1,019 results on '"Markwick A"'
Search Results
2. Cooling and Instabilities in Colliding Radiative Flows with Toroidal Magnetic Fields
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Markwick, R. N., Frank, A., Blackman, E. G., Carroll-Nellenback, J., Lebedev, S. V., Russell, D. R., Halliday, J. W. D., Suttle, L. G., and Hartigan, P. M.
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Astrophysics - High Energy Astrophysical Phenomena ,Physics - Plasma Physics - Abstract
We report on the results of a simulation based study of colliding magnetized plasma flows. Our set-up mimics pulsed power laboratory astrophysical experiments but, with an appropriate frame change, are relevant to astrophysical jets with internal velocity variations. We track the evolution of the interaction region where the two flows collide. Cooling via radiative loses are included in the calculation. We systematically vary plasma beta ($\beta_m$) in the flows, the strength of the cooling ($\Lambda_0$) and the exponent ($\alpha$) of temperature-dependence of the cooling function. We find that for strong magnetic fields a counter-propagating jet called a "spine" is driven by pressure from shocked toroidal fields. The spines eventually become unstable and break apart. We demonstrate how formation and evolution of the spines depends on initial flow parameters and provide a simple analytic model that captures the basic features of the flow., Comment: 14 pages, 16 figures. Submitted to MNRAS
- Published
- 2023
3. The UMIST Database for Astrochemistry 2022
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Millar, T J, Walsh, C, Van de Sande, M, and Markwick, A J
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics ,Physics - Chemical Physics - Abstract
Detailed astrochemical models are a key component to interpret the observations of interstellar and circumstellar molecules since they allow important physical properties of the gas and its evolutionary history to be deduced. We update one of the most widely used astrochemical databases to reflect advances in experimental and theoretical estimates of rate coefficients and to respond to the large increase in the number of molecules detected in space since our last release in 2013. We present the sixth release of the UMIST Database for Astrochemistry (UDfA), a major expansion of the gas-phase chemistry that describes the synthesis of interstellar and circumstellar molecules. Since our last release, we have undertaken a major review of the literature which has increased the number of reactions by over 40% to a total of 8767 and increased the number of species by over 55% to 737. We have made a particular attempt to include many of the new species detected in space over the past decade, including those from the QUIJOTE and GOTHAM surveys, as well as providing references to the original data sources. We use the database to investigate the gas-phase chemistries appropriate to O-rich and C-rich conditions in TMC-1 and to the circumstellar envelope of the C-rich AGB star IRC+10216 and identify successes and failures of gas-phase only models. This update is a significant improvement to the UDfA database. For the dark cloud and C-rich circumstellar envelope models, calculations match around 60% of the abundances of observed species to within an order of magnitude. There are a number of detected species, however, that are not included in the model either because their gas-phase chemistry is unknown or because they are likely formed via surface reactions on icy grains. Future laboratory and theoretical work is needed to include such species in reaction networks., Comment: 26 pages, 8 figures, accepted for publication in A&A
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- 2023
4. Semantic Information in a model of Resource Gathering Agents
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Sowinski, Damian R, Carroll-Nellenback, Jonathan, Markwick, Robert N, Piñero, Jordi, Gleiser, Marcelo, Kolchinsky, Artemy, Ghoshal, Gourab, and Frank, Adam
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Condensed Matter - Statistical Mechanics ,Computer Science - Information Theory ,Nonlinear Sciences - Cellular Automata and Lattice Gases ,Physics - Biological Physics ,Quantitative Biology - Quantitative Methods - Abstract
We explore the application of a new theory of Semantic Information to the well-motivated problem of a resource foraging agent. Semantic information is defined as the subset of correlations, measured via the transfer entropy, between agent $A$ and environment $E$ that is necessary for the agent to maintain its viability $V$. Viability, in turn, is endogenously defined as opposed to the use of exogenous quantities like utility functions. In our model, the forager's movements are determined by its ability to measure, via a sensor, the presence of an individual unit of resource, while the viability function is its expected lifetime. Through counterfactual interventions -- scrambling the correlations between agent and environment via noising the sensor -- we demonstrate the presence of a critical value of the noise parameter, $\eta_c$, above which the forager's expected lifetime is dramatically reduced. On the other hand, for $\eta < \eta_c$ there is little-to-no effect on its ability to survive. We refer to this boundary as the semantic threshold, quantifying the subset of agent-environment correlations that the agent actually needs to maintain its desired state of staying alive. Each bit of information affects the agent's ability to persist both above and below the semantic threshold. Modeling the viability curve and its semantic threshold via forager/environment parameters, we show how the correlations are instantiated. Our work provides a useful model for studies of established agents in terms of semantic information. It also shows that such semantic thresholds may prove useful for understanding the role information plays in allowing systems to become autonomous agents., Comment: 17 pages, 10 figures, 5 appendices
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- 2023
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5. Morphology of Shocked Lateral Outflows in Colliding Hydrodynamic Flows
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Markwick, R. N., Frank, A., Carroll-Nellenback, J., Blackman, E. G., Hartigan, P. M., Lebedev, S. V., Russel, D. R., Halliday, J. W. D., and Suttle, L. G.
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Astrophysics - High Energy Astrophysical Phenomena ,Physics - Fluid Dynamics ,Physics - Plasma Physics - Abstract
Supersonic interacting flows occurring in phenomena such as protostellar jets give rise to strong shocks, and have been demonstrated in several laboratory experiments. To study such colliding flows, we use the AstroBEAR AMR code to conduct hydrodynamic simulations in three dimensions. We introduce variations in the flow parameters of density, velocity, and cross sectional radius of the colliding flows %radius in order to study the propagation and conical shape of the bow shock formed by collisions between two, not necessarily symmetric, hypersonic flows. We find that the motion of the interaction region is driven by imbalances in ram pressure between the two flows, while the conical structure of the bow shock is a result of shocked lateral outflows (SLOs) being deflected from the horizontal when the flows are of differing cross-section.
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- 2022
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6. Probiotic potential of acetic acid bacteria isolated from kombucha in New Zealand in vitro
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Boying Wang, Kay Rutherfurd-Markwick, Ninghui Liu, Xue-Xian Zhang, and Anthony N. Mutukumira
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Kombucha ,Fermentation ,Probiotics ,Acetic acid bacteria ,Microbiology ,QR1-502 - Abstract
Kombucha is a fermented tea beverage containing live microorganisms, mostly beneficial strains of yeast and acetic acid bacteria (AAB), but empirical evidence is limited supporting the probiotic potential of kombucha. This study reports the in vitro probiotic potential of 36 AAB strains isolated from three Kombucha samples commercially available in New Zealand. Nine representative AAB strains, belonging to three species (Komagataeibacter rhaeticus, Acetobacter musti and Gluconobacter potus), were examined for their primary probiotic characteristics such as tolerance to bile salts, NaCl, and low pH, and temperature. Three non-cellulose forming strains (A. musti LOAAB1, G. potus LOAAB2 and G. potus GBAAB3) were assayed for their cell surface characteristics such as auto-aggregation, co-aggregation with pathogenic bacteria, and hydrophobicity. Antimicrobial, antioxidant activities and enzymatic activities were also investigated for the strains of interest. Results indicated that nine strains were able to grow under low pH in the presence of bile salts, suggesting their potential to survive in the human gut. Six K. rhaeticus strains produced cellulosic pellicles, a potential source of prebiotics for beneficial bacteria. The three AAB strains LOAAB1, LOAAB2 and GBAAB3 showed promising cell surface characteristics, such as auto-aggregation rates (>80 %), co-aggregation with four pathogenic bacteria (13.24–43.47 %), hydrophobicity (42.12 % to 50.20 %), and antioxidant activities (>90 %). All nine strains tested negative for enzymatic activities (haemolytic, proteolytic, phospholipase, and gelatinase), suggesting that they are safe to consume. Together, these data indicate the potential for the three AAB strains to be further investigated as probiotic sources with more in vivo tests for applications in the food and beverages industry.
