Sample records for n-mer frequency profiles

  1. Robust k-mer frequency estimation using gapped k-mers

    PubMed Central

    Ghandi, Mahmoud; Mohammad-Noori, Morteza

    2013-01-01

    Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome. PMID:23861010

  2. Robust k-mer frequency estimation using gapped k-mers.

    PubMed

    Ghandi, Mahmoud; Mohammad-Noori, Morteza; Beer, Michael A

    2014-08-01

    Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome.

  3. 3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012

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

    Johnson, Reed F., E-mail: johnsonreed@mail.nih.gov; Bagci, Ulas; Center for Research in Computer Vision

    Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the causative agent of a severe, lethal respiratory disease occurring across several countries in the Middle East. To date there have been over 1600 laboratory confirmed cases of MERS-CoV in 26 countries with a case fatality rate of 36%. Given the endemic region, it is possible that MERS-CoV could spread during the annual Hajj pilgrimage, necessitating countermeasure development. In this report, we describe the clinical and radiographic changes of rhesus monkeys following infection with 5×10{sup 6} PFU MERS-CoV Jordan-n3/2012. Two groups of NHPs were treated with either a humanmore » anti-MERS monoclonal antibody 3B11-N or E410-N, an anti-HIV antibody. MERS-CoV Jordan-n3/2012 infection resulted in quantifiable changes by computed tomography, but limited other clinical signs of disease. 3B11-N treated subjects developed significantly reduced lung pathology when compared to infected, untreated subjects, indicating that this antibody may be a suitable MERS-CoV treatment. - Highlights: • MERS-CoV Jordan-n3/2012 challenge of rhesus monkeys results in a mild disease. • CT can be used to monitor disease progression to aid models of human disease. • Treatment with the human monoclonal antibody 3B11-N resulted in decreased disease.« less

  4. 3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012.

    PubMed

    Johnson, Reed F; Bagci, Ulas; Keith, Lauren; Tang, Xianchun; Mollura, Daniel J; Zeitlin, Larry; Qin, Jing; Huzella, Louis; Bartos, Christopher J; Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H; Paulty, Michael H; Velasco, Jesus; Whaley, Kevin J; Johnson, Joshua C; Pettitt, James; Ork, Britini L; Solomon, Jeffrey; Oberlander, Nicholas; Zhu, Quan; Sun, Jiusong; Holbrook, Michael R; Olinger, Gene G; Baric, Ralph S; Hensley, Lisa E; Jahrling, Peter B; Marasco, Wayne A

    2016-03-01

    Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the causative agent of a severe, lethal respiratory disease occurring across several countries in the Middle East. To date there have been over 1600 laboratory confirmed cases of MERS-CoV in 26 countries with a case fatality rate of 36%. Given the endemic region, it is possible that MERS-CoV could spread during the annual Hajj pilgrimage, necessitating countermeasure development. In this report, we describe the clinical and radiographic changes of rhesus monkeys following infection with 5×10(6) PFU MERS-CoV Jordan-n3/2012. Two groups of NHPs were treated with either a human anti-MERS monoclonal antibody 3B11-N or E410-N, an anti-HIV antibody. MERS-CoV Jordan-n3/2012 infection resulted in quantifiable changes by computed tomography, but limited other clinical signs of disease. 3B11-N treated subjects developed significantly reduced lung pathology when compared to infected, untreated subjects, indicating that this antibody may be a suitable MERS-CoV treatment. Published by Elsevier Inc.

  5. Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease

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

    Johnson, Reed F., E-mail: johnsonreed@mail.nih.gov; Via, Laura E.; Kumar, Mia R.

    Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT),more » with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication. - Highlights: • Common marmosets infected with MERS-EMC and MERS-JOR did not develop lethal disease. • Infected subjects developed transient signs of clinical disease. • CT indicated few differences between the infected and control groups. • Marmosets do not faithfully replicate human MERS pathogenesis.« less

  6. Middle East Respiratory Syndrome (MERS)

    MedlinePlus

    Middle East Respiratory Syndrome Coronavirus; MERS-CoV; Novel coronavirus; nCoV ... for Disease Control and Prevention website. Middle East Respiratory Syndrome (MERS): Frequently asked questions and answers. www. ...

  7. Admittance–voltage profiling of Al{sub x}Ga{sub 1−x}N/GaN heterostructures: Frequency dependence of capacitance and conductance

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

    Köhler, K.; Pletschen, W.; Godejohann, B.

    2015-11-28

    Admittance–voltage profiling of Al{sub x}Ga{sub 1−x}N/GaN heterostructures was used to determine the frequency dependent capacitance and conductance of FET devices in the frequency range from 50 Hz to 1 MHz. The nominally undoped low pressure metal-organic vapor-phase epitaxy structures were grown with an Al-content of 30%. An additional 1 nm thick AlN interlayer was placed in one structure before the Al{sub 0.3}Ga{sub 0.7}N layer growth. For frequencies below 10{sup 8} Hz it is convenient to use equivalent circuits to represent electric or dielectric properties of a material, a method widely used, for example, in impedance spectroscopy. We want to emphasize the relation betweenmore » frequency dependent admittance–voltage profiling and the corresponding equivalent circuits to the complex dielectric function. Debye and Drude models are used for the description of the frequency dependent admittance profiles in a range of depletion onset of the two-dimensional electron gas. Capacitance- and conductance-frequency profiles are fitted in the entire measured range by combining both models. Based on our results, we see contributions to the two-dimensional electron gas for our samples from surface states (80%) as well as from background doping in the Al{sub 0.3}Ga{sub 0.7}N barriers (20%). The specific resistance of the layers below the gate is above 10{sup 5} Ω cm for both samples and increases with increasing negative bias, i.e., the layers below the gate are essentially depleted. We propose that the resistance due to free charge carriers, determined by the Drude model, is located between gate and drain and, because of the AlN interlayer, the resistance is lowered by a factor of about 30 if compared to the sample without an AlN layer.« less

  8. Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

    PubMed Central

    Mohammad-Noori, Morteza; Beer, Michael A.

    2014-01-01

    Abstract Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem. PMID:25033408

  9. Enhanced regulatory sequence prediction using gapped k-mer features.

    PubMed

    Ghandi, Mahmoud; Lee, Dongwon; Mohammad-Noori, Morteza; Beer, Michael A

    2014-07-01

    Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.

  10. MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

    DOE PAGES

    Menachery, Vineet D.; Schafer, Alexandra; Burnum-Johnson, Kristin E.; ...

    2018-01-16

    Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways in order to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems based approach, we examined differential regulation of IFNγ dependent genes following infection with highly pathogenic viruses including influenza (H5N1-VN1203, H1N1-CA04) and coronaviruses (SARS-CoV, MERS-CoV). Categorizing by function, we observed down regulation of genes associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down regulation of antigenmore » presentation genes and was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation rather than histone modification plays a crucial role in MERS-CoV mediated antagonism of antigen presentation genes; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Altogether, the results indicate a common approach utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.« less

  11. MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

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

    Menachery, Vineet D.; Schäfer, Alexandra; Burnum-Johnson, Kristin E.

    Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways in order to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems based approach, we examined differential regulation of IFNγ dependent genes following infection with highly pathogenic viruses including influenza (H5N1-VN1203, H1N1-CA04) and coronaviruses (SARS-CoV, MERS-CoV). Categorizing by function, we observed down regulation of genes associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down regulation of antigenmore » presentation genes and was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation rather than histone modification plays a crucial role in MERS-CoV mediated antagonism of antigen presentation genes; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Together, the results indicate a common approach utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.« less

  12. Probing the mer- to fac-isomerization of tris-cyclometallated homo- and heteroleptic (C,N)3 iridium(III) complexes.

    PubMed

    McDonald, Aidan R; Lutz, Martin; von Chrzanowski, Lars S; van Klink, Gerard P M; Spek, Anthony L; van Koten, Gerard

    2008-08-04

    We have developed techniques which allow for covalent tethering, via a "hetero" cyclometallating ligand, of heteroleptic tris-cyclometallated iridium(III) complexes to polymeric supports (for application in light-emitting diode technologies). This involved the selective synthesis and thorough characterization of heteroleptic [Ir(C,N) 2(C',N')] tris-cyclometallated iridium(III) complexes. Furthermore, the synthesis and characterization of heteroleptic [Ir(C,N) 2OR] complexes is presented. Under standard thermal conditions for the synthesis of the facial ( fac) isomer of tris-cyclometallated complexes, it was not possible to synthesize pure heteroleptic complexes of the form [Ir(C,N) 2(C',N')]. Instead, a mixture of homo- and heteroleptic complexes was acquired. It was found that a stepwise procedure involving the synthesis of a pure meridonial ( mer) isomer followed by photochemical isomerization of this mer to the fac isomer was necessary to synthesize pure fac-[Ir(C,N) 2(C',N')] complexes. Under thermal isomerization conditions, the conversion of mer-[Ir(C,N) 2(C',N')] to fac-[Ir(C,N) 2(C',N')] was also not a clean reaction, with again a mixture of homo- and heteroleptic complexes acquired. An investigation into the thermal mer to fac isomerization of both homo- and heteroleptic tris-cyclometallated complexes is presented. It was found that the process is an alcohol-catalyzed reaction with the formation of an iridium alkoxide [Ir(C,N) 2OR] intermediate in the isomerization process. This catalyzed reaction can be carried out between 50 and 100 degrees C, the first such example of low-temperature mer-fac thermal isomerization. We have synthesized analogous complexes and have shown that they do indeed react so as to give fac-tris-cyclometallated products. A detailed explanation of the intermediates (and all of their stereoisomers, in particular when systems of the generic formula [M(a,b) 2(a',b')] are synthesized) formed in the mer to fac isomerization process is

  13. Nitrogen and 15N in the Mer Bleue peatland

    NASA Astrophysics Data System (ADS)

    Moore, Tim

    2017-04-01

    Although much of our attention in peatlands has focussed on carbon, as CO2, CH4 and DOC processing and fluxes, N plays an important role in the functioning of these ecosystems. Here, I present information on the distribution of N and 15N in plant and peat tissues and relate them to the cycling of N. N concentration in foliar tissues, ranged from 0.67 to 1.3% in evergreen shrubs and trees and mosses with little seasonal variation, and with a strong seasonal variation from 0.5 to 3.5% in the deciduous forbs, shrubs and trees, with a strong overall relationship to [chlorophyll]. Although the proportion of shrubs and mosses varied with microtopography the spatial foliar mass of N varied little with water table position, resulting in minor spatial variations in photosynthetic potential. Decomposition of plant tissues through litter to peat resulted in a decrease in the C:N ratio from about 50:1 to about 30:1 at the base of the profile, representing peat about 8000 yr old. This marginally larger loss of N through decomposition (mainly as TDN, 0.4 g N m-2 yr-1) compared to C produced a long-term N accumulation rate of 0.9 g N m-2 yr-1, being smaller in the bog phase, 0.6 N m-2 yr-1, and over past 150 yr, 0.8 g N m-2 yr-1. Although N is 'hard won' through N2 fixation, northern peatlands are significant global sinks of N and have limited N availability. del15N in foliar tissues ranged from -4 to -9 ‰ in evergreen and deciduous shrubs and trees, from -4 to -5 ‰ in mosses and from -1 to +1 ‰ in sedges and forbs. This appears to be a function of the mycorhizzal infection of the shrubs and trees, compared to sedges and forbs and the values for mosses may partially reflect the signature of atmospheric N deposition. There was no strong correlation between foliar [N] and del15N. In peat profiles from bog and fen sections of Mer Bleue, del15N values in peat fell from -5 to -2 ‰ in the top 10 cm to values of -1 to +1 ‰ at a depth of 40 cm and remained close to 0 ‰ below

  14. MER SPICE Interface

    NASA Technical Reports Server (NTRS)

    Sayfi, Elias

    2004-01-01

    MER SPICE Interface is a software module for use in conjunction with the Mars Exploration Rover (MER) mission and the SPICE software system of the Navigation and Ancillary Information Facility (NAIF) at NASA's Jet Propulsion Laboratory. (SPICE is used to acquire, record, and disseminate engineering, navigational, and other ancillary data describing circumstances under which data were acquired by spaceborne scientific instruments.) Given a Spacecraft Clock value, MER SPICE Interface extracts MER-specific data from SPICE kernels (essentially, raw data files) and calculates values for Planet Day Number, Local Solar Longitude, Local Solar Elevation, Local Solar Azimuth, and Local Solar Time (UTC). MER SPICE Interface was adapted from a subroutine, denoted m98SpiceIF written by Payam Zamani, that was intended to calculate SPICE values for the Mars Polar Lander. The main difference between MER SPICE Interface and m98SpiceIf is that MER SPICE Interface does not explicitly call CHRONOS, a time-conversion program that is part of a library of utility subprograms within SPICE. Instead, MER SPICE Interface mimics some portions of the CHRONOS code, the advantage being that it executes much faster and can efficiently be called from a pipeline of events in a parallel processing environment.

  15. Effective inhibition of MERS-CoV infection by resveratrol.

    PubMed

    Lin, Shih-Chao; Ho, Chi-Tang; Chuo, Wen-Ho; Li, Shiming; Wang, Tony T; Lin, Chi-Chen

    2017-02-13

    Middle East Respiratory Syndrome coronavirus (MERS-CoV) is an emerging viral pathogen that causes severe morbidity and mortality. Up to date, there is no approved or licensed vaccine or antiviral medicines can be used to treat MERS-CoV-infected patients. Here, we analyzed the antiviral activities of resveratrol, a natural compound found in grape seeds and skin and in red wine, against MERS-CoV infection. We performed MTT and neutral red uptake assays to assess the survival rates of MERS-infected Vero E6 cells. In addition, quantitative PCR, western blotting, and immunofluorescent assays determined the intracellular viral RNA and protein expression. For viral productivity, we utilized plaque assays to confirm the antiviral properties of resveratrol against MERS-CoV. Resveratrol significantly inhibited MERS-CoV infection and prolonged cellular survival after virus infection. We also found that the expression of nucleocapsid (N) protein essential for MERS-CoV replication was decreased after resveratrol treatment. Furthermore, resveratrol down-regulated the apoptosis induced by MERS-CoV in vitro. By consecutive administration of resveratrol, we were able to reduce the concentration of resveratrol while achieving inhibitory effectiveness against MERS-CoV. In this study, we first demonstrated that resveratrol is a potent anti-MERS agent in vitro. We perceive that resveratrol can be a potential antiviral agent against MERS-CoV infection in the near future.

  16. Debate on MERS-CoV respiratory precautions: surgical mask or N95 respirators?

    PubMed Central

    Chung, Jasmine Shimin; Ling, Moi Lin; Seto, Wing Hong; Ang, Brenda Sze Peng; Tambyah, Paul Anantharajah

    2014-01-01

    Since the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in mid-2012, there has been controversy over the respiratory precaution recommendations in different guidelines from various international bodies. Our understanding of MERS-CoV is still evolving. Current recommendations on infection control practices are heavily influenced by the lessons learnt from severe acute respiratory syndrome. A debate on respiratory precautions for MERS-CoV was organised by Infection Control Association (Singapore) and the Society of Infectious Disease (Singapore). We herein discuss and present the evidence for surgical masks for the protection of healthcare workers from MERS-CoV. PMID:25017402

  17. Implementation of hierarchical clustering using k-mer sparse matrix to analyze MERS-CoV genetic relationship

    NASA Astrophysics Data System (ADS)

    Bustamam, A.; Ulul, E. D.; Hura, H. F. A.; Siswantining, T.

    2017-07-01

    Hierarchical clustering is one of effective methods in creating a phylogenetic tree based on the distance matrix between DNA (deoxyribonucleic acid) sequences. One of the well-known methods to calculate the distance matrix is k-mer method. Generally, k-mer is more efficient than some distance matrix calculation techniques. The steps of k-mer method are started from creating k-mer sparse matrix, and followed by creating k-mer singular value vectors. The last step is computing the distance amongst vectors. In this paper, we analyze the sequences of MERS-CoV (Middle East Respiratory Syndrome - Coronavirus) DNA by implementing hierarchical clustering using k-mer sparse matrix in order to perform the phylogenetic analysis. Our results show that the ancestor of our MERS-CoV is coming from Egypt. Moreover, we found that the MERS-CoV infection that occurs in one country may not necessarily come from the same country of origin. This suggests that the process of MERS-CoV mutation might not only be influenced by geographical factor.

  18. Turtle: identifying frequent k-mers with cache-efficient algorithms.

    PubMed

    Roy, Rajat Shuvro; Bhattacharya, Debashish; Schliep, Alexander

    2014-07-15

    Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k-mers and not in the, typically much larger, total number of k-mers in the read library. We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high-coverage libraries and large genomes such as human. Our method is designed to minimize cache misses in a cache-efficient manner by using a pattern-blocked Bloom filter to remove infrequent k-mers from consideration in combination with a novel sort-and-compact scheme, instead of a hash, for the actual counting. Although this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant of method can resort to a counting Bloom filter for even larger savings in memory at the expense of false-negative rates in addition to the false-positive rates common to all Bloom filter-based approaches. A comparison with the state-of-the-art shows reduced memory requirements and running times. The tools are freely available for download at http://bioinformatics.rutgers.edu/Software/Turtle and http://figshare.com/articles/Turtle/791582. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Characterization of MER Landing Sites Using MOC and MOLA

    NASA Technical Reports Server (NTRS)

    Anderson, F. S.; Parker, T. J.

    2002-01-01

    The MOC images for MER are compared with MOLA data to characterize and locate each image. MOLA profiles show that Hematite remains benign, Melas and Isidis are rougher, and Athabasca and Gusev have regions of significant small scale topography. Additional information is contained in the original extended abstract.

  20. Mapping Potential Amplification and Transmission Hotspots for MERS-CoV, Kenya.

    PubMed

    Gikonyo, Stephen; Kimani, Tabitha; Matere, Joseph; Kimutai, Joshua; Kiambi, Stella G; Bitek, Austine O; Juma Ngeiywa, K J Z; Makonnen, Yilma J; Tripodi, Astrid; Morzaria, Subhash; Lubroth, Juan; Rugalema, Gabriel; Fasina, Folorunso Oludayo

    2018-03-16

    Dromedary camels have been implicated consistently as the source of Middle East respiratory syndrome coronavirus (MERS-CoV) human infections and attention to prevent and control it has focused on camels. To understanding the epidemiological role of camels in the transmission of MERS-CoV, we utilized an iterative empirical process in Geographic Information System (GIS) to identify and qualify potential hotspots for maintenance and circulation of MERS-CoV, and produced risk-based surveillance sites in Kenya. Data on camel population and distribution were used to develop camel density map, while camel farming system was defined using multi-factorial criteria including the agro-ecological zones (AEZs), production and marketing practices. Primary and secondary MERS-CoV seroprevalence data from specific sites were analyzed, and location-based prevalence matching with camel densities was conducted. High-risk convergence points (migration zones, trade routes, camel markets, slaughter slabs) were profiled and frequent cross-border camel movement mapped. Results showed that high camel-dense areas and interaction (markets and migration zones) were potential hotspot for transmission and spread. Cross-border contacts occurred with in-migrated herds at hotspot locations. AEZ differential did not influence risk distribution and plausible risk factors for spatial MERS-CoV hotspots were camel densities, previous cases of MERS-CoV, high seroprevalence and points of camel convergences. Although Kenyan camels are predisposed to MERS-CoV, no shedding is documented to date. These potential hotspots, determined using anthropogenic, system and trade characterizations should guide selection of sampling/surveillance sites, high-risk locations, critical areas for interventions and policy development in Kenya, as well as instigate further virological examination of camels.

  1. A Novel Role of MerC in Methylmercury Transport and Phytoremediation of Methylmercury Contamination.

    PubMed

    Sone, Yuka; Uraguchi, Shimpei; Takanezawa, Yasukazu; Nakamura, Ryosuke; Pan-Hou, Hidemitsu; Kiyono, Masako

    2017-01-01

    MerC, encoded by merC in the transposon Tn21 mer operon, is a heavy metal transporter with potential applications for phytoremediation of heavy metals such as mercuric ion and cadmium. In this study, we demonstrate that MerC also acts as a transporter for methylmercury. When MerC was expressed in Escherichia coli XL1-Blue, cells became hypersensitive to CH 3 Hg(I) and the uptake of CH 3 Hg(I) by these cells was higher than that by cells of the isogenic strain. Moreover, transgenic Arabidopsis plants expressing bacterial MerC or MerC fused to plant soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) accumulated CH 3 Hg(I) effectively and their growth was comparable to the wild-type plants. These results demonstrate that when the bacterium-derived merC gene is ectopically introduced in genetically modified plants, MerC expression in the transgenic plants promotes the transport and sequestration of methylmercury. Thus, our results show that the expression of merC in Arabidopsis results in transgenic plants that could be used for the phytoremediation and elimination of toxic methylmercury from the environment.

  2. MER Telemetry Processor

    NASA Technical Reports Server (NTRS)

    Lee, Hyun H.

    2012-01-01

    MERTELEMPROC processes telemetered data in data product format and generates Experiment Data Records (EDRs) for many instruments (HAZCAM, NAVCAM, PANCAM, microscopic imager, Moessbauer spectrometer, APXS, RAT, and EDLCAM) on the Mars Exploration Rover (MER). If the data is compressed, then MERTELEMPROC decompresses the data with an appropriate decompression algorithm. There are two compression algorithms (ICER and LOCO) used in MER. This program fulfills a MER specific need to generate Level 1 products within a 60-second time requirement. EDRs generated by this program are used by merinverter, marscahv, marsrad, and marsjplstereo to generate higher-level products for the mission operations. MERTELEPROC was the first GDS program to process the data product. Metadata of the data product is in XML format. The software allows user-configurable input parameters, per-product processing (not streambased processing), and fail-over is allowed if the leading image header is corrupted. It is used within the MER automated pipeline. MERTELEMPROC is part of the OPGS (Operational Product Generation Subsystem) automated pipeline, which analyzes images returned by in situ spacecraft and creates level 1 products to assist in operations, science, and outreach.

  3. Syntheses and multi-NMR study of fac- and mer-OsO(3)F(2)(NCCH(3)) and the X-ray crystal structure (n = 2) and Raman spectrum (n = 0) of fac-OsO(3)F(2)(NCCH(3)).nCH(3)CN.

    PubMed

    Hughes, Michael J; Gerken, Michael; Mercier, Hélène P A; Schrobilgen, Gary J

    2010-06-07

    Dissolution of the infinite chain polymer, (OsO(3)F(2))(infinity), in CH(3)CN solvent at -40 degrees C followed by solvent removal under vacuum at -40 degrees C yielded fac-OsO(3)F(2)(NCCH(3)).nCH(3)CN (n >/= 2). Continued pumping at -40 degrees C with removal of uncoordinated CH(3)CN yielded fac-OsO(3)F(2)(NCCH(3)). Both fac-OsO(3)F(2)(NCCH(3)).nCH(3)CN and fac-OsO(3)F(2)(NCCH(3)) are yellow-brown solids and were characterized by low-temperature (-150 degrees C) Raman spectroscopy. The crystal structure (-173 degrees C) of fac-OsO(3)F(2)(NCCH(3)).2CH(3)CN consists of two co-crystallized CH(3)CN molecules and a pseudo-octahedral OsO(3)F(2).NCCH(3) molecule in which three oxygen atoms are in a facial arrangement and CH(3)CN is coordinated trans to an oxygen atom in an end-on fashion. The Os---N bond length (2.205(3) A) is among the shortest M---N adduct bonds observed for a d(0) transition metal oxide fluoride. The (19)F NMR spectrum of (OsO(3)F(2))(infinity) in CH(3)CN solvent (-40 degrees C) is a singlet (-99.6 ppm) corresponding to fac-OsO(3)F(2)(NCCH(3)). The (1)H, (15)N, (13)C, and (19)F NMR spectra of (15)N-enriched OsO(3)F(2)(NCCH(3)) were recorded in SO(2)ClF solvent (-84 degrees C). Nitrogen-15 enrichment resulted in splitting of the (19)F resonance of fac-OsO(3)F(2)((15)NCCH(3)) into a doublet ((2)J((15)N-(19)F), 21 Hz). In addition, a doublet of doublets ((2)J((19)F(ax)-(19)F(eq)), 134 Hz; (2)J((15)N-(19)F(eq)), 18 Hz) and a doublet ((2)J((19)F(ax)-(19)F(eq)), 134 Hz) were observed in the (19)F NMR spectrum that have been assigned to mer-OsO(3)F(2)((15)NCCH(3)); however, coupling of (15)N to the axial fluorine-on-osmium environment could not be resolved. The nitrogen atom of CH(3)CN is coordinated trans to a fluorine ligand in the mer-isomer. Quantum-chemical calculations at the SVWN and B3LYP levels of theory were used to calculate the energy-minimized gas-phase geometries, vibrational frequencies of fac- and mer-OsO(3)F(2)(NCCH(3)) and of CH(3)CN. The

  4. Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards.

    PubMed

    Kim, Sung-Han; Chang, So Young; Sung, Minki; Park, Ji Hoon; Bin Kim, Hong; Lee, Heeyoung; Choi, Jae-Phil; Choi, Won Suk; Min, Ji-Young

    2016-08-01

    The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) outside the Middle East occurred in South Korea in 2015 and resulted in 186 laboratory-confirmed infections, including 36 (19%) deaths. Some hospitals were considered epicenters of infection and voluntarily shut down most of their operations after nearly half of all transmissions occurred in hospital settings. However, the ways that MERS-CoV is transmitted in healthcare settings are not well defined. We explored the possible contribution of contaminated hospital air and surfaces to MERS transmission by collecting air and swabbing environmental surfaces in 2 hospitals treating MERS-CoV patients. The samples were tested by viral culture with reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescence assay (IFA) using MERS-CoV Spike antibody, and electron microscopy (EM). The presence of MERS-CoV was confirmed by RT-PCR of viral cultures of 4 of 7 air samples from 2 patients' rooms, 1 patient's restroom, and 1 common corridor. In addition, MERS-CoV was detected in 15 of 68 surface swabs by viral cultures. IFA on the cultures of the air and swab samples revealed the presence of MERS-CoV. EM images also revealed intact particles of MERS-CoV in viral cultures of the air and swab samples. These data provide experimental evidence for extensive viable MERS-CoV contamination of the air and surrounding materials in MERS outbreak units. Thus, our findings call for epidemiologic investigation of the possible scenarios for contact and airborne transmission, and raise concern regarding the adequacy of current infection control procedures. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  5. Etude de la performance des radars hautes-frequences CODAR et WERA pour la mesure des courants marins en presence partielle de glace de mer

    NASA Astrophysics Data System (ADS)

    Kamli, Emna

    Les radars hautes-frequences (RHF) mesurent les courants marins de surface avec une portee pouvant atteindre 200 kilometres et une resolution de l'ordre du kilometre. Cette etude a pour but de caracteriser la performance des RHF, en terme de couverture spatiale, pour la mesure des courants de surface en presence partielle de glace de mer. Pour ce faire, les mesures des courants de deux radars de type CODAR sur la rive sud de l'estuaire maritime du Saint-Laurent, et d'un radar de type WERA sur la rive nord, prises pendant l'hiver 2013, ont ete utilisees. Dans un premier temps, l'aire moyenne journaliere de la zone ou les courants sont mesures par chaque radar a ete comparee a l'energie des vagues de Bragg calculee a partir des donnees brutes d'acceleration fournies par une bouee mouillee dans la zone couverte par les radars. La couverture des CODARs est dependante de la densite d'energie de Bragg, alors que la couverture du WERA y est pratiquement insensible. Un modele de fetch appele GENER a ete force par la vitesse du vent predite par le modele GEM d'Environnement Canada pour estimer la hauteur significative ainsi que la periode modale des vagues. A partir de ces parametres, la densite d'energie des vagues de Bragg a ete evaluee pendant l'hiver a l'aide du spectre theorique de Bretschneider. Ces resultats permettent d'etablir la couverture normale de chaque radar en absence de glace de mer. La concentration de glace de mer, predite par le systeme canadien operationnel de prevision glace-ocean, a ete moyennee sur les differents fetchs du vent selon la direction moyenne journaliere des vagues predites par GENER. Dans un deuxieme temps, la relation entre le ratio des couvertures journalieres obtenues pendant l'hiver 2013 et des couvertures normales de chaque radar d'une part, et la concentration moyenne journaliere de glace de mer d'autre part, a ete etablie. Le ratio des couvertures decroit avec l'augmentation de la concentration de glace de mer pour les deux types

  6. The MER/CIP Portal for Ground Operations

    NASA Technical Reports Server (NTRS)

    Chan, Louise; Desai, Sanjay; DOrtenzio, Matthew; Filman, Robtert E.; Heher, Dennis M.; Hubbard, Kim; Johan, Sandra; Keely, Leslie; Magapu, Vish; Mak, Ronald

    2003-01-01

    We developed the Mars Exploration Rover/Collaborative Information Portal (MER/CIP) to facilitate MER operations. MER/CIP provides a centralized, one-stop delivery platform integrating science and engineering data from several distributed heterogeneous data sources. Key issues for MER/CIP include: 1) Scheduling and schedule reminders; 2) Tracking the status of daily predicted outputs; 3) Finding and analyzing data products; 4) Collaboration; 5) Announcements; 6) Personalization.

  7. Middle East Respiratory Syndrome (MERS)

    MedlinePlus

    ... Controls Cancel Submit Search The CDC Middle East Respiratory Syndrome (MERS) Note: Javascript is disabled or is ... Recommend on Facebook Tweet Share Compartir Middle East Respiratory Syndrome (MERS) is viral respiratory illness that was ...

  8. Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.

    PubMed

    Alnazawi, Mohamed; Altaher, Abdallah; Kandeel, Mahmoud

    2017-01-01

    Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.

  9. First confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in the United States, updated information on the epidemiology of MERS-CoV infection, and guidance for the public, clinicians, and public health authorities - May 2014.

    PubMed

    Bialek, Stephanie R; Allen, Donna; Alvarado-Ramy, Francisco; Arthur, Ray; Balajee, Arunmozhi; Bell, David; Best, Susan; Blackmore, Carina; Breakwell, Lucy; Cannons, Andrew; Brown, Clive; Cetron, Martin; Chea, Nora; Chommanard, Christina; Cohen, Nicole; Conover, Craig; Crespo, Antonio; Creviston, Jeanean; Curns, Aaron T; Dahl, Rebecca; Dearth, Stephanie; DeMaria, Alfred; Echols, Fred; Erdman, Dean D; Feikin, Daniel; Frias, Mabel; Gerber, Susan I; Gulati, Reena; Hale, Christa; Haynes, Lia M; Heberlein-Larson, Lea; Holton, Kelly; Ijaz, Kashef; Kapoor, Minal; Kohl, Katrin; Kuhar, David T; Kumar, Alan M; Kundich, Marianne; Lippold, Susan; Liu, Lixia; Lovchik, Judith C; Madoff, Larry; Martell, Sandra; Matthews, Sarah; Moore, Jessica; Murray, Linda R; Onofrey, Shauna; Pallansch, Mark A; Pesik, Nicki; Pham, Huong; Pillai, Satish; Pontones, Pam; Pringle, Kimberly; Pritchard, Scott; Rasmussen, Sonja; Richards, Shawn; Sandoval, Michelle; Schneider, Eileen; Schuchat, Anne; Sheedy, Kristine; Sherin, Kevin; Swerdlow, David L; Tappero, Jordan W; Vernon, Michael O; Watkins, Sharon; Watson, John

    2014-05-16

    Since mid-March 2014, the frequency with which cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection have been reported has increased, with the majority of recent cases reported from Saudi Arabia and United Arab Emirates (UAE). In addition, the frequency with which travel-associated MERS cases have been reported and the number of countries that have reported them to the World Health Organization (WHO) have also increased. The first case of MERS in the United States, identified in a traveler recently returned from Saudi Arabia, was reported to CDC by the Indiana State Department of Health on May 1, 2014, and confirmed by CDC on May 2. A second imported case of MERS in the United States, identified in a traveler from Saudi Arabia having no connection with the first case, was reported to CDC by the Florida Department of Health on May 11, 2014. The purpose of this report is to alert clinicians, health officials, and others to increase awareness of the need to consider MERS-CoV infection in persons who have recently traveled from countries in or near the Arabian Peninsula. This report summarizes recent epidemiologic information, provides preliminary descriptions of the cases reported from Indiana and Florida, and updates CDC guidance about patient evaluation, home care and isolation, specimen collection, and travel as of May 13, 2014.

  10. Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis.

    PubMed

    Sharmin, Refat; Islam, Abul B M M K

    2016-01-01

    MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the degree of conserved antigenic sites among them. It is of importance to elucidate the shared antigenic-sites and extent of conservation between them to understand the evolutionary dynamics of MERS-CoV. Multiple sequence alignment of the spike (S), membrane (M), enveloped (E) and nucleocapsid (N) proteins was employed to identify the sequence conservation among MERS and Bat (HKU4, HKU5) coronaviruses. We used various in silico tools to predict the conserved antigenic sites. We found that MERS-CoV shared 30 % of its S protein antigenic sites with HKU4 and 70 % with HKU5 bat-CoV. Whereas 100 % of its E, M and N protein's antigenic sites are found to be conserved with those in HKU4 and HKU5. This sharing suggests that in case of pathogenicity MERS-CoV is more closely related to HKU5 bat-CoV than HKU4 bat-CoV. The conserved epitopes indicates their evolutionary relationship and ancestry of pathogenicity.

  11. Frequency of MMPI Profile Types in Three Chronic Illness Populations.

    ERIC Educational Resources Information Center

    Naliboff, Bruce D.; And Others

    1983-01-01

    Developed sorting rules to identify Minnesota Multiphasic Personality Inventory configurations and applied these to patients with chronic low back pain, migraine headaches, hypertension, and diabetes (N=157). Results showed that profile types did not differ in frequency among the groups but were more elevated in the back pain patients. (LLL)

  12. KAnalyze: a fast versatile pipelined k-mer toolkit.

    PubMed

    Audano, Peter; Vannberg, Fredrik

    2014-07-15

    Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language. As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes. KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/. © The Author 2014. Published by Oxford University Press.

  13. Molecular interaction study of commercial cyclic peptides and MERS-COV papain-like protease as novel drug candidate for MERS-COV

    NASA Astrophysics Data System (ADS)

    Nasution, M. A. F.; Azzuhdi, M. G.; Tambunan, U. S. F.

    2017-07-01

    Middle-east respiratory syndrome coronavirus (MERS-CoV) has become the current outbreak, MERS-CoV infection results in illness at the respiratory system, digestive, and even lead to death with an average mortality caused by MERS-CoV infection reaches 50 %. Until now, there is not any effective vaccine or drug to ward off MERS-CoV infection. Papain-like protease (PLpro) is responsible for cleavage of a nonstructural protein that is essential for viral maturation. Inhibition of PLpro with a ligand will block the cleavage process of nonstructural protein, thus reduce the infection of MERS-CoV. Through of bioinformatics study with molecular docking and binding interaction analysis of commercial cyclic peptides, aldosterone secretion inhibiting factor (1-35) (bovine) was obtained as an inhibitor for PLpro. Thus, aldosterone secretion inhibiting factor (1-35) (bovine) has a potential as a novel candidate drug for treating MERS-CoV.

  14. KAnalyze: a fast versatile pipelined K-mer toolkit

    PubMed Central

    Audano, Peter; Vannberg, Fredrik

    2014-01-01

    Motivation: Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language. Results: As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes. Availability and implementation: KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/ Contact: fredrik.vannberg@biology.gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24642064

  15. Transmission characteristics of MERS and SARS in the healthcare setting: a comparative study.

    PubMed

    Chowell, Gerardo; Abdirizak, Fatima; Lee, Sunmi; Lee, Jonggul; Jung, Eunok; Nishiura, Hiroshi; Viboud, Cécile

    2015-09-03

    highly across individual hospital outbreaks (Kruskal-Wallis test; P < 0.0001), with significantly higher transmission heterogeneity in the distribution of secondary cases for MERS than SARS. Simulations indicate a 2-fold higher probability of occurrence of large outbreaks (>100 cases) for SARS than MERS (2 % versus 1 %); however, owing to higher transmission heterogeneity, the largest outbreaks of MERS are characterized by sharper incidence peaks. The probability of occurrence of MERS outbreaks larger than the South Korean cluster (n = 186) is of the order of 1 %. Our study suggests that the South Korean outbreak followed a similar progression to previously described hospital clusters involving coronaviruses, with early super-spreading events generating a disproportionately large number of secondary infections, and the transmission potential diminishing greatly in subsequent generations. Differences in relative exposure patterns and transmission heterogeneity of MERS and SARS could point to changes in hospital practices since 2003 or differences in transmission mechanisms of these coronaviruses.

  16. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

    PubMed Central

    Sims, Gregory E.; Kim, Sung-Hou

    2011-01-01

    A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (∼8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions of core features with low frequency and low variability (∼0.56 million features), which account for ∼69% of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal. Shigella appears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show that Shigella consists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup. PMID:21536867

  17. Isomerization Reaction of mer- to fac-Tris(2-phenylpyridinato-N,C2')Iridium(III) Monitored by Using Surface-Enhanced Raman Spectroscopy.

    PubMed

    Wu, Bo-Han; Huang, Min-Jie; Lai, Cheng-Chang; Cheng, Chien-Hong; Chen, I-Chia

    2018-04-16

    We developed a new method by enclosing the complex tris(2-phenylpyridinato-N,C2')Iridium(III), Ir(ppy) 3 with surfactant cetyltrimethylammonium bromide (CATB), coated with a thin layer of silica then bonded to the surface of silver nanoparticle. These samples were used to acquire surface-enhanced Raman scattering (SERS) spectra. The thickness of silica layer was controlled to have efficient phosphorescence quenching and Raman enhancement by metal nanoparticle. The SERS spectra of fac- and mer-Ir(ppy) 3 , recorded at 633 nm excitation, display distinct ring breathing mode features because the total symmetric vibrational bands were enhanced. This provides a convenient means to differentiate these isomers with great sensitivity and to study their isomerization process. A direct conversion reaction of mer- to fac- isomerization is identified with time constant 3.1 min when mer was irradiated with Xe light. Via thermal activation, under moderate conditions (pH 5.5 and 343 K), we observed an intermediate particularly with new bands 320/662 cm -1 after heating for 17.5 h, and then those bands disappeared to form fac-Ir(ppy) 3 . On the basis of DFT calculations, the intermediate is proposed to contain octahedral N-N Ir(ppy) 3 -HO-silica structure; band at 320 cm -1 is assigned to iridium oxygen stretching mode ν Ir-O of this intermediate. Under acidic conditions, pH 1-2 catalyzed by silanol in silica, byproduct with band at 353 cm -1 was observed. According to the SERS bands and the calculation, this byproduct is assigned to be iridium(III) siloxide, and the new band is assigned to ν Ir-O .

  18. From SARS to MERS: evidence and speculation.

    PubMed

    Gao, Hainv; Yao, Hangping; Yang, Shigui; Li, Lanjuan

    2016-12-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel zoonotic pathogen. In 2012, the infectious outbreak caused by MERS-CoV in Saudi Arabia has spread to more than 1600 patients in 26 countries, resulting in over 600 deaths.Without a travel history, few clinical and radiological features can reliably differentiate MERS from SARS. But in real world, comparing with SARS, MERS presents more vaguely defined epidemiology, more severe symptoms, and higher case fatality rate. In this review, we summarize the recent findings in the field of MERS-CoV, especially its molecular virology, interspecies mechanisms, clinical features, antiviral therapies, and the further investigation into this disease. As a newly emerging virus, many questions are not fully answered, including the exact mode of transmission chain, geographical distribution, and animal origins. Furthermore, a new protocol needs to be launched to rapidly evaluate the effects of unproven antiviral drugs and vaccine to fasten the clinical application of new drugs.

  19. MERS transmission and risk factors: a systematic review.

    PubMed

    Park, Ji-Eun; Jung, Soyoung; Kim, Aeran; Park, Ji-Eun

    2018-05-02

    Since Middle East respiratory syndrome (MERS) infection was first reported in 2012, many studies have analysed its transmissibility and severity. However, the methodology and results of these studies have varied, and there has been no systematic review of MERS. This study reviews the characteristics and associated risk factors of MERS. We searched international (PubMed, ScienceDirect, Cochrane) and Korean databases (DBpia, KISS) for English- or Korean-language articles using the terms "MERS" and "Middle East respiratory syndrome". Only human studies with > 20 participants were analysed to exclude studies with low representation. Epidemiologic studies with information on transmissibility and severity of MERS as well as studies containing MERS risk factors were included. A total of 59 studies were included. Most studies from Saudi Arabia reported higher mortality (22-69.2%) than those from South Korea (20.4%). While the R 0 value in Saudi Arabia was < 1 in all but one study, in South Korea, the R 0 value was 2.5-8.09 in the early stage and decreased to < 1 in the later stage. The incubation period was 4.5-5.2 days in Saudi Arabia and 6-7.8 days in South Korea. Duration from onset was 4-10 days to confirmation, 2.9-5.3 days to hospitalization, 11-17 days to death, and 14-20 days to discharge. Older age and concomitant disease were the most common factors related to MERS infection, severity, and mortality. The transmissibility and severity of MERS differed by outbreak region and patient characteristics. Further studies assessing the risk of MERS should consider these factors.

  20. Prevalence of Diabetes in the 2009 Influenza A (H1N1) and the Middle East Respiratory Syndrome Coronavirus: A Systematic Review and Meta-Analysis.

    PubMed

    Badawi, Alaa; Ryoo, Seung Gwan

    2016-12-09

    Over the past two decades a number of severe acute respiratory infection outbreaks such as the 2009 influenza A (H1N1) and the Middle East respiratory syndrome coronavirus (MERS-CoV) have emerged and presented a considerable global public health threat. Epidemiologic evidence suggests that diabetic subjects are more susceptible to these conditions. However, the prevalence of diabetes in H1N1 and MERS-CoV has not been systematically described. The aim of this study is to conduct a systematic review and meta-analysis of published reports documenting the prevalence of diabetes in H1N1 and MERS-CoV and compare its frequency in the two viral conditions. Meta-analysis for the proportions of subjects with diabetes was carried out in 29 studies for H1N1 ( n =92,948) and 9 for MERS-CoV ( n =308). Average age of H1N1 patients (36.2±6.0 years) was significantly younger than that of subjects with MERS-CoV (54.3±7.4 years, P<0.05). Compared to MERS-CoV patients, subjects with H1N1 exhibited 3-fold lower frequency of cardiovascular diseases and 2- and 4-fold higher prevalence of obesity and immunosuppression, respectively. The overall prevalence of diabetes in H1N1 was 14.6% (95% CI: 12.3-17.0%; P<0.001), a 3.6-fold lower than in MERS-CoV (54.4%; 95% CI: 29.4-79.5; P<0.001). The prevalence of diabetes among H1N1 cases from Asia and North America was ~two-fold higher than those from South America and Europe. The prevalence of diabetes in MERS-CoV cases is higher than in H1N1. Regional comparisons suggest that an etiologic role of diabetes in MERS-CoV may exist distinctive from that in H1N1.

  1. Deciphering MERS-CoV Evolution in Dromedary Camels.

    PubMed

    Du, Lin; Han, Guan-Zhu

    2016-02-01

    The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) poses a potential threat to global public health. Many aspects of the evolution and transmission of MERS-CoV in its animal reservoir remain unclear. A recent study provides new insights into the evolution and transmission of MERS-CoV in dromedary camels. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. 28-mer Fragment Derived from Enterocin CRL35 Displays an Unexpected Bactericidal Effect on Listeria Cells.

    PubMed

    Masias, Emilse; Sanches, Paulo R S; Dupuy, Fernando G; Acuna, Leonardo; Bellomio, Augusto; Cilli, Eduardo; Saavedra, Lucila; Minahk, Carlos

    2015-01-01

    Two shorter peptides derived from enterocin CRL35, a 43-mer bacteriocin, were synthesized i.e. the N-terminal fragment spanning from residues 1 to 15, and a 28-mer fragment that represents the C-terminal of enterocin CRL35, the residues 16 to 43. The separate peptides showed no activity when combined. On one hand, the 28-mer peptide displayed an unpredicted antimicrobial activity. On the other, 15- mer peptide had no consistent anti-Listeria effect. The dissociation constants calculated from experimental data indicated that all peptides could bind at similar extent to the sensitive cells. However, transmembrane electrical potential was not dissipated to the same level by the different peptides; whereas the full-length and the C-terminal 28-mer fragment induced almost full dissipation, 15-mer fragment produced only a slow and incomplete effect. Furthermore, a different interaction of each peptide with membranes was demonstrated based on studies carried out with liposomes, which led us to conclude that activity was related to structure rather than to net positive charges. These results open up the possibility of designing new peptides based on the 28-mer fragment with enhanced activity, which would represent a promising approach for combating Listeria and other pathogens.

  3. Human Centered Design and Development for NASA's MerBoard

    NASA Technical Reports Server (NTRS)

    Trimble, Jay

    2003-01-01

    This viewgraph presentation provides an overview of the design and development process for NASA's MerBoard. These devices are large interactive display screens which can be shown on the user's computer, which will allow scientists in many locations to interpret and evaluate mission data in real-time. These tools are scheduled to be used during the 2003 Mars Exploration Rover (MER) expeditions. Topics covered include: mission overview, Mer Human Centered Computers, FIDO 2001 observations and MerBoard prototypes.

  4. Chinese social media reaction to the MERS-CoV and avian influenza A(H7N9) outbreaks

    PubMed Central

    2013-01-01

    Background As internet and social media use have skyrocketed, epidemiologists have begun to use online data such as Google query data and Twitter trends to track the activity levels of influenza and other infectious diseases. In China, Weibo is an extremely popular microblogging site that is equivalent to Twitter. Capitalizing on the wealth of public opinion data contained in posts on Weibo, this study used Weibo as a measure of the Chinese people’s reactions to two different outbreaks: the 2012 Middle East Respiratory Syndrome Coronavirus (MERS-CoV) outbreak, and the 2013 outbreak of human infection of avian influenza A(H7N9) in China. Methods Keyword searches were performed in Weibo data collected by The University of Hong Kong’s Weiboscope project. Baseline values were determined for each keyword and reaction values per million posts in the days after outbreak information was released to the public. Results The results show that the Chinese people reacted significantly to both outbreaks online, where their social media reaction was two orders of magnitude stronger to the H7N9 influenza outbreak that happened in China than the MERS-CoV outbreak that was far away from China. Conclusions These results demonstrate that social media could be a useful measure of public awareness and reaction to disease outbreak information released by health authorities. PMID:24359669

  5. Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa

    NASA Astrophysics Data System (ADS)

    Wang, Dan; Huang, Shanqing; Liu, Pingying; Liu, Xichun; He, Yafeng; Chen, Weizhong; Hu, Qingyuan; Wei, Tianbiao; Gan, Jianhua; Ma, Jing; Chen, Hao

    2016-09-01

    The metalloprotein MerR is a mercury(II)-dependent transcriptional repressor-activator that responds to mercury(II) with extraordinary sensitivity and selectivity. It’s widely distributed in both Gram-negative and Gram-positive bacteria but with barely detectable sequence identities between the two sources. To provide structural basis for the considerable biochemical and biophysical experiments previously performed on Tn501 and Tn21 MerR from Gram-negative bacteria, we analyzed the crystal structure of mercury(II)-bound Tn501 MerR. The structure in the metal-binding domain provides Tn501 MerR with a high affinity for mercury(II) and the ability to distinguish mercury(II) from other metals with its unique planar trigonal coordination geometry, which is adopted by both Gram-negative and Gram-positive bacteria. The mercury(II) coordination state in the C-terminal metal-binding domain is transmitted through the allosteric network across the dimer interface to the N-terminal DNA-binding domain. Together with the previous mutagenesis analyses, the present data indicate that the residues in the allosteric pathway have a central role in maintaining the functions of Tn501 MerR. In addition, the complex structure exhibits significant differences in tertiary and quaternary structural arrangements compared to those of Bacillus MerR from Gram-positive bacteria, which probably enable them to function with specific promoter DNA with different spacers between -35 and -10 elements.

  6. Thermally induced defluorination during a mer to fac transformation of a blue-green phosphorescent cyclometalated iridium(III) complex.

    PubMed

    Zheng, Yonghao; Batsanov, Andrei S; Edkins, Robert M; Beeby, Andrew; Bryce, Martin R

    2012-01-02

    The new homoleptic tris-cyclometalated [Ir(C^N)(3)] complexes mer-8, fac-8, and fac-9 incorporating γ-carboline ligands are reported. Reaction of 3-(2,4-difluorophenyl)-5-(2-ethylhexyl)-pyrido[4,3-b]indole 6 with iridium(III) chloride under standard cyclometalating conditions gave the homoleptic complex mer-8 in 63% yield. The X-ray crystal structure of mer-8 is described. The Ir-C and Ir-N bonds show the expected bond length alternations for the differing trans influence of phenyl and pyridyl ligands. mer-8 quantitatively isomerized to fac-8 upon irradiation with UV light. However, heating mer-8 at 290 °C in glycerol led to an unusual regioselective loss of one fluorine atom from each of the ligands, yielding fac-9 in 58% yield. fac-8 is thermally very stable: no decomposition was observed when fac-8 was heated in glycerol at 290 °C for 48 h. The γ-carboline system of fac-8 enhances thermal stability compared to the pyridyl analogue fac-Ir(46dfppy)(3)10, which decomposes extensively upon being heated in glycerol at 290 °C for 2 h. Complexes mer-8, fac-8, and fac-9 are emitters of blue-green light (λ(max)(em) = 477, 476, and 494 nm, respectively). The triplet lifetimes for fac-8 and fac-9 are ~4.5 μs at room temperature; solution Φ(PL) values are 0.31 and 0.22, respectively.

  7. SARS and MERS: recent insights into emerging coronaviruses.

    PubMed

    de Wit, Emmie; van Doremalen, Neeltje; Falzarano, Darryl; Munster, Vincent J

    2016-08-01

    The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 marked the second introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The continuing introductions of MERS-CoV from dromedary camels, the subsequent travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates highlight the need for prophylactic and therapeutic measures. Scientific advancements since the 2002-2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. In this Review, we detail our present understanding of the transmission and pathogenesis of SARS-CoV and MERS-CoV, and discuss the current state of development of measures to combat emerging coronaviruses.

  8. Translating MAPGEN to ASPEN for MER

    NASA Technical Reports Server (NTRS)

    Rabideau, Gregg R.; Knight, Russell L.; Lenda, Matthew; Maldague, Pierre F.

    2013-01-01

    This software translates MAPGEN (Europa and APGEN) domains to ASPEN, and the resulting domain can be used to perform planning for the Mars Exploration Rover (MER). In other words, this is a conversion of two distinct planning languages (both declarative and procedural) to a third (declarative) planning language in order to solve the problem of faithful translation from mixed-domain representations into the ASPEN Modeling Language. The MAPGEN planning system is an example of a hybrid procedural/declarative system where the advantages of each are leveraged to produce an effective planner/scheduler for MER tactical planning. The adaptation of the planning system (ASPEN) was investigated, and, with some translation, much of the procedural knowledge encoding is amenable to declarative knowledge encoding. The approach was to compose translators from the core languages used for adapting MAGPEN, which consists of Europa and APGEN. Europa is a constraint- based planner/scheduler where domains are encoded using a declarative model. APGEN is also constraint-based, in that it tracks constraints on resources and states and other variables. Domains are encoded in both constraints and code snippets that execute according to a forward sweep through the plan. Europa and APGEN communicate to each other using proxy activities in APGEN that represent constraints and/or tokens in Europa. The composition of a translator from Europa to ASPEN was fairly straightforward, as ASPEN is also a declarative planning system, and the specific uses of Europa for the MER domain matched ASPEN s native encoding fairly closely. On the other hand, translating from APGEN to ASPEN was considerably more involved. On the surface, the types of activities and resources one encodes in APGEN appear to match oneto- one to the activities, state variables, and resources in ASPEN. But, when looking into the definitions of how resources are profiled and activities are expanded, one sees code snippets that access

  9. Deterministic and stochastic models for middle east respiratory syndrome (MERS)

    NASA Astrophysics Data System (ADS)

    Suryani, Dessy Rizki; Zevika, Mona; Nuraini, Nuning

    2018-03-01

    World Health Organization (WHO) data stated that since September 2012, there were 1,733 cases of Middle East Respiratory Syndrome (MERS) with 628 death cases that occurred in 27 countries. MERS was first identified in Saudi Arabia in 2012 and the largest cases of MERS outside Saudi Arabia occurred in South Korea in 2015. MERS is a disease that attacks the respiratory system caused by infection of MERS-CoV. MERS-CoV transmission occurs directly through direct contact between infected individual with non-infected individual or indirectly through contaminated object by the free virus. Suspected, MERS can spread quickly because of the free virus in environment. Mathematical modeling is used to illustrate the transmission of MERS disease using deterministic model and stochastic model. Deterministic model is used to investigate the temporal dynamic from the system to analyze the steady state condition. Stochastic model approach using Continuous Time Markov Chain (CTMC) is used to predict the future states by using random variables. From the models that were built, the threshold value for deterministic models and stochastic models obtained in the same form and the probability of disease extinction can be computed by stochastic model. Simulations for both models using several of different parameters are shown, and the probability of disease extinction will be compared with several initial conditions.

  10. Rapid detection of MERS coronavirus-like viruses in bats: pote1ntial for tracking MERS coronavirus transmission and animal origin.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Chen, Yixin; Wong, Emily Y M; Chan, Kwok-Hung; Chen, Honglin; Zhang, Libiao; Xia, Ningshao; Yuen, Kwok-Yung

    2018-03-07

    Recently, we developed a monoclonal antibody-based rapid nucleocapsid protein detection assay for diagnosis of MERS coronavirus (MERS-CoV) in humans and dromedary camels. In this study, we examined the usefulness of this assay to detect other lineage C betacoronaviruses closely related to MERS-CoV in bats. The rapid MERS-CoV nucleocapsid protein detection assay was tested positive in 24 (88.9%) of 27 Tylonycteris bat CoV HKU4 (Ty-BatCoV-HKU4) RNA-positive alimentary samples of Tylonycteris pachypus and 4 (19.0%) of 21 Pipistrellus bat CoV HKU5 (Pi-BatCoV-HKU5) RNA-positive alimentary samples of Pipistrellus abramus. There was significantly more Ty-BatCoV-HKU4 RNA-positive alimentary samples than Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive by the rapid MERS-CoV nucleocapsid protein detection assay (P < 0.001 by Chi-square test). The rapid assay was tested negative in all 51 alimentary samples RNA-positive for alphacoronaviruses (Rhinolophus bat CoV HKU2, Myotis bat CoV HKU6, Miniopterus bat CoV HKU8 and Hipposideros batCoV HKU10) and 32 alimentary samples positive for lineage B (SARS-related Rhinolophus bat CoV HKU3) and lineage D (Rousettus bat CoV HKU9) betacoronaviruses. No significant difference was observed between the viral loads of Ty-BatCoV-HKU4/Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive and negative by the rapid test (Mann-Witney U test). The rapid MERS-CoV nucleocapsid protein detection assay is able to rapidly detect lineage C betacoronaviruses in bats. It detected significantly more Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5 because MERS-CoV is more closely related to Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5. This assay will facilitate rapid on-site mass screening of animal samples for ancestors of MERS-CoV and tracking transmission in the related bat species.

  11. Improvement of an enzyme-linked immunosorbent assay for equine herpesvirus type 4 by using a synthetic-peptide 24-mer repeat sequence of glycoprotein G as an antigen.

    PubMed

    Bannai, Hiroshi; Nemoto, Manabu; Tsujimura, Koji; Yamanaka, Takashi; Maeda, Ken; Kondo, Takashi

    2016-02-01

    To increase the sensitivity of an enzyme-linked immunosorbent assay (ELISA) for equine herpesvirus type 4 (EHV-4) that uses a 12-mer peptide of glycoprotein G (gG4-12-mer: MKNNPIYSEGSL) [4], we used a longer peptide consisting of a 24-mer repeat sequence (gG4-24-mer: MKNNPIYSEGSLMLNVQHDDSIHT) as an antigen. Sera of horses experimentally infected with EHV-4 reacted much more strongly to the gG4-24-mer peptide than to the gG4-12-mer peptide. We used peptide ELISAs to test paired sera from horses naturally infected with EHV-4 (n=40). gG4-24-mer ELISA detected 37 positive samples (92.5%), whereas gG4-12-mer ELISA detected only 28 (70.0%). gG4-24-mer ELISA was much more sensitive than gG4-12-mer ELISA.

  12. K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

    PubMed Central

    Sievers, Aaron; Bosiek, Katharina; Bisch, Marc; Dreessen, Chris; Riedel, Jascha; Froß, Patrick; Hausmann, Michael; Hildenbrand, Georg

    2017-01-01

    In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of

  13. Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa

    PubMed Central

    Wang, Dan; Huang, Shanqing; Liu, Pingying; Liu, Xichun; He, Yafeng; Chen, Weizhong; Hu, Qingyuan; Wei, Tianbiao; Gan, Jianhua; Ma, Jing; Chen, Hao

    2016-01-01

    The metalloprotein MerR is a mercury(II)-dependent transcriptional repressor-activator that responds to mercury(II) with extraordinary sensitivity and selectivity. It’s widely distributed in both Gram-negative and Gram-positive bacteria but with barely detectable sequence identities between the two sources. To provide structural basis for the considerable biochemical and biophysical experiments previously performed on Tn501 and Tn21 MerR from Gram-negative bacteria, we analyzed the crystal structure of mercury(II)-bound Tn501 MerR. The structure in the metal-binding domain provides Tn501 MerR with a high affinity for mercury(II) and the ability to distinguish mercury(II) from other metals with its unique planar trigonal coordination geometry, which is adopted by both Gram-negative and Gram-positive bacteria. The mercury(II) coordination state in the C-terminal metal-binding domain is transmitted through the allosteric network across the dimer interface to the N-terminal DNA-binding domain. Together with the previous mutagenesis analyses, the present data indicate that the residues in the allosteric pathway have a central role in maintaining the functions of Tn501 MerR. In addition, the complex structure exhibits significant differences in tertiary and quaternary structural arrangements compared to those of Bacillus MerR from Gram-positive bacteria, which probably enable them to function with specific promoter DNA with different spacers between −35 and −10 elements. PMID:27641146

  14. A mouse model for MERS coronavirus-induced acute respiratory distress syndrome.

    PubMed

    Cockrell, Adam S; Yount, Boyd L; Scobey, Trevor; Jensen, Kara; Douglas, Madeline; Beall, Anne; Tang, Xian-Chun; Marasco, Wayne A; Heise, Mark T; Baric, Ralph S

    2016-11-28

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel virus that emerged in 2012, causing acute respiratory distress syndrome (ARDS), severe pneumonia-like symptoms and multi-organ failure, with a case fatality rate of ∼36%. Limited clinical studies indicate that humans infected with MERS-CoV exhibit pathology consistent with the late stages of ARDS, which is reminiscent of the disease observed in patients infected with severe acute respiratory syndrome coronavirus. Models of MERS-CoV-induced severe respiratory disease have been difficult to achieve, and small-animal models traditionally used to investigate viral pathogenesis (mouse, hamster, guinea-pig and ferret) are naturally resistant to MERS-CoV. Therefore, we used CRISPR-Cas9 gene editing to modify the mouse genome to encode two amino acids (positions 288 and 330) that match the human sequence in the dipeptidyl peptidase 4 receptor, making mice susceptible to MERS-CoV infection and replication. Serial MERS-CoV passage in these engineered mice was then used to generate a mouse-adapted virus that replicated efficiently within the lungs and evoked symptoms indicative of severe ARDS, including decreased survival, extreme weight loss, decreased pulmonary function, pulmonary haemorrhage and pathological signs indicative of end-stage lung disease. Importantly, therapeutic countermeasures comprising MERS-CoV neutralizing antibody treatment or a MERS-CoV spike protein vaccine protected the engineered mice against MERS-CoV-induced ARDS.

  15. Improvement of an enzyme-linked immunosorbent assay for equine herpesvirus type 4 by using a synthetic-peptide 24-mer repeat sequence of glycoprotein G as an antigen

    PubMed Central

    BANNAI, Hiroshi; NEMOTO, Manabu; TSUJIMURA, Koji; YAMANAKA, Takashi; MAEDA, Ken; KONDO, Takashi

    2015-01-01

    To increase the sensitivity of an enzyme-linked immunosorbent assay (ELISA) for equine herpesvirus type 4 (EHV-4) that uses a 12-mer peptide of glycoprotein G (gG4-12-mer: MKNNPIYSEGSL) [4], we used a longer peptide consisting of a 24-mer repeat sequence (gG4-24-mer: MKNNPIYSEGSLMLNVQHDDSIHT) as an antigen. Sera of horses experimentally infected with EHV-4 reacted much more strongly to the gG4-24-mer peptide than to the gG4-12-mer peptide. We used peptide ELISAs to test paired sera from horses naturally infected with EHV-4 (n=40). gG4-24-mer ELISA detected 37 positive samples (92.5%), whereas gG4-12-mer ELISA detected only 28 (70.0%). gG4-24-mer ELISA was much more sensitive than gG4-12-mer ELISA. PMID:26424485

  16. KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

    PubMed

    Mapleson, Daniel; Garcia Accinelli, Gonzalo; Kettleborough, George; Wright, Jonathan; Clavijo, Bernardo J

    2017-02-15

    De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . bernardo.clavijo@earlham.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  17. Evaluation of candidate vaccine approaches for MERS-CoV

    DOE PAGES

    Wang, Lingshu; Shi, Wei; Joyce, M. Gordon; ...

    2015-07-28

    The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV vaccine development. Efforts focused solely on the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein may not optimize neutralizing antibody (NAb) responses. Here we show that immunogens based on full-length S DNA and S1 subunit protein elicit robust serum-neutralizing activity against several MERS-CoV strains in mice and non-human primates. Serological analysis and isolation of murine monoclonal antibodies revealed that immunization elicits NAbs to RBD and, non-RBD portions of S1 and S2 subunit. Multiple neutralization mechanismsmore » were demonstrated by solving the atomic structure of a NAb-RBD complex, through sequencing of neutralization escape viruses and by constructing MERS-CoV S variants for serological assays. Immunization of rhesus macaques confers protection against MERS-CoV-induced radiographic pneumonia, as assessed using computerized tomography, supporting this strategy as a promising approach for MERS-CoV vaccine development.« less

  18. Evaluation of candidate vaccine approaches for MERS-CoV

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

    Wang, Lingshu; Shi, Wei; Joyce, M. Gordon

    The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV vaccine development. Efforts focused solely on the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein may not optimize neutralizing antibody (NAb) responses. Here we show that immunogens based on full-length S DNA and S1 subunit protein elicit robust serum-neutralizing activity against several MERS-CoV strains in mice and non-human primates. Serological analysis and isolation of murine monoclonal antibodies revealed that immunization elicits NAbs to RBD and, non-RBD portions of S1 and S2 subunit. Multiple neutralization mechanismsmore » were demonstrated by solving the atomic structure of a NAb-RBD complex, through sequencing of neutralization escape viruses and by constructing MERS-CoV S variants for serological assays. Immunization of rhesus macaques confers protection against MERS-CoV-induced radiographic pneumonia, as assessed using computerized tomography, supporting this strategy as a promising approach for MERS-CoV vaccine development.« less

  19. MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

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

    White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.

    MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

  20. Mars Exploration Rover (MER) aeroshell

    NASA Image and Video Library

    2003-01-31

    In the Payload Hazardous Servicing Facility, workers prepare the Mars Exploration Rover (MER) aeroshell for transfer to a rotation stand. Set to launch in 2003, the MER Mission will consist of two identical rovers designed to cover roughly 110 yards (100 meters) each Martian day. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. The rovers will be identical to each other, but will land at different regions of Mars. The first rover has a launch window opening May 30, and the second rover a window opening June 25, 2003.

  1. Lexical Frequency Profiles and Zipf's Law

    ERIC Educational Resources Information Center

    Edwards, Roderick; Collins, Laura

    2011-01-01

    Laufer and Nation (1995) proposed that the Lexical Frequency Profile (LFP) can estimate the size of a second-language writer's productive vocabulary. Meara (2005) questioned the sensitivity and the reliability of LFPs for estimating vocabulary sizes, based on the results obtained from probabilistic simulations of LFPs. However, the underlying…

  2. Analyzing MER Uplink Reports

    NASA Technical Reports Server (NTRS)

    Savin, Stephen C.

    2005-01-01

    The MER project includes two rovers working simultaneously on opposite sides of Mars each receiving commands only once a day. Creating this uplink is critical, since a failed uplink means a lost day and a waste of money. Examining the process of creating this uplink, I tracked the use of the system developed for requesting observations as well as the development, from stage to stage, in forming an activity plan. I found the system for requesting observations was commonly misused, if used at all. There are half a dozen reports to document the creation of the uplink plan and often there are discrepancies among them. Despite this, the uplink process worked very well and MER has been one of the most successful missions for NASA in recent memory. Still it is clear there is room for improvement.

  3. Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction

    PubMed Central

    Omrani, Ali S.; Al-Tawfiq, Jaffar A.

    2015-01-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel enzootic betacoronavirus that was first described in September 2012. The clinical spectrum of MERS-CoV infection in humans ranges from an asymptomatic or mild respiratory illness to severe pneumonia and multi-organ failure; overall mortality is around 35.7%. Bats harbour several betacoronaviruses that are closely related to MERS-CoV but more research is needed to establish the relationship between bats and MERS-CoV. The seroprevalence of MERS-CoV antibodies is very high in dromedary camels in Eastern Africa and the Arabian Peninsula. MERS-CoV RNA and viable virus have been isolated from dromedary camels, including some with respiratory symptoms. Furthermore, near-identical strains of MERS-CoV have been isolated from epidemiologically linked humans and camels, confirming inter-transmission, most probably from camels to humans. Though inter-human spread within health care settings is responsible for the majority of reported MERS-CoV cases, the virus is incapable at present of causing sustained human-to-human transmission. Clusters can be readily controlled with implementation of appropriate infection control procedures. Phylogenetic and sequencing data strongly suggest that MERS-CoV originated from bat ancestors after undergoing a recombination event in the spike protein, possibly in dromedary camels in Africa, before its exportation to the Arabian Peninsula along the camel trading routes. MERS-CoV serosurveys are needed to investigate possible unrecognized human infections in Africa. Amongst the important measures to control MERS-CoV spread are strict regulation of camel movement, regular herd screening and isolation of infected camels, use of personal protective equipment by camel handlers and enforcing rules banning all consumption of unpasteurized camel milk and urine. PMID:26924345

  4. Potential MER Landing Site in Melas Chasma

    NASA Technical Reports Server (NTRS)

    Weitz, C. M.; Parker, Timothy J.; Anderson, F. Scott

    2001-01-01

    We have selected one area in Valles Marineris as a potential landing site for the Mars Exploration Rover (MER) mission. After 30 years of analyses, the formation of the Valles Marineris system of troughs and its associated deposits still remains an enigma. Understanding all aspects of the Valles Marineris would significantly contribute to deciphering the internal and external history of Mars. A landing site within Melas Chasma could provide insight into both the formation of Valles Marineris and the composition and origin of the interior layered deposits (ILDs). The ILDs have been proposed as: (1) sedimentary deposits formed in lakes mass wasted material from the walls; (3) remnants of the wall rock; (4) carbonate deposits; (5) aeolian deposits; and (6) volcanic. More recently, Malin and Edgett suggest that the fine-scale, rhythmic layering seen in the interior deposits, as well as other layered deposits in craters, supports a sedimentary origin. Because an understanding of the formation of Valles Marineris and its interior deposits is so important to deciphering the history of Mars, we have proposed a landing site for the MER mission on an exposure of interior deposits in western Melas Chasma. Either MER-A and MER-B could land at this same location.

  5. Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis)

    PubMed Central

    Munster, Vincent J.; Adney, Danielle R.; van Doremalen, Neeltje; Brown, Vienna R.; Miazgowicz, Kerri L.; Milne-Price, Shauna; Bushmaker, Trenton; Rosenke, Rebecca; Scott, Dana; Hawkinson, Ann; de Wit, Emmie; Schountz, Tony; Bowen, Richard A.

