11) at a sampling rate of 3 h-1. The second is an online continuous flow hydride generator. A sampling rate of 3-12 h-1 can be achieved with samples of 0.1-0.51. In addition, shipboard operation eliminates major problems related to sample pretreatment, transport and storage. Ultra-trace multi-element determination is finally performed in the laboratory by cryogenic GC hyphenated with ICP-MS. Routine detection limits of 0.5-10 pg (as metal) for 0.51 water samples were achieved for the selected alkyl-metal(loid) species of arsenic, germanium, mercury and tin. Concentrations of various species, obtained from water samples taken from the Rhine estuary, are also presented. These species include alkylated arsenic compounds, other than methyl derivatives, that have been tentatively identified and are reported here for the first time.

  18. 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. PMID:27451225

  19. 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.

  20. 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

    2011-12-01

    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.

  1. 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.

  2. Simultaneous analysis of multiple classes of antibiotics by ion trap LC/MS/MS for assessing surface water and groundwater contamination.

    PubMed

    Batt, Angela L; Aga, Diana S

    2005-05-01

    Solid-phase extraction (SPE) and liquid chromatography in combination with ion trap mass spectrometry (LC/MS/MS) conditions were optimized for the simultaneous analysis of 13 antibiotics belonging to multiple classes and caffeine in 3 different water matrixes. The single-cartridge extraction step was developed using a reversed-phase cartridge, resulting in recoveries for the 14 compounds ranging from 71 to 119% with relative standard deviations of 16% or lower. The analytes were separated in one chromatographic run, and the SPE-LC/MS/MS detection limits ranged from 0.03 to 0.19 microg/L. The SPE procedure was validated in groundwater, surface water, and wastewater. The analysis of samples from each of the three water matrixes revealed clindamycin (1.1 microg/L) in surface water and multiple antibiotics in wastewater (0.10-1.3 microg/L). The use of identification points to unambiguously assign the identity of antibiotics in various water matrixes was applied to an ion trap data-dependent scanning method, which simultaneously collects full scan and full scan MS/MS data for the unequivocal identification of target analytes.

  3. 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...

  4. Simple method for the rapid simultaneous screening of photocatalytic activity over multiple positions of self-cleaning films.

    PubMed

    Kafizas, Andreas; Adriaens, Davy; Mills, Andrew; Parkin, Ivan P

    2009-10-01

    An intelligent ink, previously shown to be capable of rapidly assessing photocatalytic activity, was simply applied via a felt-pen onto a commercially available piece of Activ self-cleaning glass. The ink, comprising of redox dye resazurin and the sacrificial electron donor glycerol within an aqueous hydroxy ethyl cellulose (HEC) polymer media, was photocatalytically degraded in a two-step process. The key initial stage was the photo-reductive conversion of resazurin to resorufin, whereby a colour change from blue to pink occurred. The latter stage was the subsequent photo-reduction of the resorufin, where a slower change from pink to colourless was seen. Red and green components of red-green-blue colour extracted from flat-bed scanner digital images of resazurin ink coated photocatalytic films at intervals during the photocatalysis reaction were inversely proportional to the changes seen via UV-visible absorption spectroscopy and indicative of reaction kinetics. A 3 x 3 grid of intelligent ink was drawn onto a piece of Activ and a glass blank. The photocatalysis reaction was monitored solely by flat-bed digital scanning. Red-green-blue values of respective positions on the grid were extracted using a custom-built program entitled RGB Extractor. The program was capable of extracting a number of 5 x 5 pixel averages of red-green-blue components simultaneously. Allocation of merely three coordinates allowed for the automatic generation of a grid, with scroll-bars controlling the number of positions to be extracted on the grid formed. No significant change in red and green components for any position on the glass blank was observed; however, the Activ film displayed a homogenous photo-reduction of the dye, reaching maxima in red and minima in green components in 23 +/- 3 and 14 +/- 2 min, respectively. A compositionally graded N-doped titania film synthesised in house via a combinatorial APCVD reaction was also photocatalytically tested by this method where 247

  5. 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.

  6. 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.

  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. 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.

  9. Simultaneous Expression of Multiple Proteins Under a Single Promoter in Caenorhabditis elegans via a Versatile 2A-Based Toolkit

    PubMed Central

    Ahier, Arnaud; Jarriault, Sophie

    2014-01-01

    Caenorhabditis elegans is a powerful in vivo model in which transgenesis is highly developed. However, while the analysis of biological phenomena often require the expression of more than one protein of interest, no reliable tool exists to ensure efficient concomitant and equivalent expression of more than two polypeptides from a single promoter. We report the use of viral 2A peptides, which trigger a “ribosomal-skip” or “STOP&GO” mechanism during translation, to express multiple proteins from a single vector in C. elegans. Although none of the viruses known to infect C. elegans contain 2A-like sequences, our results show that 2A peptides allow the production of separate functional proteins in all cell types and at all developmental stages tested in the worm. In addition, we constructed a toolkit including a 2A-based polycistronic plasmid and reagents to generate 2A-tagged fosmids. 2A peptides constitute an important tool to ensure the delivery of multiple polypeptides in specific cells, enabling several novel applications such as the reconstitution of multi-subunit complexes. PMID:24361941

  10. Micropatterned superhydrophobic structures for the simultaneous culture of multiple cell types and the study of cell-cell communication.

