Browsing by Subject "SHAPE"

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  • Turc, L.; Fontaine, D.; Savoini, P.; Hietala, H.; Kilpua, E. K. J. (2013)
  • Bleyer, Ismael Rodrigo; Lybeck, Lasse; Auvinen, Harri; Airaksinen, Manu; Alku, Paavo; Siltanen, Samuli (2017)
    A new method is proposed for solving the glottal inverse filtering (GIF) problem. The goal of GIF is to separate an acoustical speech signal into two parts: the glottal airflow excitation and the vocal tract filter. To recover such information one has to deal with a blind deconvolution problem. This ill-posed inverse problem is solved under a deterministic setting, considering unknowns on both sides of the underlying operator equation. A stable reconstruction is obtained using a double regularization strategy, alternating between fixing either the glottal source signal or the vocal tract filter. This enables not only splitting the nonlinear and nonconvex problem into two linear and convex problems, but also allows the use of the best parameters and constraints to recover each variable at a time. This new technique, called alternating minimization glottal inverse filtering (AM-GIF), is compared with two other approaches: Markov chain Monte Carlo glottal inverse filtering (MCMC-GIF), and iterative adaptive inverse filtering (IAIF), using synthetic speech signals. The recent MCMC-GIF has good reconstruction quality but high computational cost. The state-of-the-art IAIF method is computationally fast but its accuracy deteriorates, particularly for speech signals of high fundamental frequency (F0). The results show the competitive performance of the new method: With high F0, the reconstruction quality is better than that of IAIF and close to MCMC-GIF while reducing the computational complexity by two orders of magnitude.
  • Muinonen, K.; Torppa, J.; Wang, X-B; Cellino, A.; Penttilä, A. (2020)
    Context. We assess statistical inversion of asteroid rotation periods, pole orientations, shapes, and phase curve parameters from photometric lightcurve observations, here sparse data from the ESA Gaia space mission (Data Release 2) or dense and sparse data from ground-based observing programs.Aims. Assuming general convex shapes, we develop inverse methods for characterizing the Bayesian a posteriori probability density of the parameters (unknowns). We consider both random and systematic uncertainties (errors) in the observations, and assign weights to the observations with the help of Bayesian a priori probability densities.Methods. For general convex shapes comprising large numbers of parameters, we developed a Markov-chain Monte Carlo sampler (MCMC) with a novel proposal probability density function based on the simulation of virtual observations giving rise to virtual least-squares solutions. We utilized these least-squares solutions to construct a proposal probability density for MCMC sampling. For inverse methods involving triaxial ellipsoids, we update the uncertainty model for the observations.Results. We demonstrate the utilization of the inverse methods for three asteroids with Gaia photometry from Data Release 2: (21) Lutetia, (26) Proserpina, and (585) Bilkis. First, we validated the convex inverse methods using the combined ground-based and Gaia data for Lutetia, arriving at rotation and shape models in agreement with those derived with the help of Rosetta space mission data. Second, we applied the convex inverse methods to Proserpina and Bilkis, illustrating the potential of the Gaia photometry for setting constraints on asteroid light scattering as a function of the phase angle (the Sun-object-observer angle). Third, with the help of triaxial ellipsoid inversion as applied to Gaia photometry only, we provide additional proof that the absolute Gaia photometry alone can yield meaningful photometric slope parameters. Fourth, for (585) Bilkis, we report, with 1-sigma uncertainties, a refined rotation period of (8.5750559 0.0000026) h, pole longitude of 320.6 degrees +/- 1.2 degrees, pole latitude of - 25.6 degrees +/- 1.7 degrees, and the first shape model and its uncertainties from convex inversion.Conclusions. We conclude that the inverse methods provide realistic uncertainty estimators for the lightcurve inversion problem and that the Gaia photometry can provide an asteroid taxonomy based on the phase curves.
