scholarly journals Testing accuracy in 2D and 3D geometric morphometric methods for cut mark identification and classification

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5133 ◽  
Author(s):  
Lloyd A. Courtenay ◽  
Miguel Ángel Maté-González ◽  
Julia Aramendi ◽  
José Yravedra ◽  
Diego González-Aguilera ◽  
...  
Keyword(s):  
Empirical Support ◽  
Microscopic Analysis ◽  
Geometric Morphometric ◽  
Cut Marks ◽  
Morphometric Methods ◽  
Testing Accuracy ◽  
Technological Improvements ◽  
3D Methods ◽  
2D And 3D ◽  
First Time

The analysis of bone surface modifications (BSMs) is a prominent part of paleoanthropological studies, namely taphonomic research. Behavioral interpretations of the fossil record hinge strongly upon correct assessment of BSMs. With the significant impact of microscopic analysis to the study of BSMs, multiple authors have discussed the reliability of these technological improvements for gaining resolution in BSM discrimination. While a certain optimism is present, some important questions are ignored and others overemphasized without appropriate empirical support. This specifically affects the study of cut marks. A diversity of geometric morphometric approaches applied to the study of cut marks have resulted in the coexistence (and competition) of different 2D and 3D methods. The present work builds upon the foundation of experiments presented by Maté-González et al. (2015), Courtenay et al. (2017) and Otárola-Castillo et al. (2018) to contrast for the first time 2D and 3D methods in their resolution of cut mark interpretation and classification. The results presented here show that both approaches are equally valid and that the use of sophisticated 3D methods do not contribute to an improvement in accuracy.

scholarly journals Arothron: An R package for geometric morphometric methods and virtual anthropology applications

2021 ◽  
Author(s):  
Profico Antonio ◽  
Buzi Costantino ◽  
Castiglione Silvia ◽  
Melchionna Marina ◽  
Piras Paolo ◽  
...  
Keyword(s):  
R Package ◽  
Geometric Morphometric ◽  
Morphometric Methods ◽  
Virtual Anthropology

scholarly journals Doppler Tomography in 2D and 3D of the X-ray Binary Cyg X-1 for June 2007

2011 ◽  
Vol 7 (S282) ◽  
pp. 201-202 ◽  
Author(s):  
O. I. Sharova ◽  
M. I. Agafonov ◽  
E. A. Karitskaya ◽  
N. G. Bochkarev ◽  
S. V. Zharikov ◽  
...  
Keyword(s):  
Binary System ◽  
Spectral Data ◽  
Inclination Angle ◽  
Tomographic Reconstruction ◽  
Orbital Plane ◽  
National Observatory ◽  
Doppler Tomography ◽  
X Ray ◽  
2D And 3D ◽  
First Time

AbstractThe 2D and 3D Doppler tomograms of X-ray binary system Cyg X-1 (V1357 Cyg) were reconstructed from spectral data for the line HeII 4686Å obtained with 2-m telescope of the Peak Terskol Observatory (Russia) and 2.1-m telescope of the Mexican National Observatory in June, 2007. Information about gas motions outside the orbital plane, using all of the three velocity components Vx, Vy, Vz, was obtained for the first time. The tomographic reconstruction was carried out for the system inclination angle of 45°. The equal resolution (50 × 50 × 50 km/s) is realized in this case, in the orbital plane (Vx, Vy) and also in the perpendicular direction Vz. The checkout tomograms were realized also for the inclination angle of 40° because of the angle uncertainty. Two versions of the result showed no qualitative discrepancy. Details of the structures revealed by the 3D Doppler tomogram were analyzed.

scholarly journals Comparing skull formation of the Hungarian (Hortobágy) Zackel sheep breed by geometrics morphometrics

2015 ◽  
pp. 29-33
Author(s):  
Zsuzsanna Csóri ◽  
András Gáspárdy ◽  
András Jávor
Keyword(s):  
Morphological Changes ◽  
Time Change ◽  
Carpathian Basin ◽  
Sheep Breed ◽  
Geometric Morphometric ◽  
The Past ◽  
Morphometric Methods ◽  
Skull Formation ◽  
Over Time

This work seeks to explore the morphological changes of the Hungarian (Hortobágy) Zackel sheep's skull, which occurred in the past 50–70 years. In this study, we compared individuals skull forms by geometric morphometric methods. The origin of the breed is not known, we do not know when entering the Carpathian Basin. Therefore, the comparison involved the only known early archaeological findings. We have shown that there is no difference between each period colour variations, but over time change has occurred in the skull formation of the breed.

scholarly journals ­Geometric morphometric analysis of snout shape in extant ruminants (Ungulata, Artiodactyla)

2013 ◽  
Author(s):  
Jonathan P. Tennant ◽  
Norman MacLeod
Keyword(s):  
Feeding Strategy ◽  
Functional Ecology ◽  
Intake Rate ◽  
Ecological Groups ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Ruminant Species ◽  
Under Sampling ◽  
Geometric Morphometric Analysis ◽  
First Time