    PubMed

    Efremov, Alexander N; Stanganello, Eliana; Welle, Alexander; Scholpp, Steffen; Levkin, Pavel A

    2013-02-01

    The ability to control spatial arrangement and geometry of different cell types while keeping them separated and in close proximity for a long time is crucial to mimic and study variety of biological processes in vitro. Although the existing cell patterning technologies allow co-culturing of different cell types, they are usually limited to relatively simple geometry. The methods used for obtaining complex geometries are usually applicable for patterning only one or two cell types. Here we introduce a convenient method for creating patterns of multiple (up to twenty) different cell types on one substrate. The method virtually allows any complexity of cell pattern geometry. Cell positioning on the substrate is realized by a parallel formation of multiple cell-containing microreservoirs confined to the geometry of highly hydrophilic regions surrounded by superhydrophobic borders built-in a fine nanoporous polymer film. As a case study we showed the cross-talk between two cell populations via Wnt signaling molecules propagation during co-culture in a mutual culture medium. PMID:23228425

  11. Multiple infections and diversity of cytoplasmic incompatibility in a haplodiploid species.

    PubMed

    Mouton, L; Henri, H; Boulétreau, M; Vavre, F

    2005-02-01

    Cytoplasmic incompatibility (CI) is a sperm-egg incompatibility commonly induced by the intracellular endosymbiont bacterium Wolbachia that, in diploid species, results in embryo mortality. In haplodiploid species, two types of CI exist depending on whether the incompatible fertilized eggs develop into males (male development (MD)) or abort (female mortality (FM)). CI allows multiple infections to be maintained in host populations, and thus allows interactions to occur between co-infecting strains. In Leptopilina heterotoma, three Wolbachia strains coexist naturally (wLhet1, wLhet2, wLhet3). When these three strains are all present, they induce a CI of FM type, whereas wLhet1 alone expresses a CI phenotype intermediate between MD and FM. Here, we compare CI effects in crosses involving insect lines sharing the same nuclear background, but harboring different mixtures of strains. Mating experiments showed that: (i) wLhet2 and wLhet3 also induce an intermediate CI when acting alone, and show a bidirectional incompatibility; (ii) there is no interaction between the co-infecting strains in CI expression; (iii) the diversity of Wolbachia present within a male host influences the expression of CI: an increase in the number of strains is correlated with a decrease in the proportion of the MD type, which is also correlated with an increase in bacterial density. All these data suggest that the CI of FM type results from a stronger effect than the MD type, which conflicts with the conventional hypotheses used to explain CI diversity in haplodiploids, and could provide some new information about CI mechanisms in insects. PMID:15562287

  12. A new acid-fast trichrome stain for simultaneous detection of Cryptosporidium parvum and microsporidial species in stool specimens.

    PubMed

    Ignatius, R; Lehmann, M; Miksits, K; Regnath, T; Arvand, M; Engelmann, E; Futh, U; Hahn, H; Wagner, J

    1997-02-01

    The detection in stool specimens of Cryptosporidium parvum and microsporidia, the most frequent parasitic pathogens causing diarrhea in AIDS patients, until now has depended on two different staining methods. However, since double infections occur and minimization of laboratory costs is mandatory, development of a method for simultaneous detection of these parasites appeared desirable. We report on a new, inexpensive, and easy-to-perform staining procedure to demonstrate both acid-fast oocysts of C. parvum and other coccidia, as well as microsporidial spores. This acid-fast trichrome stain yields results comparable to those obtained by the Kinyoun and modified trichrome methods and considerably reduces the time necessary for microscopic examination.

  13. 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

  14. Single-Isocenter Frameless Intensity-Modulated Stereotactic Radiosurgery for Simultaneous Treatment of Multiple Brain Metastases: Clinical Experience

    SciTech Connect

    Nath, Sameer K.; Lawson, Joshua D.; Simpson, Daniel R.

    2010-09-01

    Purpose: To describe our clinical experience using a unique single-isocenter technique for frameless intensity-modulated stereotactic radiosurgery (IM-SRS) to treat multiple brain metastases. Methods and Materials: Twenty-six patients with a median of 5 metastases (range, 2-13) underwent optically guided frameless IM-SRS using a single, centrally located isocenter. Median prescription dose was 18 Gy (range, 14-25). Follow-up magnetic resonance imaging (MRI) and clinical examination occurred every 2-4 months. Results: Median follow-up for all patients was 3.3 months (range, 0.2-21.3), with 20 of 26 patients (77%) followed up until their death. For the remaining 6 patients alive at the time of analysis, median follow-up was 14.6 months (range, 9.3-18.0). Total treatment time ranged from 9.0 to 38.9 minutes (median, 21.0). Actuarial 6- and 12-month overall survivals were 50% (95% confidence interval [C.I.], 31-70%) and 38% (95% C.I., 19-56%), respectively. Actuarial 6- and 12-month local control (LC) rates were 97% (95% C.I., 93-100%) and 83% (95% C.I., 71-96%), respectively. Tumors {<=}1.5 cm had a better 6-month LC than those >1.5 cm (98% vs. 90%, p = 0.008). New intracranial metastatic disease occurring outside of the treatment volume was observed in 7 patients. Grade {>=}3 toxicity occurred in 2 patients (8%). Conclusion: Frameless IM-SRS using a single-isocenter approach for treating multiple intracranial metastases can produce clinical outcomes that compare favorably with those of conventional SRS in a much shorter treatment time (<40 minutes). Given its faster treatment time, this technique is appealing to both patients and personnel in busy clinics.

  15. 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.