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- 2024
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7. Reducing FODMAPs in bread - the case for sourdough fermentation
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Mutukumira, Anthony N, Tian, Haojing, and Rutherfurd-Markwick, Kay
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- 2021
8. On not becoming a teacher
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Doyle-Markwick, Caitlin
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- 2021
9. Cooling and Instabilities in Colliding Flows
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Markwick, R. N., Frank, A., Carroll-Nellenback, J., Liu, B., Blackman, E. G., Lebedev, S. V., and Hartigan, P. M.
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Astrophysics - High Energy Astrophysical Phenomena ,Physics - Fluid Dynamics - Abstract
Collisional self-interactions occurring in protostellar jets give rise to strong shocks, the structure of which can be affected by radiative cooling within the flow. To study such colliding flows, we use the AstroBEAR AMR code to conduct hydrodynamic simulations in both one and three dimensions with a power law cooling function. The characteristic length and time scales for cooling are temperature dependent and thus may vary as shocked gas cools. When the cooling length decreases sufficiently rapidly the system becomes unstable to the radiative shock instability, which produces oscillations in the position of the shock front; these oscillations can be seen in both the one and three dimensional cases. Our simulations show no evidence of the density clumping characteristic of a thermal instability, even when the cooling function meets the expected criteria. In the three-dimensional case, the nonlinear thin shell instability (NTSI) is found to dominate when the cooling length is sufficiently small. When the flows are subjected to the radiative shock instability, oscillations in the size of the cooling region allow NTSI to occur at larger cooling lengths, though larger cooling lengths delay the onset of NTSI by increasing the oscillation period., Comment: 12 pages, 21 figures. Accepted for publication in MNRAS
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- 2021
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10. Iron deficiency and risk factors in pre-menopausal females living in Auckland, New Zealand
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Lim, Kimberley, Beck, Kathryn Louise, Von Hurst, Pamela Ruth, Rutherfurd-Markwick, Kay Jenice, and Badenhorst, Claire Evelyn
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- 2020
11. Evaluation of the probiotic potential of yeast isolated from kombucha in New Zealand
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Wang, Boying, Rutherfurd-Markwick, Kay, Liu, Ninghui, Zhang, Xue-Xian, and Mutukumira, Anthony N.
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- 2024
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12. Assessing Cost-Effectiveness in Obesity (ACE-Obesity): an overview of the ACE approach, economic methods and cost results
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Swinburn Boyd, Vos Theo, Magnus Anne, Markwick Alison, Moodie Marj, Carter Rob, and Haby Michele M
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Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background The aim of the ACE-Obesity study was to determine the economic credentials of interventions which aim to prevent unhealthy weight gain in children and adolescents. We have reported elsewhere on the modelled effectiveness of 13 obesity prevention interventions in children. In this paper, we report on the cost results and associated methods together with the innovative approach to priority setting that underpins the ACE-Obesity study. Methods The Assessing Cost Effectiveness (ACE) approach combines technical rigour with 'due process' to facilitate evidence-based policy analysis. Technical rigour was achieved through use of standardised evaluation methods, a research team that assembles best available evidence and extensive uncertainty analysis. Cost estimates were based on pathway analysis, with resource usage estimated for the interventions and their 'current practice' comparator, as well as associated cost offsets. Due process was achieved through involvement of stakeholders, consensus decisions informed by briefing papers and 2nd stage filter analysis that captures broader factors that influence policy judgements in addition to cost-effectiveness results. The 2nd stage filters agreed by stakeholders were 'equity', 'strength of the evidence', 'feasibility of implementation', 'acceptability to stakeholders', 'sustainability' and 'potential for side-effects'. Results The intervention costs varied considerably, both in absolute terms (from cost saving [6 interventions] to in excess of AUD50m per annum) and when expressed as a 'cost per child' estimate (from Conclusion The use of consistent methods enables valid comparison of potential intervention costs and cost-offsets for each of the interventions. ACE-Obesity informs policy-makers about cost-effectiveness, health impact, affordability and 2nd stage filters for important options for preventing unhealthy weight gain in children. In related articles cost-effectiveness results and second stage filter considerations for each intervention assessed will be presented and analysed.
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- 2009
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13. Bayesian nonparametric Hawkes processes with applications
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Markwick, Dean
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519.5 - Abstract
Many statistical problems involve modelling the times at which events occur. There are cases where events can occur in clusters with sudden jumps in the total number of occurrences. To model such data an intensity function can be constructed which describes the probability of an event occurring at a specific time. The Hawkes process is a point process model with a conditional intensity function that provides a change in intensity for each event occurrence and as such the Hawkes process can be used to explain event clustering. The flexibility and extendability of the Hawkes process will be highlighted in this thesis. I extend the Hawkes process by using nonparametric Bayesian methods where different components of the Hawkes process are constructed using a Dirichlet process which is a Bayesian prior for distributions. This allows for a data driven approach and removes the need for parametric assumptions. This Bayesian approach also allows for a hierarchical structure to be integrated in the models where appropriate. These extended Hawkes process are applied to different application domains including: extreme value theory, financial trading and soccer goal occurrence modelling. Each new application introduces a different extension to the Hawkes process and illustrates how it improves on existing methodology. From this research I also wrote a new software package for using Dirichlet processes. This software enables users to easily construct Dirichlet process objects that can incorporated into existing inference workflows. This allows users to introduce nonparametric methods without needing to program their own inference methods.
- Published
- 2020
14. Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery
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Markwick, Phineus RL, Peacock, Riley B, and Komives, Elizabeth A
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Analytical Chemistry ,Chemical Sciences ,1.1 Normal biological development and functioning ,Underpinning research ,Allosteric Regulation ,Allosteric Site ,Humans ,Hydrogen Deuterium Exchange-Mass Spectrometry ,Molecular Dynamics Simulation ,Point Mutation ,Thrombin ,Physical Sciences ,Biological Sciences ,Biophysics ,Biological sciences ,Chemical sciences ,Physical sciences - Abstract
Amide hydrogen/deuterium exchange mass spectrometry (HDXMS) of proteins has become extremely popular for identifying ligand-binding sites, protein-protein interactions, intrinsic disorder, and allosteric changes upon protein modification. Such phenomena are revealed when amide exchange is measured in the fast limit, that is, within a few minutes of exchange in deuterated buffer. The HDXMS data have a resolution of the length of peptides and are difficult to interpret because many different phenomena lead to changes in hydrogen/deuterium exchange. We present a quantitative analysis of accelerated molecular dynamics simulations that provides impressive agreement with peptide-length HDXMS data. Comparative analysis of thrombin and a single-point mutant reveals that the simulation analysis can distinguish the subtle differences in exchange due to mutation. In addition, the results provide a deeper understanding of the underlying changes in dynamics revealed by the HDXMS that extend far from the site of mutation.
