Projection distortion analysis for flattened image mosaicing from straight uniform generalized cylinders

This paper presents a new approach for reconstructing images mapped or painted on straight uniform generalized cylinders (SUGC). A set of monocular images is taken from different viewpoints in order to be mosaiced and to represent the entire scene in detail. The expressions of the SUGC's projection axis are derived from two cross-sections projected onto the image plane. Based on these axes we derive the SUGC localization in the camera coordinate system. We explain how we can find a virtual image representation when the intersection of the two axes is matched to the image center. We analyze the perspective distortions when flattening a scene which is mapped on a SUGC. We evaluate the lower and the upper bounds of the necessary number of views in order to represent the entire scene from a SUGC, by considering the distortions produced by perspective projection. A region matching based mosaicing method is proposed to be applied on the flattened images in order to obtain the complete scene. The mosaiced scene is visualized on a new synthetic surface by a mapping procedure. The proposed algorithm is used for the representation of mural paintings located on SUGCs with closed cross-sections (circles for columns), or opened cross-sections (ellipses or parabolas for vaults). (C) 2001 Pattern Recognition Society. Published by Elsevier Science Ltd. All rights reserved

Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bors, E. K., Herrera, S., Morris, J. A., Jr., & Shank, T. M. Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure. Ecology and Evolution, 9(6), (2019):3306-3320, doi:10.1002/ece3.4952.Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo‐Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme‐associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D‐loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between‐basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.We thank the many participants of the Gulf and Caribbean Fisheries Institute for providing lionfish samples from around the Caribbean region, as well as Dr. Bernard Castillo at the University of the Virgin Islands and Kristian Rogers at the Biscayne Bay National Park. We would like to acknowledge Alex Bogdanoff at NOAA, Beaufort NC, for assistance with sample acquisition; Camrin Braun at WHOI, for assistance with the calculation of oceanic distances between sites; Dr. Tom Schultz at Duke Marine Lab and Dr. Margaret Hunter at USGS for discussions concerning ongoing population genetic projects; and Jack Cook at the WHOI Graphics department for his assistance in generating maps of the study area. We would like to extend a special thank you to Dr. John Wakeley of Harvard University for assistance in the interpretation of data. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374. Sequencing funding was provided in part by the PADI Foundation Grant No. 14904. Additional research support was provided by the Woods Hole Oceanographic Institution (WHOI) Ocean Ventures Fund, the Coastal Ocean Institute at WHOI, the National Science Foundation (OCE‐1131620 to TMS), and the James Education Fund for Ocean Exploration within the Ocean Exploration Institute at WHOI. Publication of this paper was supported, in part, by the Henry Mastin Graduate Student Fund administered by the Oregon State University Department of Fisheries and Wildlife. Finally, we sincerely thank the reviewers and editors who helped to strengthen this manuscript

A provenance task abstraction framework

Visual analytics tools integrate provenance recording to externalize analytic processes or user insights. Provenance can be captured on varying levels of detail, and in turn activities can be characterized from different granularities. However, current approaches do not support inferring activities that can only be characterized across multiple levels of provenance. We propose a task abstraction framework that consists of a three stage approach, composed of (1) initializing a provenance task hierarchy, (2) parsing the provenance hierarchy by using an abstraction mapping mechanism, and (3) leveraging the task hierarchy in an analytical tool. Furthermore, we identify implications to accommodate iterative refinement, context, variability, and uncertainty during all stages of the framework. A use case describes exemplifies our abstraction framework, demonstrating how context can influence the provenance hierarchy to support analysis. The paper concludes with an agenda, raising and discussing challenges that need to be considered for successfully implementing such a framework

A novel approach to task abstraction to make better sense of provenance data

Working Group Report in 'Provenance and Logging for Sense Making' report from Dagstuhl Seminar 18462: Provenance and Logging for Sense Making, Dagstuhl Reports, Volume 8, Issue 1

In vitro embryo rescue and plant regeneration following self-pollination with irradiated pollen in cassava (Manihot esculenta Crantz)

Cassava is a highly heterozygous species; hence, current methods used in classical cassava breedingcannot match the urgent need to high yielding varieties. Recently, progress was made through androgenesis and gynogenesis as pathways for raising doubled cassava haploid lines to overcome problems associated with cassava’s inherent reproductive biology, but these efforts were limited (nocandidate cassava plantlets were regenerated). For the first time, this study shows that pollen irradiation coupled with self-pollination and embryo rescue regenerated 62 candidate cassava plantlets. Plants of an elite cassava variety, Nase14, served as a mother plant and as the pollen donor for the irradiation. Irradiation dosages of 50 to 250 Gray studied across five pollination events and 300 or 500 Gray in one pollination event caused a reduction in pollen germination up to 67.0%. By 15 days after pollination (DAP) with irradiated pollen, up to 89.7% of the pollinated flowers had aborted. By embryo rescue time (42 DAP), significant differences were observed in number of fruits, seeds and embryos generated, with the non-irradiated pollen treatments having significantly higher numbers. Sixteen (16) heterozygous SSR markers in the parent and ploidy analysis showed that none of the regenerated plants was haploid or homozygous. However, the plantlets resulting from pollination with non-irradiated pollen had 56.2% homozygous loci, while progeny derived from irradiated treatments had frequencies of homozygous loci between 28.1 and 55.0%. This is the first time to use irradiated pollen in cassava as a pathway to generate candidate plantlets as an initial step in double haploid production.Key words: Cassava, doubled haploids, embryo rescue, plant regeneration, pollen germination, pollenirradiation