  • Macri, Simone; Savriama, Yoland; Khan, Imran; Di-Poi, Nicolas (2019)
    Ecomorphological studies evaluating the impact of environmental and biological factors on the brain have so far focused on morphology or size measurements, and the ecological relevance of potential multi-level variations in brain architecture remains unclear in vertebrates. Here, we exploit the extraordinary ecomorphological diversity of squamates to assess brain phenotypic diversification with respect to locomotor specialization, by integrating single-cell distribution and transcriptomic data along with geometric morphometric, phylogenetic, and volumetric analysis of high-definition 3D models. We reveal significant changes in cerebellar shape and size as well as alternative spatial layouts of cortical neurons and dynamic gene expression that all correlate with locomotor behaviours. These findings show that locomotor mode is a strong predictor of cerebellar structure and pattern, suggesting that major behavioural transitions in squamates are evolutionarily correlated with mosaic brain changes. Furthermore, our study amplifies the concept of 'cerebrotype', initially proposed for vertebrate brain proportions, towards additional shape characters.
  • Räsänen, Aleksi; Juutinen, Sari; Tuittila, Eeva-Stiina; Aurela, Mika; Virtanen, Tarmo (2019)
  • Snäll, Johanna; Narjus-Sterba, M.; Toivari, M.; Wilkman, T.; Thoren, H. (2019)
    PurposeThe aim of this study was to investigate the relationship between intraorbital volume change caused by orbital fracture and globe malposition (GMP) in blow-out fracture patients undergoing surgery and to clarify the significance of different radiologically detected predictors associated with GMP.Patients and methodsA 6-month prospective follow-up study of unilateral isolated orbital fractures was designed and implemented. The main outcome variable was GMP (present or absent); the secondary outcome was orientation of GMP (horizontal or vertical). The primary predictor variable was postoperative orbital volume difference determined as the difference between the fractured and non-fractured orbit (measured in milliliter and analyzed in milliliter and percentages). The explanatory variables were gender, age, treatment delay from trauma to surgery, fracture site, horizontal depth of the fracture, fracture area, maximum vertical dislocation of the fracture, and preoperative volume difference.ResultsA total of 15 patients fulfilled the inclusion criteria and were followed for 6months from a larger cohort. GMP was detected in 6/15 patients (40.0%). GMP was more often present in large (2.5cm(2)) fractures (55.6%), in combined orbital fractures (50.0%), and in fractures with preoperative volume difference 2.5ml (62.5%) regardless of the postoperative volume correction. Postoperatively, patients with and without GMP displayed overcorrection of orbital volume; 4.15% corresponded to 1.15ml (with GMP) and 7.6% corresponded to 1.9ml (without GMP).ConclusionGMP was present in large and combined orbital fractures. Clinically detectable postoperative GMP occurred despite satisfactory orbital reconstruction and overcorrection. Mild GMP, however, is not significant for the patient.
  • Ridolfo, Roxane; Tavakoli, Shirin; Junnuthula, Vijayabhaskarreddy; Williams, David S.; Urtti, Arto; van Hest, Jan C. M. (2021)
    Nanoparticle morphology (size, shape, and composition) and surface chemistry are the determining factors underpinning the efficacy of such materials in therapeutic applications. The size, shape, and surface chemistry of a nanoparticle can strongly influence key properties such as interactions with diverse biological fluids and interfaces and, in turn, impact the delivery of bioactive cargo, modulating therapeutic performance. This is exemplified in ocular drug delivery, where potential therapeutics must navigate complex biological media such as the gel-like vitreal fluid and the retina. Biodegradable block copolymer amphiphiles are a robust tool for the engineering of various types of self-assembled nanoparticles with diverse morphologies ranging from spherical and tubular polymersomes to spherical and worm-like micelles. Here, we explore the effect of morphological features such as shape and surface chemistry upon the interactions of a series of copolymer nanoparticles with retinal (ARPE-19) cells and the release of a low solubility drug (dexamethasone) that is currently used in ocular therapy and study their diffusion in vitreous using ex vivo eyes. We demonstrate that both aspect ratio and surface chemistry of nanoparticles will influence their performance in terms of cell uptake, drug release, and diffusion with high aspect ratio shapes demonstrating enhanced properties in relation to their spherical counterparts.