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- 2019
15. Phenotypic and genotypic characterisation of Lactobacillus and yeast isolates from a traditional New Zealand Māori potato starter culture
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Sun, Jia, Silander, Olin, Rutherfurd-Markwick, Kay, Wen, Daying, Davy, Tanya Poi-poi, and Mutukumira, Anthony N.
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- 2022
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16. Isolation and characterisation of dominant acetic acid bacteria and yeast isolated from Kombucha samples at point of sale in New Zealand
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Wang, Boying, Rutherfurd-Markwick, Kay, Zhang, Xue-Xian, and Mutukumira, Anthony N.
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- 2022
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17. Promoting Inuit health through a participatory whiteboard video
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Rigolet Inuit Community Government, Nunatsiavut Government, IHACC Research Team, Saini, Manpreet, Roche, Steven, Papadopoulos, Andrew, Markwick, Nicole, Shiwak, Inez, Flowers, Charlie, Wood, Michele, Edge, Victoria L., Ford, James, Wright, Carlee, and Harper, Sherilee L.
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- 2020
18. The DeepMIP contribution to PMIP4: experimental design for model simulations of the EECO, PETM, and pre-PETM (version 1.0)
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Lunt, Daniel J, Huber, Matthew, Anagnostou, Eleni, Baatsen, Michiel LJ, Caballero, Rodrigo, DeConto, Rob, Dijkstra, Henk A, Donnadieu, Yannick, Evans, David, Feng, Ran, Foster, Gavin L, Gasson, Ed, von der Heydt, Anna S, Hollis, Chris J, Inglis, Gordon N, Jones, Stephen M, Kiehl, Jeff, Turner, Sandy Kirtland, Korty, Robert L, Kozdon, Reinhardt, Krishnan, Srinath, Ladant, Jean-Baptiste, Langebroek, Petra, Lear, Caroline H, LeGrande, Allegra N, Littler, Kate, Markwick, Paul, Otto-Bliesner, Bette, Pearson, Paul, Poulsen, Christopher J, Salzmann, Ulrich, Shields, Christine, Snell, Kathryn, Staerz, Michael, Super, James, Tabor, Clay, Tierney, Jessica E, Tourte, Gregory JL, Tripati, Aradhna, Upchurch, Garland R, Wade, Bridget S, Wing, Scott L, Winguth, Arne ME, Wright, Nicky M, Zachos, James C, and Zeebe, Richard E
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Earth Sciences - Abstract
Abstract. Past warm periods provide an opportunity to evaluate climate models under extreme forcing scenarios, in particular high ( > 800 ppmv) atmospheric CO2 concentrations. Although a post hoc intercomparison of Eocene ( ∼ 50 Ma) climate model simulations and geological data has been carried out previously, models of past high-CO2 periods have never been evaluated in a consistent framework. Here, we present an experimental design for climate model simulations of three warm periods within the early Eocene and the latest Paleocene (the EECO, PETM, and pre-PETM). Together with the CMIP6 pre-industrial control and abrupt 4 × CO2 simulations, and additional sensitivity studies, these form the first phase of DeepMIP – the Deep-time Model Intercomparison Project, itself a group within the wider Paleoclimate Modelling Intercomparison Project (PMIP). The experimental design specifies and provides guidance on boundary conditions associated with palaeogeography, greenhouse gases, astronomical configuration, solar constant, land surface processes, and aerosols. Initial conditions, simulation length, and output variables are also specified. Finally, we explain how the geological data sets, which will be used to evaluate the simulations, will be developed.
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- 2017
19. Identification of dominant lactic acid bacteria and yeast in rice sourdough produced in New Zealand
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Yang, Qiwei, Rutherfurd-Markwick, Kay, and Mutukumira, Anthony N.
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- 2021
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20. Microbiological and Physico-Chemical Characteristics of Black Tea Kombucha Fermented with a New Zealand Starter Culture
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Boying Wang, Kay Rutherfurd-Markwick, Naran Naren, Xue-Xian Zhang, and Anthony N. Mutukumira
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kombucha ,acetic acid bacteria ,yeast ,Komagataeibacter rhaeticus ,Zygosaccharomyces lentus ,Debaryomyces prosopidis ,Chemical technology ,TP1-1185 - Abstract
Kombucha is a popular sparkling sugared tea, fermented by a symbiotic culture of acetic acid bacteria (AAB) and yeast. The demand for kombucha continues to increase worldwide, mainly due to its perceived health benefits and appealing sensory properties. This study isolated and characterised the dominant AAB and yeast from a starter culture and kombucha broth after 0, 1, 3, 5, 7, 9, 11, and 14 days of fermentation at ambient temperature (22 °C). Yeast and AAB were isolated from the Kombucha samples using glucose yeast extract mannitol ethanol acetic acid (GYMEA) and yeast extract glucose chloramphenicol (YGC) media, respectively. The phenotypic and taxonomic identification of AAB and yeast were determined by morphological and biochemical characterisation, followed by a sequence analysis of the ribosomal RNA gene (16S rRNA for AAB and ITS for yeast). The changes in the microbial composition were associated with variations in the physico-chemical characteristics of kombucha tea, such as pH, titratable acidity, and total soluble solids (TSS). During fermentation, the acidity increased and the TSS decreased. The yield, moisture content, and water activity of the cellulosic pellicles which had developed at the end of fermentation were attributed to the presence of AAB. The dominant AAB species in the cellulosic pellicles and kombucha broth were identified as Komagataeibacter rhaeticus. The yeast isolates belonged to Debaryomyces prosopidis and Zygosaccharomyces lentus.
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- 2023
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21. Cooling and instabilities in colliding radiative flows with toroidal magnetic fields
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Markwick, R N, primary, Frank, A, additional, Blackman, E G, additional, Carroll-Nellenback, J, additional, Lebedev, S V, additional, Russell, D R, additional, Halliday, J W D, additional, Suttle, L G, additional, and Hartigan, P M, additional
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- 2024
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22. Regulation of DAG lipase activity : implications for 'on-demand' endocannabinoid signalling
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Markwick, Rachel Loretta Lane, Williams, Gareth, and Doherty, Patrick
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572 - Abstract
The diacylglycerol lipases (DAGL α and β) are key enzymes in the biosynthesis of 2-AG, the major endocannabinoid (eCB) in the brain. 2-AG acts on CB1 and/or CB2 receptors and DAGL-dependent eCB signalling regulates a large number of responses including axonal growth during development, as well as neurogenesis and retrograde synaptic plasticity in the adult. The enzymes also play a major role in driving pathogenic inflammatory responses via a DAGL/MAGL pathway that generates arachidonic acid as a precursor to prostaglandin synthesis. DAGL antagonists are being developed as novel therapeutics based on their ability to regulate eCB-mediated signalling and/or inflammatory responses, but the mechanisms underlying the regulation of these enzymes is poorly understood. The DAGLs appear to display ‘on-demand’ synthesis, generating increasing amounts of 2-AG in response to cellular messengers. Using a bioinformatics approach, we have postulated that phosphorylation is key mechanism for regulation of DAGL function. We overexpressed each enzyme in U2OS cells that harbour the Tango assay system. We showed the transgenic DAGLs to be expressed at the membrane, and DAGLα to be active using surrogate substrates. We measured an eCB-dependent CB1 response in the Tango assay, with evidence for kinase activation-dependent eCB signalling, but only a portion of this response appeared to be DAGL-dependent. As a result, we are pursuing a genetic strategy to systematically ‘switch off’ endogenous eCB production. We first targeted the DAGLs using the CRISPR/Cas9 system, using both wild-type and nickase Cas9. Our next strategy will be to knockout other eCB-producing enzymes in these cells to tease out which enzymes are resulting in the eCB-CB1 activation in the Tango assay. This will also provide us with a ‘parent’ cell line to support future mutagenesis studies to understand which (if any) phospho-sites are important for DAGL regulation.
