Hierarchical octree and k-d tree grids for 3D radiative transfer simulations

A crucial ingredient for numerically solving the 3D radiative transfer problem is the choice of the grid that discretizes the transfer medium. Many modern radiative transfer codes, whether using Monte Carlo or ray tracing techniques, are equipped with hierarchical octree-based grids to accommodate a wide dynamic range in densities. We critically investigate two different aspects of octree grids in the framework of Monte Carlo dust radiative transfer. Inspired by their common use in computer graphics applications, we test hierarchical k-d tree grids as an alternative for octree grids. On the other hand, we investigate which node subdivision-stopping criteria are optimal for constructing of hierarchical grids. We implemented a k-d tree grid in the 3D radiative transfer code SKIRT and compared it with the previously implemented octree grid. We also considered three different node subdivision-stopping criteria (based on mass, optical depth, and density gradient thresholds). Based on a small suite of test models, we compared the efficiency and accuracy of the different grids, according to various quality metrics. For a given set of requirements, the k-d tree grids only require half the number of cells of the corresponding octree. Moreover, for the same number of grid cells, the k-d tree is characterized by higher discretization accuracy. Concerning the subdivision stopping criteria, we find that an optical depth criterion is not a useful alternative to the more standard mass threshold, since the resulting grids show a poor accuracy. Both criteria can be combined; however, in the optimal combination, for which we provide a simple approximate recipe, this can lead to a 20% reduction in the number of cells needed to reach a certain grid quality. An additional density gradient threshold criterion can be added that solves the problem of poorly resolving sharp edges and... (abridged).Comment: 10 pages, 6 figures. Accepted for publication in A&

Large and small-scale structures and the dust energy balance problem in spiral galaxies

The interstellar dust content in galaxies can be traced in extinction at optical wavelengths, or in emission in the far-infrared. Several studies have found that radiative transfer models that successfully explain the optical extinction in edge-on spiral galaxies generally underestimate the observed FIR/submm fluxes by a factor of about three. In order to investigate this so-called dust energy balance problem, we use two Milky Way-like galaxies produced by high-resolution hydrodynamical simulations. We create mock optical edge-on views of these simulated galaxies (using the radiative transfer code SKIRT), and we then fit the parameters of a basic spiral galaxy model to these images (using the fitting code FitSKIRT). The basic model includes smooth axisymmetric distributions along a S\'ersic bulge and exponential disc for the stars, and a second exponential disc for the dust. We find that the dust mass recovered by the fitted models is about three times smaller than the known dust mass of the hydrodynamical input models. This factor is in agreement with previous energy balance studies of real edge-on spiral galaxies. On the other hand, fitting the same basic model to less complex input models (e.g. a smooth exponential disc with a spiral perturbation or with random clumps), does recover the dust mass of the input model almost perfectly. Thus it seems that the complex asymmetries and the inhomogeneous structure of real and hydrodynamically simulated galaxies are a lot more efficient at hiding dust than the rather contrived geometries in typical quasi-analytical models. This effect may help explain the discrepancy between the dust emission predicted by radiative transfer models and the observed emission in energy balance studies for edge-on spiral galaxies.Comment: 9 pages, 5 figures, accepted for publication in A&

Woodland caribou persistence and extirpation in relic populations on Lake Superior

