Covering Partial Cubes with Zones

A partial cube is a graph having an isometric embedding in a hypercube. Partial cubes are characterized by a natural equivalence relation on the edges, whose classes are called zones. The number of zones determines the minimal dimension of a hypercube in which the graph can be embedded. We consider the problem of covering the vertices of a partial cube with the minimum number of zones. The problem admits several special cases, among which are the problem of covering the cells of a line arrangement with a minimum number of lines, and the problem of finding a minimum-size fibre in a bipartite poset. For several such special cases, we give upper and lower bounds on the minimum size of a covering by zones. We also consider the computational complexity of those problems, and establish some hardness results

Gene Expression Pattern Analysis of Anterior Hox Genes during Zebrafish (Danio rerio) Embryonic Development Reveals Divergent Expression Patterns from Other Teleosts

The regional identity of organs and organ systems along the anterior-posterior axis during embryonic development is patterned, in part, by Hox genes, which encode transcription factor proteins that activate or repress the expression of downstream target genes. Divergent nested Hox gene expression patterns may have had a role in facilitating morphological divergence of structures, such as the pharyngeal jaw apparatus, among evolutionarily divergent teleost fishes. Recent studies from several evolutionarily divergent teleosts, such as the Japanese Medaka (Oryzias latipes) and the Nile Tilapia (Oreochromis niloticus), have shown the presence of divergent expression patterns of several Hox genes within paralog groups 2–5 between these species. Specifically, these expression patterns were documented in the pharyngeal arches, which give rise to the pharyngeal jaw apparatus. While the expression patterns of several Zebrafish (Danio rerio) Hox genes that are orthologous to those of Medaka and Tilapia have been documented within the developing hindbrain and pharyngeal arches, many still have yet to be documented, especially within the pharyngeal arches during the postmigratory cranial neural crest cell stages. Here, we present the expression patterns of six Zebrafish Hox genes, hoxc3a, d3a, a4a, d4a, b5a, and c5a, within the pharyngeal arches during a postmigratory cranial neural crest cell stage and compare them to their orthologous genes of Medaka and Tilapia at similar stages. We show that while hoxc3a, d3a, and c5a of Zebrafish are absent from the pharyngeal arches, hoxa4a, d4a, and b5a show divergent expression patterns from their orthologs in Medaka and Tilapia. These observed divergences may be, in part, responsible for the divergent pharyngeal jaw apparatus structures exhibited by these fishes

Dermocystid infection and associated skin lesions in free-living palmate newts (Lissotriton helveticus) from Southern France

Since the early 1900s, mesomycetozoan parasites have been reported in both European anuran and caudate species. These reports have primarily been descriptive, which has made assessing the impact of these parasites on host populations difficult. Anecdotal reports of Dermocystidium-like parasites are becoming widespread across Europe, possibly indicating that these mesomycetozoan parasites are increasing in distribution and/or abundance. This highlights the need for further investigations into the occurrence, pathogenesis and effects on host health of these parasitic infections for free-living amphibian populations, particularly those which are already stressed or threatened by other factors. Here we report the results of pathological, microbiological and molecular investigations used to characterize unidentified skin lesions in palmate newts (Lissotriton helveticus) from Larzac, France. We confirm that the lesions are the result of infection with a novel dermocystidium-like parasite, which is related to Amphybiocystidium ranae. We also show that the same parasite is distributed across several newt breeding sites. The lesions that result from infection with this parasite range from single or few vesicular or nodular cutaneous lesions to multiple coalescing skin ulcers with extensive hemorrhages. The latter have not been previously described in amphibians due to mesomycetozoan parasitic infection. Dermocystid DNA was detected only in newts that showed lesions, providing comparative evidence of the parasite's pathogenicity. We discuss the potential significance of the presence of this pathogen in the context of the population health of palmate newts

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

BACKGROUND: The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific assays in T and B cell lines, we provide compelling evidence that redefines causal genes at the 6q23 locus, one of the most important loci that confers autoimmunity risk. RESULTS: Although the function of disease-associated non-coding single nucleotide polymorphisms (SNPs) at 6q23 is unknown, the association is generally assigned to TNFAIP3, the closest gene. However, the DNA fragment containing the associated SNPs interacts through chromatin looping not only with TNFAIP3, but also with IL20RA, located 680 kb upstream. The risk allele of the most likely causal SNP, rs6927172, is correlated with both a higher frequency of interactions and increased expression of IL20RA, along with a stronger binding of both the NFκB transcription factor and chromatin marks characteristic of active enhancers in T-cells. CONCLUSIONS: Our results highlight the importance of gene assignment for translating GWAS findings into biologically meaningful mechanisms of disease and potential therapeutic targets; indeed, monoclonal antibody therapy targeting IL-20 is effective in the treatment of rheumatoid arthritis and psoriasis, both with strong GWAS associations to this region

Involving research participants in a pan-European research initiative: the EPAD participant panel experience

Abstract: Background: Including participants in patient and public involvement activities is increasingly acknowledged as a key pillar of successful research activity. Such activities can influence recruitment and retention, as well as researcher experience and contribute to decision making in research studies. However, there are few established methodologies of how to set up and manage participant involvement activities. Further, there is little discussion of how to do so when dealing with collaborative projects that run across countries and operate in multiple linguistic and regulatory contexts. Methods: In this paper we describe the set-up, running and experiences of the EPAD participant panel. The EPAD study was a pan-European cohort study with the aim to understand risks for developing Alzheimer’s disease and build a readiness cohort for Phase 2 clinical trials. Due to the longitudinal nature of this study, combined with the enrolment of healthy volunteers and those with mild cognitive impairments, the EPAD team highlighted participant involvement as crucial to the success of this project. The EPAD project employed a nested model, with local panels meeting in England, France, Scotland, Spain and The Netherlands, and feeding into a central study panel. The local panels were governed by terms of reference which were adaptable to local needs. Results: The impact of the panels has been widespread, and varies from feedback on documentation, to supporting with design of media materials and representation of the project at national and international meetings. Conclusions: The EPAD panels have contributed to the success of the project and the model established is easily transferable to other disease areas investigating healthy or at-risk populations

Some implications of superconducting quantum interference to the application of master equations in engineering quantum technologies

In this paper we consider the modeling and simulation of open quantum systems from a device engineering perspective. We derive master equations at different levels of approximation for a superconducting quantum interference device (SQUID) ring coupled to an ohmic bath. We demonstrate that the master equations we consider produce decoherences that are qualitatively and quantitatively dependent on both the level of approximation and the ring's external flux bias. We discuss the issues raised when seeking to obtain Lindbladian dissipation and show, in this case, that the external flux (which may be considered to be a control variable in some applications) is not confined to the Hamiltonian, as often assumed in quantum control, but also appears in the Lindblad terms

External costs of atmospheric Pb emissions: valuation of neurotoxic impacts due to inhalation

<p>Abstract</p> <p>Background</p> <p>The Impact Pathway Approach (IPA) is an innovative methodology to establish links between emissions, related impacts and monetary estimates. Only few attempts have so far been presented regarding emissions of metals; in this study the external costs of airborne lead (Pb) emissions are assessed using the IPA. Exposure to Pb is known to provoke impacts especially on children's cognition. As cognitive abilities (measured as IQ, intelligence quotient) are known to have implications for lifetime income, a pathway can be established leading from figures for Pb emissions to the implied loss in earnings, and on this basis damage costs per unit of Pb emission can be assessed.</p> <p>Methods</p> <p>Different types of models are here linked. It is relatively straightforward to establish the relationship between Pb emissions and consequent increase in air-Pb concentration, by means of a Gaussian plume dispersion model (OML). The exposed population can then be modelled by linking the OML-output to population data nested in geo-referenced grid cells. Less straightforward is to establish the relationship between exposure to air-Pb concentrations and the resulting blood-Pb concentration. Here an Age-Dependent Biokinetic Model (ADBM) for Pb is applied. On basis of previous research which established links between increases in blood-Pb concentrations during childhood and resulting IQ-loss we arrive at our results.</p> <p>Results</p> <p>External costs of Pb airborne emissions, even at low doses, in our site are in the range of 41-83 €/kg emitted Pb, depending on the considered meteorological year. This estimate applies only to the initial effects of air-Pb, as our study does not address the effects due to the Pb environmental-accumulation and to the subsequent Pb re-exposure. These are likely to be between one and two orders of magnitude higher.</p> <p>Conclusions</p> <p>Biokinetic modelling is a novel tool not previously included when applying the IPA to explore impacts of Pb emissions and related external costs; it allows for more fine-tuned, age-dependent figures for the external costs from low-dose exposure. Valuation of additional health effects and impacts e.g. due to exposure via ingestion appear to be feasible when extending the insights from the present pilot study.</p