  • Zhao, Junlei; Cao, Lu; Palmer, Richard E.; Nordlund, Kai; Djurabekova, Flyura (2017)
    In this paper, we study the mechanisms of growth of Ag nanoclusters in a solid Ar matrix and the emission of these nanoclusters from the matrix by a combination of experimental and theoretical methods. The molecular dynamics simulations show that the cluster growth mechanism can be described as "thermal spike-enhanced clustering" in multiple sequential ion impact events. We further show that experimentally observed large sputtered metal clusters cannot be formed by direct sputtering of Ag mixed in the Ar. Instead, we describe the mechanism of emission of the metal nanocluster that, at first, is formed in the cryogenic matrix due to multiple ion impacts, and then is emitted as a result of the simultaneous effects of interface boiling and spring force. We also develop an analytical model describing this size-dependent cluster emission. The model bridges the atomistic simulations and experimental time and length scales, and allows increasing the controllability of fast generation of nanoclusters in experiments with a high production rate.
  • Adamo, Martino; Mammola, Stefano; Noble, Virgile; Mucciarelli, Marco (2020)
    We studied the ecology, distribution, and phylogeography of Tephroseris balbisiana, a rare plant whose range is centered to the South-Western Alps. Our aim was to assess the extent of intraspecific variability within the nominal species and the conservation status of isolated populations. We studied genetic diversity across the whole species range. We analyzed leaf traits, which are distinctive morphological characters within the Tephroseris genus. A clear pattern of genetic variation was found among populations of T. balbisiana, which clustered according to their geographic position. On the contrary, there was a strong overlap in the morphological space of individuals across the species' range, with few peripheral populations diverging in their leaf morphology. Studying habitat suitability by means of species distribution models, we observed that T. balbisiana range is primarily explained by solar radiation and precipitation seasonality. Environmental requirements could explain the genetic and morphological uniformity of T. balbisiana in its core distribution area and justify genetic, morphological, and ecological divergences found among the isolated populations of the Apennines. Our findings emphasize the need to account for the whole diversity of a species, comprising peripheral populations, in order to better estimate its status and to prioritize areas for its conservation.
  • Prevost, Coline; Zhao, Hongxia; Manzi, John; Lemichez, Emmanuel; Lappalainen, Pekka; Callan-Jones, Andrew; Bassereau, Patricia (2015)
    BAR domain proteins contribute to membrane deformation in diverse cellular processes. The inverted-BAR (I-BAR) protein IRSp53, for instance, is found on the inner leaflet of the tubular membrane of filopodia; however its role in the formation of these structures is incompletely understood. Here we develop an original assay in which proteins are encapsulated in giant unilamellar vesicles connected to membrane nanotubes. Our results demonstrate that I-BAR dimers sense negative membrane curvature. Experiment and theory reveal that the I-BAR displays a non-monotonic sorting with curvature, and expands the tube at high imposed tension while constricting it at low tension. Strikingly, at low protein density and tension, protein-rich domains appear along the tube. This peculiar behaviour is due to the shallow intrinsic curvature of I-BAR dimers. It allows constriction of weakly curved membranes coupled to local protein enrichment at biologically relevant conditions. This might explain how IRSp53 contributes in vivo to the initiation of filopodia.
