DeepOrientation: convolutional neural network for fringe pattern orientation map estimation

Fringe pattern based measurement techniques are the state-of-the-art in full-field optical metrology. They are crucial both in macroscale, e.g., fringe projection profilometry, and microscale, e.g., label-free quantitative phase microscopy. Accurate estimation of the local fringe orientation map can significantly facilitate the measurement process on various ways, e.g., fringe filtering (denoising), fringe pattern boundary padding, fringe skeletoning (contouring/following/tracking), local fringe spatial frequency (fringe period) estimation and fringe pattern phase demodulation. Considering all of that the accurate, robust and preferably automatic estimation of local fringe orientation map is of high importance. In this paper we propose novel numerical solution for local fringe orientation map estimation based on convolutional neural network and deep learning called DeepOrientation. Numerical simulations and experimental results corroborate the effectiveness of the proposed DeepOrientation comparing it with the representative of the classical approach to orientation estimation called combined plane fitting/gradient method. The example proving the effectiveness of DeepOrientation in fringe pattern analysis, which we present in this paper is the application of DeepOrientation for guiding the phase demodulation process in Hilbert spiral transform. In particular, living HeLa cells quantitative phase imaging outcomes verify the method as an important asset in label-free microscopy

Single-shot fringe pattern phase retrieval using improved period-guided bidimensional empirical mode decomposition and Hilbert transform

Fringe pattern analysis is the central aspect of numerous optical measurement methods, e.g., interferometry, fringe projection, digital holography, quantitative phase microscopy. Experimental fringe patterns always contain significant features originating from fluctuating environment, optical system and illumination quality, and the sample itself that severely affect analysis outcome. Before the stage of phase retrieval (information decoding) interferogram needs proper filtering, which minimizes the impact of mentioned issues. In this paper we propose fully automatic and adaptive fringe pattern pre-processing technique - improved period guided bidimensional empirical mode decomposition algorithm (iPGBEMD). It is based on our previous work about PGBEMD which eliminated the mode-mixing phenomenon and made the empirical mode decomposition fully adaptive. In present work we overcame key problems of original PGBEMD – we have considerably increased algorithm’s application range and shortened computation time several-fold. We proposed three solutions to the problem of erroneous decomposition for very low fringe amplitude images, which limited original PGBEMD significantly and we have chosen the best one among them after comprehensive analysis. Several acceleration methods were also proposed and merged to ensure the best results. We combined our improved pre-processing algorithm with the Hilbert Spiral Transform to receive complete, consistent, and versatile fringe pattern analysis path. Quality and effectiveness evaluation, in comparison with selected reference methods, is provided using numerical simulations and experimental fringe data

Revisiting predictive biomarkers of musculoskeletal injury in thoroughbred racehorses: longitudinal study in polish population

Abstract Background High prevalence of musculoskeletal disorders in racehorses and its impact on horse welfare and racing economics call for improved measures of injury diagnosis and prevention. Serum biomarkers of bone and cartilage metabolism have previously shown promise in prediction of musculoskeletal injuries in horses. This study aimed to re-evaluate usability of the predictive serum biomarkers identified in North American Thoroughbred racehorses in a geographically distinct group of Polish Thoroughbreds. Results Serum concentrations of bone and cartilage biomarkers: osteocalcin, c-terminal telopeptide of type I collagen, total glycosaminoglycans (GAG), chondroitin sulfate epitope and c-propeptide of type II procollagen (CPII) were evaluated in the beginning and the next 3 months of one racing season in a cohort of twenty-six 2-year-old Polish racehorses. Exit criteria were diagnosis of musculoskeletal injury, leading to > 5 days off training (n = 8), or completion of 3 study months with no training interruptions (n = 18). Normalized results and matching archival data from 35 2-year-old North American racehorses was used for logistic regression analysis to identify universal predictors of injury. Mean GAG and CPII levels were lower in injured group comparing to control, which is consistent with previous findings in racehorses. These biomarkers were also identified as predictors of injury in the mixed population model. Population origin had no significant effect on predictive value of evaluated biomarkers (Wald test p = 0.137). Decreased osteocalcin and increased c-terminal telopeptide of type I collagen levels in injured horses comparing to controls were specific for Polish population and signalized disruption in bone turnover homeostasis. Conclusions Changes in serum GAG and CPII in racehorses at risk of injury appear to be similar across distinct populations while dynamics of serum bone marker is more population-specific

Integrative Taxonomy for Continental-Scale Terrestrial Insect Observations

Although 21st century ecology uses unprecedented technology at the largest spatio-temporal scales in history, the data remain reliant on sound taxonomic practices that derive from 18th century science. The importance of accurate species identifications has been assessed repeatedly and in instances where inappropriate assignments have been made there have been costly consequences. The National Ecological Observatory Network (NEON) will use a standardized system based upon an integrative taxonomic foundation to conduct observations of the focal terrestrial insect taxa, ground beetles and mosquitoes, at the continental scale for a 30 year monitoring program. The use of molecular data for continental-scale, multi-decadal research conducted by a geographically widely distributed set of researchers has not been evaluated until this point. The current paper addresses the development of a reference library for verifying species identifications at NEON and the key ways in which this resource will enhance a variety of user communities

Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

Background: DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings: A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance: Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies

Serum iron, ferritin, transferrin and haptoglobin concentration variations during repeated show jumping competition in horse

Modifications of the iron profile in athlete horses during two international three star (***) show jumping competitions performed in two consecutive weekends were evaluated. Serum iron, ferritin, transferrin, and haptoglobin were assessed in 12 well-trained Italian Saddle horses. Blood samplings were performed before the first day of competition (R1), within 10 min from the end of each competition (J1, J2) and on the day after competition (R2). The same plan was followed during the second weekend (J3, J4 and R3). One-way repeated measures analysis of variance (ANOVA) was applied on obtained data, and a significant effect of exercise (P < 0.05) on all studied indices was found. These results suggest that serum iron, transferrin, ferritin and haptoglobin are responsive to intense exercise and could be considered important indicators that may give important information about the horse’s performance

DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors

<p>Abstract</p> <p>Background</p> <p>Mosquitoes belonging to the Albitarsis Group (<it>Anopheles</it>: <it>Nyssorhynchus</it>) are of importance as malaria vectors across the Neotropics. The Group currently comprises six known species, and recent studies have indicated further hidden biodiversity within the Group. DNA barcoding has been proposed as a highly useful tool for species recognition, although its discriminatory utility has not been verified in closely related taxa across a wide geographic distribution.</p> <p>Methods</p> <p>DNA barcodes (658 bp of the mtDNA <it>Cytochrome c Oxidase </it>- <it>COI</it>) were generated for 565 <it>An. albitarsis </it>s.l. collected in Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela over the past twenty years, including specimens from type series and type localities. Here we test the utility of currently advocated barcoding methodologies, including the Kimura-two-parameter distance model (K2P) and Neighbor-joining analysis (NJ), for determining species delineation within mosquitoes of the Neotropical Albitarsis Group of malaria vectors (<it>Anopheles</it>: <it>Nyssorhynchus</it>), and compare results with Bayesian analysis.</p> <p>Results</p> <p>Species delineation through barcoding analysis and Bayesian phylogenetic analysis, fully concur. Analysis of 565 sequences (302 unique haplotypes) resolved nine NJ tree clusters, with less than 2% intra-node variation. Mean intra-specific variation (K2P) was 0.009 (range 0.002 - 0.014), whereas mean inter-specific divergence were several-fold higher at 0.041 (0.020 - 0.056), supporting the reported "barcoding gap". These results show full support for separate species status of the six known species in the Albitarsis Group (<it>An. albitarsis </it>s.s., <it>An. albitarsis </it>F, <it>An. deaneorum</it>, <it>An. janconnae</it>, <it>An. marajoara </it>and <it>An. oryzalimnetes</it>), and also support species level status for two previously detected lineages - <it>An. albitarsis </it>G &<it>An. albitarsis </it>I (designated herein). In addition, we highlight the presence of a unique mitochondrial lineage close to <it>An. deaneorum </it>and <it>An. marajoara </it>(<it>An. albitarsis </it>H) from Rondônia and Mato Grosso in southwestern Brazil. Further integrated studies are required to confirm the status of this lineage.</p> <p>Conclusions</p> <p>DNA barcoding provides a reliable means of identifying both known and undiscovered biodiversity within the closely related taxa of the Albitarsis Group. We advocate its usage in future studies to elucidate the vector competence and respective distributions of all eight species in the Albitarsis Group and the novel mitochondrial lineage (<it>An. albitarsis </it>H) recovered in this study.</p

A Comprehensive DNA Barcode Library for the Looper Moths (Lepidoptera: Geometridae) of British Columbia, Canada

The construction of comprehensive reference libraries is essential to foster the development of DNA barcoding as a tool for monitoring biodiversity and detecting invasive species. The looper moths of British Columbia (BC), Canada present a challenging case for species discrimination via DNA barcoding due to their considerable diversity and limited taxonomic maturity.By analyzing specimens held in national and regional natural history collections, we assemble barcode records from representatives of 400 species from BC and surrounding provinces, territories and states. Sequence variation in the barcode region unambiguously discriminates over 93% of these 400 geometrid species. However, a final estimate of resolution success awaits detailed taxonomic analysis of 48 species where patterns of barcode variation suggest cases of cryptic species, unrecognized synonymy as well as young species.A catalog of these taxa meriting further taxonomic investigation is presented as well as the supplemental information needed to facilitate these investigations