Investigating hookworm genomes by comparative analysis of two Ancylostoma species

Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum. Results Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae. Conclusion The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics

Do primordial Lithium abundances imply there's no Dark Energy?

Explaining the well established observation that the expansion rate of the universe is apparently accelerating is one of the defining scientific problems of our age. Within the standard model of cosmology, the repulsive 'dark energy' supposedly responsible has no explanation at a fundamental level, despite many varied attempts. A further important dilemma in the standard model is the Lithium problem, which is the substantial mismatch between the theoretical prediction for 7-Li from Big Bang Nucleosynthesis and the value that we observe today. This observation is one of the very few we have from along our past worldline as opposed to our past lightcone. By releasing the untested assumption that the universe is homogeneous on very large scales, both apparent acceleration and the Lithium problem can be easily accounted for as different aspects of cosmic inhomogeneity, without causing problems for other cosmological phenomena such as the cosmic microwave background. We illustrate this in the context of a void model.Comment: 14 pages, 4 figures. v2: minor rearrangements in the text, comments and references expanded, results unchange

Herd-level risk factors of bovine tuberculosis in England and Wales after the 2001 foot-and-mouth disease epidemic

We present the results of a 2005 case–control study of bovine tuberculosis (bTB) breakdowns in English and Welsh herds. The herd management, farming practices, and environmental factors of 401matched pairs of case and control herds were investigated to provide a picture of herd-level risk factors in areas of varying bTB incidence. A global conditional logistic regression model, with region-specific variants, was used to compare case herds that had experienced a confirmed bTB breakdown to contemporaneous control herds matched on region, herd type, herd size, and parish testing interval. Contacts with cattle from contiguous herds and sourcing cattle from herds with a recent history of bTB were associated with an increased risk in both the global and regional analyses. Operating a farm over several premises, providing cattle feed inside the housing, and the presence of badgers were also identified as significantly associated with an increased bTB risk. Steps taken to minimize cattle contacts with neighboring herds and altering trading practices could have the potential to reduce the size of the bTB epidemic. In principle, limiting the interactions between cattle and wildlife may also be useful; however this study did not highlight any specific measures to implement

Cosmological background solutions and cosmological backreactions

The cosmological backreaction proposal, which attempts to account for observations without a primary dark energy source in the stress-energy tensor, has been developed and discussed by means of different approaches. Here, we focus on the concept of cosmological background solutions in order to develop a framework to study different backreaction proposals.Comment: 14 pages, 5 figures; major changes, replaced to match the version published in General Relativity and Gravitatio

Observable Effects of Scalar Fields and Varying Constants

We show by using the method of matched asymptotic expansions that a sufficient condition can be derived which determines when a local experiment will detect the cosmological variation of a scalar field which is driving the spacetime variation of a supposed constant of Nature. We extend our earlier analyses of this problem by including the possibility that the local region is undergoing collapse inside a virialised structure, like a galaxy or galaxy cluster. We show by direct calculation that the sufficient condition is met to high precision in our own local region and we can therefore legitimately use local observations to place constraints upon the variation of "constants" of Nature on cosmological scales.Comment: Invited Festscrift Articl

Estimating North American background ozone in U.S. surface air with two independent global models: Variability, uncertainties, and recommendations

Accurate estimates for North American background (NAB) ozone (O3) in surface air over the United States are needed for setting and implementing an attainable national O3 standard. These estimates rely on simulations with atmospheric chemistry-transport models that set North American anthropogenic emissions to zero, and to date have relied heavily on one global model. We examine NAB estimates for spring and summer 2006 with two independent global models (GEOS-Chem and GFDL AM3). We evaluate the base simulations, which include North American anthropogenic emissions, with mid-tropospheric O3 retrieved from space and ground-level O3 measurements. The models often bracket the observed values, implying value in developing a multi-model approach to estimate NAB O3. Consistent with earlier studies, the models robustly simulate the largest nation-wide NAB levels at high-altitude western U.S. sites (seasonal average maximum daily 8-h values of ∼40–50 ppb in spring and ∼25–40 ppb in summer) where it correlates with observed O3. At these sites, a 27-year GFDL AM3 simulation simulates observed O3 events above 60 ppb and indicates that year-to-year variations in NAB O3 influence their annual frequency (with NAB contributing 50–60 ppb or more during individual events). During summer over the eastern United States (EUS), when photochemical production from regional anthropogenic emissions peaks, NAB is largely uncorrelated with observed values and it is lower than at high-altitude sites (average values of ∼20–30 ppb). Four processes contribute substantially to model differences in specific regions and seasons: lightning NOx, biogenic isoprene emissions and chemistry, wildfires, and stratosphere-to-troposphere transport. Differences in the representations of these processes within the GFDL AM3 and GEOS-Chem models contribute more to uncertainty in NAB estimates, particularly in spring when NAB is highest, than the choice of horizontal resolution within a single model (GEOS-Chem). We propose that future efforts seek to constrain these processes with targeted analysis of multi-model simulations evaluated with observations of O3 and related species from multiple platforms, and thereby reduce the error on NAB estimates needed for air quality planning.Engineering and Applied Science

Dimensionless cosmology

Although it is well known that any consideration of the variations of fundamental constants should be restricted to their dimensionless combinations, the literature on variations of the gravitational constant $G$ is entirely dimensionful. To illustrate applications of this to cosmology, we explicitly give a dimensionless version of the parameters of the standard cosmological model, and describe the physics of Big Bang Neucleosynthesis and recombination in a dimensionless manner. The issue that appears to have been missed in many studies is that in cosmology the strength of gravity is bound up in the cosmological equations, and the epoch at which we live is a crucial part of the model. We argue that it is useful to consider the hypothetical situation of communicating with another civilization (with entirely different units), comparing only dimensionless constants, in order to decide if we live in a Universe governed by precisely the same physical laws. In this thought experiment, we would also have to compare epochs, which can be defined by giving the value of any {\it one} of the evolving cosmological parameters. By setting things up carefully in this way one can avoid inconsistent results when considering variable constants, caused by effectively fixing more than one parameter today. We show examples of this effect by considering microwave background anisotropies, being careful to maintain dimensionlessness throughout. We present Fisher matrix calculations to estimate how well the fine structure constants for electromagnetism and gravity can be determined with future microwave background experiments. We highlight how one can be misled by simply adding $G$ to the usual cosmological parameter set

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

Genome Instability and Cance