  • Bainbridge, Hannah E.; Brien, Melanie N.; Morochz, Carlos; Salazar, Patricio A.; Rastas, Pasi; Nadeau, Nicola J. (2020)
    Mimetic systems allow us to address the question of whether the same genes control similar phenotypes in different species. Although widespread parallels have been found for major effect loci, much less is known about genes that control quantitative trait variation. In this study, we identify and compare the loci that control subtle changes in the size and shape of forewing pattern elements in twoHeliconiusbutterfly co-mimics. We use quantitative trait locus (QTL) analysis with a multivariate phenotyping approach to map the variation in red pattern elements across the whole forewing surface ofHeliconius eratoandHeliconius melpomene. These results are compared with a QTL analysis of univariate trait changes, and show that our resolution for identifying small effect loci is somewhat improved with the multivariate approach, but also that different loci are detected with these different approaches. QTL likely corresponding to the known patterning geneoptixwere found in both species but otherwise, a remarkably low level of genetic parallelism was found. This lack of similarity indicates that the genetic basis of convergent traits may not be as predictable as assumed from studies that focus solely on Mendelian traits.
  • Ludtka, Christopher; Schwan, Stefan; Friedmann, Andrea; Brehm, Walther; Wiesner, Ingo; Goehre, Felix (2017)
    The primary goal of this study is to clearly define and evaluate new intervertebral disc height parameters in analysing the morphological pathology of disc degeneration for application in damage model and regeneration therapy development, as well as applying traditional variables to 3-D characterization methods. A posterolateral surgical approach was used to induce disc degeneration in an ovine model. At 12-months post-operation, sheep vertebral segments were removed and characterized using micro-CT to evaluate disc height parameters in regard to injury localization. Statistically significant differences between the disc height loss of the left and right side of the disc, consistent with the lateral surgical approach used were seen using the modified average disc height method by Dabbs et al. However, convexity index and the newly proposed Cross Tilt Index did not conclusively demonstrate a difference. Two-dimensional morphological evaluations can be applied in 3-D to provide a more complete picture of disc height loss for injury models. New 3-D parameters that are tailored to the type of surgical approach used should be investigated, with the 9-point system described herein providing a useful basis for derived values. Additionally, the surgical approach chosen when artificially injuring the disc can result in asymmetrical degeneration, as indicated by uneven disc height loss.
  • Matamoro-Vidal, Alexis; Huang, Yunxian; Salazar-Ciudad, Isaac; Shimmi, Osamu; Houle, David (2018)
    Quantitative genetic variation in morphology is pervasive in all species and is the basis for the evolution of differences among species. The measurement of morphological form in adults is now beginning to be combined with comparable measurements of form during development. Here we compare the shape of the developing wing to its adult form in a holometabolous insect, Drosophila melanogaster. We used protein expression patterns to measure shape in the developing precursors of the final adult wing. Three developmental stages were studied: late larval third instar, post-pupariation and in the adult fly. We studied wild-type animals in addition to mutants of two genes (shf and ds) that have known effects on adult wing shape and size. Despite experimental noise related to the difficulty of comparing developing structures, we found consistent differences in wing shape and size at each developmental stage between genotypes. Quantitative comparisons of variation arising at different developmental stages with the variation in the final structure enable us to determine when variation arises, and to generate hypotheses about the causes of that variation. In addition we provide linear rules allowing us to link wing morphology in the larva, with wing morphology in the pupa. Our approach provides a framework to analyze quantitative morphological variation in the developing fly wing. This framework should help to characterize the natural variation of the larval and pupal wing shape, and to measure the contribution of the processes occurring during these developmental stages to the natural variation in adult wing morphology.
