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Case Stud

A search for molecules in damped Lyman-alpha absorbers occulting millimetre-loud quasars

We have used the SEST 15-metre and Onsala 20-metre telescopes to perform deep (r.m.s. >~ 30 mJy) integrations of various molecular rotational transitions towards damped Lyman-alpha absorption systems (DLAs) known to occult millimetre-loud quasars. We have observed 6 new systems and improved the existing limits for 11 transitions. These limits may be approaching the sensitivities required to detect new systems and we present a small number of candidate systems which we believe warrant further observation.Comment: 7 pages, 1 PS figure, 4 tables. Accepted by A&

A complete sample of 21-cm absorbers at z~1.3: Giant Metrewave Radio Telescope Survey Using MgII Systems

We present the results of a systematic Giant Metrewave Radio Telescope (GMRT) survey of 21-cm absorption in a representative and unbiased sample of 35 strong MgII systems in the redshift range: zabs~1.10-1.45, 33 of which have W_r>1 \AA. The survey using ~400hrs of telescope time has resulted in 9 new 21-cm detections and stringent 21-cm optical depth upper limits (median 3-sigma optical depth per 10 km/s of 0.017) for the remaining 26 systems. This is by far the largest number of 21-cm detections from any single survey of intervening absorbers. Prior to our survey no intervening 21-cm system was known in the above redshift range and only one system was known in the redshift range 0.7<z<1.5. We discuss the relation between the detectability of 21-cm absorption and various properties of UV absorption lines. We show that if MgII systems are selected with the following criteria, MgII doublet ratio <1.3 and W_r(MgI)/W_r(MgII)>0.3, then a detection rate of 21-cm absorption up to 90% can be achieved. We estimate n_{21}, the number per unit redshift of 21-cm absorbers with W_r(Mg(II)>W_o and integrated optical depth Tau_{21}>Tau_o and show that n_{21} decreases with increasing redshift. In particular, for W_o=1.0 \AA and Tau_o>0.3 km\s, n_{21} falls by a factor 4 from =0.5 to =1.3. The evolution seems to be stronger for stronger MgII systems. Using a subsample of systems for which high frequency VLBA images are available, we show that the effect is not related to the structure of the background radio sources and is most probably due to the evolution of the cold neutral medium filling factor in MgII systems. We find no correlation between the velocity spread of the 21-cm absorption feature and W_r(MgII) at z~1.3.Comment: 22 pages, 8 tables, 12 figures, accepted for publication in MNRA

A Pycellerator Tutorial.

We present a tutorial on using Pycellerator for biomolecular simulations. Models are described in human readable (and editable) text files (UTF8 or ASCII) containing collections of reactions, assignments, initial conditions, function definitions, and rate constants. These models are then converted into a Python program that can optionally solve the system, e.g., as a system of differential equations using ODEINT, or be run by another program. The input language implements an extended version of the Cellerator arrow notation, including mass action, Hill functions, S-Systems, MWC, and reactions with user-defined kinetic laws. Simple flux balance analysis is also implemented. We will demonstrate the implementation and analysis of progressively more complex models, starting from simple mass action through indexed cascades. Pycellerator can be used as a library that is integrated into other programs, run as a command line program, or in iPython notebooks. It is implemented in Python 2.7 and available under an open source GPL license

A new fireworm (Amphinomidae) from the Cretaceous of Lebanon identified from three-dimensionally preserved myoanatomy

© 2015 Parry et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

Diagnosis of breast cancer using elastic-scattering spectroscopy: preliminary clinical results

