915 research outputs found
Early detection of Haemonchus contortus infection in sheep using three different faecal occult blood tests
Haemonchus contortus is a blood-sucking parasite causing the presence of faecal occult blood (FOB). The objective was to study three different FOB tests in order to have a new indicator of H. contortus infection in sheep that could be included in the genetic evaluation system as an alternative selection criterion to faecal worm egg count (FEC). A total of 29 Corriedale lambs were experimentally infected with 10.000 larvae of H. contortus. Stool samples were recorded for FEC and FOB tests (Hexagon, HematestŸ and MultistixŸ), blood for packed cell volume (PCV), haemoglobin, white and red blood cell count (RBC), and FAMACHA© for scoring anaemia. At the end of the experiment lambs were slaughtered to worm burden count. Field infection was achieved in 309 Merino lambs under natural parasite challenge. FEC data were normalized through logarithmic transformation (LnFEC). Pearson correlation was estimated to examine the relationship between all traits. The three tests were able to detect the presence of FOB at day 11. FEC, PCV and RBC decreased to sub-normal values from day 18. FAMACHA© score 3 was considered to be indicative of anaemia. Most of the correlations were of high magnitude, with the exception of MultistixŸ test that was moderately correlated with haematological parameters, LnFEC and FEC. In field infection, most samples were negative to FOB tests and the correlations were lower than those calculated under experimental infection. In conclusion, FOB tests were able to detect haemonchosis earlier than FEC under high experimental parasite challenge. However, they were not able to detect FOB under natural mixed parasite challenge. FAMACHA© and PCV demonstrated to be good indicators of Haemonchosis, having moderate to high correlations with FEC.Keywords: Faecal occult blood test, Faecal worm egg count, Haemonchosis, Sheep
Computer-aided verification in mechanism design
In mechanism design, the gold standard solution concepts are dominant
strategy incentive compatibility and Bayesian incentive compatibility. These
solution concepts relieve the (possibly unsophisticated) bidders from the need
to engage in complicated strategizing. While incentive properties are simple to
state, their proofs are specific to the mechanism and can be quite complex.
This raises two concerns. From a practical perspective, checking a complex
proof can be a tedious process, often requiring experts knowledgeable in
mechanism design. Furthermore, from a modeling perspective, if unsophisticated
agents are unconvinced of incentive properties, they may strategize in
unpredictable ways.
To address both concerns, we explore techniques from computer-aided
verification to construct formal proofs of incentive properties. Because formal
proofs can be automatically checked, agents do not need to manually check the
properties, or even understand the proof. To demonstrate, we present the
verification of a sophisticated mechanism: the generic reduction from Bayesian
incentive compatible mechanism design to algorithm design given by Hartline,
Kleinberg, and Malekian. This mechanism presents new challenges for formal
verification, including essential use of randomness from both the execution of
the mechanism and from the prior type distributions. As an immediate
consequence, our work also formalizes Bayesian incentive compatibility for the
entire family of mechanisms derived via this reduction. Finally, as an
intermediate step in our formalization, we provide the first formal
verification of incentive compatibility for the celebrated
Vickrey-Clarke-Groves mechanism
Shortest paths in nearly conservative digraphs
We introduce the following notion: a digraph D = (V, A) with arc weights c: A â R is called nearly conservative if every negative cycle consists of two arcs. Computing shortest paths in nearly conservative digraphs is NP-hard, and even deciding whether a digraph is nearly conservative is coNP-complete. We show that the âAll Pairs Shortest Pathâ problem is fixed parameter tractable with various parameters for nearly conservative digraphs. The results also apply for the special case of conservative mixed graphs
Finding Connected Dense -Subgraphs
Given a connected graph on vertices and a positive integer ,
a subgraph of on vertices is called a -subgraph in . We design
combinatorial approximation algorithms for finding a connected -subgraph in
such that its density is at least a factor
of the density of the densest -subgraph
in (which is not necessarily connected). These particularly provide the
first non-trivial approximations for the densest connected -subgraph problem
on general graphs
Discrete Convex Functions on Graphs and Their Algorithmic Applications
The present article is an exposition of a theory of discrete convex functions
on certain graph structures, developed by the author in recent years. This
theory is a spin-off of discrete convex analysis by Murota, and is motivated by
combinatorial dualities in multiflow problems and the complexity classification
of facility location problems on graphs. We outline the theory and algorithmic
applications in combinatorial optimization problems
Generating natural language specifications from UML class diagrams
Early phases of software development are known to be problematic, difficult to manage and errors occurring during these phases are expensive to correct. Many systems have been developed to aid the transition from informal Natural Language requirements to semistructured or formal specifications. Furthermore, consistency checking is seen by many software engineers as the solution to reduce the number of errors occurring during the software development life cycle and allow early verification and validation of software systems. However, this is confined to the models developed during analysis and design and fails to include the early Natural Language requirements. This excludes proper user involvement and creates a gap between the original requirements and the updated and modified models and implementations of the system. To improve this process, we propose a system that generates Natural Language specifications from UML class diagrams. We first investigate the variation of the input language used in naming the components of a class diagram based on the study of a large number of examples from the literature and then develop rules for removing ambiguities in the subset of Natural Language used within UML. We use WordNet,a linguistic ontology, to disambiguate the lexical structures of the UML string names and generate semantically sound sentences. Our system is developed in Java and is tested on an independent though academic case study
Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites.
The acquisition of genes by horizontal transfer can impart entirely new biological functions and provide an important route to major evolutionary innovation. Here we have used ancient gene reconstruction and functional assays to investigate the impact of a single horizontally transferred nucleotide transporter into the common ancestor of the Microsporidia, a major radiation of intracellular parasites of animals and humans. We show that this transporter provided early microsporidians with the ability to steal host ATP and to become energy parasites. Gene duplication enabled the diversification of nucleotide transporter function to transport new substrates, including GTP and NAD+, and to evolve the proton-energized net import of nucleotides for nucleic acid biosynthesis, growth and replication. These innovations have allowed the loss of pathways for mitochondrial and cytosolic energy generation and nucleotide biosynthesis that are otherwise essential for free-living eukaryotes, resulting in the highly unusual and reduced cells and genomes of contemporary Microsporidia
Conjunctions of Among Constraints
Many existing global constraints can be encoded as a conjunction of among
constraints. An among constraint holds if the number of the variables in its
scope whose value belongs to a prespecified set, which we call its range, is
within some given bounds. It is known that domain filtering algorithms can
benefit from reasoning about the interaction of among constraints so that
values can be filtered out taking into consideration several among constraints
simultaneously. The present pa- per embarks into a systematic investigation on
the circumstances under which it is possible to obtain efficient and complete
domain filtering algorithms for conjunctions of among constraints. We start by
observing that restrictions on both the scope and the range of the among
constraints are necessary to obtain meaningful results. Then, we derive a
domain flow-based filtering algorithm and present several applications. In
particular, it is shown that the algorithm unifies and generalizes several
previous existing results.Comment: 15 pages plus appendi
Progressive, Transgenerational Changes in Offspring Phenotype and Epigenotype following Nutritional Transition
Induction of altered phenotypes during development in response to environmental input involves epigenetic changes. Phenotypic traits can be passed between generations by a variety of mechanisms, including direct transmission of epigenetic states or by induction of epigenetic marks de novo in each generation. To distinguish between these possibilities we measured epigenetic marks over four generations in rats exposed to a sustained environmental challenge. Dietary energy was increased by 25% at conception in F0 female rats and maintained at this level to generation F3. F0 dams showed higher pregnancy weight gain, but lower weight gain and food intake during lactation than F1 and F2 dams. On gestational day 8, fasting plasma glucose concentration was higher and ÎČ-hydroxybutyrate lower in F0 and F1 dams than F2 dams. This was accompanied by decreased phosphoenolpyruvate carboxykinase (PEPCK) and increased PPARα and carnitine palmitoyl transferase-1 mRNA expression. PEPCK mRNA expression was inversely related to the methylation of specific CpG dinucleotides in its promoter. DNA methyltransferase (Dnmt) 3a2, but not Dnmt1 or Dnmt3b, expression increased and methylation of its promoter decreased from F1 to F3 generations. These data suggest that the regulation of energy metabolism during pregnancy and lactation within a generation is influenced by the maternal phenotype in the preceding generation and the environment during the current pregnancy. The transgenerational effects on phenotype were associated with altered DNA methylation of specific genes in a manner consistent with induction de novo of epigenetic marks in each generation
CR1 Knops blood group alleles are not associated with severe malaria in the Gambia
The Knops blood group antigen erythrocyte polymorphisms have been associated with reduced falciparum malaria-based in vitro rosette formation (putative malaria virulence factor). Having previously identified single-nucleotide polymorphisms (SNPs) in the human complement receptor 1 (CR1/CD35) gene underlying the Knops antithetical antigens Sl1/Sl2 and McC(a)/McC(b), we have now performed genotype comparisons to test associations between these two molecular variants and severe malaria in West African children living in the Gambia. While SNPs associated with Sl:2 and McC(b+) were equally distributed among malaria-infected children with severe malaria and control children not infected with malaria parasites, high allele frequencies for Sl 2 (0.800, 1,365/1,706) and McC(b) (0.385, 658/1706) were observed. Further, when compared to the Sl 1/McC(a) allele observed in all populations, the African Sl 2/McC(b) allele appears to have evolved as a result of positive selection (modified Nei-Gojobori test Ka-Ks/s.e.=1.77, P-value <0.05). Given the role of CR1 in host defense, our findings suggest that Sl 2 and McC(b) have arisen to confer a selective advantage against infectious disease that, in view of these case-control study data, was not solely Plasmodium falciparum malaria. Factors underlying the lack of association between Sl 2 and McC(b) with severe malaria may involve variation in CR1 expression levels
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