Extended: The hypothesis was proposed that woodland caribou (Rangifer tarandus caribou) in North America had declined due to wolf predation and over-hunting rather than from a shortage of winter lichens (Bergerud, 1974). In 1974, two study areas were selected for testing: for the lichen hypothesis, we selected the Slate Islands in Lake Superior (36 km2), a closed canopy forest without terrestrial lichens, wolves, bears, or moose; for the predation hypothesis, we selected the nearby Pukaskwa National Park (PNP) where terrestrial lichens, wolves, bears, and moose were present. Both areas were monitored from 1974 to 2003 (30 years). The living and dead caribou on the Slates were estimated by the ‘King census’ strip transect (mean length 108±9.3 km, extremes 22-190, total 3026 km) and the Lincoln Index (mean tagged 45±3.6, extremes 15-78). The mean annual population on the Slate Islands based on the strip transects was 262±22 animals (extremes 104-606), or 7.3/km2 (29 years) and from the Lincoln Index 303±64 (extremes 181-482), or 8.4/km2 (23 years). These are the highest densities in North America and have persisted at least since 1949 (56 years). Mountain maple (Acer spicatum) interacted with caribou density creating a record in its age structure which corroborates persistence at relatively high density from c. 1930. The mean percentage of calves was 14.8±0.34% (20 years) in the fall and 14.1±1.95% (19 years) in late winter. The Slate Islands herd was regulated by the density dependent abundance of summer green foods and fall physical condition rather than density independent arboreal lichen availability and snow depths. Two wolves (1 wolf/150 caribou) crossed to the islands in 1993-94 and reduced two calf cohorts (3 and 4.9 per cent calves) while female adult survival declined from a mean of 82% to 71% and the population declined ≈100 animals. In PNP, caribou/moose/wolf populations were estimated by aerial surveys (in some years assisted by telemetry). The caribou population estimates ranged from 31 in 1979 to 9 in 2003 (Y=1267 - 0.628X, r=-0.783, n=21, P<0.01) and extirpation is forecast in 2018. Animals lived within 3 km of Lake Superior (Bergerud, 1985) with an original density of 0.06/km2, similar to many other woodland herds coexisting with wolves (Bergerud, 1992), and 100 times less than the density found on the Slate Islands. The mean moose population was 0.25±0.016/km2 and the wolf population averaged 8.5±0.65/1000 km2. Late winter calf percentages in PNP averaged 16.2±1.89 (25 years); the population was gradually reduced by winter wolf predation (Bergerud, 1989; 1996). The refuge habitat available is apparently insufficient for persistence in an area where the continuous distribution of woodland caribou is fragmented due to moose exceeding 0.10/km2 and thereby supporting wolf densities ≥6.5/1000 km2. A second experimental study was to introduce Slate Island caribou to areas with and without wolves. A release to Bowman Island, where wolves and moose were present, failed due to predation. Bowman Island is adjacent to St. Ignace Island where caribou had persisted into the late 1940s. A second release in 1989 to the mainland in Lake Superior Provincial Park of 39 animals has persisted (<10 animals) because the animals utilize off-shore islands but numbers are also declining. A third release to Montréal Island in 1984 doubled in numbers (up to 20 animals) until Lake Superior froze in 1994 and wolves reached the island. A fourth release was to Michipicoten Island (188 km2) in 1982 where wolves were absent and few lichens were available. This herd increased at λ= 1.18 (8 to ±200, 160 seen 2001) in 19 years. This was the island envisioned for the crucial test of the lichen/predation hypotheses (Bergerud, 1974: p.769). These studies strongly support the idea that ecosystems without predators are limited bottom–up by food and those with wolves top-down by predation; however the proposed crucial test which has been initiated on Michipicoten Island remains to be completed and there is a limited window of opportunity for unequivocal results

Ultrafocused electromagnetic field pulses with a hollow cylindrical waveguide

We theoretically show that a dipole externally driven by a pulse with a lower-bounded temporal width, and placed inside a cylindrical hollow waveguide, can generate a train of arbitrarily short and focused electromagnetic pulses. The waveguide encloses vacuum with perfect electric conducting walls. A dipole driven by a single short pulse, which is properly engineered to exploit the linear spectral filtering of the cylindrical hollow waveguide, excites longitudinal waveguide modes that are coherently refocused at some particular instances of time, thereby producing arbitrarily short and focused electromagnetic pulses. We numerically show that such ultrafocused pulses persist outside the cylindrical waveguide at distances comparable to its radius