    2016-01-01

    The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) highlights the zoonotic potential of Betacoronaviruses. Investigations into the origin of MERS-CoV have focused on two potential reservoirs: bats and camels. Here, we investigated the role of bats as a potential reservoir for MERS-CoV. In vitro, the MERS-CoV spike glycoprotein interacted with Jamaican fruit bat (Artibeus jamaicensis) dipeptidyl peptidase 4 (DPP4) receptor and MERS-CoV replicated efficiently in Jamaican fruit bat cells, suggesting there is no restriction at the receptor or cellular level for MERS-CoV. To shed light on the intrinsic host-virus relationship, we inoculated 10 Jamaican fruit bats with MERS-CoV. Although all bats showed evidence of infection, none of the bats showed clinical signs of disease. Virus shedding was detected in the respiratory and intestinal tract for up to 9 days. MERS-CoV replicated transiently in the respiratory and, to a lesser extent, the intestinal tracts and internal organs; with limited histopathological changes observed only in the lungs. Analysis of the innate gene expression in the lungs showed a moderate, transient induction of expression. Our results indicate that MERS-CoV maintains the ability to replicate in bats without clinical signs of disease, supporting the general hypothesis of bats as ancestral reservoirs for MERS-CoV. PMID:26899616

  6. KMC 2: fast and resource-frugal k-mer counting.

    PubMed

    Deorowicz, Sebastian; Kokot, Marek; Grabowski, Szymon; Debudaj-Grabysz, Agnieszka

    2015-05-15

    Building the histogram of occurrences of every k-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of k-mer counting. Its applications include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. The tremendous amounts of NGS data require fast algorithms for k-mer counting, preferably using moderate amounts of memory. We present a novel method for k-mer counting, on large datasets about twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12 GB (or less) of RAM. Our disk-based method bears some resemblance to MSPKmerCounter, yet replacing the original minimizers with signatures (a carefully selected subset of all minimizers) and using (k, x)-mers allows to significantly reduce the I/O and a highly parallel overall architecture allows to achieve unprecedented processing speeds. For example, KMC 2 counts the 28-mers of a human reads collection with 44-fold coverage (106 GB of compressed size) in about 20 min, on a 6-core Intel i7 PC with an solid-state disk. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Synthesis, structure, luminescence, and magnetic properties of a single-ion magnet "mer"-[tris(N-[(imidazol-4-yl)-methylidene]-DL-phenylalaninato)terbium(III) and related "fac"-DL-alaninato derivative.

    PubMed

    Yamauchi, Suguru; Fujinami, Takeshi; Matsumoto, Naohide; Mochida, Naotaka; Ishida, Takayuki; Sunatsuki, Yukinari; Watanabe, Masayuki; Tsuchimoto, Masanobu; Coletti, Cecilia; Re, Nazzareno

    2014-06-16

    Two Tb(III) complexes with the same N6O3 donor atoms but different coordination geometries, "fac"-[Tb(III)(HL(DL-ala))3]·7H2O (1) and "mer"-[Tb(III)(HL(DL-phe))3]·7H2O (2), were synthesized, where H2L(DL-ala) and H2L(DL-phe) are N-[(imidazol-4-yl)methylidene]-DL-alanine and -DL-phenylalanine, respectively. Each Tb(III) ion is coordinated by three electronically mononegative NNO tridentate ligands to form a coordination geometry of a tricapped trigonal prism. Compound 1 consists of enantiomers "fac"-[Tb(III)(HL(D-ala))3] and "fac"-[Tb(III)(HL(L-ala))3], while 2 consists of "mer"-[Tb(III)(HL(D-phe))2(HL(L-phe))] and "mer"-[Tb(III)(HL(D-phe))(HL(L-phe))2]. Magnetic data were analyzed by a spin Hamiltonian including the crystal field effect on the Tb(III) ion (4f(8), J = 6, S = 3, L = 3, gJ = 3/2, (7)F6). The Stark splitting of the ground state (7)F6 was evaluated from magnetic analysis, and the energy diagram pattern indicated easy-plane and easy-axis (Ising type) magnetic anisotropies for 1 and 2, respectively. Highly efficient luminescences with Φ = 0.50 and 0.61 for 1 and 2, respectively, were observed, and the luminescence fine structure due to the (5)D4 → (7)F6 transition is in good accordance with the energy diagram determined from magnetic analysis. The energy diagram of 1 shows an approximate single-well potential curve, whereas that of 2 shows a double- or quadruple-well potential within the (7)F6 multiplets. Complex 2 displayed an onset of the out-of-phase signal in alternating current (ac) susceptibility at a direct current bias field of 1000 Oe on cooling down to 1.9 K. A slight frequency dependence was recorded around 2 K. On the other hand, 1 did not show any meaningful out-of-phase ac susceptibility. Pulsed-field magnetizations of 1 and 2 were measured below 1.6 K, and only 2 exhibited magnetic hysteresis. This finding agrees well with the energy diagram pattern from crystal field calculation on 1 and 2. DFT calculation allowed us to estimate the

  8. Tremor Frequency Profile as a Function of Level of Mental Retardation

    ERIC Educational Resources Information Center

    Sprague, Robert L.; Deutsch, Katherine M.; Newell, Karl M.

    2007-01-01

    The characteristic slowness of movement initiation and execution in adult individuals with mental retardation may be driven by the slower frequency profile of the dynamics of the system. To investigate this hypothesis, we examined the resting and postural finger tremor frequency profile (single and dual limb) of adults as a function of level of…

  9. Development of Animal Models Against Emerging Coronaviruses: From SARS to MERS coronavirus

    PubMed Central

    Sutton, Troy C; Subbarao, Kanta

    2016-01-01

    Two novel coronaviruses have emerged to cause severe disease in humans. While bats may be the primary reservoir for both viruses, SARS coronavirus (SARS-CoV) likely crossed into humans from civets in China, and MERS coronavirus (MERS-CoV) has been transmitted from camels in the Middle East. Unlike SARS-CoV that resolved within a year, continued introductions of MERS-CoV present an on-going public health threat. Animal models are needed to evaluate countermeasures against emerging viruses. With SARS-CoV, several animal species were permissive to infection. In contrast, most laboratory animals are refractory or only semi-permissive to infection with MERS-CoV. This host-range restriction is largely determined by sequence heterogeneity in the MERS-CoV receptor. We describe animal models developed to study coronaviruses, with a focus on host-range restriction at the level of the viral receptor and discuss approaches to consider in developing a model to evaluate countermeasures against MERS-CoV. PMID:25791336

  10. Engineered Single-Chain, Antiparallel, Coiled Coil Mimics the MerR Metal Binding Site

    PubMed Central

    Song, Lingyun; Caguiat, Jonathan; Li, Zhongrui; Shokes, Jacob; Scott, Robert A.; Olliff, Lynda; Summers, Anne O.

    2004-01-01

    The repressor-activator MerR that controls transcription of the mercury resistance (mer) operon is unusual for its high sensitivity and specificity for Hg(II) in in vivo and in vitro transcriptional assays. The metal-recognition domain of MerR resides at the homodimer interface in a novel antiparallel arrangement of α-helix 5 that forms a coiled-coil motif. To facilitate the study of this novel metal binding motif, we assembled this antiparallel coiled coil into a single chain by directly fusing two copies of the 48-residue α-helix 5 of MerR. The resulting 107-residue polypeptide, called the metal binding domain (MBD), and wild-type MerR were overproduced and purified, and their metal-binding properties were determined in vivo and in vitro. In vitro MBD bound ca. 1.0 equivalent of Hg(II) per pair of binding sites, just as MerR does, and it showed only a slightly lower affinity for Hg(II) than did MerR. Extended X-ray absorption fine structure data showed that MBD has essentially the same Hg(II) coordination environment as MerR. In vivo, cells overexpressing MBD accumulated 70 to 100% more 203Hg(II) than cells bearing the vector alone, without deleterious effects on cell growth. Both MerR and MBD variously bound other thiophilic metal ions, including Cd(II), Zn(II), Pb(II), and As(III), in vitro and in vivo. We conclude that (i) it is possible to simulate in a single polypeptide chain the in vitro and in vivo metal-binding ability of dimeric, full-length MerR and (ii) MerR's specificity in transcriptional activation does not reside solely in the metal-binding step. PMID:14996817

  11. Mouse-adapted MERS coronavirus causes lethal lung disease in human DPP4 knockin mice.

    PubMed

    Li, Kun; Wohlford-Lenane, Christine L; Channappanavar, Rudragouda; Park, Jung-Eun; Earnest, James T; Bair, Thomas B; Bates, Amber M; Brogden, Kim A; Flaherty, Heather A; Gallagher, Tom; Meyerholz, David K; Perlman, Stanley; McCray, Paul B

    2017-04-11

    The Middle East respiratory syndrome (MERS) emerged in Saudi Arabia in 2012, caused by a zoonotically transmitted coronavirus (CoV). Over 1,900 cases have been reported to date, with ∼36% fatality rate. Lack of autopsies from MERS cases has hindered understanding of MERS-CoV pathogenesis. A small animal model that develops progressive pulmonary manifestations when infected with MERS-CoV would advance the field. As mice are restricted to infection at the level of DPP4, the MERS-CoV receptor, we generated mice with humanized exons 10-12 of the mouse Dpp4 locus. Upon inoculation with MERS-CoV, human DPP4 knockin (KI) mice supported virus replication in the lungs, but developed no illness. After 30 serial passages through the lungs of KI mice, a mouse-adapted virus emerged (MERS MA ) that grew in lungs to over 100 times higher titers than the starting virus. A plaque-purified MERS MA clone caused weight loss and fatal infection. Virus antigen was observed in airway epithelia, pneumocytes, and macrophages. Pathologic findings included diffuse alveolar damage with pulmonary edema and hyaline membrane formation associated with accumulation of activated inflammatory monocyte-macrophages and neutrophils in the lungs. Relative to the parental MERS-CoV, MERS MA viruses contained 13-22 mutations, including several within the spike (S) glycoprotein gene. S-protein mutations sensitized viruses to entry-activating serine proteases and conferred more rapid entry kinetics. Recombinant MERS MA bearing mutant S proteins were more virulent than the parental virus in hDPP4 KI mice. The hDPP4 KI mouse and the MERS MA provide tools to investigate disease causes and develop new therapies.

  12. Increase methylmercury accumulation in Arabidopsis thaliana expressing bacterial broad-spectrum mercury transporter MerE

    PubMed Central

    2013-01-01

    The bacterial merE gene derived from the Tn21 mer operon encodes a broad-spectrum mercury transporter that governs the transport of methylmercury and mercuric ions across bacterial cytoplasmic membranes, and this gene is a potential molecular tool for improving the efficiency of methylmercury phytoremediation. A transgenic Arabidopsis engineered to express MerE was constructed and the impact of expression of MerE on methylmercury accumulation was evaluated. The subcellular localization of transiently expressed GFP-tagged MerE was examined in Arabidopsis suspension-cultured cells. The GFP-MerE was found to localize to the plasma membrane and cytosol. The transgenic Arabidopsis expressing MerE accumulated significantly more methymercury and mercuric ions into plants than the wild-type Arabidopsis did. The transgenic plants expressing MerE was significantly more resistant to mercuric ions, but only showed more resistant to methylmercury compared with the wild type Arabidopsis. These results demonstrated that expression of the bacterial mercury transporter MerE promoted the transport and accumulation of methylmercury in transgenic Arabidopsis, which may be a useful method for improving plants to facilitate the phytoremediation of methylmercury pollution. PMID:24004544

  13. MERS in the U.S.

    MedlinePlus

    ... traveler departed Riyadh, Saudi Arabia and traveled by plane to London, England, then to Chicago, Illinois. The ... MERS. On May 1, the patient traveled by plane from Jeddah, Saudi Arabia to London, England; to ...

  14. Low-frequency pulse profile variation in PSR B2217+47: evidence for echoes from the interstellar medium

    NASA Astrophysics Data System (ADS)

    Michilli, D.; Hessels, J. W. T.; Donner, J. Y.; Grießmeier, J.-M.; Serylak, M.; Shaw, B.; Stappers, B. W.; Verbiest, J. P. W.; Deller, A. T.; Driessen, L. N.; Stinebring, D. R.; Bondonneau, L.; Geyer, M.; Hoeft, M.; Karastergiou, A.; Kramer, M.; Osłowski, S.; Pilia, M.; Sanidas, S.; Weltevrede, P.

    2018-05-01

    We have observed a complex and continuous change in the integrated pulse profile of PSR B2217+47, manifested as additional components trailing the main peak. These transient components are detected over 6 yr at 150 MHz using the LOw Frequency ARray (LOFAR), but they are not seen in contemporaneous Lovell observations at 1.5 GHz. We argue that propagation effects in the ionized interstellar medium (IISM) are the most likely cause. The putative structures in the IISM causing the profile variation are roughly half-way between the pulsar and the Earth and have transverse radii R ˜ 30 au. We consider different models for the structures. Under the assumption of spherical symmetry, their implied average electron density is \\overline{n}_e ˜ 100 cm-3. Since PSR B2217+47 is more than an order of magnitude brighter than the average pulsar population visible to LOFAR, similar profile variations would not have been identified in most pulsars, suggesting that subtle profile variations in low-frequency profiles might be more common than we have observed to date. Systematic studies of these variations at low frequencies can provide a new tool to investigate the proprieties of the IISM and the limits to the precision of pulsar timing.

  15. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

    PubMed Central

    Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

    2009-01-01

    Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

  16. WATER ON MARS: EVIDENCE FROM MER MISSION RESULTS

    NASA Technical Reports Server (NTRS)

    Landis, Geoffrey A.

    2006-01-01

    The Mars Exploration Rover (MER) mission landed two rovers on Mars, equipped with a highly-capable suite of science instruments. The Spirit rover landed on the inside Gusev Crater on January 5, 2004, and the Opportunity rover three weeks later on Meridiani Planum. This paper summarizes some of the findings from the MER rovers related to the NASA science strategy of investigating past and present water on Mars.

  17. Preventing cleavage of Mer promotes efferocytosis and suppresses acute lung injury in bleomycin treated mice

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

    Lee, Ye-Ji; Tissue Injury Defense Research Center, School of Medicine, Ewha Womans University, Seoul; Lee, Seung-Hae

    2012-08-15

    Mer receptor tyrosine kinase (Mer) regulates macrophage activation and promotes apoptotic cell clearance. Mer activation is regulated through proteolytic cleavage of the extracellular domain. To determine if membrane-bound Mer is cleaved during bleomycin-induced lung injury, and, if so, how preventing the cleavage of Mer enhances apoptotic cell uptake and down-regulates pulmonary immune responses. During bleomycin-induced acute lung injury in mice, membrane-bound Mer expression decreased, but production of soluble Mer and activity as well as expression of disintegrin and metalloproteinase 17 (ADAM17) were enhanced . Treatment with the ADAM inhibitor TAPI-0 restored Mer expression and diminished soluble Mer production. Furthermore, TAPI-0more » increased Mer activation in alveolar macrophages and lung tissue resulting in enhanced apoptotic cell clearance in vivo and ex vivo by alveolar macrophages. Suppression of bleomycin-induced pro-inflammatory mediators, but enhancement of hepatocyte growth factor induction were seen after TAPI-0 treatment. Additional bleomycin-induced inflammatory responses reduced by TAPI-0 treatment included inflammatory cell recruitment into the lungs, levels of total protein and lactate dehydrogenase activity in bronchoalveolar lavage fluid, as well as caspase-3 and caspase-9 activity and alveolar epithelial cell apoptosis in lung tissue. Importantly, the effects of TAPI-0 on bleomycin-induced inflammation and apoptosis were reversed by coadministration of specific Mer-neutralizing antibodies. These findings suggest that restored membrane-bound Mer expression by TAPI-0 treatment may help resolve lung inflammation and apoptosis after bleomycin treatment. -- Highlights: ►Mer expression is restored by TAPI-0 treatment in bleomycin-stimulated lung. ►Mer signaling is enhanced by TAPI-0 treatment in bleomycin-stimulated lung. ►TAPI-0 enhances efferocytosis and promotes resolution of lung injury.« less

  18. Development of animal models against emerging coronaviruses: From SARS to MERS coronavirus.

    PubMed

    Sutton, Troy C; Subbarao, Kanta

    2015-05-01

    Two novel coronaviruses have emerged to cause severe disease in humans. While bats may be the primary reservoir for both viruses, SARS coronavirus (SARS-CoV) likely crossed into humans from civets in China, and MERS coronavirus (MERS-CoV) has been transmitted from camels in the Middle East. Unlike SARS-CoV that resolved within a year, continued introductions of MERS-CoV present an on-going public health threat. Animal models are needed to evaluate countermeasures against emerging viruses. With SARS-CoV, several animal species were permissive to infection. In contrast, most laboratory animals are refractory or only semi-permissive to infection with MERS-CoV. This host-range restriction is largely determined by sequence heterogeneity in the MERS-CoV receptor. We describe animal models developed to study coronaviruses, with a focus on host-range restriction at the level of the viral receptor and discuss approaches to consider in developing a model to evaluate countermeasures against MERS-CoV. Copyright © 2015. Published by Elsevier Inc.

  19. Power Supply for Variable Frequency Induction Heating Using MERS Soft-Switching High Frequency Inverter

    NASA Astrophysics Data System (ADS)

    Isobe, Takanori; Kitahara, Tadayuki; Fukutani, Kazuhiko; Shimada, Ryuichi

    Variable frequency induction heating has great potential for industrial heating applications due to the possibility of achieving heating distribution control; however, large-scale induction heating with variable frequency has not yet been introduced for practical use. This paper proposes a high frequency soft-switching inverter for induction heating that can achieve variable frequency operation. One challenge of variable frequency induction heating is increasing power electronics ratings. This paper indicates that its current source type dc-link configuration and soft-switching characteristics can make it possible to build a large-scale system with variable frequency capability. A 90-kVA 150-1000Hz variable frequency experimental power supply for steel strip induction heating was developed. Experiments confirmed the feasibility of variable frequency induction heating with proposed converter and the advantages of variable frequency operation.

  20. Unraveling the drivers of MERS-CoV transmission

    PubMed Central

    Cauchemez, Simon; Nouvellet, Pierre; Cori, Anne; Jombart, Thibaut; Clapham, Hannah; Moore, Sean; Mills, Harriet Linden; Salje, Henrik; Collins, Caitlin; Rodriquez-Barraquer, Isabel; Riley, Steven; Truelove, Shaun; Algarni, Homoud; Alhakeem, Rafat; AlHarbi, Khalid; Turkistani, Abdulhafiz; Aguas, Ricardo J.; Cummings, Derek A. T.; Van Kerkhove, Maria D.; Donnelly, Christl A.; Lessler, Justin; Fraser, Christophe; Al-Barrak, Ali; Ferguson, Neil M.

    2016-01-01

    With more than 1,700 laboratory-confirmed infections, Middle East respiratory syndrome coronavirus (MERS-CoV) remains a significant threat for public health. However, the lack of detailed data on modes of transmission from the animal reservoir and between humans means that the drivers of MERS-CoV epidemics remain poorly characterized. Here, we develop a statistical framework to provide a comprehensive analysis of the transmission patterns underlying the 681 MERS-CoV cases detected in the Kingdom of Saudi Arabia (KSA) between January 2013 and July 2014. We assess how infections from the animal reservoir, the different levels of mixing, and heterogeneities in transmission have contributed to the buildup of MERS-CoV epidemics in KSA. We estimate that 12% [95% credible interval (CI): 9%, 15%] of cases were infected from the reservoir, the rest via human-to-human transmission in clusters (60%; CI: 57%, 63%), within (23%; CI: 20%, 27%), or between (5%; CI: 2%, 8%) regions. The reproduction number at the start of a cluster was 0.45 (CI: 0.33, 0.58) on average, but with large SD (0.53; CI: 0.35, 0.78). It was >1 in 12% (CI: 6%, 18%) of clusters but fell by approximately one-half (47% CI: 34%, 63%) its original value after 10 cases on average. The ongoing exposure of humans to MERS-CoV from the reservoir is of major concern, given the continued risk of substantial outbreaks in health care systems. The approach we present allows the study of infectious disease transmission when data linking cases to each other remain limited and uncertain. PMID:27457935

  1. A Rapid and Specific Assay for the Detection of MERS-CoV

    PubMed Central

    Huang, Pei; Wang, Hualei; Cao, Zengguo; Jin, Hongli; Chi, Hang; Zhao, Jincun; Yu, Beibei; Yan, Feihu; Hu, Xingxing; Wu, Fangfang; Jiao, Cuicui; Hou, Pengfei; Xu, Shengnan; Zhao, Yongkun; Feng, Na; Wang, Jianzhong; Sun, Weiyang; Wang, Tiecheng; Gao, Yuwei; Yang, Songtao; Xia, Xianzhu

    2018-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that can cause human respiratory disease. The development of a detection method for this virus that can lead to rapid and accurate diagnosis would be significant. In this study, we established a nucleic acid visualization technique that combines the reverse transcription loop-mediated isothermal amplification technique and a vertical flow visualization strip (RT-LAMP-VF) to detect the N gene of MERS-CoV. The RT-LAMP-VF assay was performed in a constant temperature water bath for 30 min, and the result was visible by the naked eye within 5 min. The RT-LAMP-VF assay was capable of detecting 2 × 101 copies/μl of synthesized RNA transcript and 1 × 101 copies/μl of MERS-CoV RNA. The method exhibits no cross-reactivities with multiple CoVs including SARS-related (SARSr)-CoV, HKU4, HKU1, OC43 and 229E, and thus exhibits high specificity. Compared to the real-time RT-PCR (rRT-PCR) method recommended by the World Health Organization (WHO), the RT-LAMP-VF assay is easy to handle, does not require expensive equipment and can rapidly complete detection within 35 min. PMID:29896174

  2. Prophylaxis With a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)–Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection

    PubMed Central

    Houser, Katherine V.; Gretebeck, Lisa; Ying, Tianlei; Wang, Yanping; Vogel, Leatrice; Lamirande, Elaine W.; Bock, Kevin W.; Moore, Ian N.; Dimitrov, Dimiter S.; Subbarao, Kanta

    2016-01-01

    With >1600 documented human infections with Middle East respiratory syndrome coronavirus (MERS-CoV) and a case fatality rate of approximately 36%, medical countermeasures are needed to prevent and limit the disease. We examined the in vivo efficacy of the human monoclonal antibody m336, which has high neutralizing activity against MERS-CoV in vitro. m336 was administered to rabbits intravenously or intranasally before infection with MERS-CoV. Prophylaxis with m336 resulted in a reduction of pulmonary viral RNA titers by 40–9000-fold, compared with an irrelevant control antibody with little to no inflammation or viral antigen detected. This protection in rabbits supports further clinical development of m336. PMID:26941283

  3. An Investigation into the Use of Word Frequency Lists in Computing Vocabulary Profiles.

    ERIC Educational Resources Information Center

    Coniam, David

    1999-01-01

    Investigates word frequency as an indicator of language proficiency in the written English of Grade 13 learners of English in Hong Kong. The study develops Laufer and Nation's (1995) work on Lexical Frequency Profile in which student writing was analyzed for the frequency of word families, with vocabulary profiles produced from the scripts on the…

  4. Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment.

    PubMed

    Ní Chadhain, Sinéad M; Schaefer, Jeffra K; Crane, Sharron; Zylstra, Gerben J; Barkay, Tamar

    2006-10-01

    The reduction of ionic mercury to elemental mercury by the mercuric reductase (MerA) enzyme plays an important role in the biogeochemical cycling of mercury in contaminated environments by partitioning mercury to the atmosphere. This activity, common in aerobic environments, has rarely been examined in anoxic sediments where production of highly toxic methylmercury occurs. Novel degenerate PCR primers were developed which span the known diversity of merA genes in Gram-negative bacteria and amplify a 285 bp fragment at the 3' end of merA. These primers were used to create a clone library and to analyse merA diversity in an anaerobic sediment enrichment collected from a mercury-contaminated site in the Meadowlands, New Jersey. A total of 174 sequences were analysed, representing 71 merA phylotypes and four novel MerA clades. This first examination of merA diversity in anoxic environments suggests an untapped resource for novel merA sequences.

  5. Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013.

    PubMed

    Meyer, Benjamin; Müller, Marcel A; Corman, Victor M; Reusken, Chantal B E M; Ritz, Daniel; Godeke, Gert-Jan; Lattwein, Erik; Kallies, Stephan; Siemens, Artem; van Beek, Janko; Drexler, Jan F; Muth, Doreen; Bosch, Berend-Jan; Wernery, Ulrich; Koopmans, Marion P G; Wernery, Renate; Drosten, Christian

    2014-04-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) has caused an ongoing outbreak of severe acute respiratory tract infection in humans in the Arabian Peninsula since 2012. Dromedary camels have been implicated as possible viral reservoirs. We used serologic assays to analyze 651 dromedary camel serum samples from the United Arab Emirates; 151 of 651 samples were obtained in 2003, well before onset of the current epidemic, and 500 serum samples were obtained in 2013. Recombinant spike protein-specific immunofluorescence and virus neutralization tests enabled clear discrimination between MERS-CoV and bovine CoV infections. Most (632/651, 97.1%) camels had antibodies against MERS-CoV. This result included all 151 serum samples obtained in 2003. Most (389/651, 59.8%) serum samples had MERS-CoV-neutralizing antibody titers >1,280. Dromedary camels from the United Arab Emirates were infected at high rates with MERS-CoV or a closely related, probably conspecific, virus long before the first human MERS cases.

  6. Mobile Three Frequency Radar as Research Platform for Precipitation Profiling

    NASA Astrophysics Data System (ADS)

    Schmidt, Walter; Rautiainen, Kimmo; Harri, Ari-Matti

    2014-05-01

    Precipitation profiling at the frequency bands of Ku, Ka and W bands are becoming increasingly popular in the studies of atmospheric microphysics. Ever since the introduction of Ku / Ka pair of frequencies for the Global Precipitation Measurement mission (GPM) and the success of W band in Cloudsat, the interest in precipitation profiling using these frequencies has increased. The profiling observations will also serve as ground validation instruments for several space missions such as GPM and EarthCARE [1]. In order to get better information to retrieve ice microphysics as well as to enhance sensitivity, we need to move from the standard S- and C-band weather radars to higher frequencies [2]. As was recently shown, the use of multi- frequency profiling yields important additional information compared to single-frequency radar mapping [3]. During the past four years a consortium of research, academic and private industries in Finland has been developing a flexible low-cost mobile three-band radar system for precipitation profiling. The feasibility of the concept is being demonstrated by implementing the Ku- and Ka-band part of the system. The antenna structure with antennas for Ku-, Ka- and W-band is completed allowing the pointing of all three antenna systems into the same direction during an azimuth and elevation scan. Using a freely programmable digital waveform generator and decoding electronics for the received data, the implementation of different wave form generation, compression and decoding schemes and their influence on the radar performance in the different bands can be evaluated and optimized. The modular design allows the connection of different transmitter control and receiver decoding units to any of the three band front-end electronics to evaluate the performance of different approaches in the various bands simultaneously. A real-time analysis software supports the data interpretation and system optimization during field tests. Via mobile internet

  7. Monoclonal Antibody Shows Promise as Potential Therapeutic for MERS | Poster

    Cancer.gov

    A monoclonal antibody has proven effective in preventing Middle Eastern Respiratory Syndrome (MERS) in lab animals, suggesting further development as a potential intervention for the deadly disease in humans, according to new research. MERS is a newly emerged coronavirus first detected in humans in 2012. Most cases have occurred in the Middle East, but the disease has appeared elsewhere. In all, MERS has infected more than 1,700 individuals and killed more than 600, according to the World Health Organization. No vaccines or antiviral therapies currently exist. Several candidate vaccines are being developed, and some have been tested in animal models, a prerequisite to human clinical trials.

  8. Demonstration of Mer-Cure Technology for Enhanced Mercury Control

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

    John Marion; Dave O'Neill; Kevin Taugher

    2008-06-01

    Alstom Power Inc. has completed a DOE/NETL-sponsored program (under DOE Cooperative Agreement No. De-FC26-07NT42776) to demonstrate Mer-Cure{trademark}, one of Alstom's mercury control technologies for coal-fired boilers. The Mer-Cure{trademark}system utilizes a small amount of Mer-Clean{trademark} sorbent that is injected into the flue gas stream for oxidation and adsorption of gaseous mercury. Mer-Clean{trademark} sorbents are carbon-based and prepared with chemical additives that promote oxidation and capture of mercury. The Mer-Cure{trademark} system is unique in that the sorbent is injected into an environment where the mercury capture kinetics is accelerated. The full-scale demonstration program originally included test campaigns at two host sites: LCRA's 480-MW{sub e} Fayette Unit No.3 and Reliant Energy's 190-MW{sub e} Shawville Unit No.3. The only demonstration tests actually done were the short-term tests at LCRA due to budget constraints. This report gives a summary of the demonstration testing at Fayette Unit No.3. The goals for this Mercury Round 3 program, established by DOE/NETL under the original solicitation, were to reduce the uncontrolled mercury emissions by 90% at a cost significantly less than 50% of the previous target ofmore » $$60,000/lb mercury removed. The results indicated that Mer-Cure{trademark} technology could achieve mercury removal of 90% based on uncontrolled stack emissions. The estimated costs for 90% mercury control, at a sorbent cost of $$0.75 to $2.00/lb respectively, were $13,400 to $18,700/lb Hg removed. In summary, the results from demonstration testing show that the goals established by DOE/NETL were met during this test program. The goal of 90% mercury reduction was achieved. Estimated mercury removal costs were 69-78% lower than the benchmark of $60,000/lb mercury removed, significantly less than 50% of the baseline removal cost.« less

  9. MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity.

    PubMed

    Chu, Daniel K W; Hui, Kenrie P Y; Perera, Ranawaka A P M; Miguel, Eve; Niemeyer, Daniela; Zhao, Jincun; Channappanavar, Rudragouda; Dudas, Gytis; Oladipo, Jamiu O; Traoré, Amadou; Fassi-Fihri, Ouafaa; Ali, Abraham; Demissié, Getnet F; Muth, Doreen; Chan, Michael C W; Nicholls, John M; Meyerholz, David K; Kuranga, Sulyman A; Mamo, Gezahegne; Zhou, Ziqi; So, Ray T Y; Hemida, Maged G; Webby, Richard J; Roger, Francois; Rambaut, Andrew; Poon, Leo L M; Perlman, Stanley; Drosten, Christian; Chevalier, Veronique; Peiris, Malik

    2018-03-20

    Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of zoonotic infection. Although MERS-CoV infection is ubiquitous in dromedaries across Africa as well as in the Arabian Peninsula, zoonotic disease appears confined to the Arabian Peninsula. MERS-CoVs from Africa have hitherto been poorly studied. We genetically and phenotypically characterized MERS-CoV from dromedaries sampled in Morocco, Burkina Faso, Nigeria, and Ethiopia. Viruses from Africa (clade C) are phylogenetically distinct from contemporary viruses from the Arabian Peninsula (clades A and B) but remain antigenically similar in microneutralization tests. Viruses from West (Nigeria, Burkina Faso) and North (Morocco) Africa form a subclade, C1, that shares clade-defining genetic signatures including deletions in the accessory gene ORF4b Compared with human and camel MERS-CoV from Saudi Arabia, virus isolates from Burkina Faso (BF785) and Nigeria (Nig1657) had lower virus replication competence in Calu-3 cells and in ex vivo cultures of human bronchus and lung. BF785 replicated to lower titer in lungs of human DPP4-transduced mice. A reverse genetics-derived recombinant MERS-CoV (EMC) lacking ORF4b elicited higher type I and III IFN responses than the isogenic EMC virus in Calu-3 cells. However, ORF4b deletions may not be the major determinant of the reduced replication competence of BF785 and Nig1657. Genetic and phenotypic differences in West African viruses may be relevant to zoonotic potential. There is an urgent need for studies of MERS-CoV at the animal-human interface. Copyright © 2018 the Author(s). Published by PNAS.

  10. Mild encephalitis/encephalopathy with reversible splenial lesion (MERS) in adults-a case report and literature review.

    PubMed

    Yuan, Junliang; Yang, Shuna; Wang, Shuangkun; Qin, Wei; Yang, Lei; Hu, Wenli

    2017-05-25

    Mild encephalitis/encephalopathy with reversible splenial lesion (MERS) is a rare clinico-radiological entity characterized by the magnetic resonance imaging (MRI) finding of a reversible lesion in the corpus callosum, sometimes involved the symmetrical white matters. Many cases of child-onset MERS with various causes have been reported. However, adult-onset MERS is relatively rare. The clinical characteristics and pathophysiologiccal mechanisms of adult-onset MERS are not well understood. We reviewed the literature on adult-onset MERS in order to describe the characteristics of MERS in adults and to provide experiences for clinician. We reported a case of adult-onset MERS with acute urinary retension and performed literature search from PubMed and web of science databases to identify other adult-onset MERS reports from Januarary 2004 to March 2016. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed on selection process. And then we summarized the clinico-radiological features of adult-onset MERS. Twenty-nine adult-onset MERS cases were reviewed from available literature including the case we have. 86.2% of the cases (25/29) were reported in Asia, especially in Japan. Ages varied between 18 and 59 years old with a 12:17 female-to-male ratio. The major cause was infection by virus or bacteria. Fever and headache were the most common clinical manifestation, and acute urinary retention was observed in 6 patients. All patients recovered completely within a month. Adult-onset MERS is an entity with a broad clinico-radiological spectrum because of the various diseases and conditions. There are similar characteristics between MERS in adults and children, also some differences.

  11. Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter.

    PubMed

    Mohamed Hashim, Ezzeddin Kamil; Abdullah, Rosni

    2015-12-21

    Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  12. Monoclonal Antibody Shows Promise as Potential Therapeutic for MERS | Poster

    Cancer.gov

    A monoclonal antibody has proven effective in preventing Middle Eastern Respiratory Syndrome (MERS) in lab animals, suggesting further development as a potential intervention for the deadly disease in humans, according to new research. MERS is a newly emerged coronavirus first detected in humans in 2012. Most cases have occurred in the Middle East, but the disease has appeared

  13. KMC 3: counting and manipulating k-mer statistics.

    PubMed

    Kokot, Marek; Dlugosz, Maciej; Deorowicz, Sebastian

    2017-09-01

    Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems. Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc . sebastian.deorowicz@polsl.pl. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  14. Activated Microglia Desialylate and Phagocytose Cells via Neuraminidase, Galectin-3, and Mer Tyrosine Kinase

    PubMed Central

    Nomura, Koji; Vilalta, Anna; Allendorf, David H.; Hornik, Tamara C.

    2017-01-01

    Activated microglia can phagocytose dying, stressed, or excess neurons and synapses via the phagocytic receptor Mer tyrosine kinase (MerTK). Galectin-3 (Gal-3) can cross-link surface glycoproteins by binding galactose residues that are normally hidden below terminal sialic acid residues. Gal-3 was recently reported to opsonize cells via activating MerTK. We found that LPS-activated BV-2 microglia rapidly released Gal-3, which was blocked by calcineurin inhibitors. Gal-3 bound to MerTK on microglia and to stressed PC12 (neuron-like) cells, and it increased microglial phagocytosis of PC12 cells or primary neurons, which was blocked by inhibition of MerTK. LPS-activated microglia exhibited a sialidase activity that desialylated PC12 cells and could be inhibited by Tamiflu, a neuraminidase (sialidase) inhibitor. Sialidase treatment of PC12 cells enabled Gal-3 to bind and opsonize the live cells for phagocytosis by microglia. LPS-induced microglial phagocytosis of PC12 was prevented by small interfering RNA knockdown of Gal-3 in microglia, lactose inhibition of Gal-3 binding, inhibition of neuraminidase with Tamiflu, or inhibition of MerTK by UNC569. LPS-induced phagocytosis of primary neurons by primary microglia was also blocked by inhibition of MerTK. We conclude that activated microglia release Gal-3 and a neuraminidase that desialylates microglial and PC12 surfaces, enabling Gal-3 binding to PC12 cells and their phagocytosis via MerTK. Thus, Gal-3 acts as an opsonin of desialylated surfaces, and inflammatory loss of neurons or synapses may potentially be blocked by inhibiting neuraminidases, Gal-3, or MerTK. PMID:28500071

  15. Microbial Certification of the MER spacecraft

    NASA Technical Reports Server (NTRS)

    Schubert, W. W.; Arakelian, T.; Barengoltz, J. B.; Chough, N. G.; Chung, S. Y.; Law, J.; Kirschner, L.; Koukol, R. C.; Newlin, L. E.; Morales, F.

    2003-01-01

    Spacecraft such as the Mars Exploration Rovers (MER) must meet acceptable microbial population levels prior to launch. Sensitive parts and materials prevent any single sterilization method from being used as a final step on the assembled spacecraft.

  16. MERS, SARS and other coronaviruses as causes of pneumonia.

    PubMed

    Yin, Yudong; Wunderink, Richard G

    2018-02-01

    Human coronaviruses (HCoVs) have been considered to be relatively harmless respiratory pathogens in the past. However, after the outbreak of the severe acute respiratory syndrome (SARS) and emergence of the Middle East respiratory syndrome (MERS), HCoVs have received worldwide attention as important pathogens in respiratory tract infection. This review focuses on the epidemiology, pathogenesis and clinical characteristics among SARS-coronaviruses (CoV), MERS-CoV and other HCoV infections. © 2017 Asian Pacific Society of Respirology.

  17. Asy2/Mer2: an evolutionarily conserved mediator of meiotic recombination, pairing, and global chromosome compaction

    PubMed Central

    Tessé, Sophie; Bourbon, Henri-Marc; Debuchy, Robert; Budin, Karine; Dubois, Emeline; Liangran, Zhang; Antoine, Romain; Piolot, Tristan; Kleckner, Nancy; Zickler, Denise; Espagne, Eric

    2017-01-01

    Meiosis is the cellular program by which a diploid cell gives rise to haploid gametes for sexual reproduction. Meiotic progression depends on tight physical and functional coupling of recombination steps at the DNA level with specific organizational features of meiotic-prophase chromosomes. The present study reveals that every step of this coupling is mediated by a single molecule: Asy2/Mer2. We show that Mer2, identified so far only in budding and fission yeasts, is in fact evolutionarily conserved from fungi (Mer2/Rec15/Asy2/Bad42) to plants (PRD3/PAIR1) and mammals (IHO1). In yeasts, Mer2 mediates assembly of recombination–initiation complexes and double-strand breaks (DSBs). This role is conserved in the fungus Sordaria. However, functional analysis of 13 mer2 mutants and successive localization of Mer2 to axis, synaptonemal complex (SC), and chromatin revealed, in addition, three further important functions. First, after DSB formation, Mer2 is required for pairing by mediating homolog spatial juxtaposition, with implications for crossover (CO) patterning/interference. Second, Mer2 participates in the transfer/maintenance and release of recombination complexes to/from the SC central region. Third, after completion of recombination, potentially dependent on SUMOylation, Mer2 mediates global chromosome compaction and post-recombination chiasma development. Thus, beyond its role as a recombinosome–axis/SC linker molecule, Mer2 has important functions in relation to basic chromosome structure. PMID:29021238

  18. MERS-CoV infection: Mind the public knowledge gap.

    PubMed

    Bawazir, Amen; Al-Mazroo, Eman; Jradi, Hoda; Ahmed, Anwar; Badri, Motasim

    In August 2015, the Corona outbreak caused by Middle East respiratory syndrome coronavirus (MERS-CoV) was the 9th episode since June 2012 in Saudi Arabia. Little is known about the public awareness toward the nature or prevention of the disease. The aim of this work was to assess the knowledge of the adult population in Riyadh toward the MERS-CoV. In this cross-sectional survey, a self-administrated questionnaire was distributed to randomly selected participants visiting malls in Riyadh. The questionnaire contained measurable epidemiological and clinical MERS-CoV knowledge level variables and relevant source of information. The study included 676 participants. Mean age was 32.5 (±SD 8.6) years and 353 (47.8%) were males. Almost all participants heard about the corona disease and causative agent. The study showed a fair overall knowledge (66.0%), less knowledge on epidemiological features of the disease (58.3%), and good knowledge (90.7%) on the clinical manifestation of the MERS-CoV. Internet was the major (89.0%) source of disease information, and other sources including health care providers, SMS, television, magazines and books were low rated (all <25%). In a multivariate logistic regression analysis age ≤30 years (Odds Ratio (OR)=1.647, 95%CI 1.048-2.584, P=0.030), male gender (OR=1.536, 95%CI 1.105-2.134, P=0.01), and no tertiary education (OR=1.957, 95%CI 1.264-3.030, P=0.003) were independent significant predictors of poor epidemiological knowledge. This study concludes that there was inadequate epidemiological knowledge received by the public and the reliance mostly on the clinical manifestations to recognizing the MERS-CoV disease. Comprehensive public health education programs is important to increase awareness of simple epidemiological determinants of the disease is warranted. Copyright © 2017. Published by Elsevier Ltd.

  19. Challenges presented by MERS corona virus, and SARS corona virus to global health.

    PubMed

    Al-Hazmi, Ali

    2016-07-01

    Numerous viral infections have arisen and affected global healthcare facilities. Millions of people are at severe risk of acquiring several evolving viral infections through several factors. In the present article we have described about risk factors, chance of infection, and prevention methods of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and severe acute respiratory syndrome (SARS-CoV), human coronaviruses (CoVs) frequently cause a normal cold which is mild and self-restricting. Zoonotic transmission of CoVs such as the newly discovered MERS-CoV and SARS-CoV, may be associated with severe lower respiratory tract infection. The present review provides the recent clinical and pathological information on MERS and SARS. The task is to transform these discoveries about MERS and SARS pathogenesis and to develop intervention methods that will eventually allow the effective control of these recently arising severe viral infections. Global health sector has learnt many lessons through the recent outbreak of MERS and SARS, but the need for identifying new antiviral treatment was not learned. In the present article we have reviewed the literature on the several facets like transmission, precautions and effectiveness of treatments used in patients with MERS-CoV and SARS infections.

  20. Worry experienced during the 2015 Middle East Respiratory Syndrome (MERS) pandemic in Korea

    PubMed Central

    Ro, Jun-Soo; Lee, Jin-Seok; Kang, Sung-Chan; Jung, Hye-Min

    2017-01-01

    Background Korea failed in its risk communication during the early stage of the Middle East Respiratory Syndrome (MERS) outbreak; consequently, it faced difficulties in managing MERS, while disease-related worry increased. Disease-related worry can help disease prevention and management, but can also have a detrimental effect. This study measured the overall level of disease-related worry during the MERS outbreak period in Korea and the influencing factors and levels of disease-related worry during key outbreak periods. Methods The cross-sectional survey included 1,000 adults who resided in Korea. An ordinal logistic regression was performed for the overall level of MERS-related worry, and influencing factors of worry were analyzed. A reliability test was performed on the levels of MERS-related worry during key outbreak periods. Results The overall level of MERS-related worry was 2.44. Multivariate analysis revealed that women and respondents w very poor subjective health status had higher levels of worry. Respondents with very high stress in daily life had higher levels of worry than those who reported having little stress. The reliability test results on MERS-related worry scores during key outbreak periods showed consistent scores during each period. Conclusion Level of worry increased in cases having higher perceived susceptibility and greater trust in informal information, while initial stage of outbreak was closely associated with that at later stages. These findings suggest the importance of managing the level of worry by providing timely and accurate disease-related information during the initial stage of disease outbreak. PMID:28273131

  1. Asy2/Mer2: an evolutionarily conserved mediator of meiotic recombination, pairing, and global chromosome compaction.

    PubMed

    Tessé, Sophie; Bourbon, Henri-Marc; Debuchy, Robert; Budin, Karine; Dubois, Emeline; Liangran, Zhang; Antoine, Romain; Piolot, Tristan; Kleckner, Nancy; Zickler, Denise; Espagne, Eric

    2017-09-15

    Meiosis is the cellular program by which a diploid cell gives rise to haploid gametes for sexual reproduction. Meiotic progression depends on tight physical and functional coupling of recombination steps at the DNA level with specific organizational features of meiotic-prophase chromosomes. The present study reveals that every step of this coupling is mediated by a single molecule: Asy2/Mer2. We show that Mer2, identified so far only in budding and fission yeasts, is in fact evolutionarily conserved from fungi (Mer2/Rec15/Asy2/Bad42) to plants (PRD3/PAIR1) and mammals (IHO1). In yeasts, Mer2 mediates assembly of recombination-initiation complexes and double-strand breaks (DSBs). This role is conserved in the fungus Sordaria However, functional analysis of 13 mer2 mutants and successive localization of Mer2 to axis, synaptonemal complex (SC), and chromatin revealed, in addition, three further important functions. First, after DSB formation, Mer2 is required for pairing by mediating homolog spatial juxtaposition, with implications for crossover (CO) patterning/interference. Second, Mer2 participates in the transfer/maintenance and release of recombination complexes to/from the SC central region. Third, after completion of recombination, potentially dependent on SUMOylation, Mer2 mediates global chromosome compaction and post-recombination chiasma development. Thus, beyond its role as a recombinosome-axis/SC linker molecule, Mer2 has important functions in relation to basic chromosome structure. © 2017 Tessé et al.; Published by Cold Spring Harbor Laboratory Press.

  2. Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes.

    PubMed

    Lin, Min-Han; Moses, David C; Hsieh, Chih-Hua; Cheng, Shu-Chun; Chen, Yau-Hung; Sun, Chiao-Yin; Chou, Chi-Yuan

    2018-02-01

    Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in late 2002 and caused a global outbreak with a fatality rate around 10% in 2003. Ten years later, a second highly pathogenic human CoV, MERS-CoV, emerged in the Middle East and has spread to other countries in Europe, North Africa, North America and Asia. As of November 2017, MERS-CoV had infected at least 2102 people with a fatality rate of about 35% globally, and hence there is an urgent need to identify antiviral drugs that are active against MERS-CoV. Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL pro s) of MERS-CoV and SARS-CoV. Our findings suggest that disulfiram acts as an allosteric inhibitor of MERS-CoV PL pro but as a competitive (or mixed) inhibitor of SARS-CoV PL pro . The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL pro by disulfiram, while synergistic inhibition of MERS-CoV PL pro by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. The Ballerina Experiment on the Rømer Mission

    NASA Astrophysics Data System (ADS)

    Brandt, Soren

    The Rømer mission has recently been approved as the next mission within the Danish Small Satellite Program. The scientific payload will consist of two separate experiments, the MONS and the Ballerina payloads. The primary objective of Ballerina is to provide accurate, real-time positions relayed to ground for ~ 70 Gamma Ray Bursts (GRBs) per year, and to study the temporal and spectral evolution of the early GRB X-ray afterglow. As an additional goal, Ballerina will detect and study bright X-ray transients, in particular X-ray novae and micro-quasar systems. R{\\o}mer is currently scheduled for launch in late 2003.

  4. Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.

    PubMed

    Almutairy, Meznah; Torng, Eric

    2018-01-01

    Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.

  5. Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches

    PubMed Central

    Torng, Eric

    2018-01-01

    Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method. PMID:29389989

  6. Taking aim at Mer and Axl receptor tyrosine kinases as novel therapeutic targets in solid tumors

    PubMed Central

    Linger, Rachel M.A.; Keating, Amy K.; Earp, H. Shelton

    2010-01-01

    Importance of the field Axl and/or Mer expression correlates with poor prognosis in several cancers. Until recently, the specific role of these receptor tyrosine kinases (RTKs) in the development and progression of cancer remained unexplained. Studies demonstrating that Axl and Mer contribute to mechanisms of cell survival, migration, invasion, metastasis, and chemosensitivity justify further investigation of Axl and Mer as novel therapeutic targets in cancer. Areas covered in this review Axl and Mer signaling pathways in cancer cells are summarized and evidence validating these RTKs as therapeutic targets in glioblastoma multiforme, non-small cell lung cancer, and breast cancer is examined. A comprehensive discussion of Axl and/or Mer inhibitors in development is also provided. What the reader will gain Potential toxicities associated with Axl or Mer inhibition are addressed. We hypothesize that the probable action of Mer and Axl inhibitors on cells within the tumor microenvironment will provide a unique therapeutic opportunity to target both tumor cells and the stromal components which facilitate disease progression. Take home message Axl and Mer mediate multiple oncogenic phenotypes and activation of these RTKs constitutes a mechanism of chemoresistance in a variety of solid tumors. Targeted inhibition of these RTKs may be effective as anti-tumor and/or anti-metastatic therapy, particularly if combined with standard cytotoxic therapies. PMID:20809868

  7. Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

    PubMed

    Pan, Tony; Flick, Patrick; Jain, Chirag; Liu, Yongchao; Aluru, Srinivas

    2017-10-09

    Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance parallel k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Kmerind's k-mer counter performs similarly or better than the best existing k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts k-mers in a 120 GB sequence read dataset in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1% of the k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. Kmerind is the first k-mer indexing library for distributed memory environments, and the first extensible library for general k-mer indexing and counting. Kmerind is available at https://github.com/ParBLiSS/kmerind.

  8. MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

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

    Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.

    ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation.In vitroreplication attenuation also extends toin vivomodels, allowing use of dORF3-5 as a live attenuated vaccine platform.more » Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. IMPORTANCEThe initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants.« less

  9. Simrank: Rapid and sensitive general-purpose k-mer search tool

    PubMed Central

    2011-01-01

    Background Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Results Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Conclusions Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity. PMID:21524302

  10. Nordic Winter and Cold: Their Correspondence with Tomas Tranströmer's Poetry

    ERIC Educational Resources Information Center

    Hosian, Mohammad Akbar

    2015-01-01

    The Nobel Prize winning poet Tomas Tranströmer was born and bred in Sweden, a remarkably Scandinavian country. Topographically, Scandinavian countries are locations of extreme cold and snowing. This distinguishing climatic condition has had a dominant influence and impact on almost all Scandinavian art and literature, including Tomas Tranströmer's…

  11. Phenetic Comparison of Prokaryotic Genomes Using k-mers

    PubMed Central

    Déraspe, Maxime; Raymond, Frédéric; Boisvert, Sébastien; Culley, Alexander; Roy, Paul H.; Laviolette, François; Corbeil, Jacques

    2017-01-01

    Abstract Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets. PMID:28957508

  12. Large supramolecular structures of 33-mer gliadin peptide activate toll-like receptors in macrophages.

    PubMed

    Herrera, María Georgina; Pizzuto, Malvina; Lonez, Caroline; Rott, Karsten; Hütten, Andreas; Sewald, Norbert; Ruysschaert, Jean-Marie; Dodero, Veronica Isabel

    2018-04-22

    Gliadin, an immunogenic protein present in wheat, is not fully degraded by humans and after the normal gastric and pancreatic digestion, the immunodominant 33-mer gliadin peptide remains unprocessed. The 33-mer gliadin peptide is found in human faeces and urine, proving not only its proteolytic resistance in vivo but more importantly its transport through the entire human body. Here, we demonstrate that 33-mer supramolecular structures larger than 220 nm induce the overexpression of nuclear factor kappa B (NF-κB) via a specific Toll-like Receptor (TLR) 2 and (TLR) 4 dependent pathway and the secretion of pro-inflammatory cytokines such as IP-10/CXCL10 and TNF-α. Using helium ion microscopy, we elucidated the initial stages of oligomerisation of 33-mer gliadin peptide, showing that rod-like oligomers are nucleation sites for protofilament formation. The relevance of the 33-mer supramolecular structures in the early stages of the disease is paving new perspectives in the understanding of gluten-related disorders. Copyright © 2018. Published by Elsevier Inc.

  13. Public response to MERS-CoV in the Middle East: iPhone survey in six countries.

    PubMed

    Alqahtani, Amani S; Rashid, Harunor; Basyouni, Mada H; Alhawassi, Tariq M; BinDhim, Nasser F

    Gulf Cooperation Council (GCC) countries bear the heaviest brunt of MERS-CoV. This study aims to compare public awareness and practice around MERS-CoV across GCC countries. A cross-sectional survey was conducted using the Gulf Indicators (GI) smartphone app among people in the six GCC countries, namely Saudi Arabia, Kuwait, the United Arab Emirates, Qatar, Bahrain, and Oman. A total of 1812 participants recruited. All were aware of MERS-CoV, yet the perception and practice around MERS-CoV varied widely between countries. Over two thirds were either "not concerned" or "slightly concerned" about contracting MERS-CoV; believing that they were under Allah's (God's) protection (40%) was the most cited reason. While 79% were aware that the disease can transmit through droplet from infected person, only 12% stated that MERS-CoV transmits via camels; people in Saudi Arabia were better aware of the transmission. Nevertheless, only 22% of respondents believed that camels are the zoonotic reservoir of MERS-CoV. Those who were concerned about contracting MERS-CoV (aOR: 1.6, 95% CI: 1.2-2.1, p<0.01) and those who thought MERS-CoV to be a severe disease only for those with high-risk conditions (aOR: 1.5, 95% CI: 1.1-2.1, p<0.01) were more likely to believe that camels are the zoonotic source. However, residents of KSA (aOR: 0.03, 95% CI: 0.01-0.07, p<0.01), UAE (aOR: 0.01, 95% CI: 0.004-0.02, p<0.01) and Kuwait (aOR: 0.03, 95% CI: 0.01-0.07, p<0.01) were less likely to believe that camels are the main zoonotic source compared to respondents from the other countries. Hygienic measures were more commonly adopted than avoidance of camels or their raw products, yet there was a discrepancy between the countries. This study highlights that despite being aware of the ongoing MERS-CoV epidemic; many people lack accurate understanding about MERS-CoV transmission, prevention, and are not fully compliant with preventive measures. Copyright © 2017 The Authors. Published by Elsevier Ltd

  14. Determining geographical spread pattern of MERS-CoV by distance method using Kimura model

    NASA Astrophysics Data System (ADS)

    Amiroch, Siti; Rohmatullah, Arif

    2017-03-01

    MERS-CoV or generally called as Middle East Respiratory Syndrome Coronavirus, a respiratory disease syndrome caused by a corona virus that attacks the respiratory tract ranging from mild to severe acute indication of fever, cough and shortness of breath. The cases happened relate to the countries in the Arabian Peninsula (Middle East) and there were 356 deaths have been reported due to the spread of the epidemic MERS. The data used in the case of MERS are the data DNA sequences taken from Genbank, the online database of the United States that stores the results of molecular biological experiments from all over the world (http://www.ncbi.nlm.nih.gov). In this case, bioinformatics plays an important role of reading sequences of DNA and genetic information by using the main device in the form of software that is supported by the availability of the Internet, while the analysis there in made and proven with mathematical methods. In similar research conducted by molecular biologists and physicians, the process of DNA sequencing is done with software that is already available like BLAST. In order to determine the MERS geographical distribution patterns in the Arabian Peninsula is done with program Clustal W, Bayesian, Phylip, etc. In this study, the writer use the Matlab simulation for all processes starting sequence alignment, counting the number of transitions and transversion substitutions for each sequence and its location up to the process of forming a phylogenetic tree that figures out the pattern of spread of the epidemic MERS. Mathematical analysis performed on a decline in the formula is to find Kimura evolutionary models and the process of forming a phylogenetic tree (the pattern of the epidemic MERS distribution) with neighbor joining algorithm. Finally it was obtained the pattern of geographical spread with 6 groups epidemic of MERS which ultimately turns out that all the MERS viruses that were spread in the Arabian Peninsula everything are almost the same as

  15. Building predictive models for MERS-CoV infections using data mining techniques.

    PubMed

    Al-Turaiki, Isra; Alshahrani, Mona; Almutairi, Tahani

    Recently, the outbreak of MERS-CoV infections caused worldwide attention to Saudi Arabia. The novel virus belongs to the coronaviruses family, which is responsible for causing mild to moderate colds. The control and command center of Saudi Ministry of Health issues a daily report on MERS-CoV infection cases. The infection with MERS-CoV can lead to fatal complications, however little information is known about this novel virus. In this paper, we apply two data mining techniques in order to better understand the stability and the possibility of recovery from MERS-CoV infections. The Naive Bayes classifier and J48 decision tree algorithm were used to build our models. The dataset used consists of 1082 records of cases reported between 2013 and 2015. In order to build our prediction models, we split the dataset into two groups. The first group combined recovery and death records. A new attribute was created to indicate the record type, such that the dataset can be used to predict the recovery from MERS-CoV. The second group contained the new case records to be used to predict the stability of the infection based on the current status attribute. The resulting recovery models indicate that healthcare workers are more likely to survive. This could be due to the vaccinations that healthcare workers are required to get on regular basis. As for the stability models using J48, two attributes were found to be important for predicting stability: symptomatic and age. Old patients are at high risk of developing MERS-CoV complications. Finally, the performance of all the models was evaluated using three measures: accuracy, precision, and recall. In general, the accuracy of the models is between 53.6% and 71.58%. We believe that the performance of the prediction models can be enhanced with the use of more patient data. As future work, we plan to directly contact hospitals in Riyadh in order to collect more information related to patients with MERS-CoV infections. Copyright © 2016

  16. Efficacy of a Mer and Flt3 tyrosine kinase small molecule inhibitor, UNC1666, in acute myeloid leukemia

    PubMed Central

    Lee-Sherick, Alisa B.; Zhang, Weihe; Menachof, Kelly K.; Hill, Amanda A.; Rinella, Sean; Kirkpatrick, Gregory; Page, Lauren S.; Stashko, Michael A.; Jordan, Craig T.; Wei, Qi; Liu, Jing; Zhang, Dehui; DeRyckere, Deborah; Wang, Xiaodong; Frye, Stephen; Earp, H. Shelton; Graham, Douglas K.

    2015-01-01

    Mer and Flt3 receptor tyrosine kinases have been implicated as therapeutic targets in acute myeloid leukemia (AML). In this manuscript we describe UNC1666, a novel ATP-competitive small molecule tyrosine kinase inhibitor, which potently diminishes Mer and Flt3 phosphorylation in AML. Treatment with UNC1666 mediated biochemical and functional effects in AML cell lines expressing Mer or Flt3 internal tandem duplication (ITD), including decreased phosphorylation of Mer, Flt3 and downstream effectors Stat, Akt and Erk, induction of apoptosis in up to 98% of cells, and reduction of colony formation by greater than 90%, compared to treatment with vehicle. These effects were dose-dependent, with inhibition of downstream signaling and functional effects correlating with the degree of Mer or Flt3 kinase inhibition. Treatment of primary AML patient samples expressing Mer and/or Flt3-ITD with UNC1666 also inhibited Mer and Flt3 intracellular signaling, induced apoptosis, and inhibited colony formation. In summary, UNC1666 is a novel potent small molecule tyrosine kinase inhibitor that decreases oncogenic signaling and myeloblast survival, thereby validating dual Mer/Flt3 inhibition as an attractive treatment strategy for AML. PMID:25762638

  17. Effects of Human Recombinant PEDF Protein and PEDF-Derived Peptide 34-mer on Choroidal Neovascularization

    PubMed Central

    Amaral, Juan

    2010-01-01

    Purpose. Pigment epithelium-derived factor (PEDF) is a serpin with antiangiogenic properties. Previously, the authors showed that PEDF injected into the subconjunctiva reaches the choroid. Here, they examined the effects of PEDF polypeptide fragments on vessel sprouting and on choroidal neovascularization (CNV) after subconjunctival administration. Methods. Recombinant human PEDF (rhuPEDF) was cleaved at its serpin-exposed loop by limited chymotrypsin proteolysis. Synthetic PEDF peptides 34-mer (Asp44-Asn77) and 44-mer (Val78-Thr121) were used. Ex vivo chick aortic vessel sprouting assays were performed. CNV was induced in rats by laser injury of Bruch's membrane. Daily subconjunctival injections (0.01–10 pmol/d protein) were performed for 5 days starting at day of injury or at the seventh day after injury. New vessel volumes were quantified using optical sections of choroid/RPE flat-mounts labeled with isolectin-Ib4. PEDF distribution was evaluated by immunofluorescence of choroid/RPE/retina cross-sections. Results. Full-length rhuPEDF, cleaved rhuPEDF, or peptide 34-mer exhibited ex vivo antiangiogenic activity, but peptide 44-mer was inefficient. PEDF immunostaining around CNV lesions diminished after laser injury. Subconjunctival administration of rhuPEDF or 34-mer at 0.1 pmol/d decreased CNV lesion volumes by 52% and 47%, respectively, whereas those of 44-mer were similar to vehicle injections. Doses of 0.1 and 1 pmol/d rhuPEDF decreased fully developed CNV complex volumes by 45% and 50%, respectively, compared with vehicle injections. Conclusions. A functional region for the inhibition of vessel sprouting and CNV resides within the 34-mer region of PEDF. Furthermore, subconjunctival administration of optimal range dosages of rhuPEDF or 34-mer can suppress and regress rat CNV lesions, demonstrating that these agents reach the choroid/RPE complex as functionally active molecules. PMID:19850839

  18. Sparse evidence of MERS-CoV infection among animal workers living in Southern Saudi Arabia during 2012

    PubMed Central

    Memish, Ziad A; Alsahly, Ahmad; Masri, Malak al; Heil, Gary L; Anderson, Benjamin D; Peiris, Malik; Khan, Salah Uddin; Gray, Gregory C

    2015-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging viral pathogen that primarily causes respiratory illness. We conducted a seroprevalence study of banked human serum samples collected in 2012 from Southern Saudi Arabia. Sera from 300 animal workers (17% with daily camel exposure) and 50 non-animal-exposed controls were examined for serological evidence of MERS-CoV infection by a pseudoparticle MERS-CoV spike protein neutralization assay. None of the sera reproducibly neutralized the MERS-CoV-pseudotyped lentiviral vector. These data suggest that serological evidence of zoonotic transmission of MERS-CoV was not common among animal workers in Southern Saudi Arabia during July 2012. PMID:25470665

  19. Mercuric ion reduction and resistance in transgenic Arabidopsis thaliana plants expressing a modified bacterial merA gene.

    PubMed Central

    Rugh, C L; Wilde, H D; Stack, N M; Thompson, D M; Summers, A O; Meagher, R B

    1996-01-01

    With global heavy metal contamination increasing, plants that can process heavy metals might provide efficient and ecologically sound approaches to sequestration and removal. Mercuric ion reductase, MerA, converts toxic Hg2+ to the less toxic, relatively inert metallic mercury (Hg0) The bacterial merA sequence is rich in CpG dinucleotides and has a highly skewed codon usage, both of which are particularly unfavorable to efficient expression in plants. We constructed a mutagenized merA sequence, merApe9, modifying the flanking region and 9% of the coding region and placing this sequence under control of plant regulatory elements. Transgenic Arabidopsis thaliana seeds expressing merApe9 germinated, and these seedlings grew, flowered, and set seed on medium containing HgCl2 concentrations of 25-100 microM (5-20 ppm), levels toxic to several controls. Transgenic merApe9 seedlings evolved considerable amounts of Hg0 relative to control plants. The rate of mercury evolution and the level of resistance were proportional to the steady-state mRNA level, confirming that resistance was due to expression of the MerApe9 enzyme. Plants and bacteria expressing merApe9 were also resistant to toxic levels of Au3+. These and other data suggest that there are potentially viable molecular genetic approaches to the phytoremediation of metal ion pollution. Images Fig. 2 Fig. 3 Fig. 4 PMID:8622910

  20. The effect of multiple external representations (MERs) worksheets toward complex system reasoning achievement

    NASA Astrophysics Data System (ADS)

    Sumarno; Ibrahim, M.; Supardi, Z. A. I.

    2018-03-01

    The application of a systems approach to assessing biological systems provides hope for a coherent understanding of cell dynamics patterns and their relationship to plant life. This action required the reasoning about complex systems. In other sides, there were a lot of researchers who provided the proof about the instructional successions. They involved the multiple external representations which improved the biological learning. The researcher conducted an investigation using one shoot case study design which involved 30 students in proving that the MERs worksheets could affect the student's achievement of reasoning about complex system. The data had been collected based on test of reasoning about complex system and student's identification result who worked through MERs. The result showed that only partially students could achieve reasoning about system complex, but their MERs skill could support their reasoning ability of complex system. This study could bring a new hope to develop the MERs worksheet as a tool to facilitate the reasoning about complex system.

  1. Feasibility of Using Convalescent Plasma Immunotherapy for MERS-CoV Infection, Saudi Arabia.

    PubMed

    Arabi, Yaseen M; Hajeer, Ali H; Luke, Thomas; Raviprakash, Kanakatte; Balkhy, Hanan; Johani, Sameera; Al-Dawood, Abdulaziz; Al-Qahtani, Saad; Al-Omari, Awad; Al-Hameed, Fahad; Hayden, Frederick G; Fowler, Robert; Bouchama, Abderrezak; Shindo, Nahoko; Al-Khairy, Khalid; Carson, Gail; Taha, Yusri; Sadat, Musharaf; Alahmadi, Mashail

    2016-09-01

    We explored the feasibility of collecting convalescent plasma for passive immunotherapy of Middle East respiratory syndrome coronavirus (MERS-CoV) infection by using ELISA to screen serum samples from 443 potential plasma donors: 196 patients with suspected or laboratory-confirmed MERS-CoV infection, 230 healthcare workers, and 17 household contacts exposed to MERS-CoV. ELISA-reactive samples were further tested by indirect fluorescent antibody and microneutralization assays. Of the 443 tested samples, 12 (2.7%) had a reactive ELISA result, and 9 of the 12 had reactive indirect fluorescent antibody and microneutralization assay titers. Undertaking clinical trials of convalescent plasma for passive immunotherapy of MERS-CoV infection may be feasible, but such trials would be challenging because of the small pool of potential donors with sufficiently high antibody titers. Alternative strategies to identify convalescent plasma donors with adequate antibody titers should be explored, including the sampling of serum from patients with more severe disease and sampling at earlier points during illness.

  2. Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates

    PubMed Central

    Lau, Susanna K P; Wernery, Renate; Wong, Emily Y M; Joseph, Sunitha; Tsang, Alan K L; Patteril, Nissy Annie Georgy; Elizabeth, Shyna K; Chan, Kwok-Hung; Muhammed, Rubeena; Kinne, Jöerg; Yuen, Kwok-Yung; Wernery, Ulrich; Woo, Patrick C Y

    2016-01-01

    Little is known regarding the molecular epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) circulating in dromedaries outside Saudi Arabia. To address this knowledge gap, we sequenced 10 complete genomes of MERS-CoVs isolated from 2 live and 8 dead dromedaries from different regions in the United Arab Emirates (UAE). Phylogenetic analysis revealed one novel clade A strain, the first detected in the UAE, and nine clade B strains. Strain D998/15 had a distinct phylogenetic position within clade A, being more closely related to the dromedary isolate NRCE-HKU205 from Egypt than to the human isolates EMC/2012 and Jordan-N3/2012. A comparison of predicted protein sequences also demonstrated the existence of two clade A lineages with unique amino acid substitutions, A1 (EMC/2012 and Jordan-N3/2012) and A2 (D998/15 and NRCE-HKU205), circulating in humans and camels, respectively. The nine clade B isolates belong to three distinct lineages: B1, B3 and B5. Two B3 strains, D1271/15 and D1189.1/15, showed evidence of recombination between lineages B4 and B5 in ORF1ab. Molecular clock analysis dated the time of the most recent common ancestor (tMRCA) of clade A to March 2011 and that of clade B to November 2011. Our data support a polyphyletic origin of MERS-CoV in dromedaries and the co-circulation of diverse MERS-CoVs including recombinant strains in the UAE. PMID:27999424

  3. Nucleation and Growth Kinetics from LaMer Burst Data.

    PubMed

    Chu, Daniel B K; Owen, Jonathan S; Peters, Baron

    2017-10-12

    In LaMer burst nucleation, the individual nucleation events happen en masse, quasi-simultaneously, and at nearly identical homogeneous conditions. These properties make LaMer burst nucleation important for applications that require monodispersed particles and also for theoretical analyses. Sugimoto and co-workers predicted that the number of nuclei generated during a LaMer burst depends only on the solute supply rate and the growth rate, independent of the nucleation kinetics. Some experiments confirm that solute supply kinetics control the number of nuclei, but flaws in the original theoretical analysis raise questions about the predicted roles of growth and nucleation kinetics. We provide a rigorous analysis of the coupled equations that govern concentrations of nuclei and solutes. Our analysis confirms that the number of nuclei is largely determined by the solute supply and growth rates, but our predicted relationship differs from that of Sugimoto et al. Moreover, we find that additional nucleus size dependent corrections should emerge in systems with slow growth kinetics. Finally, we show how the nucleation kinetics determine the particle size distribution. We suggest that measured particle size distributions might therefore provide ways to test theoretical models of homogeneous nucleation kinetics.