  16. Infestation of Wild-caught American Bullfrogs (Rana catesbeiana) by Multiple Species of Metazoan Parasites

    PubMed Central

    Lemke, Laura B; Dronen, Norman; Fox, James G; Nambiar, Prashant R

    2008-01-01

    The American bullfrog (Rana catesbeiana) is an aquatic, carnivorous member of the family Ranidae that is used extensively in physiology education programs and in various physiology, toxicology, sensorineural, and genetics research. Eleven bullfrogs purchased from a vendor distributing wild-caught frogs for use in a physiology research protocol were emaciated but otherwise showed no apparent clinical signs of illness. Necropsies performed on selected emaciated frogs indicated heavy infestation with multiple species of endoparasites. Identified helminths included Gorgodera amplicava, Haematolechus breviplexus, Clinostomum spp, Contracaecum spp, Cosmocercoides dukae, and Eustrongyloides spp. Grossly, parasitized bullfrogs showed encysted trematode larvae within skeletal muscle, nematode impaction of the intestinal tract, and lack of coelemic fat stores. Histopathologic lesions were restricted primarily to the gastrointestinal tract and consisted of parasitic granulomas associated with Contracaecum spp. The parasitic lesions may have been associated with the poor body condition of the bullfrogs. Food crickets maintained in-house were negative for parasite larvae or ova. Heavy parasitism of wild-caught bullfrogs may confound research protocols and markedly impair animal health. We encourage researchers to purchase laboratory-bred and -reared bullfrogs and to routinely monitor the parasite status of colony frogs. PMID:18459712

  17. Infestation of wild-caught American bullfrogs (Rana catesbeiana) by multiple species of metazoan parasites.

    PubMed

    Lemke, Laura B; Dronen, Norman; Fox, James G; Nambiar, Prashant R

    2008-05-01

    The American bullfrog (Rana catesbeiana) is an aquatic, carnivorous member of the family Ranidae that is used extensively in physiology education programs and in various physiology, toxicology, sensorineural, and genetics research. Eleven bullfrogs purchased from a vendor distributing wild-caught frogs for use in a physiology research protocol were emaciated but otherwise showed no apparent clinical signs of illness. Necropsies performed on selected emaciated frogs indicated heavy infestation with multiple species of endoparasites. Identified helminths included Gorgodera amplicava, Haematolechus breviplexus, Clinostomum spp, Contracaecum spp, Cosmocercoides dukae, and Eustrongyloides spp. Grossly, parasitized bullfrogs showed encysted trematode larvae within skeletal muscle, nematode impaction of the intestinal tract, and lack of coelemic fat stores. Histopathologic lesions were restricted primarily to the gastrointestinal tract and consisted of parasitic granulomas associated with Contracaecum spp. The parasitic lesions may have been associated with the poor body condition of the bullfrogs. Food crickets maintained in-house were negative for parasite larvae or ova. Heavy parasitism of wild-caught bullfrogs may confound research protocols and markedly impair animal health. We encourage researchers to purchase laboratory-bred and -reared bullfrogs and to routinely monitor the parasite status of colony frogs. PMID:18459712

  18. Infestation of wild-caught American bullfrogs (Rana catesbeiana) by multiple species of metazoan parasites.

    PubMed

    Lemke, Laura B; Dronen, Norman; Fox, James G; Nambiar, Prashant R

    2008-05-01

    The American bullfrog (Rana catesbeiana) is an aquatic, carnivorous member of the family Ranidae that is used extensively in physiology education programs and in various physiology, toxicology, sensorineural, and genetics research. Eleven bullfrogs purchased from a vendor distributing wild-caught frogs for use in a physiology research protocol were emaciated but otherwise showed no apparent clinical signs of illness. Necropsies performed on selected emaciated frogs indicated heavy infestation with multiple species of endoparasites. Identified helminths included Gorgodera amplicava, Haematolechus breviplexus, Clinostomum spp, Contracaecum spp, Cosmocercoides dukae, and Eustrongyloides spp. Grossly, parasitized bullfrogs showed encysted trematode larvae within skeletal muscle, nematode impaction of the intestinal tract, and lack of coelemic fat stores. Histopathologic lesions were restricted primarily to the gastrointestinal tract and consisted of parasitic granulomas associated with Contracaecum spp. The parasitic lesions may have been associated with the poor body condition of the bullfrogs. Food crickets maintained in-house were negative for parasite larvae or ova. Heavy parasitism of wild-caught bullfrogs may confound research protocols and markedly impair animal health. We encourage researchers to purchase laboratory-bred and -reared bullfrogs and to routinely monitor the parasite status of colony frogs.

  19. 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. PMID:18508807

  20. Progesterone supplementation during multiple ovulation treatment in buffalo species (Bubalus bubalis).

    PubMed

    Neglia, Gianluca; Gasparrini, Bianca; Vecchio, Domenico; Rubessa, Marcello; Di Palo, Rossella; Zicarelli, Luigi; Campanile, Giuseppe

    2010-08-01

    The aim of this study was to evaluate the effect of exogenous progesterone supplementation on superovulatory response in buffaloes that has undergone a multiple ovulation program. Fourteen Mediterranean buffaloes were divided into two groups and received a 4-day decreasing dosage of an equal mixture of 500 IU of FSH and LH starting on day 8 of the cycle. In group A (n = 7) a progesterone-releasing intravaginal device was removed on day 8, whereas in group B (n = 7) it was left till day 10, when PGF2alpha was administered. Eighty hours later, buffaloes were artificially inseminated and after 6 days they undergone uterine flushing. A higher (P < 0.05) number of corpora lutea (8.3 vs. 5.7) and embryo/flushing/buffalo (2.3 vs. 1.3) were recorded in group B vs. group A if responsive buffaloes are considered (n = 12) and the number of corpora lutea was highly correlated with the number of embryos (r = 0.65; P < 0.05). In conclusion, progesterone supplementation during the first 2 days of the superovulation treatment seems to enhance the recovery rate in buffalo species. A high ovulation rate, associated with a high number of corpora lutea, can represent a parameter for estimating embryo recovery. PMID:20411328

  1. A tomographic technique for the simultaneous imaging of temperature, chemical species, and pressure in reactive flows using absorption spectroscopy with frequency-agile lasers

    SciTech Connect

    Cai, Weiwei; Kaminski, Clemens F.

