Mod/Resc Parsimony Inference

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.Comment: 11 pages, 3 figure

Experimental evidence that livestock grazing intensity affects the activity of a generalist predator

Open Access funded by Natural Environment Research CouncilPeer reviewedPublisher PD

Minimal unsatisfiable formulas with bounded clause-variable difference are fixed-parameter tractable

Recognition of minimal unsatisfiable CNF formulas (unsatisfiable CNF formulas which become satisfiable if any clause is removed) is a classical DP-complete problem. It was shown recently that minimal unsatisfiable formulas with n variables and n+k clauses can be recognized in time . We improve this result and present an algorithm with time complexity ; hence the problem turns out to be fixed-parameter tractable (FTP) in the sense of Downey and Fellows (Parameterized Complexity, 1999). Our algorithm gives rise to a fixed-parameter tractable parameterization of the satisfiability problem: If for a given set of clauses F, the number of clauses in each of its subsets exceeds the number of variables occurring in the subset at most by k, then we can decide in time whether F is satisfiable; k is called the maximum deficiency of F and can be efficiently computed by means of graph matching algorithms. Known parameters for fixed-parameter tractable satisfiability decision are tree-width or related to tree-width. Tree-width and maximum deficiency are incomparable in the sense that we can find formulas with constant maximum deficiency and arbitrarily high tree-width, and formulas where the converse prevails

Reducing Livestock Effects on Public Lands in the Western United States as the Climate Changes: A Reply to Svejcar et al.

Beschta et al. (2013) synthesized the ecological effects 41 of climate change and ungulate grazing on western public lands, grounding their recommendations in ecological considerations and federal agency legal authority and obligations. Svejcar et al. (2014) suggest that Beschta et al. (2013) neither “present a balanced synthesis of the scientific literature” nor “reflect the complexities associated with herbivore grazing.” Svejcar et al. (2014) “dispute the notion that eliminating [livestock] grazing will provide a solution to problems created by climate change,” although we made no such claim. Instead, Beschta et al. (2013: p. 474) indicate that removal or reduction of livestock across large areas of public land will reduce a pervasive ecological stress, diminishing cumulative impacts on these ecosystems under climate change. We respond to three livestock grazing issues raised by Svejcar et al. (2014): (1) legacy vs. contemporary effects, (2) fuels reduction and fire effects, and (3) grazing complexity and restoration.Keywords: Climate change, Public lands, Restoration, Ungulates, Livestock grazing, Biodiversit

Arboreality increases reptile community resistance to disturbance from livestock grazing

1. Domestic livestock grazing directly alters ground-level habitat but its effects on arboreal habitat are poorly known. Similarly, the response to grazing of ground-dwelling fauna has been examined, but there are few studies of arboreal fauna. Globally, grazing has been implicated in the decline of vertebrate fauna species, but some species appear resistant to the effects of grazing, either benefiting from the structural changes at ground level or avoiding them, as may be the case with arboreal species. Here we examine arboreal and terrestrial habitat responses and reptile community responses to grazing, to determine whether arboreal reptile species are more resistant than terrestrial reptile species. 2. We conducted arboreal and terrestrial reptile surveys on four different grazing treatments, at a 19-year experimental grazing trial in northern Australia. To compare the grazing response of arboreal and terrestrial reptile assemblages, we used community, functional group and individual species-level analyses. Species responses were modelled in relation to landscape-scale and microhabitat variables. 3. Arboreal reptile species were resistant to the impact of grazing, whereas terrestrial reptiles were negatively affected by heavy grazing. Terrestrial reptiles were positively associated with complex ground structures, which were greatly reduced in heavily grazed areas. Arboreal lizards responded positively to microhabitat features such as tree hollows. 4. Synthesis and applications. Arboreal and terrestrial reptiles have different responses to the impact of livestock grazing. This has implications for rangeland management, particularly if management objectives include goals relating to conserving certain species or functional groups. Arboreal reptiles showed resistance in a landscape that is grazed, but where trees have not been cleared. We highlight the importance of retaining trees in rangelands for both terrestrial and arboreal microhabitats

Structural and functional studies of ligandin, a major renal organic anion-binding protein.

Sephadex gel filtration of the 1000,000 g supernate of homogenates of rat kidney revealed binding of various organic anions (penicillin, Bromsulphalein [BSP], bilirubin, phenolsulfonphthalein [PSP], phlorizin, glutathione [GSH], p-amino hippurate (PAH), probenecid, conjugated bilirubin, and BSP-GSH) to a nonalbumin-containing protein fraction (Y), which precipated on addition of monospecific anti-rat liver ligandin (Y protein)-IgG, but not control IgG. Quantitatively similar organic anion binding was observed in vivo after injection of BSP, BSP-GSH, phlorizin, probenecid, conjugated bilirubin, PAH, or penicillin. The binding protein was purified to apparent homogeneity and is a basic protein (pI 8.9) of 44,000 daltons with two apparently identical subunits of 22,000 daltons. Monospecific antibody was produced against the renal protein. The results of binding studies in vivo and in vitro and phsicochemical, immunologic, structural, and binding site investigations indicate that the renal protein is identical to hepatic ligandin. Immunofluorescent studies utilizing anti-ligandin IgG previously localized ligandin in the kidney to all proximal tubular cells. By quantitative radial immunodiffusion, the concentration of renal ligandin was 31.2 plus or minus 2.2 mug/mg supernatant protein and was increased 160% above basal values by pretreatment of rats with tetrachloro-dibenzo-p-dioxin. Pretreatment with phenobarbital, DDT, or pregnene-16alpha-carbonitrile did not increase renal ligandin concentration but doubled hepatic ligandin concentration. Circular dichroism studies of renal ligandin revealed percent helical structure similar to hepatic ligandin and primary association contrasts were derived for BSP (10-6 M-1) and PAH, probenecid, and penicillin (10-3 M-1). Administration of BSP or probenecid simultaneously with [C14] penicillin resulted in increased plasma retention and reduced kidney and urinary bladder content of [14C] penicillin and a correlation coefficient of -0.8 between total kidney/plasma radioactivity and percent of protein-bound radioactivity bound to ligandin in the kidney. These studies indicate that renal and hepatic ligandin are identical. Their response to drugs and chemicals varies. Competitive binding between several organic anions for ligandin correlated with their renal uptake from plasma, which suggests that ligandin may function in the proximal tubular cell as a component of the renal organic anion transport system