  4. The impact of multichannel microelectrode recording (MER) in deep brain stimulation of the basal ganglia.

    PubMed

    Kinfe, Thomas M; Vesper, Jan

    2013-01-01

    Deep brain stimulation (DBS) of the basal ganglia (Ncl. subthalamicus, Ncl. ventralis intermedius thalami, globus pallidus internus) has become an evidence-based and well-established treatment option in otherwise refractory movement disorders. The Ncl. subthalamicus (STN) is the target of choice in Parkinson's disease.However, a considerable discussion is currently ongoing with regard to the necessity for micro-electrode recording (MER) in DBS surgery.The present review provides an overview on deep brain stimulation and (MER) of the STN in patients with Parkinson's disease. Detailed description is given concerning the multichannel MER systems nowadays available for DBS of the basal ganglia, especially of the STN, as a useful tool for target refinement. Furthermore, an overview is given of the historical aspects, spatial mapping of the STN by MER, and its impact for accuracy and precision in current functional stereotactic neurosurgery.The pros concerning target refinement by MER means on the one hand, and cons including increased bleeding risk, increased operation time, local or general anesthesia, and single versus multichannel microelectrode recording are discussed in detail. Finally, the authors favor the use of MER with intraoperative testing combined with imaging to achieve a more precise electrode placement, aiming to ameliorate clinical outcome in therapy-resistant movement disorders.

  5. Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

    PubMed Central

    Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

    2017-01-01

    Abstract Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k-mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k-mer co-occurrence information with recent advances in deep learning. Results: We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k-mer embedding. We first split DNA sequences into k-mers and pre-train k-mer embedding vectors based on the co-occurrence matrix of k-mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k-mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. Availability and implementation: The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm. Contact: tingchen@tsinghua.edu.cn or ruijiang

  6. Managing PV Power on Mars - MER Rovers

    NASA Technical Reports Server (NTRS)

    Stella, Paul M.; Chin, Keith; Wood, Eric; Herman, Jennifer; Ewell, Richard

    2009-01-01

    The MER Rovers have recently completed over 5 years of operation! This is a remarkable demonstration of the capabilities of PV power on the Martian surface. The extended mission required the development of an efficient process to predict the power available to the rovers on a day-to-day basis. The performance of the MER solar arrays is quite unlike that of any other Space array and perhaps more akin to Terrestrial PV operation, although even severe by that comparison. The impact of unpredictable factors, such as atmospheric conditions and dust accumulation (and removal) on the panels limits the accurate prediction of array power to short time spans. Based on the above, it is clear that long term power predictions are not sufficiently accurate to allow for detailed long term planning. Instead, the power assessment is essentially a daily activity, effectively resetting the boundary points for the overall predictive power model. A typical analysis begins with the importing of the telemetry from each rover's previous day's power subsystem activities. This includes the array power generated, battery state-of-charge, rover power loads, and rover orientation, all as functions of time. The predicted performance for that day is compared to the actual performance to identify the extent of any differences. The model is then corrected for these changes. Details of JPL's MER power analysis procedure are presented, including the description of steps needed to provide the final prediction for the mission planners. A dust cleaning event of the solar array is also highlighted to illustrate the impact of Martian weather on solar array performance

  7. Dromedary camels and the transmission of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

    PubMed Central

    Hemida, Maged G; Elmoslemany, Ahmed; Al-Hizab, Fahad; Alnaeem, Abdulmohsen; Almathen, Faisal; Faye, Bernard; Chu, Daniel KW; Perera, Ranawaka A; Peiris, Malik

    2015-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is an existential threat to global public health. The virus has been repeatedly detected in dromedary camels (Camelus dromedarius). Adult animals in many countries in the Middle East as well as in North and East Africa showed high (>90%) sero-prevalence to the virus. MERS-CoV isolated from dromedaries is genetically and phenotypically similar to viruses from humans. We summarise current understanding of the ecology of MERS-CoV in animals and transmission at the animal-human interface. We review aspects of husbandry, animal movements and trade and the use and consumption of camel dairy and meat products in the Middle East that may be relevant to the epidemiology of MERS. We also highlight the gaps in understanding the transmission of this virus in animals and from animals to humans. PMID:26256102

  8. Cell Surface Display of MerR on Saccharomyces cerevisiae for Biosorption of Mercury.

    PubMed

    Wei, Qinguo; Yan, Jiakuo; Chen, Yao; Zhang, Lei; Wu, Xiaoyang; Shang, Shuai; Ma, Shisheng; Xia, Tian; Xue, Shuyu; Zhang, Honghai

    2018-01-01

    The metalloregulatory protein MerR which plays important roles in mer operon system exhibits high affinity and selectivity toward mercury (II) (Hg 2+ ). In order to improve the adsorption ability of Saccharomyces cerevisiae for Hg 2+ , MerR was displayed on the surface of S. cerevisiae for the first time with an α-agglutinin-based display system in this study. The merR gene was synthesized after being optimized and added restriction endonuclease sites EcoR I and Mlu I. The display of MerR was indirectly confirmed by the enhanced adsorption ability of S. cerevisiae for Hg 2+ and colony PCR. The hydride generation atomic absorption spectrometry was applied to measure the Hg 2+ content in water. The engineered yeast strain not only showed higher tolerance to Hg, but also their adsorption ability was much higher than that of origin and control strains. The engineered yeast could adsorb Hg 2+ under a wide range of pH levels, and it could also adsorb Hg 2+ effectively with Cd 2+ and Cu 2+ coexistence. Furthermore, the engineered yeast strain could adsorb ultra-trace Hg 2+ effectively. The results above showed that the surface-engineered yeast strain could adsorb Hg 2+ under complex environmental conditions and could be used for the biosorption and bioremediation of environmental Hg contaminants.

  9. Influence of anisotropy on percolation and jamming of linear k-mers on square lattice with defects

    NASA Astrophysics Data System (ADS)

    Tarasevich, Yu Yu; Laptev, V. V.; Burmistrov, A. S.; Shinyaeva, T. S.

    2015-09-01

    By means of the Monte Carlo simulation, we study the layers produced by the random sequential adsorption of the linear rigid objects (k-mers also known as rigid or stiff rods, sticks, needles) onto the square lattice with defects in the presence of an external field. The value of k varies from 2 to 32. The point defects randomly and uniformly placed on the substrate hinder adsorption of the elongated objects. The external field affects isotropic deposition of the particles, consequently the deposited layers are anisotropic. We study the influence of the defect concentration, the length of the objects, and the external field on the percolation threshold and the jamming concentration. Our main findings are (i) the critical defect concentration at which the percolation never occurs even at jammed state decreases for short k-mers (k < 16) and increases for long k-mers (k > 16) as anisotropy increases, (ii) the corresponding critical k-mer concentration decreases with anisotropy growth, (iii) the jamming concentration decreases drastically with growth of k-mer length for any anisotropy, (iv) for short k-mers, the percolation threshold is almost insensitive to the defect concentration for any anisotropy.

  10. Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County, Kenya

    PubMed Central

    Deem, Sharon L.; Fèvre, Eric M.; Kinnaird, Margaret; Browne, A. Springer; Muloi, Dishon; Godeke, Gert-Jan; Koopmans, Marion; Reusken, Chantal B.

    2015-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently identified virus causing severe viral respiratory illness in people. Little is known about the reservoir in the Horn of Africa. In Kenya, where no human MERS cases have been reported, our survey of 335 dromedary camels, representing nine herds in Laikipia County, showed a high seroprevalence (46.9%) to MERS-CoV antibodies. Between herd differences were present (14.3%– 82.9%), but was not related to management type or herd isolation. Further research should focus on identifying similarity between MERS-CoV viral isolates in Kenya and clinical isolates from the Middle East and elsewhere. PMID:26473733

  11. Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County, Kenya.

    PubMed

    Deem, Sharon L; Fèvre, Eric M; Kinnaird, Margaret; Browne, A Springer; Muloi, Dishon; Godeke, Gert-Jan; Koopmans, Marion; Reusken, Chantal B

    2015-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently identified virus causing severe viral respiratory illness in people. Little is known about the reservoir in the Horn of Africa. In Kenya, where no human MERS cases have been reported, our survey of 335 dromedary camels, representing nine herds in Laikipia County, showed a high seroprevalence (46.9%) to MERS-CoV antibodies. Between herd differences were present (14.3%- 82.9%), but was not related to management type or herd isolation. Further research should focus on identifying similarity between MERS-CoV viral isolates in Kenya and clinical isolates from the Middle East and elsewhere.

  12. Histopathology of Middle East respiratory syndrome coronovirus (MERS-CoV) infection - clinicopathological and ultrastructural study.

    PubMed

    Alsaad, Khaled O; Hajeer, Ali H; Al Balwi, Mohammed; Al Moaiqel, Mohammed; Al Oudah, Nourah; Al Ajlan, Abdulaziz; AlJohani, Sameera; Alsolamy, Sami; Gmati, Giamal E; Balkhy, Hanan; Al-Jahdali, Hamdan H; Baharoon, Salim A; Arabi, Yaseen M

    2018-02-01

    The pathogenesis, viral localization and histopathological features of Middle East respiratory syndrome - coronavirus (MERS-CoV) in humans are not described sufficiently. The aims of this study were to explore and define the spectrum of histological and ultrastructural pathological changes affecting various organs in a patient with MERS-CoV infection and represent a base of MERS-CoV histopathology. We analysed the post-mortem histopathological findings and investigated localisation of viral particles in the pulmonary and extrapulmonary tissue by transmission electron microscopic examination in a 33-year-old male patient of T cell lymphoma, who acquired MERS-CoV infection. Tissue needle biopsies were obtained from brain, heart, lung, liver, kidney and skeletal muscle. All samples were collected within 45 min from death to reduce tissue decomposition and artefact. Histopathological examination showed necrotising pneumonia, pulmonary diffuse alveolar damage, acute kidney injury, portal and lobular hepatitis and myositis with muscle atrophic changes. The brain and heart were histologically unremarkable. Ultrastructurally, viral particles were localised in the pneumocytes, pulmonary macrophages, renal proximal tubular epithelial cells and macrophages infiltrating the skeletal muscles. The results highlight the pulmonary and extrapulmonary pathological changes of MERS-CoV infection and provide the first evidence of the viral presence in human renal tissue, which suggests tissue trophism for MERS-CoV in kidney. © 2017 John Wiley & Sons Ltd.

  13. Tuning in and catching on? Examining the relationship between pandemic communication and awareness and knowledge of MERS in the USA.

    PubMed

    Lin, Leesa; McCloud, Rachel F; Bigman, Cabral A; Viswanath, Kasisomayajula

    2017-06-01

    Large-scale influenza outbreaks over the last decade, such as SARS and H1N1, have brought to global attention the importance of emergency risk communication and prompted the international community to develop communication responses. Since pandemic outbreaks are relatively infrequent, there is a dearth of evidence addressing the following questions: (i) Have the resources invested in strategic and routine communication for past pandemic outbreaks yielded public health preparedness benefits? (ii) Have past efforts sensitized people to pay attention to new pandemic threats? The Middle East Respiratory Syndrome (MERS) that was followed closely by major media outlets in the USA provides an opportunity to examine the relationship between exposure to public communication about epidemics and public awareness and knowledge about new risks. In December, 2013, we surveyed a nationally representative sample of 627 American adults and examined the associations between people's awareness to prior pandemics and their awareness of and knowledge about MERS. Awareness of prior pandemics was significantly associated with awareness and knowledge of MERS. The most common sources from which people first heard about MERS were also identified. Communication inequalities were observed between racial/ethnic and socioeconomic positions, suggesting a need for more effective pandemic communication. © The Author 2016. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.

    PubMed

    Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

    2017-07-15

    Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning. We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k -mer embedding. We first split DNA sequences into k -mers and pre-train k -mer embedding vectors based on the co-occurrence matrix of k -mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k -mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm . tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn. Supplementary materials are available at

  15. The receptor tyrosine kinase MerTK activates phospholipase C γ2 during recognition of apoptotic thymocytes by murine macrophages

    PubMed Central

    Todt, Jill C.; Hu, Bin; Curtis, Jeffrey L.

    2008-01-01

    Apoptotic leukocytes must be cleared efficiently by macrophages (Mø). Apoptotic cell phagocytosis by Mø requires the receptor tyrosine kinase (RTK) MerTK (also known as c-Mer and Tyro12), the phosphatidylserine receptor (PS-R), and the classical protein kinase C (PKC) isoform βII, which translocates to Mø membrane and cytoskeletal fractions in a PS-R-dependent fashion. How these molecules cooperate to induce phagocytosis is unknown. Because the phosphatidylinositol-specific phospholipase (PI-PLC) PLC γ2 is downstream of RTKs in some cell types and can activate classical PKCs, we hypothesized that MerTK signals via PLC γ2. To test this hypothesis, we examined the interaction of MerTK and PLC γ2 in resident murine PMø and in the murine Mø cell line J774A.1 (J774) following exposure to apoptotic thymocytes. We found that, as with PMø, J774 phagocytosis of apoptotic thymocytes was inhibited by antibody against MerTK. Western blotting and immunoprecipitation showed that exposure to apoptotic cells produced three time-dependent changes in PMø and J774: (1) tyrosine phosphorylation of MerTK; (2) association of PLC γ2 with MerTK; and (3) tyrosine phosphorylation of PLC γ2. Phosphorylation of PLC γ2 and its association with MerTK was also induced by cross-linking MerTK using antibody. A PI-PLC appears to be required for phagocytosis of apoptotic cells because the PI-PLC inhibitor Et-18-OCH3 and the PLC inhibitor U73122, but not the inactive control U73343, blocked phagocytosis without impairing adhesion. On apoptotic cell adhesion to Mø, MerTK signals at least in part via PLC γ2. PMID:14704368

  16. Identifying Monoclonal Antibodies that Potently Inhibit MERS-CoV | Center for Cancer Research

    Cancer.gov

    The Middle East respiratory syndrome coronavirus (MERS-CoV), first isolated in September 2012, infects cells lining the human airway, causing severe flu-like symptoms that, in some cases, lead to death. As of July 2, 2014, 824 confirmed cases of MERS-CoV infection, including at least 286 related deaths, have been reported to the World Health Organization. While there are

  17. Identifying Monoclonal Antibodies that Potently Inhibit MERS-CoV | Center for Cancer Research

    Cancer.gov

    The Middle East respiratory syndrome coronavirus (MERS-CoV), first isolated in September 2012, infects cells lining the human airway, causing severe flu-like symptoms that, in some cases, lead to death. As of July 2, 2014, 824 confirmed cases of MERS-CoV infection, including at least 286 related deaths, have been reported to the World Health Organization. While there are currently no effective therapies against the virus, monoclonal antibodies (MAbs) may be a promising candidate. Having previously developed MAbs against other viruses, including the related severe acute respiratory syndrome coronavirus or SARS-CoV, Dimiter Dimitrov, Ph.D., of CCR’s Laboratory of Experimental Immunology (LEI), and his colleagues decided to pan a library of antigen binding fragments (Fab) for activity against MERS-CoV.

  18. An assessment of the level of concern among hospital-based health-care workers regarding MERS outbreaks in Saudi Arabia.

    PubMed

    Abolfotouh, Mostafa A; AlQarni, Ali A; Al-Ghamdi, Suliman M; Salam, Mahmoud; Al-Assiri, Mohammed H; Balkhy, Hanan H

    2017-01-03

    Middle East Respiratory Syndrome (MERS) is caused by MERS coronavirus (MERS-CoV). More than 80% of reported cases have occurred in Saudi Arabia, with a mortality exceeding 50%. Health-care workers (HCWs) are at risk of acquiring and transmitting this virus, so the concerns of HCWs in Saudi Arabia regarding MERS were evaluated. An anonymous, self-administered, previously validated questionnaire was given to 1031 HCWs at three tertiary hospitals in Saudi Arabia from October to December, 2014. Concerns regarding the disease, its severity and governmental efforts to contain it, as well as disease outcomes were assessed using 31 concern statements in five distinct domains. A total concern score was calculated for each HCW. Multiple regression analyses were used to identify predictors of high concern scores. The average age of participants was 37.1 ± 9.0 years, 65.8% were married and 59.1% were nurses. The majority of respondents (70.4%) felt at risk of contracting a MERS-CoV infection at work, 69.1% felt threatened if a colleague contracted MERS-CoV, 60.9% felt obliged to care for patients infected with MERS-CoV and 87.8% did not feel safe at work using standard precautions. In addition, 87.7% believed that the government should isolate patients with MERS in specialized hospitals, 73.7% agreed with travel restriction to and from areas affected by MERS and 65.3% agreed with avoiding inviting expatriates from such areas. After adjustment for covariates, high concern scores were significantly associated with being a Saudi national (p < 0.001), a non-physician (p < 0.001) and working in the central region (p < 0.001). The majority of respondents reported concern regarding MERS-CoV infection from exposure at work. The overall level of concern may be influenced by previous experience of MERS outbreaks and related cultural issues. The concerns of HCWs may affect their overall effectiveness in an outbreak and should be addressed by incorporating management

  19. Environmental Conditions Constrain the Distribution and Diversity of Archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

    USGS Publications Warehouse

    Wang, Y.; Boyd, E.; Crane, S.; Lu-Irving, P.; Krabbenhoft, D.; King, S.; Dighton, J.; Geesey, G.; Barkay, T.

    2011-01-01

    The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient. ?? 2011 Springer Science+Business Media, LLC.

  20. Environmental conditions constrain the distribution and diversity of archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

    PubMed

    Wang, Yanping; Boyd, Eric; Crane, Sharron; Lu-Irving, Patricia; Krabbenhoft, David; King, Susan; Dighton, John; Geesey, Gill; Barkay, Tamar

    2011-11-01

    The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient.

  1. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen

    PubMed Central

    Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S.; Wrapp, Daniel; Kirchdoerfer, Robert N.; Turner, Hannah L.; Cottrell, Christopher A.; Becker, Michelle M.; Wang, Lingshu; Shi, Wei; Kong, Wing-Pui; Andres, Erica L.; Kettenbach, Arminja N.; Denison, Mark R.; Chappell, James D.; Graham, Barney S.; Ward, Andrew B.

    2017-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. PMID:28807998

  2. Planning Mars Memory: Learning from the MER Mission

    NASA Technical Reports Server (NTRS)

    Charlotte, Linde

    2004-01-01

    This viewgraph presentation discusses ways in which the lessons learned from a mission can be systematically remembered, retained, and applied by individuals and by an organization as a whole. The presentation cites lessons learned from the Mars Exploration Rover (MER) Mission as examples.

  3. The Role of an Aggrecan 32mer Fragment in Post-Traumatic Osteoarthritis

    DTIC Science & Technology

    2017-10-01

    Award Number: W81XWH-16-1-0706 TITLE: The Role of an Aggrecan 32mer Fragment in Post -Traumatic Osteoarthritis PRINCIPAL INVESTIGATOR: Professor...TITLE AND SUBTITLE The Role of an Aggrecan 32mer Fragment in Post - Traumatic Osteoarthritis 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-16-1-0706 5c...reduction in knee hyperalgesia, but not mechanical allodynia, in mice at 8 weeks post -surgery. This trend was not statistically significant, however, we are

  4. Impact of defects on percolation in random sequential adsorption of linear k-mers on square lattices.

    PubMed

    Tarasevich, Yuri Yu; Laptev, Valeri V; Vygornitskii, Nikolai V; Lebovka, Nikolai I

    2015-01-01

    The effect of defects on the percolation of linear k-mers (particles occupying k adjacent sites) on a square lattice is studied by means of Monte Carlo simulation. The k-mers are deposited using a random sequential adsorption mechanism. Two models L(d) and K(d) are analyzed. In the L(d) model it is assumed that the initial square lattice is nonideal and some fraction of sites d is occupied by nonconducting point defects (impurities). In the K(d) model the initial square lattice is perfect. However, it is assumed that some fraction of the sites in the k-mers d consists of defects, i.e., is nonconducting. The length of the k-mers k varies from 2 to 256. Periodic boundary conditions are applied to the square lattice. The dependences of the percolation threshold concentration of the conducting sites p(c) vs the concentration of defects d are analyzed for different values of k. Above some critical concentration of defects d(m), percolation is blocked in both models, even at the jamming concentration of k-mers. For long k-mers, the values of d(m) are well fitted by the functions d(m)∝k(m)(-α)-k(-α) (α=1.28±0.01 and k(m)=5900±500) and d(m)∝log(10)(k(m)/k) (k(m)=4700±1000) for the L(d) and K(d) models, respectively. Thus, our estimation indicates that the percolation of k-mers on a square lattice is impossible even for a lattice without any defects if k⪆6×10(3).

  5. Successful recovery of MERS CoV pneumonia in a patient with acquired immunodeficiency syndrome: a case report.

    PubMed

    Shalhoub, Sarah; AlZahrani, Abdulwahab; Simhairi, Raed; Mushtaq, Adnan

    2015-01-01

    Middle East Respiratory Syndrome Coronavirus (MERS CoV) may cause severe pneumonia with significant morbidity and mortality, particularly in patients with multiple comorbid condition. MERS CoV pneumonia has not been previously reported in patients with Human Immunodeficiency Virus (HIV). Herein, we report a case of MERS CoV pneumonia with a successful outcome in a patient recently diagnosed with HIV. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Disk-based k-mer counting on a PC

    PubMed Central

    2013-01-01

    Background The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. Results We propose a simple, yet efficient, parallel disk-based algorithm for counting k-mers. Experiments show that it usually offers the fastest solution to the considered problem, while demanding a relatively small amount of memory. In particular, it is capable of counting the statistics for short-read human genome data, in input gzipped FASTQ file, in less than 40 minutes on a PC with 16 GB of RAM and 6 CPU cores, and for long-read human genome data in less than 70 minutes. On a more powerful machine, using 32 GB of RAM and 32 CPU cores, the tasks are accomplished in less than half the time. No other algorithm for most tested settings of this problem and mammalian-size data can accomplish this task in comparable time. Our solution also belongs to memory-frugal ones; most competitive algorithms cannot efficiently work on a PC with 16 GB of memory for such massive data. Conclusions By making use of cheap disk space and exploiting CPU and I/O parallelism we propose a very competitive k-mer counting procedure, called KMC. Our results suggest that judicious resource management may allow to solve at least some bioinformatics problems with massive data on a commodity personal computer. PMID:23679007

  7. Value, Market Preferences and Trade of Beche-De-Mer from Pacific Island Sea Cucumbers

    PubMed Central

    Purcell, Steven W.

    2014-01-01

    Market preferences of natural resources contribute to shape their exploitation and production. Beche-de-mer, the product after gutting, cooking, salting and drying sea cucumbers, is exported worldwide to Asian dried seafood markets. A better understanding of the trade, value and market preferences of Pacific island beche-de-mer could identify critical postharvest processing techniques and management strategies for fisheries and aquaculture. Data were collected on export prices and trade of beche-de-mer from Kiribati, Fiji, Tonga and New Caledonia, and the selling prices, respective sizes and organoleptic properties of the products in stores in China. Export prices varied considerably within and among the four countries and low-value species were the most exported by volume. Most of the beche-de-mer from the four Pacific islands is exported to Hong Kong, where quality products are sold and others are distributed to mainland China. Prices of the beche-de-mer in Chinese stores varied up to ten-fold and were mostly influenced by species, body size and, to a lesser extent, physical damage to the products. Market prices across species (averaging US$15–385 kg−1) appear to have mostly increased six- to twelve-fold over the past decade. The data allude that fisheries for Holothuria scabra, H. lessoni, H. fuscogilva, H. whitmaei and Thelenota ananas should be most carefully managed because they were the highest-value species and under greatest demand. The relationships between size of beche-de-mer and sale price were species specific and highly varied. This study also highlights the need for better regulations and/or enforcement of minimum size limits in sea cucumber fisheries, which can help to maximise economic benefits of wild stocks. PMID:24736374

  8. Value, market preferences and trade of Beche-de-mer from Pacific Island sea cucumbers.

    PubMed

    Purcell, Steven W

    2014-01-01

    Market preferences of natural resources contribute to shape their exploitation and production. Beche-de-mer, the product after gutting, cooking, salting and drying sea cucumbers, is exported worldwide to Asian dried seafood markets. A better understanding of the trade, value and market preferences of Pacific island beche-de-mer could identify critical postharvest processing techniques and management strategies for fisheries and aquaculture. Data were collected on export prices and trade of beche-de-mer from Kiribati, Fiji, Tonga and New Caledonia, and the selling prices, respective sizes and organoleptic properties of the products in stores in China. Export prices varied considerably within and among the four countries and low-value species were the most exported by volume. Most of the beche-de-mer from the four Pacific islands is exported to Hong Kong, where quality products are sold and others are distributed to mainland China. Prices of the beche-de-mer in Chinese stores varied up to ten-fold and were mostly influenced by species, body size and, to a lesser extent, physical damage to the products. Market prices across species (averaging US$15-385 kg-1) appear to have mostly increased six- to twelve-fold over the past decade. The data allude that fisheries for Holothuria scabra, H. lessoni, H. fuscogilva, H. whitmaei and Thelenota ananas should be most carefully managed because they were the highest-value species and under greatest demand. The relationships between size of beche-de-mer and sale price were species specific and highly varied. This study also highlights the need for better regulations and/or enforcement of minimum size limits in sea cucumber fisheries, which can help to maximise economic benefits of wild stocks.

  9. Healthcare Workers Emotions, Perceived Stressors and Coping Strategies During a MERS-CoV Outbreak.

    PubMed

    Khalid, Imran; Khalid, Tabindeh J; Qabajah, Mohammed R; Barnard, Aletta G; Qushmaq, Ismael A

    2016-03-01

    Healthcare workers (HCWs) are at high risk of contracting Middle East respiratory syndrome coronavirus (MERS-CoV) during an epidemic. We explored the emotions, perceived stressors, and coping strategies of healthcare workers who worked during a MERS-CoV outbreak in our hospital. A cross-sectional descriptive survey design. A tertiary care hospital. HCWs (150) who worked in high risk areas during the April-May 2014 MERS-CoV outbreak that occurred in Jeddah, Saudi Arabia. We developed and administered a "MERS-CoV staff questionnaire" to study participants. The questionnaire consisted of 5 sections with 72 questions. The sections evaluated hospital staffs emotions, perceived stressors, factors that reduced their stress, coping strategies, and motivators to work during future outbreaks. Responses were scored on a scale from 0-3. The varying levels of stress or effectiveness of measures were reported as mean and standard deviation, as appropriate. Completed questionnaires were returned by 117 (78%) of the participants. The results had many unique elements. HCWs ethical obligation to their profession pushed them to continue with their jobs. The main sentiments centered upon fear of personal safety and well-being of colleagues and family. Positive attitudes in the workplace, clinical improvement of infected colleagues, and stoppage of disease transmission among HCWs after adopting strict protective measures alleviated their fear and drove them through the epidemic. They appreciated recognition of their efforts by hospital management and expected similar acknowledgment, infection control guidance, and equipment would entice them to work during future epidemics. The MERS-CoV outbreak was a distressing time for our staff. Hospitals can enhance HCWs experiences during any future MERS-CoV outbreak by focusing on the above mentioned aspects. © 2016 Marshfield Clinic.

  10. One-Pot Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting MERS-CoV

    PubMed Central

    Lee, Se Hee; Baek, Yun Hee; Kim, Yang-Hoon; Choi, Young-Ki; Song, Min-Suk; Ahn, Ji-Young

    2017-01-01

    Due to the limitation of rapid development of specific antiviral drug or vaccine for novel emerging viruses, an accurate and rapid diagnosis is a key to manage the virus spread. We developed an efficient and rapid method with high specificity for the Middle East Respiratory Syndrome coronavirus (MERS-CoV), based on one-pot reverse transcription loop-mediated isothermal amplification (one-pot RT-LAMP). A set of six LAMP primers [F3, B3, FIP, BIP, LF (Loop-F), and LB (Loop-B)] were designed using the sequence of nucleocapsid (N) gene with optimized RT-LAMP enzyme conditions: 100 U M-MLV RTase and 4 U Bst polymerase, implying that the reaction was able to detect four infectious viral genome copies of MERS-CoV within a 60 min reaction time period. Significantly, EvaGreen dye has better signal read-out properties in one-pot RT-LAMP reaction and is more compatible with DNA polymerase than SYBR green I. Isothermally amplified specific N genes were further evaluated using field-deployable microchamber devices, leading to the specific identification of as few as 0.4 infectious viral genome copies, with no cross-reaction to the other acute respiratory disease viruses, including influenza type A (H1N1 and H3N2), type B, human coronavirus 229E, and human metapneumovirus. This sensitive, specific and feasible method provides a large-scale technical support in emergencies, and is also applied as a sample-to-detection module in Point of Care Testing devices. PMID:28119682

  11. Replication and Shedding of MERS-CoV in Upper Respiratory Tract of Inoculated Dromedary Camels

    PubMed Central

    Adney, Danielle R.; van Doremalen, Neeltje; Brown, Vienna R.; Bushmaker, Trenton; Scott, Dana; de Wit, Emmie; Munster, Vincent J.

    2014-01-01

    In 2012, a novel coronavirus associated with severe respiratory disease in humans emerged in the Middle East. Epidemiologic investigations identified dromedary camels as the likely source of zoonotic transmission of Middle East respiratory syndrome coronavirus (MERS-CoV). Here we provide experimental support for camels as a reservoir for MERS-CoV. We inoculated 3 adult camels with a human isolate of MERS-CoV and a transient, primarily upper respiratory tract infection developed in each of the 3 animals. Clinical signs of the MERS-CoV infection were benign, but each of the camels shed large quantities of virus from the upper respiratory tract. We detected infectious virus in nasal secretions through 7 days postinoculation, and viral RNA up to 35 days postinoculation. The pattern of shedding and propensity for the upper respiratory tract infection in dromedary camels may help explain the lack of systemic illness among naturally infected camels and the means of efficient camel-to-camel and camel-to-human transmission. PMID:25418529

  12. T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV.

    PubMed

    Liu, William J; Zhao, Min; Liu, Kefang; Xu, Kun; Wong, Gary; Tan, Wenjie; Gao, George F

    2017-01-01

    Over 12 years have elapsed since severe acute respiratory syndrome (SARS) triggered the first global alert for coronavirus infections. Virus transmission in humans was quickly halted by public health measures and human infections of SARS coronavirus (SARS-CoV) have not been observed since. However, other coronaviruses still pose a continuous threat to human health, as exemplified by the recent emergence of Middle East respiratory syndrome (MERS) in humans. The work on SARS-CoV widens our knowledge on the epidemiology, pathophysiology and immunology of coronaviruses and may shed light on MERS coronavirus (MERS-CoV). It has been confirmed that T-cell immunity plays an important role in recovery from SARS-CoV infection. Herein, we summarize T-cell immunological studies of SARS-CoV and discuss the potential cross-reactivity of the SARS-CoV-specific immunity against MERS-CoV, which may provide useful recommendations for the development of broad-spectrum vaccines against coronavirus infections. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. ARM - Midlatitude Continental Convective Clouds Experiment (MC3E): Multi-Frequency Profilers, 449 MHz Profiler(williams-449_prof)

    DOE Data Explorer

    Williams, Christopher; Jensen, Mike

    2012-11-06

    This data was collected by the NOAA 449-MHz and 2.8-GHz profilers in support of the Department of Energy (DOE) and NASA sponsored Mid-latitude Continental Convective Cloud Experiment (MC3E). The profiling radars were deployed in Northern Oklahoma at the DOE Atmospheric Radiation Mission (ARM) Southern Great Plans (SGP) Central Facility from 22 April through 6 June 2011. NOAA deployed three instruments: a Parsivel disdrometer, a 2.8-GHz profiler, and a 449-MHz profiler. The parasivel provided surface estimates of the raindrop size distribution and is the reference used to absolutely calibrate the 2.8 GHz profiler. The 2.8-GHz profiler provided unattenuated reflectivity profiles of the precipitation. The 449-MHz profiler provided estimates of the vertical air motion during precipitation from near the surface to just below the freezing level. By using the combination of 2.8-GHz and 449-MHz profiler observations, vertical profiles of raindrop size distributions can be retrieved. The profilers are often reference by their frequency band: the 2.8-GHz profiler operates in the S-band and the 449-MHz profiler operates in the UHF band. The raw observations are available as well as calibrated spectra and moments. This document describes how the instruments were deployed, how the data was collected, and the format of the archived data.

  14. EDs on heightened alert for MERS-CoV as first cases reach the US.

    PubMed

    2014-07-01

    The first cases of Middle East Respiratory Syndrome coronavirus (MERS-CoV) have turned up in the United States. First, in late April, a patient tested positive for the virus at a hospital in Munster, IN, and then shortly thereafter, a second patient tested positive at a hospital in Orlando, FL. While both patients have since recovered from the virus and been released, the cases have raised awareness of the infectious threat of MERS-CoV, and they have put EDs and other frontline providers on heightened alert for patients with severe respiratory symptoms and other risk factors. While MERS-CoV is not yet as contagious as seasonal influenza or the severe acute respiratory syndrome (SARS) that started in China and then swept around the globe in 2003, it is more deadly. The World Health Organization reports that roughly one-quarter of 514 people who have tested positive for the virus have died. Experts note that health care workers make up a large percentage of the documented cases of MERS-CoV, and they point out that most human-to-human transmissions of the virus occur in the hospital setting. Public health officials urge emergency personnel to pay strict attention to infection control practices, and to query patients who present with fever and respiratory distress about recent travel to the Arabian Peninsula and/or close contact with a person who has a confirmed or probable case of MERS-CoV.

  15. 21 CFR 177.1040 - Acrylonitrile/styrene copoly-mer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Acrylonitrile/styrene copoly-mer. 177.1040 Section 177.1040 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... Internal Standard Method”; “Infrared Spectrophotometric Determination of Polymer Extracted from Barex 210...

  16. Diversification of the celiac disease α-gliadin complex in wheat: a 33-mer peptide with six overlapping epitopes, evolved following polyploidization.

    PubMed

    Ozuna, Carmen V; Iehisa, Julio C M; Giménez, María J; Alvarez, Juan B; Sousa, Carolina; Barro, Francisco

    2015-06-01

    The gluten proteins from wheat, barley and rye are responsible both for celiac disease (CD) and for non-celiac gluten sensitivity, two pathologies affecting up to 6-8% of the human population worldwide. The wheat α-gliadin proteins contain three major CD immunogenic peptides: p31-43, which induces the innate immune response; the 33-mer, formed by six overlapping copies of three highly stimulatory epitopes; and an additional DQ2.5-glia-α3 epitope which partially overlaps with the 33-mer. Next-generation sequencing (NGS) and Sanger sequencing of α-gliadin genes from diploid and polyploid wheat provided six types of α-gliadins (named 1-6) with strong differences in their frequencies in diploid and polyploid wheat, and in the presence and abundance of these CD immunogenic peptides. Immunogenic variants of the p31-43 peptide were found in most of the α-gliadins. Variants of the DQ2.5-glia-α3 epitope were associated with specific types of α-gliadins. Remarkably, only type 1 α-gliadins contained 33-mer epitopes. Moreover, the full immunodominant 33-mer fragment was only present in hexaploid wheat at low abundance, probably as the result of allohexaploidization events from subtype 1.2 α-gliadins found only in Aegilops tauschii, the D-genome donor of hexaploid wheat. Type 3 α-gliadins seem to be the ancestral type as they are found in most of the α-gliadin-expressing Triticeae species. These findings are important for reducing the incidence of CD by the breeding/selection of wheat varieties with low stimulatory capacity of T cells. Moreover, advanced genome-editing techniques (TALENs, CRISPR) will be easier to implement on the small group of α-gliadins containing only immunogenic peptides. © 2015 Society for Experimental Biology and John Wiley & Sons Ltd.

  17. Sulforaphane rescues amyloid-β peptide-mediated decrease in MerTK expression through its anti-inflammatory effect in human THP-1 macrophages.

    PubMed

    Jhang, Kyoung A; Park, Jin-Sun; Kim, Hee-Sun; Chong, Young Hae

    2018-03-12

    Mer tyrosine kinase (MerTK) activity necessary for amyloid-stimulated phagocytosis strongly implicates that MerTK dysregulation might contribute to chronic inflammation implicated in Alzheimer's disease (AD) pathology. However, the precise mechanism involved in the regulation of MerTK expression by amyloid-β (Aβ) in proinflammatory environment has not yet been ascertained. The objective of this study was to determine the underlying mechanism involved in Aβ-mediated decrease in MerTK expression through Aβ-mediated regulation of MerTK expression and its modulation by sulforaphane in human THP-1 macrophages challenged with Aβ1-42. We used protein preparation, Ca 2+ influx fluorescence imaging, nuclear fractionation, Western blotting techniques, and small interfering RNA (siRNA) knockdown to perform our study. Aβ1-42 elicited a marked decrease in MerTK expression along with increased intracellular Ca 2+ level and induction of proinflammatory cytokines such as IL-1β and TNF-α. Ionomycin A and thapsigargin also increased intracellular Ca 2+ levels and production of IL-1β and TNF-α, mimicking the effect of Aβ1-42. In contrast, the Aβ1-42-evoked responses were attenuated by depletion of Ca 2+ with ethylene glycol tetraacetic acid. Furthermore, recombinant IL-1β or TNF-α elicited a decrease in MerTK expression. However, immunodepletion of IL-1β or TNF-α with neutralizing antibodies significantly inhibited Aβ1-42-mediated downregulation of MerTK expression. Notably, sulforaphane treatment potently inhibited Aβ1-42-induced intracellular Ca 2+ level and rescued the decrease in MerTK expression by blocking nuclear factor-κB (NF-κB) nuclear translocation, thereby decreasing IL-1β and TNF-α production upon Aβ1-42 stimulation. Such adverse effects of sulforaphane were replicated by BAY 11-7082, a NF-κB inhibitor. Moreover, sulforaphane's anti-inflammatory effects on Aβ1-42-induced production of IL-1β and TNF-α were significantly diminished by si

  18. Prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels in Abu Dhabi Emirate, United Arab Emirates.

    PubMed

    Yusof, Mohammed F; Eltahir, Yassir M; Serhan, Wissam S; Hashem, Farouk M; Elsayed, Elsaeid A; Marzoug, Bahaaeldin A; Abdelazim, Assem Si; Bensalah, Oum Keltoum A; Al Muhairi, Salama S

    2015-06-01

    High seroprevalence of Middle East respiratory syndrome corona virus (MERS-CoV) in dromedary camels has been previously reported in United Arab Emirates (UAE). However, the molecular detection of the virus has never been reported before in UAE. Of the 7,803 nasal swabs tested in the epidemiological survey, MERS-CoV nucleic acid was detected by real-time PCR in a total of 126 (1.6 %) camels. Positive camels were detected at the borders with Saudi Arabia and Oman and in camels' slaughter houses. MERS-CoV partial sequences obtained from UAE camels were clustering with human- and camel-derived MERS-CoV sequences in the same geographic area. Results provide further evidence of MERS-CoV zoonosis.

  19. Transmission of SARS and MERS coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination.

    PubMed

    Otter, J A; Donskey, C; Yezli, S; Douthwaite, S; Goldenberg, S D; Weber, D J

    2016-03-01

    Viruses with pandemic potential including H1N1, H5N1, and H5N7 influenza viruses, and severe acute respiratory syndrome (SARS)/Middle East respiratory syndrome (MERS) coronaviruses (CoV) have emerged in recent years. SARS-CoV, MERS-CoV, and influenza virus can survive on surfaces for extended periods, sometimes up to months. Factors influencing the survival of these viruses on surfaces include: strain variation, titre, surface type, suspending medium, mode of deposition, temperature and relative humidity, and the method used to determine the viability of the virus. Environmental sampling has identified contamination in field-settings with SARS-CoV and influenza virus, although the frequent use of molecular detection methods may not necessarily represent the presence of viable virus. The importance of indirect contact transmission (involving contamination of inanimate surfaces) is uncertain compared with other transmission routes, principally direct contact transmission (independent of surface contamination), droplet, and airborne routes. However, influenza virus and SARS-CoV may be shed into the environment and be transferred from environmental surfaces to hands of patients and healthcare providers. Emerging data suggest that MERS-CoV also shares these properties. Once contaminated from the environment, hands can then initiate self-inoculation of mucous membranes of the nose, eyes or mouth. Mathematical and animal models, and intervention studies suggest that contact transmission is the most important route in some scenarios. Infection prevention and control implications include the need for hand hygiene and personal protective equipment to minimize self-contamination and to protect against inoculation of mucosal surfaces and the respiratory tract, and enhanced surface cleaning and disinfection in healthcare settings. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  20. Dating a tropical ice core by time-frequency analysis of ion concentration depth profiles

    NASA Astrophysics Data System (ADS)

    Gay, M.; De Angelis, M.; Lacoume, J.-L.

    2014-09-01

    Ice core dating is a key parameter for the interpretation of the ice archives. However, the relationship between ice depth and ice age generally cannot be easily established and requires the combination of numerous investigations and/or modelling efforts. This paper presents a new approach to ice core dating based on time-frequency analysis of chemical profiles at a site where seasonal patterns may be significantly distorted by sporadic events of regional importance, specifically at the summit area of Nevado Illimani (6350 m a.s.l.), located in the eastern Bolivian Andes (16°37' S, 67°46' W). We used ion concentration depth profiles collected along a 100 m deep ice core. The results of Fourier time-frequency and wavelet transforms were first compared. Both methods were applied to a nitrate concentration depth profile. The resulting chronologies were checked by comparison with the multi-proxy year-by-year dating published by de Angelis et al. (2003) and with volcanic tie points. With this first experiment, we demonstrated the efficiency of Fourier time-frequency analysis when tracking the nitrate natural variability. In addition, we were able to show spectrum aliasing due to under-sampling below 70 m. In this article, we propose a method of de-aliasing which significantly improves the core dating in comparison with annual layer manual counting. Fourier time-frequency analysis was applied to concentration depth profiles of seven other ions, providing information on the suitability of each of them for the dating of tropical Andean ice cores.

  1. N(h) profile data at World Data Centers

    NASA Technical Reports Server (NTRS)

    Allen, J. H.; Conkright, R.; Bilitza, D.; Feldstein, A. IA.; Willis, D. M.

    1990-01-01

    The data base for ionospheric electron density profiles at the World Data Centers is assessed. Past and future N(h) profiling from ionograms and profiles from incoherent scatter radar measurements are considered.

  2. Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon–Metal Bond Cleavage

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

    Wahba, Haytham M.; Stevenson, Michael J.; Mansour, Ahmed

    2017-01-03

    The organomercurial lyase MerB has the unique ability to cleave carbon–Hg bonds, and structural studies indicate that three residues in the active site (C96, D99, and C159 in E. coli MerB) play important roles in the carbon–Hg bond cleavage. However, the role of each residue in carbon–metal bond cleavage has not been well-defined. To do so, we have structurally and biophysically characterized the interaction of MerB with a series of organotin and organolead compounds. Studies with two known inhibitors of MerB, dimethyltin (DMT) and triethyltin (TET), reveal that they inhibit by different mechanisms. In both cases the initial binding ismore » to D99, but DMT subsequently binds to C96, which induces a conformation change in the active site. In contrast, diethyltin (DET) is a substrate for MerB and the SnIV product remains bound in the active site in a coordination similar to that of HgII following cleavage of organomercurial compounds. The results with analogous organolead compounds are similar in that trimethyllead (TML) is not cleaved and binds only to D99, whereas diethyllead (DEL) is a substrate and the PbIV product remains bound in the active site. Binding and cleavage is an exothermic reaction, while binding to D99 has negligible net heat flow. These results show that initial binding of organometallic compounds to MerB occurs at D99 followed, in some cases, by cleavage and loss of the organic moieties and binding of the metal ion product to C96, D99, and C159. The N-terminus of MerA is able to extract the bound PbVI but not the bound SnIV. These results suggest that MerB could be utilized for bioremediation applications, but certain organolead and organotin compounds may present an obstacle by inhibiting the enzyme.« less

  3. TAM receptors Tyro3 and Mer as novel targets in colorectal cancer.

    PubMed

    Schmitz, Robin; Valls, Aida Freire; Yerbes, Rosario; von Richter, Sophie; Kahlert, Christoph; Loges, Sonja; Weitz, Jürgen; Schneider, Martin; Ruiz de Almodovar, Carmen; Ulrich, Alexis; Schmidt, Thomas

    2016-08-30

    CRC remains the third most common cancer worldwide with a high 5-year mortality rate in advanced cases. Combined with chemotherapy, targeted therapy is an additional treatment option. However as CRC still escapes targeted therapy the vigorous search for new targets is warranted to increase patients´ overall survival. In this study we describe a new role for Gas6/protein S-TAM receptor interaction in CRC. Gas6, expressed by tumor-infiltrating M2-like macrophages, enhances malignant properties of tumor cells including proliferation, invasion and colony formation. Upon chemotherapy macrophages increase Gas6 synthesis, which significantly attenuates the cytotoxic effect of 5-FU chemotherapy on tumor cells. The anti-coagulant protein S has similar effects as Gas6.In CRC patient samples Tyro3 was overexpressed within the tumor. In-vitro inhibition of Tyro3 and Mer reduces tumor cell proliferation and sensitizes tumor cells to chemotherapy. Moreover high expression of Tyro3 and Mer in tumor tissue significantly shortens CRC patients´ survival. Various in vitro models were used to investigate the role of Gas6 and its TAM receptors in human CRC cells, by stimulation (rhGas6) and knockdown (siRNA) of Axl, Tyro3 and Mer. In terms of a translational research, we additionally performed an expression analysis in human CRC tissue and analyzed the medical record of these patients. Tyro3 and Mer represent novel therapeutic targets in CRC and warrant further preclinical and clinical investigation in the future.

  4. Inferences of Strength of Soil Deposits along MER Rover Traverses

    NASA Astrophysics Data System (ADS)

    Richter, L.; Schmitz, N.; Weiss, S.; Mer/Athena Team

    As the two MER Mars Exploration Rovers ,Spirit' and ,Opportunity' traverse terrains within Gusev crater and at Meridiani Planum, respectively, they leave behind wheel tracks that are routinely imaged by the different sets of cameras as part of the Athena instrument suite. Stereo observations of these tracks reveal wheel sinkage depths which are diagnostic of the strength of the soil-like deposits crossed by the vehicles, and observations of track morphology at different imaging scales - including that of the Microscopic Imager - allow estimations of soil grain size distributions. This presentation will discuss results of systematic analyses of MER-A and -B wheel track observations with regard to solutions for soil bearing strength and soil shear strength. Data are analyzed in the context of wheel-soil theory calibrated to the shape of the MER wheel and by consulting comparisons with terrestrial soils. Results are applicable to the top ˜20-30 cm of the soil deposits, the depth primarily affected by the stress distribution under the wheels. The large number of wheel track observations per distance travelled enables investigations of variations of soil physical properties as a function of spatial scale, type of surface feature encountered, and local topography. Exploiting relationships between soil strength and degree of soil consolidation known from lunar regolith and dry terrestrial soils allows one to relate inferred soil strengths to bulk density. This provides a means to ground-truth radar Fresnel reflection coefficients obtained for the landing sites from Earth-based observations. Moreover, bulk density is correlated with soil dielectric constant, a parameter of direct relevance also for Mars-orbiting radars. The obtained estimates for soil bulk density are also used to determine local thermal conductivity of near-surface materials, based on correlations between the two quantities, and to subsequently estimate thermal inertia. This represents an independent

  5. The MER Mossbauer Spectrometers: 40 Months of Operation on the Martian Surface

    NASA Technical Reports Server (NTRS)

    Fleischer, Iris; Rodionov, D.; Schroeder, C.; Morris, R.; Yen, A.; Ming, D.; McCoy, T.; Mittlefehldt, D.; Gellert, R.; Cohen, B.; hide

    2007-01-01

    The primary MER objectives have been successfully completed. The total integration time of all MB measurements exceeds the duration of the primary 90-sols-mission for Spirit's MB spectrometer, and approaches this value for Opportunity's MB spectrometer. Both MB spectrometers continue to accumulate valuable scientific data after three years of operation (data is available for download [13]) The identification of aqueous minerals such as goethite in Gusev crater and jarosite at Meridiani Planum by the MER Mossbauer spectrometers is strong evidence for past water activity at the two landing sites.

  6. Science Activity Planner for the MER Mission

    NASA Technical Reports Server (NTRS)

    Norris, Jeffrey S.; Crockett, Thomas M.; Fox, Jason M.; Joswig, Joseph C.; Powell, Mark W.; Shams, Khawaja S.; Torres, Recaredo J.; Wallick, Michael N.; Mittman, David S.

    2008-01-01

    The Maestro Science Activity Planner is a computer program that assists human users in planning operations of the Mars Explorer Rover (MER) mission and visualizing scientific data returned from the MER rovers. Relative to its predecessors, this program is more powerful and easier to use. This program is built on the Java Eclipse open-source platform around a Web-browser-based user-interface paradigm to provide an intuitive user interface to Mars rovers and landers. This program affords a combination of advanced display and simulation capabilities. For example, a map view of terrain can be generated from images acquired by the High Resolution Imaging Science Explorer instrument aboard the Mars Reconnaissance Orbiter spacecraft and overlaid with images from a navigation camera (more precisely, a stereoscopic pair of cameras) aboard a rover, and an interactive, annotated rover traverse path can be incorporated into the overlay. It is also possible to construct an overhead perspective mosaic image of terrain from navigation-camera images. This program can be adapted to similar use on other outer-space missions and is potentially adaptable to numerous terrestrial applications involving analysis of data, operations of robots, and planning of such operations for acquisition of scientific data.

  7. The effects of low-frequency vibrations on hepatic profile of blood

    NASA Astrophysics Data System (ADS)

    Damijan, Z.

    2008-02-01

    Body vibrations training has become popular in sports training, fitness activity, it is still a rare form of physical rehabilitation.. Vibrations are transmitted onto the whole body or some body parts of an exercising person via a vibration platform subjected to mechanical vertical vibrations. During the training session a participant has to maintain his body position or do exercises that engage specific muscles whilst vibrations of the platform are transmitted onto the person's body. This paper is the continuation of the earlier study covering the effects of low-frequency vibrations on selected physiological parameters of the human body. The experiments were conducted to find the answer to the question if vibration exposure (total duration of training sessions 6 hours 20 min) should produce any changes in hepatic profile of blood. Therefore a research program was undertaken at the University of Science and Technology AGH UST to investigate the effects of low-frequency vibration on selected parameters of hepatic profile of human blood. Cyclic fluctuations of bone loading were induced by the applied harmonic vibration 3.5 Hz and amplitude 0.004 m. The experiments utilizing two vibrating platforms were performed in the Laboratory of Structural Acoustics and Biomedical Engineering AGH-UST. The applied vibrations were harmless and not annoying, in accordance with the standard PN-EN ISO 130901-1, 1998. 23 women volunteers had 19 sessions on subsequent working days, at the same time of day. during the tests the participants remained in the standing position, passive. The main hypothesis has it that short-term low-frequency vibration exposure might bring about the changes of the hepatic profile of blood, including: bilirubin (BILIRUBIN), alkaline phosphatase (Alp), alanine aminotransferase (ALT), aspartate aminotransferase (AST) and albumin (ALBUMIN) levels. Research data indicate the low-frequency vibrations exposure produces statistically significant decrease of

  8. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

    PubMed

    Wang, Dapeng; Xu, Jiayue; Yu, Jun

    2015-09-16

    The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

  9. Estimating Potential Incidence of MERS-CoV Associated with Hajj Pilgrims to Saudi Arabia, 2014

    PubMed Central

    Lessler, Justin; Rodriguez-Barraquer, Isabel; Cummings, Derek A.T.; Garske, Tini; Van Kerkhove, Maria; Mills, Harriet; Truelove, Shaun; Hakeem, Rafat; Albarrak, Ali; Ferguson, Neil M.; Aguas, Ricardo; Algarni, Homud; AlHarbi, Khalid; Cauchemez, Simon; Clapham, Hannah; Collins, Caitlin; Cori, Anne; Donnelly, Christl; Fraser, Christophe; Jombart, Thibaut; Moore, Sean M.; Nouvellet, Pierre; Riley, Steven; Salje, Henrik; Turkistani, Abdulhafiz

    2014-01-01

    Between March and June 2014 the Kingdom of Saudi Arabia (KSA) had a large outbreak of MERS-CoV, renewing fears of a major outbreak during the Hajj this October. Using KSA Ministry of Health data, the MERS-CoV Scenario and Modeling Working Group forecast incidence under three scenarios. In the expected incidence scenario, we estimate 6.2 (95% Prediction Interval [PI]: 1–17) pilgrims will develop MERS-CoV symptoms during the Hajj, and 4.0 (95% PI: 0–12) foreign pilgrims will be infected but return home before developing symptoms. In the most pessimistic scenario, 47.6 (95% PI: 32–66) cases will develop symptoms during the Hajj, and 29.0 (95% PI: 17–43) will be infected but return home asymptomatic. Large numbers of MERS-CoV cases are unlikely to occur during the 2014 Hajj even under pessimistic assumptions, but careful monitoring is still needed to detect possible mass infection events and minimize introductions into other countries.   PMID:25685624

  10. Up-Regulation of Soluble Axl and Mer Receptor Tyrosine Kinases Negatively Correlates with Gas6 in Established Multiple Sclerosis Lesions

    PubMed Central

    Weinger, Jason G.; Omari, Kakuri M.; Marsden, Kurt; Raine, Cedric S.; Shafit-Zagardo, Bridget

    2009-01-01

    Multiple sclerosis is a disease that is characterized by inflammation, demyelination, and axonal damage; it ultimately forms gliotic scars and lesions that severely compromise the function of the central nervous system. Evidence has shown previously that altered growth factor receptor signaling contributes to lesion formation, impedes recovery, and plays a role in disease progression. Growth arrest-specific protein 6 (Gas6), the ligand for the TAM receptor tyrosine kinase family, consisting of Tyro3, Axl, and Mer, is important for cell growth, survival, and clearance of debris. In this study, we show that levels of membrane-bound Mer (205 kd), soluble Mer (∼150 kd), and soluble Axl (80 kd) were all significantly elevated in homogenates from established multiple sclerosis lesions comprised of both chronic active and chronic silent lesions. Whereas in normal tissue Gas6 positively correlated with soluble Axl and Mer, there was a negative correlation between Gas6 and soluble Axl and Mer in established multiple sclerosis lesions. In addition, increased levels of soluble Axl and Mer were associated with increased levels of mature ADAM17, mature ADAM10, and Furin, proteins that are associated with Axl and Mer solubilization. Soluble Axl and Mer are both known to act as decoy receptors and block Gas6 binding to membrane-bound receptors. These data suggest that in multiple sclerosis lesions, dysregulation of protective Gas6 receptor signaling may prolong lesion activity. PMID:19541935

  11. Protection of rat liver against hepatic ischemia-reperfusion injury by a novel selenocysteine-containing 7-mer peptide

    PubMed Central

    Jiang, Qianqian; Pan, Yu; Cheng, Yupeng; Li, Huiling; Li, Hui

    2016-01-01

    Hepatic ischemia-reperfusion (I-R) injury causes acute organ damage or dysfunction, and remains a problem for liver transplantation. In the I-R phase, the generation of reactive oxygen species aggravates the injury. In the current study, a novel selenocysteine-containing 7-mer peptide (H-Arg-Sec-Gly-Arg-Asn-Ala-Gln-OH) was constructed to imitate the active site of an antioxidant enzyme, glutathione peroxidase (GPX). The 7-mer peptide which has a lower molecular weight, and improved water-solubility, higher stability and improved cell membrane permeability compared with other GPX mimics. Its GPX activity reached 13 U/µmol, which was 13 times that of ebselen (a representative GPX mimic). The effect of this GPX mimic on I-R injury of the liver was assessed in rats. The 7-mer peptide significantly inhibited the increase in serum hepatic amino-transferases, tissue malondialdehyde, nitric oxide contents, myeloperoxidase activity and decrease of GPX activity compared with I-R tissue. Following treatment with the 7-mer peptide, the expression of B-cell CLL/lymphoma-2 (Bcl-2) was significantly upregulated at the mRNA and protein level compared with the I-R group, as determined by reverse transcription-polymerase chain reaction and immunohistochemistry, respectively. By contrast, Bcl-2 associated X protein (Bax) was downregulated by the 7-mer peptide compared the I-R group. Histological and ultrastructural changes of the rat liver tissue were also compared among the experimental groups. The results of the current study suggest that the 7-mer peptide protected the liver against hepatic I-R injury via suppression of oxygen-derived free radicals and regulation of Bcl-2 and Bax expression, which are involved in the apoptosis of liver cells. The findings of the present study will further the investigation of the 7-mer peptide as an effective therapeutic agent in hepatic I-R injury. PMID:27431272

  12. A high-frequency sonar for profiling small-scale subaqueous bedforms

    USGS Publications Warehouse

    Dingler, J.R.; Boylls, J.C.; Lowe, R.L.

    1977-01-01

    A high-resolution ultrasonic profiler has been developed which permits both laboratory and field studies of small-scale subaqueous bedforms. The device uses a 2.5-cm diameter piezoelectric ceramic crystal pulsed at a frequency of 4.5 MHz to obtain vertical accuracy and resolution of at least 1 mm. Compared to other small-scale profiling methods, this ultrasonic technique profiles the bottom more accurately and more rapidly without disturbing the bedforms. These characteristics are vital in wave-dominated nearshore zones where oscillatory flow and low visibility for the most part have stymied detailed bedform studies. In the laboratory the transducer is mounted directly to an instrument carriage. For field work the transducer housing is mounted in a 2 m long aluminum frame which is situated and operated by scuba divers. Observations using the device include ripple geometry and migration, the suspension height of sand during sheet flow, and long-term erosion/deposition at a point. ?? 1977.

  13. Electrical conductivity of a monolayer produced by random sequential adsorption of linear k -mers onto a square lattice

    NASA Astrophysics Data System (ADS)

    Tarasevich, Yuri Yu.; Goltseva, Valeria A.; Laptev, Valeri V.; Lebovka, Nikolai I.

    2016-10-01

    The electrical conductivity of a monolayer produced by the random sequential adsorption (RSA) of linear k -mers (particles occupying k adjacent adsorption sites) onto a square lattice was studied by means of computer simulation. Overlapping with predeposited k -mers and detachment from the surface were forbidden. The RSA process continued until the saturation jamming limit, pj. The isotropic (equiprobable orientations of k -mers along x and y axes) and anisotropic (all k -mers aligned along the y axis) depositions for two different models—of an insulating substrate and conducting k -mers (C model) and of a conducting substrate and insulating k -mers (I model)—were examined. The Frank-Lobb algorithm was applied to calculate the electrical conductivity in both the x and y directions for different lengths (k =1 - 128) and concentrations (p =0 - pj) of the k -mers. The "intrinsic electrical conductivity" and concentration dependence of the relative electrical conductivity Σ (p ) (Σ =σ /σm for the C model and Σ =σm/σ for the I model, where σm is the electrical conductivity of substrate) in different directions were analyzed. At large values of k the Σ (p ) curves became very similar and they almost coincided at k =128 . Moreover, for both models the greater the length of the k -mers the smoother the functions Σx y(p ) ,Σx(p ) and Σy(p ) . For the more practically important C model, the other interesting findings are (i) for large values of k (k =64 ,128 ), the values of Σx y and Σy increase rapidly with the initial increase of p from 0 to 0.1; (ii) for k ≥16 , all the Σx y(p ) and Σx(p ) curves intersect with each other at the same isoconductivity points; (iii) for anisotropic deposition, the percolation concentrations are the same in the x and y directions, whereas, at the percolation point the greater the length of the k -mers the larger the anisotropy of the electrical conductivity, i.e., the ratio σy/σx (>1 ).

  14. “Don’t forget the migrants”: exploring preparedness and response strategies to combat the potential spread of MERS-CoV virus through migrant workers in Sri Lanka

    PubMed Central

    Agampodi, Suneth B

    2013-01-01

    From September 2012 to July 2013, 81 laboratory-confirmed cases of infection with Middle East respiratory syndrome coronavirus (MERS-CoV), including 45 deaths (a case fatality ratio of 55%) have been reported from eight countries. Human-to-human transmission is now confirmed showing potential for another pandemic of zoonotic disease, with an extremely high mortality rate. Effective surveillance strategies are required in countries with a high influx of migrants from the Middle East to mitigate the probable importation of MERS-CoV. We discuss here the risk of MERS-CoV in major labor sending countries and list the probable strategies for control and prevention of MERS-CoV using Sri Lanka as an example. It is conservatively estimated that 10% of Sri Lanka’s population work as international labor migrants (1.8 to 2 million workers), with 93% residing in the Middle East. An average of 720 workers depart each day, with the majority of these workers (71%) departing to the Kingdom of Saudi Arabia (the country with 81.5% of total MERS-CoV cases). We also describe other inbound migration categories such as tourists and resident visa holders relevant to the context of preparedness and planning. The importance of partnerships between public health authorities at national and regional levels with labor migration networks to establish institutional and/or policy mechanisms are highlighted for ensuring effective preparedness and response planning. Strategies that can be taken by public health authorities working in both labor sending and labor receiving counties are also described.  The strategies described here may be useful for other labor sending country contexts in Asia with a high frequency and volume of migrant workers to and from the Gulf region. PMID:24555078

  15. Multi-Agent Modeling and Simulation Approach for Design and Analysis of MER Mission Operations

    NASA Technical Reports Server (NTRS)

    Seah, Chin; Sierhuis, Maarten; Clancey, William J.

    2005-01-01

    A space mission operations system is a complex network of human organizations, information and deep-space network systems and spacecraft hardware. As in other organizations, one of the problems in mission operations is managing the relationship of the mission information systems related to how people actually work (practices). Brahms, a multi-agent modeling and simulation tool, was used to model and simulate NASA's Mars Exploration Rover (MER) mission work practice. The objective was to investigate the value of work practice modeling for mission operations design. From spring 2002 until winter 2003, a Brahms modeler participated in mission systems design sessions and operations testing for the MER mission held at Jet Propulsion Laboratory (JPL). He observed how designers interacted with the Brahms tool. This paper discussed mission system designers' reactions to the simulation output during model validation and the presentation of generated work procedures. This project spurred JPL's interest in the Brahms model, but it was never included as part of the formal mission design process. We discuss why this occurred. Subsequently, we used the MER model to develop a future mission operations concept. Team members were reluctant to use the MER model, even though it appeared to be highly relevant to their effort. We describe some of the tool issues we encountered.

  16. Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV.

    PubMed

    Lee, Hyun; Lei, Hao; Santarsiero, Bernard D; Gatuz, Joseph L; Cao, Shuyi; Rice, Amy J; Patel, Kavankumar; Szypulinski, Michael Z; Ojeda, Isabel; Ghosh, Arun K; Johnson, Michael E

    2015-06-19

    The Middle East Respiratory Syndrome coronavirus (MERS-CoV) papain-like protease (PLpro) blocking loop 2 (BL2) structure differs significantly from that of SARS-CoV PLpro, where it has been proven to play a crucial role in SARS-CoV PLpro inhibitor binding. Four SARS-CoV PLpro lead inhibitors were tested against MERS-CoV PLpro, none of which were effective against MERS-CoV PLpro. Structure and sequence alignments revealed that two residues, Y269 and Q270, responsible for inhibitor binding to SARS-CoV PLpro, were replaced by T274 and A275 in MERS-CoV PLpro, making critical binding interactions difficult to form for similar types of inhibitors. High-throughput screening (HTS) of 25 000 compounds against both PLpro enzymes identified a small fragment-like noncovalent dual inhibitor. Mode of inhibition studies by enzyme kinetics and competition surface plasmon resonance (SPR) analyses suggested that this compound acts as a competitive inhibitor with an IC50 of 6 μM against MERS-CoV PLpro, indicating that it binds to the active site, whereas it acts as an allosteric inhibitor against SARS-CoV PLpro with an IC50 of 11 μM. These results raised the possibility that inhibitor recognition specificity of MERS-CoV PLpro may differ from that of SARS-CoV PLpro. In addition, inhibitory activity of this compound was selective for SARS-CoV and MERS-CoV PLpro enzymes over two human homologues, the ubiquitin C-terminal hydrolases 1 and 3 (hUCH-L1 and hUCH-L3).

  17. Risk of global spread of Middle East respiratory syndrome coronavirus (MERS-CoV) via the air transport network.

    PubMed

    Gardner, Lauren M; Chughtai, Abrar A; MacIntyre, C Raina

    2016-06-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) emerged from the Kingdom of Saudi Arabia (KSA) in 2012 and has since spread to 26 countries. All cases reported so far have either been in the Middle East or linked to the region through passenger air travel, with the largest outbreak outside KSA occurring in South Korea. Further international spread is likely due to the high travel volumes of global travel, as well as the occurrence of large annual mass gathering such as the Haj and Umrah pilgrimages that take place in the region. In this study, a transport network modelling framework was used to quantify the risk of MERS-CoV spreading internationally via air travellers. All regions connected to MERS-CoV affected countries via air travel are considered, and the countries at highest risk of travel-related importations of MERS-CoV were identified, ranked and compared with actual spread of MERS cases. The model identifies all countries that have previously reported a travel acquired case to be in the top 50 at-risk countries. India, Pakistan and Bangladesh are the highest risk countries which have yet to report a case, and should be prepared for the possibility of (pilgrims and general) travellers returning infected with MERS-CoV. In addition, the UK, Egypt, Turkey and the USA are at risk of more cases. We have demonstrated a risk-analysis approach, using travel patterns, to prioritize countries at highest risk for MERS-CoV importations. In order to prevent global outbreaks such as the one seen in South Korea, it is critical for high-risk countries to be prepared and have appropriate screening and triage protocols in place to identify travel-related cases of MERS-CoV. The results from the model can be used by countries to prioritize their airport and hospital screening and triage protocols. © International Society of Travel Medicine, 2016. All rights reserved. Published by Oxford University Press. For permissions, please e-mail: journals.permissions@oup.com.

  18. Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures

    PubMed Central

    Wang, Ying; Fu, Lei; Ren, Jie; Yu, Zhaoxia; Chen, Ting; Sun, Fengzhu

    2018-01-01

    Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered “group-specific” in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers. We developed a long k-mer (k ≥ 30 bps)-based computational pipeline to detect group-specific sequences at strain resolution free from reference sequences, sequence alignments, and metagenome-wide de novo assembly. We called our method MetaGO: Group-specific oligonucleotide analysis for metagenomic samples. An open-source pipeline on Apache Spark was developed with parallel computing. We applied MetaGO to one simulated and three real metagenomic datasets to evaluate the discriminative capability of identified group-specific markers. In the simulated dataset, 99.11% of group-specific logical 40-mers covered 98.89% disease-specific regions from the disease-associated strain. In addition, 97.90% of group-specific numerical 40-mers covered 99.61 and 96.39% of differentially abundant genome and regions between two groups, respectively. For a large-scale metagenomic liver cirrhosis (LC)-associated dataset, we identified 37,647 group-specific 40-mer features. Any one of the features can predict disease status of the training samples with the average of sensitivity and specificity higher than 0.8. The random forests classification using the top 10 group-specific features yielded a higher AUC (from ∼0.8 to ∼0.9) than that of previous studies. All group-specific 40-mers were present in LC patients, but not healthy controls. All the assembled 11 LC-specific sequences can be mapped to two

  19. NCI Researchers Discover Exceptionally Potent Antibodies with Potential for Prophylaxis and Therapy of MERS-Coronavirus Infections | Poster

    Cancer.gov

    By Andrea Frydl, Contributing Writer In a recent article published in the Journal of Virology, Tianlei Ying, Ph.D., Dimiter Dimitrov, Ph.D., and their colleagues in the Laboratory of Experimental Immunology (LEI), Cancer and Inflammation Program, NCI Center for Cancer Research, reported the identification of three human monoclonal antibodies (m336, m337, and m338) that target the part of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) that is responsible for binding to its receptor. These antibodies are exceptionally potent inhibitors of MERS-CoV infection and also provide a basis for creating a future MERS-CoV vaccine.