    2014-01-20

    This paper proposes a technique that can simultaneously retrieve distributions of temperature, concentration of chemical species, and pressure based on broad bandwidth, frequency-agile tomographic absorption spectroscopy. The technique holds particular promise for the study of dynamic combusting flows. A proof-of-concept numerical demonstration is presented, using representative phantoms to model conditions typically prevailing in near-atmospheric or high pressure flames. The simulations reveal both the feasibility of the proposed technique and its robustness. Our calculations indicate precisions of ∼70 K at flame temperatures and ∼0.05 bars at high pressure from reconstructions featuring as much as 5% Gaussian noise in the projections.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Simultaneous determination of multiple amino acids in plasma in critical illness by high performance liquid chromatography with ultraviolet and fluorescence detection.

    PubMed

    Wang, Hao; McNeil, Yvette R; Yeo, Tsin W; Anstey, Nicholas M

    2013-12-01

    There is increasing recognition that the host response to critical illness includes derangement of multiple amino acid pathways, including amino acids (AAs) central to metabolism and immune, endothelial and neurological function. To characterise concentration changes of these plasma amino acid we report the development and validation of a method for the quantification of AAs in small volumes of plasma (50μL) using HPLC with simultaneous UV and fluorescence (FL) detection. Protein precipitation and pre-column derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) is followed by reversed phase HPLC separation. Calibration curves were built with norleucine as an internal standard. Thirty-three (including the 20 proteinogenic) AAs, were selected as standards and their corresponding concentrations in the plasma of healthy human controls and patients with severe falciparum malaria were quantified. This method enables the detection of perturbations in arginine metabolism, aromatic amino acid pathways, methionine transsulfuration and transmethylation pathways and other metabolic pathways.

  11. 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.

  12. 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. PMID:19610365

  13. Simultaneous Quantification of Apolipoprotein A-I and Apolipoprotein B by Liquid-Chromatography–Multiple-Reaction–Monitoring Mass Spectrometry

    PubMed Central

    Agger, Sean A.; Marney, Luke C.; Hoofnagle, Andrew N.

    2011-01-01

    BACKGROUND If liquid-chromatography–multiple-reaction–monitoring mass spectrometry (LC-MRM/MS) could be used in the large-scale preclinical verification of putative biomarkers, it would obviate the need for the development of expensive immunoassays. In addition, the translation of novel biomarkers to clinical use would be accelerated if the assays used in preclinical studies were the same as those used in the clinical laboratory. To validate this approach, we developed a multiplexed assay for the quantification of 2 clinically well-known biomarkers in human plasma, apolipoprotein A-I and apolipoprotein B (apoA-I and apoB). METHODS We used PeptideAtlas to identify candidate peptides. Human samples were denatured with urea or trifluoroethanol, reduced and alkylated, and digested with trypsin. We compared reversed-phase chromatographic separation of peptides with normal flow and microflow, and we normalized endogenous peptide peak areas to internal standard peptides. We evaluated different methods of calibration and compared the final method with a nephelometric immunoassay. RESULTS We developed a final method using trifluoroethanol denaturation, 21-h digestion, normal flow chromatography-electrospray ionization, and calibration with a single normal human plasma sample. For samples injected in duplicate, the method had intraassay CVs <6% and interassay CVs <12% for both proteins, and compared well with immunoassay (n = 47; Deming regression, LC-MRM/MS = 1.17 × immunoassay – 36.6; Sx|y = 10.3 for apoA-I and LC-MRM/MS = 1.21 × immunoassay + 7.0; Sx|y = 7.9 for apoB). CONCLUSIONS Multiplexed quantification of proteins in human plasma/serum by LC-MRM/MS is possible and compares well with clinically useful immunoassays. The potential application of single-point calibration to large clinical studies could simplify efforts to reduce day-to-day digestion variability. PMID:20923952

  14. Quality Evaluation of Scrophulariae Radix Processed by Different 'Sweating' Methods Based on Simultaneous Determination of Multiple Bioactive Constituents Combined with Grey Relational Analysis.

    PubMed

    Wang, Shengnan; Hua, Yujiao; Xu, Li; Zou, Lisi; Liu, Xunhong; Luo, Yiyuan; Liu, Juanxiu; Yan, Ying

    2016-01-01

    Scrophulariae Radix is one of the most popular traditional Chinese medicines (TCMs), which needs to be processed by 'sweating' methods. Primary processing of Scrophulariae Radix is an important link which closely relates to the quality of products in this TCM. To facilitate selection of the suitable 'sweating' processing method for Scrophulariae Radix, in this study the quality of Scrophulariae Radix processed by different 'sweating' methods was evaluated based on simultaneous determination of multiple bioactive constituents combined with grey relational analysis. The contents of iridoid glycosides, phenylpropanoid glycosides, and organic acids in Scrophulariae Radix processed by different 'sweating' methods were simultaneously determined using ultra high performance liquid chromatography coupled with triple quadrupole-linear ion trap mass spectrometry (UPLC-QTRAP-MS/MS). Furthermore, grey relational analysis (GRA) was performed to evaluate the 'sweating' processed samples according to the contents of twelve constituents. All of the results demonstrated that the quality of Scrophulariae Radix processed by oven drying at 35 °C and 'sweating' for three days was better. The developed method was useful for the overall assessment on quality of Scrophulariae Radix, and this study may provide the foundation and support for 'sweating' processing of Scrophulariae Radix in normalization and standardization. PMID:27367656

  15. 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).