Tachyonic preheating using 2PI-1/N dynamics and the classical approximation

We study the process of tachyonic preheating using approximative quantum equations of motion derived from the 2PI effective action. The O(N) scalar (Higgs) field is assumed to experience a fast quench which is represented by an instantaneous flip of the sign of the mass parameter. The equations of motion are solved numerically on the lattice, and the Hartree and 1/N-NLO approximations are compared to the classical approximation. Classical dynamics is expected to be valid, since the occupation numbers can rise to large values during tachyonic preheating. We find that the classical approximation performs excellently at short and intermediate times, even for couplings in the larger region currently allowed for the SM Higgs. This is reassuring, since all previous numerical studies of tachyonic preheating and baryogenesis during tachyonic preheating have used classical dynamics. We also compare different initializations for the classical simulations.Comment: 32 pages, 21 figures. Published version: Some details added, section added, references added, conclusions unchange

Komplex molekuláris genetikai vizsgálati algoritmus myeloproliferativ neoplasiák diagnosztikájában

Introduction: Mutations in Janus kinase 2, calreticulin and thrombopoietin receptor genes have been identified in the genetic background of Philadelphia chromosome negative, "classic" myeloproliferative neoplasms. Aim: The aim of the authors was to identify driver mutations in a large myeloproliferative cohort of 949 patients. Method: A complex array of molecular techniques (qualitative and quantitative allele-specific polymerase chain reactions, fragment analyzes, high resolution melting and Sanger sequencing) was applied. Results: All 354 patients with polycythemia vera carried Janus kinase 2 mutations (V617F 98.6%, exon 12: 1.4%). In essential thrombocythemia (n = 468), the frequency of V617F was 61.3% (n = 287), that of calreticulin 25.2% (n = 118), and that of thrombopoietin receptor mutations 2.1% (n = 10), while 11.3% (n = 53) were triple-negative. Similar distribution was observed in primary myelofibrosis (n = 127): 58.3% (n = 74) V617F, 23.6% (n = 30) calreticulin, 6.3% (n = 8) thrombopoietin receptor mutation positive and 11.8% (n = 15) triple-negative. Conclusions: The recent discovery of calreticulin gene mutations led to definite molecular diagnostics in around 90% of clonal myeloproliferative cases. Orv. Hetil., 2014, 155(52), 2074-2081

Distinct clinical characteristics of myeloproliferative neoplasms with calreticulin mutations

Somatic insertions/deletions in the calreticulin gene have recently been discovered to be causative alterations in myeloproliferative neoplasms. A combination of qualitative and quantitative allele-specific polymerase chain reaction, fragment-sizing, high resolution melting and Sanger-sequencing was applied for the detection of three driver mutations (in Janus kinase 2, calreticulin and myeloproliferative leukemia virus oncogene genes) in 289 cases of essential thrombocythemia and 99 cases of primary myelofibrosis. In essential thrombocythemia, 154 (53%) Janus kinase 2 V617F, 96 (33%) calreticulin, 9 (3%) myeloproliferative leukemia virus oncogene gene mutation-positive and 30 triple-negative (11%) cases were identified, while in primary myelofibrosis 56 (57%) Janus kinase 2 V617F, 25 (25%) calreticulin, 7 (7%) myeloproliferative leukemia virus oncogene gene mutation-positive and 11 (11%) triple-negative cases were identified. Patients positive for the calreticulin mutation were younger and had higher platelet counts compared to Janus kinase 2 mutation-positive counterparts. Calreticulin mutation-positive patients with essential thrombocythemia showed a lower risk of developing venous thrombosis, but no difference in overall survival. Calreticulin mutation-positive patients with primary myelofibrosis had a better overall survival compared to that of the Janus kinase 2 mutation-positive (P=0.04) or triple-negative cases (P=0.01). Type 2 calreticulin mutation occurred more frequently in essential thrombocythemia than in primary myelofibrosis (P=0.049). In essential thrombocythemia, the calreticulin mutational load was higher than the Janus kinase 2 mutational load (P<0.001), and increased gradually in advanced stages. Calreticulin mutational load influenced blood counts even at the time point of diagnosis in essential thrombocythemia. We confirm that calreticulin mutation is associated with distinct clinical characteristics and explored relationships between mutation type, load and clinical outcome