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- 2015
23. Perceived racism may partially explain the gap in health between Aboriginal and non-Aboriginal Victorians: A cross-sectional population based study
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Markwick, Alison, Ansari, Zahid, Clinch, Darren, and McNeil, John
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- 2019
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24. The UMIST database for astrochemistry 2012
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McElroy, D., Walsh, C., Markwick, A. J., Cordiner, M. A., Smith, K., and Millar, T. J.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
We present the fifth release of the UMIST Database for Astrochemistry (UDfA). The new reaction network contains 6173 gas-phase reactions, involving 467 species, 47 of which are new to this release. We have updated rate coefficients across all reaction types. We have included 1171 new anion reactions and updated and reviewed all photorates. In addition to the usual reaction network, we also now include, for download, state-specific deuterated rate coefficients, deuterium exchange reactions and a list of surface binding energies for many neutral species. Where possible, we have referenced the original source of all new and existing data. We have tested the main reaction network using a dark cloud model and a carbon-rich circumstellar envelope model. We present and briefly discuss the results of these models.
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- 2012
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25. The crystalline fraction of interstellar silicates in starburst galaxies
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Kemper, F., Markwick, A. J., and Woods, Paul M.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We present a model using the evolution of the stellar population in a starburst galaxy to predict the crystallinity of the silicates in the interstellar medium of this galaxy. We take into account dust production in stellar ejecta, and amorphisation and destruction in the interstellar medium and find that a detectable amount of crystalline silicates may be formed, particularly at high star formation rates, and in case supernovae are efficient dust producers. We discuss the effect of dust destruction and amorphisation by supernovae, and the effect of a low dust-production efficiency by supernovae, and find that when taking this into account, crystallinity in the interstellar medium becomes hard to detect. Levels of 6.5-13% crystallinity in the interstellar medium of starburst galaxies have been observed and thus we conclude that not all these crystalline silicates can be of stellar origin, and an additional source of crystalline silicates associated with the Active Galactic Nucleus must be present., Comment: 8 pages, 6 figures, accepted by MNRAS
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- 2010
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26. Rusty old stars: a source of the missing interstellar iron?
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McDonald, Iain, Sloan, Gregory C., Zijlstra, Albert A., Matsunaga, Noriyuki, Matsuura, Mikako, Kraemer, Kathleen E., Bernard-Salas, Jeronimo, and Markwick, Andrew J.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Iron, the Universe's most abundant refractory element, is highly depleted in both circumstellar and interstellar environments, meaning it exists in solid form. The nature of this solid is unknown. In this Letter, we provide evidence that metallic iron grains are present around oxygen-rich AGB stars, where it is observationally manifest as a featureless mid-infrared excess. This identification is made using Spitzer Space Telescope observations of evolved globular cluster stars, where iron dust production appears ubiquitous and in some cases can be modelled as the only observed dust product. In this context, FeO is examined as the likely carrier for the 20-micron feature observed in some of these stars. Metallic iron appears to be an important part of the dust condensation sequence at low metallicity, and subsequently plays an influential role in the interstellar medium. We explore the stellar metallicities and luminosities at which iron formation is observed, and how the presence of iron affects the outflow and its chemistry. The conditions under which iron can provide sufficient opacity to drive a wind remain unclear., Comment: 7 pages. 4 figures, accepted ApJL
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- 2010
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27. The abundance of HNCO and its use as a diagnostic of environment
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Tideswell, D. M., Fuller, G. A., Millar, T. J., and Markwick, A. J.
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Astrophysics - Astrophysics of Galaxies - Abstract
We aim to investigate the chemistry and gas phase abundance of HNCO and the variation of the HNCO/CS abundance ratio as a diagnostic of the physics and chemistry in regions of massive star formation. A numerical-chemical model has been developed which self-consistently follows the chemical evolution of a hot core. The model comprises of two distinct stages. An initial collapse phase is immediately followed by an increase in temperature which represents the switch on of a central massive star and the subsequent evolution of the chemistry in a hot, dense gas cloud (the hot core). During the collapse phase, gas species are allowed to accrete on to grain surfaces where they can participate in further reactions. During the hot core phase surface species thermally desorb back in to the ambient gas and further chemical evolution takes place. For comparison, the chemical network was also used to model a simple dark cloud and photodissociation regions. Our investigation reveals that HNCO is inefficiently formed when only gas-phase formation pathways are considered in the chemical network with reaction rates consistent with existing laboratory data. Using currently measured gas phase reaction rates, obtaining the observed HNCO abundances requires its formation on grain surfaces. However our model shows that the gas phase HNCO in hot cores is not a simple direct product of the evaporation of grain mantles. We also show that the HNCO/CS abundance ratio varies as a function of time in hot cores and can match the range of values observed. This ratio is not unambiguously related to the ambient UV field as been suggested - our results are inconsistent with the hypothesis of Martin et al (2008). In addition, our results show that this ratio is extremely sensitive to the initial sulphur abundance., Comment: Accepted for publication in Astronomy and Astrophysics
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- 2009
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28. The Mass-Loss Return From Evolved Stars to the LMC: Empirical Relations for Excess Emission at 8 and 24 \mu m
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Srinivasan, Sundar, Meixner, Margaret, Leitherer, Claus, Vijh, Uma, Volk, Kevin, Blum, Robert D., Babler, Brian L., Block, Miwa, Bracker, Steve, Cohen, Martin, Engelbracht, Charles W., For, Bi-Qing, Gordon, Karl D., Harris, Jason, Hora, Joseph L., Indebetouw, Remy, Markwick-Kemper, Francisca, Meade, Marilyn, Misselt, Karl A., Sewilo, Marta, and Whitney, Barbara
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Astrophysics - Cosmology and Extragalactic Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present empirical relations describing excess emission from evolved stars in the Large Magellanic Cloud (LMC) using data from the SAGE (Surveying the Agents of a Galaxy's Evolution) survey which includes the IRAC 3.6, 4.5, 5.8 and 8.0 \mu m and MIPS 24, 70 and 160 \mu m bands. We combine the SAGE data with the Two Micron All Sky Survey (2MASS; J, H and Ks) and the optical Magellanic Cloud Photometric Survey (MCPS; U, B, V and I) point source catalogs to create complete spectral energy distributions (SEDs) of the asymptotic giant branch (AGB) star candidates in the LMC. AGB star outflows are among the main producers of dust in a galaxy, and this mass loss results in an excess in the fluxes observed in the 8 and 24 \mic m bands. We identify oxygen-rich, carbon-rich and extreme AGB star populations in our sample based on their 2MASS and IRAC colors. We calculate excesses fluxes in the mid-IR bands by comparison of the SEDs with model photospheres. We find about 16,000 O-rich, 6300 C-rich and 1000 extreme sources with reliable 8 \mu m excesses, and about 4500 O-rich, 5300 C-rich and 960 extreme sources with reliable 24 \mic m excesses. The excesses are in the range 0.1 mJy--5 Jy. The 8 and 24 \mic m excesses for all three types of AGB candidates show a general increasing trend with luminosity. The dust color temperature derived from the ratio of the 8 and 24 \mic m excesses decreases with an increase in excess, while the 24 \mic m optical depth increases with excess. The extreme AGB candidates are the major contributors to the mass loss, and we estimate the total AGB mass-loss return to the LMC to be (5.9--13)\times 10^{-3} Msun yr^{-1}., Comment: 41 pages, 18 figures, accepted for publication in the Astronomical Journal
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- 2009
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29. The UMIST database for astrochemistry 2022
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Millar, T. J., primary, Walsh, C., additional, Van de Sande, M., additional, and Markwick, A. J., additional
- Published
- 2023
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30. Complete 2mm Spectral Line Survey (130-170 GHz) of Sgr B2N, Sgr B2OH, IRC +10 216, Orion (KL), Orion-S, W51M, and W3(IRS5)
- Author
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Remijan, Anthony. J., Leigh, Diane P., Markwick-Kemper, A. J., and Turner, B. E.