  16. 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.

  17. Flow injection simultaneous determination of synthetic colorants in food using multiple pulse amperometric detection with a boron-doped diamond electrode.

    PubMed

    Medeiros, Roberta A; Lourencao, Bruna C; Rocha-Filho, Romeu C; Fatibello-Filho, Orlando

    2012-09-15

    A single-line flow injection system and multiple pulse amperometric detection using a boron-doped diamond electrode were employed to develop and optimize a simple, low-cost, and rapid method for the simultaneous determination of two pairs of food colorants: tartrazine and sunset yellow (TT-SY) or brilliant blue and SY (BB-SY). A dual-potential waveform was used: E(det.1)=-150 mV (400 ms duration) and E(det.2)=-450 mV (100 ms duration) vs. Ag/AgCl (3.0 mol L(-1) KCl). Polarization at E(det.1) or E(det.2) causes reduction of SY or the respective pair of colorants, TT-SY or BB-SY; hence, with proper current correction, both colorants in each pair can be determined. The obtained linear response ranges (detection limits) were 5.0-60.0 (2.5) and 1.0-50.0 (0.80) μmol L(-1), for TT and SY, or 5.0-60.0 (3.5) and 1.0-50.0 (0.85) μmol L(-1), for BB and SY, respectively. Investigation of possible interferents (other food colorants or additives) showed no significant interference with the methods here proposed, which were then used to simultaneously determine the pairs of colorants in industrialized food samples, with results that showed good agreement with those obtained using a comparative HPLC method.

  18. Simultaneous use of camera and probe diagnostics to unambiguously identify and study the dynamics of multiple underlying instabilities during the route to plasma turbulence.

    PubMed

    Thakur, S C; Brandt, C; Light, A; Cui, L; Gosselin, J J; Tynan, G R

    2014-11-01

    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.

  19. 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...

  20. 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...

  1. Importance of Simultaneous Evaluation of Multiple Risk Factors for Hemodialysis Patients’ Mortality and Development of a Novel Index: Dialysis Outcomes and Practice Patterns Study

    PubMed Central

    2015-01-01

    Background For hemodialysis (HD) patients, many risk factors for death are associated with each other intricately. However, they are often considered separately in clinical settings. We evaluated the maintenance HD patients’ risk of death within one year from multiple risk factors simultaneously considering their interrelationships using a novel index (survival index, SI) for HD patients in the United States developed using data from the Dialysis Outcomes and Practice Patterns Study (DOPPS). Methods We analyzed data from 3899 and 3765 patients to develop and validate SI, respectively. To predict death within one year, candidate models were developed using logistic regression models. The final model was determined by comparing the accuracy among the models for the prediction of deaths. Results The model included age; body mass index; serum creatinine, albumin, total cholesterol and phosphorus levels; history of cardiovascular diseases; and arteriovenous fistula use. SI showed a higher accuracy in predicting death (c-statistic, 0.739) than geriatric nutritional risk index (0.647) and serum albumin level (0.637). The probability of death predicted on the basis of SI matched the observed number of deaths. Cox proportional hazard models for time-dependent SI showed that patients with low SI had a higher risk of death than patients with high SI [reference, Group 4 (26.1≤SI)]; Group 1 (SI<12.7), adjusted hazard ratio, 7.97 (95% CI, 5.02, 12.65); Group 2 (12.7≤SI<19.0), 3.18 (95% CI, 1.96, 5.16); Group 3 (19.0≤SI<26.1), 2.20 (95% CI, 1.33, 3.66). Conclusion Results of this study suggest that the simultaneous evaluation of multiple risk factors can more accurately assess patients’ prognosis and identify patients at an increased risk of death than single factors. PMID:26030526

  2. Simultaneous determination of eight coumarins in Angelica gigas and in various other Angelica species by high performance liquid chromatography and comparative micro-morphology study of Angelica species.

    PubMed

    Avula, Bharathi; Joshi, Vaishali C; Reddy V L, Niranjan; Choi, Young-Whan; Khan, Ikhlas A

    2007-11-01

    This article outlines the development of a simple and specific analytical method for the quantitative determination of eight coumarin constituents from the methanolic extract of the roots of Angelica gigas. The coumarin constituents present in the roots of Angelica gigas were separated using an acetonitrile (0.1 % acetic acid)-water (0.1 % acetic acid)-reagent alcohol gradient solvent system at a flow rate of 1.0 mL per minute. The HPLC separation was performed using a Phenomenex C12 reversed phase column with detection at 328 nm. The method was successfully used to study the percentage compositions of eight coumarins present in various Angelica species procured from S. Korea. Additionally, this manuscript provides a detailed microscopic account for the authentication of Angelica gigas and compared it with other Angelica species. The microscopic evaluation of plant tissue samples plays a vital role in botanical authentication. The combination of these two methodologies will provide additional tools for the evaluation of various Angelica species.

  3. New method for the simultaneous identification of cow, sheep, goat, and water buffalo in dairy products by analysis of short species-specific mitochondrial DNA targets.