  20. Carbo-biphenyls and Carbo-terphenyls: Oligo(phenylene ethynylene) Ring Carbo-mers.

    PubMed

    Zhu, Chongwei; Poater, Albert; Duhayon, Carine; Kauffmann, Brice; Saquet, Alix; Maraval, Valérie; Chauvin, Remi

    2018-05-14

    Ring carbo-mers of oligo(phenylene ethynylene)s (OPEn, n=0-2), made of C 2 -catenated C 18 carbo-benzene rings, have been synthesized and characterized by NMR and UV-vis spectroscopy, crystallography and voltammetry. Analyses of crystal and DFT-optimized structures show that the C 18 rings preserve their individual aromatic character according to structural and magnetic criteria (NICS indices). Carbo-terphenyls (n=2) are reversibly reduced at ca. -0.42 V/SCE, i.e. 0.41 V more readily than the corresponding carbo-benzene (-0.83 V/SCE), thus revealing efficient inter-ring π-conjugation. An accurate linear fit of E 1/2 red1 vs. the DFT LUMO energy suggests a notably higher value (-0.30 V/SCE) for a carbo-quaterphenyl congener (n=3). Increase with n of the effective π-conjugation is also evidenced by a red shift of two of the three main visible light absorption bands, all being assigned to TDDFT-calculated excited states, one of them restricting to a HOMO→LUMO main one-electron transition. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. KENNEDY SPACE CENTER, FLA. - An overhead crane lifts the Mars Exploration Rover 2 (MER-2) entry vehicle from its stand to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - An overhead crane lifts the Mars Exploration Rover 2 (MER-2) entry vehicle from its stand to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

  2. KENNEDY SPACE CENTER, FLA. - With help from workers, the overhead crane lowers the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - With help from workers, the overhead crane lowers the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

  3. KENNEDY SPACE CENTER, FLA. - An overhead crane moves the Mars Exploration Rover 2 (MER-2) entry vehicle across the Payload Hazardous Servicing Facility toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - An overhead crane moves the Mars Exploration Rover 2 (MER-2) entry vehicle across the Payload Hazardous Servicing Facility toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

  4. KENNEDY SPACE CENTER, FLA. - Workers in the Payload Hazardous Servicing Facility help guide the Mars Exploration Rover 2 (MER-2) entry vehicle toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - Workers in the Payload Hazardous Servicing Facility help guide the Mars Exploration Rover 2 (MER-2) entry vehicle toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

  5. KENNEDY SPACE CENTER, FLA. - The overhead crane settles the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - The overhead crane settles the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

  6. Characterization of novel monoclonal antibodies against the MERS-coronavirus spike protein and their application in species-independent antibody detection by competitive ELISA.

    PubMed

    Fukushi, Shuetsu; Fukuma, Aiko; Kurosu, Takeshi; Watanabe, Shumpei; Shimojima, Masayuki; Shirato, Kazuya; Iwata-Yoshikawa, Naoko; Nagata, Noriyo; Ohnishi, Kazuo; Ato, Manabu; Melaku, Simenew Keskes; Sentsui, Hiroshi; Saijo, Masayuki

    2018-01-01

    Since discovering the Middle East respiratory syndrome coronavirus (MERS-CoV) as a causative agent of severe respiratory illness in the Middle East in 2012, serological testing has been conducted to assess antibody responses in patients and to investigate the zoonotic reservoir of the virus. Although the virus neutralization test is the gold standard assay for MERS diagnosis and for investigating the zoonotic reservoir, it uses live virus and so must be performed in high containment laboratories. Competitive ELISA (cELISA), in which a labeled monoclonal antibody (MAb) competes with test serum antibodies for target epitopes, may be a suitable alternative because it detects antibodies in a species-independent manner. In this study, novel MAbs against the spike protein of MERS-CoV were produced and characterized. One of these MAbs was used to develop a cELISA. The cELISA detected MERS-CoV-specific antibodies in sera from MERS-CoV-infected rats and rabbits immunized with the spike protein of MERS-CoV. The MAb-based cELISA was validated using sera from Ethiopian dromedary camels. Relative to the neutralization test, the cELISA detected MERS-CoV-specific antibodies in 66 Ethiopian dromedary camels with a sensitivity and specificity of 98% and 100%, respectively. The cELISA and neutralization test results correlated well (Pearson's correlation coefficients=0.71-0.76, depending on the cELISA serum dilution). This cELISA may be useful for MERS epidemiological investigations on MERS-CoV infection. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update.

    PubMed

    Aly, Mahmoud; Elrobh, Mohamed; Alzayer, Maha; Aljuhani, Sameera; Balkhy, Hanan

    2017-01-01

    The emergence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections has become a global issue of dire concerns. MERS-CoV infections have been identified in many countries all over the world whereas high level occurrences have been documented in the Middle East and Korea. MERS-CoV is mainly spreading across the geographical region of the Middle East, especially in the Arabian Peninsula, while some imported sporadic cases were reported from the Europe, North America, Africa, and lately Asia. The prevalence of MERS-CoV infections across the Gulf Corporation Council (GCC) countries still remains unclear. Therefore, the objective of the current study was to report the prevalence of MERS-CoV in the GCC countries and to also elucidate on its demographics in the Arabian Peninsula. To date, the World Health Organization (WHO) has reported 1,797 laboratory-confirmed cases of MERS-CoV infection since June 2012, involving 687 deaths in 27 different countries worldwide. Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. Our data comprise a total of 1550 cases (67.1% male and 32.9% female). The age-specific prevalence and distribution of MERS-CoV was as follow: <20 yrs (36 cases: 3.28%), 20-39 yrs (331 cases: 30.15%), 40-59 yrs (314 cases: 28.60%), and the highest-risk elderly group aged ≥60 yrs (417 cases: 37.98%). The case distribution among GCC countries was as follows: Saudi Arabia (1441 cases: 93%), Kuwait (4 cases: 0.3%), Bahrain (1 case: 0.1%), Oman (8 cases: 0.5%), Qatar (16 cases: 1.0%), and United Arab Emirates (80 cases: 5.2%). Thus, MERS-CoV was found to be more prevalent in Saudi Arabia especially in Riyadh, where 756 cases (52.4%) were the worst hit area of the country identified, followed by the western region Makkah where 298 cases (20.6%) were recorded. This prevalence update

  8. Development of a procedure to model high-resolution wind profiles from smoothed or low-frequency data

    NASA Technical Reports Server (NTRS)

    Camp, D. W.

    1977-01-01

    The derivation of simulated Jimsphere wind profiles from low-frequency rawinsonde data and a generated set of white noise data are presented. A computer program is developed to model high-resolution wind profiles based on the statistical properties of data from the Kennedy Space Center, Florida. Comparison of the measured Jimsphere data, rawinsonde data, and the simulated profiles shows excellent agreement.

  9. Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response.

    PubMed

    Kindler, E; Thiel, V; Weber, F

    2016-01-01

    Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells. © 2016 Elsevier Inc. All rights reserved.

  10. MERS-CoV at the Animal–Human Interface: Inputs on Exposure Pathways from an Expert-Opinion Elicitation

    PubMed Central

    Funk, Anna L.; Goutard, Flavie Luce; Miguel, Eve; Bourgarel, Mathieu; Chevalier, Veronique; Faye, Bernard; Peiris, J. S. Malik; Van Kerkhove, Maria D.; Roger, Francois Louis

    2016-01-01

    Nearly 4 years after the first report of the emergence of Middle-East respiratory syndrome Coronavirus (MERS-CoV) and nearly 1800 human cases later, the ecology of MERS-CoV, its epidemiology, and more than risk factors of MERS-CoV transmission between camels are poorly understood. Knowledge about the pathways and mechanisms of transmission from animals to humans is limited; as of yet, transmission risks have not been quantified. Moreover the divergent sanitary situations and exposures to animals among populations in the Arabian Peninsula, where human primary cases appear to dominate, vs. other regions in the Middle East and Africa, with no reported human clinical cases and where the virus has been detected only in dromedaries, represents huge scientific and health challenges. Here, we have used expert-opinion elicitation in order to obtain ideas on relative importance of MERS-CoV risk factors and estimates of transmission risks from various types of contact between humans and dromedaries. Fourteen experts with diverse and extensive experience in MERS-CoV relevant fields were enrolled and completed an online questionnaire that examined pathways based on several scenarios, e.g., camels–camels, camels–human, bats/other species to camels/humans, and the role of diverse biological substances (milk, urine, etc.) and potential fomites. Experts believed that dromedary camels play the largest role in MERS-CoV infection of other dromedaries; however, they also indicated a significant influence of the season (i.e. calving or weaning periods) on transmission risk. All experts thought that MERS-CoV-infected dromedaries and asymptomatic humans play the most important role in infection of humans, with bats and other species presenting a possible, but yet undefined, risk. Direct and indirect contact of humans with dromedary camels were identified as the most risky types of contact, when compared to consumption of various camel products, with estimated “most likely

  11. Ray Meta: scalable de novo metagenome assembly and profiling

    PubMed Central

    2012-01-01

    Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

  12. KENNEDY SPACE CENTER, FLA. - In the foreground, three solid rocket boosters (SRBs) suspended in the launch tower flank the Delta II rocket (in the background) that will launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-15

    KENNEDY SPACE CENTER, FLA. - In the foreground, three solid rocket boosters (SRBs) suspended in the launch tower flank the Delta II rocket (in the background) that will launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  13. Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

    NASA Astrophysics Data System (ADS)

    Kritee, K.; Barkay, Tamar; Blum, Joel D.

    2009-03-01

    Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg

  14. Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

    PubMed

    Douglas, Madeline G; Kocher, Jacob F; Scobey, Trevor; Baric, Ralph S; Cockrell, Adam S

    2018-04-01

    We recently established a mouse model (288-330 +/+ ) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 10 6 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 10 3 and 10 5 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10-1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Vaccines for emerging infectious diseases: Lessons from MERS coronavirus and Zika virus.

    PubMed

    Maslow, Joel N

    2017-12-02

    The past decade and a half has been characterized by numerous emerging infectious diseases. With each new threat, there has been a call for rapid vaccine development. Pathogens such as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and the Zika virus represent either new viral entities or viruses emergent in new geographic locales and characterized by novel complications. Both serve as paradigms for the global spread that can accompany new pathogens. In this paper, we review the epidemiology and pathogenesis of MERS-CoV and Zika virus with respect to vaccine development. The challenges in vaccine development and the approach to clinical trial design to test vaccine candidates for disease entities with a changing epidemiology are discussed.

  16. Within treatment therapeutic alliance ratings profiles predict posttreatment frequency of alcohol use

    PubMed Central

    Prince, Mark A.; Connors, Gerard J.; Maisto, Stephen A.; Dearing, Ronda L.

    2016-01-01

    While past research has demonstrated a positive relationship between the therapeutic alliance (TA) and improved drinking outcomes, specific aspects of the alliance have received less attention. In this study, we examined the association between alliance characteristics during treatment and 4-month follow-up drinking reports. 65 treatment-seeking alcohol dependent clients who participated in 12 weeks of individual outpatient treatment provided weekly TA ratings during treatment and reported on pre-treatment, during treatment, and post-treatment alcohol use. Latent profile analysis was conducted to discern distinct profiles of client and therapist ratings of therapeutic alliance with similar alliance characteristics. TA profiles were based on clients’ and therapists’ mean alliance rating, minimum alliance rating, maximum alliance rating, the range of alliance ratings, and the difference in session number between maximum and minimum alliance ratings. 1- through 4- class models were fit to the data. Model fit was judged by comparative fit indices, substantive interpretability, and parsimony. Wald tests of mean equality determined whether classes differed on follow-up percentage of days abstinent (PDA) at 4 months posttreatment. 3-profile solutions provided the best fit for both client and therapist ratings of the therapeutic alliance. Client alliance rating profiles predicted drinking in the follow-up period, but therapist rating profiles did not. These results suggest that distinct profiles of the therapeutic alliance can be identified and that client alliance rating profiles are associated with frequency of alcohol use following outpatient treatment. PMID:26999350

  17. Thermophysical properties of the MER and Beagle II landing site regions on Mars

    NASA Astrophysics Data System (ADS)

    Jakosky, Bruce M.; Hynek, Brian M.; Pelkey, Shannon M.; Mellon, Michael T.; Martínez-Alonso, Sara; Putzig, Nathaniel E.; Murphy, Nate; Christensen, Philip R.

    2006-08-01

    We analyzed remote-sensing observations of the Isidis Basin, Gusev Crater, and Meridiani Planum landing sites for Beagle II, MER-A Spirit, and MER-B Opportunity spacecraft, respectively. We emphasized the thermophysical properties using daytime and nighttime radiance measurements from the Mars Global Surveyor (MGS) Thermal Emission Spectrometer and Mars Odyssey Thermal Emission Imaging System (THEMIS) and thermal inertias derived from nighttime data sets. THEMIS visible images, MGS Mars Orbiter Camera (MOC) narrow-angle images, and MGS Mars Orbiter Laser Altimeter (MOLA) data are incorporated as well. Additionally, the remote-sensing data were compared with ground-truth at the MER sites. The Isidis Basin surface layer has been shaped by aeolian processes and erosion by slope winds coming off of the southern highlands and funneling through notches between massifs. In the Gusev region, surface materials of contrasting thermophysical properties have been interpreted as rocks or bedrock, duricrust, and dust deposits; these are consistent with a complex geological history dominated by volcanic and aeolian processes. At Meridiani Planum the many layers having different thermophysical and erosional properties suggest periodic deposition of differing sedimentological facies possibly related to clast size, grain orientation and packing, or mineralogy.

  18. High-Resolution Topomapping of Mars: Life After MER Site Selection

    NASA Technical Reports Server (NTRS)

    Kirk, R. L.; Howington-Kraus, E.; Hare, T. M.; Soricone, R.; Ross, K.; Weller, L.; Rosiek, M.; Redding, B.; Galuszka, D.; Haldemann, A. F. C.

    2004-01-01

    In this abstract we describe our ongoing use of high-resolution images from the Mars Global Surveyor Mars Orbiter Camera Narrow-Angle subsystem (MGS MOC-NA) to derive quantitative topographic and slope data for the martian surface at 3 - 10-m resolution. Our efforts over the past several years focused on assessment of candidate landing sites for the Mars Exploration Rovers (MER) and culminated in the selection of sites in Gusev crater and Meridiani Planum as safe as well as scientifically compelling. As of this writing, MER-A (Spirit) has landed safely in Gusev and we are performing a limited amount of additional mapping near the landing point to support localization of the lander and rover operations planning. The primary focus of our work, however, has been extending our techniques to sample a variety of geologic terrains planetwide to support both a variety of geoscientific studies and planning and data analysis for missions such as Mars Express, Mars Reconnaissance Orbiter, and Phoenix.

  19. Mild encephalopathy/encephalitis with a reversible splenial lesion (MERS): A report of five neonatal cases.

    PubMed

    Sun, Dan; Chen, Wen-Hong; Baralc, Suraj; Wang, Juan; Liu, Zhi-Sheng; Xia, Yuan-Peng; Chen, Lei

    2017-06-01

    Mild encephalopathy/encephalitis with a reversible splenial (MERS) lesion is a clinic-radiological entity. The clinical features of MERS in neonates are still not systemically reported. This paper presents five cases of MERS, and the up-to-date reviews of previously reported cases were collected and analyzed in the literature. Here we describe five cases clinically diagnosed with MERS. All of them were neonates and the average age was about 4 days. They were admitted for the common neurological symptoms such as hyperspasmia, poor reactivity and delirium. Auxiliary examinations during hospitalization also exhibited features in common. In this report, we reached following conclusions. Firstly, magnetic resonance imaging revealed solitary or comprehensive lesions in the splenium of corpus callosum, some of them extending to almost the whole corpus callosum. The lesions showed low intensity signal on T1-weighted images, homogeneously hyperintense signal on T2-weighted images, fluid-attenuated inversion recovery and diffusion-weighted images, and exhibited an obvious reduced diffusion on apparent diffusion coefficient map. Moreover, the lesions in the magnetic resonance imaging disappeared very quickly even prior to the clinical recovery. Secondly, all the cases depicted here suffered electrolyte disturbances especially hyponatremia which could be easily corrected. Lastly, all of the cases recovered quickly over one week to one month and majority of them exhibited signs of infections and normal electroencephalography.

  20. Statistical properties and time-frequency analysis of temperature, salinity and turbidity measured by the MAREL Carnot station in the coastal waters of Boulogne-sur-Mer (France)

    NASA Astrophysics Data System (ADS)

    Kbaier Ben Ismail, Dhouha; Lazure, Pascal; Puillat, Ingrid

    2016-10-01

    In marine sciences, many fields display high variability over a large range of spatial and temporal scales, from seconds to thousands of years. The longer recorded time series, with an increasing sampling frequency, in this field are often nonlinear, nonstationary, multiscale and noisy. Their analysis faces new challenges and thus requires the implementation of adequate and specific methods. The objective of this paper is to highlight time series analysis methods already applied in econometrics, signal processing, health, etc. to the environmental marine domain, assess advantages and inconvenients and compare classical techniques with more recent ones. Temperature, turbidity and salinity are important quantities for ecosystem studies. The authors here consider the fluctuations of sea level, salinity, turbidity and temperature recorded from the MAREL Carnot system of Boulogne-sur-Mer (France), which is a moored buoy equipped with physico-chemical measuring devices, working in continuous and autonomous conditions. In order to perform adequate statistical and spectral analyses, it is necessary to know the nature of the considered time series. For this purpose, the stationarity of the series and the occurrence of unit-root are addressed with the Augmented-Dickey Fuller tests. As an example, the harmonic analysis is not relevant for temperature, turbidity and salinity due to the nonstationary condition, except for the nearly stationary sea level datasets. In order to consider the dominant frequencies associated to the dynamics, the large number of data provided by the sensors should enable the estimation of Fourier spectral analysis. Different power spectra show a complex variability and reveal an influence of environmental factors such as tides. However, the previous classical spectral analysis, namely the Blackman-Tukey method, requires not only linear and stationary data but also evenly-spaced data. Interpolating the time series introduces numerous artifacts to the

  1. Critical Spacecraft-to-Earth Communications for Mars Exploration Rover (MER) entry, descent and landing

    NASA Technical Reports Server (NTRS)

    Hurd, William J.; Estabrook, Polly; Racho, Caroline S.; Satorius, Edgar H.

    2002-01-01

    For planetary lander missions, the most challenging phase of the spacecraft to ground communications is during the entry, descent, and landing (EDL). As each 2003 Mars Exploration Rover (MER) enters the Martian atmosphere, it slows dramatically. The extreme acceleration and jerk cause extreme Doppler dynamics on the X-band signal received on Earth. When the vehicle slows sufficiently, the parachute is deployed, causing almost a step in deceleration. After parachute deployment, the lander is lowered beneath the parachute on a bridle. The swinging motion of the lander imparts high Doppler dynamics on the signal and causes the received signal strength to vary widely, due to changing antenna pointing angles. All this time, the vehicle transmits important health and status information that is especially critical if the landing is not successful. Even using the largest Deep Space Network antennas, the weak signal and high dynamics render it impossible to conduct reliable phase coherent communications. Therefore, a specialized form of frequency-shift-keying will be used. This paper describes the EDL scenario, the signal conditions, the methods used to detect and frequency-track the carrier and to detect the data modulation, and the resulting performance estimates.

  2. Meter-scale slopes of candidate MER landing sites from point photoclinometry

    USGS Publications Warehouse

    Beyer, R.A.; McEwen, A.S.; Kirk, R.L.

    2003-01-01

    Photoclinometry was used to analyze the small-scale roughness of areas that fall within the proposed Mars Exploration Rover (MER) 2003 landing ellipses. The landing ellipses presented in this study were those in Athabasca Valles, Elysium Planitia, Eos Chasma, Gusev Crater, Isidis Planitia, Melas Chasma, and Meridiani Planum. We were able to constrain surface slopes on length scales comparable to the image resolution (1.5 to 12 m/pixel). The MER 2003 mission has various engineering constraints that each candidate landing ellipse must satisfy. These constraints indicate that the statistical slope values at 5 m baselines are an important criterion. We used our technique to constrain maximum surface slopes across large swaths of each image, and built up slope statistics for the images in each landing ellipse. We are confident that all MER 2003 landing site ellipses in this study, with the exception of the Melas Chasma ellipse, are within the small-scale roughness constraints. Our results have provided input into the landing hazard assessment process. In addition to evaluating the safety of the landing sites, our mapping of small-scale roughnesses can also be used to better define and map morphologic units. The morphology of a surface is characterized by the slope distribution and magnitude of slopes. In looking at how slopes are distributed, we can better define landforms and determine the boundaries of morphologic units. Copyright 2003 by the American Geophysical Union.

  3. Using High Frequency Focused Water-Coupled Ultrasound for 3-D Surface Depression Profiling

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

    1999-01-01

    Surface topography is an important variable in the performance of many industrial components and is normally measured with diamond-tip profilometry over a small area or using optical scattering methods for larger area measurement. A prior study was performed demonstrating that focused air-coupled ultrasound at 1 MHz was capable of profiling surfaces with 25 micron depth resolution and 400 micron lateral resolution over a 1.4 mm depth range. In this article, the question of whether higher-frequency focused water-coupled ultrasound can improve on these specifications is addressed. 10 and 25 MHz focused ultrasonic transducers were employed in the water-coupled mode. Time-of-flight images of the sample surface were acquired and converted to depth / surface profile images using the simple relation (d = V*t/2) between distance (d), time-of-flight (t), and the velocity of sound in water (V). Results are compared for the two frequencies used and with those from the 1 MHz air-coupled configuration.

  4. Geology of the MER 2003 "Elysium" candidate landing site in southeastern Utopia Planitia, Mars

    USGS Publications Warehouse

    Tanaka, K.L.; Carr, M.H.; Skinner, J.A.; Gilmore, M.S.; Hare, T.M.

    2003-01-01

    The NASA Mars Exploration Rover (MER) Project has been considering a landing-site ellipse designated EP78B2 in southeastern Utopia Planitia, southwest of Elysium Mons. The site appears to be relatively safe for a MER landing site because of its predicted low wind velocities in mesoscale atmospheric circulation models and its low surface roughness at various scales as indicated by topographic and imaging data sets. Previously, the site's surface rocks have been interpreted to be marine sediments or lava flows. In addition, we suggest that Late Noachian to Early Hesperian collapse and mass wasting of Noachian highland rocks contributed to the deposition of detritus in the area of the ellipse. Furthermore, we document partial Late Hesperian to Early Amazonian resurfacing of the ellipse by flows and vents that may be of mud or silicate volcanic origin. A rover investigation of the Utopia landing site using the MER Athena instrument package might address some fundamental aspects of Martian geologic evolution, such as climate change, hydrologic evolution, and magmatic and tectonic history. Copyright 2003 by the American Geophysical Union.

  5. Vaccines for emerging infectious diseases: Lessons from MERS coronavirus and Zika virus

    PubMed Central

    Maslow, Joel N.

    2017-01-01

    ABSTRACT The past decade and a half has been characterized by numerous emerging infectious diseases. With each new threat, there has been a call for rapid vaccine development. Pathogens such as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and the Zika virus represent either new viral entities or viruses emergent in new geographic locales and characterized by novel complications. Both serve as paradigms for the global spread that can accompany new pathogens. In this paper, we review the epidemiology and pathogenesis of MERS-CoV and Zika virus with respect to vaccine development. The challenges in vaccine development and the approach to clinical trial design to test vaccine candidates for disease entities with a changing epidemiology are discussed. PMID:28846484

  6. Characterization of Martian Rock Shape for MER Airbag Drop Tests

    NASA Astrophysics Data System (ADS)

    Dimaggio, E. N.; Schroeder, R.; Castle, N.; Golombek, M.

    2002-12-01

    Rock distributions for the final platforms used in airbag drop tests are currently being designed for the Mars Exploration Rovers (MER) scheduled to launch in 2003. Like Mars Pathfinder (MPF), launched in 1996, MER will use a series of airbags to cushion its landing on the surface of Mars. Previous MER airbag drop tests have shown that sharp, angular (triangular) rocks >20 cm high may be hazardous. To aid in defining the rock distributions for the final airbag tests, images from the Viking Landers 1 and 2 and MPF were used to identify rocks that are >20 cm high, and characterize them as triangular, square or round. Approximately 33% of all rocks analyzed are triangular. Of the rocks analyzed that are ~20-60 cm high, ~14% are triangular. Most of these triangular rocks are small, ~20-30 cm high. Rock distributions of previous airbag platforms were similarly classified and show a greater percentage of triangular and square rocks that are ~20-60 cm high than at the landing sites. The burial of a rock (perched, partially buried or buried) was also considered because perched rocks may pose less of a threat to the airbags than those buried because perched rocks can be dislodged and roll during impact. Approximately 19% of all rocks analyzed, and ~19% of rocks that are ~20-60 cm high, are triangular and partially buried or buried. These data suggest that the platform rock distributions appropriately represented the risks to the airbags associated with triangular rocks. A similar percentage of >20 cm high triangular rocks will be added to the drop test platforms to represent landing site rock distributions.

  7. Autonomous Navigation Results from the Mars Exploration Rover (MER) Mission

    NASA Technical Reports Server (NTRS)

    Maimone, Mark; Johnson, Andrew; Cheng, Yang; Willson, Reg; Matthies, Larry H.

    2004-01-01

    In January, 2004, the Mars Exploration Rover (MER) mission landed two rovers, Spirit and Opportunity, on the surface of Mars. Several autonomous navigation capabilities were employed in space for the first time in this mission. ]n the Entry, Descent, and Landing (EDL) phase, both landers used a vision system called the, Descent Image Motion Estimation System (DIMES) to estimate horizontal velocity during the last 2000 meters (m) of descent, by tracking features on the ground with a downlooking camera, in order to control retro-rocket firing to reduce horizontal velocity before impact. During surface operations, the rovers navigate autonomously using stereo vision for local terrain mapping and a local, reactive planning algorithm called Grid-based Estimation of Surface Traversability Applied to Local Terrain (GESTALT) for obstacle avoidance. ]n areas of high slip, stereo vision-based visual odometry has been used to estimate rover motion, As of mid-June, Spirit had traversed 3405 m, of which 1253 m were done autonomously; Opportunity had traversed 1264 m, of which 224 m were autonomous. These results have contributed substantially to the success of the mission and paved the way for increased levels of autonomy in future missions.

  8. Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

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

    Borucki, Monica K.; Lao, Victoria; Hwang, Mona

    Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater thanmore » 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Lastly, many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.« less

  9. Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

    DOE PAGES

    Borucki, Monica K.; Lao, Victoria; Hwang, Mona; ...

    2016-01-20

    Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater thanmore » 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Lastly, many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.« less

  10. KENNEDY SPACE CENTER, FLA. - The fairing for the Mars Exploration Rover 2 (MER-2/MER-A) arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - The fairing for the Mars Exploration Rover 2 (MER-2/MER-A) arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  11. KENNEDY SPACE CENTER, FLA. - An overhead crane is in place to lift the Mars Exploration Rover 2 (MER-2) entry vehicle to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - An overhead crane is in place to lift the Mars Exploration Rover 2 (MER-2) entry vehicle to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

  12. Exploring Gusev with MER A

    NASA Astrophysics Data System (ADS)

    Grin, E. A.; Cabrol, N. A.; Des Marais, D.; Farmer, J.; Greeley, R.; Carr, M.; Kramer, M.; Moore, J.; Sutter, B.; Fike, D.; Kuzmin, R.; Grant, F.; Barlow, N.; Newsom, H.; Tanaka, K.; Urquhart, M.; de Goursac, O.; Grisby, B.

    2002-12-01

    Gusev will be an outstanding candidate to achieve the 2003 MER mission goals. The crater has collected sediments from a diversity of parent rocks in the vast Maadim Vallis watershed over a period of three billion years. Because of the interaction between Gusev and Maadim, it has been proposed that a significant volume of the sedimentary material in the crater is of aqueous origin. Mars Odyssey has shown that the hydrogen abundance in the Gusev region is higher than average at corresponding latitudes. This observation could be consistent with a past long lived aqueous activity. The presence of aqueous material is central to the MER mission because it can provide clues about the past water history, climate changes, and the potential habitability of Mars. However, while Gusev is recognized as a primary site because of its past fluvio lacustrine activity, the geological diversity and history of its immediate surroundings makes it exceptional and provides the foundation for an exciting exploration leading to key discoveries. In addition to aqueous, many other processes can have contributed to the material in the crater basin: volcanic, Apollinaris patera is only 200 km away, aeolian, glacial, and global airfall processes. How to identify the signature of each process? What was their succession in time? Do we see the evolution from perennial to more episodic lakes? Do we see interaction between volcanic, glacial, aeolian and lacustrine processes? What was the recurrence of dry episodes? What type of measurements can provide a definitive answer for each of these questions in the 600 m traverse range that the rover will accomplish? What diversity can we also expect in this range? Finally, the uniqueness and potential of Gusev does not reside only in this exceptional diversity. As there is evidence for long lived lake episodes, Gusev also offers the unique possibility to study for the first time the results of the in situ formation of aqueous sediments and minerals in their

  13. KENNEDY SPACE CENTER, FLA. - Workers on the launch tower of Complex 17-A, Cape Canaveral Air Force Station, stand by while a solid rocket booster (SRB) is lifted to vertical. It is one of nine that will help launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-15

    KENNEDY SPACE CENTER, FLA. - Workers on the launch tower of Complex 17-A, Cape Canaveral Air Force Station, stand by while a solid rocket booster (SRB) is lifted to vertical. It is one of nine that will help launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  14. Follow-up chest radiographic findings in patients with MERS-CoV after recovery

    PubMed Central

    Das, Karuna M; Lee, Edward Y; Singh, Rajvir; Enani, Mushira A; Al Dossari, Khalid; Van Gorkom, Klaus; Larsson, Sven G; Langer, Ruth D

    2017-01-01

    Purpose: To evaluate the follow-up chest radiographic findings in patients with Middle East respiratory syndrome coronavirus (MERS-CoV) who were discharged from the hospital following improved clinical symptoms. Materials and Methods: Thirty-six consecutive patients (9 men, 27 women; age range 21–73 years, mean ± SD 42.5 ± 14.5 years) with confirmed MERS-CoV underwent follow-up chest radiographs after recovery from MERS-CoV. The 36 chest radiographs were obtained at 32 to 230 days with a median follow-up of 43 days. The reviewers systemically evaluated the follow-up chest radiographs from 36 patients for lung parenchymal, airway, pleural, hilar and mediastinal abnormalities. Lung parenchyma and airways were assessed for consolidation, ground-glass opacity (GGO), nodular opacity and reticular opacity (i.e., fibrosis). Follow-up chest radiographs were also evaluated for pleural thickening, pleural effusion, pneumothorax and lymphadenopathy. Patients were categorized into two groups: group 1 (no evidence of lung fibrosis) and group 2 (chest radiographic evidence of lung fibrosis) for comparative analysis. Patient demographics, length of ventilations days, number of intensive care unit (ICU) admission days, chest radiographic score, chest radiographic deterioration pattern (Types 1-4) and peak lactate dehydrogenase level were compared between the two groups using the student t-test, Mann-Whitney U test and Fisher's exact test. Results: Follow-up chest radiographs were normal in 23 out of 36 (64%) patients. Among the patients with abnormal chest radiographs (13/36, 36%), the following were found: lung fibrosis in 12 (33%) patients GGO in 2 (5.5%) patients, and pleural thickening in 2 (5.5%) patients. Patients with lung fibrosis had significantly greater number of ICU admission days (19 ± 8.7 days; P value = 0.001), older age (50.6 ± 12.6 years; P value = 0.02), higher chest radiographic scores [10 (0-15.3); P value = 0.04] and higher peak lactate dehydrogenase

  15. Fac and mer isomers of Ru(II) tris(pyrazolyl-pyridine) complexes as models for the vertices of coordination cages: structural characterisation and hydrogen-bonding characteristics.

    PubMed

    Metherell, Alexander J; Cullen, William; Stephenson, Andrew; Hunter, Christopher A; Ward, Michael D

    2014-01-07

    We have prepared a series of mononuclear fac and mer isomers of Ru(II) complexes containing chelating pyrazolyl-pyridine ligands, to examine their differing ability to act as hydrogen-bond donors in MeCN. This was prompted by our earlier observation that octanuclear cube-like coordination cages that contain these types of metal vertex can bind guests such as isoquinoline-N-oxide (K = 2100 M(-1) in MeCN), with a significant contribution to binding being a hydrogen-bonding interaction between the electron-rich atom of the guest and a hydrogen-bond donor site on the internal surface of the cage formed by a convergent set of CH2 protons close to a 2+ metal centre. Starting with [Ru(L(H))3](2+) [L(H) = 3-(2-pyridyl)-1H-pyrazole] the geometric isomers were separated by virtue of the fact that the fac isomer forms a Cu(I) adduct which the mer isomer does not. Alkylation of the pyrazolyl NH group with methyl iodide or benzyl bromide afforded [Ru(L(Me))3](2+) and [Ru(L(bz))3](2+) respectively, each as their fac and mer isomers; all were structurally characterised. In the fac isomers the convergent group of pendant -CH2R or -CH3 protons defines a hydrogen-bond donor pocket; in the mer isomer these protons do not converge and any hydrogen-bonding involving these protons is expected to be weaker. For both [Ru(L(Me))3](2+) and [Ru(L(bz))3](2+), NMR titrations with isoquinoline-N-oxide in MeCN revealed weak 1 : 1 binding (K ≈ 1 M(-1)) between the guest and the fac isomer of the complex that was absent with the mer isomer, confirming a difference in the hydrogen-bond donor capabilities of these complexes associated with their differing geometries. The weak binding compared to the cage however occurs because of competition from the anions, which are free to form ion-pairs with the mononuclear complex cations in a way that does not happen in the cage complexes. We conclude that (i) the presence of fac tris-chelate sites in the cage to act as hydrogen-bond donors, and (ii

  16. Association of Spicy Food Consumption Frequency with Serum Lipid Profiles in Older People in China.

    PubMed

    Yu, K; Xue, Y; He, T; Guan, L; Zhao, A; Zhang, Y

    2018-01-01

    There has been recent interest in spicy foods and their bioactive ingredients for cardiovascular health. This study aims to explore relationship between spicy food consumption frequency and serum lipid profiles in a cross-sectional sample of older Chinese from China Health and Nutrition Survey (CHNS). A total of 1549 participant aged 65 years and above from CHNS 2009 were included in the analysis. Information on spicy food consumption was obtained using a questionnaire survey and 24h dietary recalls over three consecutive days combined with weighted food inventory. Fasting blood samples were analyzed for total cholesterol (TC), triglycerides, high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), apolipoprotein A1 (apoA1) and apolipoprotein B (apoB). Correlations between spicy food consumption frequency and serum lipid profiles were evaluated by multivariate linear regression models. The result shows a significant positive association between frequency of spicy food consumption estimated by the frequency question and daily spicy food intake calculated from 24h recall. After adjustment for potential lifestyle and dietary confounding factors, men with higher frequency of spicy food consumption showed higher apoA1 level, and lower ratio of LDL-C/apoB (p for trend <0.05). For female, frequency of spicy food consumption was significantly associated with TC, LDL-C, apoB, LDL-C/HDL-C, and apoB/apoA1 in an inverse manner, and positively correlated with apoA1 level (p for trend <0.05). In this study with Chinese aged 65y and above, increased spicy food consumption frequency may favorably associated with some risk factors for cardiovascular diseases.

  17. Geology of a Proposed MER Landing Site in Western Melas Chasma

    NASA Technical Reports Server (NTRS)

    Weitz, C. M.; Parker, T. J.; Anderson, F. S.; Grant, J. A.

    2002-01-01

    A proposed landing site for the Mars Exploration Rover (MER) has been identified in western Melas Chasma. The landing ellipse contains a blocky, bright deposit which we propose formed as a landslide, perhaps beneath a former lake. Additional information is contained in the original extended abstract.

  18. Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman.

    PubMed

    Al-Abaidani, I S; Al-Maani, A S; Al-Kindi, H S; Al-Jardani, A K; Abdel-Hady, D M; Zayed, B E; Al-Harthy, K S; Al-Shaqsi, K H; Al-Abri, S S

    2014-12-01

    Several countries in the Middle East and around 22 countries worldwide have reported cases of human infection with the Middle East respiratory syndrome coronavirus (MERS-CoV). The exceptionally high fatality rate resulting from MERS-CoV infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. Copyright © 2014. Published by Elsevier Ltd.

  19. Enhanced inflammation in New Zealand white rabbits when MERS-CoV reinfection occurs in the absence of neutralizing antibody

    PubMed Central

    Houser, Katherine V.; Gretebeck, Lisa; Vogel, Leatrice; Sutton, Troy; Orandle, Marlene; Moore, Ian N.

    2017-01-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that was first detected in humans in 2012 as a cause of severe acute respiratory disease. As of July 28, 2017, there have been 2,040 confirmed cases with 712 reported deaths. While many infections have been fatal, there have also been a large number of mild or asymptomatic cases discovered through monitoring and contact tracing. New Zealand white rabbits are a possible model for asymptomatic infection with MERS-CoV. In order to discover more about non-lethal infections and to learn whether a single infection with MERS-CoV would protect against reinfection, we inoculated rabbits with MERS-CoV and monitored the antibody and inflammatory response. Following intranasal infection, rabbits developed a transient dose-dependent pulmonary infection with moderately high levels of viral RNA, viral antigen, and perivascular inflammation in multiple lung lobes that was not associated with clinical signs. The rabbits developed antibodies against viral proteins that lacked neutralizing activity and the animals were not protected from reinfection. In fact, reinfection resulted in enhanced pulmonary inflammation, without an associated increase in viral RNA titers. Interestingly, passive transfer of serum from previously infected rabbits to naïve rabbits was associated with enhanced inflammation upon infection. We further found this inflammation was accompanied by increased recruitment of complement proteins compared to primary infection. However, reinfection elicited neutralizing antibodies that protected rabbits from subsequent viral challenge. Our data from the rabbit model suggests that people exposed to MERS-CoV who fail to develop a neutralizing antibody response, or persons whose neutralizing antibody titers have waned, may be at risk for severe lung disease on re-exposure to MERS-CoV. PMID:28817732

  20. A camel-derived MERS-CoV with a variant spike protein cleavage site and distinct fusion activation properties

    PubMed Central

    Millet, Jean Kaoru; Goldstein, Monty E; Labitt, Rachael N; Hsu, Hung-Lun; Daniel, Susan; Whittaker, Gary R

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) continues to circulate in both humans and camels, and the origin and evolution of the virus remain unclear. Here we characterize the spike protein of a camel-derived MERS-CoV (NRCE-HKU205) identified in 2013, early in the MERS outbreak. NRCE-HKU205 spike protein has a variant cleavage motif with regard to the S2′ fusion activation site—notably, a novel substitution of isoleucine for the otherwise invariant serine at the critical P1′ cleavage site position. The substitutions resulted in a loss of furin-mediated cleavage, as shown by fluorogenic peptide cleavage and western blot assays. Cell–cell fusion and pseudotyped virus infectivity assays demonstrated that the S2′ substitutions decreased spike-mediated fusion and viral entry. However, cathepsin and trypsin-like protease activation were retained, albeit with much reduced efficiency compared with the prototypical EMC/2012 human strain. We show that NRCE-HKU205 has more limited fusion activation properties possibly resulting in more restricted viral tropism and may represent an intermediate in the complex pattern of MERS-CoV ecology and evolution. PMID:27999426

  1. The Synechocystis PCC6803 MerA-like enzyme operates in the reduction of both mercury and uranium under the control of the glutaredoxin 1 enzyme.

    PubMed

    Marteyn, Benoit; Sakr, Samer; Farci, Sandrine; Bedhomme, Mariette; Chardonnet, Solenne; Decottignies, Paulette; Lemaire, Stéphane D; Cassier-Chauvat, Corinne; Chauvat, Franck

    2013-09-01

    In a continuing effort to analyze the selectivity/redundancy of the three glutaredoxin (Grx) enzymes of the model cyanobacterium Synechocystis PCC6803, we have characterized an enzyme system that plays a crucial role in protection against two toxic metal pollutants, mercury and uranium. The present data show that Grx1 (Slr1562 in CyanoBase) selectively interacts with the presumptive mercuric reductase protein (Slr1849). This MerA enzyme plays a crucial role in cell defense against both mercuric and uranyl ions, in catalyzing their NADPH-driven reduction. Like MerA, Grx1 operates in cell protection against both mercury and uranium. The Grx1-MerA interaction requires cysteine 86 (C86) of Grx1 and C78 of MerA, which is critical for its reductase activity. MerA can be inhibited by glutathionylation and subsequently reactivated by Grx1, likely through deglutathionylation. The two Grx1 residues C31, which belongs to the redox active site (CX(2)C), and C86, which operates in MerA interactions, are both required for reactivation of MerA. These novel findings emphasize the role of glutaredoxins in tolerance to metal stress as well as the evolutionary conservation of the glutathionylation process, so far described mostly for eukaryotes.

  2. The Synechocystis PCC6803 MerA-Like Enzyme Operates in the Reduction of Both Mercury and Uranium under the Control of the Glutaredoxin 1 Enzyme

    PubMed Central

    Marteyn, Benoit; Sakr, Samer; Farci, Sandrine; Bedhomme, Mariette; Chardonnet, Solenne; Decottignies, Paulette; Lemaire, Stéphane D.; Cassier-Chauvat, Corinne

    2013-01-01

    In a continuing effort to analyze the selectivity/redundancy of the three glutaredoxin (Grx) enzymes of the model cyanobacterium Synechocystis PCC6803, we have characterized an enzyme system that plays a crucial role in protection against two toxic metal pollutants, mercury and uranium. The present data show that Grx1 (Slr1562 in CyanoBase) selectively interacts with the presumptive mercuric reductase protein (Slr1849). This MerA enzyme plays a crucial role in cell defense against both mercuric and uranyl ions, in catalyzing their NADPH-driven reduction. Like MerA, Grx1 operates in cell protection against both mercury and uranium. The Grx1-MerA interaction requires cysteine 86 (C86) of Grx1 and C78 of MerA, which is critical for its reductase activity. MerA can be inhibited by glutathionylation and subsequently reactivated by Grx1, likely through deglutathionylation. The two Grx1 residues C31, which belongs to the redox active site (CX2C), and C86, which operates in MerA interactions, are both required for reactivation of MerA. These novel findings emphasize the role of glutaredoxins in tolerance to metal stress as well as the evolutionary conservation of the glutathionylation process, so far described mostly for eukaryotes. PMID:23852862

  3. Association between Australian Hajj Pilgrims' awareness of MERS-CoV, and their compliance with preventive measures and exposure to camels.

    PubMed

    Alqahtani, Amani S; Wiley, Kerrie E; Mushta, Sami M; Yamazaki, Kaoruko; BinDhim, Nasser F; Heywood, Anita E; Booy, Robert; Rashid, Harunor

    2016-05-01

    Through a prospective cohort study the relationship between travellers' awareness of MERS-CoV, and compliance with preventive measures and exposure to camels was evaluated among Australian Hajj pilgrims who attended Hajj in 2015. Only 28% of Australian Hajj pilgrims were aware of MERS-CoV in Saudi Arabia. Those who were aware of MERS-CoV were more likely to receive recommended vaccines [odds ratio (OR) 3.1, 95% confidence interval (CI): 1.5-5.9, P < 0.01], but there was no significant difference in avoiding camels or their raw products during Hajj between those who were aware of MERS-CoV and those who were not (OR 1.2, 95% CI: 0.3-5.2, P = 0.7). Hajj pilgrims' awareness is reflected in some of their practices but not in all. © International Society of Travel Medicine, 2016. All rights reserved. Published by Oxford University Press. For permissions, please e-mail: journals.permissions@oup.com.

  4. From Prime to Extended Mission: Evolution of the MER Tactical Uplink Process

    NASA Technical Reports Server (NTRS)

    Mishkin, Andrew H.; Laubach, Sharon

    2006-01-01

    To support a 90-day surface mission for two robotic rovers, the Mars Exploration Rover mission designed and implemented an intensive tactical operations process, enabling daily commanding of each rover. Using a combination of new processes, custom software tools, a Mars-time staffing schedule, and seven-day-a-week operations, the MER team was able to compress the traditional weeks-long command-turnaround for a deep space robotic mission to about 18 hours. However, the pace of this process was never intended to be continued indefinitely. Even before the end of the three-month prime mission, MER operations began evolving towards greater sustainability. A combination of continued software tool development, increasing team experience, and availability of reusable sequences first reduced the mean process duration to approximately 11 hours. The number of workshifts required to perform the process dropped, and the team returned to a modified 'Earth-time' schedule. Additional process and tool adaptation eventually provided the option of planning multiple Martian days of activity within a single workshift, making 5-day-a-week operations possible. The vast majority of the science team returned to their home institutions, continuing to participate fully in the tactical operations process remotely. MER has continued to operate for over two Earth-years as many of its key personnel have moved on to other projects, the operations team and budget have shrunk, and the rovers have begun to exhibit symptoms of aging.

  5. Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion

    PubMed Central

    Duroc, Yann; Kumar, Rajeev; Ranjha, Lepakshi; Adam, Céline; Guérois, Raphaël; Md Muntaz, Khan; Marsolier-Kergoat, Marie-Claude; Dingli, Florent; Laureau, Raphaëlle; Loew, Damarys; Llorente, Bertrand; Charbonnier, Jean-Baptiste; Cejka, Petr; Borde, Valérie

    2017-01-01

    Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations. DOI: http://dx.doi.org/10.7554/eLife.21900.001 PMID:28051769

  6. High frequency longitudinal profiling reveals hydrologic controls on solute sourcing, transport and processing in a karst river

    NASA Astrophysics Data System (ADS)

    Hensley, R. T.; Cohen, M. J.; Spangler, M.; Gooseff, M. N.

    2017-12-01

    The lower Santa Fe River is a large, karst river of north Florida, fed by numerous artesian springs and also containing multiple sink-rise systems. We performed repeated longitudinal profiles collecting very high frequency measurements of multiple stream parameters including temperature, dissolved oxygen, carbon dioxide, pH, dissolved organic matter, nitrate, ammonium, phosphate and turbidity. This high frequency dataset provided a spatially explicit understanding of solute sources and coupled biogeochemical processing rates along the 25 km study reach. We noted marked changes in river profiles as the river transitioned from low to high flow during the onset of the wet season. The role of lateral inflow from springs as the primary solute source was greatly reduced under high flow conditions. Effects of sink-rise systems, which under low flow conditions allow the majority of flow to bypass several kilometer long sections of the main channel, virtually disappeared under high flow conditions. Impeded light transmittance at high flow reduced primary production and by extension assimilatory nutrient uptake. This study demonstrates how high frequency longitudinal profiling can be used to observe how hydrologic conditions can alter groundwater-surface water interactions and modulate the sourcing, transport and biogeochemical processing of stream solutes.

  7. The Merli-Missiroli-Pozzi Two-Slit Electron-Interference Experiment.

    PubMed

    Rosa, Rodolfo

    In 2002 readers of Physics World voted Young's double-slit experiment with single electrons as "the most beautiful experiment in physics" of all time. Pier Giorgio Merli, Gian Franco Missiroli, and Giulio Pozzi carried out this experiment in a collaboration between the Italian Research Council and the University of Bologna almost three decades earlier. I examine their experiment, place it in historical context, and discuss its philosophical implications.

  8. Estimation of basic reproduction number of the Middle East respiratory syndrome coronavirus (MERS-CoV) during the outbreak in South Korea, 2015.

    PubMed

    Chang, Hyuk-Jun

    2017-06-13

    In South Korea, an outbreak of Middle East respiratory syndrome (MERS) occurred in 2015. It was the second largest MERS outbreak. As a result of the outbreak in South Korea, 186 infections were reported, and 36 patients died. At least 16,693 people were isolated with suspicious symptoms. This paper estimates the basic reproduction number of the MERS coronavirus (CoV), using data on the spread of MERS in South Korea. The basic reproduction number of an epidemic is defined as the average number of secondary cases that an infected subject produces over its infectious period in a susceptible and uninfected population. To estimate the basic reproduction number of the MERS-CoV, we employ data from the 2015 South Korea MERS outbreak and the susceptible-infected-removed (SIR) model, a mathematical model that uses a set of ordinary differential equations (ODEs). We fit the model to the epidemic data of the South Korea outbreak minimizing the sum of the squared errors to identify model parameters. Also we derive the basic reproductive number as the terms of the parameters of the SIR model. Then we determine the basic reproduction number of the MERS-CoV in South Korea in 2015 as 8.0977. It is worth comparing with the basic reproductive number of the 2014 Ebola outbreak in West Africa including Guinea, Sierra Leone, and Liberia, which had values of 1.5-2.5. There was no intervention to control the infection in the early phase of the outbreak, thus the data used here provide the best conditions to evaluate the epidemic characteristics of MERS, such as the basic reproduction number. An evaluation of basic reproduction number using epidemic data could be problematic if there are stochastic fluctuations in the early phase of the outbreak, or if the report is not accurate and there is bias in the data. Such problems are not relevant to this study because the data used here were precisely reported and verified by Korea Hospital Association.

  9. A predictive wheel-soil interaction model for planetary rovers validated in testbeds and against MER Mars rover performance data

    NASA Astrophysics Data System (ADS)

    Richter, L.; Ellery, A.; Gao, Y.; Michaud, S.; Schmitz, N.; Weiss, S.

    Successful designs of vehicles intended for operations on planetary objects outside the Earth demand, just as for terrestrial off-the-road vehicles, a careful assessment of the terrain relevant for the vehicle mission and predictions of the mobility performance to allow rational trade-off's to be made for the choice of the locomotion concept and sizing. Principal issues driving the chassis design for rovers are the stress-strain properties of the planetary surface soil, the distribution of rocks in the terrain representing potential obstacles to movement, and the gravity level on the celestial object in question. Thus far, planetary rovers have been successfully designed and operated for missions to the Earth's moon and to the planet Mars, including NASA's Mars Exploration Rovers (MER's) `Spirit' and `Opportunity' being in operation on Mars since their landings in January 2004. Here we report on the development of a wheel-soil interaction model with application to wheel sizes and wheel loads relevant to current and near-term robotic planetary rovers, i.e. wheel diameters being between about 200 and 500 mm and vertical quasistatic wheel loads in operation of roughly 100 to 200 N. Such a model clearly is indispensable for sizings of future rovers to analyse the aspect of rover mobility concerned with motion across soils. This work is presently funded by the European Space Agency (ESA) as part of the `Rover Chassis Evaluation Tools' (RCET) effort which has developed a set of S/W-implemented models for predictive mobility analysis of rovers in terms of movement on soils and across obstacles, coupled with dedicated testbeds to validate the wheel-soil models. In this paper, we outline the details of the wheel-soil modelling performed within the RCET work and present comparisons of predictions of wheel performance (motion resistance, torque vs. slip and drawbar pull vs. slip) for specific test cases with the corresponding measurements performed in the RCET single wheel

  10. The effects of parity, litter size, physiological state, and milking frequency on the metabolic profile of Lacaune dairy ewes.

    PubMed

    González-García, E; Tesniere, A; Camous, S; Bocquier, F; Barillet, F; Hassoun, P

    2015-01-01

    Effects of parity (primiparous, PRIM vs multiparous, MULT) and litter size (singletons, SING vs twins, TWIN) on metabolic profiles from 1 wk before lambing to the end of lactation were studied in 48 Lacaune dairy ewes reared in confinement during most of the year and grazed on improved pastures at the end of lactation (summer). Another group of 48 ewes was incorporated during the milking period (ie, from 1 wk after weaning), to measure the effects of milking frequency (1 vs 2 milkings per day) on intake, milk production and composition, and body energy usage. Thus, in a 2 × 2 × 2 factorial design, ewes (n = 96) were allocated to homogeneous groups according to body weight (BW) and body condition score (BCS) and were monitored from late pregnancy to late lactation as a function of parity (PRIM, n = 48; MULT, n = 48), litter size (LSi) (SING, n = 40; TWIN, n = 56) and daily milking frequency (FREQ; milked once, ONE; n = 48; or twice, TWO; n = 48). Individual BW, BCS, plasma metabolites, and metabolic hormones were measured regularly (ie, 9 consecutive sampling dates). The BW was higher in MULT but no differences because of LSi or FREQ were detected at the intra-parity group level. The BCS was higher in MULT and in ewes with SING throughout the experiment. The latter was related to the demands for body reserves mobilization, as expressed by higher nonesterified fatty acids and β-hydroxybutyrate concentrations in ewes with TWIN from late pregnancy to weaning (35 d postpartum) in both PRIM and MULT ewes. This was consistent with higher insulin in MULT and higher triiodothyronine, leptin and insulin-like growth factor 1 in ewes with SING during this period. Differences in energy balance because of FREQ were evident after interpretation of plasma nonesterified fatty acids, glucose, insulin, and leptin concentration during the milking period. At similar feed intakes, ewes in ONE were in positive balance with regard to TWO. Overall, clear effects of parity, LSi

  11. Frequency and magnetic field mapping of magnetoelastic spin pumping in high overtone bulk acoustic wave resonator

    NASA Astrophysics Data System (ADS)

    Polzikova, N. I.; Alekseev, S. G.; Pyataikin, I. I.; Luzanov, V. A.; Raevskiy, A. O.; Kotov, V. A.

    2018-05-01

    We report on the first observation of microvolt-scale inverse spin Hall effect (ISHE) dc voltage driven by an acoustic spin pumping (ASP) in a bulk acoustic wave (BAW) resonator formed by a Al-ZnO-Al-YIG(1)-GGG-YIG(2)-Pt structure. When 2 mW power is applied to an Al-ZnO-Al transducer, the voltage VISHE ˜ 4 μV in the Pt film is observed as a result of resonant ASP from YIG(2) to Pt in the area ˜ 170 μm. The results of frequency and magnetic field mapping of VISHE(f,H) together with reflectivity of the resonator show an obvious agreement between the positions of the voltage maxima and BAW resonance frequencies fn(H) on the (f, H) plane. At the same time a significant asymmetry of the VISHE(fn(H)) value in reference to the magnetoelastic resonance (MER) line fMER(H) position is revealed, which is explained by asymmetry of the magnetoelastic waves dispersion law.

  12. Overexpression of a bacterial mercury transporter MerT in Arabidopsis enhances mercury tolerance.

    PubMed

    Xu, Sheng; Sun, Bin; Wang, Rong; He, Jia; Xia, Bing; Xue, Yong; Wang, Ren

    2017-08-19

    The phytoremediation by using of green plants in the removal of environmental pollutant is an environment friendly, green technology that is cost effective and energetically inexpensive. By using Agrobacterium-mediated gene transfer, we generated transgenic Arabidopsis plants ectopically expressing mercuric transport protein gene (merT) from Pseudomonas alcaligenes. Compared with wild-type (WT) plants, overexpressing PamerT in Arabidopsis enhanced the tolerance to HgCl 2 . Further results showed that the enhanced total activities or corresponding transcripts of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POD) were observed in transgenic Arabidopsis under HgCl 2 stress. These results were confirmed by the alleviation of oxidative damage, as indicated by the decrease of thiobarbituric acid reactive substances (TBARS) contents and reactive oxygen species (ROS) accumulation. In addition, localization analysis of PaMerT in Arabidopsis protoplast showed that it is likely to be associated with vacuole. In all, PamerT increased mercury (Hg) tolerance in transgenic Arabidopsis, and decreased production of Hg-induced ROS, thereby protecting plants from oxidative damage. The present study has provided further evidence that bacterial MerT plays an important role in the plant tolerance to HgCl 2 and in reducing the production of ROS induced by HgCl 2 . Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Complementary modulation of N2 and CRN by conflict frequency.

    PubMed

    Grützmann, Rosa; Riesel, Anja; Klawohn, Julia; Kathmann, Norbert; Endrass, Tanja

    2014-08-01

    The present study investigated the modulation of the N2 and the correct-related negativity (CRN) by conflict frequency. Conflict costs, as measured by reaction times and error rate, were reduced with increasing conflict frequency, indicating improved conflict resolution. N2 amplitudes in incompatible trials increased with higher conflict frequency, while postresponse CRN amplitudes decreased. In concert with behavioral findings of reduced conflict costs and greater interference suppression, the increase of N2 might reflect enhanced conflict resolution during stimulus processing. The CRN, however, might reflect postresponse implementation of cognitive control, which is reduced when conflict is already adequately resolved during stimulus processing. Furthermore, N2 and CRN in incompatible trials were inversely related on the between- and within-subject level, implying that the two modes of implementing cognitive control are applied complementarily. Copyright © 2014 Society for Psychophysiological Research.

  14. GaN transistors on Si for switching and high-frequency applications

    NASA Astrophysics Data System (ADS)

    Ueda, Tetsuzo; Ishida, Masahiro; Tanaka, Tsuyoshi; Ueda, Daisuke

    2014-10-01

    In this paper, recent advances of GaN transistors on Si for switching and high-frequency applications are reviewed. Novel epitaxial structures including superlattice interlayers grown by metal organic chemical vapor deposition (MOCVD) relieve the strain and eliminate the cracks in the GaN over large-diameter Si substrates up to 8 in. As a new device structure for high-power switching application, Gate Injection Transistors (GITs) with a p-AlGaN gate over an AlGaN/GaN heterostructure successfully achieve normally-off operations maintaining high drain currents and low on-state resistances. Note that the GITs on Si are free from current collapse up to 600 V, by which the drain current would be markedly reduced after the application of high drain voltages. Highly efficient operations of an inverter and DC-DC converters are presented as promising applications of GITs for power switching. The high efficiencies in an inverter, a resonant LLC converter, and a point-of-load (POL) converter demonstrate the superior potential of the GaN transistors on Si. As for high-frequency transistors, AlGaN/GaN heterojuction field-effect transistors (HFETs) on Si designed specifically for microwave and millimeter-wave frequencies demonstrate a sufficiently high output power at these frequencies. Output powers of 203 W at 2.5 GHz and 10.7 W at 26.5 GHz are achieved by the fabricated GaN transistors. These devices for switching and high-frequency applications are very promising as future energy-efficient electronics because of their inherent low fabrication cost and superior device performance.

  15. Predicting the binding preference of transcription factors to individual DNA k-mers.

    PubMed

    Alleyne, Trevis M; Peña-Castillo, Lourdes; Badis, Gwenael; Talukder, Shaheynoor; Berger, Michael F; Gehrke, Andrew R; Philippakis, Anthony A; Bulyk, Martha L; Morris, Quaid D; Hughes, Timothy R

    2009-04-15

    Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members. We employed a new dataset consisting of the relative preferences of mouse homeodomains for all eight-base DNA sequences in order to ask how well we can predict the binding profiles of homeodomains when only their protein sequences are given. We evaluated a panel of standard statistical inference techniques, as well as variations of the protein features considered. Nearest neighbour among functionally important residues emerged among the most effective methods. Our results underscore the complexity of TF-DNA recognition, and suggest a rational approach for future analyses of TF families.

  16. The MerR-like regulator BrlR confers biofilm tolerance by activating multidrug efflux pumps in Pseudomonas aeruginosa biofilms.

    PubMed

    Liao, Julie; Schurr, Michael J; Sauer, Karin

    2013-08-01

    A defining characteristic of biofilms is antibiotic tolerance that can be up to 1,000-fold greater than that of planktonic cells. In Pseudomonas aeruginosa, biofilm tolerance to antimicrobial agents requires the biofilm-specific MerR-type transcriptional regulator BrlR. However, the mechanism by which BrlR mediates biofilm tolerance has not been elucidated. Genome-wide transcriptional profiling indicated that brlR was required for maximal expression of genes associated with antibiotic resistance, in particular those encoding the multidrug efflux pumps MexAB-OprM and MexEF-OprN. Chromatin immunoprecipitation (ChIP) analysis revealed a direct regulation of these genes by BrlR, with DNA binding assays confirming BrlR binding to the promoter regions of the mexAB-oprM and mexEF-oprN operons. Quantitative reverse transcriptase PCR (qRT-PCR) analysis further indicated BrlR to be an activator of mexAB-oprM and mexEF-oprN gene expression. Moreover, immunoblot analysis confirmed increased MexA abundance in cells overexpressing brlR. Inactivation of both efflux pumps rendered biofilms significantly more susceptible to five different classes of antibiotics by affecting MIC but not the recalcitrance of biofilms to killing by bactericidal agents. Overexpression of either efflux pump in a ΔbrlR strain partly restored tolerance of ΔbrlR biofilms to antibiotics. Expression of brlR in mutant biofilms lacking both efflux pumps partly restored antimicrobial tolerance of biofilms to wild-type levels. Our results indicate that BrlR acts as an activator of multidrug efflux pumps to confer tolerance to P. aeruginosa biofilms and to resist the action of antimicrobial agents.

  17. Photochemistry in a 3D metal-organic framework (MOF): monitoring intermediates and reactivity of the fac-to-mer photoisomerization of Re(diimine)(CO)3Cl incorporated in a MOF.

    PubMed

    Easun, Timothy L; Jia, Junhua; Calladine, James A; Blackmore, Danielle L; Stapleton, Christopher S; Vuong, Khuong Q; Champness, Neil R; George, Michael W

    2014-03-03

    The mechanism and intermediates in the UV-light-initiated ligand rearrangement of fac-Re(diimine)(CO)3Cl to form the mer isomer, when incorporated into a 3D metal-organic framework (MOF), have been investigated. The structure hosting the rhenium diimine complex is a 3D network with the formula {Mn(DMF)2[LRe(CO)3Cl]}∞ (ReMn; DMF = N,N-dimethylformamide), where the diimine ligand L, 2,2'-bipyridine-5,5'-dicarboxylate, acts as a strut of the MOF. The incorporation of ReMn into a KBr disk allows spatial distribution of the mer-isomer photoproduct in the disk to be mapped and spectroscopically characterized by both Fourier transform infrared and Raman microscopy. Photoisomerization has been monitored by IR spectroscopy and proceeds via dissociation of a CO to form more than one dicarbonyl intermediate. The dicarbonyl species are stable in the solid state at 200 K. The photodissociated CO ligand appears to be trapped within the crystal lattice and, upon warming above 200 K, readily recombines with the dicarbonyl intermediates to form both the fac-Re(diimine)(CO)3Cl starting material and the mer-Re(diimine)(CO)3Cl photoproduct. Experiments over a range of temperatures (265-285 K) allow estimates of the activation enthalpy of recombination for each process of ca. 16 (±6) kJ mol(-1) (mer formation) and 23 (±4) kJ mol(-1) (fac formation) within the MOF. We have compared the photochemistry of the ReMn MOF with a related alkane-soluble Re(dnb)(CO)3Cl complex (dnb = 4,4'-dinonyl-2,2'-bipyridine). Time-resolved IR measurements clearly show that, in an alkane solution, the photoinduced dicarbonyl species again recombines with CO to both re-form the fac-isomer starting material and form the mer-isomer photoproduct. Density functional theory calculations of the possible dicarbonyl species aids the assignment of the experimental data in that the ν(CO) IR bands of the CO loss intermediate are, as expected, shifted to lower energy when the metal is bound to DMF rather than to an

  18. Novel chimeric virus-like particles vaccine displaying MERS-CoV receptor-binding domain induce specific humoral and cellular immune response in mice.

    PubMed

    Wang, Chong; Zheng, Xuexing; Gai, Weiwei; Wong, Gary; Wang, Hualei; Jin, Hongli; Feng, Na; Zhao, Yongkun; Zhang, Weijiao; Li, Nan; Zhao, Guoxing; Li, Junfu; Yan, Jinghua; Gao, Yuwei; Hu, Guixue; Yang, Songtao; Xia, Xianzhu

    2017-04-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) has continued spreading since its emergence in 2012 with a mortality rate of 35.6%, and is a potential pandemic threat. Prophylactics and therapies are urgently needed to address this public health problem. We report here the efficacy of a vaccine consisting of chimeric virus-like particles (VLP) expressing the receptor binding domain (RBD) of MERS-CoV. In this study, a fusion of the canine parvovirus (CPV) VP2 structural protein gene with the RBD of MERS-CoV can self-assemble into chimeric, spherical VLP (sVLP). sVLP retained certain parvovirus characteristics, such as the ability to agglutinate pig erythrocytes, and structural morphology similar to CPV virions. Immunization with sVLP induced RBD-specific humoral and cellular immune responses in mice. sVLP-specific antisera from these animals were able to prevent pseudotyped MERS-CoV entry into susceptible cells, with neutralizing antibody titers reaching 1: 320. IFN-γ, IL-4 and IL-2 secreting cells induced by the RBD were detected in the splenocytes of vaccinated mice by ELISpot. Furthermore, mice inoculated with sVLP or an adjuvanted sVLP vaccine elicited T-helper 1 (Th1) and T-helper 2 (Th2) cell-mediated immunity. Our study demonstrates that sVLP displaying the RBD of MERS-CoV are promising prophylactic candidates against MERS-CoV in a potential outbreak situation. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. The Effects of the Mars Exploration Rovers (MER) Work Schedule Regime on Locomotor Activity Circadian Rhythms, Sleep and Fatigue

    NASA Technical Reports Server (NTRS)

    DeRoshia, Charles W.; Colletti, Laura C.; Mallis, Melissa M.

    2008-01-01

    This study assessed human adaptation to a Mars sol by evaluating sleep metrics obtained by actigraphy and subjective responses in 22 participants, and circadian rhythmicity in locomotor activity in 9 participants assigned to Mars Exploration Rover (MER) operational work schedules (24.65 hour days) at the Jet Propulsion Laboratory in 2004. During MER operations, increased work shift durations and reduced sleep durations and time in bed were associated with the appearance of pronounced 12-hr (circasemidian) rhythms with reduced activity levels. Sleep duration, workload, and circadian rhythm stability have important implications for adaptability and maintenance of operational performance not only of MER operations personnel but also in space crews exposed to a Mars sol of 24.65 hours during future Mars missions.

  20. Understanding M-ligand bonding and mer-/fac-isomerism in tris(8-hydroxyquinolinate) metallic complexes.

    PubMed

    Lima, Carlos F R A C; Taveira, Ricardo J S; Costa, José C S; Fernandes, Ana M; Melo, André; Silva, Artur M S; Santos, Luís M N B F

    2016-06-28

    Tris(8-hydroxyquinolinate) metallic complexes, Mq3, are one of the most important classes of organic semiconductor materials. Herein, the nature of the chemical bond in Mq3 complexes and its implications on their molecular properties were investigated by a combined experimental and computational approach. Various Mq3 complexes, resulting from the alteration of the metal and substitution of the 8-hydroxyquinoline ligand in different positions, were prepared. The mer-/fac-isomerism in Mq3 was explored by FTIR and NMR spectroscopy, evidencing that, irrespective of the substituent, mer- and fac-are the most stable molecular configurations of Al(iii) and In(iii) complexes, respectively. The relative M-ligand bond dissociation energies were evaluated experimentally by electrospray ionization tandem mass spectrometry (ESI-MS-MS), showing a non-monotonous variation along the group (Al > In > Ga). The results reveal a strong covalent character in M-ligand bonding, which allows for through-ligand electron delocalization, and explain the preferred molecular structures of Mq3 complexes as resulting from the interplay between bonding and steric factors. The mer-isomer reduces intraligand repulsions, being preferred for smaller metals, while the fac-isomer is favoured for larger metals where stronger covalent M-ligand bonds can be formed due to more extensive through-ligand conjugation mediated by metal "d" orbitals.

  1. MAPGEN : mixed initiative planning and scheduling for the Mars '03 MER mission

    NASA Technical Reports Server (NTRS)

    Ai-Chang, Mitchell; Bresina, John; Charest, Len; Jonsson, Ari; Hsu, Jennifer; Kanefsky, Bob; Maldague, Pierre; Morris, Paul; Rajan, Kanna; Yglesias, Jeffrey

    2003-01-01

    The Mars Exploration Rovers Mars '03 mission is one of NASA's most ambitious science missions to date. The rovers will be launched in the summer of 2003 with each rover carrying instruments to conduct remote and in-situ observation to elucidate the planet's past climate, water activity, and habitability. Science is the primary driver of MER and, as a consequence, making best use of the scientific instruments, within the available resources, is a crucial aspect of the mission. To address this critically, the MER project has selected MAPGEN (Mixed-Initiative Activity Plan GENerator) as an activity planning tool. MAPGEN combines two exiting systems, each with a strong heritage: APGEN the Activity Planning tool from the Jet Propulsion Laboratory and the Europs Planning/Scheduling system from NASA Ames Research Center. This paper discusses the issues arising from combining these tools in the context of this mission.

