Solving the discretised neutron diffusion equations using neural networks

This paper presents a new approach which uses the tools within artificial intelligence (AI) software libraries as an alternative way of solving partial differential equations (PDEs) that have been discretised using standard numerical methods. In particular, we describe how to represent numerical discretisations arising from the finite volume and finite element methods by pre-determining the weights of convolutional layers within a neural network. As the weights are defined by the discretisation scheme, no training of the network is required and the solutions obtained are identical (accounting for solver tolerances) to those obtained with standard codes often written in Fortran or C++. We also explain how to implement the Jacobi method and a multigrid solver using the functions available in AI libraries. For the latter, we use a U-Net architecture which is able to represent a sawtooth multigrid method. A benefit of using AI libraries in this way is that one can exploit their built-in technologies to enable the same code to run on different computer architectures (such as central processing units, graphics processing units or new-generation AI processors) without any modification. In this article, we apply the proposed approach to eigenvalue problems in reactor physics where neutron transport is described by diffusion theory. For a fuel assembly benchmark, we demonstrate that the solution obtained from our new approach is the same (accounting for solver tolerances) as that obtained from the same discretisation coded in a standard way using Fortran. We then proceed to solve a reactor core benchmark using the new approach. For both benchmarks we give timings for the neural network implementation run on a CPU and a GPU, and a serial Fortran code run on a CPU

Predicting cortical bone adaptation to axial loading in the mouse tibia

The development of predictive mathematical models can contribute to a deeper understanding of the specific stages of bone mechanobiology and the process by which bone adapts to mechanical forces. The objective of this work was to predict, with spatial accuracy, cortical bone adaptation to mechanical load, in order to better understand the mechanical cues that might be driving adaptation. The axial tibial loading model was used to trigger cortical bone adaptation in C57BL/6 mice and provide relevant biological and biomechanical information. A method for mapping cortical thickness in the mouse tibia diaphysis was developed, allowing for a thorough spatial description of where bone adaptation occurs. Poroelastic finite-element (FE) models were used to determine the structural response of the tibia upon axial loading and interstitial fluid velocity as the mechanical stimulus. FE models were coupled with mechanobiological governing equations, which accounted for non-static loads and assumed that bone responds instantly to local mechanical cues in an on–off manner. The presented formulation was able to simulate the areas of adaptation and accurately reproduce the distributions of cortical thickening observed in the experimental data with a statistically significant positive correlation (Kendall's τ rank coefficient τ = 0.51, p < 0.001). This work demonstrates that computational models can spatially predict cortical bone mechanoadaptation to a time variant stimulus. Such models could be used in the design of more efficient loading protocols and drug therapies that target the relevant physiological mechanisms

Necromass in forests of Madre de Dios, Peru: A comparison between terra firme and lowland forests

This is the final version of the article. Available from Universidad Nacional Mayor de San Marcos, Facultad de Ciencias Biológicas via the DOI in this record.Stocks of dead wood or necromass represent an important portion of biomass and nutrients in tropical forests. The objectives of this study were: 1) to evaluate and compare the necromass of “terra firme” and lowlands forests, (2) to study the relationship between necromass, above-ground biomass and wood density, and (3) to estimate the necromass of the department of Madre de Dios, Peru. Stocks of necromass and above-ground biomass were estimated at three different locations using permanent plots and line intercept transects. The average volume of necromass for the three sites was 72.9 m3 ha-1 with an average weight varying between 24.8 and 30.7 Mg ha-1, depending on the estimations of dead wood density used for the calculations. Terra firme forests had significantly higher stocks of necromass than lowland forests. The amount of necromass was 11% of the total above-ground biomass in Madre de Dios forests. The total stock of carbon stored in dead wood for the entire department of Madre de Dios was estimated to be approximately 100 mega tonnes of carbon. This is ten times more than the annual fossil fuel emissions of Peru between 2000 and 2008. The substantial stocks of necromass emphasize the importance of these types of field studies, considering that this component of tropical forest carbon cannot be detected using other methods such as satellite remote sensing

Necromass in forests of Madre de Dios, Peru: a comparison between terra firme and lowland forests