Using hierarchical octrees in Monte Carlo radiative transfer simulations

A crucial aspect of 3D Monte Carlo radiative transfer is the choice of the spatial grid used to partition the dusty medium. We critically investigate the use of octree grids in Monte Carlo dust radiative transfer, with two different octree construction algorithms (regular and barycentric subdivision) and three different octree traversal algorithms (top-down, neighbour list, and the bookkeeping method). In general, regular octree grids need higher levels of subdivision compared to the barycentric grids for a fixed maximum cell mass threshold criterion. The total number of grid cells, however, depends on the geometry of the model. Surprisingly, regular octree grid simulations turn out to be 10 to 20% more efficient in run time than the barycentric grid simulations, even for those cases where the latter contain fewer grid cells than the former. Furthermore, we find that storing neighbour lists for each cell in an octree, ordered according to decreasing overlap area, is worth the additional memory and implementation overhead: using neighbour lists can cut down the grid traversal by 20% compared to the traditional top-down method. In conclusion, the combination of a regular node subdivision and the neighbour list method results in the most efficient octree structure for Monte Carlo radiative transfer simulations.Comment: 6 pages, 1 figure, accepted for publication in Astronomy and Astrophysic

The genome of Romanomermis culicivorax:revealing fundamental changes in the core developmental genetic toolkit in Nematoda

Background: The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored. Results: We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination. Conclusions: Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model

Weight loss-induced stress in subcutaneous adipose tissue is related to weight regain

Initial successful weight loss is often followed by weight regain after the dietary intervention. Compared with lean people, cellular stress in adipose tissue is increased in obese subjects. However, the relation between cellular stress and the risk for weight regain after weight loss is unclear. Therefore, we determined the expression levels of stress proteins during weight loss and weight maintenance in relation to weight regain. In vivo findings were compared with results from in vitro cultured human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes. In total, eighteen healthy subjects underwent an 8-week diet programme with a 10-month follow-up. Participants were categorised as weight maintainers or weight regainers (WR) depending on their weight changes during the intervention. Abdominal subcutaneous adipose tissue biopsies were obtained before and after the diet and after the follow-up. In vitro differentiated SGBS adipocytes were starved for 96 h with low (0.55 mm) glucose. Levels of stress proteins were determined by Western blotting. WR showed increased expressions of beta-actin, calnexin, heat shock protein (HSP) 27, HSP60 and HSP70. Changes of beta-actin, HSP27 and HSP70 are linked to HSP60, a proposed key factor in weight regain after weight loss. SGBS adipocytes showed increased levels of beta-actin and HSP60 after 96 h of glucose restriction. The increased level of cellular stress proteins in the adipose tissue of WR probably resides in the adipocytes as shown by in vitro experiments. Cellular stress accumulated in adipose tissue during weight loss may be a risk factor for weight regain

Nurse Practitioner Led Services in Primary Health Care in Rural NSW– Two Case Studies

Background Nurse Practitioners (NPs) are a relatively new advanced nursing role. It was hoped that NPs would reduce some of the challenges facing health care, address workforce shortages and improve access to services for rural populations. The most recent census of Australian NPs showed that just twelve of 208 working NPs were located in primary health care settings. It also showed the majority of NPs were employed in metropolitan areas. Few previous studies describe NP roles in detail, or in rural primary health care settings. Aims This study aims to describe, in detail, the roles of two NPs in rural New South Wales in primary health care settings. One case study focuses on the delivery of an integrated mental health service and the other on leadership in aged care. Methods A case study methodology was employed, using multiple data sources. Data were gathered using semi-structured interviews with 31 key stakeholders, the examination of key documentation, and observation of the NPs within these settings. In the first case study, quantitative data were also analysed. Interview data were analysed thematically. Results The case studies offer an in-depth description of why and how these roles were established, what the NPs do and their impact within the context of small rural towns. They illustrate how NPs established intersectoral partnerships, new service delivery models and advocacy regarding the way health care was provided. The case studies also provide valuable information on how to best incorporate NPs into rural primary health care. Conclusion This study details the complexity of two NP roles within rural primary health care settings. The two case studies show that in these settings, NPs are providing leadership, supporting other services, helping to address workforce shortages, improving access to services for rural populations, and therefore demonstrating the positive impact of NPs working in these settings