-Generic Computability, Turing Reducibility and Asymptotic Density

Generic computability has been studied in group theory and we now study it in the context of classical computability theory. A set A of natural numbers is generically computable if there is a partial computable function f whose domain has density 1 and which agrees with the characteristic function of A on its domain. A set A is coarsely computable if there is a computable set C such that the symmetric difference of A and C has density 0. We prove that there is a c.e. set which is generically computable but not coarsely computable and vice versa. We show that every nonzero Turing degree contains a set which is not coarsely computable. We prove that there is a c.e. set of density 1 which has no computable subset of density 1. As a corollary, there is a generically computable set A such that no generic algorithm for A has computable domain. We define a general notion of generic reducibility in the spirt of Turing reducibility and show that there is a natural order-preserving embedding of the Turing degrees into the generic degrees which is not surjective

Multipass automata and group word problems

We introduce the notion of multipass automata as a generalization of pushdown automata and study the classes of languages accepted by such machines. The class of languages accepted by deterministic multipass automata is exactly the Boolean closure of the class of deterministic context-free languages while the class of languages accepted by nondeterministic multipass automata is exactly the class of poly-context-free languages, that is, languages which are the intersection of finitely many context-free languages. We illustrate the use of these automata by studying groups whose word problems are in the above classes

The 2-Dimensional Quantum Euclidean Algebra

The algebra dual to Woronowicz's deformation of the 2-\-di\-men\-sion\-al Euclidean group is constructed. The same algebra is obtained from $SU_{q}(2)$ via contraction on both the group and algebra levels.Comment: 8 pages, LBL-31711 and UCB-PTH-92/0

Region-Wide Ecological Responses of Arid Wyoming Big Sagebrush Communities to Fuel Treatments

If arid sagebrush ecosystems lack resilience to disturbances or resistance to annual invasives, then alternative successional states dominated by annual invasives, especially cheatgrass (Bromus tectorum L.), are likely after fuel treatments. We identified six Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis Beetle & Young) locations (152–381 mm precipitation) that we believed had sufficient resilience and resistance for recovery. We examined impacts of woody fuel reduction (fire, mowing, the herbicide tebuthiuron, and untreated controls, all with and without the herbicide imazapic) on short-term dominance of plant groups and on important land health parameters with the use of analysis of variance (ANOVA). Fire and mowing reduced woody biomass at least 85% for 3 yr, but herbaceous fuels were reduced only by fire (72%) and only in the first year. Herbaceous fuels produced at least 36% more biomass with mowing than untreated areas during posttreatment years. Imazapic only reduced herbaceous biomass after fires (34%). Tebuthiuron never affected herbaceous biomass. Perennial tall grass cover was reduced by 59% relative to untreated controls in the first year after fire, but it recovered by the second year. Cover of all remaining herbaceous groups was not changed by woody fuel treatments. Only imazapic reduced significantly herbaceous cover. Cheatgrass cover was reduced at least 63% with imazapic for 3 yr. Imazapic reduced annual forb cover by at least 45%, and unexpectedly, perennial grass cover by 49% (combination of tall grasses and Sandberg bluegrass [Poa secunda J. Presl.]). Fire reduced density of Sandberg bluegrass between 40% and 58%, decreased lichen and moss cover between 69% and 80%, and consequently increased bare ground between 21% and 34% and proportion of gaps among perennial plants &spigt; 2 m (at least 28% during the 3 yr). Fire, mowing, and imazapic may be effective in reducing fuels for 3 yr, but each has potentially undesirable consequences on plant communities

Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections

Exserohilum rostratum was the cause of most cases of fungal meningitis and other infections associated with the injection of contaminated methylprednisolone acetate produced by the New England Compounding Center (NECC). Until this outbreak, very few human cases of Exserohilum infection had been reported, and very little was known about this dematiaceous fungus, which usually infects plants. Here, we report using whole-genome sequencing (WGS) for the detection of single nucleotide polymorphisms (SNPs) and phylogenetic analysis to investigate the molecular origin of the outbreak using 22 isolates of E. rostratum retrieved from 19 case patients with meningitis or epidural/spinal abscesses, 6 isolates from contaminated NECC vials, and 7 isolates unrelated to the outbreak. Our analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb. A total of 8 SNPs were detected among the outbreak genomes, with no more than 2 SNPs separating any 2 of the 28 genomes. The outbreak genomes were separated from the next most closely related control strain by ∼136,000 SNPs. We also observed significant genomic variability among strains unrelated to the outbreak, which may suggest the possibility of cryptic speciation in E. rostratum

Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens

Melioidosis is an emerging infectious disease caused by the soil bacterium Burkholderia pseudomallei. In diagnostic and forensic settings, molecular detection assays need not only high sensitivity with low limits of detection but also high specificity. In a direct comparison of published and newly developed TaqMan PCR assays, we found the TTS1-orf2 assay to be superior in detecting B. pseudomallei directly from clinical specimens. The YLF/BTFC multiplex assay (targeting the Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region) also showed high diagnostic sensitivity and provides additional information on possible geographic origin