Stocks of dead wood or necromass represent an important portion of biomass and nutrients in tropical forests. The objectives of this study were: 1) to evaluate and compare the necromass of "terra firme" and lowlands forests, (2) to study the relationship between necromass, above-ground biomass and wood density, and (3) to estimate the necromass of the department of Madre de Dios, Peru. Stocks of necromass and above-ground biomass were estimated at three different locations using permanent plots and line intercept transects. The average volume of necromass for the three sites was 72.9 m3 ha-1 with an average weight varying between 24.8 and 30.7 Mg ha-1, depending on the estimations of dead wood density used for the calculations. Terra firme forests had significantly higher stocks of necromass than lowland forests. The amount of necromass was 11% of the total above-ground biomass in Madre de Dios forests. The total stock of carbon stored in dead wood for the entire department of Madre de Dios was estimated to be approximately 100 mega tonnes of carbon. This is ten times more than the annual fossil fuel emissions of Peru between 2000 and 2008. The substantial stocks of necromass emphasize the importance of these types of field studies, considering that this component of tropical forest carbon cannot be detected using other methods such as satellite remote sensing

Increased HIV Incidence in Men Who Have Sex with Men Despite High Levels of ART-Induced Viral Suppression: Analysis of an Extensively Documented Epidemic

Background: There is interest in expanding ART to prevent HIV transmission, but in the group with the highest levels of ART use, men-who-have-sex-with-men (MSM), numbers of new infections diagnosed each year have not decreased as ART coverage has increased for reasons which remain unclear. Methods: We analysed data on the HIV-epidemic in MSM in the UK from a range of sources using an individual-based simulation model. Model runs using parameter sets found to result in good model fit were used to infer changes in HIV-incidence and risk behaviour. Results: HIV-incidence has increased (estimated mean incidence 0.30/100 person-years 1990–1997, 0.45/100 py 1998–2010), associated with a modest (26%) rise in condomless sex. We also explored counter-factual scenarios: had ART not been introduced, but the rise in condomless sex had still occurred, then incidence 2006–2010 was 68% higher; a policy of ART initiation in all diagnosed with HIV from 2001 resulted in 32% lower incidence; had levels of HIV testing been higher (68% tested/year instead of 25%) incidence was 25% lower; a combination of higher testing and ART at diagnosis resulted in 62% lower incidence; cessation of all condom use in 2000 resulted in a 424% increase in incidence. In 2010, we estimate that undiagnosed men, the majority in primary infection, accounted for 82% of new infections. Conclusion: A rise in HIV-incidence has occurred in MSM in the UK despite an only modest increase in levels of condomless sex and high coverage of ART. ART has almost certainly exerted a limiting effect on incidence. Much higher rates of HIV testing combined with initiation of ART at diagnosis would be likely to lead to substantial reductions in HIV incidence. Increased condom use should be promoted to avoid the erosion of the benefits of ART and to prevent other serious sexually transmitted infections

Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease

Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries, with major public health and economic implications in West Africa. Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circulating levels of a large array of inflammatory mediators, without impacting on the leukocyte composition of peripheral blood. Notably, several proteins contributing to acute phase reaction, lipid metabolism, coagulation and tissue remodelling were also impacted. Their down-regulation was selective and persisted after the elimination of bacteria with antibiotic therapy. It involved proteins with various functions and origins, suggesting that M. ulcerans infection causes global and chronic defects in the host’s protein metabolism. Accordingly, patients had reduced levels of total serum proteins and blood urea, in the absence of signs of malnutrition, or functional failure of liver or kidney. Interestingly, slow healers had deeper metabolic and coagulation defects at the start of antibiotic therapy. In addition to providing novel insight into Buruli ulcer pathogenesis, our study therefore identifies a unique proteomic signature for this disease

SN 2005hj: Evidence for Two Classes of Normal-Bright SNe Ia and Implications for Cosmology

HET Optical spectra covering the evolution from about 6 days before to about 5 weeks after maximum light and the ROTSE-IIIb unfiltered light curve of the "Branch-normal" Type Ia Supernova SN 2005hj are presented. The host galaxy shows HII region lines at redshift of z=0.0574, which puts the peak unfiltered absolute magnitude at a somewhat over-luminous -19.6. The spectra show weak and narrow SiII lines, and for a period of at least 10 days beginning around maximum light these profiles do not change in width or depth and they indicate a constant expansion velocity of ~10,600 km/s. We analyzed the observations based on detailed radiation dynamical models in the literature. Whereas delayed detonation and deflagration models have been used to explain the majority of SNe Ia, they do not predict a long velocity plateau in the SiII minimum with an unvarying line profile. Pulsating delayed detonations and merger scenarios form shell-like density structures with properties mostly related to the mass of the shell, M_shell, and we discuss how these models may explain the observed SiII line evolution; however, these models are based on spherical calculations and other possibilities may exist. SN 2005hj is consistent with respect to the onset, duration, and velocity of the plateau, the peak luminosity and, within the uncertainties, with the intrinsic colors for models with M_shell=0.2 M_sun. Our analysis suggests a distinct class of events hidden within the Branch-normal SNe Ia. If the predicted relations between observables are confirmed, they may provide a way to separate these two groups. We discuss the implications of two distinct progenitor classes on cosmological studies employing SNe Ia, including possible differences in the peak luminosity to light curve width relation.Comment: ApJ accepted, 31 page