- Subjects
Astrophysics - Abstract
We report a complete 2mm spectral line survey (130-170 GHz) taken with the NRAO 12m Telescope between 1993 and 1995 toward the following sources: Sgr B2N, Sgr B2OH, IRC +10 216, Orion (KL), Orion-S, W51M, and W3(IRS5). Until very recently, this project was entirely the work of B. E. Turner. He wrote the original proposal, given below without changes or updates, and did all of the observing. B.E. Turner has fallen seriously ill and can no longer continue to work on the analysis of these data. The notes that follow the proposal give further information about the project and important information for users of these data. The data are distributed using the Spectral Line Search Engine (SLiSE) developed by A. J. Remijan and M. J. Remijan. SLiSE is a data display tool that will contain all the fully reduced and calibrated archived data taken as part of this 2mm survey. SLiSE is fast, easy to use, and contains the necessary functionality to display the data taken from spectral line searches. For example, SLiSE contains functions to overlay possible molecule identifications based on a current line catalog as well as overlaying H and He recombination lines. It is a Java-based applet, so it is platform independent and easily accessed online. The only caveat is that SLiSE was built using Java 1.5, so an update to the user's Java may be necessary. We request users of these data to give B.E. Turner and this work the appropriate citation and credit., Comment: 22 pages, 6 figures
- Published
- 2008
31. Kombucha: Production and Microbiological Research
- Author
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Boying Wang, Kay Rutherfurd-Markwick, Xue-Xian Zhang, and Anthony N. Mutukumira
- Subjects
Kombucha ,fermentation ,acetic acid bacteria ,yeast ,microbial identification ,Chemical technology ,TP1-1185 - Abstract
Kombucha is a sparkling sugared tea commonly prepared using a sugared tea infusion and fermented at ambient temperature for several days using a cellulose pellicle also called tea fungus that is comprised of acetic acid bacteria and yeast. Consumption of Kombucha has been reported as early as 220 B.C. with various reported potential health benefits and appealing sensory properties. During Kombucha fermentation, sucrose is hydrolysed by yeast cells into fructose and glucose, which are then metabolised to ethanol. The ethanol is then oxidised by acetic acid bacteria (AAB) to produce acetic acid which is responsible for the reduction of the pH and also contributes to the sour taste of Kombucha. Characterisation of the AAB and yeast in the Kombucha starter culture can provide a better understanding of the fermentation process. This knowledge can potentially aid in the production of higher quality products as these microorganisms affect the production of metabolites such as organic acids which are associated with potential health benefits, as well as sensory properties. This review presents recent advances in the isolation, enumeration, biochemical characteristics, conventional phenotypic identification system, and modern genetic identification techniques of AAB and yeast present in Kombucha to gain a better understanding of the microbial diversity of the beverage.
- Published
- 2022
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32. Dust in the wind: Crystalline silicates, corundum and periclase in PG 2112+059
- Author
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Markwick-Kemper, F., Gallagher, S. C., Hines, D. C., and Bouwman, J.
- Subjects
Astrophysics - Abstract
We have determined the mineralogical composition of dust in the Broad Absorption Line (BAL) quasar PG 2112+059 using mid-infrared spectroscopy obtained with the Spitzer Space Telescope. From spectral fitting of the solid state features, we find evidence for Mg-rich amorphous silicates with olivine stoichiometry, as well as the first detection of corundum (Al_2O_3) and periclase (MgO) in quasars. This mixed composition provides the first direct evidence for a clumpy density structure of the grain forming region. The silicates in total encompass 56.5% of the identified dust mass, while corundum takes up 38 wt.%. Depending on the choice of continuum, a range of mass fractions is observed for periclase ranging from 2.7% in the most conservative case to 9% in a less constrained continuum. In addition, we identify a feature at 11.2 micron as the crystalline silicate forsterite, with only a minor contribution from polycyclic aromatic hydrocarbons. The 5% crystalline silicate fraction requires high temperatures such as those found in the immediate quasar environment in order to counteract rapid destruction from cosmic rays., Comment: 2 figures
- Published
- 2007
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33. The variable mass loss of the AGB star WX Psc as traced by the CO J=1-0 through 7-6 lines and the dust emission
- Author
-
Decin, L., Hony, S., de Koter, A., Molenberghs, G., Dehaes, S., and Markwick-Kemper, F.
- Subjects
Astrophysics - Abstract
Low and intermediate mass stars lose a significant fraction of their mass through a dust-driven wind during the Asymptotic Giant Branch (AGB) phase. Recent studies show that winds from late-type stars are far from being smooth. Mass-loss variations occur on different time scales, from years to tens of thousands of years. The variations appear to be particularly prominent towards the end of the AGB evolution. The occurrence, amplitude and time scale of these variations are still not well understood. The goal of our study is to gain insight into the structure of the circumstellar envelope (CSE) of WX Psc and map the possible variability of the late-AGB mass-loss phenomenon. We have performed an in-depth analysis of the extreme infrared AGB star WX Psc by modeling (1) the CO J=1-0 through 7-6 rotational line profiles and the full spectral energy distribution (SED) ranging from 0.7 to 1300 micron. We hence are able to trace a geometrically extended region of the CSE. Both mass-loss diagnostics bear evidence of the occurrence of mass-loss modulations during the last ~2000 yr. In particular, WX Psc went through a high mass-loss phase (Mdot~5e-5 Msun/yr) some 800 yr ago. This phase lasted about 600 yr and was followed by a long period of low mass loss (Mdot~5e-8 Msun/yr). The present day mass-loss rate is estimated to be ~6e-6 Msun/yr. The AGB star WX Psc has undergone strong mass-loss rate variability on a time scale of several hundred years during the last few thousand years. These variations are traced in the strength and profile of the CO rotational lines and in the SED. We have consistently simulated the behaviour of both tracers using radiative transfer codes that allow for non-constant mass-loss rates., Comment: 12 pages, accepted for publication in A&A
- Published
- 2007
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34. Observations of chemical differentiation in clumpy molecular clouds
- Author
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Buckle, J. V., Rodgers, S. D., Wirström, E. S., Charnley, S. B., Markwick-Kemper, A. J., Butner, H. M., and Takakuwa, S.
