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

Distribution of mosquitoes in the South East of Argentina and first report on the analysis based on 18S rDNA and COI sequences

Although Mar del Plata is the most important city on the Atlantic coast of Argentina, mosquitoes inhabiting such area are almost uncharacterized. To increase our knowledge in their distribution, we sampled specimens of natural populations. After the morphological identification based on taxonomic keys, sequences of DNA from small ribosomal subunit (18S rDNA) and cytochrome c oxidase I (COI) genes were obtained from native species and the phylogenetic analysis of these sequences were done. Fourteen species from the genera Uranotaenia, Culex, Ochlerotatus and Psorophora were found and identified. Our 18S rDNA and COI-based analysis indicates the relationships among groups at the supra-species level in concordance with mosquito taxonomy. The introduction and spread of vectors and diseases carried by them are not known in Mar del Plata, but some of the species found in this study were reported as pathogen vectors

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

Effect of high-pressure carbon dioxide combined with modified atmosphere packaging on the quality of fresh-cut squash during storage

The study evaluated the application of a novel high-pressure microbial inactivation method combining dense carbon dioxide with modified atmosphere packaging on organic fresh-cut squash (Cucurbita moschata). Approximately 4 g or 32 g of squash was packed in plastic pouches filled with CO2 to test two different gas-to-product ratios and treated with the high-pressure method at previously optimized process conditions (45 °C, 6.0 MPa and 40 min). The products were then stored for 21 days at 4 °C and assessed for enzymatic activity, product quality, sugar content, bioaccessibility (polyphenols, DPPH antioxidant activity, and carotenoids), and sensory acceptance, with products packed in air and CO2 serving as controls. The high-pressure treatment effectively inactivated inoculated E. coli to undetectable levels (inactivation >3.63 ± 0.53 Log CFU/g) and reduced the activity of the browning-responsible enzymes up to 50 %. During the shelf life, treated samples exhibited significantly higher scavenging activity for DPPH, ABTS, OH, O2−, and NO compared to non-treated samples, with minor exceptions at a high gas-to-product ratio. Additionally, treated samples showed increased levels of glucose and fructose and a comparable or higher bioaccessibility of antioxidants with respect to the products packed in air or in CO2. Sensory evaluation indicated that the treatment enhanced color and smell appreciation among panelists, demonstrating the potential of this method to improve both safety and quality of fresh-cut squash

Subnormothermic Oxygenated Machine Perfusion (24 h) in DCD Kidney Transplantation

Background: Ex vivo kidney perfusion is an evolving platform that demonstrates promise in preserving and rehabilitating the kidney grafts. Despite this, there is little consensus on the optimal perfusion conditions. Hypothermic perfusion offers limited functional assessment, whereas normothermic perfusion requires a more complex mechanical system and perfusate. Subnormothermic machine perfusion (SNMP) has the potential to combine the advantages of both approaches but has undergone limited investigation. Therefore, the present study sought to determine the suitability of SNMP for extended kidney preservation. Methods: SNMP at 22-25 °C was performed on a portable device for 24 h with porcine kidneys. Graft assessment included measurement of mechanical parameters and biochemical analysis of the perfusate using point-of-care tests. To investigate the viability of kidneys preserved by SNMP, porcine kidney autotransplants were performed in a donation after circulatory death (DCD) model. SNMP was also compared with static cold storage (SCS). Finally, follow-up experiments were conducted in a subset of human kidneys to test the translational significance of findings in porcine kidneys. Results: In the perfusion-only cohort, porcine kidneys all displayed successful perfusion for 24 h by SNMP, evidenced by stable mechanical parameters and biological markers of graft function. Furthermore, in the transplant cohort, DCD grafts with 30 min of warm ischemic injury demonstrated superior posttransplant graft function when preserved by SNMP in comparison with SCS. Finally, human kidneys that underwent 24-h perfusion exhibited stable functional and biological parameters consistent with observations in porcine organs. Conclusions: These observations demonstrate the suitability and cross-species generalizability of subnormothermic machine perfusion to maintain stable kidney perfusion and provide foundational evidence for improved posttransplant graft function of DCD kidneys after SNMP compared with SCS

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

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