Spiny lobster development: where does successful metamorphosis to the puerulus occur?: a review

This review re-addresses the question: Where does metamorphosis to the puerulus mainly take place among the shallow-water palinurids? A decade ago we reviewed this ecological question in a paper that focused on phyllosomal development of the western rock lobster, Panulirus cygnus. The main region of occurrence of its metamorphosis was found to be in the slope region beyond the shelf break. Because the puerulus of P. cygnus is a non-feeding stage, it was hypothesised that metamorphosis will not occur until the final phyllosoma has reached some critical, and specific, level of stored energy reserves. For late larval development and successful metamorphosis of P. cygnus, the richest food resources seem to be located in the slope waters adjoining the shelf break off Western Australia. This, like most shelf break areas, is a region of higher zooplankton and micronekton biomass than is usually found further offshore, and is dominated (in winter-spring months) by the warm south-flowing Leeuwin Current. In this new review, distribution and abundance data of final phyllosomas and pueruli are examined from, Panulirusargus, Panulirus cygnus, Panulirus japonicus, Panulirus ornatus and Jasus edwardsii, and where possible, related to features of the satellite imagery of the areas in which they occur. We hypothesise that metamorphosis will occur where the final stages have partaken of sufficient, appropriate nutrition to provide them with a reserve of bioenergetic resources, and this can occur where oceanographic fronts effect greater planktonic productivity and concentrations of food organisms. This may be near the shelf-break, or out to large distances offshore, because of large-scale oceanographic events such as the prevailing current system, its off-shoots, mesoscale eddy fronts, counter-currents, etc. However, we contend that, in terms of population recruitment, metamorphosis in most shallow-water palinurid species occurs mainly in the slope waters adjoining the shelf break of the region to which the species is endemic. Although some final phyllosomas may metamorphose much further offshore, it is unlikely that these pueruli will reach the shore, let alone settle and successfully moult to the juvenile stage. All of the data indicate that successful metamorphosis from the final-stage phyllosoma to the puerulus stage in all species occurs offshore but close to the continental shelf

Discovery of a Supernova Explosion at Half the Age of the Universe and its Cosmological Implications

The ultimate fate of the universe, infinite expansion or a big crunch, can be determined by measuring the redshifts, apparent brightnesses, and intrinsic luminosities of very distant supernovae. Recent developments have provided tools that make such a program practicable: (1) Studies of relatively nearby Type Ia supernovae (SNe Ia) have shown that their intrinsic luminosities can be accurately determined; (2) New research techniques have made it possible to schedule the discovery and follow-up observations of distant supernovae, producing well over 50 very distant (z = 0.3 -- 0.7) SNe Ia to date. These distant supernovae provide a record of changes in the expansion rate over the past several billion years. By making precise measurements of supernovae at still greater distances, and thus extending this expansion history back far enough in time, we can distinguish the slowing caused by the gravitational attraction of the universe's mass density Omega_M from the effect of a possibly inflationary pressure caused by a cosmological constant Lambda. We report here the first such measurements, with our discovery of a Type Ia supernova (SN 1997ap) at z = 0.83. Measurements at the Keck II 10-m telescope make this the most distant spectroscopically confirmed supernova. Over two months of photometry of SN 1997ap with the Hubble Space Telescope and ground-based telescopes, when combined with previous measurements of nearer SNe Ia, suggests that we may live in a low mass-density universe. Further supernovae at comparable distances are currently scheduled for ground and space-based observations.Comment: 12 pages and 4 figures (figure 4 is repeated in color and black and white) Nature, scheduled for publication in the 1 January, 1998 issue. Also available at http://www-supernova.lbl.go