Potential Theory on Trees, Graphs and Ahlfors Regular Metric Spaces

We investigate connections between potential theories on a Ahlfors-regular metric space X, on a graph G associated with X, and on the tree T obtained by removing the "horizontal edges" in G. Applications to the calculation of set capacity are given.Comment: 45 pages; presentation improved based on referee comment

Reports Of Conferences, Institutes, And Seminars

This quarter\u27s column offers coverage of multiple sessions from the 2016 Electronic Resources & Libraries (ER&L) Conference, held April 3–6, 2016, in Austin, Texas. Topics in serials acquisitions dominate the column, including reports on altmetrics, cost per use, demand-driven acquisitions, and scholarly communications and the use of subscriptions agents; ERMS, access, and knowledgebases are also featured

Morphology of the Reproductive System of Tetrix arenosa angusta (Hancock) (Orthoptera, Tetrigidae)

The internal reproductive organs of the male include a pair of testes, each composed of about 37 follicles and connected to a short vas efferens; a pair of vasa deferentia; about 12 paired accessory glands; a twice folded ejaculatory duct and a membranous, extensible intromittent organ. The external structures of the male include a chitinous collar, pallial complex and ninth abdominal sternum. The internal reproductive organs of the female include a pair of ovaries, each composed of 11 ovarioles; paired lateral oviducts; a short median oviduct; a terminal genital chamber; a trilobed spermatheca attached to a spermathecal gland, and a pair of median glands. The external structures of the female include the ovipositor and its related sclerites and apodemes

Benchmarking of long-read assemblers for prokaryote whole genome sequencing.

Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled - one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of eight long-read assemblers (Canu, Flye, Miniasm/Minipolish, NECAT, NextDenovo/NextPolish, Raven, Redbean and Shasta) across a wide variety of genomes and read parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, contig circularisation and computational resources used. Results: Canu v2.1 produced reliable assemblies and was good with plasmids, but it performed poorly with circularisation and had the longest runtimes of all assemblers tested. Flye v2.8 was also reliable and made the smallest sequence errors, though it used the most RAM. Miniasm/Minipolish v0.3/v0.1.3 was the most likely to produce clean contig circularisation. NECAT v20200803 was reliable and good at circularisation but tended to make larger sequence errors. NextDenovo/NextPolish v2.3.1/v1.3.1 was reliable with chromosome assembly but bad with plasmid assembly. Raven v1.3.0 was reliable for chromosome assembly, though it did not perform well on small plasmids and had circularisation issues. Redbean v2.5 and Shasta v0.7.0 were computationally efficient but more likely to produce incomplete assemblies. Conclusions: Of the assemblers tested, Flye, Miniasm/Minipolish, NextDenovo/NextPolish and Raven performed best overall. However, no single tool performed well on all metrics, highlighting the need for continued development on long-read assembly algorithms

Connection between global conservation status, geographical range size, midpoint latitude, female carapace length, and clutch size of Testudines

The need for species conservation is only magnified with each passing day. Testudines are one of the taxonomic orders most at risk of extinction on Earth. Over 70% of Testudines are globally listed on the IUCN Red List and over 60% of those are at risk of extinction. Testudines face many threats including habitat loss and degradation. At time of data collection there were 258 turtles globally listed on the IUCN Red List. Following justified additions there were recognized to be 266 turtle species globally listed on the IUCN Red List for the purpose of this study. I collected data for 357 turtle species and examined the association of conservation status with geographic range size, midpoint latitude, female carapace length, and clutch size to determine if any of these attributes would be useful for determining extinction risk. IUCN status rank for species was most highly correlated with mean female carapace length. IUCN status rank for species was most highly correlated with mean female carapace length. The positive association of risk with increasing body size supports concerns about the impact of harvesting or poaching of turtles and tortoises by humans. Testudines are clearly in need of conservation efforts

Classical simulation of noninteracting-fermion quantum circuits

We show that a class of quantum computations that was recently shown to be efficiently simulatable on a classical computer by Valiant corresponds to a physical model of noninteracting fermions in one dimension. We give an alternative proof of his result using the language of fermions and extend the result to noninteracting fermions with arbitrary pairwise interactions, where gates can be conditioned on outcomes of complete von Neumann measurements in the computational basis on other fermionic modes in the circuit. This last result is in remarkable contrast with the case of noninteracting bosons where universal quantum computation can be achieved by allowing gates to be conditioned on classical bits (quant-ph/0006088).Comment: 26 pages, 1 figure, uses wick.sty; references added to recent results by E. Knil

Nitrous oxide fluxes and nitrogen cycling along a pasture chronosequence in Central Amazonia, Brazil

International audienceWe studied nitrous oxide (N2O) fluxes and soil nitrogen (N) cycling following forest conversion to pasture in the central Amazon near Santarém, Pará, Brazil. Two undisturbed forest sites and 27 pasture sites of 0.5 to 60 years were sampled once each during wet and dry seasons. In addition to soil-atmosphere fluxes of N2O we measured 27 soil chemical, soil microbiological and soil physical variables. Soil N2O fluxes were higher in the wet season than in the dry season. Fluxes of N2O from forest soils always exceeded fluxes from pasture soils and showed no consistent trend with pasture age. At our forest sites, nitrate was the dominant form of inorganic N both during wet and dry season. At our pasture sites nitrate generally dominated the inorganic N pools during the wet season and ammonium dominated during the dry season. Net mineralization and nitrification rates displayed large variations. During the dry season net immobilization of N was observed in some pastures. Compared to forest sites, young pasture sites (?2 years) had low microbial biomass N and protease activities. Protease activity and microbial biomass N peaked in pastures of intermediate age (4 to 8 years) followed by consistently lower values in older pasture (10 to 60 years). The C/N ratio of litter was low at the forest sites (~25) and rapidly increased with pasture age reaching values of 60-70 at pastures of 15 years and older. Nitrous oxide emissions at our sites were controlled by C and N availability and soil aeration. Fluxes of N2O were negatively correlated to leaf litter C/N ratio, NH4+-N and the ratio of NO3--N to the sum of NO3--N + NH4+-N (indicators of N availability), and methane fluxes and bulk density (indicators of soil aeration status) during the wet season. During the dry season fluxes of N2O were positively correlated to microbial biomass N, ?-glucosidase activity, total inorganic N stocks and NH4+-N. In our study region, pastures of all age emitted less N2O than old-growth forests, because of a progressive decline in N availability with pasture age combined with strongly anaerobic conditions in some pastures during the wet season

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormaechei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormaechei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species