    PubMed

    Gonçalves, Joana; Pereira, Filipe; Amorim, António; van Asch, Barbara

    2012-10-24

    A novel method is presented here as an analytical tool for food control and authentication of dairy products manufactured from the milk of cow, sheep, goat, and buffalo. The method is based on multiplex polymerase chain reaction (PCR) of species-specific mitochondrial DNA (mtDNA) targets followed by fragment size analysis by capillary electrophoresis. The method includes (a) simultaneous detection of four species, (b) internal control for DNA extraction and PCR, (c) mtDNA as a target for PCR, (d) amplicons of <200 bp, and (e) flexibility in the electrophoresis and fragment size detection method. Species identification proved to be straightforward, efficient, sensitive, and robust. The method is sensitive to an at least 1% (v/v) relative proportion of milk in binary mixtures. A survey of commercial products showed that 12.5% failed to conform to the description of the contents, by either the introduction or absence of listed species, thus demonstrating the relevance of this type of testing.

  4. 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.

  5. 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. PMID:26686075

  6. 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.

  7. 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

  8. The Consequences of Multiple Simultaneous C-Type Lectin–Ligand Interactions: DCIR Alters the Endo-Lysosomal Routing of DC-SIGN

    PubMed Central

    García-Vallejo, Juan J.; Bloem, Karien; Knippels, Léon M. J.; Garssen, Johan; van Vliet, Sandra J.; van Kooyk, Yvette

    2015-01-01

    Antigen-presenting cells (APCs) are equipped with multiple receptors to allow proper pathogen recognition and capture. C-type lectin receptors (CLRs) recognize glycan structures on pathogens and endogenous glycoproteins for internalization and antigen processing and presentation. Often, the glycan specificity of these receptors is overlapping and/or pathogens are decorated with ligands for multiple CLRs, posing the question whether interference or cooperativity within the CLR family exists. Here, we used imaging flow cytometry to investigate the internalization properties of four different CLRs [mannose receptor, DC-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), macrophage galactose-type lectin, and dendritic cell immunoreceptor (DCIR)] on different APCs, as well as their intracellular routing. Although the internalization score of the investigated CLRs was similar on monocytes, macrophages, and dendritic cells (DCs), DCIR internalization rates were lower compared to the other CLRs. Upon triggering, DCIR routed to intracellular compartments outside of the classical endo-lysosomal pathway, resulting in poor CD4+ T-cell stimulation. Although DC maturation reduced CLR expression levels, it did not affect their internalization rates. Although CLR internalization appeared to be independently regulated, DC-SIGN routing was affected when DCIR was triggered simultaneously. In conclusion, our results provide new insights for the design of DC-based immunotherapeutic strategies and suggest that DCIR is an inferior target in this respect. PMID:25806031

  9. Plasticity in above- and belowground resource acquisition traits in response to single and multiple environmental factors in three tree species.

    PubMed

    Freschet, Grégoire T; Bellingham, Peter J; Lyver, Philip O'B; Bonner, Karen I; Wardle, David A

    2013-04-01

    Functional trait plasticity is a major component of plant adjustment to environmental stresses. Here, we explore how multiple local environmental gradients in resources required by plants (light, water, and nutrients) and soil disturbance together influence the direction and amplitude of intraspecific changes in leaf and fine root traits that facilitate capture of these resources. We measured population-level analogous above- and belowground traits related to resource acquisition, i.e. "specific leaf area"-"specific root length" (SLA-SRL), and leaf and root N, P, and dry matter content (DMC), on three dominant understory tree species with contrasting carbon and nutrient economics across 15 plots in a temperate forest influenced by burrowing seabirds. We observed similar responses of the three species to the same single environmental influences, but partially species-specific responses to combinations of influences. The strength of intraspecific above- and belowground trait responses appeared unrelated to species resource acquisition strategy. Finally, most analogous leaf and root traits (SLA vs. SRL, and leaf versus root P and DMC) were controlled by contrasting environmental influences. The decoupled responses of above- and belowground traits to these multiple environmental factors together with partially species-specific adjustments suggest complex responses of plant communities to environmental changes, and potentially contrasting feedbacks of plant traits with ecosystem properties. We demonstrate that despite the growing evidence for broadly consistent resource-acquisition strategies at the whole plant level among species, plants also show partially decoupled, finely tuned strategies between above- and belowground parts at the intraspecific level in response to their environment. This decoupling within species suggests a need for many species-centred ecological theories on how plants respond to their environments (e.g. competitive/stress-tolerant/ruderal and

  10. Plasticity in above- and belowground resource acquisition traits in response to single and multiple environmental factors in three tree species

    PubMed Central

    Freschet, Grégoire T; Bellingham, Peter J; Lyver, Philip O'B; Bonner, Karen I; Wardle, David A

    2013-01-01

    Functional trait plasticity is a major component of plant adjustment to environmental stresses. Here, we explore how multiple local environmental gradients in resources required by plants (light, water, and nutrients) and soil disturbance together influence the direction and amplitude of intraspecific changes in leaf and fine root traits that facilitate capture of these resources. We measured population-level analogous above- and belowground traits related to resource acquisition, i.e. “specific leaf area”–“specific root length” (SLA–SRL), and leaf and root N, P, and dry matter content (DMC), on three dominant understory tree species with contrasting carbon and nutrient economics across 15 plots in a temperate forest influenced by burrowing seabirds. We observed similar responses of the three species to the same single environmental influences, but partially species-specific responses to combinations of influences. The strength of intraspecific above- and belowground trait responses appeared unrelated to species resource acquisition strategy. Finally, most analogous leaf and root traits (SLA vs. SRL, and leaf versus root P and DMC) were controlled by contrasting environmental influences. The decoupled responses of above- and belowground traits to these multiple environmental factors together with partially species-specific adjustments suggest complex responses of plant communities to environmental changes, and potentially contrasting feedbacks of plant traits with ecosystem properties. We demonstrate that despite the growing evidence for broadly consistent resource-acquisition strategies at the whole plant level among species, plants also show partially decoupled, finely tuned strategies between above- and belowground parts at the intraspecific level in response to their environment. This decoupling within species suggests a need for many species-centred ecological theories on how plants respond to their environments (e.g. competitive

  11. 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

  12. Phylogenetic Reconstruction and DNA Barcoding for Closely Related Pine Moth Species (Dendrolimus) in China with Multiple Gene Markers

    PubMed Central

    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

  13. 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

  14. 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.

