Trade-offs, condition dependence and stopover site selection by migrating sandpipers

Western sandpipers Calidris mauri on southward migration fly over the Gulf of Alaska to the Strait of Georgia, British Columbia, where they stop for a few days to replenish reserves before continuing. In the Strait, individuals captured on the extensive tidal mudflats of the Fraser estuary (∼25000 ha) are significantly heavier (2.71 g, or >10% of lean body mass) than those captured on the small (<100 ha) mudflat of nearby Sidney Island. Previous work has shown that the difference cannot be attributed to seasonal timing, size, age or gender effects, and here we compare predictions made by six hypotheses about a diverse set of data to explain why, partway through a migratory journey of ∼10000 km, birds have such different body masses at two stopover sites within 40 km of each other. The ‘trade-off’ hypothesis – that the large Fraser estuary offers safety from predators, but a lower fattening rate, while the small Sidney Island site is more dangerous, but offers a higher fattening rate – made six successful predictions, all of which were upheld by the data. All other hypotheses failed at least one prediction. We infer that calidrid sandpipers arriving in the Strait of Georgia with little fat remaining (and therefore low body mass) choose to take advantage of the high feeding rate at small sites like Sidney Island because they are less vulnerable to avian predators than are individuals with higher fat reserves, who instead elect to feed at large open sites like the Fraser estuary mudflats

Using local dispersal data to reduce bias in annual apparent survival and mate fidelity

Citation: Taylor, C. M., Lank, D. B., & Sandercock, B. K. (2015). Using local dispersal data to reduce bias in annual apparent survival and mate fidelity. Condor, 117(4), 598-608. doi:10.1650/condor-14-184.1In mark-recapture studies conducted on fixed-area study sites, apparent (or "local") survival (phi) is the product of the probabilities of true survival (S) and site fidelity to the sampling area (F). If marked individuals permanently emigrate from the study site, apparent survival will be biased low relative to true survival. Similarly, estimates of mate fidelity will be biased high because site fidelity is typically higher for individuals that reunite with their previous mates than among pairs that divorce. Here, we develop a method for calculating site fidelity that takes plot boundaries into account, based on a dispersal model estimated from local movements within a fixed study site. We use dispersal estimates to adjust apparent survival and mate fidelity for the effects of short-distance movements out of a fixed area. We demonstrate our method with a retrospective analysis of a published study of 2 species of sandpipers breeding sympatrically at a field site in western Alaska. Estimates of survival probability increased by 0.01-0.03 for males and 0.07-0.08 for females in both species. The larger adjustments for females were expected based on their longer local dispersal movements. Adjusted mate fidelity estimates were lower than the original estimates by 0.04-0.07. Use of local movement data to estimate site fidelity cannot account for permanent emigration due to long-distance movements and, if such movements occur, our adjusted estimates of phi remain a function of true survival and site fidelity. Nevertheless, our method can reduce bias in demographic parameters resulting from local dispersal movements, improving estimates of annual survival and mate fidelity for use in demographic models

Creating Your Bubble: Personal Space On and Around Large Public Displays

We describe an empirical study that explores how users establish and use personal space around large public displays (LPDs). Our study complements field studies in this space by more fully characterizing interpersonal distances based on coupling and confirms the use of on-screen territories on vertical displays. Finally, we discuss implications for future research: limitations of proxemics and territoriality, how user range can augment existing theory, and the influence of display size on personal space

Subtle and Personal Workspace Requirements for Visual Search Tasks on Public Displays

This is the author’s version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in the Proceedings of the 2017 International Conference on Human Factors in Computing Systems on the ACM Digital Library http://dx.doi.org/10.1145/3025453.3025500We explore how users approach and define personal space on large, public displays. Our results show that users of public displays use one of two strategies for visual search tasks: minimizers create a small window and work up close to the display, and maximizers expand content to its full resolution and work at a distance. We show that these interaction styles match predicted `personal' and `subtle' interaction zones, characterize typical width and height requirements for these interactions, and show that these requirements are independent of the on-screen content's dimensions. Finally, we suggest practical guidelines for defining workspaces during personal and subtle interaction on large, public displays

Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping

Located on Chromosome 6p21, classical human leukocyte antigen genes are highly polymorphic. HLA alleles associate with a variety of phenotypes, such as narcolepsy, autoimmunity, as well as immunologic response to infectious disease. Moreover, high resolution genotyping of these loci is critical to achieving long-term survival of allogeneic transplants. Development of methods to obtain high resolution analysis of HLA genotypes will lead to improved understanding of how select alleles contribute to human health and disease risk. Genomic DNAs were obtained from a cohort of n = 383 subjects recruited as part of an Ulcerative Colitis study and analyzed for HLA-DRB1. HLA genotypes were determined using sequence specific oligonucleotide probes and by next-generation sequencing using the Roche/454 GSFLX instrument. The Clustering and Alignment of Polymorphic Sequences (CAPSeq) software application was developed to analyze next-generation sequencing data. The application generates HLA sequence specific 6-digit genotype information from next-generation sequencing data using MUMmer to align sequences and the R package diffusionMap to classify sequences into their respective allelic groups. The incorporation of Bootstrap Aggregating, Bagging to aid in sorting of sequences into allele classes resulted in improved genotyping accuracy. Using Bagging iterations equal to 60, the genotyping results obtained using CAPSeq when compared with sequence specific oligonucleotide probe characterized 4-digit genotypes exhibited high rates of concordance, matching at 759 out of 766 (99.1%) alleles. © 2013 Ringquist et al

Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff

By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black- and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation

Road Quality Classification

Automatické vyhodnocování kvality vozovky může být užitečné jak správním orgánům, tak i těm účastníkům silničního provozu, kteří vyhledávají vozovky s kvalitním povrchem pro co největší potěšení z jízdy. Tato práce se zabývá návrhem modelu, který klasifikuje obrázky silnic do pěti kvalitativních kategorií na základě jejich celkového vzhledu. V práci prezentujeme nový ručně anotovaný dataset, obsahující fotografie ze služby Google Street View. Anotace datasetu byla navržena pro motorkáře, ale může být použita i pro jiné účastníky silničního provozu. Experimentovali jsme jak s předučenými konvolučními neuronovými sítěmi, jako jsou MobileNet či DenseNet, tak s vlastními architekturami konvolučních neuronových sítí. Dále jsme vyzkoušeli různé techniky předzpracování dat, např. odstraňování stínů či kontrastně-limitní adaptabilní histogramovou ekvalizací (CLAHE). Námi navrhovaný klasifikační model využívá CLAHE a na testovací sadě dosahuje 71&amp;amp;amp;#37; přesnosti. Vizuální kontrola ukázala, že navrhovaný model je i s touto přesností využitelný za účelem, pro který byl navržen.Automated evaluation of road quality can be helpful to authorities and also road users who seek high-quality roads to maximize their driving pleasure. This thesis proposes a model which classifies road images into five qualitative categories based on overall appearance. We present a new manually annotated dataset, collected from Google Street View. The dataset classes were designed for motorcyclists, but they are also applicable to other road users. We experimented with Convolutions Neural Networks, involving custom architectures and pre-trained networks, such as MobileNet or DenseNet. Also, many experiments with preprocessing methods such as shadow removal or CLAHE. Our proposed classification model uses CLAHE and achieves 71&amp;amp;amp;#37; accuracy on a test set. A visual check showed the model is applicable for its designed purpose despite the modest accuracy since the image data are often controversial and hard to label even for humans