PRECIS: Protein reports engineered from concise information in SWISS-PROT

Motivation: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords. Availability: The software is accessible online at: http://www.bioinf.man.ac.uk/cgi-bin/dbbrowser/precis/blast_precis.cg

Target studies for accelerator-based boron neutron capture therapy

Two new concepts, NIFTI and DISCOS, are described. These concepts enable the efficient production of epithermal neutrons for BNCT (Boron Neutron Capture Therapy) medical treatment, utilizing a low current, low energy proton beam impacting on a lithium target. The NIFTI concept uses an iron layer that strongly impedes the transmission of neutrons with energies above 24 KeV. Lower energy neutrons readily pass through this iron ``filter``, which has a deep ``window`` in its scattering cross section at 24 KeV. The DISCOS concept uses a rapidly rotating, high g disc to create a series of thin ({approximately} 1 micron thickness) liquid lithium targets in the form of continuous films through which the proton beam passes. The average energy lost by a proton as it passes through a single target is small, approximately 10 KeV. Between the targets, the proton beam is reaccelerated by an applied DC electric field. The DISCOS approach enables the accelerator -- target facility to operate with a beam energy only slightly above the threshold value for neutron production -- resulting in an output beam of low-energy epithermal neutrons -- while achieving a high yield of neutrons per milliamp of proton beam current

New concepts for compact accelerator/target for Boron Neutron Capture Therapy

Two new target concepts, NIFTI and DISCOS, that enable a large reduction in the proton beam current needed to produce epithermal neutrons for BNCT (Boron Neutron Capture Therapy) are described. In the NIFTI concept, high energy neutrons produced by (p, n) reactions of 2.5 MeV protons on Li are down scattered to treatment energies ({approximately} 20 keV) by relatively thin layers of PbF{sub 2} and iron. In the DISCOS concept, treatment energy neutrons are produced directly in a succession of thin ({approximately} 1 micron) liquid Li films on rotating Be foils. These foils interact with a proton beam that operates just above threshold for the (p, n) reaction, with an applied DC field to re-accelerate the proton beam between the target foils

Embodying militarism: exploring the spaces and bodies in-between

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Microbial competition for phosphorus limits the CO2 response of a mature forest

The capacity for terrestrial ecosystems to sequester additional carbon (C) with rising CO2 concentrations depends on soil nutrient availability1,2. Previous evidence suggested that mature forests growing on phosphorus (P)-deprived soils had limited capacity to sequester extra biomass under elevated CO2 (refs. 3–6), but uncertainty about ecosystem P cycling and its CO2 response represents a crucial bottleneck for mechanistic prediction of the land C sink under climate change7. Here, by compiling the first comprehensive P budget for a P-limited mature forest exposed to elevated CO2, we show a high likelihood that P captured by soil microorganisms constrains ecosystem P recycling and availability for plant uptake. Trees used P efficiently, but microbial pre-emption of mineralized soil P seemed to limit the capacity of trees for increased P uptake and assimilation under elevated CO2 and, therefore, their capacity to sequester extra C. Plant strategies to stimulate microbial P cycling and plant P uptake, such as increasing rhizosphere C release to soil, will probably be necessary for P-limited forests to increase C capture into new biomass. Our results identify the key mechanisms by which P availability limits CO2 fertilization of tree growth and will guide the development of Earth system models to predict future long-term C storage

Magnetic fields in supernova remnants and pulsar-wind nebulae

We review the observations of supernova remnants (SNRs) and pulsar-wind nebulae (PWNe) that give information on the strength and orientation of magnetic fields. Radio polarimetry gives the degree of order of magnetic fields, and the orientation of the ordered component. Many young shell supernova remnants show evidence for synchrotron X-ray emission. The spatial analysis of this emission suggests that magnetic fields are amplified by one to two orders of magnitude in strong shocks. Detection of several remnants in TeV gamma rays implies a lower limit on the magnetic-field strength (or a measurement, if the emission process is inverse-Compton upscattering of cosmic microwave background photons). Upper limits to GeV emission similarly provide lower limits on magnetic-field strengths. In the historical shell remnants, lower limits on B range from 25 to 1000 microGauss. Two remnants show variability of synchrotron X-ray emission with a timescale of years. If this timescale is the electron-acceleration or radiative loss timescale, magnetic fields of order 1 mG are also implied. In pulsar-wind nebulae, equipartition arguments and dynamical modeling can be used to infer magnetic-field strengths anywhere from about 5 microGauss to 1 mG. Polarized fractions are considerably higher than in SNRs, ranging to 50 or 60% in some cases; magnetic-field geometries often suggest a toroidal structure around the pulsar, but this is not universal. Viewing-angle effects undoubtedly play a role. MHD models of radio emission in shell SNRs show that different orientations of upstream magnetic field, and different assumptions about electron acceleration, predict different radio morphology. In the remnant of SN 1006, such comparisons imply a magnetic-field orientation connecting the bright limbs, with a non-negligible gradient of its strength across the remnant.Comment: 20 pages, 24 figures; to be published in SpSciRev. Minor wording change in Abstrac

The Political Economy of US Military Spending

The causes of the dramatic rise in military spending in the post-war era have been the subject of much political and academic controversy. No extant formulation seems to provide a compelling explanation of the dynamics involved in the levels of, and rates of change in, such spending. In light of this, the authors develop a new model, based mainly on a political-business cycle argument, to account for these dynamics. The basic proposition in this model is that variations in national defense spending arise from political considerations which are related to real and desired conditions within the national economy. Applying this model to the experience of the United States 1948-1976, the authors show that it has a large measure of empirical validity. If one removes the effects of war-time mobilization, it is clear that for the United States the principal driving forces in military spending dynamics were (1) the perceived utility of such spending in stabilizing aggregate demand, (2) the political or electoral value of the perceived economic effects arising out of such spending, and (3) the pressures of institutional-constituency demands.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68958/2/10.1177_002234337901600202.pd

Synthesizing Systems with Optimal Average-Case Behavior for Ratio Objectives

We show how to automatically construct a system that satisfies a given logical specification and has an optimal average behavior with respect to a specification with ratio costs. When synthesizing a system from a logical specification, it is often the case that several different systems satisfy the specification. In this case, it is usually not easy for the user to state formally which system she prefers. Prior work proposed to rank the correct systems by adding a quantitative aspect to the specification. A desired preference relation can be expressed with (i) a quantitative language, which is a function assigning a value to every possible behavior of a system, and (ii) an environment model defining the desired optimization criteria of the system, e.g., worst-case or average-case optimal. In this paper, we show how to synthesize a system that is optimal for (i) a quantitative language given by an automaton with a ratio cost function, and (ii) an environment model given by a labeled Markov decision process. The objective of the system is to minimize the expected (ratio) costs. The solution is based on a reduction to Markov Decision Processes with ratio cost functions which do not require that the costs in the denominator are strictly positive. We find an optimal strategy for these using a fractional linear program.Comment: In Proceedings iWIGP 2011, arXiv:1102.374

The fate of carbon in a mature forest under carbon dioxide enrichment

Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1 5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. Although evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3 5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7 10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving the fate of additional carbon fixed under eCO2 unclear4,5,7 11. Here using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responded to four years of eCO2 exposure. We show that, although the eCO2 treatment of +150 parts per million (+38 per cent) above ambient levels induced a 12 per cent (+247 grams of carbon per square metre per year) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone accounting for half of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on ubiquitous CO2 fertilization as a driver of increased carbon sinks in global forests. © 2020, The Author(s), under exclusive licence to Springer Nature Limited