We report on the first stages of a clinical study designed to test elastic-scattering spectroscopy, mediated by fiberoptic probes, for three specific clinical applications in breast-tissue diagnosis: (1) a transdermal-needle (interstitial) measurement for instant diagnosis with minimal invasiveness similar to fine-needle aspiration but with sensitivity to a larger tissue volume, (2) a hand-held diagnostic probe for use in assessing tumor/resection margins during open surgery, and (3) use of the same probe for real-time assessment of the `sentinel' node during surgery to determine the presence or absence of tumor (metastatic). Preliminary results from in vivo measurements on 31 women are encouraging. Optical spectra were measured on 72 histology sites in breast tissue, and 54 histology sites in sentinel nodes. Two different artificial intelligence methods of spectral classification were studied. Artificial neural networks yielded sensitivities of 69% and 58%, and specificities of 85% and 93%, for breast tissue and sentinel nodes, respectively. Hierarchical cluster analysis yielded sensitivities of 67% and 91%, and specificities of 79% and 77%, for breast tissue and sentinel nodes, respectively. These values are expected to improve as the data sets continue to grow and more sophisticated data preprocessing is employed. The study will enroll up to 400 patients over the next two years

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches

A New Stalked Filter-Feeder from the Middle Cambrian Burgess Shale, British Columbia, Canada

Burgess Shale-type deposits provide invaluable insights into the early evolution of body plans and the ecological structure of Cambrian communities, but a number of species, continue to defy phylogenetic interpretations. Here we extend this list to include a new soft-bodied animal, Siphusauctum gregarium n. gen. and n. sp., from the Tulip Beds (Campsite Cliff Shale Member, Burgess Shale Formation) of Mount Stephen (Yoho National Park, British Columbia). With 1,133 specimens collected, S. gregarium is clearly the most abundant animal from this locality

Three novel components of the human exosome

Contains fulltext : 186951.pdf (publisher's version ) (Open Access)The yeast exosome is a complex of 3' --> 5' exoribonucleases. Sequence analysis identified putative human homologues for exosome components, although several were found only as expressed sequence tags. Here we report the cloning of full-length cDNAs, which encode putative human homologues of the Rrp40p, Rrp41p, and Rrp46p components of the exosome. Recombinant proteins were expressed and used to raise rabbit antisera. In Western blotting experiments, these decorated HeLa cell proteins of the predicted sizes. All three human proteins were enriched in the HeLa cells nucleus and nucleolus, but were also clearly detected in the cytoplasm. Size exclusion chromatography revealed that hRrp40p, hRrp41p, and hRrp46p were present in a large complex. This cofractionated with the human homologues of other exosome components, hRrp4p and PM/Scl-100. Anti-PM/Scl-positive patient sera coimmunoprecipitated hRrp40p, hRrp41p, and hRrp46p demonstrating their physical association. The immunoprecipitated complex exhibited 3' --> 5' exoribonuclease activity in vitro. hRrp41p was expressed in yeast and shown to suppress the lethality of genetic depletion of yeast Rrp41p. We conclude that hRrp40p, hRrp41p, and hRrp46p represent novel components of the human exosome complex

A search for damped Lyman-alpha systems towards radio-loud quasars I: The optical survey

We present the results from the optical component of a survey for damped Lyman-alpha systems (DLAs) towards radio-loud quasars. Our quasar sample is drawn from the Texas radio survey with the following primary selection criteria: z_em > 2.4, optical magnitudes B < 22 and 365 MHz flux density S_365 > 400 mJy. We obtained spectra for a sample of 45 QSOs with the William Herschel Telescope, Very Large Telescope and Gemini-North, resulting in a survey redshift path Delta z = 38.79. We detect nine DLAs and one sub-DLA with a mean absorption redshift = 2.44. The DLA number density is n(z) = 0.23^{+0.11}_{-0.07}, in good agreement with the value derived for DLAs detected in the Sloan Digital Sky Survey at this redshift. The DLA number density of our sample is also in good agreement with optically-complete radio-selected samples, supporting previous claims that n(z) is not significantly affected by dust obscuration bias. We present N(HI) column density determinations and metal line equivalent width measurements for all our DLAs. The low frequency flux density selection criterion used for the quasar sample implies that all absorbers will be suitable for follow-up absorption spectroscopy in the redshifted HI 21 cm line. A following paper (Kanekar et al.) will present HI 21 cm absorption studies of, and spin temperature determinations for, our DLA sample.Comment: Accepted for publication in the MNRA