- Subjects
Astrophysics - Abstract
We have extensively mapped a sample of dense molecular clouds (L1512, TMC-1C, L1262, Per 7, L1389, L1251E) in lines of HC3N, CH3OH, SO and C^{18}O. We demonstrate that a high degree of chemical differentiation is present in all of the observed clouds. We analyse the molecular maps for each cloud, demonstrating a systematic chemical differentiation across the sample, which we relate to the evolutionary state of the cloud. We relate our observations to the cloud physical, kinematical and evolutionary properties, and also compare them to the predictions of simple chemical models. The implications of this work for understanding the origin of the clumpy structures and chemical differentiation observed in dense clouds are discussed., Comment: 20 pages, 7 figures. Higher quality figures appear in the published journal article
- Published
- 2007
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35. The shape and composition of interstellar silicate grains
- Author
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Min, M., Waters, L. B. F. M., de Koter, A., Hovenier, J. W., Keller, L. P., and Markwick-Kemper, F.
- Subjects
Astrophysics - Abstract
We investigate the composition and shape distribution of silicate dust grains in the interstellar medium. The effect of the amount of magnesium in the silicate lattice is studied. We fit the spectral shape of the interstellar 10 mu extinction feature as observed towards the galactic center. We use very irregularly shaped coated and non-coated porous Gaussian Random Field particles as well as a statistical approach to model shape effects. For the dust materials we use amorphous and crystalline silicates with various composition and SiC. The results of our analysis of the 10 mu feature are used to compute the shape of the 20 mu silicate feature and to compare this with observations. By using realistic particle shapes we are, for the first time, able to derive the magnesium fraction in interstellar silicates. We find that the interstellar silicates are highly magnesium rich (Mg/(Fe+Mg)>0.9) and that the stoichiometry lies between pyroxene and olivine type silicates. This composition is not consistent with that of the glassy material found in GEMS in interplanetary dust particles indicating that these are, in general, not unprocessed remnants from the interstellar medium. Also, we find a significant fraction of SiC (~3%). We discuss the implications of our results for the formation and evolutionary history of cometary and circumstellar dust. We argue that the fact that crystalline silicates in cometary and circumstellar grains are almost purely magnesium silicates is a natural consequence of our findings that the amorphous silicates from which they were formed were already magnesium rich., Comment: Accepted for publication in A&A
- Published
- 2006
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36. Spitzer SAGE survey of the Large Magellanic Cloud II: Evolved Stars and Infrared Color Magnitude Diagrams
- Author
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Blum, R. D., Mould, J. R., Olsen, K. A., Frogel, J. A., Werner, M., Meixner, M., Markwick-Kemper, F., Indebetouw, R., Whitney, B., Meade, M., Babler, B., Churchwell, E. B., Gordon, K., Engelbracht, C., For, B. -Q., Misselt, K., Vijh, U., Leitherer, C., Volk, K., Points, S., Reach, W., Hora, J. L., Bernard, J. -P., Boulanger, F., Bracker, S., Cohen, M., Fukui, Y., Gallagher, J., Gorjian, V., Harris, J., Kelly, D., Kawamura, A., Latter, W. B., Madden, S., Mizuno, A., Mizuno, N., Nota, A., Oey, M. S., Onishi, T., Paladini, R., Panagia, N., Perez-Gonzalez, P., Shibai, H., Sato, S., Smith, L., Staveley-Smith, L., Tielens, A. G. G. M., Ueta, T., Van Dyk, S., and Zaritsky, D.
- Subjects
Astrophysics - Abstract
Color-magnitude diagrams (CMDs) are presented for the Spitzer SAGE (Surveying the Agents of a Galaxy's Evolution) survey of the Large Magellanic Cloud (LMC). IRAC and MIPS 24 um epoch one data are presented. These data represent the deepest, widest mid-infrared CMDs of their kind ever produced in the LMC. Combined with the 2MASS survey, the diagrams are used to delineate the evolved stellar populations in the Large Magellanic Cloud as well as Galactic foreground and extragalactic background populations. Some 32000 evolved stars brighter than the tip of the red giant branch are identified. Of these, approximately 17500 are classified as oxygen-rich, 7000 carbon-rich, and another 1200 as ``extreme'' asymptotic giant branch (AGB) stars. Brighter members of the latter group have been called ``obscured'' AGB stars in the literature owing to their dusty circumstellar envelopes. A large number (1200) of luminous oxygen--rich AGB stars/M supergiants are also identified. Finally, there is strong evidence from the 24 um MIPS channel that previously unexplored, lower luminosity oxygen-rich AGB stars contribute significantly to the mass loss budget of the LMC (1200 such sources are identified)., Comment: LaTex, 31 pages, 10 figures. Accepted for publication in the Astronomical Journal
- Published
- 2006
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37. Spitzer Survey of the Large Magellanic Cloud, Surveying the Agents of a Galaxy's Evolution (SAGE) I: Overview and Initial Results
- Author
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Meixner, Margaret, Gordon, Karl D., Indebetouw, Remy, Hora, Joseph L., Whitney, Barbara, Blum, Robert, Reach, William, Bernard, Jean-Philippe, Meade, Marilyn, Babler, Brian, Engelbracht, Charles W., For, Bi-Qing, Misselt, Karl, Vijh, Uma, Leitherer, Claus, Cohen, Martin, Churchwell, Ed B., Boulanger, Francois, Frogel, Jay A., Fukui, Yasuo, Gallagher, Jay, Gorjian, Varoujan, Harris, Jason, Kelly, Douglas, Kawamura, Akiko, Kim, SoYoung, Latter, William B., Madden, Suzanne, Markwick-Kemper, Ciska, Mizuno, Akira, Mizuno, Norikazu, Mould, Jeremy, Nota, Antonella, Oey, M. S., Olsen, Knut, Onishi, Toshikazu, Paladini, Roberta, Panagia, Nino, Perez-Gonzalez, Pablo, Shibai, Hiroshi, Shuji, Sato, Smith, Linda, Staveley-Smith, Lister, Tielens, A. G. G. M., Ueta, Toshiya, Van Dyk, Schuyler, Volk, Kevin, Werner, Michael, and Zaritsky, Dennis
- Subjects
Astrophysics - Abstract
We are performing a uniform and unbiased, ~7x7 degrees imaging survey of the Large Magellanic Cloud (LMC), using the IRAC and MIPS instruments on board the Spitzer Space Telescope in order to survey the agents of a galaxy's evolution (SAGE), the interstellar medium (ISM) and stars in the LMC. The detection of diffuse ISM with column densities >1.2x10^21 H cm^-2 permits detailed studies of dust processes in the ISM. SAGE's point source sensitivity enables a complete census of newly formed stars with masses >3 solar masses that will determine the current star formation rate in the LMC. SAGE's detection of evolved stars with mass loss rates >1x10^-8 solar masses per year will quantify the rate at which evolved stars inject mass into the ISM of the LMC. The observing strategy includes two epochs in 2005, separated by three months, that both mitigate instrumental artifacts and constrain source variability. The SAGE data are non-proprietary. The data processing includes IRAC and MIPS pipelines and a database for mining the point source catalogs, which will be released to the community in support of Spitzer proposal cycles 4 and 5. We present initial results on the epoch 1 data with a special focus on the N79 and N83 region. The SAGE epoch 1 point source catalog has ~4 million sources. The point source counts are highest for the IRAC 3.6 microns band and decrease dramatically towards longer wavelengths consistent with the fact that stars dominate the point source catalogs and that the dusty objects, e.g. young stellar objects and dusty evolved stars that detected at the longer wavelengths, are rare in comparison. We outline a strategy for identifying foreground MW stars, that may comprise as much as 18% of the source list, and background galaxies, that may comprise ~12% of the source list., Comment: Accepted by the Astronomical Journal
- Published
- 2006
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38. Mid-Infrared Spectroscopy of Disks around Classical T Tauri Stars
- Author
-
Forrest, W. J., Sargent, B., Furlan, E., D'Alessio, P., Calvet, N., Hartmann, L., Uchida, K. I., Green, J. D., Watson, D. M., Chen, C. H., Markwick-Kemper, F., Keller, L. D., Sloan, G. C., Herter, T. L., Brandl, B. R., Houck, J. R., Barry, D. J., Hall, P., Morris, P. W., Najita, J., and Myers, P. C.