  2. KENNEDY SPACE CENTER, FLA. - At right is the Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, that will launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-15

    KENNEDY SPACE CENTER, FLA. - At right is the Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, that will launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

  3. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2) is installed around the Mars Exploration Rover 2 (MER-2). MER-2 is one of NASA's twin Mars Exploration Rovers designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can't yet go. MER-2 is scheduled to launch no earlier than June 8 as MER-A, with two launch opportunities each day during the launch period that closes on June 19.

    NASA Image and Video Library

    2003-05-31

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2) is installed around the Mars Exploration Rover 2 (MER-2). MER-2 is one of NASA's twin Mars Exploration Rovers designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can't yet go. MER-2 is scheduled to launch no earlier than June 8 as MER-A, with two launch opportunities each day during the launch period that closes on June 19.

  4. Photophysical properties of the series fac- and mer-(1-phenylisoquinolinato-N∧C2')(x)(2-phenylpyridinato-N∧C2')(3-x)iridium(III) (x = 1-3).

    PubMed

    Deaton, Joseph C; Young, Ralph H; Lenhard, Jerome R; Rajeswaran, Manju; Huo, Shouquan

    2010-10-18

    The photophysical properties of tris-cyclometalated iridium(III) complexes have been probed by chemical and geometric variation through the series fac- and mer-Ir(piq)(x)(ppy)(3-x) (x = 1-3; piq = 1-phenylisoquinolinato-N(∧)C(2'), ppy = 2-phenylpyridinato-N(∧)C(2')). The phosphorescent decays were recorded in solution at 295 K and in polymer films from 2 to 295 K. In the heteroleptic complexes, emission occurs based solely on the piq ligand(s), at least by the nanosecond time scale, as its excited states are the lowest energy. Because fac-Ir(piq)(3) and fac-Ir(ppy)(3) possess practically the same oxidation potential, comparison of photophysical properties through the series fac-Ir(piq)(x)(ppy)(3-x) (x = 1-3) revealed the effects of having one, two, or three emissive piq ligands with no confounding effects from differences in electron withdrawing or donating properties between the spectator ppy ligands and the piq ligands. Effects of placement of piq ligands in different coordination geometries were elucidated by comparisons to the mer series.

  5. RBS Depth Profiling Analysis of (Ti, Al)N/MoN and CrN/MoN Multilayers.

    PubMed

    Han, Bin; Wang, Zesong; Devi, Neena; Kondamareddy, K K; Wang, Zhenguo; Li, Na; Zuo, Wenbin; Fu, Dejun; Liu, Chuansheng

    2017-12-01

    (Ti, Al)N/MoN and CrN/MoN multilayered films were synthesized on Si (100) surface by multi-cathodic arc ion plating system with various bilayer periods. The elemental composition and depth profiling of the films were investigated by Rutherford backscattering spectroscopy (RBS) using 2.42 and 1.52 MeV Li 2+ ion beams and different incident angles (0°, 15°, 37°, and 53°). The microstructures of (Ti, Al)N/MoN multilayered films were evaluated by X-ray diffraction. The multilayer periods and thickness of the multilayered films were characterized by scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HR-TEM) and then compared with RBS results.

  6. The clinical and virological features of the first imported case causing MERS-CoV outbreak in South Korea, 2015.

    PubMed

    Lee, Ji Yeon; Kim, You-Jin; Chung, Eun Hee; Kim, Dae-Won; Jeong, Ina; Kim, Yeonjae; Yun, Mi-Ran; Kim, Sung Soon; Kim, Gayeon; Joh, Joon-Sung

    2017-07-14

    In 2015, the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside the Middle East occurred in South Korea. We summarized the epidemiological, clinical, and laboratory findings of the first Korean case of MERS-CoV and analyzed whole-genome sequences of MERS-CoV derived from the patient. A 68-year-old man developed fever and myalgia 7 days after returning to Korea, following a 10-day trip to the Middle East. Before diagnosis, he visited 4 hospitals, potentially resulting in secondary transmission to 28 patients. On admission to the National Medical Center (day 9, post-onset of clinical illness), he presented with drowsiness, hypoxia, and multiple patchy infiltrations on the chest radiograph. He was intubated (day 12) because of progressive acute respiratory distress syndrome (ARDS) and INF-α2a and ribavirin treatment was commenced. The treatment course was prolonged by superimposed ventilator associated pneumonia. MERS-CoV PCR results converted to negative from day 47 and the patient was discharged (day 137), following rehabilitation therapy. The complete genome sequence obtained from a sputum sample (taken on day 11) showed the highest sequence similarity (99.59%) with the virus from an outbreak in Riyadh, Saudi Arabia, in February 2015. The first case of MERS-CoV infection had high transmissibility and was associated with a severe clinical course. The patient made a successful recovery after early treatment with antiviral agents and adequate supportive care. This first case in South Korea became a super-spreader because of improper infection control measures, rather than variations of the virus.

  7. Synthetic range profiling in ground penetrating radar

    NASA Astrophysics Data System (ADS)

    Kaczmarek, Pawel; Lapiński, Marian; Silko, Dariusz

    2009-06-01

    The paper describes stepped frequency continuous wave (SFCW) ground penetrating radar (GPR), where signal's frequency is discretely increased in N linear steps, each separated by a fixed ▵f increment from the previous one. SFCW radar determines distance from phase shift in a reflected signal, by constructing synthetic range profile in spatial time domain using the IFFT. Each quadrature sample is termed a range bin, as it represents the signal from a range window of length cτ/2, where τ is duration of single frequency segment. IFFT of those data samples resolves the range bin in into fine range bins of c/2N▵f width, thus creating the synthetic range profile in a GPR - a time domain approximation of the frequency response of a combination of the medium through which electromagnetic waves propagates (soil) and any targets or dielectric interfaces (water, air, other types of soil) present in the beam width of the radar. In the paper, certain practical measurements done by a monostatic SFCW GPR were presented. Due to complex nature of signal source, E5062A VNA made by Agilent was used as a signal generator, allowing number of frequency steps N to go as high as 1601, with generated frequency ranging from 300kHz to 3 GHz.

  8. KENNEDY SPACE CENTER, FLA. - After arriving at Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off its transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - After arriving at Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off its transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  9. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  10. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) reaches the top of the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) reaches the top of the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  11. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off the transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off the transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  12. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, a crane is in place to lift the fairing for the Mars Exploration Rover 2 (MER-2/MER-A). The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, a crane is in place to lift the fairing for the Mars Exploration Rover 2 (MER-2/MER-A). The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  13. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is moved inside the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5..

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is moved inside the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5..

  14. Depth Profiles of Mg, Si, and Zn Implants in GaN by Trace Element Accelerator Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Ravi Prasad, G. V.; Pelicon, P.; Mitchell, L. J.; McDaniel, F. D.

    2003-08-01

    GaN is one of the most promising electronic materials for applications requiring high-power, high frequencies, or high-temperatures as well as opto-electronics in the blue to ultraviolet spectral region. We have recently measured depth profiles of Mg, Si, and Zn implants in GaN substrates by the TEAMS particle counting method for both matrix and trace elements, using a gas ionization chamber. Trace Element Accelerator Mass Spectrometry (TEAMS) is a combination of Secondary Ion Mass Spectrometry (SIMS) and Accelerator Mass Spectrometry (AMS) to measure trace elements at ppb levels. Negative ions from a SIMS like source are injected into a tandem accelerator. Molecular interferences inherent with the SIMS method are eliminated in the TEAMS method. Negative ion currents are extremely low with GaN as neither gallium nor nitrogen readily forms negative ions making the depth profile measurements more difficult. The energies of the measured ions are in the range of 4-8 MeV. A careful selection of mass/charge ratios of the detected ions combined with energy-loss behavior of the ions in the ionization chamber eliminated molecular interferences.

  15. The TAM-family receptor Mer mediates production of HGF through the RhoA-dependent pathway in response to apoptotic cells.

    PubMed

    Park, Hyun-Jung; Baen, Ji-Yeon; Lee, Ye-Ji; Choi, Youn-Hee; Kang, Jihee Lee

    2012-08-01

    The TAM receptor protein tyrosine kinases Tyro3, Axl, and Mer play important roles in macrophage function. We investigated the roles of the TAM receptors in mediating the induction of hepatocyte growth factor (HGF) during the interaction of macrophages with apoptotic cells. Mer-specific neutralizing antibody, small interfering RNA (siRNA), and a recombinant Mer protein (Mer/Fc) inhibited HGF mRNA and protein expression, as well as activation of RhoA, Akt, and specific mitogen-activated protein (MAP) kinases in response to apoptotic cells. Inhibition of Axl or Tyro3 with specific antibodies, siRNA, or Fc-fusion proteins did not prevent apoptotic cell-induced HGF mRNA and protein expression and did not inhibit activation of the postreceptor signaling molecules RhoA and certain MAP kinases, including extracellular signal-regulated protein kinase and c-Jun NH(2)-terminal kinase. However, Axl- and Tyro3-specific blockers did inhibit the activation of Akt and p38 MAP kinase in response to apoptotic cells. In addition, none of the TAM receptors mediated the effects of apoptotic cells on transforming growth factor-β or epidermal growth factor mRNA expression. However, they were involved in the induction of vascular endothelial growth factor mRNA expression. Our data provide evidence that when macrophages interact with apoptotic cells, only Mer of the TAM-family receptors is responsible for mediating transcriptional HGF production through a RhoA-dependent pathway.

  16. MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

    PubMed Central

    Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.; Gralinski, Lisa E.; Yount, Boyd L.; Graham, Rachel L.; McAnarney, Eileen T.; Douglas, Madeline G.; Scobey, Trevor; Beall, Anne; Dinnon, Kenneth; Kocher, Jacob F.; Hale, Andrew E.; Stratton, Kelly G.; Waters, Katrina M.

    2017-01-01

    ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. PMID:28830941

  17. The Ames MER microscopic imager toolkit

    USGS Publications Warehouse

    Sargent, R.; Deans, Matthew; Kunz, C.; Sims, M.; Herkenhoff, K.

    2005-01-01

    12The Mars Exploration Rovers, Spirit and Opportunity, have spent several successful months on Mars, returning gigabytes of images and spectral data to scientists on Earth. One of the instruments on the MER rovers, the Athena Microscopic Imager (MI), is a fixed focus, megapixel camera providing a ??3mm depth of field and a 31??31mm field of view at a working distance of 63 mm from the lens to the object being imaged. In order to maximize the science return from this instrument, we developed the Ames MI Toolkit and supported its use during the primary mission. The MI Toolkit is a set of programs that operate on collections of MI images, with the goal of making the data more understandable to the scientists on the ground. Because of the limited depth of field of the camera, and the often highly variable topography of the terrain being imaged, MI images of a given rock are often taken as a stack, with the Instrument Deployment Device (IDD) moving along a computed normal vector, pausing every few millimeters for the MI to acquire an image. The MI Toolkit provides image registration and focal section merging, which combine these images to form a single, maximally in-focus image, while compensating for changes in lighting as well as parallax due to the motion of the camera. The MI Toolkit also provides a 3-D reconstruction of the surface being imaged using stereo and can embed 2-D MI images as texture maps into 3-D meshes produced by other imagers on board the rover to provide context. The 2-D images and 3-D meshes output from the Toolkit are easily viewed by scientists using other mission tools, such as Viz or the MI Browser.This paper describes the MI Toolkit in detail, as well as our experience using it with scientists at JPL during the primary MER mission. ?? 2005 IEEE.

  18. The Ames MER Microscopic Imager Toolkit

    NASA Technical Reports Server (NTRS)

    Sargent, Randy; Deans, Matthew; Kunz, Clayton; Sims, Michael; Herkenhoff, Ken

    2005-01-01

    The Mars Exploration Rovers, Spirit and Opportunity, have spent several successful months on Mars, returning gigabytes of images and spectral data to scientists on Earth. One of the instruments on the MER rovers, the Athena Microscopic Imager (MI), is a fixed focus, megapixel camera providing a plus or minus mm depth of field and a 3lx31mm field of view at a working distance of 63 mm from the lens to the object being imaged. In order to maximize the science return from this instrument, we developed the Ames MI Toolkit and supported its use during the primary mission. The MI Toolkit is a set of programs that operate on collections of MI images, with the goal of making the data more understandable to the scientists on the ground. Because of the limited depth of field of the camera, and the often highly variable topography of the terrain being imaged, MI images of a given rock are often taken as a stack, with the Instrument Deployment Device (IDD) moving along a computed normal vector, pausing every few millimeters for the MI to acquire an image. The MI Toolkit provides image registration and focal section merging, which combine these images to form a single, maximally in-focus image, while compensating for changes in lighting as well as parallax due to the motion of the camera. The MI Toolkit also provides a 3-D reconstruction of the surface being imaged using stereo and can embed 2-D MI images as texture maps into 3-D meshes produced by other imagers on board the rover to provide context. The 2-D images and 3-D meshes output from the Toolkit are easily viewed by scientists using other mission tools, such as Viz or the MI Browser. This paper describes the MI Toolkit in detail, as well as our experience using it with scientists at JPL during the primary MER mission.

  19. Generation and characterization of electron bunches with ramped current profiles in a dual-frequency superconducting linear accelerator.

    PubMed

    Piot, P; Behrens, C; Gerth, C; Dohlus, M; Lemery, F; Mihalcea, D; Stoltz, P; Vogt, M

    2012-01-20

    We report on the successful experimental generation of electron bunches with ramped current profiles. The technique relies on impressing nonlinear correlations in the longitudinal phase space using a superconducing radio frequency linear accelerator operating at two frequencies and a current-enhancing dispersive section. The produced ~700-MeV bunches have peak currents of the order of a kilo-Ampère. Data taken for various accelerator settings demonstrate the versatility of the method and, in particular, its ability to produce current profiles that have a quasilinear dependency on the longitudinal (temporal) coordinate. The measured bunch parameters are shown, via numerical simulations, to produce gigavolt-per-meter peak accelerating electric fields with transformer ratios larger than 2 in dielectric-lined waveguides. © 2012 American Physical Society

  20. ARM - Midlatitude Continental Convective Clouds Experiment (MC3E): Multi-Frequency Profilers, Surface Meteorology (williams-surfmet)

    DOE Data Explorer

    Williams, Christopher; Jensen, Mike

    2012-11-06

    This data was collected by the NOAA 449-MHz and 2.8-GHz profilers in support of the Department of Energy (DOE) and NASA sponsored Mid-latitude Continental Convective Cloud Experiment (MC3E). The profiling radars were deployed in Northern Oklahoma at the DOE Atmospheric Radiation Mission (ARM) Southern Great Plans (SGP) Central Facility from 22 April through 6 June 2011. NOAA deployed three instruments: a Parsivel disdrometer, a 2.8-GHz profiler, and a 449-MHz profiler. The parasivel provided surface estimates of the raindrop size distribution and is the reference used to absolutely calibrate the 2.8 GHz profiler. The 2.8-GHz profiler provided unattenuated reflectivity profiles of the precipitation. The 449-MHz profiler provided estimates of the vertical air motion during precipitation from near the surface to just below the freezing level. By using the combination of 2.8-GHz and 449-MHz profiler observations, vertical profiles of raindrop size distributions can be retrieved. The profilers are often reference by their frequency band: the 2.8-GHz profiler operates in the S-band and the 449-MHz profiler operates in the UHF band. The raw observations are available as well as calibrated spectra and moments. This document describes how the instruments were deployed, how the data was collected, and the format of the archived data.

  1. ARM - Midlatitude Continental Convective Clouds Experiment (MC3E): Multi-Frequency Profilers, Parcivel Disdrometer (williams-disdro)

    DOE Data Explorer

    Williams, Christopher; Jensen, Mike

    2012-11-06

    This data was collected by the NOAA 449-MHz and 2.8-GHz profilers in support of the Department of Energy (DOE) and NASA sponsored Mid-latitude Continental Convective Cloud Experiment (MC3E). The profiling radars were deployed in Northern Oklahoma at the DOE Atmospheric Radiation Mission (ARM) Southern Great Plans (SGP) Central Facility from 22 April through 6 June 2011. NOAA deployed three instruments: a Parsivel disdrometer, a 2.8-GHz profiler, and a 449-MHz profiler. The parasivel provided surface estimates of the raindrop size distribution and is the reference used to absolutely calibrate the 2.8 GHz profiler. The 2.8-GHz profiler provided unattenuated reflectivity profiles of the precipitation. The 449-MHz profiler provided estimates of the vertical air motion during precipitation from near the surface to just below the freezing level. By using the combination of 2.8-GHz and 449-MHz profiler observations, vertical profiles of raindrop size distributions can be retrieved. The profilers are often reference by their frequency band: the 2.8-GHz profiler operates in the S-band and the 449-MHz profiler operates in the UHF band. The raw observations are available as well as calibrated spectra and moments. This document describes how the instruments were deployed, how the data was collected, and the format of the archived data.

  2. Multi-Frequency Microwaves Plasma Production for Active Profile Control of Ion Beams on a Large Bore ECR Ion Source with Permanent Magnets

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

    Sakamoto, Naoki; Kato, Yushi; Kiriyama, Ryutaro

    2011-01-07

    A new concept on magnetic field of plasma production and confinement by using permanent magnets, i.e. cylindrically comb-shaped magnets, has been proposed to enhance efficiency of an electron cyclotron resonance (ECR) plasma for broad and dense ion beam source under the low pressure and also the low microwave power. The resonance zones corresponding to the fundamental ECR for 2.45 GHz and 11-13 GHz frequency are constructed at different positions. The profiles of the plasma parameters in the ECR ion source are different from each frequency of microwave. Large bore extractor is set at the opposite side against the microwave feeds.more » It is found that differences of their profiles also appear at those of ion beam profiles. We conducted to launch simultaneously multiplex frequency microwaves controlled individually, and tried to control the profiles of the plasma parameters and then those of extracted ion beam.« less

  3. The effects of downwelling radiance on MER surface spectra: the evil that atmospheres do

    NASA Astrophysics Data System (ADS)

    Wolff, M.; Ghosh, A.; Arvidson, R.; Christensen, P.; Guinness, E.; Ruff, S.; Seelos, F.; Smith, M.; Athena Science

    2004-11-01

    While it may not be surprising to some that downwelling radiation in the martian atmosphere may contribute a non-negligible fraction of the radiance for a given surface scene, others remain shocked and surprised (and often dismayed) to discover this fact; particularly with regard to mini-TES observations. Naturally, the relative amplitude of this sky ``contamination'' is often a complicated function of meteorological conditions, viewing geometry, surface properties, and (for the IR) surface temperature. Ideally, one would use a specialized observations to mimic the actual hemispherical-directional nature of the problem. Despite repeated attempts to obtain Pancam complete sky observations and mini-TES sky octants, such observations are not available in the MER observational database. As a result, one is left with the less-enviable, though certainly more computationally intensive, task of connecting point observations (radiance and derived meteorological parameters) to a hemispherical integral of downwelling radiance. Naturally, one must turn to a radiative transfer analysis, despite oft-repeated attempts to assert otherwise. In our presentation, we offer insight into the conditions under which one must worry about atmospheric removal, as well as semi-empirical approaches (based upon said radiative transfer efforts) for producing the correction factors from the available MER atmospheric observations. This work is proudly supported by the MER program through NASA/JPL Contract No. 1242889 (MJW), as well as the contracts for the co-authors.

  4. Rapid and Effective Virucidal Activity of Povidone-Iodine Products Against Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and Modified Vaccinia Virus Ankara (MVA).

    PubMed

    Eggers, Maren; Eickmann, Markus; Zorn, Juergen

    2015-12-01

    Since the first case of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infection was reported in 2012, the virus has infected more than 1300 individuals in 26 countries, and caused more than 480 deaths. Human-to-human transmission requires close contact, and has typically occurred in the healthcare setting. Improved global awareness, together with improved hygiene practices in healthcare facilities, has been highlighted as key strategies in controlling the spread of MERS-CoV. This study tested the in vitro efficacy of three formulations of povidone iodine (PVP-I: 4% PVP-I skin cleanser, 7.5% PVP-I surgical scrub, and 1% PVP-I gargle/mouthwash) against a reference virus (Modified vaccinia virus Ankara, MVA) and MERS-CoV. According to EN14476, a standard suspension test was used to assess virucidal activity against MVA and large volume plating was used for MERS-CoV. All products were tested under clean (0.3 g/L bovine serum albumin, BSA) and dirty conditions (3.0 g/L BSA + 3.0 mL/L erythrocytes), with application times of 15, 30, and 60 s for MVA, and 15 s for MERS-CoV. The products were tested undiluted, 1:10 and 1:100 diluted against MVA, and undiluted against MERS-CoV. A reduction in virus titer of ≥4 log10 (corresponding to an inactivation of ≥99.99%) was regarded as evidence of virucidal activity. This was achieved versus MVA and MERS-CoV, under both clean and dirty conditions, within 15 s of application of each undiluted PVP-I product. These data indicate that PVP-I-based hand wash products for potentially contaminated skin, and PVP-I gargle/mouthwash for reduction of viral load in the oral cavity and the oropharynx, may help to support hygiene measures to prevent transmission of MERS-CoV. Mundipharma Research GmbH & Co.

  5. [Profiles of high-frequency users of primary care services and associations with depressive anxiety disorders in Cali, Colombia].

    PubMed

    Rodriguez-Lopez, Mérida; Arrivillaga, Marcela; Holguín, Jorge; León, Hoover; Ávila, Alfonso; Hernández, Carlos; Rincón-Hoyos, Hernán G

    2016-01-01

    To determine the profiles of highly frequent users of primary care services and the associations of these profiles with depressive anxiety disorders in Cali, Colombia. A case-control study, high-frequency cases were defined as those involving patients with a percentile >75 with regard to the frequency of spontaneous use of outpatient facilities in the last 12 months; controls were defined as those with a percentile <25. A multiple correspondence analysis was used to describe patient profiles, and the influences of depression and anxiety on frequent attendance was determined via logistic regression. Among the 780 participating patients, differences in the profiles among frequent users and controls were related to predisposing factors such as sex, age, and education, capacity factors such as the time required to visit the institution and the means of transport used, and need factors such as health perceptions, social support, family function, and the presence of anxiety or depressive disorders. A depression or anxiety disorder was found to associate positively with frequent attendance (adjusted odds ratio [aOR]: 1.99, 95% confidence interval [CI]: 1.19-3.31) and a referral system (aOR: 1.61, 95% CI: 1.01-2.76), but negatively with mild or no family dysfunction (aOR: 0.79; 95% CI: 0.48-0.88) after adjusting for age, sex, ethnicity, and health service-providing institutions. The profiles of high-frequency patients differ from control patients with respect to factors related to capacity, need, and willingness; in particular, the latter were independently associated with frequent attendance. Notably, the presence of an anxious or depressive disorder doubled the risk of highfrequency attendance at a primary care facility.

  6. Real-Time Sequence-Validated Loop-Mediated Isothermal Amplification Assays for Detection of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

    PubMed Central

    Bhadra, Sanchita; Jiang, Yu Sherry; Kumar, Mia R.; Johnson, Reed F.; Hensley, Lisa E.; Ellington, Andrew D.

    2015-01-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens. PMID:25856093

  7. Computational modeling of the bat HKU4 coronavirus 3CLpro inhibitors as a tool for the development of antivirals against the emerging Middle East respiratory syndrome (MERS) coronavirus.

    PubMed

    Abuhammad, Areej; Al-Aqtash, Rua'a A; Anson, Brandon J; Mesecar, Andrew D; Taha, Mutasem O

    2017-11-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus that poses a major challenge to clinical management. The 3C-like protease (3CL pro ) is essential for viral replication and thus represents a potential target for antiviral drug development. Presently, very few data are available on MERS-CoV 3CL pro inhibition by small molecules. We conducted extensive exploration of the pharmacophoric space of a recently identified set of peptidomimetic inhibitors of the bat HKU4-CoV 3CL pro . HKU4-CoV 3CL pro shares high sequence identity (81%) with the MERS-CoV enzyme and thus represents a potential surrogate model for anti-MERS drug discovery. We used 2 well-established methods: Quantitative structure-activity relationship (QSAR)-guided modeling and docking-based comparative intermolecular contacts analysis. The established pharmacophore models highlight structural features needed for ligand recognition and revealed important binding-pocket regions involved in 3CL pro -ligand interactions. The best models were used as 3D queries to screen the National Cancer Institute database for novel nonpeptidomimetic 3CL pro inhibitors. The identified hits were tested for HKU4-CoV and MERS-CoV 3CL pro inhibition. Two hits, which share the phenylsulfonamide fragment, showed moderate inhibitory activity against the MERS-CoV 3CL pro and represent a potential starting point for the development of novel anti-MERS agents. To the best of our knowledge, this is the first pharmacophore modeling study supported by in vitro validation on the MERS-CoV 3CL pro . MERS-CoV is an emerging virus that is closely related to the bat HKU4-CoV. 3CL pro is a potential drug target for coronavirus infection. HKU4-CoV 3CL pro is a useful surrogate model for the identification of MERS-CoV 3CL pro enzyme inhibitors. dbCICA is a very robust modeling method for hit identification. The phenylsulfonamide scaffold represents a potential starting point for MERS coronavirus 3CL pro inhibitors

  8. Determination of the effect of source intensity profile on speckle contrast using coherent spatial frequency domain imaging

    PubMed Central

    Rice, Tyler B.; Konecky, Soren D.; Owen, Christopher; Choi, Bernard; Tromberg, Bruce J.

    2012-01-01

    Laser Speckle Imaging (LSI) is fast, noninvasive technique to image particle dynamics in scattering media such as biological tissue. While LSI measurements are independent of the overall intensity of the laser source, we find that spatial variations in the laser source profile can impact measured flow rates. This occurs due to differences in average photon path length across the profile, and is of significant concern because all lasers have some degree of natural Gaussian profile in addition to artifacts potentially caused by projecting optics. Two in vivo measurement are performed to show that flow rates differ based on location with respect to the beam profile. A quantitative analysis is then done through a speckle contrast forward model generated within a coherent Spatial Frequency Domain Imaging (cSFDI) formalism. The model predicts remitted speckle contrast as a function of spatial frequency, optical properties, and scattering dynamics. Comparison with experimental speckle contrast images were done using liquid phantoms with known optical properties for three common beam shapes. cSFDI is found to accurately predict speckle contrast for all beam shapes to within 5% root mean square error. Suggestions for improving beam homogeneity are given, including a widening of the natural beam Gaussian, proper diffusing glass spreading, and flat top shaping using microlens arrays. PMID:22741080

  9. Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

    PubMed

    Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

    2016-02-23

    In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

  10. Customized Oligonucleotide Array-Based Comparative Genomic Hybridization as a Clinical Assay for Genomic Profiling of Chronic Lymphocytic Leukemia

    PubMed Central

    Sargent, Rachel; Jones, Dan; Abruzzo, Lynne V.; Yao, Hui; Bonderover, Jaime; Cisneros, Marissa; Wierda, William G.; Keating, Michael J.; Luthra, Rajyalakshmi

    2009-01-01

    Chromosome gains and losses used for risk stratification in chronic lymphocytic leukemia (CLL) are commonly assessed by multiprobe fluorescence in situ hybridization (FISH) studies. We designed and validated a customized array-comparative genomic hybridization (aCGH) platform as a clinical assay for CLL genomic profiling. A 60-mer, 44,000-probe oligonucleotide array with a 50-kb average spatial resolution was augmented with high-density probe tiling at loci that are frequently aberrant in CLL. Aberrations identified by aCGH were compared with those identified by a FISH panel, including locus-specific probes to ATM (11q22.3), the centromeric region of chromosome 12 (12p11.1–q11), D13S319 (13q14.3), LAMP1 (13q34), and TP53 (17p13.1). In 100 CLL samples, aCGH/FISH concordance was seen for 89% of FISH-called aberrations at the ATM (n = 18), D13S319 (n = 42), LAMP (n = 12), and TP53 (n = 22) loci and for chromosome 12 (n = 14). Eighty-four percentage of FISH/aCGH discordant calls were in samples either at or below the limit of aCGH sensitivity (10% to 25% FISH aberration-containing cells). Therefore, aCGH profiling is a feasible routine clinical test with comparable results to multiprobe FISH studies; however, it may be less sensitive than FISH in cases with low-level aberrations. Further, a customized array design can provide comprehensive genomic profiling with additional accuracy in both identifying and defining the extent of small aberrations at target loci. PMID:19074592

  11. Low-frequency microwave radiometer for N-ROSS

    NASA Astrophysics Data System (ADS)

    Hollinger, J. P.; Lo, R. C.

    1985-04-01

    The all weather, global determination of sea surface temperature (SST) has been identified as a requirement needed to support naval operations. The target SST accuracy is + or - 1.0 K with a surface resolution of 10 km. Investigations of the phenomenology and technology of remote passive microwave sensing of the ocean environment over the past decade have demonstrated that this objective is presently attainable. Preliminary specification and trade off studies were conducted to define the frequency, polarization, scan geometry, antenna size, and other esstential parameters of the low frequency microwave radiometer (LFMR). It will be a dual polarized, dual frequency system at 5.2 and 10.4 GHz using a 4.9 meter deployable mesh surface antenna. It is to be flown on the Navy-Remote Ocean Sensing System (N-ROSS) satellite scheduled to be launched in late 1988.

  12. Low-frequency microwave radiometer for N-ROSS

    NASA Technical Reports Server (NTRS)

    Hollinger, J. P.; Lo, R. C.

    1985-01-01

    The all weather, global determination of sea surface temperature (SST) has been identified as a requirement needed to support naval operations. The target SST accuracy is + or - 1.0 K with a surface resolution of 10 km. Investigations of the phenomenology and technology of remote passive microwave sensing of the ocean environment over the past decade have demonstrated that this objective is presently attainable. Preliminary specification and trade off studies were conducted to define the frequency, polarization, scan geometry, antenna size, and other esstential parameters of the low frequency microwave radiometer (LFMR). It will be a dual polarized, dual frequency system at 5.2 and 10.4 GHz using a 4.9 meter deployable mesh surface antenna. It is to be flown on the Navy-Remote Ocean Sensing System (N-ROSS) satellite scheduled to be launched in late 1988.

  13. Phagocytosis of microparticles by alveolar macrophages during acute lung injury requires MerTK.

    PubMed

    Mohning, Michael P; Thomas, Stacey M; Barthel, Lea; Mould, Kara J; McCubbrey, Alexandria L; Frasch, S Courtney; Bratton, Donna L; Henson, Peter M; Janssen, William J

    2018-01-01

    Microparticles are a newly recognized class of mediators in the pathophysiology of lung inflammation and injury, but little is known about the factors that regulate their accumulation and clearance. The primary objective of our study was to determine whether alveolar macrophages engulf microparticles and to elucidate the mechanisms by which this occurs. Alveolar microparticles were quantified in bronchoalveolar fluid of mice with lung injury induced by LPS and hydrochloric acid. Microparticle numbers were greatest at the peak of inflammation and declined as inflammation resolved. Isolated, fluorescently labeled particles were placed in culture with macrophages to evaluate ingestion in the presence of endocytosis inhibitors. Ingestion was blocked with cytochalasin D and wortmannin, consistent with a phagocytic process. In separate experiments, mice were treated intratracheally with labeled microparticles, and their uptake was assessed though microscopy and flow cytometry. Resident alveolar macrophages, not recruited macrophages, were the primary cell-ingesting microparticles in the alveolus during lung injury. In vitro, microparticles promoted inflammatory signaling in LPS primed epithelial cells, signifying the importance of microparticle clearance in resolving lung injury. Microparticles were found to have phosphatidylserine exposed on their surfaces. Accordingly, we measured expression of phosphatidylserine receptors on macrophages and found high expression of MerTK and Axl in the resident macrophage population. Endocytosis of microparticles was markedly reduced in MerTK-deficient macrophages in vitro and in vivo. In conclusion, microparticles are released during acute lung injury and peak in number at the height of inflammation. Resident alveolar macrophages efficiently clear these microparticles through MerTK-mediated phagocytosis.

  14. A Computerized Microelectrode Recording to Magnetic Resonance Imaging Mapping System for Subthalamic Nucleus Deep Brain Stimulation Surgery.

    PubMed

    Dodani, Sunjay S; Lu, Charles W; Aldridge, J Wayne; Chou, Kelvin L; Patil, Parag G

    2018-06-01

    Accurate electrode placement is critical to the success of deep brain stimulation (DBS) surgery. Suboptimal targeting may arise from poor initial target localization, frame-based targeting error, or intraoperative brain shift. These uncertainties can make DBS surgery challenging. To develop a computerized system to guide subthalamic nucleus (STN) DBS electrode localization and to estimate the trajectory of intraoperative microelectrode recording (MER) on magnetic resonance (MR) images algorithmically during DBS surgery. Our method is based upon the relationship between the high-frequency band (HFB; 500-2000 Hz) signal from MER and voxel intensity on MR images. The HFB profile along an MER trajectory recorded during surgery is compared to voxel intensity profiles along many potential trajectories in the region of the surgically planned trajectory. From these comparisons of HFB recordings and potential trajectories, an estimate of the MER trajectory is calculated. This calculated trajectory is then compared to actual trajectory, as estimated by postoperative high-resolution computed tomography. We compared 20 planned, calculated, and actual trajectories in 13 patients who underwent STN DBS surgery. Targeting errors for our calculated trajectories (2.33 mm ± 0.2 mm) were significantly less than errors for surgically planned trajectories (2.83 mm ± 0.2 mm; P = .01), improving targeting prediction in 70% of individual cases (14/20). Moreover, in 4 of 4 initial MER trajectories that missed the STN, our method correctly indicated the required direction of targeting adjustment for the DBS lead to intersect the STN. A computer-based algorithm simultaneously utilizing MER and MR information potentially eases electrode localization during STN DBS surgery.

  15. KENNEDY SPACE CENTER, FLA. - The Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, is having solid rocket boosters (SRBs) installed that will help launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-15

    KENNEDY SPACE CENTER, FLA. - The Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, is having solid rocket boosters (SRBs) installed that will help launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

  16. Comparing K-mer based methods for improved classification of 16S sequences.

    PubMed

    Vinje, Hilde; Liland, Kristian Hovde; Almøy, Trygve; Snipen, Lars

    2015-07-01

    The need for precise and stable taxonomic classification is highly relevant in modern microbiology. Parallel to the explosion in the amount of sequence data accessible, there has also been a shift in focus for classification methods. Previously, alignment-based methods were the most applicable tools. Now, methods based on counting K-mers by sliding windows are the most interesting classification approach with respect to both speed and accuracy. Here, we present a systematic comparison on five different K-mer based classification methods for the 16S rRNA gene. The methods differ from each other both in data usage and modelling strategies. We have based our study on the commonly known and well-used naïve Bayes classifier from the RDP project, and four other methods were implemented and tested on two different data sets, on full-length sequences as well as fragments of typical read-length. The difference in classification error obtained by the methods seemed to be small, but they were stable and for both data sets tested. The Preprocessed nearest-neighbour (PLSNN) method performed best for full-length 16S rRNA sequences, significantly better than the naïve Bayes RDP method. On fragmented sequences the naïve Bayes Multinomial method performed best, significantly better than all other methods. For both data sets explored, and on both full-length and fragmented sequences, all the five methods reached an error-plateau. We conclude that no K-mer based method is universally best for classifying both full-length sequences and fragments (reads). All methods approach an error plateau indicating improved training data is needed to improve classification from here. Classification errors occur most frequent for genera with few sequences present. For improving the taxonomy and testing new classification methods, the need for a better and more universal and robust training data set is crucial.

  17. Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

    PubMed Central

    Kingsford, Carl

    2017-01-01

    With the rapidly increasing volume of deep sequencing data, more efficient algorithms and data structures are needed. Minimizers are a central recent paradigm that has improved various sequence analysis tasks, including hashing for faster read overlap detection, sparse suffix arrays for creating smaller indexes, and Bloom filters for speeding up sequence search. Here, we propose an alternative paradigm that can lead to substantial further improvement in these and other tasks. For integers k and L > k, we say that a set of k-mers is a universal hitting set (UHS) if every possible L-long sequence must contain a k-mer from the set. We develop a heuristic called DOCKS to find a compact UHS, which works in two phases: The first phase is solved optimally, and for the second we propose several efficient heuristics, trading set size for speed and memory. The use of heuristics is motivated by showing the NP-hardness of a closely related problem. We show that DOCKS works well in practice and produces UHSs that are very close to a theoretical lower bound. We present results for various values of k and L and by applying them to real genomes show that UHSs indeed improve over minimizers. In particular, DOCKS uses less than 30% of the 10-mers needed to span the human genome compared to minimizers. The software and computed UHSs are freely available at github.com/Shamir-Lab/DOCKS/ and acgt.cs.tau.ac.il/docks/, respectively. PMID:28968408

  18. Searching for animal models and potential target species for emerging pathogens: Experience gained from Middle East respiratory syndrome (MERS) coronavirus.

    PubMed

    Vergara-Alert, Júlia; Vidal, Enric; Bensaid, Albert; Segalés, Joaquim

    2017-06-01

    Emerging and re-emerging pathogens represent a substantial threat to public health, as demonstrated with numerous outbreaks over the past years, including the 2013-2016 outbreak of Ebola virus in western Africa. Coronaviruses are also a threat for humans, as evidenced in 2002/2003 with infection by the severe acute respiratory syndrome coronavirus (SARS-CoV), which caused more than 8000 human infections with 10% fatality rate in 37 countries. Ten years later, a novel human coronavirus (Middle East respiratory syndrome coronavirus, MERS-CoV), associated with severe pneumonia, arose in the Kingdom of Saudi Arabia. Until December 2016, MERS has accounted for more than 1800 cases and 35% fatality rate. Finding an animal model of disease is key to develop vaccines or antivirals against such emerging pathogens and to understand its pathogenesis. Knowledge of the potential role of domestic livestock and other animal species in the transmission of pathogens is of importance to understand the epidemiology of the disease. Little is known about MERS-CoV animal host range. In this paper, experimental data on potential hosts for MERS-CoV is reviewed. Advantages and limitations of different animal models are evaluated in relation to viral pathogenesis and transmission studies. Finally, the relevance of potential new target species is discussed.

  19. Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier.

    PubMed

    Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Rao, A R

    2016-11-05

    DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Application of State Analysis and Goal-based Operations to a MER Mission Scenario

    NASA Technical Reports Server (NTRS)

    Morris, John Richard; Ingham, Michel D.; Mishkin, Andrew H.; Rasmussen, Robert D.; Starbird, Thomas W.

    2006-01-01

    State Analysis is a model-based systems engineering methodology employing a rigorous discovery process which articulates operations concepts and operability needs as an integrated part of system design. The process produces requirements on system and software design in the form of explicit models which describe the system behavior in terms of state variables and the relationships among them. By applying State Analysis to an actual MER flight mission scenario, this study addresses the specific real world challenges of complex space operations and explores technologies that can be brought to bear on future missions. The paper first describes the tools currently used on a daily basis for MER operations planning and provides an in-depth description of the planning process, in the context of a Martian day's worth of rover engineering activities, resource modeling, flight rules, science observations, and more. It then describes how State Analysis allows for the specification of a corresponding goal-based sequence that accomplishes the same objectives, with several important additional benefits.

  1. Application of State Analysis and Goal-Based Operations to a MER Mission Scenario

    NASA Technical Reports Server (NTRS)

    Morris, J. Richard; Ingham, Michel D.; Mishkin, Andrew H.; Rasmussen, Robert D.; Starbird, Thomas W.

    2006-01-01

    State Analysis is a model-based systems engineering methodology employing a rigorous discovery process which articulates operations concepts and operability needs as an integrated part of system design. The process produces requirements on system and software design in the form of explicit models which describe the behavior of states and the relationships among them. By applying State Analysis to an actual MER flight mission scenario, this study addresses the specific real world challenges of complex space operations and explores technologies that can be brought to bear on future missions. The paper describes the tools currently used on a daily basis for MER operations planning and provides an in-depth description of the planning process, in the context of a Martian day's worth of rover engineering activities, resource modeling, flight rules, science observations, and more. It then describes how State Analysis allows for the specification of a corresponding goal-based sequence that accomplishes the same objectives, with several important additional benefits.

  2. ARM - Midlatitude Continental Convective Clouds Experiment (MC3E): Multi-Frequency Profilers, Vertical Air Motion (williams-vertair)

    DOE Data Explorer

    Williams, Christopher; Jensen, Mike

    2012-11-06

    This data was collected by the NOAA 449-MHz and 2.8-GHz profilers in support of the Department of Energy (DOE) and NASA sponsored Mid-latitude Continental Convective Cloud Experiment (MC3E). The profiling radars were deployed in Northern Oklahoma at the DOE Atmospheric Radiation Mission (ARM) Southern Great Plans (SGP) Central Facility from 22 April through 6 June 2011. NOAA deployed three instruments: a Parsivel disdrometer, a 2.8-GHz profiler, and a 449-MHz profiler. The parasivel provided surface estimates of the raindrop size distribution and is the reference used to absolutely calibrate the 2.8 GHz profiler. The 2.8-GHz profiler provided unattenuated reflectivity profiles of the precipitation. The 449-MHz profiler provided estimates of the vertical air motion during precipitation from near the surface to just below the freezing level. By using the combination of 2.8-GHz and 449-MHz profiler observations, vertical profiles of raindrop size distributions can be retrieved. The profilers are often reference by their frequency band: the 2.8-GHz profiler operates in the S-band and the 449-MHz profiler operates in the UHF band. The raw observations are available as well as calibrated spectra and moments. This document describes how the instruments were deployed, how the data was collected, and the format of the archived data.

  3. Heterodyne frequency measurements on N2O at 5.3 and 9.0 microns

    NASA Technical Reports Server (NTRS)

    Wells, J. S.; Jennings, D. A.; Hinz, A.; Murray, J. S.; Maki, A. G.

    1985-01-01

    Heterodyne frequency measurements on the 01(1)1-00(0)0 band of N2O have been made with the use of a tunable-diode laser, CO laser transfer oscillator, and a CO2 laser frequency synthesizer. A beat frequency was measured between a CO laser and tunable-diode laser whose frequency was locked to the peak of N2O absorption features. The frequency of the CO laser was simultaneously determined by neasuring the beat frequency with respect to a reference synthesized from two CO2 lasers. New rovibrational constants are given for the 01(1)1 state of N2O, which are in excellent agreement with previous results, although the band center is 4 MHz higher than in the previous measurements. A table for the line frequencies and their absolute uncertainties is given for the N2O absorption lines in the wave-number region from 1830 to 1920 kaysers. Some additional frequency measurements near the lower-frequency end of the 02(0)0-00(0)0 band have also been made with respect to a C-12)(0-18)2 laser.

  4. Treatment outcomes for patients with Middle Eastern Respiratory Syndrome Coronavirus (MERS CoV) infection at a coronavirus referral center in the Kingdom of Saudi Arabia.

    PubMed

    Al Ghamdi, Mohammed; Alghamdi, Khalid M; Ghandoora, Yasmeen; Alzahrani, Ameera; Salah, Fatmah; Alsulami, Abdulmoatani; Bawayan, Mayada F; Vaidya, Dhananjay; Perl, Trish M; Sood, Geeta

    2016-04-21

    Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV) is a poorly understood disease with no known treatments. We describe the clinical features and treatment outcomes of patients with laboratory confirmed MERS-CoV at a regional referral center in the Kingdom of Saudi Arabia. In 2014, a retrospective chart review was performed on patients with a laboratory confirmed diagnosis of MERS-CoV to determine clinical and treatment characteristics associated with death. Confounding was evaluated and a multivariate logistic regression was performed to assess the independent effect of treatments administered. Fifty-one patients had an overall mortality of 37 %. Most patients were male (78 %) with a mean age of 54 years. Almost a quarter of the patients were healthcare workers (23.5 %) and 41 % had a known exposure to another person with MERS-CoV. Survival was associated with male gender, working as a healthcare worker, history of hypertension, vomiting on admission, elevated respiratory rate, abnormal lung exam, elevated alanine transaminase (ALT), clearance of MERS-CoV on repeat PCR polymerase chain reaction (PCR) testing, and mycophenolate mofetil treatment. Survival was reduced in the presence of coronary artery disease, hypotension, hypoxemia, CXR (chest X-ray) abnormalities, leukocytosis, creatinine >1 · 5 mg/dL, thrombocytopenia, anemia, and renal failure. In a multivariate analysis of treatments administered, severity of illness was the greatest predictor of reduced survival. Care for patients with MERS-CoV remains a challenge. In this retrospective cohort, interferon beta and mycophenolate mofetil treatment were predictors of increased survival in the univariate analysis. Severity of illness was the greatest predictor of reduced survival in the multivariate analysis. Larger randomized trials are needed to better evaluate the efficacy of these treatment regimens for MERS-CoV.

  5. Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt, August 2015 to January 2016

    PubMed Central

    Ali, Mohamed; El-Shesheny, Rabeh; Kandeil, Ahmed; Shehata, Mahmoud; Elsokary, Basma; Gomaa, Mokhtar; Hassan, Naglaa; El Sayed, Ahmed; El-Taweel, Ahmed; Sobhy, Heba; Oludayo, Fasina Folorunso; Dauphin, Gwenaelle; El Masry, Ihab; Wolde, Abebe Wossene; Daszak, Peter; Miller, Maureen; VonDobschuetz, Sophie; Gardner, Emma; Morzaria, Subhash; Lubroth, Juan; Makonnen, Yilma Jobre

    2017-01-01

    A cross-sectional study was conducted in Egypt to determine the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in imported and resident camels and bats, as well as to assess possible transmission of the virus to domestic ruminants and equines. A total of 1,031 sera, 1,078 nasal swabs, 13 rectal swabs, and 38 milk samples were collected from 1,078 camels in different types of sites. In addition, 145 domestic animals and 109 bats were sampled. Overall, of 1,031 serologically-tested camels, 871 (84.5%) had MERS-CoV neutralising antibodies. Seroprevalence was significantly higher in imported (614/692; 88.7%) than resident camels (257/339; 5.8%) (p < 0.05). Camels from Sudan (543/594; 91.4%) had a higher seroprevalence than those from East Africa (71/98; 72.4%) (p < 0.05). Sampling site and age were also associated with MERS-CoV seroprevalence (p < 0.05). All tested samples from domestic animals and bats were negative for MERS-CoV antibodies except one sheep sample which showed a 1:640 titre. Of 1,078 camels, 41 (3.8%) were positive for MERS-CoV genetic material. Sequences obtained were not found to cluster with clade A or B MERS-CoV sequences and were genetically diverse. The presence of neutralising antibodies in one sheep apparently in contact with seropositive camels calls for further studies on domestic animals in contact with camels. PMID:28333616

  6. PEDF and PEDF-derived peptide 44mer inhibit oxygen-glucose deprivation-induced oxidative stress through upregulating PPARγ via PEDF-R in H9c2 cells.

    PubMed

    Zhuang, Wei; Zhang, Hao; Pan, Jiajun; Li, Zhimin; Wei, Tengteng; Cui, Huazhu; Liu, Zhiwei; Guan, Qiuhua; Dong, Hongyan; Zhang, Zhongming

    2016-04-08

    Pigment epithelial-derived factor (PEDF) is a glycoprotein with broad biological activities including inhibiting oxygen-glucose deprivation(OGD)-induced cardiomyocytes apoptosis through its anti-oxidative properties. PEDF derived peptide-44mer shows similar cytoprotective effect to PEDF. However, the molecular mechanisms mediating cardiomyocytes apoptosis have not been fully established. Here we found that PEDF and 44mer decreased the content of ROS. This content was abolished by either PEDF-R small interfering RNA (siRNA) or PPARγ antagonist. The level of Lysophosphatidic acid (LPA) and phospholipase A2 (PLA2) was observed as drawn from the ELISA assays. PEDF and 44mer sequentially induced PPARγ expression was observed both in qPCR and Western blot assays. The level of LPA and PLA2 and PPARγ expression increased by PEDF and 44mer was significantly attenuated by PEDF-R siRNA. However, PEDF and 44mer inhibited the H9c2 cells and cultured neonatal rat myocardial cells apoptosis rate. On the other hand, TUNEL assay and cleavage of procaspase-3 showed that PEDF-R siRNA or PPARγ antagonist increased the apoptosis again. We conclude that under OGD condition, PEDF and 44mer reduce H9c2 cells apoptosis and inhibit OGD-induced oxidative stress via its receptor PEDF-R and the PPARγ signaling pathway. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  8. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  9. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) nears the top of the launch tower. The fairing will be installed around the payload for protection during launch on a Delta II rocket. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) nears the top of the launch tower. The fairing will be installed around the payload for protection during launch on a Delta II rocket. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  10. Using Mars and the Mer Mission to Teach Science: A Curriculum Designed for Teachers and Their Students

    NASA Astrophysics Data System (ADS)

    Aubele, J. C.; Stanley, J.; Grochowski, A.; Jones, K.; Aragon, J.

    2006-12-01

    Learning opportunities can be exceptionally successful when linked to national, newsworthy events. Planetary missions are particularly exciting in engaging teachers, and their students, because they combine the human "stories" of scientists and engineers with cutting-edge technology and new science. Planetary suface missions, such as the Mars Exploration Rover (MER) mission, return beautiful and human-scale images that can virtually transport the viewer to another world. The MER mission allows children and adults to participate in the exploration of one of our nearest neighbors in space. New discoveries in the natural history of Mars have been used as the basis of a new integrated curriculum created by Museum and class-room educators designed to serve informal (family learning) and formal (classroom) audiences. The curriculum uses Mars and the MER mission as a "hook" to teach a wide range of topics that relate to all of the sciences, mathematics, social studies (history and exploration), science and society, career readiness, language and literacy, and visual arts. The curriculum, entitled "Making Tracks on Mars: Teacher Resource and Activity Guide," includes the following key features that have contributed to its success and usefulness: (1) basic information about Mars, Mars missions, and the MER mission providing teachers with the knowledge they may lack; (2) activities that follow a standardized format and include necessary information, pre-lesson preparation and post-lesson closure and extensions, and all information and/or images needed; (3) activities that cross the curriculum and can be used to address many different standards; (4) relevant state and national standards listed for each activity; (5) annotated MER image file and PowerPoint presentation for easy classroom use; (6) lists of additional Mars-related resources; (7) emphasis on local connections to the mission to enable teachers and students to feel personally connected; (8) elementary through high

  11. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

    PubMed Central

    LeProust, Emily M.; Peck, Bill J.; Spirin, Konstantin; McCuen, Heather Brummel; Moore, Bridget; Namsaraev, Eugeni; Caruthers, Marvin H.

    2010-01-01

    We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology). PMID:20308161

  12. Cultivation of Hard-To-Culture Subsurface Mercury-Resistant Bacteria and Discovery of New merA Gene Sequences▿

    PubMed Central

    Rasmussen, L. D.; Zawadsky, C.; Binnerup, S. J.; Øregaard, G.; Sørensen, S. J.; Kroer, N.

    2008-01-01

    Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments. PMID:18441111

  13. Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion.

    PubMed

    Pulsipher, Katherine W; Villegas, Jose A; Roose, Benjamin W; Hicks, Tacey L; Yoon, Jennifer; Saven, Jeffery G; Dmochowski, Ivan J

    2017-07-18

    Protein cage self-assembly enables encapsulation and sequestration of small molecules, macromolecules, and nanomaterials for many applications in bionanotechnology. Notably, wild-type thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) exists as a stable dimer of four-helix bundle proteins at a low ionic strength, and the protein forms a hollow assembly of 24 protomers at a high ionic strength (∼800 mM NaCl). This assembly process can also be initiated by highly charged gold nanoparticles (AuNPs) in solution, leading to encapsulation. These data suggest that salt solutions or charged AuNPs can shield unfavorable electrostatic interactions at AfFtn dimer-dimer interfaces, but specific "hot-spot" residues controlling assembly have not been identified. To investigate this further, we computationally designed three AfFtn mutants (E65R, D138K, and A127R) that introduce a single positive charge at sites along the dimer-dimer interface. These proteins exhibited different assembly kinetics and thermodynamics, which were ranked in order of increasing 24mer propensity: A127R < wild type < D138K ≪ E65R. E65R assembled into the 24mer across a wide range of ionic strengths (0-800 mM NaCl), and the dissociation temperature for the 24mer was 98 °C. X-ray crystal structure analysis of the E65R mutant identified a more compact, closed-pore cage geometry. A127R and D138K mutants exhibited wild-type ability to encapsulate and stabilize 5 nm AuNPs, whereas E65R did not encapsulate AuNPs at the same high yields. This work illustrates designed protein cages with distinct assembly and encapsulation properties.

  14. Delta II Heavy MER-B Prelaunch

    NASA Image and Video Library

    2003-07-07

    On Launch Complex 17-B, Cape Canaveral Air Force Station, the Delta II Heavy launch vehicle carrying the rover "Opportunity" for the second Mars Exploration Rover mission is poised for launch after rollback of the Mobile Service Tower. Opportunity will reach Mars on Jan. 25, 2004. Together the two MER rovers, Spirit (launched June 10) and Opportunity, seek to determine the history of climate and water at two sites on Mars where conditions may once have been favorable to life. The rovers are identical. They will navigate themselves around obstacles as they drive across the Martian surface, traveling up to about 130 feet each Martian day. Each rover carries five scientific instruments including a panoramic camera and microscope, plus a rock abrasion tool that will grind away the outer surfaces of rocks to expose their interiors for examination. Each rover’s prime mission is planned to last three months on Mars.

  15. mer and fac isomerism in tris chelate diimine metal complexes.

    PubMed

    Dabb, Serin L; Fletcher, Nicholas C

    2015-03-14

    In this perspective, we highlight the issue of meridional (mer) and facial (fac) orientation of asymmetrical diimines in tris-chelate transition metal complexes. Diimine ligands have long been the workhorse of coordination chemistry, and whilst there are now good strategies to isolate materials where the inherent metal centered chirality is under almost complete control, and systematic methodologies to isolate heteroleptic complexes, the conceptually simple geometrical isomerism has not been widely investigated. In systems where the two donor atoms are significantly different in terms of the σ-donor and π-accepting ability, the fac isomer is likely to be the thermodynamic product. For the diimine complexes with two trigonal planar nitrogen atoms there is much more subtlety to the system, and external factors such as the solvent, lattice packing and the various steric considerations play a delicate role in determining the observed and isolable product. In this article we discuss the possibilities to control the isomeric ratio in labile systems, consider the opportunities to separate inert complexes and discuss the observed differences in their spectroscopic properties. Finally we report on the ligand orientation in supramolecular systems where facial coordination leads to simple regular structures such as helicates and tetrahedra, but the ability of the ligand system to adopt a mer orientation enables self-assembled structures of considerable beauty and complexity.

  16. Nutrient availability at Mer Bleue bog measured by PRSTM probes

    NASA Astrophysics Data System (ADS)

    Wang, M.; Moore, T. R.; Talbot, J.

    2015-12-01

    Bogs, covering ~0.7 million km2 in Canada, store a large amount of C and N. As nutrient deficient ecosystems, it's critical to examine the nutrient availabilities and seasonal dynamics. We used Plant Root Simulators (PRSTM) at Mer Bleue bog to provide some baseline data on nutrient availability and its variability. In particular, we focused on ammonium, nitrate, phosphate, calcium, magnesium and potassium, iron, sulphate and aluminum. We placed PRS probes at a depth of 5 - 15 cm in pristine plots and plots with long term N, P and K fertilization for 4 weeks and determined the availability of these nutrients, from spring through to fall. Probes were also placed beneath the water table in hummock and hollow microtopography and along a transect including part of the bog which had been drained through the creation of a ditch 80 years ago. The result showed that there was limited available ammonium, nitrate and phosphate in the bog, the seasonal variation of nutrient availabilities probably due to mineralization, an increase in the availability of some nutrients between different water table depths or as a result of drainage, and the relative availability of nutrients compared to the input from fertilization. We suggest that PRS probes could be a useful tool to examine nutrient availability and dynamics in wetlands, with careful consideration of installing condition, for example, proper exposure period, depth relative to water table etc.

  17. Enhancement by O6-benzyl-N2-acetylguanosine of N'-[2-chloroethyl]-N-[2-(methylsulphonyl)ethyl]-N'-nitrosourea therapeutic index on nude mice bearing resistant human melanoma.

    PubMed Central

    Debiton, E.; Cussac-Buchdhal, C.; Mounetou, E.; Rapp, M.; Dupuy, J. M.; Maurizis, J. C.; Veyre, A.; Madelmont, J. C.

    1997-01-01

    The exposure of cells to O6-benzyl-N2-acetylguanosine (BNAG) and several guanine derivatives is known to reduce the activity of O6-alkylguanine-DNA alkyltransferase (MGMT) and to enhance the sensitivity of Mer+ (methyl enzyme repair positive) tumour cells to chloroethylnitrosoureas (CENUs) in vitro and in vivo. High water solubility and the pharmacokinetic properties of BNAG make it a candidate for simultaneous administration with CENUs by the i.v. route in human clinical use. In vivo we have shown previously that BNAG significantly increases the efficiency of N'-[2-chloroethyl]-N-[2-(methylsulphonyl)ethyl]-N'-nitrosourea (cystemustine) against M4Beu melanoma cells (Mer+) through its cytostatic activity by the i.p. route, but also increases its toxicity. To investigate the toxicity of BNAG and cystemustine when administered simultaneously in mice, we compared the maximum tolerated dose and LD50 doses of cystemustine alone or in combination with 40 mg kg(-1) BNAG by the i.p. route. The toxicity of cystemustine was enhanced by a factor of almost 1.44 when combined with BNAG. To compare the therapeutic index of cystemustine alone and the cystemustine/BNAG combination, pharmacological tests were carried out in nude mice bearing Mer+ M4Beu human melanoma cells. Isotoxic doses were calculated using the 1.44 ratio. The treatments were administered three times by the i.v. route on days 1, 5 and 9 after s.c. inoculation of tumour cells. Although the toxicities of the treatments were equal, BNAG strongly enhanced tumour growth inhibition. These results demonstrate the increase of the therapeutic index of cystemustine by BNAG and justify the use of BNAG to enhance nitrosourea efficiency in vivo by i.v. co-injection. PMID:9365163

  18. Radarclinometry: Bootstrapping the radar reflectance function from the image pixel-signal frequency distribution and an altimetry profile

    USGS Publications Warehouse

    Wildey, R.L.

    1988-01-01

    A method is derived for determining the dependence of radar backscatter on incidence angle that is applicable to the region corresponding to a particular radar image. The method is based on enforcing mathematical consistency between the frequency distribution of the image's pixel signals (histogram of DN values with suitable normalizations) and a one-dimensional frequency distribution of slope component, as might be obtained from a radar or laser altimetry profile in or near the area imaged. In order to achieve a unique solution, the auxiliary assumption is made that the two-dimensional frequency distribution of slope is isotropic. The backscatter is not derived in absolute units. The method is developed in such a way as to separate the reflectance function from the pixel-signal transfer characteristic. However, these two sources of variation are distinguishable only on the basis of a weak dependence on the azimuthal component of slope; therefore such an approach can be expected to be ill-conditioned unless the revision of the transfer characteristic is limited to the determination of an additive instrumental background level. The altimetry profile does not have to be registered in the image, and the statistical nature of the approach minimizes pixel noise effects and the effects of a disparity between the resolutions of the image and the altimetry profile, except in the wings of the distribution where low-number statistics preclude accuracy anyway. The problem of dealing with unknown slope components perpendicular to the profiling traverse, which besets the one-to-one comparison between individual slope components and pixel-signal values, disappears in the present approach. In order to test the resulting algorithm, an artificial radar image was generated from the digitized topographic map of the Lake Champlain West quadrangle in the Adirondack Mountains, U.S.A., using an arbitrarily selected reflectance function. From the same map, a one-dimensional frequency

  19. Tolerance or avoidance: drought frequency determines the response of an N2 -fixing tree.

    PubMed

    Minucci, Jeffrey M; Miniat, Chelcy Ford; Teskey, Robert O; Wurzburger, Nina

    2017-07-01

    Climate change is increasing drought frequency, which may affect symbiotic N 2 fixation (SNF), a process that facilitates ecosystem recovery from disturbance. Here, we assessed the effect of drought frequency on the ecophysiology and SNF rate of a common N 2 -fixing tree in eastern US forests. We grew Robinia pseudoacacia seedlings under the same mean soil moisture, but with different drought frequency caused by wet-dry cycles of varying periodicity. We found no effect of drought frequency on final biomass or mean SNF rate. However, seedlings responded differently to wet and dry phases depending on drought frequency. Under low-frequency droughts, plants fixed carbon (C) and nitrogen (N) at similar rates during wet and dry phases. Conversely, under high-frequency droughts, plants fixed C and N at low rates during dry phases and at high rates during wet phases. Our findings suggest that R. pseudoacacia growth is resistant to increased drought frequency because it employs two strategies - drought tolerance or drought avoidance, followed by compensation. SNF may play a role in both by supplying N to leaf tissues for acclimation and by facilitating compensatory growth following drought. Our findings point to SNF as a mechanism for plants and ecosystems to cope with drought. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  20. Iodine-stabilized single-frequency green InGaN diode laser.

    PubMed

    Chen, Yi-Hsi; Lin, Wei-Chen; Shy, Jow-Tsong; Chui, Hsiang-Chen

    2018-01-01

    A 520-nm InGaN diode laser can emit a milliwatt-level, single-frequency laser beam when the applied current slightly exceeds the lasing threshold. The laser frequency was less sensitive to diode temperature and could be finely tuned by adjusting the applied current. Laser frequency was stabilized onto a hyperfine component in an iodine transition through the saturated absorption spectroscopy. The uncertainty of frequency stabilization was approximately 8×10 -9 at a 10-s integration time. This compact laser system can replace the conventional green diode-pumped solid-state laser and applied as a frequency reference. A single longitudinal mode operational region with diode temperature, current, and output power was investigated.

  1. MicroRNA categorization using sequence motifs and k-mers.

    PubMed

    Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, Jens

    2017-03-14

    Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.

  2. MER Atmospheric Results: Pancam and Mini-TES

    NASA Astrophysics Data System (ADS)

    Wolff, M. J.

    2004-12-01

    Although at first glance, the Mars Exploration Rover (MER) payload may be perceived as primarily suited to geological investigation, it is in fact quite well-suited to carry out a robust and dynamic program of atmospheric monitoring and characterization with a particular emphasis on the planetary boundary layer. More to the point, it has been doing so at both the Gusev and Meridiani locations for more than 200 days. Ongoing atmospheric observations include (1) periodic thermal infrared spectra of the Martian sky by the Miniature Thermal Emission Spectrometer (Mini-TES). The actual sequences consist of both standard 200-second integrations and long ``stares'' of up to (almost) an hour. These data are highly diagnostic of vertical thermal structure (from 10 meters to 3-5 kilometers), aerosol optical depth along with particle size, and under the right conditions, the water column. (2) direct solar imaging using the Panoramic Camera (Pancam) and 440/880 nm + neutral density (ND5) filters, providing accurate measurement visible optical depths. (3) near-sun and ``sky-arc'' sequences using the full suite of geological filters, intended to capture the forward-diffraction peak and the phase function characteristics of the aerosol particles. (4) carbon dioxide (15 micrometer band) profiling of the Mini-TES surface observations, providing an average near-surface (1 m) air temperature. The above activities have been (and will continue to be) used to characterize diurnal and secular temporal trends and to examine the spatial variability of such trends. In addition, serendipity has provided the unique opportunities of watching the decay of a moderate dust storm from two widely-separated sites as well as of multiple simultaneous orbiter-rover observing ``campaigns.'' The latter includes thus far the Mars Express and Mars Global Surveyor over-flights. During our presentation, we will summarize the atmospheric results obtained and analyzed through the end of the first 200 days of

  3. MIMOS II on MER One Year of Mossbauer Spectroscopy on the Surface of Mars: From Jarosite at Meridiani Planum to Goethite at Gusev Crater

    NASA Technical Reports Server (NTRS)

    Klingelhoefer, G.; Rodionov, D. S.; Morris, R. V.; Schroeder, C.; deSouza, P. A.; Ming, D. W.; Yen, A. S.; Bernhardt, B.; Renz, F.; Fleischer, I.

    2005-01-01

    The miniaturized Mossbauer (MB) spectrometer MIMOS II [1] is part of the Athena payload of NASA s twin Mars Exploration Rovers "Spirit" (MER-A) and "Opportunity" (MER-B). It determines the Fe-bearing mineralogy of Martian soils and rocks at the Rovers respective landing sites, Gusev crater and Meridiani Planum. Both spectrometers performed successfully during first year of operation. Total integration time is about 49 days for MERA (79 samples) and 34 days for MER-B (85 samples). For curiosity it might be interesting to mention that the total odometry of the oscillating part of the MB drive exceeds 35 km for both rovers.

  4. Low frequency microwave radiometer for N-ROSS

    NASA Astrophysics Data System (ADS)

    Hollinger, J. P.; Lo, R. C.

    1984-01-01

    The all weather, global determination of sea surface temperature (SST) has been identified as a requirement needed to support naval operations.The target SST accuracy is + or 1.0 K with a surface resolution of 10 km. Investigations of the phenomenology and technology of remote passive microwave sensing of the ocean environment over the past decade have demonstrated that this objective is presently attainable. Preliminary specification and trade off studies were conducted to define the frequency, polarization, scan geometry, antenna size, and other essential parameters of the low frequency microwave radiometer (LFMR). It will be a meter deployable mesh surface antenna. It is to be flown on the Navy-Remote Ocean Sensing System (N-ROSS) satellite scheduled to be launched in late 1988.

  5. NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies.

    PubMed

    Sauk, Martin; Žilina, Olga; Kurg, Ants; Ustav, Eva-Liina; Peters, Maire; Paluoja, Priit; Roost, Anne Mari; Teder, Hindrek; Palta, Priit; Brison, Nathalie; Vermeesch, Joris R; Krjutškov, Kaarel; Salumets, Andres; Kaplinski, Lauris

    2018-04-04

    Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/ .

  6. Differential mercury volatilization by tobacco organs expressing a modified bacterial merA gene.

    PubMed

    He, Y K; Sun, J G; Feng, X Z; Czakó, M; Márton, L

    2001-09-01

    Mercury pollution is a major environmental problem accompanying industrial activities. Most of the mercury released ends up and retained in the soil as complexes of the toxic ionic mercury (Hg2+), which then can be converted by microbes into the even more toxic methylmercury which tends to bioaccumulate. Mercury detoxification of the soil can also occur by microbes converting the ionic mercury into the least toxic metallic mercury (Hg0) form, which then evaporates. The remediation potential of transgenic plants carrying the MerA gene from E. coli encoding mercuric ion reductase could be evaluated. A modified version of the gene, optimized for plant codon preferences (merApe9, Rugh et al. 1996), was introduced into tobacco by Agrobacterium-mediated leaf disk transformation. Transgenic seeds were resistant to HgCl2 at 50 microM, and some of them (10-20% ) could germinate on media containing as much as 350 microM HgCl2, while the control plants were fully inhibited or died on 50 microM HgCl2. The rate of elemental mercury evolution from Hg2+ (added as HgCl2) was 5-8 times higher for transgenic plants than the control. Mercury volatilization by isolated organs standardized for fresh weight was higher (up to 5 times) in the roots than in shoots or the leaves. The data suggest that it is the root system of the transgenic plants that volatilizes most of the reduced mercury (Hg0). It also suggests that much of the mercury need not enter the vascular system to be transported to the leaves for volatilization. Transgenic plants with the merApe9 gene may be used to mercury detoxification for environmental improvement in mercury-contaminated regions more efficiently than it had been predicted based on data on volatilization of whole plants via the upper parts only (Rugh et al. 1996).

