Bibliography of the computer codes literature examined by the Radiation Shielding Information Center

Bibliography of computer codes on radiation and nuclear shieldin

Is the transition redshift a new cosmological number?

Observations from Supernovae Type Ia (SNe Ia) provided strong evidence for an expanding accelerating Universe at intermediate redshifts. This means that the Universe underwent a transition from deceleration to acceleration phases at a transition redshift $z_t$ of the order unity whose value in principle depends on the cosmology as well as on the assumed gravitational theory. Since cosmological accelerating models endowed with a transition redshift are extremely degenerated, in principle, it is interesting to know whether the value of $z_t$ itself can be observationally used as a new cosmic discriminator. After a brief discussion of the potential dynamic role played by the transition redshift, it is argued that future observations combining SNe Ia, the line-of-sight (or "radial") baryon acoustic oscillations, the differential age of galaxies, as well as the redshift drift of the spectral lines may tightly constrain $z_t$, thereby helping to narrow the parameter space for the most realistic models describing the accelerating Universe.Comment: 12 pages, 5 figures. Some discussions about how to estimate the transition redshift have been added. New data by Planck and H(z) data have been mentioned. New references have been adde

Domains of invasion organelle proteins from apicomplexan parasites are homologous with the Apple domains of blood coagulation factor XI and plasma pre-kallikrein and are members of the PAN module superfamily

AbstractMicronemes are specialised organelles, found in all apicomplexan parasites, which secrete molecules that are essential for parasite attachment to and invasion of host cells. Regions of several microneme proteins have sequence similarity to the Apple domains (A-domains) of blood coagulation factor XI (FXI) and plasma pre-kallikrein (PK). We have used mass spectrometry on a recombinant-expressed, putative A-domain from the microneme protein EtMIC5 from Eimeria tenella, to demonstrate that three intramolecular disulphide bridges are formed. These bridges are analogous to those that stabilise A-domains in FXI and PK. The data confirm that the apicomplexan domains are structural homologues of A-domains and are therefore novel members of the PAN module superfamily, which also includes the N-terminal domains of members of the plasminogen/hepatocyte growth factor family. The role of A-domains/PAN modules in apicomplexan parasites is not known, but their presence in the microneme suggests that they may be important for mediating protein–protein or protein–carbohydrate interactions during parasite attachment and host cell invasion

Calcium binding activity of the epidermal growth factor-like domains of the apicomplexan microneme protein EtMIC4

Microneme proteins are secreted from apicomplexan parasites during invasion of host cells and they play crucial roles in parasite-host cell adhesion. EtMIC4 is a 240 kDa transmembrane protein from Eimeria tenella that contains 31 tandemly arranged epidermal growth factor (EGF), like repeats within its extracellular domain. The majority of these repeats have calcium binding (cb) consensus sequences. Little is known about cbEGFs in apicomplexan parasites but their presence in microneme proteins suggests that they may contribute to parasite-host interactions. To investigate the potential role of cbEGFs we have expressed and correctly refolded a cbEGF triplet from EtMIC4 (cbEGF7-9) and demonstrated that this triplet binds calcium. Circular dichroism spectroscopic analysis of cbEGF7-9 demonstrates that the molecule undergoes a gradual change in conformation with increasing levels of calcium. In the presence of calcium, the triplet becomes resistant to proteolytic degradation by a variety of proteases, a characteristic feature of cbEGF repeats from higher eukaryotic proteins, such as fibrillin, suggesting that calcium binding induces the formation of a rigid conformation. Moreover, mass spectrometric mapping of the cleavage sites that are protected by calcium shows that these sites are located both close to and distant from the calcium binding sites, indicating that protection is not due to steric hindrance by calcium ions, but rather due to the overall conformation adopted by the triplet in the presence of calcium. Thus, the tandemly-arranged cbEGF repeats within EtMIC4 provide a mechanism whereby, in the calcium-rich extracellular environment, the molecule could adopt a protease-resistant, rigid structure that could favour its interaction with host cell ligands

Why is timing of bird migration advancing when individuals are not?

Recent advances in spring arrival dates have been reported in many migratory species but the mechanism driving these advances is unknown. As population declines are most widely reported in species that are not advancing migration, there is an urgent need to identify the mechanisms facilitating and constraining these advances. Individual plasticity in timing of migration in response to changing climatic conditions is commonly proposed to drive these advances but plasticity in individual migratory timings is rarely observed. For a shorebird population that has significantly advanced migration in recent decades, we show that individual arrival dates are highly consistent between years, but that the arrival dates of new recruits to the population are significantly earlier now than in previous years. Several mechanisms could drive advances in recruit arrival, none of which require individual plasticity or rapid evolution of migration timings. In particular, advances in nest-laying dates could result in advanced recruit arrival, if benefits of early hatching facilitate early subsequent spring migration. This mechanism could also explain why arrival dates of short-distance migrants, which generally return to breeding sites earlier and have greater scope for advance laying, are advancing more rapidly than long-distance migrants

On the Interface Between LENS® Deposited Stainless Steel 304L Repair Geometry and Cast or Machined Components

Laser Engineered Net Shaping™ (LENS®) is being evaluated for use as a metal component repair/modification process. A component of the evaluation is to better understand the characteristics of the interface between LENS deposited material and the substrate on which it is deposited. A processing and metallurgical evaluation was made on LENS processed material fabricated for component qualification tests. A process parameter evaluation was used to determine optimum build parameters and these parameters were used in the fabrication of tensile test specimens to study the characteristics of the interface between LENS deposited material and several types of substrates. Analyses of the interface included mechanical properties, microstructure, and metallurgical integrity. Test samples were determined for a variety of geometric configurations associated with interfaces between LENS deposited material and both wrought base material or previously deposited LENS material. Thirteen different interface configurations were fabricated for evaluation representing a spectrum of deposition conditions from complete part build, to hybrid substrate-LENS builds, to repair builds for damaged or re-designed housings. Good mechanical properties and full density were observed for all configurations. When tested to failure, fracture occurred by ductile microvoid coalescence. The repair and hybrid interfaces showed the same metallurgical integrity as, and had properties similar to, monolithic LENS deposits.Mechanical Engineerin

Connecting species’ geographical distributions to environmental variables: range maps versus observed points of occurrence

Connecting the geographical occurrence of a species with underlying environmental variables is fundamental for many analyses of life history evolution and for modeling species distributions for both basic and practical ends. However, raw distributional information comes principally in two forms: points of occurrence (specific geographical coordinates where a species has been observed), and expert-prepared range maps. Each form has potential short-comings: range maps tend to overestimate the true occurrence of a species, whereas occurrence points (because of their frequent non-random spatial distribution) tend to underestimate it. Whereas previous comparisons of the two forms have focused on how they may differ when estimating species richness, less attention has been paid to the extent to which the two forms actually differ in their representation of a species’ environmental associations. We assess such differences using the globally distributed avian order Galliformes (294 species). For each species we overlaid range maps obtained from IUCN and point-of-occurrence data obtained from GBIF on global maps of four climate variables and elevation. Over all species, the median difference in distribution centroids was 234 km, and median values of all five environmental variables were highly correlated, although there were a few species outliers for each variable. We also acquired species’ elevational distribution mid-points (mid-point between minimum and maximum elevational extent) from the literature; median elevations from point occurrences and ranges were consistently lower (median −420 m) than mid-points. We concluded that in most cases occurrence points were likely to produce better estimates of underlying environmental variables than range maps, although differences were often slight. We also concluded that elevational range mid-points were biased high, and that elevation distributions based on either points or range maps provided better estimates

Laser cooling of trapped ytterbium ions with an ultraviolet diode laser

We demonstrate an ultraviolet diode laser system for cooling of trapped ytterbium ions. The laser power and linewidth are comparable to previous systems based on resonant frequency doubling, but the system is simpler, more robust, and less expensive. We use the laser system to cool small numbers of ytterbium ions confined in a linear Paul trap. From the observed spectra, we deduce final temperatures < 270 mK.Comment: submitted to Opt. Let

Type-Inference Based Short Cut Deforestation (nearly) without Inlining

Deforestation optimises a functional program by transforming it into another one that does not create certain intermediate data structures. In [ICFP'99] we presented a type-inference based deforestation algorithm which performs extensive inlining. However, across module boundaries only limited inlining is practically feasible. Furthermore, inlining is a non-trivial transformation which is therefore best implemented as a separate optimisation pass. To perform short cut deforestation (nearly) without inlining, Gill suggested to split definitions into workers and wrappers and inline only the small wrappers, which transfer the information needed for deforestation. We show that Gill's use of a function build limits deforestation and note that his reasons for using build do not apply to our approach. Hence we develop a more general worker/wrapper scheme without build. We give a type-inference based algorithm which splits definitions into workers and wrappers. Finally, we show that we can deforest more expressions with the worker/wrapper scheme than the algorithm with inlining