  15. 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.

  16. 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. PMID:22300167

  17. 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. PMID:27033598

  18. 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.

  19. 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

  20. 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

    2015-01-01

    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

  1. 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.

  2. 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.

  3. 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.

  4. 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%.

  5. 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%. PMID:25872425

  6. Multiple origins of BBCC allopolyploid species in the rice genus (Oryza).

    PubMed

    Zou, Xin-Hui; Du, Yu-Su; Tang, Liang; Xu, Xin-Wei; Doyle, Jeff J; Sang, Tao; Ge, Song

    2015-01-01

    In the rice genus (Oryza), about one half of the species are allopolyploids. These species are not only important resources for rice breeding but also provide a unique opportunity for studying evolution of polyploid species. In the present study, we sequenced four biparentally inherited nuclear loci and three maternally inherited chloroplast fragments from all diploid and tetraploid species with the B- and C-genome types in this genus. We detected at least three independent origins of three BC-genome tetraploid species. Specifically, the diploid O. punctata (B-genome) and O. officinalis (C-genome) were the parental progenitors of O. minuta and O. malampuzhaensis with O. punctata being the maternal donors, whereas the diploid O. punctata and O. eichingeri (C-genome) were the progenitors of tetraploid O. punctata with O. punctata being the paternal donor. Our relaxed clock analyses suggest that all the BBCC species originated within the last one million years, which is coincident with the severe climate oscillations occurred during the last ice age, implying the potential impact of climate change on their formations and dispersals. In addition, our results support previous taxonomic arguments that the tetraploid O. punctata might be better treated as a separate species (O. schweinfurthiana).

  7. 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.

  8. 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

  9. Analysis of multiple tsetse fly populations in Uganda reveals limited diversity and species-specific gut microbiota.

    PubMed

    Aksoy, Emre; Telleria, Erich L; Echodu, Richard; Wu, Yineng; Okedi, Loyce M; Weiss, Brian L; Aksoy, Serap; Caccone, Adalgisa

    2014-07-01

    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 (10(4) to 10(6) 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

  10. 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. PMID:27140784

  11. 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.

  12. Statistical framework for the utilization of simultaneous pupil plane and focal plane telemetry for exoplanet imaging I Accounting for aberrations in multiple planes

    NASA Astrophysics Data System (ADS)

    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 exo-planetary 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 ADI and SDI. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

    PubMed

    Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

    2013-07-01

    Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems. PMID:23229391

  17. Beam dynamics of a double-gap acceleration cell for ion implantation with multiple atomic species

    SciTech Connect

    Wadlinger, E.A.; Lysenko, W.P.; Rusnak, B.; Saadatmand, K.

    1997-02-01

    As a result of our work on ion implantation, we derived equations for the beam dynamics of a two-gap-resonator cavity for accelerating and bunching various ion species of varying energies with the cavity designed for one particular ion species of a given energy (the design-reference particle). A two gap structure is useful at low resonant frequencies where lumped circuit elements (inductors) can be used and the structure kept small. A single gap structure has the advantage that each gap can be independently phased to produce the desired beam dynamics behavior for various ion species and ion energies. However at low frequencies, single gap resonant structures can be large. We find that the two-gap structure, where the phase difference between gaps, for the design reference particle, is fixed at {pi} radians can give acceptable performance provided that the individual two gap cells in the entire accelerator are optimized for the ion species having the largest mass to charge ratio and having the maximum required output energy. Our equations show how to adjust the cavity phases and electric fields to obtain equivalent first-order accelerator performance for various ion species and energies. These equations allow for the effective evaluation of various accelerator concepts and can facilitate the tuning of a linac when changing energies and ion species. Extensive simulations have confirmed the efficacy of our equations. {copyright} {ital 1997 American Institute of Physics.}

  18. 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.

  19. Multiple phenological responses to climate change among 42 plant species in Xi'an, China.

    PubMed

    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.

  20. Strength in numbers? Effects of multiple natural enemy species on plant performance.

    PubMed

    Stephens, Andrea E A; Srivastava, Diane S; Myers, Judith H

    2013-06-01

    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.

  1. 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.

  2. 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

  3. 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.

  4. 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. PMID:24491701

  5. Multiple Ant Species Tending Lac Insect Kerria yunnanensis (Hemiptera: Kerriidae) Provide Asymmetric Protection against Parasitoids

    PubMed Central

    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

  6. 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

  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. Multiple species of wild tree peonies gave rise to the 'king of flowers', Paeonia suffruticosa Andrews.

    PubMed

    Zhou, Shi-Liang; Zou, Xin-Hui; Zhou, Zhi-Qin; Liu, Jing; Xu, Chao; Yu, Jing; Wang, Qiang; Zhang, Da-Ming; Wang, Xiao-Quan; Ge, Song; Sang, Tao; Pan, Kai-Yu; Hong, De-Yuan

    2014-12-22

    The origin of cultivated tree peonies, known as the 'king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.