  7. Risk factors for MERS coronavirus infection in dromedary camels in Burkina Faso, Ethiopia, and Morocco, 2015

    PubMed Central

    Miguel, Eve; Chevalier, Véronique; Ayelet, Gelagay; Ben Bencheikh, Med Nadir; Boussini, Hiver; Chu, Daniel KW; El Berbri, Ikhlass; Fassi-Fihri, Ouaffa; Faye, Bernard; Fekadu, Getnet; Grosbois, Vladimir; Ng, Bryan CY; Perera, Ranawaka APM; So, TY; Traore, Amadou; Roger, François; Peiris, Malik

    2017-01-01

    Understanding Middle East respiratory syndrome coronavirus (MERS-CoV) transmission in dromedary camels is important, as they consitute a source of zoonotic infection to humans. To identify risk factors for MERS-CoV infection in camels bred in diverse conditions in Burkina Faso, Ethiopia and Morocco, blood samples and nasal swabs were sampled in February–March 2015. A relatively high MERS-CoV RNA rate was detected in Ethiopia (up to 15.7%; 95% confidence interval (CI): 8.2–28.0), followed by Burkina Faso (up to 12.2%; 95% CI: 7–20.4) and Morocco (up to 7.6%; 95% CI: 1.9–26.1). The RNA detection rate was higher in camels bred for milk or meat than in camels for transport (p = 0.01) as well as in younger camels (p = 0.06). High seropositivity rates (up to 100%; 95% CI: 100–100 and 99.4%; 95% CI: 95.4–99.9) were found in Morocco and Ethiopia, followed by Burkina Faso (up to 84.6%; 95% CI: 77.2–89.9). Seropositivity rates were higher in large/medium herds (≥51 camels) than small herds (p = 0.061), in camels raised for meat or milk than for transport (p = 0.01), and in nomadic or sedentary herds than in herds with a mix of these lifestyles (p < 0.005). PMID:28382915

  8. Risk factors for MERS coronavirus infection in dromedary camels in Burkina Faso, Ethiopia, and Morocco, 2015.

    PubMed

    Miguel, Eve; Chevalier, Véronique; Ayelet, Gelagay; Ben Bencheikh, Med Nadir; Boussini, Hiver; Chu, Daniel Kw; El Berbri, Ikhlass; Fassi-Fihri, Ouaffa; Faye, Bernard; Fekadu, Getnet; Grosbois, Vladimir; Ng, Bryan Cy; Perera, Ranawaka Apm; So, T Y; Traore, Amadou; Roger, François; Peiris, Malik

    2017-03-30

    Understanding Middle East respiratory syndrome coronavirus (MERS-CoV) transmission in dromedary camels is important, as they consitute a source of zoonotic infection to humans. To identify risk factors for MERS-CoV infection in camels bred in diverse conditions in Burkina Faso, Ethiopia and Morocco, blood samples and nasal swabs were sampled in February-March 2015. A relatively high MERS-CoV RNA rate was detected in Ethiopia (up to 15.7%; 95% confidence interval (CI): 8.2-28.0), followed by Burkina Faso (up to 12.2%; 95% CI: 7-20.4) and Morocco (up to 7.6%; 95% CI: 1.9-26.1). The RNA detection rate was higher in camels bred for milk or meat than in camels for transport (p = 0.01) as well as in younger camels (p = 0.06). High seropositivity rates (up to 100%; 95% CI: 100-100 and 99.4%; 95% CI: 95.4-99.9) were found in Morocco and Ethiopia, followed by Burkina Faso (up to 84.6%; 95% CI: 77.2-89.9). Seropositivity rates were higher in large/medium herds (≥51 camels) than small herds (p = 0.061), in camels raised for meat or milk than for transport (p = 0.01), and in nomadic or sedentary herds than in herds with a mix of these lifestyles (p < 0.005). This article is copyright of The Authors, 2017.

  9. Microstructural, electrical and frequency-dependent properties of Au/p-Cu2ZnSnS4/n-GaN heterojunction.

    PubMed

    Rajagopal Reddy, V; Janardhanam, V; Won, Jonghan; Choi, Chel-Jong

    2017-08-01

    An Au/Cu 2 ZnSnS 4 (CZTS)/n-GaN heterojunction (HJ) is fabricated with a CZTS interlayer and probed its chemical states, structural, electrical and frequency-dependent characteristics by XPS, TEM, I-V and C-V measurements. XPS and TEM results confirmed that the CZTS films are formed on the n-GaN surface. The band gap of deposited CZTS film is found to be 1.55eV. The electrical properties of HJ correlated with the Au/n-GaN Schottky junction (SJ). The Au/CZTS/n-GaN HJ reveals a good rectification nature with high barrier height (0.82eV) compared to the Au/n-GaN SJ (0.69eV), which suggests the barrier height is influenced by the CZTS interlayer. The barrier height values assessed by I-V, Cheung's and Norde functions are closely matched with one other, thus the methods used here are reliable and valid. The extracted interface state density (N SS ) of Au/CZTS/n-GaN HJ is lower compared to the Au/n-GaN SJ that suggests the CZTS interlayer plays an important role in the reduction of N SS . Moreover, the capacitance-frequency (C-f) and conductance-frequency (G-f) characteristics of SJ and HJ are measured in the range of 1kHz-1MHz, and found that the capacitance and conductance strappingly dependent on frequency. It is found that the N SS estimated from C-f and G-f characteristics is lower compared to those estimated from I-V characteristics. Analysis confirmed that Poole-Frenkel emission dominates the reverse leakage current in both SJ and HJ, probably related to the structural defects and trap levels in the CZTS interlayer. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. ARM - Midlatitude Continental Convective Clouds Experiment (MC3E): Multi-Frequency Profilers, S-band Radar (williams-s_band)

    DOE Data Explorer

    Williams, Christopher

    2012-11-06

    This data was collected by the NOAA 449-MHz and 2.8-GHz profilers in support of the Department of Energy (DOE) and NASA sponsored Mid-latitude Continental Convective Cloud Experiment (MC3E). The profiling radars were deployed in Northern Oklahoma at the DOE Atmospheric Radiation Mission (ARM) Southern Great Plans (SGP) Central Facility from 22 April through 6 June 2011. NOAA deployed three instruments: a Parsivel disdrometer, a 2.8-GHz profiler, and a 449-MHz profiler. The parasivel provided surface estimates of the raindrop size distribution and is the reference used to absolutely calibrate the 2.8 GHz profiler. The 2.8-GHz profiler provided unattenuated reflectivity profiles of the precipitation. The 449-MHz profiler provided estimates of the vertical air motion during precipitation from near the surface to just below the freezing level. By using the combination of 2.8-GHz and 449-MHz profiler observations, vertical profiles of raindrop size distributions can be retrieved. The profilers are often reference by their frequency band: the 2.8-GHz profiler operates in the S-band and the 449-MHz profiler operates in the UHF band. The raw observations are available as well as calibrated spectra and moments. This document describes how the instruments were deployed, how the data was collected, and the format of the archived data.

  11. Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody

    DOE PAGES

    Ying, Tianlei; Prabakaran, Ponraj; Du, Lanying; ...

    2015-09-15

    The MERS-CoV is an emerging virus, which already infected more than 1,300 humans with high (~36%) mortality. Here, we show that m336, an exceptionally potent human anti-MERS-CoV antibody, is almost germline with only one somatic mutation in the heavy chain. The structure of Fab m336 in complex with the MERS-CoV receptor-binding domain reveals that its IGHV1-69-derived heavy chain provides more than 85% binding surface and that its epitope almost completely overlaps with the receptor-binding site. Analysis of antibodies from 69 healthy humans suggests an important role of the V(D)J recombination-generated junctional and allele-specific residues for achieving high affinity of bindingmore » at such low levels of somatic hypermutation. Our results also have important implications for development of vaccine immunogens based on the newly identified m336 epitope as well as for elucidation of mechanisms of neutralization by m336-like antibodies and their elicitation in vivo.« less

  12. Strength and Deformability of Light-toned Layered Deposits Observed by MER Opportunity: Eagle to Erebus Craters

    NASA Astrophysics Data System (ADS)

    Okubo, C. H.; Schultz, R. A.; Nahm, A. L.

    2007-07-01

    The strength and deformability of light-toned layered deposits are estimated based on measurements of porosity from Microscopic Imager data acquired by MER Opportunity during its traverse from Eagle Crater to Erebus Crater.

  13. Analysis of electronic parameters and frequency-dependent properties of Au/NiO/ n-GaN heterojunctions

    NASA Astrophysics Data System (ADS)

    Reddy, Varra Niteesh; Padma, R.; Gunasekhar, K. R.

    2018-01-01

    The electrical and frequency-dependent properties of ten Au/NiO/ n-GaN heterojunctions fabricated with similar conditions are assessed by I-V, C-V, and G-V measurement methods. In addition, C-f and G-f measurements are conducted in the frequency range of 1 kHz-1 MHz. The electronic parameters are changed from junction to junction even if they are fabricated in the similar way. The calculated barrier height and ideality factor values are fitted by the Gaussian distribution function. Statistical analysis of the data provides the mean barrier height and ideality factor values of 0.84 eV and 2.70 for the heterojunction. Besides, the mean barrier height ( V b), donor concentration ( N d), space charge layer width ( W D), and Fermi level ( E F) are determined from the C-V data and the corresponding values are 1.30 eV, 2.00 × 1017 cm-3, 8.222 × 10-6 cm, and 0.018 eV, respectively. The interface state density ( N SS) and relaxation time (τ) are assessed from C-f and G-f measurements. Moreover, the dielectric constant ( ɛ'), dielectric loss ( ɛ″), tangent loss (tan δ), and electrical conductivity ( σ ac) are determined from C-f and G-f data in the frequency range of 1 kHz-1 MHz with various biases (0.1-0.6 V). ɛ' and ɛ″ are decreased with increasing frequency.

  14. Comparison of incubation period distribution of human infections with MERS-CoV in South Korea and Saudi Arabia.

    PubMed

    Virlogeux, Victor; Fang, Vicky J; Park, Minah; Wu, Joseph T; Cowling, Benjamin J

    2016-10-24

    The incubation period is an important epidemiologic distribution, it is often incorporated in case definitions, used to determine appropriate quarantine periods, and is an input to mathematical modeling studies. Middle East Respiratory Syndrome coronavirus (MERS) is an emerging infectious disease in the Arabian Peninsula. There was a large outbreak of MERS in South Korea in 2015. We examined the incubation period distribution of MERS coronavirus infection for cases in South Korea and in Saudi Arabia. Using parametric and nonparametric methods, we estimated a mean incubation period of 6.9 days (95% credibility interval: 6.3-7.5) for cases in South Korea and 5.0 days (95% credibility interval: 4.0-6.6) among cases in Saudi Arabia. In a log-linear regression model, the mean incubation period was 1.42 times longer (95% credibility interval: 1.18-1.71) among cases in South Korea compared to Saudi Arabia. The variation that we identified in the incubation period distribution between locations could be associated with differences in ascertainment or reporting of exposure dates and illness onset dates, differences in the source or mode of infection, or environmental differences.

  15. NCI Scientists Solve Structure of Protein that Enables MERS Virus to Spread | Poster

    Cancer.gov

    Scientists at the Frederick National Lab have produced three crystal structures that reveal a specific part of a protein that can be targeted to fight the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an emerging viral respiratory illness. Senior Investigator David Waugh, Ph.D., Macromolecular Crystallography Laboratory, has solved the structure of an

  16. Relation of Cloud Occurrence Frequency, Overlap, and Effective Thickness Derived from CALIPSO and CloudSat Merged Cloud Vertical Profiles

    NASA Technical Reports Server (NTRS)

    Kato, Seiji; Sun-Mack, Sunny; Miller, Walter F.; Rose, Fred G.; Chen, Yan; Minnis, Patrick; Wielicki, Bruce A.

    2009-01-01

    A cloud frequency of occurrence matrix is generated using merged cloud vertical profile derived from Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and Cloud Profiling Radar (CPR). The matrix contains vertical profiles of cloud occurrence frequency as a function of the uppermost cloud top. It is shown that the cloud fraction and uppermost cloud top vertical pro les can be related by a set of equations when the correlation distance of cloud occurrence, which is interpreted as an effective cloud thickness, is introduced. The underlying assumption in establishing the above relation is that cloud overlap approaches the random overlap with increasing distance separating cloud layers and that the probability of deviating from the random overlap decreases exponentially with distance. One month of CALIPSO and CloudSat data support these assumptions. However, the correlation distance sometimes becomes large, which might be an indication of precipitation. The cloud correlation distance is equivalent to the de-correlation distance introduced by Hogan and Illingworth [2000] when cloud fractions of both layers in a two-cloud layer system are the same.

  17. The Role of Social Work for Foreign Residents in an Epidemic: The MERS Crisis in the Republic of Korea.

    PubMed

    Park, Hong-Jae; Lee, Bong Joo

    2016-01-01

    This article explores the experiences of foreign residents during the period of the Middle East Respiratory Syndrome (MERS) outbreak in (South) Korea and discusses from a social work perspective the implications of their experiences and their needs. Data were obtained from interviews with 22 foreigners who either live and work or study in Korea. The data were then interpreted using a thematic analysis approach in a multilingual research context. The findings from the study show that foreign residents experienced a wide range of social and psychoemotional difficulties during the MERS health threat. Implications for social work practice in an epidemic emergency are presented.

  18. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

    PubMed

    Pettengill, James B; Pightling, Arthur W; Baugher, Joseph D; Rand, Hugh; Strain, Errol

    2016-01-01

    The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

  19. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

    DOE PAGES

    Pettengill, James B.; Pightling, Arthur W.; Baugher, Joseph D.; ...

    2016-11-10

    The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging duemore » to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). Finally, when analyzing empirical data (wholegenome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.« less

  20. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

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

    Pettengill, James B.; Pightling, Arthur W.; Baugher, Joseph D.

    The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging duemore » to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). Finally, when analyzing empirical data (wholegenome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.« less

  1. Investigation of Trap States in AlInN/AlN/GaN Heterostructures by Frequency-Dependent Admittance Analysis

    NASA Astrophysics Data System (ADS)

    Arslan, Engin; Bütün, Serkan; Şafak, Yasemin; Ozbay, Ekmel

    2010-12-01

    We present a systematic study on the admittance characterization of surface trap states in unpassivated and SiN x -passivated Al0.83In0.17N/AlN/GaN heterostructures. C- V and G/ ω- V measurements were carried out in the frequency range of 1 kHz to 1 MHz, and an equivalent circuit model was used to analyze the experimental data. A detailed analysis of the frequency-dependent capacitance and conductance data was performed, assuming models in which traps are located at the metal-AlInN surface. The density ( D t) and time constant ( τ t) of the surface trap states have been determined as a function of energy separation from the conduction-band edge ( E c - E t). The D st and τ st values of the surface trap states for the unpassivated samples were found to be D_{{st}} \\cong (4 - 13) × 10^{12} {eV}^{ - 1} {cm}^{ - 2} and τ st ≈ 3 μs to 7 μs, respectively. For the passivated sample, D st decreased to 1.5 × 10^{12} {eV}^{ - 1} {cm}^{ - 2} and τ st to 1.8 μs to 2 μs. The density of surface trap states in Al0.83In0.17N/AlN/GaN heterostructures decreased by approximately one order of magnitude with SiN x passivation, indicating that the SiN x insulator layer between the metal contact and the surface of the Al0.83In0.17N layer can passivate surface states.

  2. Relationships among cloud occurrence frequency, overlap, and effective thickness derived from CALIPSO and CloudSat merged cloud vertical profiles

    NASA Astrophysics Data System (ADS)

    Kato, Seiji; Sun-Mack, Sunny; Miller, Walter F.; Rose, Fred G.; Chen, Yan; Minnis, Patrick; Wielicki, Bruce A.

    2010-01-01

    A cloud frequency of occurrence matrix is generated using merged cloud vertical profiles derived from the satellite-borne Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and cloud profiling radar. The matrix contains vertical profiles of cloud occurrence frequency as a function of the uppermost cloud top. It is shown that the cloud fraction and uppermost cloud top vertical profiles can be related by a cloud overlap matrix when the correlation length of cloud occurrence, which is interpreted as an effective cloud thickness, is introduced. The underlying assumption in establishing the above relation is that cloud overlap approaches random overlap with increasing distance separating cloud layers and that the probability of deviating from random overlap decreases exponentially with distance. One month of Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and CloudSat data (July 2006) support these assumptions, although the correlation length sometimes increases with separation distance when the cloud top height is large. The data also show that the correlation length depends on cloud top hight and the maximum occurs when the cloud top height is 8 to 10 km. The cloud correlation length is equivalent to the decorrelation distance introduced by Hogan and Illingworth (2000) when cloud fractions of both layers in a two-cloud layer system are the same. The simple relationships derived in this study can be used to estimate the top-of-atmosphere irradiance difference caused by cloud fraction, uppermost cloud top, and cloud thickness vertical profile differences.

  3. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and Mars Exploration Rover 2 (MER-A) are ready for the third launch attempt after weather concerns postponed earlier attempts. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and Mars Exploration Rover 2 (MER-A) are ready for the third launch attempt after weather concerns postponed earlier attempts. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  4. KENNEDY SPACE CENTER, FLA. - A solid rocket booster arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-14

    KENNEDY SPACE CENTER, FLA. - A solid rocket booster arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  5. 1 μs broadband frequency sweeping reflectometry for plasma density and fluctuation profile measurements

    NASA Astrophysics Data System (ADS)

    Clairet, F.; Bottereau, C.; Medvedeva, A.; Molina, D.; Conway, G. D.; Silva, A.; Stroth, U.; ASDEX Upgrade Team; Tore Supra Team; Eurofusion Mst1 Team

    2017-11-01

    Frequency swept reflectometry has reached the symbolic value of 1 μs sweeping time; this performance has been made possible, thanks to an improved control of the ramp voltage driving the frequency source. In parallel, the memory depth of the acquisition system has been upgraded and can provide up to 200 000 signals during a plasma discharge. Additional improvements regarding the trigger delay determination of the acquisition and the voltage ramp linearity required by this ultra-fast technique have been set. While this diagnostic is traditionally dedicated to the plasma electron density profile measurement, such a fast sweeping rate can provide the study of fast plasma events and turbulence with unprecedented time and radial resolution from the edge to the core. Experimental results obtained on ASDEX Upgrade plasmas are presented to demonstrate the performances of the diagnostic.

  6. Avoiding student infection during a Middle East respiratory syndrome (MERS) outbreak: a single medical school experience.

    PubMed

    Park, Seung Won; Jang, Hye Won; Choe, Yon Ho; Lee, Kyung Soo; Ahn, Yong Chan; Chung, Myung Jin; Lee, Kyu-Sung; Lee, Kyunghoon; Han, Taehee

    2016-06-01

    In outbreaks of infectious disease, medical students are easily overlooked in the management of healthcare personnel protection although they serve in clinical clerkships in hospitals. In the early summer of 2015, Middle East respiratory syndrome (MERS) struck South Korea, and students of Sungkyunkwan University School of Medicine (SKKUSOM) were at risk of contracting the disease. The purpose of this report is to share SKKUSOM's experience against the MERS outbreak and provide suggestions for medical schools to consider in the face of similar challenges. Through a process of reflection-on-action, we examined SKKUSOM's efforts to avoid student infection during the MERS outbreak and derived a few practical guidelines that medical schools can adopt to ensure student safety in outbreaks of infectious disease. The school leadership conducted ongoing risk assessment and developed contingency plans to balance student safety and continuity in medical education. They rearranged the clerkships to another hospital and offered distant lectures and tutorials. Five suggestions are extracted for medical schools to consider in infection outbreaks: instant cessation of clinical clerkships; rational decision making on a school closure; use of information technology; constant communication with hospitals; and open communication with faculty, staff, and students. Medical schools need to take the initiative and actively seek countermeasures against student infection. It is essential that medical schools keep constant communication with their index hospitals and the involved personnel. In order to assure student learning, medical schools may consider offering distant education with online technology.

  7. Imported case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection from Oman to Thailand, June 2015

    PubMed Central

    Plipat, Tanarak; Buathong, Rome; Wacharapluesadee, Supaporn; Siriarayapon, Potjaman; Pittayawonganon, Chakrarat; Sangsajja, Chariya; Kaewpom, Thongchai; Petcharat, Sininat; Ponpinit, Teerada; Jumpasri, Jaruphan; Joyjinda, Yutthana; Rodpan, Apaporn; Ghai, Siriporn; Jittmittraphap, Akanitt; Khongwichit, Sarawut; Smith, Duncan R; Corman, Victor M; Drosten, Christian; Hemachudha, Thiravat

    2017-01-01

    Thailand reported the first Middle East respiratory syndrome (MERS) case on 18 June 2015 (day 4) in an Omani patient with heart condition who was diagnosed with pneumonia on hospital admission on 15 June 2015 (day 1). Two false negative RT-PCR on upper respiratory tract samples on days 2 and 3 led to a 48-hour diagnosis delay and a decision to transfer the patient out of the negative pressure unit (NPU). Subsequent examination of sputum later on day 3 confirmed MERS coronavirus (MERS-CoV) infection. The patient was immediately moved back into the NPU and then transferred to Bamrasnaradura Infectious Disease Institute. Over 170 contacts were traced; 48 were quarantined and 122 self-monitored for symptoms. High-risk close contacts exhibiting no symptoms, and whose laboratory testing on the 12th day after exposure was negative, were released on the 14th day. The Omani Ministry of Health (MOH) was immediately notified using the International Health Regulation (IHR) mechanism. Outbreak investigation was conducted in Oman, and was both published on the World Health Organization (WHO) intranet and shared with Thailand’s IHR focal point. The key to successful infection control, with no secondary transmission, were the collaborative efforts among hospitals, laboratories and MOHs of both countries. PMID:28840828

  8. Thermal conductivity profile determination in proton-irradiated ZrC by spatial and frequency scanning thermal wave methods

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

    Jensen, C.; Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322; Chirtoc, M.

    2013-10-07

    Using complementary thermal wave methods, the irradiation damaged region of zirconium carbide (ZrC) is characterized by quantifiably profiling the thermophysical property degradation. The ZrC sample was irradiated by a 2.6 MeV proton beam at 600 °C to a dose of 1.75 displacements per atom. Spatial scanning techniques including scanning thermal microscopy (SThM), lock-in infrared thermography (lock-in IRT), and photothermal radiometry (PTR) were used to directly map the in-depth profile of thermal conductivity on a cross section of the ZrC sample. The advantages and limitations of each system are discussed and compared, finding consistent results from all techniques. SThM provides themore » best resolution finding a very uniform thermal conductivity envelope in the damaged region measuring ∼52 ± 2 μm deep. Frequency-based scanning PTR provides quantification of the thermal parameters of the sample using the SThM measured profile to provide validation of a heating model. Measured irradiated and virgin thermal conductivities are found to be 11.9 ± 0.5 W m{sup −1} K{sup −1} and 26.7 ±1 W m{sup −1} K{sup −1}, respectively. A thermal resistance evidenced in the frequency spectra of the PTR results was calculated to be (1.58 ± 0.1) × 10{sup −6} m{sup 2} K W{sup −1}. The measured thermal conductivity values compare well with the thermal conductivity extracted from the SThM calibrated signal and the spatially scanned PTR. Combined spatial and frequency scanning techniques are shown to provide a valuable, complementary combination for thermal property characterization of proton-irradiated ZrC. Such methodology could be useful for other studies of ion-irradiated materials.« less

  9. The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study

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

    Rothenberg, Sarah E.; Keiser, Sharon; Ajami, Nadim J.

    The mechanisms by which gut microbiota contribute to methylmercury metabolism remain unclear. Among a cohort of pregnant mothers, the main objectives of our pilot study were to determine 1) associations between gut microbiota and mercury concentrations in biomarkers (stool, hair and cord blood) and 2) the contributions of gut microbial mercury methylation/demethylation to stool methylmercury. Moreover, for pregnant women (36-39 weeks gestation, n=17) donated hair and stool specimens, and cord blood was collected for a subset (n=7). The diversity of gut microbiota was determined using 16S rRNA gene profiling (n=17). For 6 stool samples with highest/lowest methylmercury concentrations, metagenomic wholemore » genome shotgun sequencing was employed to search for one mercury methylation gene (hgcA), and two mer operon genes involved in methylmercury detoxification (merA and merB). There were seventeen bacterial genera that were significantly correlated (increasing or decreasing) with stool methylmercury, stool inorganic mercury, or hair total mercury; however, aside from one genus, there was no overlap between biomarkers. No definitive matches for hgcA or merB, while merA were detected at low concentrations in all six samples. Proportional differences in stool methylmercury were not likely attributed to gut microbiota through methylation/demethylation. Gut microbiota potentially altered methylmercury metabolism using indirect pathways.« less

  10. The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study

    DOE PAGES

    Rothenberg, Sarah E.; Keiser, Sharon; Ajami, Nadim J.; ...

    2016-02-01

    The mechanisms by which gut microbiota contribute to methylmercury metabolism remain unclear. Among a cohort of pregnant mothers, the main objectives of our pilot study were to determine 1) associations between gut microbiota and mercury concentrations in biomarkers (stool, hair and cord blood) and 2) the contributions of gut microbial mercury methylation/demethylation to stool methylmercury. Moreover, for pregnant women (36-39 weeks gestation, n=17) donated hair and stool specimens, and cord blood was collected for a subset (n=7). The diversity of gut microbiota was determined using 16S rRNA gene profiling (n=17). For 6 stool samples with highest/lowest methylmercury concentrations, metagenomic wholemore » genome shotgun sequencing was employed to search for one mercury methylation gene (hgcA), and two mer operon genes involved in methylmercury detoxification (merA and merB). There were seventeen bacterial genera that were significantly correlated (increasing or decreasing) with stool methylmercury, stool inorganic mercury, or hair total mercury; however, aside from one genus, there was no overlap between biomarkers. No definitive matches for hgcA or merB, while merA were detected at low concentrations in all six samples. Proportional differences in stool methylmercury were not likely attributed to gut microbiota through methylation/demethylation. Gut microbiota potentially altered methylmercury metabolism using indirect pathways.« less

  11. Towards high frequency heterojunction transistors: Electrical characterization of N-doped amorphous silicon-graphene diodes

    NASA Astrophysics Data System (ADS)

    Strobel, C.; Chavarin, C. A.; Kitzmann, J.; Lupina, G.; Wenger, Ch.; Albert, M.; Bartha, J. W.

    2017-06-01

    N-type doped amorphous hydrogenated silicon (a-Si:H) is deposited on top of graphene (Gr) by means of very high frequency (VHF) and radio frequency plasma-enhanced chemical vapor deposition (PECVD). In order to preserve the structural integrity of the monolayer graphene, a plasma excitation frequency of 140 MHz was successfully applied during the a-Si:H VHF-deposition. Raman spectroscopy results indicate the absence of a defect peak in the graphene spectrum after the VHF-PECVD of (n)-a-Si:H. The diode junction between (n)-a-Si:H and graphene was characterized using temperature dependent current-voltage (IV) and capacitance-voltage measurements, respectively. We demonstrate that the current at the (n)-a-Si:H-graphene interface is dominated by thermionic emission and recombination in the space charge region. The Schottky barrier height (qΦB), derived by temperature dependent IV-characteristics, is about 0.49 eV. The junction properties strongly depend on the applied deposition method of (n)-a-Si:H with a clear advantage of the VHF(140 MHz)-technology. We have demonstrated that (n)-a-Si:H-graphene junctions are a promising technology approach for high frequency heterojunction transistors.

  12. Analytical & Experimental Study of Radio Frequency Cavity Beam Profile Monitor

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

    Balcazar, Mario D.; Yonehara, Katsuya

    The purpose of this analytical and experimental study is multifold: 1) To explore a new, radiation-robust, hadron beam profile monitor for intense neutrino beam applications; 2) To test, demonstrate, and develop a novel gas-filled Radio-Frequency (RF) cavity to use in this monitoring system. Within this context, the first section of the study analyzes the beam distribution across the hadron monitor as well as the ion-production rate inside the RF cavity. Furthermore a more effecient pixel configuration across the hadron monitor is proposed to provide higher sensitivity to changes in beam displacement. Finally, the results of a benchtop test of themore » tunable quality factor RF cavity will be presented. The proposed hadron monitor configuration consists of a circular array of RF cavities located at a radial distance of 7cm { corresponding to the standard deviation of the beam due to scatering { and a gas-filled RF cavity with a quality factor in the range 400 - 800.« less

  13. In vitro and in vivo characterization of a reversible synthetic heparin analog.

    PubMed

    Whelihan, Matthew F; Cooley, Brian; Xu, Yongmei; Pawlinski, Rafal; Liu, Jian; Key, Nigel S

    2016-02-01

    The global supply of unfractionated heparin (UFH) and all commercially available low molecular weight heparins (LMWH) remain dependent on animal sources, such as porcine intestine or bovine lung. Recent experience has shown that contamination of the supply chain (with over-sulfated chondroitin sulfates) can result in lethal toxicity. Fondaparinux is currently the only commercially available synthetic analog of heparin. We recently described a new class of chemoenzymatically synthesized heparin analogs. One of these compounds (S12-mer) is a dodecasaccharide consisting of an antithrombin-binding moiety with repeating units of IdoA2S-GlcNS6S and two 3-O-sulfate groups that confer the ability to bind protamine. We sought to further characterize this new compound in vitro using biochemical and global coagulation assays and in vivo using thrombosis and hemostasis assays. The anticoagulant activities of the Super 12-mer (S12-mer) and Enoxaparin in anti-factor Xa and plasma-based thrombin generation assays were roughly equivalent with a 50% reduction in peak thrombin generation occurring at approximately 325nM. When protamine was titrated against a fixed concentration of S12-mer in plasma or blood, the S12-mer displayed a significant restitution of thrombin generation and clot formation. In vivo, S12-mer inhibited venous thrombosis to a similar extent as Enoxaparin, with similar bleeding profiles. These data show that the S12-mer has almost identical efficacy to Enoxaparin in terms of FXa inhibition, while displaying significant reversibility with protamine. Taken together with the ability to ensure purity and homogeneity from batch to batch, the S12-mer is a promising new synthetic heparin analog with a potentially enhanced safety profile. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Recapitulating phylogenies using k-mers: from trees to networks.

    PubMed

    Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

    2016-01-01

    Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

  15. MER : from landing to six wheels on Mars ... twice

    NASA Technical Reports Server (NTRS)

    Krajewski, Joel; Burke, Kevin; Lewicki, Chris; Limonadi, Daniel; Trebi-Ollennu, Ashitey; Voorhees, Chris

    2005-01-01

    Application of the Pathfinder landing system design to enclose the much larger Mars Exploration Rover required a variety of Rover deployments to achieve the surface driving configuration. The project schedule demanded that software design, engineering model test, and flight hardware build to be accomplished in parallel. This challenge was met through (a) bounding unknown environments against which to design and test, (b) early mechanical prototype testing, (c) constraining the scope of on-board autonomy to survival-critical deployments, (d) executing a balance of nominal and off-nominal test cases, (e) developing off-nominal event mitigation techniques before landing, (f) flexible replanning in response to surprises during operations. Here is discussed several specific events encountered during initial MER surface operations.

  16. Depth-time interpolation of feature trends extracted from mobile microelectrode data with kernel functions.

    PubMed

    Wong, Stephen; Hargreaves, Eric L; Baltuch, Gordon H; Jaggi, Jurg L; Danish, Shabbar F

    2012-01-01

    Microelectrode recording (MER) is necessary for precision localization of target structures such as the subthalamic nucleus during deep brain stimulation (DBS) surgery. Attempts to automate this process have produced quantitative temporal trends (feature activity vs. time) extracted from mobile MER data. Our goal was to evaluate computational methods of generating spatial profiles (feature activity vs. depth) from temporal trends that would decouple automated MER localization from the clinical procedure and enhance functional localization in DBS surgery. We evaluated two methods of interpolation (standard vs. kernel) that generated spatial profiles from temporal trends. We compared interpolated spatial profiles to true spatial profiles that were calculated with depth windows, using correlation coefficient analysis. Excellent approximation of true spatial profiles is achieved by interpolation. Kernel-interpolated spatial profiles produced superior correlation coefficient values at optimal kernel widths (r = 0.932-0.940) compared to standard interpolation (r = 0.891). The choice of kernel function and kernel width resulted in trade-offs in smoothing and resolution. Interpolation of feature activity to create spatial profiles from temporal trends is accurate and can standardize and facilitate MER functional localization of subcortical structures. The methods are computationally efficient, enhancing localization without imposing additional constraints on the MER clinical procedure during DBS surgery. Copyright © 2012 S. Karger AG, Basel.

  17. Electric and Dielectric Properties of Au/ZnS-PVA/n-Si (MPS) Structures in the Frequency Range of 10-200 kHz

    NASA Astrophysics Data System (ADS)

    Baraz, Nalan; Yücedağ, İbrahim; Azizian-Kalandaragh, Yashar; Ersöz, Gülçin; Orak, İkram; Altındal, Şemsettin; Akbari, Bashir; Akbari, Hossein

    2017-07-01

    Pure polyvinyl alcohol (PVA) capped ZnS semiconductor nanocrystals were prepared by microwave-assisted method, and the optical and structural properties of the as-prepared materials were characterized by x-ray diffraction (XRD) and Ultraviolet-visible (UV-Vis) techniques. The XRD pattern shows the formation of ZnS nanocrystals, and the UV-Vis spectroscopy results show a blue shift of about 1.2 eV in its band gap due to the confinement of very small nanostructures. The concentration of donor atoms ( N D), diffusion potential ( V D), Fermi energy level ( E F), and barrier height (ΦB ( C- V)) values were obtained from the reverse bias C -2- V plots for each frequency. The voltage dependent profile of series resistance ( R s) and surface states ( N ss) were also obtained using admittance and low-high frequency methods, respectively. R s- V and N ss- V plots both have distinctive peaks in the depletion region due to the spatial distribution charge at the surface states. The effect of R s and interfacial layer on the C- V and G/ ω- V characteristics was found remarkable at high frequencies. Therefore, the high frequency C- V and G/ ω- V plots were corrected to eliminate the effect of R s. The real and imaginary parts of dielectric constant ( ɛ' and ɛ″) and electric modulus ( M' and M″), loss tangent (tan δ), and ac electrical conductivity ( σ ac) were also obtained using C and G/ ω data and it was found that these parameters are indeed strong functions of frequency and applied bias voltage. Experimental results confirmed that the N ss, R s , and interfacial layer of the MPS structure are important parameters that strongly influence both the electrical and dielectric properties. The low values of N ss ( 109 eV-1 cm-2) and the value of dielectric constant ( ɛ' = 1.3) of ZnS-PVA interfacial layer even at 10 kHz are very suitable for electronic devices when compared with the SiO2. These results confirmed that the ZnS-PVA considerably improves the performance of

  18. Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers.

    PubMed

    Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlogl, Udo; Al-Nazawi, Mohamed

    2018-08-01

    Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer was modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system, with minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at the a and d positions of HR helix were strong stabilizers of HR recognition. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. n-alkane profiles of engine lubricating oil and particulate matter by molecular sieve extraction.

    PubMed

    Caravaggio, Gianni A; Charland, Jean-Pierre; Macdonald, Penny; Graham, Lisa

    2007-05-15

    As part of the Canadian Atmospheric Fine Particle Research Program to obtain reliable primary source emission profiles, a molecular sieve method was developed to reliably determine n-alkanes in lubricating oils, vehicle emissions, and mobile source dominated ambient particulate matter (PM). This work was also initiated to better calculate carbon preference index values (CPI: the ratio of the sums of odd over even n-alkanes), a parameter for estimating anthropogenic versus biogenic contributions in PM. n-Alkanes in lubricating oil and mobile source dominated PM are difficult to identify and quantify by gas chromatography due to the presence of similar components that cannot be fully resolved. This results in a hump, the unresolved complex mixture (UCM) that leads to incorrect n-alkane concentrations and CPI values. The sieve method yielded better chromatography, unambiguous identification of n-alkanes and allowed examination of differences between n-alkane profiles in light (LDV) and heavy duty vehicle (HDV) lubricating oils that would have been otherwise difficult. These profile differences made it possible to relate the LDV profile to that of the PM samples collected during a tunnel study in August 2001 near Vancouver (British Columbia, Canada). The n-alkane PM data revealed that longer sampling times result in a negative artifact, i.e., the desorption of the more volatile n-alkanes from the filters. Furthermore, the sieve procedure yielded n-alkane data that allowed calculation of accurate CPI values for lubricating oils and PM samples. Finally, this method may prove helpful in estimating the respective diesel and gasoline contributions to ambient PM.

  20. Kuramoto model with uniformly spaced frequencies: Finite-N asymptotics of the locking threshold.

    PubMed

    Ottino-Löffler, Bertrand; Strogatz, Steven H

    2016-06-01

    We study phase locking in the Kuramoto model of coupled oscillators in the special case where the number of oscillators, N, is large but finite, and the oscillators' natural frequencies are evenly spaced on a given interval. In this case, stable phase-locked solutions are known to exist if and only if the frequency interval is narrower than a certain critical width, called the locking threshold. For infinite N, the exact value of the locking threshold was calculated 30 years ago; however, the leading corrections to it for finite N have remained unsolved analytically. Here we derive an asymptotic formula for the locking threshold when N≫1. The leading correction to the infinite-N result scales like either N^{-3/2} or N^{-1}, depending on whether the frequencies are evenly spaced according to a midpoint rule or an end-point rule. These scaling laws agree with numerical results obtained by Pazó [D. Pazó, Phys. Rev. E 72, 046211 (2005)PLEEE81539-375510.1103/PhysRevE.72.046211]. Moreover, our analysis yields the exact prefactors in the scaling laws, which also match the numerics.

  1. First density profile measurements using frequency modulation of the continuous wave reflectometry on JETa)

    NASA Astrophysics Data System (ADS)

    Meneses, L.; Cupido, L.; Sirinelli, A.; Manso, M. E.; Jet-Efds Contributors

    2008-10-01

    We present the main design options and implementation of an X-mode reflectometer developed and successfully installed at JET using an innovative approach. It aims to prove the viability of measuring density profiles with high spatial and temporal resolution using broadband reflectometry operating in long and complex transmission lines. It probes the plasma with magnetic fields between 2.4 and 3.0 T using the V band [~(0-1.4)×1019 m-3]. The first experimental results show the high sensitivity of the diagnostic when measuring changes in the plasma density profile occurring ITER relevant regimes, such as ELMy H-modes. The successful demonstration of this concept motivated the upgrade of the JET frequency modulation of the continuous wave (FMCW) reflectometry diagnostic, to probe both the edge and core. This new system is essential to prove the viability of using the FMCW reflectometry technique to probe the plasma in next step devices, such as ITER, since they share the same waveguide complexity.

  2. Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications.

    PubMed

    Kim, K H; Tandi, T E; Choi, J W; Moon, J M; Kim, M S

    2017-02-01

    Since the first case of Middle East respiratory syndrome coronavirus (MERS-CoV) in South Korea was reported on 20 th May 2015, there have been 186 confirmed cases, 38 deaths and 16,752 suspected cases. Previously published research on South Korea's MERS outbreak was limited to the early stages, when few data were available. Now that the outbreak has ended, albeit unofficially, a more comprehensive review is appropriate. Data were obtained through the MERS portal by the Ministry for Health and Welfare (MOHW) and Korea Centres for Disease Control and Prevention, press releases by MOHW, and reports by the MERS Policy Committee of the Korean Medical Association. Cases were analysed for general characteristics, exposure source, timeline and infection generation. Sex, age and underlying diseases were analysed for the 38 deaths. Beginning with the index case that infected 28 others, an in-depth analysis was conducted. The average age was 55 years, which was a little higher than the global average of 50 years. As in most other countries, more men than women were affected. The case fatality rate was 19.9%, which was lower than the global rate of 38.7% and the rate in Saudi Arabia (36.5%). In total, 184 patients were infected nosocomially and there were no community-acquired infections. The main underlying diseases were respiratory diseases, cancer and hypertension. The main contributors to the outbreak were late diagnosis, quarantine failure of 'super spreaders', familial care-giving and visiting, non-disclosure by patients, poor communication by the South Korean Government, inadequate hospital infection management, and 'doctor shopping'. The outbreak was entirely nosocomial, and was largely attributable to infection management and policy failures, rather than biomedical factors. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  3. Delta II Heavy MER-B - MST Rollback

    NASA Image and Video Library

    2003-07-07

    The Mobile Service Tower is ready to be rolled back at Launch Complex 17-B, Cape Canaveral Air Force Station, to launch the Delta II Heavy launch vehicle carrying the rover "Opportunity" on the second Mars Exploration Rover mission. Opportunity will reach Mars on Jan. 25, 2004. Together the two MER rovers, Spirit (launched June 10) and Opportunity, seek to determine the history of climate and water at two sites on Mars where conditions may once have been favorable to life. The rovers are identical. They will navigate themselves around obstacles as they drive across the Martian surface, traveling up to about 130 feet each Martian day. Each rover carries five scientific instruments including a panoramic camera and microscope, plus a rock abrasion tool that will grind away the outer surfaces of rocks to expose their interiors for examination. Each rover’s prime mission is planned to last three months on Mars.

  4. The potential of high-frequency profiling to assess vertical and seasonal patterns of phytoplankton dynamics in lakes: An extension of the Plankton Ecology Group (PEG) model

    USGS Publications Warehouse

    Brentrup, Jennifer A.; Williamson, Craig E.; Colom-Montero, William; Eckert, Werner; de Eyto, Elvira; Grossart, Hans-Peter; Huot, Yannick; Isles, Peter D. F.; Knoll, Lesley B.; Leach, Taylor H.; McBride, Christopher G.; Pierson, Don; Pomati, Francesco; Read, Jordan S.; Rose, Kevin C.; Samal, Nihar R.; Staehr, Peter A.; Winslow, Luke A.

    2016-01-01

    The use of high-frequency sensors on profiling buoys to investigate physical, chemical, and biological processes in lakes is increasing rapidly. Profiling buoys with automated winches and sensors that collect high-frequency chlorophyll fluorescence (ChlF) profiles in 11 lakes in the Global Lake Ecological Observatory Network (GLEON) allowed the study of the vertical and temporal distribution of ChlF, including the formation of subsurface chlorophyll maxima (SSCM). The effectiveness of 3 methods for sampling phytoplankton distributions in lakes, including (1) manual profiles, (2) single-depth buoys, and (3) profiling buoys were assessed. High-frequency ChlF surface data and profiles were compared to predictions from the Plankton Ecology Group (PEG) model. The depth-integrated ChlF dynamics measured by the profiling buoy data revealed a greater complexity that neither conventional sampling nor the generalized PEG model captured. Conventional sampling techniques would have missed SSCM in 7 of 11 study lakes. Although surface-only ChlF data underestimated average water column ChlF, at times by nearly 2-fold in 4 of the lakes, overall there was a remarkable similarity between surface and mean water column data. Contrary to the PEG model’s proposed negligible role for physical control of phytoplankton during the growing season, thermal structure and light availability were closely associated with ChlF seasonal depth distribution. Thus, an extension of the PEG model is proposed, with a new conceptual framework that explicitly includes physical metrics to better predict SSCM formation in lakes and highlight when profiling buoys are especially informative.

  5. Multiple Frequency Contrast Source Inversion Method for Vertical Electromagnetic Profiling: 2D Simulation Results and Analyses

    NASA Astrophysics Data System (ADS)

    Li, Jinghe; Song, Linping; Liu, Qing Huo

    2016-02-01

    A simultaneous multiple frequency contrast source inversion (CSI) method is applied to reconstructing hydrocarbon reservoir targets in a complex multilayered medium in two dimensions. It simulates the effects of a salt dome sedimentary formation in the context of reservoir monitoring. In this method, the stabilized biconjugate-gradient fast Fourier transform (BCGS-FFT) algorithm is applied as a fast solver for the 2D volume integral equation for the forward computation. The inversion technique with CSI combines the efficient FFT algorithm to speed up the matrix-vector multiplication and the stable convergence of the simultaneous multiple frequency CSI in the iteration process. As a result, this method is capable of making quantitative conductivity image reconstruction effectively for large-scale electromagnetic oil exploration problems, including the vertical electromagnetic profiling (VEP) survey investigated here. A number of numerical examples have been demonstrated to validate the effectiveness and capacity of the simultaneous multiple frequency CSI method for a limited array view in VEP.

  6. 3-D Surface Depression Profiling Using High Frequency Focused Air-Coupled Ultrasonic Pulses

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Kautz, Harold E.; Abel, Phillip B.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

    1999-01-01

    Surface topography is an important variable in the performance of many industrial components and is normally measured with diamond-tip profilometry over a small area or using optical scattering methods for larger area measurement. This article shows quantitative surface topography profiles as obtained using only high-frequency focused air-coupled ultrasonic pulses. The profiles were obtained using a profiling system developed by NASA Glenn Research Center and Sonix, Inc (via a formal cooperative agreement). (The air transducers are available as off-the-shelf items from several companies.) The method is simple and reproducible because it relies mainly on knowledge and constancy of the sound velocity through the air. The air transducer is scanned across the surface and sends pulses to the sample surface where they are reflected back from the surface along the same path as the incident wave. Time-of-flight images of the sample surface are acquired and converted to depth/surface profile images using the simple relation (d = V*t/2) between distance (d), time-of-flight (t), and the velocity of sound in air (V). The system has the ability to resolve surface depression variations as small as 25 microns, is useable over a 1.4 mm vertical depth range, and can profile large areas only limited by the scan limits of the particular ultrasonic system. (Best-case depth resolution is 0.25 microns which may be achievable with improved isolation from vibration and air currents.) The method using an optimized configuration is reasonably rapid and has all quantitative analysis facilities on-line including 2-D and 3-D visualization capability, extreme value filtering (for faulty data), and leveling capability. Air-coupled surface profilometry is applicable to plate-like and curved samples. In this article, results are shown for several proof-of-concept samples, plastic samples burned in microgravity on the STS-54 space shuttle mission, and a partially-coated cylindrical ceramic

  7. Imported case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection from Oman to Thailand, June 2015.

    PubMed

    Plipat, Tanarak; Buathong, Rome; Wacharapluesadee, Supaporn; Siriarayapon, Potjaman; Pittayawonganon, Chakrarat; Sangsajja, Chariya; Kaewpom, Thongchai; Petcharat, Sininat; Ponpinit, Teerada; Jumpasri, Jaruphan; Joyjinda, Yutthana; Rodpan, Apaporn; Ghai, Siriporn; Jittmittraphap, Akanitt; Khongwichit, Sarawut; Smith, Duncan R; Corman, Victor M; Drosten, Christian; Hemachudha, Thiravat

    2017-08-17

    Thailand reported the first Middle East respiratory syndrome (MERS) case on 18 June 2015 (day 4) in an Omani patient with heart condition who was diagnosed with pneumonia on hospital admission on 15 June 2015 (day 1). Two false negative RT-PCR on upper respiratory tract samples on days 2 and 3 led to a 48-hour diagnosis delay and a decision to transfer the patient out of the negative pressure unit (NPU). Subsequent examination of sputum later on day 3 confirmed MERS coronavirus (MERS-CoV) infection. The patient was immediately moved back into the NPU and then transferred to Bamrasnaradura Infectious Disease Institute. Over 170 contacts were traced; 48 were quarantined and 122 self-monitored for symptoms. High-risk close contacts exhibiting no symptoms, and whose laboratory testing on the 12th day after exposure was negative, were released on the 14th day. The Omani Ministry of Health (MOH) was immediately notified using the International Health Regulation (IHR) mechanism. Outbreak investigation was conducted in Oman, and was both published on the World Health Organization (WHO) intranet and shared with Thailand's IHR focal point. The key to successful infection control, with no secondary transmission, were the collaborative efforts among hospitals, laboratories and MOHs of both countries. This article is copyright of The Authors, 2017.

  8. Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors.

    PubMed

    Kumar, Vathan; Tan, Kian-Pin; Wang, Ying-Ming; Lin, Sheng-Wei; Liang, Po-Huang

    2016-07-01

    Severe acute respiratory syndrome (SARS) led to a life-threatening form of atypical pneumonia in late 2002. Following that, Middle East Respiratory Syndrome (MERS-CoV) has recently emerged, killing about 36% of patients infected globally, mainly in Saudi Arabia and South Korea. Based on a scaffold we reported for inhibiting neuraminidase (NA), we synthesized the analogues and identified compounds with low micromolar inhibitory activity against 3CL(pro) of SARS-CoV and MERS-CoV. Docking studies show that a carboxylate present at either R(1) or R(4) destabilizes the oxyanion hole in the 3CL(pro). Interestingly, 3f, 3g and 3m could inhibit both NA and 3CL(pro) and serve as a starting point to develop broad-spectrum antiviral agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Public Health Network Structure and Collaboration Effectiveness during the 2015 MERS Outbreak in South Korea: An Institutional Collective Action Framework

    PubMed Central

    Andrew, Simon A.

    2017-01-01

    Following the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to examine the structural effect of public health network explaining collaboration effectiveness, which is defined as joint efforts to improve quality of service provision, cost savings, and coordination. We tested the bonding and bridging effects on collaboration effectiveness during the MERS outbreak response by utilizing an institutional collective action framework. The analysis results of 114 organizations responding during the crisis show a significant association between the bonding effect and the effectiveness of collaboration, as well as a positive association between risk communication in disseminating public health information and the effectiveness of collaboration. PMID:28914780

  10. Regional N2O fluxes in Amazonia derived from aircraft vertical profiles

    NASA Astrophysics Data System (ADS)

    D'Amelio, M. T. S.; Gatti, L. V.; Miller, J. B.; Tans, P.

    2009-11-01

    Nitrous oxide (N2O) is the third most important anthropogenic greenhouse gas. Globally, the main sources of N2O are nitrification and denitrification in soils. About two thirds of the soil emissions occur in the tropics and approximately 20% originate in wet rainforest ecosystems, like the Amazon forest. The work presented here involves aircraft vertical profiles of N2O from the surface to 4 km over two sites in the Eastern and Central Amazon: Tapajós National Forest (SAN) and Cuieiras Biologic Reserve (MAN), and the estimation of N2O fluxes for regions upwind of these sites. To our knowledge, these regional scale N2O measurements in Amazonia are unique and represent a new approach to looking regional scale emissions. The fluxes upwind of MAN exhibited little seasonality, and the annual mean was 2.1±1.0 mg N2O m-2 day-1, higher than that for fluxes upwind of SAN, which averaged 1.5±1.6 mg N2O m-2 day-1. The higher rainfall around the MAN site could explain the higher N2O emissions, as a result of increased soil moisture accelerating microbial nitrification and denitrification processes. For fluxes from the coast to SAN seasonality is present for all years, with high fluxes in the months of March through May, and in November through December. The first peak of N2O flux is strongly associated with the wet season. The second peak of high N2O flux recorded at SAN occurs during the dry season and can not be easily explained. However, about half of the dry season profiles exhibit significant correlations with CO, indicating a larger than expected source of N2O from biomass burning. The average CO:N2O ratio for all profiles sampled during the dry season is 94±77 mol CO:mol N2O and suggests a larger biomass burning contribution to the global N2O budget than previously reported.

  11. Regional N2O fluxes in Amazonia derived from aircraft vertical profiles

    NASA Astrophysics Data System (ADS)

    D'Amelio, M. T. S.; Gatti, L. V.; Miller, J. B.; Tans, P.

    2009-08-01

    Nitrous oxide (N2O) is the third most important anthropogenic greenhouse gas. Globally, the main sources of N2O are nitrification and denitrification in soils. About two thirds of the soil emissions occur in the tropics and approximately 20% originate in wet rainforest ecosystems, like the Amazon forest. The work presented here involves aircraft vertical profiles of N2O from the surface to 4 km over two sites in the Eastern and Central Amazon: Tapajós National Forest (SAN) and Cuieiras Biologic Reserve (MAN), and the estimation of N2O fluxes for regions upwind of these sites. To our knowledge, these regional scale N2O measurements in Amazonia are unique and represent a new approach to looking regional scale emissions. The fluxes upwind of MAN exhibited little seasonality, and the annual mean was 2.1±1.0 mg N2O m-2 day-1, higher than that for fluxes upwind of SAN, which averaged 1.5±1.6 mg N2O m-2 day-1. The higher rainfall around the MAN site could explain the higher N2O emissions. For fluxes from the coast to SAN seasonality is present for all years, with high fluxes in the months of March through May, and in November through December. The first peak of N2O flux is strongly associated with the wet season. The second peak of high N2O flux recorded at SAN occurs during the dry season and can not be easily explained. However, about half of the dry season profiles exhibit significant correlations with CO, indicating a larger than expected source of N2O from biomass burning. The average CO:N2O ratio for all profiles sampled during the dry season is 94±77 mol CO:mol N2O and suggests a larger biomass burning contribution to the global N2O budget than previously reported.

  12. Role of ionization and electron drift velocity profile to Rayleigh instability in a Hall thruster plasma

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

    Singh, Sukhmander; Malik, Hitendra K.

    Role of ionization to Rayleigh instability is clarified in a Hall thruster plasma under the variety of profiles of electron drift velocity, namely, step-like profile (SLP) and two different super-Gaussian profiles (SGP1 and SGP2). For this, a relevant Rayleigh equation is derived and solved numerically using fourth-order Runge-Kutta method. Interestingly, an upper cutoff frequency of oscillations {omega}{sub max} is realized for the occurrence of the instability that shows dependence on the ionization rate {alpha}, electron drift velocity u{sub 0}, electron cyclotron frequency {Omega}, azimuthal wave number k{sub y}, plasma density n{sub 0}, density gradient {partial_derivative}n{sub 0}/{partial_derivative}x, ion (electron) thermal speedmore » V{sub thI}(V{sub thE}), and ion (electron) plasma frequency {omega}{sub pi}({omega}{sub pe}). The frequency {omega}{sub max} follows the trend {omega}{sub max} (for SGP2) >{omega}{sub max} (for SLP) >{omega}{sub max} (for SGP1) and shows a similar behaviour with ionization for all types of the velocity profiles. The instability is found to grow faster for the higher {alpha} and the ion temperature but it acquires lower rate under the effect of the higher electron temperature; the perturbed potential also varies in accordance with the growth rate. The electron temperature influences the growth rate and cutoff frequency less significantly in comparison with the ion temperature.« less

  13. Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.

    PubMed

    Nims, Raymond W; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera; Elmore, Eugene

    2010-12-01

    The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.

  14. KENNEDY SPACE CENTER, FLA. - Leaving smoke and steam behind, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - Leaving smoke and steam behind, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  15. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  16. KENNEDY SPACE CENTER, FLA. - Amid billows of smoke and steam, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - Amid billows of smoke and steam, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  17. KENNEDY SPACE CENTER, FLA. - A third solid rocket booster (SRB) is lifted up the launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station. They are three of nine SRBs that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-14

    KENNEDY SPACE CENTER, FLA. - A third solid rocket booster (SRB) is lifted up the launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station. They are three of nine SRBs that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  18. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, workers complete raising a solid rocket booster to a vertical position. It will be lifted up the launch tower and mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-14

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, workers complete raising a solid rocket booster to a vertical position. It will be lifted up the launch tower and mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  19. KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the outside of the launch tower. Visible on another side is the Delta II rocket that will carry the payload into space. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

    NASA Image and Video Library

    2003-04-30

    KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the outside of the launch tower. Visible on another side is the Delta II rocket that will carry the payload into space. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

  20. Productivity depends more on the rate than the frequency of N addition in a temperate grassland.

    PubMed

    Zhang, Yunhai; Feng, Jinchao; Isbell, Forest; Lü, Xiaotao; Han, Xingguo

    2015-07-28

    Nitrogen (N) is a key limiting resource for aboveground net primary productivity (ANPP) in diverse terrestrial ecosystems. The relative roles of the rate and frequency (additions yr(-1)) of N application in stimulating ANPP at both the community- and species-levels are largely unknown. By independently manipulating the rate and frequency of N input, with nine rates (from 0 to 50 g N m(-2) year(-1)) crossed with two frequencies (twice year(-1) or monthly) in a temperate steppe of northern China across 2008-2013, we found that N addition increased community ANPP, and had positive, negative, or neutral effects for individual species. There were similar ANPP responses at the community- or species-level when a particular annual amount of N was added either twice year(-1) or monthly. The community ANPP was less sensitive to soil ammonium at lower frequency of N addition. ANPP responses to N addition were positively correlated with annual precipitation. Our results suggest that, over a five-year period, there will be similar ANPP responses to a given annual N input that occurs either frequently in small amounts, as from N deposition, or that occur infrequently in larger amounts, as from application of N fertilizers.

  1. NCI Scientists Solve Structure of Protein that Enables MERS Virus to Spread | Poster

    Cancer.gov

    Scientists at the Frederick National Lab have produced three crystal structures that reveal a specific part of a protein that can be targeted to fight the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an emerging viral respiratory illness. Senior Investigator David Waugh, Ph.D., Macromolecular Crystallography Laboratory, has solved the structure of an enzyme known as the 3C-like protease (3CLpro), which, if blocked, can prevent the virus from replicating...

  2. Screening sourdough samples for gliadin-degrading activity revealed Lactobacillus casei strains able to individually metabolize the coeliac-disease-related 33-mer peptide.

    PubMed

    Alvarez-Sieiro, Patricia; Redruello, Begoña; Ladero, Victor; Martín, Maria Cruz; Fernández, María; Alvarez, Miguel A

    2016-05-01

    A selective culture medium containing acid-hydrolyzed gliadins as the sole nitrogen source was used in the search for sourdough-indigenous lactic acid bacteria (LAB) with gliadin-metabolizing activity. Twenty gliadin-degrading LAB strains were isolated from 10 sourdoughs made in different ways and from different geographical regions. Fifteen of the 20 isolated strains were identified as Lactobacillus casei, a species usually reported as subdominant in sourdough populations. The other 5 gliadin-degrading strains belonged to the more commonly encountered sourdough species Leuconostoc mesenteroides and Lactobacillus plantarum. All these strains were shown to be safe in terms of their resistance to antimicrobial agents. When individually incubated with the α2-gliadin-derived immunotoxic 33-mer peptide (97.5 ppm), half of the L. casei strains metabolized at least 50% of it within 24 h. One strain metabolized 82% of the 33-mer peptide within 8 h and made it fully disappear within 12 h. These results reveal for the first time the presence in sourdough of proteolytic L. casei strains with the capacity to individually metabolize the coeliac-disease-related 33-mer peptide.

  3. Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model.

    PubMed

    de Wilde, Adriaan H; Falzarano, Darryl; Zevenhoven-Dobbe, Jessika C; Beugeling, Corrine; Fett, Craig; Martellaro, Cynthia; Posthuma, Clara C; Feldmann, Heinz; Perlman, Stanley; Snijder, Eric J

    2017-01-15

    Currently, there is no registered treatment for infections with emerging zoonotic coronaviruses like SARS- and MERS-coronavirus. We here report that in cultured cells low-micromolar concentrations of alisporivir, a non-immunosuppressive cyclosporin A-analog, inhibit the replication of four different coronaviruses, including MERS- and SARS-coronavirus. Ribavirin was found to further potentiate the antiviral effect of alisporivir in these cell culture-based infection models, but this combination treatment was unable to improve the outcome of SARS-CoV infection in a mouse model. Nevertheless, our data provide a basis to further explore the potential of Cyp inhibitors as host-directed, broad-spectrum inhibitors of coronavirus replication. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  4. Possible Evidence for Iron Sulfates, Iron Sulfides, and Elemental Sulfur at Gusev Crater, Mars, from Mer, Crism, and Analog Data

    NASA Technical Reports Server (NTRS)

    Morris, R. V.; Ming, D. W.; Yen, A.; Arvidson, R. E.; Gruener, J.; Humm, D.; Klingelhoefer, G.; Murchie, S.; Schroeder, C.; Seelos, F., IV; hide

    2007-01-01

    The Mossbauer (MB) spectrometers on the Mars Exploration Rovers (MER) Spirit (Gusev crater) and Opportunity (Meridiani Planum) have detected 14 Fe-bearing phases, and mineralogical assignments have been made for all except 3. Identified Fe2+-bearing phases are olivine, pyroxene, ilmenite, and troilite. Magnetite and chromite are present as mixed Fe(2+) and Fe(3+) phases. Identified Fe(3+) phase are jarosite, hematite, goethite, and nanophase ferric oxide (npOx). Fe(sup 0) (iron metal) is present as kamacite. Nanophase ferric oxide (npOx) is a generic name for octahedrally coordinated Fe(3+) alteration products that cannot be otherwise mineralogically assigned on the basis of MER data. On the Earth, npOx would include ferrihydrite, iddingsite, schwertmannite, akaganeite, and superparamagnetic hematite and goethite. The Mars Reconnaissance Orbiter CRISM instrument, a visible, near-IR hyperspectral imager (approximately 0.35 to 4 micron) enables mineralogical examination of Mars with a tool that is sensitive to H2O and to M-OH (M = Al, Si, Fe, Mg, etc.) at spatial resolution of about 20 m/pixel. We examined a CRISM image of the MER region of Gusev crater (Columbia Hills and plains to the west), looking for spectral evidence of the aqueous process apparent from the MER analyses. We also searched for spectral constraints for the mineralogical composition of our unidentified Fe-bearing phases and the forms of npOx present on Mars. We also consider evidence from analogue samples that the precursor for the goethite detected by MB in Clovis Class rocks is an iron sulfide. We suggest that there is some indirect evidence that elemental sulfur might be present to different extents in Clovis Class rocks, the Fe3Sulfate-rich soils, and perhaps even typical (Laguna Class) surface soils.

  5. Photochemistry of Iron and Ruthenium Carbonyl Complexes: Evidence for Light-Induced Loss of Carbon Monoxide and Reductive Elimination of Triethylsilane from cis-mer-HM(SiEt3)(CO)3(PPh3).

    DTIC Science & Technology

    1983-05-21

    JEOL FX9OQ Fourier transform or Bruker 250 or 270 MHz Fourier transform spectrometer. Irradiations. Photochemical reactions were carried out using a...Ph 3 ) 3nd -t-Etin V,- a 313 nm quantum yield of -0.6. The process is photochemically everse if the cis-mer-HM(SiPh 3 )(CO) 3 (PPh 3) is irradiated...process is photochemically reversed if the cis-mer-HM(SiPh 3 )(CO)3 (PPh 3 ) is irradiated in t.e presence of excess Et3SiH. Irradiation of cis-mer-HM

  6. Improved modified energy ratio method using a multi-window approach for accurate arrival picking

    NASA Astrophysics Data System (ADS)

    Lee, Minho; Byun, Joongmoo; Kim, Dowan; Choi, Jihun; Kim, Myungsun

    2017-04-01

    To identify accurately the location of microseismic events generated during hydraulic fracture stimulation, it is necessary to detect the first break of the P- and S-wave arrival times recorded at multiple receivers. These microseismic data often contain high-amplitude noise, which makes it difficult to identify the P- and S-wave arrival times. The short-term-average to long-term-average (STA/LTA) and modified energy ratio (MER) methods are based on the differences in the energy densities of the noise and signal, and are widely used to identify the P-wave arrival times. The MER method yields more consistent results than the STA/LTA method for data with a low signal-to-noise (S/N) ratio. However, although the MER method shows good results regardless of the delay of the signal wavelet for signals with a high S/N ratio, it may yield poor results if the signal is contaminated by high-amplitude noise and does not have the minimum delay. Here we describe an improved MER (IMER) method, whereby we apply a multiple-windowing approach to overcome the limitations of the MER method. The IMER method contains calculations of an additional MER value using a third window (in addition to the original MER window), as well as the application of a moving average filter to each MER data point to eliminate high-frequency fluctuations in the original MER distributions. The resulting distribution makes it easier to apply thresholding. The proposed IMER method was applied to synthetic and real datasets with various S/N ratios and mixed-delay wavelets. The results show that the IMER method yields a high accuracy rate of around 80% within five sample errors for the synthetic datasets. Likewise, in the case of real datasets, 94.56% of the P-wave picking results obtained by the IMER method had a deviation of less than 0.5 ms (corresponding to 2 samples) from the manual picks.

  7. GAS6/Mer axis regulates the homing and survival of the E2A/PBX1 positive B-cell precursor acute lymphoblastic leukemia in the bone marrow niche

    PubMed Central

    Shiozawa, Yusuke; Pedersen, Elisabeth A.; Taichman, Russell S.

    2009-01-01

    Despite improvements in current combinational chemotherapy regimens, the prognosis of the (1;19)(q23;p13) translocation (E2A/PBX1) positive B-cell precursor acute lymphoblastic leukemia (ALL) is poor in pediatric leukemia patients. In this study, we examined the roles of GAS6/Mer axis in the interactions between E2A/PBX1 positive B-cell precursor ALL cells and the osteoblastic niche in the bone marrow. The data show that primary human osteoblasts secrete GAS6 in response to the Mer-over-expressed E2A/PBX1 positive ALL cells through MAPK signaling pathway and that leukemia cells migrate toward GAS6 using pathways activated by Mer. Importantly, GAS6 supports the survival and prevents apoptosis from chemotherapy of E2A/PBX1 positive ALL cells by inducing dormancy. Together, these data suggest that GAS6/Mer axis regulates the homing and survival of the E2A/PBX1 positive B-cell precursor ALL in the bone marrow niche. PMID:19922767

  8. Tolerance or avoidance: drought frequency determines the response of an N 2 -fixing tree

    Treesearch

    Jeffrey M. Minucci; Chelcy Ford Miniat; Robert O. Teskey; Nina Wurzburger

    2017-01-01

    • Climate change is increasing drought frequency, which may affect symbiotic N2 fixation (SNF), a process that facilitates ecosystem recovery from disturbance. Here, we assessed the effect of drought frequency on the ecophysiology and SNF rate of a common N2-fixing tree in eastern US forests.•We grew Robinia pseudoacacia seedlings under the same mean soil...

  9. Stratospheric N2O5, CH4, and N2O profiles from IR solar occultation spectra

    NASA Technical Reports Server (NTRS)

    Camy-Peyret, C.; Flaud, J.-M.; Perrin, A.; Rinsland, C. P.; Goldman, A.; Murcray, F. J.

    1993-01-01

    Stratospheric volume mixing ratio profiles of N2O5, CH4, and N2O have been retrieved from a set of 0.052/cm resolution (FWHM) solar occultation spectra recorded at sunrise during a balloon flight from Aire sur l'Adour, France (44 N latitude) on 12 October 1990. The N2O5 results have been derived from measurements of the integrated absorption by the 1246/cm band. Assuming a total intensity of 4.32 x 10 exp -17 cm/molecule/sq cm independent of temperature, the retrieved N2O5 volume mixing ratios in ppbv, interpolated to 2 km height spacings, are 1.64 +/- 0.49 at 37.5 km, 1.92 +/- 0.56 at 35.5 km, 2.06 +/- 0.47 at 33.5 km, 1.95 +/- 0.42 at 31.5 km, 1.60 +/- 0.33 at 29.5 km, 1.26 +/- 0.28 at 27.5 km, and 0.85 +/- 0.20 at 25.5 km. Error bars indicate the estimated 1-sigma uncertainty including the error in the total band intensity. The retrieved profiles are compared with previous measurements and photochemical model results.

  10. FInvestigation of enhancement mode HfO2 insulated N-polarity GaN/InN/GaN/In0.9Al0.1N heterostructure MISHEMT for high-frequency applications

    NASA Astrophysics Data System (ADS)

    Mohanbabu, A.; Mohankumar, N.; Godwin Raj, D.; Sarkar, Partha

    2017-08-01

    In this paper, we examined normally-OFF N-polar InN-channel Metal insulated semiconductor high-electron mobility transistors (MISHEMTs) device with a relaxed In0.9Al0.1N buffer layer. In addition, the enhancement-mode operation of the N-polar structure was investigated. The effect of scaling in N-polar MISHEMT, such as the dielectric and the channel thickness, alter the electrical behavior of the device. We have achieved a maximum drain current of 1.17 A/mm, threshold voltage (VT) =0.728 V, transconductance (gm) of 2.9 S mm-1, high ION/IOFF current ratio of 3.23×103, lowest ON-state resistance (RON) of 0.41 Ω mm and an intrinsic delay time (τ) of 1.456 Fs along with high-frequency performance with ft/ fmaxof 90 GHz/109 GHz and 180 GHz/260 GHz for TCH =0.5 nm at Vds =0.5 V and 1.0 V. The numerically simulated results of highly confined GaN/InN/GaN/In0.9Al0.1N heterostructure MISHEMT exhibits outstanding potential as one of the possibility to replace presently used N-polar MISHEMTs for delivering high power density and frequency at RF/power amplifier applications.