  • Li, Honghong; Penttinen, Petri; Mikkonen, Anu; Stoddard, Frederick L.; Lindstrom, Kristina (2020)
    Pastures are an important part of crop and food systems in cold climates. Understanding how fertilization and plant species affect soil bacterial community diversity and composition is the key for understanding the role of soil bacteria in sustainable agriculture. To study the response of soil bacteria to different fertilization and cropping managements, a 3-year (2013-2015) field study was established. In the split-plot design, fertilizer treatment (unfertilized control, organic fertilizer, and synthetic fertilizer) was the main plot factor, and plant treatment [clear fallow, red clover (Trifolium pratense), timothy (Phleum pratense), and a mixture of red clover and timothy] was the sub-plot factor. Soil bacterial community diversity and composition, soil properties, and crop growth were investigated through two growing seasons in 2014 and 2015, with different nitrogen input levels. The community diversity measures (richness, Shannon diversity, and Shannon evenness) and composition changed over time (P<0.05) and at different time scales. The community diversity was lower in 2014 than in 2015. The temporal differences were greater than the differences between treatments. The overall correlations of Shannon diversity to soil pH, NO3-, NH4+, and surplus nitrogen were positive and that of bacterial richness to crop dry matter yield was negative (P<0.05). The major differences in diversity and community composition were found between fallow and planted treatments and between organic and synthetic fertilizer treatments. The differences between the planted plots were restricted to individual operational taxonomic units (OTUs). Soil moisture, total carbon content, and total nitrogen content correlated consistently with the community composition (P<0.05). Compared to the unfertilized control, the nitrogen fertilizer loading enhanced the temporal change of community composition in pure timothy and in the mixture more than that in red clover, which further emphasizes the complexity of interactions between fertilization and cropping treatments on soil bacteria.
  • Werner, Maike; Blanquer, Sebastien B. G.; Haimi, Suvi; Korus, Gabriela; Dunlop, John W. C.; Duda, Georg N.; Grijpma, Dirk. W.; Petersen, Ansgar (2017)
    Signals from the microenvironment around a cell are known to influence cell behavior. Material properties, such as biochemical composition and substrate stiffness, are today accepted as significant regulators of stem cell fate. The knowledge of how cell behavior is influenced by 3D geometric cues is, however, strongly limited despite its potential relevance for the understanding of tissue regenerative processes and the design of biomaterials. Here, the role of surface curvature on the migratory and differentiation behavior of human mesenchymal stem cells (hMSCs) has been investigated on 3D surfaces with well-defined geometric features produced by stereolithography. Time lapse microscopy reveals a significant increase of cell migration speed on concave spherical compared to convex spherical structures and flat surfaces resulting from an upward-lift of the cell body due to cytoskeletal forces. On convex surfaces, cytoskeletal forces lead to substantial nuclear deformation, increase lamin-A levels and promote osteogenic differentiation. The findings of this study demonstrate a so far missing link between 3D surface curvature and hMSC behavior. This will not only help to better understand the role of extracellular matrix architecture in health and disease but also give new insights in how 3D geometries can be used as a cell-instructive material parameter in the field of biomaterial-guided tissue regeneration.
  • Häkkinen, Jukka; Gröhn, Lauri (2016)
    Humans perceive shape in two-dimensional shaded images, and turning such an image upside down can result in inversion of the relief of this image. Previous research indicates that this inversion is caused by assumptions related to overhead illumination, global convexity and viewpoint above the surface. In our article, we describe the inverted waves effect, in which turning an image of waves upside down changes its relief and also its perceived material properties.
  • Piedra, Patricio; Gobert, Christian; Kalume, Aimable; Pan, Yong-Le; Kocifaj, Miroslav; Muinonen, Karri; Penttilä, Antti; Zubko, Evgenij; Videen, Gorden (2020)
    We explore a technique called class-activation mapping (CAM) to investigate how a Machine Learning (ML) architecture learns to classify particles based on their light-scattering signals. We release our code, and also find that different regions of the light-scattering signals play different roles in ML classification. These regions depend on the type of particles being classified and on the nature of the data obtained and trained. For instance, the Mueller-matrix elements S-11*, S-1(2)* and S-21* had the greatest classification activation in the diffraction region. Linear polarization elements S-1(2)* and S-21* were most accurate in the backscattering region for clusters of spheres and spores, and was most accurate in the diffraction region for other particle classes. The CAM technique was able to highlight light-scattering angles that maximize the potential for discrimination of similar particle classes. Such information is useful for designing detector systems to classify particles where limited space or resources are available, including flow cytometry and satellite remote sensing. (C) 2020 The Authors. Published by Elsevier Ltd.