  9. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism

    PubMed Central

    Wang, Lijie; Zhang, Tong; Watson, David G.; Silva, Ana Marta; Coombs, Graham H.

    2015-01-01

    Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts. PMID:26368322

  10. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    PubMed

    Westrop, Gareth D; Williams, Roderick A M; Wang, Lijie; Zhang, Tong; Watson, David G; Silva, Ana Marta; Coombs, Graham H

    2015-01-01

    Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  11. Disentangling canid howls across multiple species and subspecies: Structure in a complex communication channel.

    PubMed

    Kershenbaum, Arik; Root-Gutteridge, Holly; Habib, Bilal; Koler-Matznick, Janice; Mitchell, Brian; Palacios, Vicente; Waller, Sara

    2016-03-01

    Wolves, coyotes, and other canids are members of a diverse genus of top predators of considerable conservation and management interest. Canid howls are long-range communication signals, used both for territorial defence and group cohesion. Previous studies have shown that howls can encode individual and group identity. However, no comprehensive study has investigated the nature of variation in canid howls across the wide range of species. We analysed a database of over 2000 howls recorded from 13 different canid species and subspecies. We applied a quantitative similarity measure to compare the modulation pattern in howls from different populations, and then applied an unsupervised clustering algorithm to group the howls into natural units of distinct howl types. We found that different species and subspecies showed markedly different use of howl types, indicating that howl modulation is not arbitrary, but can be used to distinguish one population from another. We give an example of the conservation importance of these findings by comparing the howls of the critically endangered red wolves to those of sympatric coyotes Canis latrans, with whom red wolves may hybridise, potentially compromising reintroduced red wolf populations. We believe that quantitative cross-species comparisons such as these can provide important understanding of the nature and use of communication in socially cooperative species, as well as support conservation and management of wolf populations.

  12. Disentangling canid howls across multiple species and subspecies: Structure in a complex communication channel.

    PubMed

    Kershenbaum, Arik; Root-Gutteridge, Holly; Habib, Bilal; Koler-Matznick, Janice; Mitchell, Brian; Palacios, Vicente; Waller, Sara

    2016-03-01

    Wolves, coyotes, and other canids are members of a diverse genus of top predators of considerable conservation and management interest. Canid howls are long-range communication signals, used both for territorial defence and group cohesion. Previous studies have shown that howls can encode individual and group identity. However, no comprehensive study has investigated the nature of variation in canid howls across the wide range of species. We analysed a database of over 2000 howls recorded from 13 different canid species and subspecies. We applied a quantitative similarity measure to compare the modulation pattern in howls from different populations, and then applied an unsupervised clustering algorithm to group the howls into natural units of distinct howl types. We found that different species and subspecies showed markedly different use of howl types, indicating that howl modulation is not arbitrary, but can be used to distinguish one population from another. We give an example of the conservation importance of these findings by comparing the howls of the critically endangered red wolves to those of sympatric coyotes Canis latrans, with whom red wolves may hybridise, potentially compromising reintroduced red wolf populations. We believe that quantitative cross-species comparisons such as these can provide important understanding of the nature and use of communication in socially cooperative species, as well as support conservation and management of wolf populations. PMID:26809021

  13. The Homogeneity of Optimal Sensor Placement Across Multiple Winged Insect Species

    NASA Astrophysics Data System (ADS)

    Jenkins, Abigail L.

    Taking inspiration from biology, control algorithms can be implemented to imitate the naturally occurring control systems present in nature. This research is primarily concerned with insect flight and optimal wing sensor placement. Many winged insects with halteres are equipped with mechanoreceptors termed campaniform sensilla. Although the exact information these receptors provide to the insect's nervous system is unknown, it is thought to have the capability of measuring inertial rotation forces. During flight, when the wing bends, the information measured by the campaniform sensilla is received by the central nervous system, and provides the insect necessary data to control flight. This research compares three insect species - the hawkmoth Manduca sexta, the honeybee Apis mellifera, and the fruit fly Drosophila melanogaster. Using an observability-based sensor placement algorithm, the optimal sensor placement for these three species is determined. Simulations resolve if this optimal sensor placement corresponds to the insect's campaniform sensilla, as well as if placement is homogeneous across species.

  14. Federated or cached searches: Providing expected performance from multiple invasive species databases

    NASA Astrophysics Data System (ADS)

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-06-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  15. Federated or cached searches: providing expected performance from multiple invasive species databases

    USGS Publications Warehouse

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-01-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  16. The product of microbial uranium reduction includes multiple species with U(IV)-phosphate coordination

    NASA Astrophysics Data System (ADS)

    Alessi, Daniel S.; Lezama-Pacheco, Juan S.; Stubbs, Joanne E.; Janousch, Markus; Bargar, John R.; Persson, Per; Bernier-Latmani, Rizlan

    2014-04-01

    Until recently, the reduction of U(VI) to U(IV) during bioremediation was assumed to produce solely the sparingly soluble mineral uraninite, UO2(s). However, results from several laboratories reveal other species of U(IV) characterized by the absence of an EXAFS U-U pair correlation (referred to here as noncrystalline U(IV)). Because it lacks the crystalline structure of uraninite, this species is likely to be more labile and susceptible to reoxidation. In the case of single species cultures, analyses of U extended X-ray fine structure (EXAFS) spectra have previously suggested U(IV) coordination to carboxyl, phosphoryl or carbonate groups. In spite of this evidence, little is unde