  11. Generation and Characterization of Electron Bunches with Ramped Current Profiles in a Dual-Frequency Superconducting Linear Accelerator

    DOE PAGES

    Piot, P.; Behrens, C.; Gerth, C.; ...

    2011-09-07

    We report on the successful experimental generation of electron bunches with ramped current profiles. The technique relies on impressing nonlinear correlations in the longitudinal phase space using a superconducing radiofrequency linear accelerator operating at two frequencies and a current-enhancing dispersive section. The produced {approx} 700-MeV bunches have peak currents of the order of a kilo-Ampere. Data taken for various accelerator settings demonstrate the versatility of the method and in particular its ability to produce current profiles that have a quasi-linear dependency on the longitudinal (temporal) coordinate. The measured bunch parameters are shown, via numerical simulations, to produce gigavolt-per-meter peak acceleratingmore » electric fields with transformer ratios larger than 2 in dielectric-lined waveguides.« less

  12. High-Frequency Focused Water-Coupled Ultrasound Used for Three-Dimensional Surface Depression Profiling

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

    2001-01-01

    To interface with other solids, many surfaces are engineered via methods such as plating, coating, and machining to produce a functional surface ensuring successful end products. In addition, subsurface properties such as hardness, residual stress, deformation, chemical composition, and microstructure are often linked to surface characteristics. Surface topography, therefore, contains the signatures of the surface and possibly links to volumetric properties, and as a result serves as a vital link between surface design, manufacturing, and performance. Hence, surface topography can be used to diagnose, monitor, and control fabrication methods. At the NASA Glenn Research Center, the measurement of surface topography is important in developing high-temperature structural materials and for profiling the surface changes of materials during microgravity combustion experiments. A prior study demonstrated that focused air-coupled ultrasound at 1 MHz could profile surfaces with a 25-m depth resolution and a 400-m lateral resolution over a 1.4-mm depth range. In this work, we address the question of whether higher frequency focused water-coupled ultrasound can improve on these specifications. To this end, we employed 10- and 25-MHz focused ultrasonic transducers in the water-coupled mode. The surface profile results seen in this investigation for 25-MHz water-coupled ultrasound, in comparison to those for 1-MHz air-coupled ultrasound, represent an 8 times improvement in depth resolution (3 vs. 25 m seen in practice), an improvement of at least 2 times in lateral resolution (180 vs. 400 m calculated and observed in practice), and an improvement in vertical depth range of 4 times (calculated).

  13. Evidence of mercury trapping in biofilm-EPS and mer operon-based volatilization of inorganic mercury in a marine bacterium Bacillus cereus BW-201B.

    PubMed

    Dash, Hirak R; Basu, Subham; Das, Surajit

    2017-04-01

    Biofilm-forming mercury-resistant marine bacterium Bacillus cereus BW-201B has been explored to evident that the bacterial biofilm-EPS (exopolymers) trap inorganic mercury but subsequently release EPS-bound mercury for induction of mer operon-mediated volatilization of inorganic mercury. The isolate was able to tolerate 50 ppm of mercury and forms biofilm in presence of mercury. mer operon-mediated volatilization was confirmed, and -SH was found to be the key functional group of bacterial EPS responsible for mercury binding. Biofilm-EPS-bound mercury was found to be internalized to the bacterial system as confirmed by reversible conformational change of -SH group and increased expression level of merA gene in a timescale experiment. Biofilm-EPS trapped Hg after 24 h of incubation, and by 96 h, the volatilization process reaches to its optimum confirming the internalization of EPS-bound mercury to the bacterial cells. Biofilm disintegration at the same time corroborates the results.

  14. High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling

    PubMed Central

    Jones, Joshua D.; Chung, Betty Y.-W.; Siddell, Stuart G.; Brierley, Ian

    2016-01-01

    Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global “snap-shot” of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal

  15. A Comparison Between Jerusalem Cross and Square Patch Frequency Selective Surfaces for Low Profile Antenna Applications

    NASA Technical Reports Server (NTRS)

    Cure, David; Weller, Thomas; Miranda, Felix A.

    2011-01-01

    In this paper, a comparison between Jerusalem Cross (JC) and Square Patch (SP) based Frequency Selected Surfaces (FSS) for low profile antenna applications is presented. The comparison is aimed at understanding the performance of low profile antennas backed by high impedance surfaces. In particular, an end loaded planar open sleeve dipole (ELPOSD) antenna is examined due to the various parameters within its configuration, offering significant design flexibility and a wide operating bandwidth. Measured data of the antennas demonstrate that increasing the number of unit cells improves the fractional bandwidth. The antenna bandwidth increased from 0.8% to 1.8% and from 0.8% to 2.7% for the JC and SP structures, respectively. The number of unit cells was increased from 48 to 80 for the JC-FSS and from 24 to 48 for the SP-FSS.

  16. AIDS, Avian flu, SARS, MERS, Ebola, Zika… what next?

    PubMed

    Reperant, Leslie A; Osterhaus, Albert D M E

    2017-08-16

    Emerging infections have threatened humanity since times immemorial. The dramatic anthropogenic, behavioral and social changes that have affected humanity and the environment in the past century have accelerated the intrusion of novel pathogens into the global human population, sometimes with devastating consequences. The AIDS and influenza pandemics have claimed and will continue to claim millions of lives. The recent SARS and Ebola epidemics have threatened populations across borders. The emergence of MERS may well be warning signals of a nascent pandemic threat, while the potential for geographical spread of vector-borne diseases, such as Zika, but also Dengue and Chikungunya is unprecedented. Novel technologies and innovative approaches have multiplied to address and improve response preparedness towards the increasing yet unpredictable threat posed by emerging pathogens. Copyright © 2017. Published by Elsevier Ltd.

  17. Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2′-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate

    PubMed Central

    Shiba, Yoshinobu; Masuda, Hirofumi; Watanabe, Naoki; Ego, Takeshi; Takagaki, Kazuchika; Ishiyama, Kouichi; Ohgi, Tadaaki; Yano, Junichi

    2007-01-01

    A long RNA oligomer, a 110mer with the sequence of a precursor-microRNA candidate, has been chemically synthesized in a single synthesizer run by means of standard automated phosphoramidite chemistry. The synthetic method involved the use of 2-cyanoethoxymethyl (CEM), a 2′-hydroxyl protecting group recently developed in our laboratory. We improved the methodology, introducing better coupling and capping conditions. The overall isolated yield of highly pure 110mer was 5.5%. Such a yield on a 1-μmol scale corresponds to 1 mg of product and emphasizes the practicality of the CEM method for synthesizing oligomers of more than 100 nt in sufficient quantity for biological research. We confirmed the identity of the 110mer by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, as well as HPLC, electrophoretic methods, and RNase-digestion experiments. The 110mer also showed sense-selective specific gene-silencing activity. As far as we know, this is the longest chemically synthesized RNA oligomer reported to date. Furthermore, the identity of the 110mer was confirmed by both physicochemical and biological methods. PMID:17459888

  18. Interpretation of frequency sweeping of n=0 mode in JET

    NASA Astrophysics Data System (ADS)

    Berk, H. L.

    2006-04-01

    Persistent rapid up and down frequency chirping modes with a toroidal mode number of zero (n=0) are observed in the JET tokamak when energetic ions, in the range of several hundred keV, are created by high field side ion cyclotron resonance frequency heating. Fokker-Planck calculations demonstrate that the heating method enables the formation of an energetically inverted ion distribution which supplies the free energy for the ions to excite a global geodesic acoustic mode (GGAM). The large frequency shifts of this mode are attributed to the formation of phase space structures whose frequencies, which are locked to an ion orbit resonance frequency, are forced to continually shift so that energetic particle energy can be released to counterbalance the energy dissipation present in the background plasma. In collaboration with C.J. Boswell, MIT; D. Borba, A.C.A. Figueiredo, Center for Nuclear Fusion Association; T. Johnson, Alfven Laboratory, KTH; M.F.F. Nave, Center for Nuclear Fusion Association; S.D. Pinches, Max Planck Institute for Plasma Physics; S.E. Sharapov, UKEA Culham Science Centre; and T. Zhou, University of Texas at Austin.

  19. When Information from Public Health Officials is Untrustworthy: The Use of Online News, Interpersonal Networks, and Social Media during the MERS Outbreak in South Korea.

    PubMed

    Jang, Kyungeun; Baek, Young Min

    2018-03-20

    Public health officials (PHOs) are responsible for providing trustworthy information during a public health crisis; however, there is little research on how the public behaves when their expectations for such information are violated. Drawing on media dependency theory and source credibility research as our primary theoretical framework, we tested how credibility of information from PHOs is associated with people's reliance on a particular communication channel in the context of the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea. Using nationally representative data (N = 1036) collected during the MERS outbreak, we found that less credible information from PHOs led to more frequent use of online news, interpersonal networks, and social media for acquiring MERS-related information. However, credibility of information from PHOs was not associated with the use of television news or print newspapers. The theoretical and practical implications of our results on communication channels usage are discussed.

  20. MER Surface Phase; Blurring the Line Between Fault Protection and What is Supposed to Happen

    NASA Technical Reports Server (NTRS)

    Reeves, Glenn E.

    2008-01-01

    An assessment on the limitations of communication with MER rovers and how such constraints drove the system design, flight software and fault protection architecture, blurring the line between traditional fault protection and expected nominal behavior, and requiring the most novel autonomous and semi-autonomous elements of the vehicle software including communication, surface mobility, attitude knowledge acquisition, fault protection, and the activity arbitration service.

  1. Theory and observations of high frequency Alfvén eigenmodes in low aspect ratio plasmas

    NASA Astrophysics Data System (ADS)

    Gorelenkov, N. N.; Fredrickson, E.; Belova, E.; Cheng, C. Z.; Gates, D.; Kaye, S.; White, R.

    2003-04-01

    New observations of sub-cyclotron frequency instability in low aspect ratio plasmas in national spherical torus experiments are reported. The frequencies of observed instabilities correlate with the characteristic Alfvén velocity of the plasma. A theory of localized compressional Alfvén eigenmodes (CAE) and global shear Alfvén eigenmodes (GAE) in low aspect ratio plasmas is presented to explain the observed high frequency instabilities. CAEs/GAEs are driven by the velocity space gradient of energetic super-Alfvénic beam ions via Doppler shifted cyclotron resonances. One of the main damping mechanisms of GAEs, the continuum damping, is treated perturbatively within the framework of ideal MHD. Properties of these cyclotron instability ions are presented.

  2. Extraintestinal manifestations of celiac disease: 33-mer gliadin binding to glutamate receptor GRINA as a new explanation.

    PubMed

    Garcia-Quintanilla, Albert; Miranzo-Navarro, Domingo

    2016-05-01

    We propose a biochemical mechanism for celiac disease and non-celiac gluten sensitivity that may rationalize many of the extradigestive disorders not explained by the current immunogenetic model. Our hypothesis is based on the homology between the 33-mer gliadin peptide and a component of the NMDA glutamate receptor ion channel - the human GRINA protein - using BLASTP software. Based on this homology the 33-mer may act as a natural antagonist interfering with the normal interactions of GRINA and its partners. The theory is supported by numerous independent data from the literature, and provides a mechanistic link with otherwise unrelated disorders, such as cleft lip and palate, thyroid dysfunction, restless legs syndrome, depression, ataxia, hearing loss, fibromyalgia, dermatitis herpetiformis, schizophrenia, toxoplasmosis, anemia, osteopenia, Fabry disease, Barret's adenocarcinoma, neuroblastoma, urinary incontinence, recurrent miscarriage, cardiac anomalies, reduced risk of breast cancer, stiff person syndrome, etc. The hypothesis also anticipates better animal models, and has the potential to open new avenues of research. © 2016 WILEY Periodicals, Inc.

  3. Patterns of Human Respiratory Viruses and Lack of MERS-Coronavirus in Patients with Acute Upper Respiratory Tract Infections in Southwestern Province of Saudi Arabia

    PubMed Central

    Alshrari, Ahmed S.; Badroon, Nassrin A.; Hassan, Ahmed M.; Alsubhi, Tagreed L.; Ejeeli, Saleh

    2017-01-01

    We undertook enhanced surveillance of those presenting with respiratory symptoms at five healthcare centers by testing all symptomatic outpatients between November 2013 and January 2014 (winter time). Nasal swabs were collected from 182 patients and screened for MERS-CoV as well as other respiratory viruses using RT-PCR and multiplex microarray. A total of 75 (41.2%) of these patients had positive viral infection. MERS-CoV was not detected in any of the samples. Human rhinovirus (hRV) was the most detected pathogen (40.9%) followed by non-MERS-CoV human coronaviruses (19.3%), influenza (Flu) viruses (15.9%), and human respiratory syncytial virus (hRSV) (13.6%). Viruses differed markedly depending on age in which hRV, Flu A, and hCoV-OC43 were more prevalent in adults and RSV, hCoV-HKU1, and hCoV-NL63 were mostly restricted to children under the age of 15. Moreover, coinfection was not uncommon in this study, in which 17.3% of the infected patients had dual infections due to several combinations of viruses. Dual infections decreased with age and completely disappeared in people older than 45 years. Our study confirms that MERS-CoV is not common in the southwestern region of Saudi Arabia and shows high diversity and prevalence of other common respiratory viruses. This study also highlights the importance and contribution of enhanced surveillance systems for better infection control. PMID:28348590

  4. Vertical Profiles as Observational Constraints on Nitrous Oxide (N2O) Emissions in an Agricultural Region

    NASA Astrophysics Data System (ADS)

    Pusede, S.; Diskin, G. S.

    2015-12-01

    We use diurnal variability in near-surface N2O vertical profiles to derive N2O emission rates. Our emissions estimates are ~3 times greater than are accounted for by inventories, a discrepancy in line with results from previous studies using different approaches. We quantify the surface N2O concentration's memory of local surface emissions on previous days to be 50-90%. We compare measured profiles both over and away from a dense N2O source region in the San Joaquin Valley, finding that profile shapes, diurnal variability, and changes in integrated near-surface column abundances are distinct according to proximity to source areas. To do this work, we use aircraft observations from the wintertime DISCOVER-AQ project in California's San Joaquin Valley, a region of intense agricultural activity.

  5. Stratospheric N2O5, CH4, and N2O Profiles from IR Solar Occultation Spectra

    NASA Technical Reports Server (NTRS)

    Peyeret, C. Camy; Flaud, J.-M.; Perrin, A.; Rinsland, C. P.; Goldman, A.; Murcray, F. J.

    1993-01-01

    Stratospheric volume mixing ratio profiles of N2O5, CH4, and N2O have been retrieved from a set of 0.052/ cm resolution (FWHM) solar occultation spectra recorded at sunrise during a balloon flight from Aire sur I'Adour, France (44 deg N latitude) on 12 October 1990. The N2O5 results have been derived from measurements of the integrated absorption by the 1246/ cm band. Assuming a total intensity of 4.32 x 10(exp 17)cm(exp -1) molecule sq cm(exp -2) independent of temperature, the retrieved N2O5 volume mixing ratios in ppbv (parts per billion by volume, 10(exp -9)), interpolated to 2 km height spacings, are 1.64 +/- 0.49 at 37.5 km, 1.92 +/- 0.56 at 35.5 km, 2.06 +/- 0.47 at 33.5 km, 1.95 +/- 0.42 at 31.5 km, 1.60 +/- 0.33 at 29.5 km, 1.26 +/- 0.28 at 27.5 km, and 0.85 +/- 0.20 at 25.5 km. Error bars indicate the estimated I-sigma uncertainty including the error in the total band intensity (+/- 20% has been assumed). The retrieved profiles are compared with previous measurements and photochemical model results.

  6. Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond.

    PubMed

    Lu, Guangwen; Wang, Qihui; Gao, George F

    2015-08-01

    Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic pathogens that crossed the species barriers to infect humans. The mechanism of viral interspecies transmission is an important scientific question to be addressed. These coronaviruses contain a surface-located spike (S) protein that initiates infection by mediating receptor-recognition and membrane fusion and is therefore a key factor in host specificity. In addition, the S protein needs to be cleaved by host proteases before executing fusion, making these proteases a second determinant of coronavirus interspecies infection. Here, we summarize the progress made in the past decade in understanding the cross-species transmission of SARS-CoV and MERS-CoV by focusing on the features of the S protein, its receptor-binding characteristics, and the cleavage process involved in priming. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Wideband profiles of stimulus-frequency otoacoustic emissions in humans

    NASA Astrophysics Data System (ADS)

    Dewey, James B.; Dhar, Sumitrajit

    2015-12-01

    Behavioral pure-tone hearing thresholds and stimulus-frequency otoacoustic emissions (SFOAEs) were measured with a high frequency resolution from 0.5-20 kHz in 15 female participants. Stimuli were calibrated in terms of forward pressure level (FPL). SFOAE responses to 36 dB FPL probes were largest near 1 kHz and declined above 8-10 kHz, though were still measurable at frequencies approaching 16 kHz in some ears. SFOAEs typically dropped in amplitude at a frequency that was roughly one octave below the "corner" frequency of the audiogram, and one-third to one-half of an octave below the frequency where thresholds departed from highly sensitive hearing. High-frequency SFOAE responses are likely limited by a reduction in the efficiency of the underlying generation mechanism and/or a diminished region of generation as the stimulus-driven excitation approaches the basal-most portion of the cochlea.

  8. Polarization-insensitive ultralow-power second-harmonic generation frequency-resolved optical gating.

    PubMed

    Miao, Houxun; Weiner, Andrew M; Langrock, Carsten; Roussev, Rostislav V; Fejer, Martin M

    2007-04-01

    We demonstrate polarization-insensitive ultralow-power second-harmonic generation frequency-resolved optical gating (FROG) measurements with a fiber-pigtailed, aperiodically poled lithium niobate waveguide. By scrambling the polarization much faster than the measurement integration time, we eliminate the impairment that frequency-independent random polarization fluctuations induce in FROG measurements. As a result we are able to retrieve intensity and phase profiles of few hundred femtosecond optical pulses with 50 MHz repetition rates at 5.2 nW coupled average power without control of the input polarization.

  9. mer, fac, and Bidentate Coordination of an Alkyl-POP Ligand in the Chemistry of Nonclassical Osmium Hydrides.

    PubMed

    Esteruelas, Miguel A; García-Yebra, Cristina; Martín, Jaime; Oñate, Enrique

    2017-01-03

    Nonclassical and classical osmium polyhydrides containing the diphosphine 9,9-dimethyl-4,5-bis(diisopropylphosphino)xanthene (xant(P i Pr 2 ) 2 ), coordinated in κ 3 -mer, κ 3 -fac, and κ 2 -P,P fashions, have been isolated during the cyclic formation of H 2 by means of the sequential addition of H + and H - or H - and H + to the classical trihydride OsH 3 Cl{xant(P i Pr 2 ) 2 } (1). This complex adds H + to form the compressed dihydride dihydrogen complex [OsCl(H···H)(η 2 -H 2 ){xant(P i Pr 2 ) 2 }] + (2). Under argon, cation 2 loses H 2 and the resulting unsaturated fragment dimerizes to give [(Os(H···H){xant(P i Pr 2 ) 2 }) 2 (μ-Cl) 2 ] 2+ (3). During the transformation the phosphine changes its coordination mode from mer to fac. The benzofuran counterpart of 1, OsH 3 Cl{dbf(P i Pr 2 ) 2 } (4; dbf(P i Pr 2 ) 2 = 4,6-bis(diisopropylphosphino)dibenzofuran), also adds H + to afford the benzofuran counterpart of 2, [OsCl(H···H)(η 2 -H 2 ){xant(P i Pr 2 ) 2 }] + (5), which in contrast to the latter is stable and does not dimerize. Acetonitrile breaks the chloride bridge of 3 to form the dihydrogen [OsCl(η 2 -H 2 )(CH 3 CN){xant(P i Pr 2 ) 2 }] + (6), regenerating the mer coordination of the diphosphine. The hydride ion also breaks the chloride bridge of 3. The addition of KH to 3 leads to 1, closing a cycle for the formation of H 2 . Complex 1 reacts with a second hydride ion to give OsH 4 {xant(P i Pr 2 ) 2 } (7) as consequence of the displacement of the chloride. Similarly to the latter, the oxygen atom of the mer-coordinated diphosphine of 7 has a tendency to be displaced by the hydride ion. Thus, the addition of KH to 7 yields [OsH 5 {xant(P i Pr 2 ) 2 }] - (8), containing a κ 2 -P,P-diphosphine. Complex 8 is easily protonated to afford OsH 6 {xant(P i Pr 2 ) 2 } (9), which releases H 2 to regenerate 7, closing a second cycle for the formation of molecular hydrogen.

  10. Sidestepping the Combinatorial Explosion: An Explanation of "n"-gram Frequency Effects Based on Naive Discriminative Learning

    ERIC Educational Resources Information Center

    Baayen, R. Harald; Hendrix, Peter; Ramscar, Michael

    2013-01-01

    Arnon and Snider ((2010). More than words: Frequency effects for multi-word phrases. "Journal of Memory and Language," 62, 67-82) documented frequency effects for compositional four-grams independently of the frequencies of lower-order "n"-grams. They argue that comprehenders apparently store frequency information about…

  11. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-09

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  12. KENNEDY SPACE CENTER, FLA. - The launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station, clears the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-09

    KENNEDY SPACE CENTER, FLA. - The launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station, clears the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  13. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are in the clear after tower rollback in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-09

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are in the clear after tower rollback in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  14. KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  15. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  16. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower (right) and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower (right) and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  17. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are viewed as the launch tower overhead rolls back. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are viewed as the launch tower overhead rolls back. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  18. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  19. KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload breaks forth from the smoke and steam into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload breaks forth from the smoke and steam into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25

  20. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload waits for rollback of the launch tower in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-09

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload waits for rollback of the launch tower in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  1. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower rolls back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts, June 8 and June 9, were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower rolls back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts, June 8 and June 9, were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  2. KENNEDY SPACE CENTER, FLA. - Blue sky and sun give a dramatic backdrop for the launch of the Delta II rocket with its Mars Exploration Rover (MER-A) payload. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - Blue sky and sun give a dramatic backdrop for the launch of the Delta II rocket with its Mars Exploration Rover (MER-A) payload. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  3. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is raised off the transporter. When vertical, it will be lifted up the launch tower and mated to the Delta rocket (in the background) to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-14

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is raised off the transporter. When vertical, it will be lifted up the launch tower and mated to the Delta rocket (in the background) to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  4. KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is moved into position to raise to vertical and lift up the launch tower. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-14

    KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is moved into position to raise to vertical and lift up the launch tower. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

  5. Soil-profile distribution of inorganic N during 6 years of integrated crop-livestock management

    USDA-ARS?s Scientific Manuscript database

    Excessive accumulation of soil nitrate-N can threaten water and air quality. How integrated crop-livestock systems might influence soil-profile nitrate-N accumulation has not been investigated. Therefore, we determined soil nitrate-N accumulation during 6 years of evaluation of diverse cropping sy...

  6. Sound level-dependent growth of N1m amplitude with low and high-frequency tones.

    PubMed

    Soeta, Yoshiharu; Nakagawa, Seiji

    2009-04-22

    The aim of this study was to determine whether the amplitude and/or latency of the N1m deflection of auditory-evoked magnetic fields are influenced by the level and frequency of sound. The results indicated that the amplitude of the N1m increased with sound level. The growth in amplitude with increasing sound level was almost constant with low frequencies (250-1000 Hz); however, this growth decreased with high frequencies (>2000 Hz). The behavior of the amplitude may reflect a difference in the increase in the activation of the peripheral and/or central auditory systems.

  7. Temperature dependent DC characterization of InAlN/(AlN)/GaN HEMT for improved reliability

    NASA Astrophysics Data System (ADS)

    Takhar, K.; Gomes, U. P.; Ranjan, K.; Rathi, S.; Biswas, D.

    2015-02-01

    InxAl1-xN/AlN/GaN HEMT device performance is analysed at various temperatures with the help of physics based 2-D simulation using commercially available BLAZE and GIGA modules from SILVACO. Various material parameters viz. band-gap, low field mobility, density of states, velocity saturation, and substrate thermal conductivity are considered as critical parameters for predicting temperature effect in InxAl1-xN/AlN/GaN HEMT. Reduction in drain current and transconductance has been observed due to the decrease of 2-DEG mobility and effective electron velocity with the increase in temperature. Degradation in cut-off frequency follows the transconductance profile as variation in gate-source/gate-drain capacitances observed very small.

  8. Impedance characterization of AlGaN/GaN Schottky diodes with metal contacts

    NASA Astrophysics Data System (ADS)

    Donahue, M.; Lübbers, B.; Kittler, M.; Mai, P.; Schober, A.

    2013-04-01

    To obtain detailed information on structural and electrical properties of AlGaN/GaN Schottky diodes and to determine an appropriate equivalent circuit, impedance spectroscopy and impedance voltage profiling are employed over a frequency range of 1 MHz-1 Hz. In contrast to the commonly assumed parallel connection of capacitive and resistive elements, an equivalent circuit is derived from impedance spectra which utilizes the constant phase element and accounts for frequency dispersion and trap states. The trap density is estimated and is in good agreement with the literature values. The resulting reduced equivalent circuit consists of a capacitor and resistor connected in series.

  9. Two-dimensional dopant profiling of gallium nitride p-n junctions by scanning capacitance microscopy

    NASA Astrophysics Data System (ADS)

    Lamhamdi, M.; Cayrel, F.; Frayssinet, E.; Bazin, A. E.; Yvon, A.; Collard, E.; Cordier, Y.; Alquier, D.

    2016-04-01

    Two-dimensional imaging of dopant profiles for n and p-type regions are relevant for the development of new power semiconductors, especially for gallium nitride (GaN) for which classical profiling techniques are not adapted. This is a challenging task since it needs a technique with simultaneously good sensitivity, high spatial resolution and high dopant gradient resolution. To face these challenges, scanning capacitance microscopy combined with Atomic Force Microscopy is a good candidate, presenting reproducible results, as demonstrated in literature. In this work, we attempt to distinguish reliably and qualitatively the various doping concentrations and type at p-n and unipolar junctions. For both p-n and unipolar junctions three kinds of samples were prepared and measured separately. The space-charge region of the p-n metallurgical junction, giving rise to different contrasts under SCM imaging, is clearly observed, enlightening the interest of the SCM technique.

  10. Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.

    PubMed

    Sheng, Zizhang; Schramm, Chaim A; Kong, Rui; Mullikin, James C; Mascola, John R; Kwong, Peter D; Shapiro, Lawrence

    2017-01-01

    Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts. We demonstrated that these gene-specific substitution profiles (GSSPs) are unique to each V gene and highly consistent between donors. We also showed that the GSSPs constructed from functional antibody repertoires are highly similar to those constructed from antibody sequences amplified from non-productively rearranged passenger alleles, which do not undergo functional selection. This suggests the types and frequencies, or mutational space, of a majority of amino acid changes sampled by the SHM machinery to be well captured by GSSPs. We further observed the rates of mutational exchange between some amino acids to be both asymmetric and context dependent and to correlate weakly with their biochemical properties. GSSPs provide an improved, position-dependent alternative to standard substitution matrices, and can be utilized to developing software for accurately modeling the SHM process. GSSPs can also be used for predicting the amino acid mutational space available for antigen-driven selection and for understanding factors modulating the maturation pathways of antibody lineages in a gene-specific context. The mGSSP method can be used to build, compare, and plot GSSPs; we report the GSSPs constructed for 69 common human V genes (DOI: 10.6084/m9.figshare.3511083) and provide high-resolution logo plots for each (DOI: 10

  11. The Synthesis and X-ray Structural Characterization of mer and fac isomers of the Technetium(I) Nitrosyl Complex [TcCl(2)(NO)(PNPpr)].

    PubMed

    Nicholson, T L; Mahmood, A; Refosco, F; Tisato, F; Müller, P; Jones, A G

    2009-08-01

    The nitrosyl complex H[TcNOCl(4)] reacts with the tridentate ligand bis[(2-diphenylphosphino)propyl]amine (PNPpr) to yield a mixture of the mer or fac isomers of [TcCl(2)(NO)(PNPpr)]. In acetonitrile, where the ligand is freely soluble, reaction occurs at room temperature to yield mostly the mer isomer with the linear nitrosyl ligand cis to the amine ligand; and the phosphine ligands arranged in a mutually trans orientation. The reaction in methanol requires reflux to dissolve the lipophilic ligand and generates the fac isomer of [TcCl2(NO)(PNPpr)] as the major product, with the tridentate ligand in a facial arrangement, leaving the chlorides and nitrosyl ligand in the remaining facial sites. The steric bulk of the tridentate ligand's diphenylphophino- moieties results in a significant distortion from octahedral geometry, with the P-Tc-P bond angle expanded to 99.48(4)°. The infrared spectra display absorptions from these nitrosyl ligands in the 1700 and 1800 cm(-1) regions for the fac and mer isomers respectively. The ESI(+) mass spectra each display the parent ion at 647 m/z.

  12. Effect of frequency on fretting wear behavior of Ti/TiN multilayer film on depleted uranium

    PubMed Central

    Zhu, Sheng-Fa; Lu, Lei; Cai, Zhen-Bing

    2017-01-01

    The Ti/TiN multi-layer film was prepared on the depleted uranium (DU) substrate by cathodic arc ion plating equipment. The character of multi-layer film was studied by SEM, XRD and AES, revealed that the surface was composed of small compact particle and the cross-section had a multi-layer structure. The fretting wear performance under different frequencies was performed by a MFT-6000 machine with a ball-on-plate configuration. The wear morphology was analyzed by white light interferometer, OM and SEM with an EDX. The result shows the Ti/TiN multi-layer film could greatly improve the fretting wear performance compared to the DU substrate. The fretting wear running and damaged behavior are strongly dependent on the film and test frequency. The fretting region of DU substrate and Ti/TiN multi-layer under low test frequency is gross slip. With the increase of test frequency, the fretting region of Ti/TiN multi-layer change from gross slip to mixed fretting, then to partial slip. PMID:28384200

  13. Effect of frequency on fretting wear behavior of Ti/TiN multilayer film on depleted uranium.

    PubMed

    Wu, Yan-Ping; Li, Zheng-Yang; Zhu, Sheng-Fa; Lu, Lei; Cai, Zhen-Bing

    2017-01-01

    The Ti/TiN multi-layer film was prepared on the depleted uranium (DU) substrate by cathodic arc ion plating equipment. The character of multi-layer film was studied by SEM, XRD and AES, revealed that the surface was composed of small compact particle and the cross-section had a multi-layer structure. The fretting wear performance under different frequencies was performed by a MFT-6000 machine with a ball-on-plate configuration. The wear morphology was analyzed by white light interferometer, OM and SEM with an EDX. The result shows the Ti/TiN multi-layer film could greatly improve the fretting wear performance compared to the DU substrate. The fretting wear running and damaged behavior are strongly dependent on the film and test frequency. The fretting region of DU substrate and Ti/TiN multi-layer under low test frequency is gross slip. With the increase of test frequency, the fretting region of Ti/TiN multi-layer change from gross slip to mixed fretting, then to partial slip.

  14. Joint time/frequency-domain inversion of reflection data for seabed geoacoustic profiles and uncertainties.

    PubMed

    Dettmer, Jan; Dosso, Stan E; Holland, Charles W

    2008-03-01

    This paper develops a joint time/frequency-domain inversion for high-resolution single-bounce reflection data, with the potential to resolve fine-scale profiles of sediment velocity, density, and attenuation over small seafloor footprints (approximately 100 m). The approach utilizes sequential Bayesian inversion of time- and frequency-domain reflection data, employing ray-tracing inversion for reflection travel times and a layer-packet stripping method for spherical-wave reflection-coefficient inversion. Posterior credibility intervals from the travel-time inversion are passed on as prior information to the reflection-coefficient inversion. Within the reflection-coefficient inversion, parameter information is passed from one layer packet inversion to the next in terms of marginal probability distributions rotated into principal components, providing an efficient approach to (partially) account for multi-dimensional parameter correlations with one-dimensional, numerical distributions. Quantitative geoacoustic parameter uncertainties are provided by a nonlinear Gibbs sampling approach employing full data error covariance estimation (including nonstationary effects) and accounting for possible biases in travel-time picks. Posterior examination of data residuals shows the importance of including data covariance estimates in the inversion. The joint inversion is applied to data collected on the Malta Plateau during the SCARAB98 experiment.

  15. AlGaN/GaN-HEMTs with a breakdown voltage higher than 100 V and maximum oscillation frequency f{sub max} as high as 100 GHz

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

    Mokerov, V. G., E-mail: vgmokerov@yandex.ru; Kuznetsov, A. L.; Fedorov, Yu. V.

    2009-04-15

    The N-Al{sub 0.27}Ga{sub 0.73}N/GaN High Electron Mobility Transistors (HEMTs) with different gate lengths L{sub g} (ranging from 170 nm to 0.5 {mu}m) and gate widths W{sub s} (ranging from 100 to 1200 {mu}m) have been studied. The S parameters have been measured; these parameters have been used to determine the current-gain cutoff frequency f{sub t}, the maximum oscillation frequency f{sub max}, and the power gain MSG/MAG and Mason's coefficients were investigated in the frequency range from 10 MHz to 67 GHz in relation to the gate length and gate width. It was found that the frequencies f{sub t} and f{submore » max} attain their maximum values of f{sub t} = 48 GHz and f{sub max} = 100 GHz at L{sub g} = 170 nm and W{sub g} = 100 {mu}m. The optimum values of W{sub g} and output power P out of the basic transistors have been determined for different frequencies of operation. It has also been demonstrated that the 170 nm Al{sub 0.27}Ga{sub 0.73}N/GaN HEMT technology provides both good frequency characteristics and high breakdown voltages and is very promising for high-frequency applications (up to 40 GHz)« less

  16. Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.

    PubMed

    Yuan, Yuan; Cao, Duanfang; Zhang, Yanfang; Ma, Jun; Qi, Jianxun; Wang, Qihui; Lu, Guangwen; Wu, Ying; Yan, Jinghua; Shi, Yi; Zhang, Xinzheng; Gao, George F

    2017-04-10

    The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.

  17. Delta II Heavy launch of "Opportunity" MER-B Rover

    NASA Image and Video Library

    2003-07-07

    On Launch Complex 17-B, Cape Canaveral Air Force Station, the Delta II Heavy launch vehicle carrying the rover "Opportunity" for the second Mars Exploration Rover mission launches at 11:18:15 p.m. EDT. Opportunity will reach Mars on Jan. 25, 2004. Together the two MER rovers, Spirit (launched June 10) and Opportunity, seek to determine the history of climate and water at two sites on Mars where conditions may once have been favorable to life. The rovers are identical. They will navigate themselves around obstacles as they drive across the Martian surface, traveling up to about 130 feet each Martian day. Each rover carries five scientific instruments including a panoramic camera and microscope, plus a rock abrasion tool that will grind away the outer surfaces of rocks to expose their interiors for examination. Each rover’s prime mission is planned to last three months on Mars.

  18. Flexible GaN for High Performance, Strainable Radio Frequency Devices (Postprint)

    DTIC Science & Technology

    2017-11-02

    devices on van der Waals (vdW) layers has been facilitated by the recent avail - ability of high -quality atomically smooth BN and graphene epi- taxial...AFRL-RX-WP-JA-2017-0333 FLEXIBLE GaN FOR HIGH PERFORMANCE, STRAINABLE RADIO FREQUENCY DEVICES (POSTPRINT) Elizabeth A. Moore and Timothy...2. REPORT TYPE 3. DATES COVERED (From - To) 5 April 2017 Interim 8 September 2014 – 5 March 2017 4. TITLE AND SUBTITLE FLEXIBLE GaN FOR HIGH

  19. kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

    PubMed

    Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

    2017-09-01

    Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

  20. LC-MS/MS Peptide Mapping with Automated Data Processing for Routine Profiling of N-Glycans in Immunoglobulins

    NASA Astrophysics Data System (ADS)

    Shah, Bhavana; Jiang, Xinzhao Grace; Chen, Louise; Zhang, Zhongqi

    2014-06-01

    Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. These methods require time-consuming sample preparations and do not provide site-specific glycosylation information. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). Experimental conditions were optimized to achieve accurate profiling of glycoforms. Glycan profiles obtained from LC-MS/MS peptide mapping were compared with those obtained from HPAEC, RPLC, and HILIC analyses of released glycans for several mAb molecules. Accuracy, reproducibility, and linearity of the LC-MS/MS peptide mapping method for glycan profiling were evaluated. The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans.

  1. CDC's Early Response to a Novel Viral Disease, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), September 2012-May 2014.

    PubMed

    Williams, Holly Ann; Dunville, Richard L; Gerber, Susan I; Erdman, Dean D; Pesik, Nicki; Kuhar, David; Mason, Karen A; Haynes, Lia; Rotz, Lisa; St Pierre, Jeanette; Poser, Sarah; Bunga, Sudhir; Pallansch, Mark A; Swerdlow, David L

    2015-01-01

    The first ever case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported in September 2012. This report describes the approaches taken by CDC, in collaboration with the World Health Organization (WHO) and other partners, to respond to this novel virus, and outlines the agency responses prior to the first case appearing in the United States in May 2014. During this time, CDC's response integrated multiple disciplines and was divided into three distinct phases: before, during, and after the initial activation of its Emergency Operations Center. CDC's response to MERS-CoV required a large effort, deploying at least 353 staff members who worked in the areas of surveillance, laboratory capacity, infection control guidance, and travelers' health. This response built on CDC's experience with previous outbreaks of other pathogens and provided useful lessons for future emerging threats.

  2. Membrane interaction of the N-terminal domain of chemokine receptor CXCR1.

    PubMed

    Haldar, Sourav; Raghuraman, H; Namani, Trishool; Rajarathnam, Krishna; Chattopadhyay, Amitabha

    2010-06-01

    The N-terminal domain of chemokine receptors constitutes one of the two critical ligand binding sites, and plays important roles by mediating binding affinity, receptor selectivity, and regulating function. In this work, we monitored the organization and dynamics of a 34-mer peptide of the CXC chemokine receptor 1 (CXCR1) N-terminal domain and its interaction with membranes by utilizing a combination of fluorescence-based approaches and surface pressure measurements. Our results show that the CXCR1 N-domain 34-mer peptide binds vesicles of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and upon binding, the tryptophan residues of the peptide experience motional restriction and exhibit red edge excitation shift (REES) of 19nm. These results are further supported by increase in fluorescence anisotropy and mean fluorescence lifetime upon membrane binding. These results constitute one of the first reports demonstrating membrane interaction of the N-terminal domain of CXCR1 and gain relevance in the context of the emerging role of cellular membranes in chemokine signaling.

  3. Vegetation change alters soil profile δ15N values at the landscape scale in a subtropical savanna

    NASA Astrophysics Data System (ADS)

    Zhou, Y.; Mushinski, R. M.; Hyodo, A.; Wu, X. B.; Boutton, T. W.

    2017-12-01

    The assessment of spatial variation in soil δ15N could provide integrative insights on soil N cycling processes across multiple spatial scales. However, little is known about spatial patterns of δ15N within soil profiles in arid and semiarid ecosystems, especially those undergoing vegetation change with a distinct shift in dominance and/or functional type. We quantified how changes from grass to woody plant dominance altered spatial patterns of δ15N throughout a 1.2 m soil profile by collecting 320 spatially-specific soil cores in a 160 m × 100 m subtropical savanna landscape that has undergone encroachment by Prosopis glandulosa (an N2-fixer) during the past century. Leaf δ15N was comparable among different plant life-forms, while fine roots from woody species had significantly lower δ15N than herbaceous species across this landscape. Woody encroachment significantly decreased soil δ15N throughout the entire soil profile, and created horizontal spatial patterns of soil δ15N that strongly resembled the spatial distribution of woody patches and were evident within each depth increment. The lower soil δ15N values that characterized areas beneath woody canopies were mostly due to the encroaching woody species, especially the N2-fixer P. glandulosa, which delivered 15N-depleted organic matter via root turnover to soils along the profile. Soil δ15N increased with depth, reached maximum values at an intermediate depth, and decreased at greater depths. Higher δ15N values at intermediate soil depths were correlated with the presence of a subsurface clay-rich argillic horizon across this landscape which may favor more rapid rates of N-cycling processes that can cause N losses and 15N enrichment of the residual soil N. These results indicate that succession from grassland to woodland has altered spatial variation in soil δ15N across the landscape and to considerable depth, suggesting significant changes in the relative rates of N-inputs vs. N-losses in this

  4. Intrinsic frequency biases and profiles across human cortex.

    PubMed

    Mellem, Monika S; Wohltjen, Sophie; Gotts, Stephen J; Ghuman, Avniel Singh; Martin, Alex

    2017-11-01

    Recent findings in monkeys suggest that intrinsic periodic spiking activity in selective cortical areas occurs at timescales that follow a sensory or lower order-to-higher order processing hierarchy (Murray JD, Bernacchia A, Freedman DJ, Romo R, Wallis JD, Cai X, Padoa-Schioppa C, Pasternak T, Seo H, Lee D, Wang XJ. Nat Neurosci 17: 1661-1663, 2014). It has not yet been fully explored if a similar timescale hierarchy is present in humans. Additionally, these measures in the monkey studies have not addressed findings that rhythmic activity within a brain area can occur at multiple frequencies. In this study we investigate in humans if regions may be biased toward particular frequencies of intrinsic activity and if a full cortical mapping still reveals an organization that follows this hierarchy. We examined the spectral power in multiple frequency bands (0.5-150 Hz) from task-independent data using magnetoencephalography (MEG). We compared standardized power across bands to find regional frequency biases. Our results demonstrate a mix of lower and higher frequency biases across sensory and higher order regions. Thus they suggest a more complex cortical organization that does not simply follow this hierarchy. Additionally, some regions do not display a bias for a single band, and a data-driven clustering analysis reveals a regional organization with high standardized power in multiple bands. Specifically, theta and beta are both high in dorsal frontal cortex, whereas delta and gamma are high in ventral frontal cortex and temporal cortex. Occipital and parietal regions are biased more narrowly toward alpha power, and ventral temporal lobe displays specific biases toward gamma. Thus intrinsic rhythmic neural activity displays a regional organization but one that is not necessarily hierarchical. NEW & NOTEWORTHY The organization of rhythmic neural activity is not well understood. Whereas it has been postulated that rhythms are organized in a hierarchical manner across

  5. Mild Airflow Limitation during N2 Sleep Increases K-complex Frequency and Slows Electroencephalographic Activity

    PubMed Central

    Nguyen, Chinh D.; Wellman, Andrew; Jordan, Amy S.; Eckert, Danny J.

    2016-01-01

    Study Objectives: To determine the effects of mild airflow limitation on K-complex frequency and morphology and electroencephalogram (EEG) spectral power. Methods: Transient reductions in continuous positive airway pressure (CPAP) during stable N2 sleep were performed to induce mild airflow limitation in 20 patients with obstructive sleep apnea (OSA) and 10 healthy controls aged 44 ± 13 y. EEG at C3 and airflow were measured in 1-min windows to quantify K-complex properties and EEG spectral power immediately before and during transient reductions in CPAP. The frequency and morphology (amplitude and latency of P200, N550 and N900 components) of K-complexes and EEG spectral power were compared between conditions. Results: During mild airflow limitation (18% reduction in peak inspiratory airflow from baseline, 0.38 ± 0.11 versus 0.31 ± 0.1 L/sec) insufficient to cause American Academy of Sleep Medicine-defined cortical arousal, K-complex frequency (9.5 ± 4.5 versus 13.7 ± 6.4 per min, P < 0.01), N550 amplitude (25 ± 3 versus 27 ± 3 μV, P < 0.01) and EEG spectral power (delta: 147 ± 48 versus 230 ± 99 μV2, P < 0.01 and theta bands: 31 ± 14 versus 34 ± 13 μV2, P < 0.01) significantly increased whereas beta band power decreased (14 ± 5 versus 11 ± 4 μV2, P < 0.01) compared to the preceding non flow-limited period on CPAP. K-complex frequency, morphology, and timing did not differ between patients and controls. Conclusion: Mild airflow limitation increases K-complex frequency, N550 amplitude, and spectral power of delta and theta bands. In addition to providing mechanistic insight into the role of mild airflow limitation on K-complex characteristics and EEG activity, these findings may have important implications for respiratory conditions in which airflow limitation during sleep is common (e.g., snoring and OSA). Citation: Nguyen CD, Wellman A, Jordan AS, Eckert DJ. Mild airflow limitation during N2 sleep increases k-complex frequency and slows

  6. The development of retrosynthetic glycan libraries to profile and classify the human serum N-linked glycome.

    PubMed

    Kronewitter, Scott R; An, Hyun Joo; de Leoz, Maria Lorna; Lebrilla, Carlito B; Miyamoto, Suzanne; Leiserowitz, Gary S

    2009-06-01

    Annotation of the human serum N-linked glycome is a formidable challenge but is necessary for disease marker discovery. A new theoretical glycan library was constructed and proposed to provide all possible glycan compositions in serum. It was developed based on established glycobiology and retrosynthetic state-transition networks. We find that at least 331 compositions are possible in the serum N-linked glycome. By pairing the theoretical glycan mass library with a high mass accuracy and high-resolution MS, human serum glycans were effectively profiled. Correct isotopic envelope deconvolution to monoisotopic masses and the high mass accuracy instruments drastically reduced the amount of false composition assignments. The high throughput capacity enabled by this library permitted the rapid glycan profiling of large control populations. With the use of the library, a human serum glycan mass profile was developed from 46 healthy individuals. This paper presents a theoretical N-linked glycan mass library that was used for accurate high-throughput human serum glycan profiling. Rapid methods for evaluating a patient's glycome are instrumental for studying glycan-based markers.

  7. 78 FR 66010 - Draft Risk Profile on Pathogens and Filth in Spices; Availability

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-04

    ... about the frequency and levels of pathogen and/or filth contamination of spices throughout the food... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2013-N-1204] Draft Risk Profile on Pathogens and Filth in Spices; Availability AGENCY: Food and Drug Administration...

  8. Design of a 2.4-GHz CMOS monolithic fractional-N frequency synthesizer

    NASA Astrophysics Data System (ADS)

    Shu, Keliu

    The wireless communication technology and market have been growing rapidly since a decade ago. The high demand market is a driving need for higher integration in the wireless transceivers. The trend is to achieve low-cost, small form factor and low power consumption. With the ever-reducing feature size, it is becoming feasible to integrate the RF front-end together with the baseband in the low-cost CMOS technology. The frequency synthesizer is a key building block in the RF front-end of the transceivers. It is used as a local oscillator for frequency translation and channel selection. The design of a 2.4-GHz low-power frequency synthesizer in 0.35mum CMOS is a challenging task mainly due to the high-speed prescaler. In this dissertation, a brief review of conventional PLL and frequency synthesizers is provided. Design techniques of a 2.4-GHz monolithic SigmaDelta fractional-N frequency synthesizer are investigated. Novel techniques are proposed to tackle the speed and integration bottlenecks of high-frequency PLL. A low-power and inherently glitch-free phase-switching prescaler and an on-chip loop filter with capacitance multiplier are developed. Compared with the existing and popular dual-path topology, the proposed loop filter reduces circuit complexity and its power consumption and noise are negligible. Furthermore, a third-order three-level digital SigmaDelta modulator topology is employed to reduce the phase noise generated by the modulator. Suitable PFD and charge-pump designs are employed to reduce their nonlinearity effects and thus minimize the folding of the SigmaDelta modulator-shaped phase noise. A prototype of the fractional-N synthesizer together with some standalone building blocks is designed and fabricated in TSMC 0.35mum CMOS through MOSIS. The prototype frequency synthesizer and standalone prescaler and loop filter are characterized. The feasibility and practicality of the proposed prescaler and loop filter are experimentally verified.

  9. BK Polyomavirus-Specific 9mer CD8 T Cell Responses Correlate With Clearance of BK Viremia in Kidney Transplant Recipients: First Report From the Swiss Transplant Cohort Study.

    PubMed

    Leboeuf, C; Wilk, S; Achermann, R; Binet, I; Golshayan, D; Hadaya, K; Hirzel, C; Hoffmann, M; Huynh-Do, U; Koller, M T; Manuel, O; Mueller, N J; Mueller, T F; Schaub, S; van Delden, C; Weissbach, F H; Hirsch, H H

    2017-10-01

    BK polyomavirus (BKPyV) causes premature kidney transplant (KT) failure in 1-15% of patients. Because antivirals are lacking, most programs screen for BKPyV-viremia and, if positive, reduce immunosuppression. To evaluate the relationship of viremia and BKPyV-specific immunity, we examined prospectively cryopreserved plasma and peripheral blood mononuclear cells at the time of transplantation (T0) and at 6 mo (T6) and 12 mo (T12) after transplant from 28 viremic KT patients and 68 nonviremic controls matched for the transplantation period. BKPyV IgG seroprevalence was comparable between cases (89.3%) and controls (91.2%; p = 0.8635), but cases had lower antibody levels (p = 0.022) at T0. Antibody levels increased at T6 and T12 but were not correlated with viremia clearance. BKPyV-specific T cell responses to pools of overlapping 15mers (15mer peptide pool [15mP]) or immunodominant CD8 9mers (9mer peptide pool [9mP]) from the early viral gene region were not different between cases and controls at T0; however, clearance of viremia was associated with stronger 9mP responses at T6 (p = 0.042) and T12 (p = 0.048), whereas 15mP responses were not informative (T6 p = 0.359; T12 p = 0.856). BKPyV-specific T cells could be expanded in vitro from all patients after transplant, permitting identification of 78 immunodominant 9mer epitopes including 50 new ones across different HLA class I. Thus, 9mP-responses may be a novel marker of reconstituting CD8 T cell function that warrants further study as a complement of plasma BKPyV loads for guiding immunosuppression reduction. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

  10. On nonlinear evolution of low-frequency Alfvén waves in weakly-expanding solar wind plasmas

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

    Nariyuki, Y.

    A multi-dimensional nonlinear evolution equation for Alfvén waves in weakly-expanding solar wind plasmas is derived by using the reductive perturbation method. The expansion of solar wind plasma parcels is modeled by an expanding box model, which includes the accelerating expansion. It is shown that the resultant equation agrees with the Wentzel-Kramers-Brillouin prediction of the low-frequency Alfvén waves in the linear limit. In the cold and one-dimensional limit, a modified derivative nonlinear Schrodinger equation is obtained. Direct numerical simulations are carried out to discuss the effect of the expansion on the modulational instability of monochromatic Alfvén waves and the propagation ofmore » Alfvén solitons. By using the instantaneous frequency, it is quantitatively shown that as far as the expansion rate is much smaller than wave frequencies, effects of the expansion are almost adiabatic. It is also confirmed that while shapes of Alfvén solitons temporally change due to the expansion, some of them can stably propagate after their collision in weakly-expanding plasmas.« less

  11. MER Field Geologic Traverse in Gusev Crater, Mars: Initial Results From the Perspective of Spirit

    NASA Technical Reports Server (NTRS)

    Crumpler, L.; Cabrol, N.; desMarais, D.; Farmer, J.; Golmbek, M.; Grant, J.; Greely, R.; Grotzinger, J.; Haskin, L.; Arvidson, R.

    2004-01-01

    This report casts the initial results of the traverse and science investigations by the Mars Exploration Rover (MER) Spirit at Gusev crater [1] in terms of data sets commonly used in field geologic investigations: Local mapping of geologic features, analyses of selected samples, and their location within the local map, and the regional context of the field traverse in terms of the larger geologic and physiographic region. These elements of the field method are represented in the MER characterization of the Gusev traverse by perspective-based geologic/morphologic maps, the placement of the results from Mossbauer, APXS, Microscopic Imager, Mini-TES and Pancam multispectral studies in context within this geologic/ morphologic map, and the placement of the overall traverse in the context of narrow-angle MOC (Mars Orbiter Camera) and descent images. A major campaign over a significance fraction of the mission will be the first robotic traverse of the ejecta from a Martian impact crater along an approximate radial from the crater center. The Mars Exploration Rovers have been conceptually described as 'robotic field geologists', that is, a suite of instruments with mobility that enables far-field traverses to multiple sites located within a regional map/image base at which in situ analyses may be done. Initial results from MER, where the field geologic method has been used throughout the initial course of the investigation, confirm that this field geologic model is applicable for remote planetary surface exploration. The field geologic method makes use of near-field geologic characteristics ('outcrops') to develop an understanding of the larger geologic context through continuous loop of rational steps focused on real-time hypothesis identification and testing. This poster equates 'outcrops' with the locations of in situ investigations and 'regional context' with the geology over distance of several kilometers. Using this fundamental field geologic method, we have

  12. MER-DIMES : a planetary landing application of computer vision

    NASA Technical Reports Server (NTRS)

    Cheng, Yang; Johnson, Andrew; Matthies, Larry

    2005-01-01

    During the Mars Exploration Rovers (MER) landings, the Descent Image Motion Estimation System (DIMES) was used for horizontal velocity estimation. The DIMES algorithm combines measurements from a descent camera, a radar altimeter and an inertial measurement unit. To deal with large changes in scale and orientation between descent images, the algorithm uses altitude and attitude measurements to rectify image data to level ground plane. Feature selection and tracking is employed in the rectified data to compute the horizontal motion between images. Differences of motion estimates are then compared to inertial measurements to verify correct feature tracking. DIMES combines sensor data from multiple sources in a novel way to create a low-cost, robust and computationally efficient velocity estimation solution, and DIMES is the first use of computer vision to control a spacecraft during planetary landing. In this paper, the detailed implementation of the DIMES algorithm and the results from the two landings on Mars are presented.

  13. The cascade of C:N:P stoichiometry in an ombrotrophic peatland: from plants to peat

    NASA Astrophysics Data System (ADS)

    Wang, Meng; Moore, Tim R.; Talbot, Julie; Richard, Pierre J. H.

    2014-01-01

    Northern peatlands are important carbon (C) sinks and while the patterns of C accumulation have been frequently investigated, nitrogen (N) and phosphorus (P) accumulation are often neglected. Here we link the C:N:P stoichiometry from foliar plant tissues, through senescent litters to peat, and determine C, N and P accumulation rates at Mer Bleue Bog, eastern Canada. Average C:N:P ratios changed from 794:17:1 in the foliar tissues to 911:10:1 in litter and 1285:32:1 in acrotelm peat. The increase in C:N and C:P ratios from mature to senescent tissues is related to nutrient resorption. The increase in C:P and N:P ratios in peat, which was contrary to that observed in Canadian forest soils, may be related to plant/mycorrhizae uptake of P. The long-term apparent rates of C, N and P accumulation were 29.5 ± 2.1 (SE) g C, 0.87 ± 0.01 g N and 0.017 ± 0.002 g P m-2 yr-1, respectively. The significant correlation between the accumulation rates of N and P and that of C suggests more attention be placed on C:N:P stoichiometry in peatland biogeochemistry, in particular in understanding why C:P ratios are so large in the lower parts of the profile.

  14. KENNEDY SPACE CENTER, FLA. - With smoke and steam billowing beneath, the Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - With smoke and steam billowing beneath, the Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  15. KENNEDY SPACE CENTER, FLA. - The Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload is viewed from under the launch tower as it moves away on Launch Complex 17-A, Cape Canaveral Air Force Station. This will be a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-09

    KENNEDY SPACE CENTER, FLA. - The Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload is viewed from under the launch tower as it moves away on Launch Complex 17-A, Cape Canaveral Air Force Station. This will be a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  16. KENNEDY SPACE CENTER, FLA. - The launch tower (right) on Launch Complex 17-A, Cape Canaveral Air Force Station, has been rolled back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload (left) in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-09

    KENNEDY SPACE CENTER, FLA. - The launch tower (right) on Launch Complex 17-A, Cape Canaveral Air Force Station, has been rolled back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload (left) in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  17. KENNEDY SPACE CENTER, FLA. - With a glimpse of the Atlantic Ocean over the horizon, the Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - With a glimpse of the Atlantic Ocean over the horizon, the Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25

  18. KENNEDY SPACE CENTER, FLA. - With a glimpse of the Atlantic Ocean over the horizon, the Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

    NASA Image and Video Library

    2003-06-10

    KENNEDY SPACE CENTER, FLA. - With a glimpse of the Atlantic Ocean over the horizon, the Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

  19. Ceramidastin, a novel bacterial ceramidase inhibitor, produced by Penicillium sp. Mer-f17067.

    PubMed

    Inoue, Hiroyuki; Someno, Tetsuya; Kato, Taira; Kumagai, Hiroyuki; Kawada, Manabu; Ikeda, Daishiro

    2009-02-01

    Decrease of ceramide in the skin is one of the aggravating factors of atopic dermatitis. The skin is often infected by ceramidase-producing bacteria, such as Pseudomonas aeruginosa. The bacterial ceramidase then degrades ceramide in the skin. To develop anti-atopic dermatitis drugs, we searched for ceramidase inhibitors, which led to the discovery of ceramidastin, a novel inhibitor of bacterial ceramidase, from the culture broth of Penicillium sp. Mer-f17067. Ceramidastin inhibited the bacterial ceramidase with an IC(50) value of 6.25 microg ml(-1). Here we describe the isolation, physicochemical properties, structure determination and biological activity of ceramidastin.

  20. Lipid profile frequency and the prevalence of dyslipidaemia from biochemical tests at Saint Louis University Hospital in Senegal.

    PubMed

    Doupa, Dominique; Mbengue, Abdou Salam; Diallo, Fatou Agne; Jobe, Modou; Ndiaye, Arame; Kane, Adama; Diatta, Alassane; Touré, Meissa

    2014-01-01

    The aim of this study was to evaluate the frequency of lipid profile requests and the prevalence of dyslipidemia in patients at the biochemistry laboratory of St. Louis University Hospital, as well as their correlation with sex and age. This was a retrospective study reviewing 14,116 laboratory results of patients of both sexes, over a period of six months (January-June 2013) regardless of the indication for the request. The lipid parameters included were: Total cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides with normal values defined as follows: Total cholesterol (<2g/l), HDL- cholesterol (>0,40g/l), LDL- cholesterol (<1,30g/l) and Triglycerides (<1,50g/l). The average age of our study population was 55.15 years with a female predorminance (M/F = 0.60). The age group most represented was that between 55-64 years. The frequency of lipid profile request in our sample was 9.41% (or 1,329). The overall prevalence of isolated hypercholesterolemia, hyperLDLaemia, hypoHDLaemia, hypertriglyceridaemia, and mixed hyperlipidemia were respectively 60.91%, 66.27%, 26.58%, 4.57% and 2.75%. Hypercholesterolemia, hyperLDLaemia, hypertriglyceridaemia and mixed hyperlipidaemia were higher in women with respectively 66.22%, 67.98%, 4.58%, 2.89% than in men (52.01%, 62.81%, 4.44% and 2.40% respectively). On the other hand, the prevalence of hypoHDLaemia was higher in males (32.19%) compared to females (23.76%). Hypercholesterolemia correlated significantly with age and sex. Our study showed a relatively low request rate for lipid profile and a high prevalence of dyslipidaemia hence the importance of conducting a major study on the prevalence of dyslipidaemia and associated factors in the Senegalese population.

  1. KvN mechanics approach to the time-dependent frequency harmonic oscillator.

    PubMed

    Ramos-Prieto, Irán; Urzúa-Pineda, Alejandro R; Soto-Eguibar, Francisco; Moya-Cessa, Héctor M

    2018-05-30

    Using the Ermakov-Lewis invariants appearing in KvN mechanics, the time-dependent frequency harmonic oscillator is studied. The analysis builds upon the operational dynamical model, from which it is possible to infer quantum or classical dynamics; thus, the mathematical structure governing the evolution will be the same in both cases. The Liouville operator associated with the time-dependent frequency harmonic oscillator can be transformed using an Ermakov-Lewis invariant, which is also time dependent and commutes with itself at any time. Finally, because the solution of the Ermakov equation is involved in the evolution of the classical state vector, we explore some analytical and numerical solutions.

  2. Biological Effects of c-Mer Receptor Tyrosine Kinase in Hematopoietic Cells Depend on the Grb2 Binding Site in the Receptor and Activation of NF-κB

    PubMed Central

    Georgescu, Maria-Magdalena; Kirsch, Kathrin H.; Shishido, Tomoyuki; Zong, Chen; Hanafusa, Hidesaburo

    1999-01-01

    The c-Mer receptor tyrosine kinase (RTK) is most closely related to chicken c-Eyk and belongs to the Axl RTK subfamily. Although not detected in normal lymphocytes, c-Mer is expressed in B- and T-cell leukemia cell lines, suggesting an association with lymphoid malignancies. To gain an understanding of the role of this receptor in lymphoid cells, we expressed in murine interleukin-3 (IL-3)-dependent Ba/F3 pro-B-lymphocyte cells a constitutively active receptor, CDMer, formed from the CD8 extracellular domain and the c-Mer intracellular domain. Cells transfected with a plasmid encoding the CDMer receptor became IL-3 independent. When tyrosine (Y)-to-phenylalanine (F) mutations were introduced into c-Mer, only the Y867 change significantly reduced the IL-3-independent cell proliferation. The Y867 residue in the CDMer receptor mediated the binding of Grb2, which recruited the p85 phosphatidylinositol 3-kinase (PI 3-kinase). Despite the difference in promotion of proliferation, both the CDMer and mutant F867 receptors activated Erk in transfected cells. On the other hand, we found that both transcriptional activation of NF-κB and activation of PI 3-kinase were significantly suppressed with the F867 mutant receptor, suggesting that the activation of antiapoptotic pathways is the major mechanism for the observed phenotypic difference. Consistent with this notion, apoptosis induced by IL-3 withdrawal was strongly prevented by CDMer but not by the F867 mutant receptor. PMID:9891051

  3. Acute viral respiratory infections among children in MERS-endemic Riyadh, Saudi Arabia, 2012-2013.

    PubMed

    Fagbo, Shamsudeen F; Garbati, Musa A; Hasan, Rami; AlShahrani, Dayel; Al-Shehri, Mohamed; AlFawaz, Tariq; Hakawi, Ahmed; Wani, Tariq Ahmad; Skakni, Leila

    2017-02-01

    The emergence of the Middle East Respiratory Syndrome (MERS) in Saudi Arabia has intensified focus on Acute Respiratory Infections [ARIs]. This study sought to identify respiratory viruses (RVs) associated with ARIs in children presenting at a tertiary hospital. Children (aged ≤13) presenting with ARI between January 2012 and December 2013 tested for 15 RVs using the Seeplex R RV15 kit were retrospectively included. Epidemiological data was retrieved from patient records. Of the 2235 children tested, 61.5% were ≤1 year with a male: female ratio of 3:2. Viruses were detected in 1364 (61.02%) children, 233 (10.4%) having dual infections: these viruses include respiratory syncytial virus (RSV) (24%), human rhinovirus (hRV) (19.7%), adenovirus (5.7%), influenza virus (5.3%), and parainfluenzavirus-3 (4.6%). Children, aged 9-11 months, were most infected (60.9%). Lower respiratory tract infections (55.4%) were significantly more than upper respiratory tract infection (45.3%) (P < 0.001). Seasonal variation of RV was directly and inversely proportional to relative humidity and temperature, respectively, for non MERS coronaviruses (NL63, 229E, and OC43). The study confirms community-acquired RV associated with ARI in children and suggests modulating roles for abiotic factors in RV epidemiology. However, community-based studies are needed to elucidate how these factors locally influence RV epidemiology. J. Med. Virol. 89:195-201, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Analysis of high-efficiency widely-tunable N-resonances in Cs vapor

    NASA Astrophysics Data System (ADS)

    Krasteva, A.; Gateva, S.; Tzvetkov, S.; Ghosh, P. N.; Sargsyan, A.; Cartaleva, S.

    2018-03-01

    The narrow-band coherent N-type resonance, promising for the development of advanced atomic clocks, can be considered as a type of three-photon resonance, where a two-photon Raman excitation is combined with a resonant optical pumping field. In this communication, we present an experimental study and a theoretical analysis related to three-photon, bi-chromatic excitation of Cs atomic vapor contained in an 8-mm long cell with 20 Torr of neon. If a coupling laser is fixed at a frequency that is lower by several GHz than the position of the absorption profile of the Fg = 4 set of transitions, and a probe laser is tuned over the D2 line (λ = 852 nm), a narrow high-contrast enhanced absorption N-resonance will be observed in the probe light profile, superimposed on the absorption profile of the Fg = 4 set of transitions. We present theoretical modeling aimed to clarify the processes behind the efficiency of the N-resonance preparation for different frequency positions of the coupling laser within the D2 line of Cs.

  5. CDC's Early Response to a Novel Viral Disease, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), September 2012–May 2014

    PubMed Central

    Dunville, Richard L.; Gerber, Susan I.; Erdman, Dean D.; Pesik, Nicki; Kuhar, David; Mason, Karen A.; Haynes, Lia; Rotz, Lisa; St. Pierre, Jeanette; Poser, Sarah; Bunga, Sudhir; Pallansch, Mark A.; Swerdlow, David L.

    2015-01-01

    The first ever case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported in September 2012. This report describes the approaches taken by CDC, in collaboration with the World Health Organization (WHO) and other partners, to respond to this novel virus, and outlines the agency responses prior to the first case appearing in the United States in May 2014. During this time, CDC's response integrated multiple disciplines and was divided into three distinct phases: before, during, and after the initial activation of its Emergency Operations Center. CDC's response to MERS-CoV required a large effort, deploying at least 353 staff members who worked in the areas of surveillance, laboratory capacity, infection control guidance, and travelers' health. This response built on CDC's experience with previous outbreaks of other pathogens and provided useful lessons for future emerging threats. PMID:26345122

  6. Gel performance in rheology and profile control under low-frequency vibration: coupling application of physical and chemical EOR techniques.

    PubMed

    Zheng, Li Ming; Pu, Chun Sheng; Liu, Jing; Ma, Bo; Khan, Nasir

    2017-01-01

    Flowing gel plugging and low-frequency vibration oil extraction technology have been widely applied in low-permeability formation. High probability of overlapping in action spheres of two technologies might lead to poor operating efficiency during gel injection. Study on flowing gel rheological properties under low-frequency vibration was essential, which was carried out indoor with viscosity measurement. Potential dynamic mechanisms were analyzed for the rheological variation. Under low-frequency vibration, gel rheological properties were found to be obviously influenced, with vibration delaying gel cross-linking in induction period, causing a two-stage gel viscosity change in acceleration period, and decreasing gel strength in stable period. Surface of gel system under vibration presented different fluctuating phenomenon from initial harmonic vibrating to heterogeneous fluctuating (droplet separation might appear) to final harmonic vibrating again. Dynamic displacement in unconsolidated sand pack revealed that low-frequency vibration during gel injection might be a measure to achieve deep profile control, with the gel injection depth increased by 65.8 % compared with the vibration-free sample. At last, suggestions for field test were given in the paper to achieve lower injection friction and better gel plugging efficiency.