- Subjects
Astrophysics - Abstract
We present the first Spitzer Infrared Spectrograph (IRS; The IRS was a collaborative venture between Cornell University and Ball Aerospace Corporation funded by NASA through the Jet Propulsion Laboratory and the Ames Research Center.) observations of the disks around classical T Tauri stars: spectra in the 5.2-30 micron range of six stars. The spectra are dominated by emission features from amorphous silicate dust, and a continuous component from 5 to 8 microns that in most cases comprises an excess above the photosphere throughout our spectral range. There is considerable variation in the silicate feature/continuum ratio, which implies variations of inclination, disk flaring, and stellar mass accretion rate. In most of our stars, structure in the silicate feature suggests the presence of a crystalline component. In one, CoKu Tau/4, no excess above the photosphere appears at wavelengths shortward of the silicate features, similar to 10 Myr old TW Hya, Hen 3-600, and HR 4796A. This indicates the optically thick inner disk is largely absent. The silicate emission features with peaks at 9.7 and 18 microns indicate small dust grains are present. The extremely low 10-20 micron color temperature of the dust excess, 135 K, indicates these grains are located more than 10 AU from the star. These features are suggestive of gravitational influence by planets or close stellar companions and grain growth in the region within 10 AU of the star, somewhat surprising for a star this young (1 Myr)., Comment: AASTEX, 10 pages text, 2 figures, 1 table, published September 2004 in The Astrophysical Journal Supplement Series
- Published
- 2006
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39. Polycyclic Aromatic Hydrocarbons Orbiting HD 233517, an Evolved Oxygen-Rich Red Giant
- Author
-
Jura, M., Bohac, J., Sargent, B., Forrest, W. J., Green, J., Watson, D. M., Sloan, G. C., Markwick-Kemper, F., Chen, C. H., and Najita, J.
- Subjects
Astrophysics - Abstract
We report spectra obtained with the Spitzer Space Telescope in the 5 to 35 micron range of HD 233517, an evolved K2 III giant with circumstellar dust. At wavelengths longer than 13 microns, the flux is a smooth continuum that varies approximately as frequency to the -5/3 power. For wavelengths shorter than 13 microns, although the star is oxygen-rich, PAH features produced by carbon-rich species at 6.3 microns, 8.2 microns, 11.3 microns and 12.7 microns are detected along with likely broad silicate emission near 20 microns. These results can be explained if there is a passive, flared disk orbiting HD 233517. Our data support the hypothesis that organic molecules in orbiting disks may be synthesized in situ as well as being incorporated from the interstellar medium., Comment: 11 pages, 2 figures, ApJ Letters, in press
- Published
- 2005
- Full Text
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40. Mid-infrared spectra of PAH emission in Herbig AeBe stars
- Author
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Sloan, G. C., Keller, L. D., Forrest, W. J., Leibensperger, E., Sargent, B., Li, A., Najita, J., Watson, D. M., Brandl, B. R., Chen, C. H., Green, J. D., Markwick-Kemper, F., Herter, T. L., D'Alessio, P., Morris, P. W., Barry, D. J., Hall, P., Myers, P. C., and Houck, J. R.
- Subjects
Astrophysics - Abstract
We present spectra of four Herbig AeBe stars obtained with the Infrared Spectrograph (IRS). on the Spitzer Space Telescope. All four of the sources show strong emission from polycyclic aromatic hydrocarbons (PAHs), with the 6.2 um emission feature shifted to 6.3 um and the strongest C-C skeletal-mode feature occuring at 7.9 um instead of at 7.7 um as is often seen. Remarkably, none of the four stars have silicate emission. The strength of the 7.9 um feature varies with respect to the 11.3 um feature among the sources, indicating that we have observed PAHs with a range of ionization fractions. The ionization fraction is higher for systems with hotter and brighter central stars. Two sources, HD 34282 and HD 169142, show emission features from aliphatic hydrocarbons at 6.85 and 7.25 um. The spectrum of HD 141569 shows a previously undetected emission feature at 12.4 um which may be related to the 12.7 um PAH feature. The spectrum of HD 135344, the coolest star in our sample, shows an unusual profile in the 7-9 um region, with the peak emission to the red of 8.0 um and no 8.6 um PAH feature., Comment: Accepted by ApJ 23 June, 2005, 8 pages (emulateapj), 5 figures (3 in color)
- Published
- 2005
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41. Spitzer detections of new dust components in the outflow of the Red Rectangle
- Author
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Markwick-Kemper, F., Green, J. D., and Peeters, E.
- Subjects
Astrophysics - Abstract
We present Spitzer high spectral resolution IRS spectroscopy of three positions in the carbon-rich outflow of post-AGB star HD 44179, better known as the Red Rectangle. Surprisingly, the spectra show some strong unknown mid-infrared resonances, in the 13-20 micron range. The shape and position of these resonances varies with position in the nebula, and are not correlated with the PAH features. We conclude these features are due to oxygen-rich minerals, located in a region which is believed to be predominantly carbon-rich. We provide possible explanations for the presence of oxygen-rich dust in the carbon-rich outflows. Simple Mg-Fe-oxides are suggested as carriers of these unidentified features., Comment: accepted by ApJL; 5 pages; 4 figures
- Published
- 2005
- Full Text
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42. Three-micron spectra of AGB stars and supergiants in nearby galaxies
- Author
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Matsuura, M., Zijlstra, A. A., van Loon, J. Th., Yamamura, I., Markwick, A. J., Whitelock, P. A., Woods, P. M., Marshall, J. R., Feast, M. W., and Waters, L. B. F. M.
- Subjects
Astrophysics - Abstract
The dependence of stellar molecular bands on the metallicity is studied using infrared L-band spectra of AGB stars (both carbon-rich and oxygen-rich) and M-type supergiants in the Large and Small Magellanic Clouds (LMC and SMC) and in the Sagittarius Dwarf Spheroidal Galaxy. The spectra cover SiO bands for oxygen-rich stars, and acetylene (C2H2), CH and HCN bands for carbon-rich AGB stars. The equivalent width of acetylene is found to be high even at low metallicity. The high C2H2 abundance can be explained with a high carbon-to-oxygen (C/O) ratio for lower metallicity carbon stars. In contrast, the HCN equivalent width is low: fewer than half of the extra-galactic carbon stars show the 3.5micron HCN band, and only a few LMC stars show high HCN equivalent width. HCN abundances are limited by both nitrogen and carbon elemental abundances. The amount of synthesized nitrogen depends on the initial mass, and stars with high luminosity (i.e. high initial mass) could have a high HCN abundance. CH bands are found in both the extra-galactic and Galactic carbon stars. None of the oxygen-rich LMC stars show SiO bands, except one possible detection in a low quality spectrum. The limits on the equivalent widths of the SiO bands are below the expectation of up to 30angstrom for LMC metallicity. Several possible explanations are discussed. The observations imply that LMC and SMC carbon stars could reach mass-loss rates as high as their Galactic counterparts, because there are more carbon atoms available and more carbonaceous dust can be formed. On the other hand, the lack of SiO suggests less dust and lower mass-loss rates in low-metallicity oxygen-rich stars. The effect on the ISM dust enrichment is discussed., Comment: accepted for A&A
- Published
- 2005
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43. Period and chemical evolution of SC stars
- Author
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Zijlstra, Albert A., Bedding, T. R., Markwick, Andrew J., Loidl-Gautschy, Rita, Tabur, Vello, Alexander, Kristen D., Jacob, Andrew P., Kiss, Laszlo L., Price, Aaron, Matsuura, Mikako, and Mattei, Janet A.