Distribution and abundance of western gray whales off northeastern Sakhalin Island, Russia, 2001’003

In 2001’003, >60,000 km of aerial surveys and 7,700 km of vessel surveys were conducted during June to November when critically endangered Korean–Okhotsk or western gray whales (Eschrichtius robustus) were present off the northeast coast of Sakhalin Island, Russia. Results of surveys in all years indicated gray whales occurred in predominantly two areas, (1) adjacent to Piltun Bay, and (2) offshore from Chayvo Bay, hereafter referred to as the Piltun and offshore feeding areas. In the Piltun feeding area, the majority of whales were observed in waters shallower than 20 m and were distributed from several hundred meters to ∼ 5 km from the shoreline. In the offshore feeding area during all years, the distribution of gray whales extended from southwest to northeast in waters 30’5 m in depth. During all years, the distribution and abundance of whales changed in both the Piltun and offshore feeding areas, and both north–south and inshore–offshore movements were documented within and between feeding seasons. The discovery of a significant number of whales feeding in the offshore area each year was a substantial finding of this study and raises questions regarding western gray whale abundance and population levels, feeding behavior and ecology, and individual site-fidelity. Fluctuations in the number of whales observed within the Piltun and offshore feeding areas and few sightings outside of these two areas indicate that gray whales move between the Piltun and offshore feeding areas during their summer–fall feeding season. Seasonal shifts in the distribution and abundance of gray whales between and within both the Piltun and offshore feeding areas are thought, in part, to be a response to seasonal changes in the distribution and abundance of prey. However, the mechanism driving the movements of whales along the northeast coast of Sakhalin Island is likely very complex and influenced by a multitude of factors

Involving research participants in a pan-European research initiative: the EPAD participant panel experience.

BACKGROUND: Including participants in patient and public involvement activities is increasingly acknowledged as a key pillar of successful research activity. Such activities can influence recruitment and retention, as well as researcher experience and contribute to decision making in research studies. However, there are few established methodologies of how to set up and manage participant involvement activities. Further, there is little discussion of how to do so when dealing with collaborative projects that run across countries and operate in multiple linguistic and regulatory contexts. METHODS: In this paper we describe the set-up, running and experiences of the EPAD participant panel. The EPAD study was a pan-European cohort study with the aim to understand risks for developing Alzheimer's disease and build a readiness cohort for Phase 2 clinical trials. Due to the longitudinal nature of this study, combined with the enrolment of healthy volunteers and those with mild cognitive impairments, the EPAD team highlighted participant involvement as crucial to the success of this project. The EPAD project employed a nested model, with local panels meeting in England, France, Scotland, Spain and The Netherlands, and feeding into a central study panel. The local panels were governed by terms of reference which were adaptable to local needs. RESULTS: The impact of the panels has been widespread, and varies from feedback on documentation, to supporting with design of media materials and representation of the project at national and international meetings. CONCLUSIONS: The EPAD panels have contributed to the success of the project and the model established is easily transferable to other disease areas investigating healthy or at-risk populations