  7. Alterations of the serum N-glycan profile in female patients with Major Depressive Disorder.

    PubMed

    Boeck, Christina; Pfister, Sophia; Bürkle, Alexander; Vanhooren, Valerie; Libert, Claude; Salinas-Manrique, Juan; Dietrich, Detlef E; Kolassa, Iris-Tatjana; Karabatsiakis, Alexander

    2018-07-01

    Glycans are short chains of saccharides linked to glycoproteins that are known to be involved in a wide range of inflammatory processes. As depression has been consistently associated with chronic low-grade inflammation, we asked whether patients with Major Depressive Disorder show alterations in the N-glycosylation pattern of serum proteins that might be linked to associated changes in inflammatory processes. In a study cohort of 21 female patients with an acute depressive episode and 21 non-depressed female control subjects aged between 50 and 69 years, we analyzed the serum N-glycan profile by DNA Sequencer Adapted-Fluorophore Assisted Carbohydrate Electrophoresis (DSA-FACE) and assessed the serum levels of interleukin (IL)- 6, tumor necrosis factor (TNF)-α and C-reactive protein (CRP) by chemiluminescence immunoassays and nephelometry. Compared to controls, MDD patients showed significant differences in the serum levels of several N-glycan structures. Alterations in the serum N-glycan profile were associated with depressive symptom severity and exploratory analyses revealed that they were most pronounced in MDD patients with a history of childhood sexual abuse. Furthermore, MDD patients showed higher levels of IL-6 and a trend for higher CRP levels, which were also associated with similar alterations in the serum N-glycan profile as those characteristic for MDD patients. The relatively small sample size and the presence of potential confounders (e.g., BMI, smoking, medication). The results offer the first evidence that specific differences in the N-glycosylation pattern of serum proteins constitute a so far unrecognized level of biological alterations that might be involved in the immune changes associated with MDD. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Quantitative Analysis of Etching Rate Profiles for 11B+-Implanted Si3N4 Film

    NASA Astrophysics Data System (ADS)

    Nakata, Jyoji; Kajiyama, Kenji

    1983-01-01

    Etching rate enhancement for 11B+-implanted Si3N4 film was investigated both experimentally and theoretically. The etching solution was concentrated H3PO4 at ˜165°C Film thicknesses were precisely measured by ellipsometry. Enhancement resulted from Si-N bond breaking. This was confirmed by a decrease of infrared absorption at a 12.0 μm wavelength for Si-N bond vibration. Main and additional peaks were observed in the etching rate profile. The former was due to nuclear damage and was well represented by the calculated etching rate profile deduced from the nuclear deposited energy density distribution. The latter existed in the surface region only when the ion projected range was shorter than the film thickness. This peak was possibly caused by charge accumulation in the insulating Si3N4 film during 11B+ implantation.

  9. High-frequency large-amplitude oscillations of a non-isothermal N/S boundary

    NASA Astrophysics Data System (ADS)

    Bezuglyj, A. I.; Shklovskij, V. A.

    2016-10-01

    Within the framework of a phenomenological approach based on the heat balance equation and the current dependence of the critical temperature of the superconductor, the effect of high-frequency current of large amplitude and arbitrary waveform on the non-isothermal balance of an oscillating N/S interface in a long superconductor was studied. Self-consistent average temperature field of the rapidly oscillating non-isothermal N/S boundary (heat kink) was introduced, which allowed us to go beyond the well-known concept of mean-square heating and consider the effect of the current waveform. With regard to experiments on the effects of high-power microwave radiation on the current-voltage (IV) characteristics of superconducting films, their classification was performed and the families of IV curves of inhomogeneous superconductors carrying a current containing a high-frequency component of large amplitude. Several IV curves exhibited a hysteresis of thermal nature.

  10. The Amorphous Component in Martian Basaltic Soil in Global Perspective from MSL and MER Missions

    NASA Technical Reports Server (NTRS)

    Morris, R. V.; Ming, D. W.; Blake, D. F.; Vaniman, D. T.; Bish, D. L.; Chipera, S. J.; Downs, R. T.; Gellert, R.; Treiman, A. H.; Yen, A. S.; hide

    2013-01-01

    The mineralogy instrument CheMin onboard the MSL rover Curiosity analyzed by transmission XRD [1] the <150 microns size fraction of putative global basaltic martian soil from scoops 4 and 5 of the Rocknest aeolian bedform (sol 81-120). Here, we combine chemical (APXS) and mineralogical (Mossbauer; MB) results from the MER rovers with chemical (APXS) and mineralogical (CheMin) results from Curiosity to constrain the relative proportions of amorphous and crystalline components, the bulk chemical composition of those components, and the

  11. Frequency-dependent Alfvén-wave Propagation in the Solar Wind: Onset and Suppression of Parametric Decay Instability

    NASA Astrophysics Data System (ADS)

    Shoda, Munehito; Yokoyama, Takaaki; Suzuki, Takeru K.

    2018-06-01

    Using numerical simulations we investigate the onset and suppression of parametric decay instability (PDI) in the solar wind, focusing on the suppression effect by the wind acceleration and expansion. Wave propagation and dissipation from the coronal base to 1 au is solved numerically in a self-consistent manner; we take into account the feedback of wave energy and pressure in the background. Monochromatic waves with various injection frequencies, f 0, are injected to discuss the suppression of PDI, while broadband waves are applied to compare the numerical results with observation. We find that high-frequency ({f}0≳ {10}-3 {Hz}) Alfvén waves are subject to PDI. Meanwhile, the maximum growth rate of the PDI of low-frequency ({f}0≲ {10}-4 {Hz}) Alfvén waves becomes negative due to acceleration and expansion effects. Medium-frequency ({f}0≈ {10}-3.5 {Hz}) Alfvén waves have a positive growth rate but do not show the signature of PDI up to 1 au because the growth rate is too small. The medium-frequency waves experience neither PDI nor reflection so they propagate through the solar wind most efficiently. The solar wind is shown to possess a frequency-filtering mechanism with respect to Alfvén waves. The simulations with broadband waves indicate that the observed trend of the density fluctuation is well explained by the evolution of PDI while the observed cross-helicity evolution is in agreement with low-frequency wave propagation.

  12. Multi-frequency ICRF diagnostic of Tokamak plasmas

    NASA Astrophysics Data System (ADS)

    Lafonteese, David James

    This thesis explores the diagnostic possibilities of a fast wave-based method for measuring the ion density and temperature profiles of tokamak plasmas. In these studies fast waves are coupled to the plasma at frequencies at the second harmonic of the ion gyrofrequency, at which wave energy is absorbed by the finite-temperature ions. As the ion gyrofrequency is dependent upon the local magnetic field, which varies as l/R in a tokamak, this power absorption is radially localized. The simultaneous launching of multiple frequencies, all resonating at different plasma positions, allows local measurements of the ion density and temperature. To investigate the profile applications of wave damping measurements in a simulated tokamak, an inhouse slab-model ICRF code is developed. A variety of analysis methods are presented, and ion density and temperature profiles are reconstructed for hydrogen plasmas for the Electric Tokamak (ET) and ITER parameter spaces. These methods achieve promising results in simulated plasmas featuring bulk ion heating, off-axis RF heating, and density ramps. The experimental results of similar studies on the Electric Tokamak, a high aspect ratio (R/a = 5), low toroidal field (2.2 kG) device are then presented. In these studies, six fast wave frequencies were coupled using a single-strap, low-field-side antenna to ET plasmas. The frequencies were variable, and could be tuned to resonate at different radii for different experiments. Four magnetic pickup loops were used to measure of the toroidal component of the wave magnetic field. The expected greater eigenmode damping of center-resonant frequencies versus edge-resonant frequencies is consistently observed. Comparison of measured aspects of fast wave behavior in ET is made with the slab code predictions, which validate the code simulations under weakly-damped conditions. A density profile is measured for an ET discharge through analysis of the fast wave measurements, and is compared to an

  13. A Single Serine Residue Determines Selectivity to Monovalent Metal Ions in Metalloregulators of the MerR Family

    PubMed Central

    Ibáñez, María M.

    2015-01-01

    ABSTRACT MerR metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. The sensor protein binds the inducer metal ion by using two conserved cysteine residues at the C-terminal metal-binding loop (MBL). Divalent metal ion sensors, such as MerR and ZntR, require a third cysteine residue, located at the beginning of the dimerization (α5) helix, for metal coordination, while monovalent metal ion sensors, such as CueR and GolS, have a serine residue at this position. This serine residue was proposed to provide hydrophobic and steric restrictions to privilege the binding of monovalent metal ions. Here we show that the presence of alanine at this position does not modify the activation pattern of monovalent metal sensors. In contrast, GolS or CueR mutant sensors with a substitution of cysteine for the serine residue respond to monovalent metal ions or Hg(II) with high sensitivities. Furthermore, in a mutant deleted of the Zn(II) exporter ZntA, they also trigger the expression of their target genes in response to either Zn(II), Cd(II), Pb(II), or Co(II). IMPORTANCE Specificity in a stressor's recognition is essential for mounting an appropriate response. MerR metalloregulators trigger the expression of specific resistance systems upon detection of heavy metal ions. Two groups of these metalloregulators can be distinguished, recognizing either +1 or +2 metal ions, depending on the presence of a conserved serine in the former or a cysteine in the latter. Here we demonstrate that the serine residue in monovalent metal ion sensors excludes divalent metal ion detection, as its replacement by cysteine renders a pan-metal ion sensor. Our results indicate that the spectrum of signals detected by these sensors is determined not only by the metal-binding ligand availability but also by the metal-binding cavity

  14. Discovering Parameters for Ancient Mars Atmospheric Profiles by Modeling Volcanic Eruptions

    NASA Astrophysics Data System (ADS)

    Meyer, A.; Clarke, A. B.; Van Eaton, A. R.; Mastin, L. G.

    2017-12-01

    Evidence of explosive volcanic deposits on Mars motivates questions about the behavior of eruption plumes in the Ancient and current Martian atmosphere. Early modeling studies suggested that Martian plumes may rise significantly higher than their terrestrial equivalents (Wilson and Head, 1994, Rev. Geophys., 32, 221-263). We revisit the issue using a steady-state 1-D model of volcanic plumes (Plumeria: Mastin, 2014, JGR, doi:10.1002/2013JD020604) along with a range of reasonable temperature and pressures. The model assumes perfect coupling of particles with the gas phase in the plume, and Stokes number analysis indicates that this is a reasonable assumption for particle diameters less than 5 mm to 1 micron. Our estimates of Knudsen numbers support the continuum assumption. The tested atmospheric profiles include an estimate of current Martian atmosphere based on data from voyager mission (Seif, A., Kirk, D.B., (1977) Geophys., 82,4364-4378), a modern Earth-like atmosphere, and several other scenarios based on variable tropopause heights and near-surface atmospheric density estimates from the literature. We simulated plume heights using mass eruption rates (MER) ranging from 1 x 103 to 1 x 1010 kg s-1 to create a series of new theoretical MER-plume height scaling relationships that may be useful for considering plume injection heights, climate impacts, and global-scale ash dispersal patterns in Mars' recent and ancient geological past. Our results show that volcanic plumes in a modern Martian atmosphere may rise up to three times higher than those on Earth. We also find that the modern Mars atmosphere does not allow eruption columns to collapse, and thus does not allow for the formation of column-collapse pyroclastic density currents, a phenomenon thought to have occurred in Mars' past based on geological observations. The atmospheric density at the surface, and especially the height of the tropopause, affect the slope of the MER-plume height curve and control

  15. Mild Airflow Limitation during N2 Sleep Increases K-complex Frequency and Slows Electroencephalographic Activity.

    PubMed

    Nguyen, Chinh D; Wellman, Andrew; Jordan, Amy S; Eckert, Danny J

    2016-03-01

    To determine the effects of mild airflow limitation on K-complex frequency and morphology and electroencephalogram (EEG) spectral power. Transient reductions in continuous positive airway pressure (CPAP) during stable N2 sleep were performed to induce mild airflow limitation in 20 patients with obstructive sleep apnea (OSA) and 10 healthy controls aged 44 ± 13 y. EEG at C3 and airflow were measured in 1-min windows to quantify K-complex properties and EEG spectral power immediately before and during transient reductions in CPAP. The frequency and morphology (amplitude and latency of P200, N550 and N900 components) of K-complexes and EEG spectral power were compared between conditions. During mild airflow limitation (18% reduction in peak inspiratory airflow from baseline, 0.38 ± 0.11 versus 0.31 ± 0.1 L/sec) insufficient to cause American Academy of Sleep Medicine-defined cortical arousal, K-complex frequency (9.5 ± 4.5 versus 13.7 ± 6.4 per min, P < 0.01), N550 amplitude (25 ± 3 versus 27 ± 3 μV, P < 0.01) and EEG spectral power (delta: 147 ± 48 versus 230 ± 99 μV(2), P < 0.01 and theta bands: 31 ± 14 versus 34 ± 13 μV(2), P < 0.01) significantly increased whereas beta band power decreased (14 ± 5 versus 11 ± 4 μV(2), P < 0.01) compared to the preceding non flow-limited period on CPAP. K-complex frequency, morphology, and timing did not differ between patients and controls. Mild airflow limitation increases K-complex frequency, N550 amplitude, and spectral power of delta and theta bands. In addition to providing mechanistic insight into the role of mild airflow limitation on K-complex characteristics and EEG activity, these findings may have important implications for respiratory conditions in which airflow limitation during sleep is common (e.g., snoring and OSA). © 2016 Associated Professional Sleep Societies, LLC.

  16. Rapid one-step construction of a Middle East Respiratory Syndrome (MERS-CoV) infectious clone system by homologous recombination.

    PubMed

    Nikiforuk, Aidan M; Leung, Anders; Cook, Bradley W M; Court, Deborah A; Kobasa, Darwyn; Theriault, Steven S

    2016-10-01

    Viral Infectious clone systems serve as robust platforms to study viral gene or replicative function by reverse genetics, formulate vaccines and adapt a wild type-virus to an animal host. Since the development of the first viral infectious clone system for the poliovirus, novel strategies of viral genome construction have allowed for the assembly of viral genomes across the identified viral families. However, the molecular profiles of some viruses make their genome more difficult to construct than others. Two factors that affect the difficulty of infectious clone construction are genome length and genome complexity. This work examines the available strategies for overcoming the obstacles of assembling the long and complex RNA genomes of coronaviruses and reports one-step construction of an infectious clone system for the Middle East Respiratory Syndrome coronavirus (MERS-CoV) by homologous recombination in S. cerevisiae. Future use of this methodology will shorten the time between emergence of a novel viral pathogen and construction of an infectious clone system. Completion of a viral infectious clone system facilitates further study of a virus's biology, improvement of diagnostic tests, vaccine production and the screening of antiviral compounds. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

  17. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana *

    PubMed Central

    Ndah, Elvis; Jonckheere, Veronique

    2017-01-01

    Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes. PMID:28432195

  18. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.

    PubMed

    Willems, Patrick; Ndah, Elvis; Jonckheere, Veronique; Stael, Simon; Sticker, Adriaan; Martens, Lennart; Van Breusegem, Frank; Gevaert, Kris; Van Damme, Petra

    2017-06-01

    Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Dust Accumulation and Solar Panel Array Performance on the Mars Exploration Rover (MER) Project

    NASA Technical Reports Server (NTRS)

    Turgay, Eren H.

    2004-01-01

    One of the most fundamental design considerations for any space vehicle is its power supply system. Many options exist, including batteries, fuel cells, nuclear reactors, radioisotopic thermal generators (RTGs), and solar panel arrays. Solar arrays have many advantages over other types of power generation. They are lightweight and relatively inexpensive, allowing more mass and funding to be allocated for other important devices, such as scientific instruments. For Mars applications, solar power is an excellent option, especially for long missions. One might think that dust storms would be a problem; however, while dust blocks some solar energy, it also scatters it, making it diffuse rather than beamed. Solar cells are still able to capture this diffuse energy and convert it into substantial electrical power. For these reasons, solar power was chosen to be used on the 1997 Mars Pathfinder mission. The success of this mission set a precedent, as NASA engineers have selected solar power as the energy system of choice for all future Mars missions, including the Mars Exploration Rover (MER) Project. Solar sells have their drawbacks, however. They are difficult to manufacture and are relatively fragile. In addition, solar cells are highly sensitive to different parts of the solar spectrum, and finding the correct balance is crucial to the success of space missions. Another drawback is that the power generated is not a constant with respect to time, but rather changes with the relative angle to the sun. On Mars, dust accumulation also becomes a factor. Over time, dust settles out of the atmosphere and onto solar panels. This dust blocks and shifts the frequency of the incoming light, degrading solar cell performance. My goal is to analyze solar panel telemetry data from the two MERs (Spirit and Opportunity) in an effort to accurately model the effect of dust accumulation on solar panels. This is no easy process due to the large number of factors involved. Changing solar

  20. The Relationship between Lexical Frequency Profiling Measures and Rater Judgements of Spoken and Written General English Language Proficiency on the CELPIP-General Test

    ERIC Educational Resources Information Center

    Douglas, Scott Roy

    2015-01-01

    Independent confirmation that vocabulary in use unfolds across levels of performance as expected can contribute to a more complete understanding of validity in standardized English language tests. This study examined the relationship between Lexical Frequency Profiling (LFP) measures and rater judgements of test-takers' overall levels of…

  1. KENNEDY SPACE CENTER, FLA. - In the Payload Hazardous Servicing Facility, workers mate the Mars Exploration Rover-2 (MER-2) to the third stage of a Delta II rocket for launch on June 5. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-23

    KENNEDY SPACE CENTER, FLA. - In the Payload Hazardous Servicing Facility, workers mate the Mars Exploration Rover-2 (MER-2) to the third stage of a Delta II rocket for launch on June 5. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-1 (MER-B) will launch June 25.

  2. The Mars Exploration Rover (MER) Transverse Impulse Rocket System (TIRS)

    NASA Technical Reports Server (NTRS)

    SanMartin, Alejandro Miguel; Bailey, Erik

    2005-01-01

    In a very short period of time the MER project successfully developed and tested a system, TIRS/DIMES, to improve the probability of success in the presence of large Martian winds. The successful development of TIRS/DIMES played a big role in the landing site selection process by enabling the landing of Spirit on Gusev crater, a site of very high scientific interest but with known high wind conditions. The performance of TIRS by Spirit at Gusev Crater was excellent. The velocity prediction error was small and Big TIRS was fired reducing the impact horizontal velocity from approximately 23 meters per second to approximately 11 meters per second, well within the airbag capabilities. The performance of TIRS by Opportunity at Meridiani was good. The velocity prediction error was rather large (approximately 6 meters per second, a less than 2 sigma value, but TIRS did not fire which was the correct action.

  3. From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.

    PubMed

    Hilgenfeld, Rolf; Peiris, Malik

    2013-10-01

    This article introduces a series of invited papers in Antiviral Research marking the 10th anniversary of the outbreak of severe acute respiratory syndrome (SARS), caused by a novel coronavirus that emerged in southern China in late 2002. Until that time, coronaviruses had not been recognized as agents causing severe disease in humans, hence, the emergence of the SARS-CoV came as a complete surprise. Research during the past ten years has revealed the existence of a diverse pool of coronaviruses circulating among various bat species and other animals, suggesting that further introductions of highly pathogenic coronaviruses into the human population are not merely probable, but inevitable. The recent emergence of another coronavirus causing severe disease, Middle East respiratory syndrome (MERS), in humans, has made it clear that coronaviruses pose a major threat to human health, and that more research is urgently needed to elucidate their replication mechanisms, identify potential drug targets, and develop effective countermeasures. In this series, experts in many different aspects of coronavirus replication and disease will provide authoritative, up-to-date reviews of the following topics: - clinical management and infection control of SARS; - reservoir hosts of coronaviruses; - receptor recognition and cross-species transmission of SARS-CoV; - SARS-CoV evasion of innate immune responses; - structures and functions of individual coronaviral proteins; - anti-coronavirus drug discovery and development; and - the public health legacy of the SARS outbreak. Each article will be identified in the last line of its abstract as belonging to the series "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses." Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Oxygen Profile of a Thermo-Haliophilic Community in the Badwater Salt Flat

    NASA Technical Reports Server (NTRS)

    Smith, H. D.; McKay, C. P.; Rainey, F.; Bebout, B.; Carpenter, S.

    2004-01-01

    Badwater is the lowest, saltiest, and hottest, place in North America. This extreme environment is 86 meters (282 feet) below sea level surrounded by four mountain ranges. Due to the geographical location Badwater does not receive moisture from the prevailing winds, this intern results in a hot, arid, and salty environment. Despite these extreme living conditions, microbes manage to flourish within the salt flat. The salt acts as an insulator making life just beneath the surface more comfortable In this paper, we compare the microbial population versus oxygen concentration; and the importance of and the role of oxygen in metabolic functions by these thermo-haliophiles. Furthermore a model of the oxygen profile will also provide an insight to the oxygen cycle in salty environments. This research has implications for the limits of life on Earth and Mars. Recent results from the MER rovers show that water on Mars was very salty. Measuring the oxygen profile in these salty environments on Earth provides a framework within which potential life on Mars can be evaluated. The use of an oxygen profile could also be used as a search criteria for life.

  5. Isolation and Characterization of Dromedary Camel Coronavirus UAE-HKU23 from Dromedaries of the Middle East: Minimal Serological Cross-Reactivity between MERS Coronavirus and Dromedary Camel Coronavirus UAE-HKU23

    PubMed Central

    Woo, Patrick C. Y.; Lau, Susanna K. P.; Fan, Rachel Y. Y.; Lau, Candy C. Y.; Wong, Emily Y. M.; Joseph, Sunitha; Tsang, Alan K. L.; Wernery, Renate; Yip, Cyril C. Y.; Tsang, Chi-Ching; Wernery, Ulrich; Yuen, Kwok-Yung

    2016-01-01

    Recently, we reported the discovery of a dromedary camel coronavirus UAE-HKU23 (DcCoV UAE-HKU23) from dromedaries in the Middle East. In this study, DcCoV UAE-HKU23 was successfully isolated in two of the 14 dromedary fecal samples using HRT-18G cells, with cytopathic effects observed five days after inoculation. Northern blot analysis revealed at least seven distinct RNA species, corresponding to predicted subgenomic mRNAs and confirming the core sequence of transcription regulatory sequence motifs as 5′-UCUAAAC-3′ as we predicted previously. Antibodies against DcCoV UAE-HKU23 were detected in 58 (98.3%) and 59 (100%) of the 59 dromedary sera by immunofluorescence and neutralization antibody tests, respectively. There was significant correlation between the antibody titers determined by immunofluorescence and neutralization assays (Pearson coefficient = 0.525, p < 0.0001). Immunization of mice using recombinant N proteins of DcCoV UAE-HKU23 and Middle East respiratory syndrome coronavirus (MERS-CoV), respectively, and heat-inactivated DcCoV UAE-HKU23 showed minimal cross-antigenicity between DcCoV UAE-HKU23 and MERS-CoV by Western blot and neutralization antibody assays. Codon usage and genetic distance analysis of RdRp, S and N genes showed that the 14 strains of DcCoV UAE-HKU23 formed a distinct cluster, separated from those of other closely related members of Betacoronavirus 1, including alpaca CoV, confirming that DcCoV UAE-HKU23 is a novel member of Betacoronavirus 1. PMID:27164099

  6. Strategy and technology to prevent hospital-acquired infections: Lessons from SARS, Ebola, and MERS in Asia and West Africa.

    PubMed

    Rajakaruna, Sanjeewa Jayachandra; Liu, Wen-Bin; Ding, Yi-Bo; Cao, Guang-Wen

    2017-10-27

    Hospital-acquired infections (HAIs) are serious problems for healthcare systems, especially in developing countries where public health infrastructure and technology for infection preventions remain undeveloped. Here, we characterized how strategy and technology could be mobilized to improve the effectiveness of infection prevention and control in hospitals during the outbreaks of Ebola, Middle East respiratory syndrome (MERS), and severe acute respiratory syndrome (SARS) in Asia and West Africa. Published literature on the hospital-borne outbreaks of SARS, Ebola, and MERS in Asia and West Africa was comprehensively reviewed. The results showed that healthcare systems and hospital management in affected healthcare facilities had poor strategies and inadequate technologies and human resources for the prevention and control of HAIs, which led to increased morbidity, mortality, and unnecessary costs. We recommend that governments worldwide enforce disaster risk management, even when no outbreaks are imminent. Quarantine and ventilation functions should be taken into consideration in architectural design of hospitals and healthcare facilities. We also recommend that health authorities invest in training healthcare workers for disease outbreak response, as their preparedness is essential to reducing disaster risk.

  7. Empirical conversion of the vertical profile of reflectivity from Ku-band to S-band frequency

    NASA Astrophysics Data System (ADS)

    Cao, Qing; Hong, Yang; Qi, Youcun; Wen, Yixin; Zhang, Jian; Gourley, Jonathan J.; Liao, Liang

    2013-02-01

    ABSTRACT This paper presents an empirical method for converting reflectivity from Ku-band (13.8 GHz) to S-band (2.8 GHz) for several hydrometeor species, which facilitates the incorporation of Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) measurements into quantitative precipitation estimation (QPE) products from the U.S. Next-Generation Radar (NEXRAD). The development of empirical dual-frequency relations is based on theoretical simulations, which have assumed appropriate scattering and microphysical models for liquid and solid hydrometeors (raindrops, snow, and ice/hail). Particle phase, shape, orientation, and density (especially for snow particles) have been considered in applying the T-matrix method to compute the scattering amplitudes. Gamma particle size distribution (PSD) is utilized to model the microphysical properties in the ice region, melting layer, and raining region of precipitating clouds. The variability of PSD parameters is considered to study the characteristics of dual-frequency reflectivity, especially the variations in radar dual-frequency ratio (DFR). The empirical relations between DFR and Ku-band reflectivity have been derived for particles in different regions within the vertical structure of precipitating clouds. The reflectivity conversion using the proposed empirical relations has been tested using real data collected by TRMM-PR and a prototype polarimetric WSR-88D (Weather Surveillance Radar 88 Doppler) radar, KOUN. The processing and analysis of collocated data demonstrate the validity of the proposed empirical relations and substantiate their practical significance for reflectivity conversion, which is essential to the TRMM-based vertical profile of reflectivity correction approach in improving NEXRAD-based QPE.

  8. Spatial distribution of acaricide profiles (Boophilus microplus strains susceptible or resistant to acaricides) in southeastern Mexico.

    PubMed

    Rodríguez-Vivas, R I; Rivas, A L; Chowell, G; Fragoso, S H; Rosario, C R; García, Z; Smith, S D; Williams, J J; Schwager, S J

    2007-05-15

    The ability of Boophilus microplus strains to be susceptible (-) or resistant (+) to amidines (Am), synthetic pyrethroids (SP), and/or organo-phosphates (OP) (or acaricide profiles) was investigated in 217 southeastern Mexican cattle ranches (located in the states of Yucatán, Quintana Roo, and Tabasco). Three questions were asked: (1) whether acaricide profiles varied at random and, if not, which one(s) explained more (or less) cases than expected, (2) whether the spatial distribution of acaricide profiles was randomly or non-randomly distributed, and (3) whether acaricide profiles were associated with farm-related covariates (frequency of annual treatments, herd size, and farm size). Three acaricide profiles explained 73.6% of the data, representing at least twice as many cases as expected (P<0.001): (1) Am-SP-, (2) Am+SP+, and (3) (among ranches that dispensed acaricides > or = 6 times/year) Am-OP+SP+. Because ticks collected in Yucatán ranches tended to be susceptible to Am, those of Quintana Roo ranches displayed, predominantly, resistance to OP/SP, and Tabasco ticks tended to be resistant to Am (all with P < or = 0.05), acaricide profiles appeared to be non-randomly disseminated over space. Across states, two farm-related covariates were associated with resistance (P < or = 0.02): (1) high annual frequency of acaricide treatments, and (2) large farm size. Findings supported the hypothesis that spatial acaricide profiles followed neither random nor homogeneous data distributions, being partially explained by agent- and/or farm-specific factors. Some profiles could not be explained by these factors. Further spatially explicit studies (addressing host-related factors) are recommended.

  9. Comparison of trap characteristics between AlGaN/GaN and AlGaN/InGaN/GaN heterostructure by frequency dependent conductance measurement

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

    Chakraborty, Apurba, E-mail: apurba.chakraborty86@gmail.com; Biswas, Dhrubes; Advanced Technology Development Centre, IIT Kharagpur, Kharagpur 721302

    2015-02-23

    Frequency dependent conductance measurement is carried out to observe the trapping effect in AlGaN/InGaN/GaN double heterostructure and compared that with conventional AlGaN/GaN single heterostructure. It is found that the AlGaN/InGaN/GaN diode structure does not show any trapping effect, whereas single heterostructure AlGaN/GaN diode suffers from two kinds of trap energy states in near depletion to higher negative voltage bias region. This conductance behaviour of AlGaN/InGaN/GaN heterostructure is owing to more Fermi energy level shift from trap energy states at AlGaN/InGaN junction compare to single AlGaN/GaN heterostructure and eliminates the trapping effects. Analysis yielded interface trap energy state in AlGaN/GaN ismore » to be with time constant of (33.8–76.5) μs and trap density of (2.38–0.656) × 10{sup 12 }eV{sup −1} cm{sup −2} in −3.2 to −4.8 V bias region, whereas for AlGaN/InGaN/GaN structure no interface energy states are found and the extracted surface trap energy concentrations and time constants are (5.87–4.39) ×10{sup 10} eV{sup −1} cm{sup −2} and (17.8–11.3) μs, respectively, in bias range of −0.8–0.0 V.« less

  10. Effects of 8-mer acidic peptide concentration on the morphology and photoluminescence of synthesized ZnO nanomaterials

    NASA Astrophysics Data System (ADS)

    Moon, Chung Hee; Tousi, Marzieh; Cheeney, Joseph; Ngo-Duc, Tam-Triet; Zuo, Zheng; Liu, Jianlin; Haberer, Elaine D.

    2015-11-01

    An 8-mer ZnO-binding peptide, VPGAAEHT, was identified using a M13 pVIII phage display library and employed as an additive during aqueous-based ZnO synthesis at 65 °C. Unlike most other well-studied ZnO-binding sequences which are strongly basic (pI > pH 7), the 8-mer peptide was overall acidic (pI < pH 7) in character, including only a single basic residue. The selected peptide strongly influenced ZnO nanostructure formation. Morphology and optical emission properties were found to be dependent on the concentration of peptide additive. Using lower peptide concentrations (<0.1 mM), single crystal hexagonal rods and platelets were produced, and using higher peptide concentrations (≥0.1 mM), polycrystalline layered platelets, yarn-like structures, and microspheres were assembled. Photoluminescence analysis revealed a characteristic ZnO band-edge peak, as well as sub-bandgap emission peaks. Defect-related green emission, typically associated with surface-related oxygen and zinc vacancies, was significantly reduced by the peptide additive, while blue emission, attributable to oxygen and zinc interstitials, emerged with increased peptide concentrations. Peptide-directed synthesis of ZnO materials may be useful for gas sensing and photocatalytic applications in which properly engineered morphology and defect levels have demonstrated enhanced performance.

  11. Low-frequency noise in AlN/AlGaN/GaN metal-insulator-semiconductor devices: A comparison with Schottky devices

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

    Le, Son Phuong; Nguyen, Tuan Quy; Shih, Hong-An

    2014-08-07

    We have systematically investigated low-frequency noise (LFN) in AlN/AlGaN/GaN metal-insulator-semiconductor (MIS) devices, where the AlN gate insulator layer was sputtering-deposited on the AlGaN surface, in comparison with LFN in AlGaN/GaN Schottky devices. By measuring LFN in ungated two-terminal devices and heterojunction field-effect transistors (HFETs), we extracted LFN characteristics in the intrinsic gated region of the HFETs. Although there is a bias regime of the Schottky-HFETs in which LFN is dominated by the gate leakage current, LFN in the MIS-HFETs is always dominated by only the channel current. Analyzing the channel-current-dominated LFN, we obtained Hooge parameters α for the gated regionmore » as a function of the sheet electron concentration n{sub s} under the gate. In a regime of small n{sub s}, both the MIS- and Schottky-HFETs exhibit α∝n{sub s}{sup −1}. On the other hand, in a middle n{sub s} regime of the MIS-HFETs, α decreases rapidly like n{sub s}{sup −ξ} with ξ ∼ 2-3, which is not observed for the Schottky-HFETs. In addition, we observe strong increase in α∝n{sub s}{sup 3} in a large n{sub s} regime for both the MIS- and Schottky-HFETs.« less

  12. Clinical Correlations of Transcriptional Profile in Patients Infected with Avian Influenza H7N9 Virus.

    PubMed

    Guan, Wenda; Wu, Nicholas C; Lee, Horace H Y; Li, Yimin; Jiang, Wenxin; Shen, Lihan; Wu, Douglas C; Chen, Rongchang; Zhong, Nanshan; Wilson, Ian A; Peiris, Malik; Yang, Zifeng; Mok, Chris K P

    2018-05-28

    Avian influenza A (H7N9) viruses emerged in China in 2013 and caused zoonotic disease associated with a case-fatality ratio of over 30%. Transcriptional profiles in peripheral blood reflect host responses and can help to elucidate disease pathogenesis. We correlated serial blood transcriptomic profiles of patients with avian influenza A (H7N9) virus infection and determined the biological significances from the analysis. We found that specific gene expression profiles in the blood were strongly correlated with the PaO2/FiO2 ratio and viral load in the lower respiratory tract (LRT). Cell cycle and leukocyte-related immunity were activated at the acute stage of the infection while T cell functions and various metabolic processes were associated with the recovery phase of the illness. A transition from systemic innate to adaptive immunity was found. We developed a novel approach for transcriptomic analysis to identify key host responses that were strongly correlated with specific clinical and virologic parameters in patients with H7N9 infection.

  13. MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

    PubMed

    Piro, Vitor C; Matschkowski, Marcel; Renard, Bernhard Y

    2017-08-14

    Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools. We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases. In a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .

  14. Evaporative purification to produce highly monodisperse polymers: Application to polystyrene for n =3 -13 and quantification of Tg from oligomer to polymer

    NASA Astrophysics Data System (ADS)

    Zhu, S.; Chai, Y.; Forrest, J. A.

    2017-07-01

    We demonstrate the use of selective thermal evaporation to separate and purify small molecular weight polymers into highly monodisperse polymers over an extended range of polymerization index. By exploiting the calculated dependence of polymer vapor pressure on polymerization index N and temperature T , we can isolate individual components (N -mers) of an initially polydisperse mixture. To demonstrate this ability, we consider polystyrene samples of Mw=600 g/mol and Mw=890 g/mol with narrow molecular weight distributions, as well as a Mw=1200 g/mol sample with a broader distribution. In each case we are able to separate the sample into milligram quantities of many different components. Using this technique, we have been able to isolate N -mers from 3 to 13. We use differential scanning calorimetry to measure the Tg values of these components, and find that the components have the same Tg values independent of the Mw or polydispersity of the sample they originate from. We find that even initially narrow molecular weight distributions have many different components whose Tg values can differ by more than 50 K. Calculations suggest the isolated components have Mw/Mn values less than 1.001 and through a second iteration of the process could become as low as 1.000 003. The measured Tg values for the N -mers as well as large N polymers are well described by a simple relation derived from the Fox equation for the Tg of mixtures.

  15. LORES: Low resolution shape program for the calculation of small angle scattering profiles for biological macromolecules in solution

    NASA Astrophysics Data System (ADS)

    Zhou, J.; Deyhim, A.; Krueger, S.; Gregurick, S. K.

    2005-08-01

    A program for determining the low resolution shape of biological macromolecules, based on the optimization of a small angle neutron scattering profile to experimental data, is presented. This program, termed LORES, relies on a Monte Carlo optimization procedure and will allow for multiple scattering length densities of complex structures. It is therefore more versatile than utilizing a form factor approach to produce low resolution structural models. LORES is easy to compile and use, and allows for structural modeling of biological samples in real time. To illustrate the effectiveness and versatility of the program, we present four specific biological examples, Apoferritin (shell model), Ribonuclease S (ellipsoidal model), a 10-mer dsDNA (duplex helix) and a construct of a 10-mer DNA/PNA duplex helix (heterogeneous structure). These examples are taken from protein and nucleic acid SANS studies, of both large and small scale structures. We find, in general, that our program will accurately reproduce the geometric shape of a given macromolecule, when compared with the known crystallographic structures. We also present results to illustrate the lower limit of the experimental resolution which the LORES program is capable of modeling. Program summaryTitle of program:LORES Catalogue identifier: ADVC Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVC Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer:SGI Origin200, SGI Octane, SGI Linux, Intel Pentium PC Operating systems:UNIX64 6.5 and LINUX 2.4.7 Programming language used:C Memory required to execute with typical data:8 MB No. of lines in distributed program, including test data, etc.:2270 No. of bytes in distributed program, including test data, etc.:13 302 Distribution format:tar.gz External subprograms used:The entire code must be linked with the MATH library

  16. Model for spontaneous frequency sweeping of an Alfvén wave in a toroidal plasma

    NASA Astrophysics Data System (ADS)

    Wang, Ge; Berk, H. L.

    2012-05-01

    We study the frequency chirping signals arising from spontaneously excited toroidial Alfvén eigenmode (TAE) waves that are being driven by an inverted energetic particle distribution whose free energy is tapped from the generic particle/wave resonance interaction. Initially a wave is excited inside the Alfvén gap with a frequency determined from the linear tip model of Rosenbluth, Berk and Van dam (RBV) [1]. Hole/clumps structures are formed and are observed to chirp towards lower energy states. We find that the chirping signals from clump enter the Alfvén continuum which eventually produce more rapid chirping signals. The accuracy of the adiabatic approximation for the mode evolution is tested and verified by demonstrating that a WKB-like decomposition of the time response for the field phase and amplitude agree with the data. Plots of the phase space structure correlate well with the chirping dependent shape of the separatrix structure. A novel aspect of the simulation is that it performed close to the wave frame of the phase space structure, which enables the numerical time step to remain the same during the simulation, independent of the rest frame frequency.

  17. Investigation of high sensitivity radio-frequency readout circuit based on AlGaN/GaN high electron mobility transistor

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Yu; Tan, Ren-Bing; Sun, Jian-Dong; Li, Xin-Xing; Zhou, Yu; Lü, Li; Qin, Hua

    2015-10-01

    An AlGaN/GaN high electron mobility transistor (HEMT) device is prepared by using a semiconductor nanofabrication process. A reflective radio-frequency (RF) readout circuit is designed and the HEMT device is assembled in an RF circuit through a coplanar waveguide transmission line. A gate capacitor of the HEMT and a surface-mounted inductor on the transmission line are formed to generate LC resonance. By tuning the gate voltage Vg, the variations of gate capacitance and conductance of the HEMT are reflected sensitively from the resonance frequency and the magnitude of the RF reflection signal. The aim of the designed RF readout setup is to develop a highly sensitive HEMT-based detector. Project supported by the National Natural Science Foundation of China (Grant No. 61107093), the Suzhou Science and Technology Project, China (Grant No. ZXG2012024), and the Youth Innovation Promotion Association, Chinese Academy of Sciences (Grant No. 2012243).

  18. Profiles of ion beams and plasma parameters on a multi-frequencies microwaves large bore electron cyclotron resonance ion source with permanent magnets

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

    Kato, Yushi; Sakamoto, Naoki; Kiriyama, Ryutaro

    2012-02-15

    In order to contribute to various applications of plasma and beams based on an electron cyclotron resonance, a new concept on magnetic field with all magnets on plasma production and confinement has been proposed with enhanced efficiency for broad and dense ion beam. The magnetic field configuration consists of a pair of comb-shaped magnet surrounding plasma chamber cylindrically. Resonance zones corresponding for 2.45 GHz and 11-13 GHz frequencies are positioned at spatially different positions. We launch simultaneously multiplex frequencies microwaves operated individually, try to control profiles of the plasma parameters and the extracted ion beams, and to measure them inmore » detail.« less

  19. Working on Mars: Understanding How Scientists, Engineers and Rovers Interacted Across Space and Time during the Mars Exploration Rover (MER) Mission

    NASA Technical Reports Server (NTRS)

    Wales, Roxana C.

    2005-01-01

    This viewgraph presentation summarizes the scheduling and planning difficulties inherent in operating the Mars Exploration Rovers (MER) during the overlapping terrestrial day and Martian sol. The presentation gives special empahsis to communication between the teams controlling the rovers from Earth, and keeping track of time on the two planets.

  20. Effect of pulse frequency on microstructural, nanomechanical, and wear properties of electrodeposited Ni-TiN composite coatings

    NASA Astrophysics Data System (ADS)

    Xia, Fafeng; Tian, Jiyu; Ma, Chunyang; Potts, Matt; Guo, Xue

    2014-12-01

    The current paper reports successful syntheses of Ni-TiN composite coatings by pulse electrodeposition. The effect of pulse frequency on the microstructures, nanomechanical, and wear properties of the coatings was investigated using transmission electron microscopy, X-ray diffraction, nanoindenter, scanning electron microscopy, and wear test instrument. The results showed that the Ni-TiN composite coating prepared at the pulse frequency of 100 Hz showed the presence of a less number of TiN particles and some degrees of aggregation in micro-regions. By contrast, in the Ni-TiN coating deposited at the pulse frequency of 500 Hz, the TiN particles were large in number and dispersed homogeneously, thereby, offering the coating a uniform and fine structure. The average grain diameters of Ni and TiN in the coating prepared at 100 Hz were 154.7 and 44.8 nm, respectively, whereas those for the coating prepared at 500 Hz were 67.3 and 25.9 nm, respectively. The maximum TiN content in the Ni-TiN coating deposited at 800 Hz was approximately 10.5 wt. %. The maximum microhardness and the Young's modulus values for the Ni-TiN composite coatings deposited at 800 Hz were 35.7 GPa and 167.4 GPa, respectively. Furthermore, the Ni-TiN composite coating prepared at 100 Hz had more severe damages, whereas the morphologies of worn surface of the coatings deposited at 500 Hz and 800 Hz were smooth and only a few small pits appeared on the surface.

  1. A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

    PubMed

    Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

    2014-03-12

    The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

  2. Broadband optical frequency comb generator based on driving N-cascaded modulators by Gaussian-shaped waveform

    NASA Astrophysics Data System (ADS)

    Hmood, Jassim K.; Harun, Sulaiman W.

    2018-05-01

    A new approach for realizing a wideband optical frequency comb (OFC) generator based on driving cascaded modulators by a Gaussian-shaped waveform, is proposed and numerically demonstrated. The setup includes N-cascaded MZMs, a single Gaussian-shaped waveform generator, and N-1 electrical time delayer. The first MZM is driven directly by a Gaussian-shaped waveform, while delayed replicas of the Gaussian-shaped waveform drive the other MZMs. An analytical model that describes the proposed OFC generator is provided to study the effect of number and chirp factor of cascaded MZM as well as pulse width on output spectrum. Optical frequency combs at frequency spacing of 1 GHz are generated by applying Gaussian-shaped waveform at pulse widths ranging from 200 to 400 ps. Our results reveal that, the number of comb lines is inversely proportional to the pulse width and directly proportional to both number and chirp factor of cascaded MZMs. At pulse width of 200 ps and chirp factor of 4, 67 frequency lines can be measured at output spectrum of two-cascaded MZMs setup. Whereas, increasing the number of cascaded stages to 3, 4, and 5, the optical spectra counts 89, 109 and 123 frequency lines; respectively. When the delay time is optimized, 61 comb lines can be achieved with power fluctuations of less than 1 dB for five-cascaded MZMs setup.

  3. Performance and data analysis aspects of the new DIII-D monostatic profile reflectometer system

    DOE PAGES

    Zeng, Lei; Peebles, William A.; Doyle, Edward J.; ...

    2014-08-07

    A new frequency-modulated (FMCW) profile reflectometer system, featuring a monostatic antenna geometry (using one microwave antenna for both launch and receive), has been installed on the DIII-D tokamak, providing a first experimental test of this measurement approach for profile reflectometry. Significant features of the new system are briefly described in this paper, including the new monostatic arrangement, use of overmoded, broadband transmission waveguide, and dual-polarization combination/demultiplexing. Updated data processing and analysis, and in-service performance aspects of the new monostatic profile reflectometer system are also presented. By using a raytracing code (GENRAY) to determine the approximate trajectory of the probe beam,more » the electron density (n e) profile can be successfully reconstructed with L-mode plasmas vertically shifted by more than 10 cm off the vessel midplane. Specifically, it is demonstrated that the new system has a capability to measure n e profiles with plasma vertical offsets of up to ±17 cm. Furthermore, examples are also presented of accurate, high time and spatial resolution density profile measurements made over a wide range of DIII-D conditions, e.g. the measured temporal evolution of the density profile across an L-H transition.« less

  4. Constraining martian atmospheric dust particle size distributions from MER Navcam observations.

    NASA Astrophysics Data System (ADS)

    Soderblom, J. M.; Smith, M. D.

    2017-12-01

    Atmospheric dust plays an important role in atmospheric dynamics by absorbing energy and influencing the thermal structure of the atmosphere [1]. The efficiency by which dust absorbs energy depends on its size and single-scattering albedo. Characterizing these properties and their variability is, thus, important in modeling atmospheric circulation. Near-sun observations of the martian sky from Viking Lander, Mars Pathfinder, and MER Pancam images have been used to characterize the atmospheric scattering phase function. The forward-scattering peak the atmospheric phase function is primarily controlled by the size of aerosol particles and is less sensitive to atmospheric opacity or particle shape and single-scattering albedo [2]. These observations, however, have been limited to scattering angles >5°. We use the MER Navcams, which experience little-to-no debilitating internal instrumental scattered light during near-Sun imaging, enabling measurements of the brightness of the martian sky down to very small scattering angles [3], making them more sensitive to aerosol particle size. Additionally, the Navcams band-pass wavelength is similar to the dust effective particle size, further increasing this sensitivity. These data sample a wide range of atmospheric conditions, including variations in the atmospheric dust loading across the entire martian year, as well as more rapid variations during the onset and dissipation of a global-scale dust storm. General circulation models (GCMs) predict a size-dependence for the transport of dust during dust storms that would result in both spatial (on regional-to-global scales) and temporal (days-to-months) variations in the dust size distribution [4]. The absolute calibration of these data, however, is limited. The instrument temperature measurement is limited to a single thermocouple on the Opportunity left Navcam CCD, and observations of the calibration target by Navcam are infrequent. We discuss ways to mitigate these

  5. 3-O sulfation of heparin leads to hepatotropism and longer circulatory half-life.

    PubMed

    Miller, Colton M; Xu, Yongmei; Kudrna, Katrina M; Hass, Blake E; Kellar, Brianna M; Egger, Andrew W; Liu, Jian; Harris, Edward N

    2018-05-17

    Heparins are common blood anticoagulants that are critical for many surgical and biomedical procedures used in modern medicine. In contrast to natural heparin derived from porcine gut mucosa, synthetic heparins are homogenous by mass, polymer length, and chemistry. Stable cell lines expressing the human and mouse Stabilin receptors were used to evaluate endocytosis of natural and synthetic heparin. We chemoenzymatically produced synthetic heparin consisting of 12 sugars (dodecamers) containing 14 sulfate groups resulting in a non-3-O sulfated structure (n12mer). Half of the n12mer was modified with a 3-O sulfate on a single GlcNS sugar producing the 3-O sulfated heparin (12mer). Wildtype (WT), Stabilin-1 knock-out (KO), and Stabilin-2 KO C57BL/6 mice were developed and used for metabolic studies and provided as a source for primary liver sinusoidal endothelial cells. Human and mouse Stabilin-2 receptors had very similar endocytosis rates of both the 12mer and n12mer, suggesting that they are functionally similar in primary cells. Subcutaneous injections of the n12mer and 12mer revealed that the 12mer had a much longer half-life in circulation and a higher accumulation in liver. The n12mer never accumulated in circulation and was readily excreted by the kidneys before liver accumulation could occur. Liver sinusoidal endothelial cells from the Stabilin-2 KO mice had lower uptake rates for both dodecamers, whereas, the Stabilin-1 KO mice had lower endocytosis rates for the 12mer than the n12mer. 3-O sulfation of heparin is correlated to both a longer circulatory half-life and hepatotropism which is largely performed by the Stabilin receptors. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. Profiling atmospheric water vapor by microwave radiometry

    NASA Technical Reports Server (NTRS)

    Wang, J. R.; Wilheit, T. T.; Szejwach, G.; Gesell, L. H.; Nieman, R. A.; Niver, D. S.; Krupp, B. M.; Gagliano, J. A.; King, J. L.

    1983-01-01

    High-altitude microwave radiometric observations at frequencies near 92 and 183.3 GHz were used to study the potential of retrieving atmospheric water vapor profiles over both land and water. An algorithm based on an extended kalman-Bucy filter was implemented and applied for the water vapor retrieval. The results show great promise in atmospheric water vapor profiling by microwave radiometry heretofore not attainable at lower frequencies.

  7. High-frequency gamma oscillations coexist with low-frequency gamma oscillations in the rat visual cortex in vitro.

    PubMed

    Oke, Olaleke O; Magony, Andor; Anver, Himashi; Ward, Peter D; Jiruska, Premysl; Jefferys, John G R; Vreugdenhil, Martin

    2010-04-01

    Synchronization of neuronal activity in the visual cortex at low (30-70 Hz) and high gamma band frequencies (> 70 Hz) has been associated with distinct visual processes, but mechanisms underlying high-frequency gamma oscillations remain unknown. In rat visual cortex slices, kainate and carbachol induce high-frequency gamma oscillations (fast-gamma; peak frequency approximately 80 Hz at 37 degrees C) that can coexist with low-frequency gamma oscillations (slow-gamma; peak frequency approximately 50 Hz at 37 degrees C) in the same column. Current-source density analysis showed that fast-gamma was associated with rhythmic current sink-source sequences in layer III and slow-gamma with rhythmic current sink-source sequences in layer V. Fast-gamma and slow-gamma were not phase-locked. Slow-gamma power fluctuations were unrelated to fast-gamma power fluctuations, but were modulated by the phase of theta (3-8 Hz) oscillations generated in the deep layers. Fast-gamma was spatially less coherent than slow-gamma. Fast-gamma and slow-gamma were dependent on gamma-aminobutyric acid (GABA)(A) receptors, alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and gap-junctions, their frequencies were reduced by thiopental and were weakly dependent on cycle amplitude. Fast-gamma and slow-gamma power were differentially modulated by thiopental and adenosine A(1) receptor blockade, and their frequencies were differentially modulated by N-methyl-D-aspartate (NMDA) receptors, GluK1 subunit-containing receptors and persistent sodium currents. Our data indicate that fast-gamma and slow-gamma both depend on and are paced by recurrent inhibition, but have distinct pharmacological modulation profiles. The independent co-existence of fast-gamma and slow-gamma allows parallel processing of distinct aspects of vision and visual perception. The visual cortex slice provides a novel in vitro model to study cortical high-frequency gamma oscillations.

  8. Anomalous waves propagating at very high frequency in the atmosphere and their disturbances due to changes in refractivity profiles

    NASA Astrophysics Data System (ADS)

    Alam, Imtiaz; Waqar, Asad; Aamir, Muhammad; Hassan, Shahzad; Shah, Syed Asim Ali

    2018-03-01

    Anomalous waves propagation is severely affected due to almost always present variations in refractivity under various environmental conditions at different time, location and frequency. These conditions, representing different state of the atmosphere including e.g. foggy, rainy and cloudy etc., not only degrade the quality of the signal but sometimes completely eradicate the communication link. Such severe impact on propagation cannot be ignored by the designers of communication systems. The aim of this research is to present correlation between experimental and modelled link losses for variations in refractivity values recommended by International Telecommunication Union-Recommendations (ITU-R) as well as that of standard profiles. To do so, a communication setup of 50 km over the Sea operating experimentally over a period of a year at 240 MHz is analyzed for different refractivity profiles and their impact on propagation. A median value is taken for every set of 6000 values taken from the recorded data set of more than 48 million experimental link losses. This reduces the huge data set of the experimental link losses to 8000 values only. This reduced data set of experimental and modelled link losses were correlated and investigated for different evaporation duct heights throughout the year. For the considered link, the ITU-R refractivity profile was found to perform better than the standard refractivity profile. However, the new findings as observed in this research, which may be helpful for the recommendations authorities, is the existing of evaporation duct up to 10 m height.

  9. Molecular basis for methoxyamine initiated mutagenesis. 1H nuclear magnetic resonance studies of base-modified oligodeoxynucleotides.

    PubMed

    Stone, M J; Nedderman, A N; Williams, D H; Lin, P K; Brown, D M

    1991-12-05

    In order to reach a more detailed understanding of the mechanism of the mutagenic action of methoxyamine and of N4-methoxycytidine and its 2'-deoxyribo-analogue, the solution structures of the self-complementary octanucleotide, d(CGAATTCG) and its analogues, d(CGAATCCG), d(CGAATMCG) and d(CGAATPCG) (designated 8mer-AT, 8mer-AC, 8mer-AM, and 8mer-AP, respectively), were investigated by 1H nuclear magnetic resonance spectroscopy; M is N4-methoxycytosine (mo4C) and P is an analogue, the bicyclic dihydropyrimido[4,5-c][1,2]oxazin-7-one, in which the N-O bond is held in the anti configuration with respect to N3 of the cytosine ring. Correlated spectroscopy and nuclear Overhauser spectroscopy allowed assignment of the base, anomeric and H2'/H2" protons in 8mers-AT, -AM and -AP, and showed that all three had features consistent with a regular B-DNA duplex structure. Duplex-to-coil transition temperatures were determined to be 52(+/- 2) degrees C (8mer-AT), 51(+/- 2) degrees C (8mer-AP), 32(+/- 2) degrees C (8mer-AM); on the chemical shift timescale, the melting transition was fast for 8mer-AT and 8mer-AP, but slow for 8mer-AM. Imino proton spectra were indicative of Watson-Crick base-pairing in 8mers-AT, -AP and -AM. The 8mer-AP duplex had a structure and melting characteristics virtually identical with those of the 8mer-AT duplex. The preferred syn configuration of the methoxyl group in M had a destabilising effect on the 8mer-AM duplex. At low temperatures, the A.M base-pair was in fast equilibrium between Watson-Crick and wobble configurations, with the methoxyl function anti-oriented, but the melting transition was accompanied by isomerization of the methoxyl group to the syn conformation. This syn-anti isomerization was the rate-determining step in the duplex-to-coil transition. The 8mer-AC oligomer did not form a stable duplex.

  10. Results from Automated Cloud and Dust Devil Detection Onboard the MER

    NASA Technical Reports Server (NTRS)

    Chien, Steve; Castano, Rebecca; Bornstein, Benjamin; Fukunaga, Alex; Castano, Andres; Biesiadecki, Jeffrey; Greeley, Ron; Whelley, Patrick; Lemmon, Mark

    2008-01-01

    We describe a new capability to automatically detect dust devils and clouds in imagery onboard rovers, enabling downlink of just the images with the targets or only portions of the images containing the targets. Previously, the MER rovers conducted campaigns to image dust devils and clouds by commanding a set of images be collected at fixed times and downloading the entire image set. By increasing the efficiency of the campaigns, more campaigns can be executed. Software for these new capabilities was developed, tested, integrated, uploaded, and operationally checked out on both rovers as part of the R9.2 software upgrade. In April 2007 on Sol 1147 a dust devil was automatically detected onboard the Spirit rover for the first time. We discuss the operational usage of the capability and present initial dust devil results showing how this preliminary application has demonstrated the feasibility and potential benefits of the approach.

  11. High-resolution topomapping of candidate MER landing sites with Mars Orbiter Camera narrow-angle images

    USGS Publications Warehouse

    Kirk, R.L.; Howington-Kraus, E.; Redding, B.; Galuszka, D.; Hare, T.M.; Archinal, B.A.; Soderblom, L.A.; Barrett, J.M.

    2003-01-01

    We analyzed narrow-angle Mars Orbiter Camera (MOC-NA) images to produce high-resolution digital elevation models (DEMs) in order to provide topographic and slope information needed to assess the safety of candidate landing sites for the Mars Exploration Rovers (MER) and to assess the accuracy of our results by a variety of tests. The mapping techniques developed also support geoscientific studies and can be used with all present and planned Mars-orbiting scanner cameras. Photogrammetric analysis of MOC stereopairs yields DEMs with 3-pixel (typically 10 m) horizontal resolution, vertical precision consistent with ???0.22 pixel matching errors (typically a few meters), and slope errors of 1-3??. These DEMs are controlled to the Mars Orbiter Laser Altimeter (MOLA) global data set and consistent with it at the limits of resolution. Photoclinometry yields DEMs with single-pixel (typically ???3 m) horizontal resolution and submeter vertical precision. Where the surface albedo is uniform, the dominant error is 10-20% relative uncertainty in the amplitude of topography and slopes after "calibrating" photoclinometry against a stereo DEM to account for the influence of atmospheric haze. We mapped portions of seven candidate MER sites and the Mars Pathfinder site. Safety of the final four sites (Elysium, Gusev, Isidis, and Meridiani) was assessed by mission engineers by simulating landings on our DEMs of "hazard units" mapped in the sites, with results weighted by the probability of landing on those units; summary slope statistics show that most hazard units are smooth, with only small areas of etched terrain in Gusev crater posing a slope hazard.

  12. Evolution of hut access facing glacier shrinkage in the Mer de Glace basin (Mont Blanc massif, France)

    NASA Astrophysics Data System (ADS)

    Mourey, Jacques; Ravanel, Ludovic

    2016-04-01

    Given the evolution of high mountain environment due to global warming, mountaineering routes and huts accesses are more and more strongly affected by glacial shrinkage and concomitant gravity processes, but almost no studies have been conducted on this relationship. The aim of this research is to describe and explain the evolution over the last century of the access to the five alpine huts around the Mer de Glace glacier (Mont Blanc massif), the larger French glacier (length = 11.5 km, area = 30 km²), a major place for Alpine tourism since 1741 and the birthplace of mountaineering, by using several methods (comparing photographs, surveying, collecting historical documents). While most of the 20th century shows no marked changes, loss of ice thickness and associated erosion of lateral moraines generate numerous and significant changes since the 1990s. Boulder falls, rockfalls and landslides are the main geomorphological processes that affect the access, while the glacier surface lowering makes access much longer and more unstable. The danger is then greatly increased and the access must be relocated and/or equipped more and more frequently (e.g. a total of 520 m of ladders has been added). This questions the future accessibility to the huts, jeopardizing an important part of mountaineering and its linked economy in the Mer de Glace area.

  13. Large-N correlator systems for low frequency radio astronomy

    NASA Astrophysics Data System (ADS)

    Foster, Griffin

    Low frequency radio astronomy has entered a second golden age driven by the development of a new class of large-N interferometric arrays. The low frequency array (LOFAR) and a number of redshifted HI Epoch of Reionization (EoR) arrays are currently undergoing commission and regularly observing. Future arrays of unprecedented sensitivity and resolutions at low frequencies, such as the square kilometer array (SKA) and the hydrogen epoch of reionization array (HERA), are in development. The combination of advancements in specialized field programmable gate array (FPGA) hardware for signal processing, computing and graphics processing unit (GPU) resources, and new imaging and calibration algorithms has opened up the oft underused radio band below 300 MHz. These interferometric arrays require efficient implementation of digital signal processing (DSP) hardware to compute the baseline correlations. FPGA technology provides an optimal platform to develop new correlators. The significant growth in data rates from these systems requires automated software to reduce the correlations in real time before storing the data products to disk. Low frequency, widefield observations introduce a number of unique calibration and imaging challenges. The efficient implementation of FX correlators using FPGA hardware is presented. Two correlators have been developed, one for the 32 element BEST-2 array at Medicina Observatory and the other for the 96 element LOFAR station at Chilbolton Observatory. In addition, calibration and imaging software has been developed for each system which makes use of the radio interferometry measurement equation (RIME) to derive calibrations. A process for generating sky maps from widefield LOFAR station observations is presented. Shapelets, a method of modelling extended structures such as resolved sources and beam patterns has been adapted for radio astronomy use to further improve system calibration. Scaling of computing technology allows for the

  14. National-Scale Changes in Soil Profile C and N in New Zealand Pastures are Determined by Land Use

    NASA Astrophysics Data System (ADS)

    Schipper, L. A.; Parfitt, R.; Ross, C.; Baisden, W. T.; Claydon, J.; Fraser, S.

    2010-12-01

    Grazed pasture is New Zealand’s predominant agricultural land-use and has been relatively recently developed from forest and native grasslands/shrub communities. From the 1850s onwards, land was cleared and exotic pastures established. Phosphorus fertilizer was increasingly used after 1950 which accelerated N fixation by clover. In the last two decades N fertilizers have been used, and grazing intensity has increased, thus affecting soil C and N. Re-sampling of 31 New Zealand soil profiles under grazed pasture measured surprisingly large losses of C and N over the last 2-3 decades (Schipper et al., 2007 Global Change Biology 13:1138-1144). These profiles were predominantly on the most intensively grazed flat land. We extended this re-sampling to 83 profiles (to 90 cm depth), to investigate whether changes in soil C and N stocks also occurred in less intensively managed pasture. Archived soils samples were analysed for total soil C and N alongside the newly collected samples. Intact cores were collected to determine bulk density through the profile. Over an average of 27 years, soils (0-30 cm) in flat dairy pastures significantly lost 0.73±0.16 Mg C ha-1y-1 and 57±16 kg N ha-1y-1 while we observed no change in soil C or N in flat pasture grazed by “dry stock” (e.g., sheep, beef), or in grazed tussock grasslands. Grazed hill country soils (0-30 cm) gained 0.52±0.18 Mg C ha-1y-1 and 66±18 kg N ha-1y-1. The losses of C and N were strongly correlated and C:N ratio has generally declined suggesting soils are becoming N saturated. Losses and gains also occurred in soil layers below 30 cm demonstrating that organic matter throughout the profile was responding to land use. The losses under dairying may be due to greater grazing pressure, fertilizer inputs and exports of C and N. There is evidence that grazing pressure reduces inputs of C below ground, reduces soil microbial C, and that dairy cow urine can mobilise C and N. Gains in hill country pastures may be due

  15. "Your Health Essential for Your Hajj": Muslim pilgrims' knowledge, attitudes and practices regarding Middle East respiratory syndrome coronavirus (MERS-CoV) during Hajj season.

    PubMed

    Alhomoud, Faten; Alhomoud, Farah

    2017-05-01

    Up to date, there have been no studies to evaluate pilgrims' knowledge, attitude and practices regarding MERS-CoV during the annual Hajj pilgrimage in order to see whether there is a need for these aspects to be improved. A cross-sectional survey study was conducted with a convenience sampling. Participants were pilgrims, aged over 18, and able to speak Arabic or English. A self-administered structured questionnaire was distributed during Hajj season in Mecca. Descriptive and multiple linear regression analysis were used in data analysis. Two hundred and fifty-seven participants completed the study, 80% of whom were female, and the median (IQR) age was 35 (24.5-43.5) years. Pilgrims had moderately correct knowledge and accurate attitudes about MERS-CoV with median scores of 5 (IQR 4-7) and 6 (IQR: 5-7) respectively. Educational level and employment status were significantly associated with knowledge whereas gender and age were significantly associated with attitude and practices respectively (P < 0.05). The correlation between knowledge, attitude and practices was significant (correlation coefficient: 0.207; P < 0.05). Better knowledge was found to be a predictor for positive practice. These findings will provide insight when designing future interventions to promote specific messages to enhance knowledge, change attitude and improve practice regarding MERS-CoV. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  16. KENNEDY SPACE CENTER, FLA. - In the Payload Hazardous Servicing Facility, workers prepare to mate the Mars Exploration Rover-2 (MER-2) to the third stage of a Delta II rocket for launch on June 5. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-1 (MER-B) will launch June 25.

    NASA Image and Video Library

    2003-05-23

    KENNEDY SPACE CENTER, FLA. - In the Payload Hazardous Servicing Facility, workers prepare to mate the Mars Exploration Rover-2 (MER-2) to the third stage of a Delta II rocket for launch on June 5. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-1 (MER-B) will launch June 25.

  17. The backshell for the Mars Exploration Rover 1 (MER-1) is moved toward the rover (foreground, left). The backshell is a protective cover for the rover. NASA's twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can't yet go. MER-1 is scheduled to launch June 25 as MER-B aboard a Delta II rocket from Cape Canaveral Air Force Station.

    NASA Image and Video Library

    2003-05-10

    The backshell for the Mars Exploration Rover 1 (MER-1) is moved toward the rover (foreground, left). The backshell is a protective cover for the rover. NASA's twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can't yet go. MER-1 is scheduled to launch June 25 as MER-B aboard a Delta II rocket from Cape Canaveral Air Force Station.

  18. Fusion and Visualization of HiRISE Super-Resolution, Shape-from-Shading DTM with MER Stereo 3D Reconstructions

    NASA Astrophysics Data System (ADS)

    Gupta, S.; Paar, G.; Muller, J. P.; Tao, Y.; Tyler, L.; Traxler, C.; Hesina, G.; Huber, B.; Nauschnegg, B.

    2014-12-01

    The FP7-SPACE project PRoViDE has assembled a major portion of the imaging data gathered so far from rover vehicles, landers and probes on extra-terrestrial planetary surfaces into a unique database, bringing them into a common planetary geospatial context and providing access to a complete set of 3D vision products. One major aim of PRoViDE is the fusion between orbiter and rover image products. To close the gap between HiRISE imaging resolution (down to 25cm for the OrthoRectified image (ORI), down to 1m for the DTM) and surface vision products, images from multiple HiRISE acquisitions are combined into a super resolution data set (Tao & Muller, 2014), increasing to 5cm resolution the Ortho images. Furthermore, shape-from-shading is applied to one of the ORIs at its original resolution for refinement of the HiRISE DTM, leading to DTM ground resolutions of up to 25 cm. After texture-based co-registration with these refined orbiter 3D products, MER PanCam and NavCam 3D image products can be smoothly pasted into a multi-resolution 3D data representation. Typical results from the MER mission are presented by a dedicated real-time rendering tool which is fed by a hierarchical 3D data structure that is able to cope with all involved scales from global planetary scale down to close-up reconstructions in the mm range. This allows us to explore and analyze the geological characteristics of rock outcrops, for example the detailed geometry and internal features of sedimentary rock layers, to aid paleoenvironmental interpretation. This integrated approach enables more efficient development of geological models of martian rock outcrops. The rendering tool also provides measurement tools to obtain geospatial data of surface points and distances between them. We report on novel scientific use cases and the added value potential of the resultant high-quality data set and presentation means to support further geologic investigations. The research leading to these results has

  19. "CH"/N substituted mer-Gaq3 and mer-Alq3 derivatives: an effective approach for the tuning of emitting color.

    PubMed

    Gahungu, Godefroid; Zhang, Jingping

    2005-09-22

    Equilibrium geometry configurations of the "CH"/N substituted Alq3 and Gaq3 derivatives are calculated by density functional theory (B3LYP/6-31G). The frontier molecular orbital and gap energy calculations for all complexes have been performed at the HF/6-31G level. It was shown that, compared to the pristine molecules, the HOMO and LUMO are stabilized, the net effect being however an increasing/decreasing of the gap (Eg) depending on the position of the substituted group. On the basis of the equilibrium geometries, the effect of the substitution on the absorption and emission spectra was evaluated using TDB3LYP/3-21G. It was shown that the change of "CH"/N substituted position on 8-hydroxyquinoline ligand is a powerful approach for the tuning of emitting color. An important blue shift was predicted for 5-substituted 8-hydroxyquinoline derivatives, an important red one being observed for 4-substituted ones. Interestingly, relatively significant blue and red shifts were also predicted for the 7- and 2-substituted derivatives. In this work, the correlation between the spectrum shifts and the metal-ligand bonding is also discussed.

  20. How Do the First Days Count? A Case Study of Qatar Experience in Emergency Risk Communication during the MERS-CoV Outbreak.

    PubMed

    Nour, Mohamed; Alhajri, Mohd; Farag, Elmoubasher A B A; Al-Romaihi, Hamad E; Al-Thani, Mohamed; Al-Marri, Salih; Savoia, Elena

    2017-12-19

    This case study is the first to be developed in the Middle East region to document what happened during the response to the 2013 MERS outbreak in Qatar. It provides a description of key epidemiologic events and news released from a prime daily newspaper and main Emergency Risk Communication (ERC) actions that were undertaken by public health authorities. Using the Crisis and Emergency Risk Communication (CERC) theoretical framework, the study analyzes how the performed ERC strategies during the first days of the outbreak might have contributed to the outbreak management. MERS-CoV related events were chronologically tracked, together with the relevant stories that were published in a major newspaper over the course of three distinct phases of the epidemic. The collected media stories were then assessed against the practiced emergency risk communication (ERC) activities during the same time frame. The Crisis & Emergency Risk Communication (CERC) framework was partially followed during the early days of the MERS-CoV epidemic, which were characterized by overwhelming uncertainty. The SCH's commitment to a proactive and open risk communication strategy since day one, contributed to creating the SCH's image as a credible source of information and allowed for the quick initiation of the overall response efforts. Yet, conflicting messages and over reassurance were among the observed pitfalls of the implemented ERC strategy. The adoption of CERC principles can help restore and maintain the credibility of responding agencies. Further work is needed to develop more rigorous and comprehensive research strategies that address sharing of information by mainstream as well as social media for a more accurate assessment of the impact of the ERC strategy.