- Subjects
Astrophysics - Abstract
The SC and CS stars are thermal-pulsing AGB stars with C/O ratio close to unity. Within this small group, the Mira variable BH Cru recently evolved from spectral type SC (showing ZrO bands) to CS (showing weak C2). Wavelet analysis shows that the spectral evolution was accompanied by a dramatic period increase, from 420 to 540 days, indicating an expanding radius. The pulsation amplitude also increased. Old photographic plates are used to establish that the period before 1940 was around 490 days. Chemical models indicate that the spectral changes were caused by a decrease in stellar temperature, related to the increasing radius. There is no evidence for a change in C/O ratio. The evolution in BH Cru is unlikely to be related to an on-going thermal pulse. Periods of the other SC and CS stars, including nine new periods, are determined. A second SC star, LX Cyg, also shows evidence for a large increase in period, and one further star shows a period inconsistent with a previous determination. Mira periods may be intrinsically unstable for C/O ~ 1; possibly because of a feedback between the molecular opacities, pulsation amplitude, and period. LRS spectra of 6 SC stars suggest a feature at wavelength > 15 micron, which resembles one recently attributed to the iron-sulfide troilite. Chemical models predict a large abundance of FeS in SC stars, in agreement with the proposed association., Comment: 14 pages, 20 figures. MNRAS, 2004, accepted for publication. Janet Mattei, one of the authors, died on 22 March, 2004. This paper is dedicated to her memory
- Published
- 2004
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44. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis
- Author
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Nguyen, Chi, Haushalter, Robert W, Lee, D John, Markwick, Phineus RL, Bruegger, Joel, Caldara-Festin, Grace, Finzel, Kara, Jackson, David R, Ishikawa, Fumihiro, O’Dowd, Bing, McCammon, J Andrew, Opella, Stanley J, Tsai, Shiou-Chuan, and Burkart, Michael D
- Subjects
Biological Sciences ,Macromolecular and Materials Chemistry ,Chemical Sciences ,Acyl Carrier Protein ,Binding Sites ,Catalytic Domain ,Cross-Linking Reagents ,Crystallography ,X-Ray ,Escherichia coli ,Fatty Acid Synthase ,Type II ,Fatty Acids ,Histidine ,Hydro-Lyases ,Magnetic Resonance Spectroscopy ,Models ,Molecular ,Molecular Dynamics Simulation ,Protein Binding ,Protein Interaction Maps ,General Science & Technology - Abstract
Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP-enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein-protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP-FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4'-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease.
- Published
- 2014
45. Correlated Motions and Residual Frustration in Thrombin
- Author
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Fuglestad, Brian, Gasper, Paul M, McCammon, J Andrew, Markwick, Phineus RL, and Komives, Elizabeth A
- Subjects
Engineering ,Chemical Sciences ,Physical Sciences ,Allosteric Regulation ,Amino Acid Chloromethyl Ketones ,Catalytic Domain ,Molecular Dynamics Simulation ,Protein Precursors ,Protein Structure ,Secondary ,Protein Structure ,Tertiary ,Thrombin ,Chemical sciences ,Physical sciences - Abstract
Thrombin is the central protease in the cascade of blood coagulation proteases. The structure of thrombin consists of a double β-barrel core surrounded by connecting loops and helices. Compared to chymotrypsin, thrombin has more extended loops that are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity. Previous experiments showed thermodynamic coupling between ligand binding at the active site and distal exosites. We present a combined approach of molecular dynamics (MD), accelerated molecular dynamics (AMD), and analysis of the residual local frustration of apo-thrombin and active-site-bound (PPACK-thrombin). Community analysis of the MD ensembles identified changes upon active site occupation in groups of residues linked through correlated motions and physical contacts. AMD simulations, calibrated on measured residual dipolar couplings, reveal that upon active site ligation, correlated loop motions are quenched, but new ones connecting the active site with distal sites where allosteric regulators bind emerge. Residual local frustration analysis reveals a striking correlation between frustrated contacts and regions undergoing slow time scale dynamics. The results elucidate a motional network that probably evolved through retention of frustrated contacts to provide facile conversion between ensembles of states.
- Published
- 2013
46. Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics
- Author
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Ortiz-Sánchez, Juan Manuel, Bucher, Denis, Pierce, Levi CT, Markwick, Phineus RL, and McCammon, J Andrew
- Subjects
Chemical Sciences ,Physical Chemistry ,Theoretical and Computational Chemistry ,Biochemistry and Cell Biology ,Computer Software ,Chemical Physics ,Physical chemistry ,Theoretical and computational chemistry - Abstract
In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra.
- Published
- 2012
47. Cultural History under Khrushchev and Brezhnev: From Social Psychology to Mentalités
- Author
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Markwick, Roger D.
- Published
- 2006
48. Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam
- Author
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Markwick, Phineus RL, Pierce, Levi CT, Goodin, David B, and McCammon, J Andrew
- Subjects
Chemical Sciences ,Neurosciences ,Neurodegenerative ,Aging ,2.1 Biological and endogenous factors ,1.1 Normal biological development and functioning ,Physical Sciences ,Chemical sciences ,Physical sciences - Abstract
An extended accelerated molecular dynamics (AMD) methodology called adaptive AMD is presented. Adaptive AMD (Ad-AMD) is an efficient and robust conformational space sampling algorithm that is particularly-well suited to proteins with highly structured potential energy surfaces exhibiting complex, large-scale collective conformational transitions. Ad-AMD simulations of substrate-free P450cam reveal that this system exists in equilibrium between a fully and partially open conformational state. The mechanism for substrate binding depends on the size of the ligand. Larger ligands enter the P450cam binding pocket, and the resulting substrate-bound system is trapped in an open conformation via a population shift mechanism. Small ligands, which fully enter the binding pocket, cause an induced-fit mechanism, resulting in the formation of an energetically stable closed conformational state. These results are corroborated by recent experimental studies and potentially provide detailed insight into the functional dynamics and conformational behavior of the entire cytochrome-P450 superfamily.
- Published
- 2011
49. Petrological, mineralogical, geochemical and geophysical studies of granulite xenoliths from beneath the European platform and northern Baltic shield
- Author
-
Markwick, Andrew John Windsor
- Subjects
552.2094713 - Published
- 2007
50. Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins
- Author
-
Markwick, Phineus RL, Cervantes, Carla F, Abel, Barrett L, Komives, Elizabeth A, Blackledge, Martin, and McCammon, J Andrew
- Subjects
Chemical Sciences ,Theoretical and Computational Chemistry ,Bioengineering ,Humans ,I-kappa B Proteins ,Molecular Dynamics Simulation ,NF-KappaB Inhibitor alpha ,Nuclear Magnetic Resonance ,Biomolecular ,Protein Conformation ,General Chemistry ,Chemical sciences ,Engineering - Abstract
A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range.
- Published
- 2010
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