Tropical theta functions and log Calabi-Yau surfaces

textWe describe combinatorial techniques for studying log Calabi-Yau surfaces. These can be viewed as generalizing the techniques for studying toric varieties in terms of their character and cocharacter lattices. These lattices are replaced by certain integral linear manifolds described in [GHK11], and monomials on toric varieties are replaced with the canonical theta functions defined in [GHK11] using ideas from mirror symmetry. We classify deformation classes of log Calabi-Yau surfaces in terms of the geometry of these integral linear manifolds. We then describe the tropicalizations of theta functions and use them to generalize the dual pairing between the character and cocharacter lattices. We use this to describe generalizations of dual cones, Newton and polar polytopes, Minkowski sums, and finite Fourier series expansions. We hope that these techniques will generalize to higher rank cluster varieties.Mathematic

Resilience of Microgrid during Catastrophic Events

Today, there is a growing number of buildings in a neighborhood and business parks that are utilizing renewable energy generation, to reduce their electric bill and carbon footprint. The most current way of implementing a renewable energy generation is to use solar panels or a windmill to generate power; then use a charge controller connected to a battery bank to store power. Once stored, the user can then access a clean source of power from these batteries instead of the main power grid. This type of power structure is utilizing a single module system in respect of one building. As the industry of renewable power generation continues to increase, we start to see a new way of implementing the infrastructure of the power system. Instead of having just individual buildings generating power, storing power, using power, and selling power there is a fifth step that can be added, sharing power. The idea of multiple buildings connected to each other to share power has been named a microgrid by the power community. With this ability to share power in a microgrid system, a catastrophic event which cause shutdowns of power production can be better managed. This paper then discusses the data from simulations and a built physical model of a resilient microgrid utilizing these principles

Correlation of Raccoon Pelt Qualities with Age, Sex, and Physical Condition

Fur harvesters and fur buyers have many intuitive ideas about how raccoons\u27 pelt qualities differ due to age, sex, or physical condition. We tried to demonstrate correlations between age classes (juvenile and adult), sex, and physical condition and the quality of raccoon pelts. Quality of pelts was described in three objective ways: size of the pelt, density of the pelage (primeness), and color of the pelage. Physical condition was measured by kidney fat index (KFI) and skin fat index (SFI). Size of the pelts was correlated with age, sex, and both measures of physical condition. Primeness of the pelts was correlated with age and both measures of physical condition but not with sex. Color of the pelts was not significantly correlated with age, sex, or either physical condition index

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.Comment: 30 pages, 1 table, 4 figures, 1 supplementary table, 3 supplementary figure

Fine-scale Genetic Structure and Social Organization in Female White-tailed Deer

Social behavior of white-tailed deer (Odocoileus virginianus) can have important management implications. The formation of matrilineal social groups among female deer has been documented and management strategies have been proposed based on this well-developed social structure. Using radiocollared (n = 17) and hunter or vehicle- killed (n = 21) does, we examined spatial and genetic structure in white-tailed deer on a 7,000-ha portion of the Savannah River Site in the upper Coastal Plain of South Carolina, USA. We used 14 microsatellite DNA loci to calculate pairwise relatedness among individual deer and to assign doe pairs to putative relationship categories. Linear distance and genetic relatedness were weakly correlated (r = –0.08, P = 0.058). Relationship categories differed in mean spatial distance, but only 60% of first-degree-related doe pairs (full sibling or mother–offspring pairs) and 38% of second-degree-related doe pairs (half sibling, grandmother–granddaughter pairs) were members of the same social group based on spatial association. Heavy hunting pressure in this population has created a young age structure among does, where the average age is4.5 years old. This—combined with potentially elevated dispersal among young does—could limit the formation of persistent, cohesive social groups. Our results question the universal applicability of recently proposed models of spatial and genetic structuring in white-tailed deer, particularly in areas with differing harvest histories

Evaluation of immunogenicity and efficacy of Fasciola hepatica Tetraspanin 2 (TSP2) fused to E. coli Heat-Labile Enterotoxin B Subunit LTB adjuvant following intranasal vaccination of cattle

Fasciolosis, caused by the liver flukes Fasciola hepatica and F. gigantica, is an economically important and globally distributed zoonotic disease. Liver fluke infections in livestock cause significant losses in production and are of particular concern to regions where drug resistance is emerging. Antigens of the F. hepatica surface tegument represent promising vaccine candidates for controlling this disease. Tetraspanins are integral tegumental antigens that have shown partial protection as vaccine candidates against other trematode species. The Escherichia coli heat-labile enterotoxin’s B subunit (LTB) is a potent mucosal adjuvant capable of inducing an immune response to fused antigens. This study investigates the potential of F. hepatica tetraspanin 2 extracellular loop 2 (rFhTSP2) as a protective vaccine antigen and determines if fusion of FhTSP2 to LTB can enhance protection in cattle. Cattle were immunised subcutaneously with rFhTSP2 mixed in the Freund’s adjuvant and intranasally with rLTB-FhTSP2 in saline, accounting for equal molar ratios of tetraspanin in both groups. Vaccination with rFhTSP2 stimulated a strong specific serum IgG response, whereas there was no significant serum IgG response following rLTB-FhTSP2 intranasal vaccination. There was no substantial antigen specific serum IgA generated in all groups across the trial. Contrastingly, after the fluke challenge, a rise in antigen specific saliva IgA was observed in both vaccination groups on Day 42, with the rLTB-FhTSP2 vaccination group showing significant mucosal IgA production at Day 84. However, neither vaccine group showed a significant reduction of fluke burden nor faecal egg output. These results suggest that intranasal vaccination with rLTB-FhTSP2 does elicit a humoral mucosal response but further work is needed to evaluate if mucosal delivery of liver fluke antigens fused to LTB is a viable vaccine strategy

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths