Halley's Comet 1909 c

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A polarizable interatomic force field for TiO2_2 parameterized using density functional theory

We report a classical interatomic force field for TiO$_2$, which has been parameterized using density functional theory forces, energies, and stresses in the rutile crystal structure. The reliability of this new classical potential is tested by evaluating the structural properties, equation of state, phonon properties, thermal expansion, and some thermodynamic quantities such as entropy, free energy, and specific heat under constant volume. The good agreement of our results with {\em ab initio} calculations and with experimental data, indicates that our force-field describes the atomic interactions of TiO$_2$ in the rutile structure very well. The force field can also describe the structures of the brookite and anatase crystals with good accuracy.Comment: Accepted for publication in Phys. Rev. B; Changes from v1 include multiple minor revisions and a re-write of the description of the force field in Section II

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

SummaryThe Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service.Availability and implementationRCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org)

Certainty Closure: Reliable Constraint Reasoning with Incomplete or Erroneous Data

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimisation problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterising the resolution methodology independently of the model. We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. The certainty closure framework brings together modelling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.Comment: Revised versio

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine

phot1 inhibition of ABCB19 primes lateral auxin fluxes in the shoot apex required for phototropism

It is well accepted that lateral redistribution of the phytohormone auxin underlies the bending of plant organs towards light. In monocots, photoreception occurs at the shoot tip above the region of differential growth. Despite more than a century of research, it is still unresolved how light regulates auxin distribution and where this occurs in dicots. Here, we establish a system in Arabidopsis thaliana to study hypocotyl phototropism in the absence of developmental events associated with seedling photomorphogenesis. We show that auxin redistribution to the epidermal sites of action occurs at and above the hypocotyl apex, not at the elongation zone. Within this region, we identify the auxin efflux transporter ATP-BINDING CASSETTE B19 (ABCB19) as a substrate target for the photoreceptor kinase PHOTOTROPIN 1 (phot1). Heterologous expression and physiological analyses indicate that phosphorylation of ABCB19 by phot1 inhibits its efflux activity, thereby increasing auxin levels in and above the hypocotyl apex to halt vertical growth and prime lateral fluxes that are subsequently channeled to the elongation zone by PIN-FORMED 3 (PIN3). Together, these results provide new insights into the roles of ABCB19 and PIN3 in establishing phototropic curvatures and demonstrate that the proximity of light perception and differential phototropic growth is conserved in angiosperm

Response of carbon dioxide emissions to sheep grazing and N application in an alpine grassland – Part 2: Effect of N application

Widespread nitrogen (N) enrichment resulting from anthropogenic activities has led to great changes in carbon exchange between the terrestrial biosphere and the atmosphere. Grassland is one of the most sensitive ecosystems to N deposition. However, the effect of N deposition on ecosystem respiration (<i>R</i>_e) in grasslands has been conducted mainly in temperate grasslands, which are limited largely by water availability, with few studies focused on alpine grasslands that are primarily constrained by low temperatures. Failure to assess the magnitude of the response in <i>R</i>_e outside the growing season (NGS) in previous studies also limits our understanding of carbon exchange under N deposition conditions. To address these knowledge gaps we used a combination of static closed chambers and gas chromatography in an alpine grassland from 2010 to 2011 to test the effects of N application on ecosystem respiration (<i>R</i>_e) both inside and outside the growing season. There was no significant change in CO₂ emissions under N application. <i>R</i>_e outside the growing season was at least equivalent to 9.4% of the CO₂ fluxes during the growing season (GS). Annual <i>R</i>_e was calculated to be 279.0–403.9 g CO₂ m⁻² yr⁻¹ in Bayinbuluk alpine grasslands. In addition, our results indicate that soil temperature was the dominant abiotic factor regulating variation in <i>R</i>_e in the cold and arid environment. Our results suggest that short-term N additions exert no significant effect on CO₂ emissions in alpine grassland

Survival efficacy of the PEGylated G-CSFs Maxy-G34 and neulasta in a mouse model of lethal H-ARS, and residual bone marrow damage in treated survivors

In an effort to expand the worldwide pool of available medical countermeasures (MCM) against radiation, the PEGylated G-CSF (PEG-G-CSF) molecules Neulasta and Maxy-G34, a novel PEG-G-CSF designed for increased half-life and enhanced activity compared to Neulasta, were examined in a murine model of the Hematopoietic Syndrome of the Acute Radiation Syndrome (H-ARS), along with the lead MCM for licensure and stockpiling, G-CSF. Both PEG-G-CSFs were shown to retain significant survival efficacy when administered as a single dose 24 h post-exposure, compared to the 16 daily doses of G-CSF required for survival efficacy. Furthermore, 0.1 mg kg of either PEG-G-CSF affected survival of lethally-irradiated mice that was similar to a 10-fold higher dose. The one dose/low dose administration schedules are attractive attributes of radiation MCM given the logistical challenges of medical care in a mass casualty event. Maxy-G34-treated mice that survived H-ARS were examined for residual bone marrow damage (RBMD) up to 9 mo post-exposure. Despite differences in Sca-1 expression and cell cycle position in some hematopoietic progenitor phenotypes, Maxy-G34-treated mice exhibited the same degree of hematopoietic stem cell (HSC) insufficiency as vehicle-treated H-ARS survivors in competitive transplantation assays of 150 purified Sca-1+cKit+lin-CD150+cells. These data suggest that Maxy-G34, at the dose, schedule, and time frame examined, did not mitigate RBMD but significantly increased survival from H-ARS at one-tenth the dose previously tested, providing strong support for advanced development of Maxy-G34, as well as Neulasta, as MCM against radiation