Snout shape is a prominent aspect of herbivore feeding ecology, controlling both forage selectivity and intake rate. Many previous investigations have suggested that ruminant feeding classes can be discriminated via snout shape, with grazing and browsing species attributed ‘blunt’ and ‘pointed’ snouts respectively, with an intermediate sub-grouping. This aspect of functional ecology is analysed for the first time using a statistically rigorous geometry-based framework to compare the two-dimensional profiles of the premaxilla in ventral aspect for a large sample of ruminant species. Our results suggest that, when a sample of browsing and grazing ruminants are classified ecologically based on a range of independent indicators of their feeding strategy, they cannot be fully discriminated on the basis of their premaxilla profile shape. Instead, our sample forms a shape variation continuum with overlap between groupings, but with a 78 percent chance of successful categorisation. Moreover, previously used terminology such as ‘pointed’ and ‘blunt’ are largely inadequate for delimiting snout shape varieties, insofar as these terms lack the descriptive power to define the morphological disparity demonstrated. These results suggest that previous attempts to use snout shape as a proxy for feeding style in ruminants may have been biased due to under-sampling of this highly diverse group and to lack of geometric rigour in the assessment of shape data. Alternatively, conflicting or inadequate evidence in defining ‘browsers’ and ‘grazers’ could have caused incorrect assignment to ecological groups, distorting our analyses. The relation between snout shape and body mass are also documented.

scholarly journals On two species of Riocypris (Crustacea, Ostracoda) from northern Patagonia and their relation to Eucypris fontana: implications in paleoenvironmental reconstructions

2018 ◽  
Vol 96 (8) ◽  
pp. 801-817 ◽  
Author(s):  
C.A. Coviaga ◽  
A.P. Pérez ◽  
L.Y. Ramos ◽  
P. Alvear ◽  
G.C. Cusminsky
Keyword(s):  
Sexual Dimorphism ◽  
Morphometric Analysis ◽  
Indicator Species ◽  
Taxonomic Status ◽  
Geometric Morphometric ◽  
Comparative Analyses ◽  
Northern Patagonia ◽  
Geometric Morphometric Analysis ◽  
The Individual ◽  
First Time

Two species of ostracods new to Patagonia, Argentina, are described. One of them, Riocypris whatleyi sp. nov., is described for the first time, and the second, Riocypris sarsi (Daday, 1902) comb. nov., is reallocated from genus Eucypris to genus Riocypris. Inter- and intra-specific variations in shape, size, and sexual dimorphism were evaluated based on geometric morphometric analysis. Moreover, morphological and morphometric comparative analyses were applied to re-examine living and quaternary specimens recovered from previous studies. Based on these results, a generic reassignment for the Patagonian Eucypris fontana (Jurine, 1820) into the genus Riocypris is proposed. Contributing to the knowledge on the systematic and autecology of this enigmatic species, widely distributed in Patagonia and frequently used in paleolimnological reconstructions, generates science-based evidence for their use as indicator species. Additionally, our results emphasize the usefulness of studying the living representatives (i.e., with valves and appendages) for elucidating the taxonomic status of the individual specimens, especially those present in paleontological records and used as bioproxies in paleolimnological studies.

3D analysis of cut marks using a new geometric morphometric methodological approach

2017 ◽  
Vol 11 (2) ◽  
pp. 651-665 ◽  
Author(s):  
Lloyd A. Courtenay ◽  
Jose Yravedra ◽  
Miguel Ángel Mate-González ◽  
Julia Aramendi ◽  
Diego González-Aguilera
Keyword(s):  
Methodological Approach ◽  
3D Analysis ◽  
Geometric Morphometric ◽  
Cut Marks

scholarly journals Cording Mycobacterium tuberculosis Bacilli Have a Key Role in the Progression towards Active Tuberculosis, Which is Stopped by Previous Immune Response

2020 ◽  
Vol 8 (2) ◽  
pp. 228 ◽  
Author(s):  
Lilibeth Arias ◽  
Paula Cardona ◽  
Martí Català ◽  
Víctor Campo-Pérez ◽  
Clara Prats ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Early Stage ◽  
Microscopic Analysis ◽  
Neutrophil Infiltration ◽  
Active Tuberculosis ◽  
Bcg Vaccination ◽  
H37rv Strain ◽  
First Time

Cording was the first virulence factor identified in Mycobacterium tuberculosis (Mtb). We aimed to ascertain its role in the induction of active tuberculosis (TB) in the mouse strain C3HeB/FeJ by testing the immunopathogenic capacity of the H37Rv strain. We have obtained two batches of the same strain by stopping their growth in Proskauer Beck liquid medium once the mid-log phase was reached, in the noncording Mtb (NCMtb) batch, and two days later in the cording Mtb (CMtb) batch, when cording could be detected by microscopic analysis. Mice were challenged with each batch intravenously and followed-up for 24 days. CMtb caused a significant increase in the bacillary load at an early stage post-challenge (day 17), when a granulomatous response started, generating exudative lesions characterized by neutrophilic infiltration, which promoted extracellular bacillary growth together with cording formation, as shown for the first time in vivo. In contrast, NCMtb experienced slight or no bacillary growth and lesions could barely be detected. Previous Bacillus Calmette-Guérin (BCG) vaccination or low dose aerosol (LDA) Mtb infection were able to delay the progression towards active TB after CMtb challenge. While BCG vaccination also reduced bacillary load when NCMtb was challenged, LDA did not, and its proliferative lesions experienced neutrophil infiltration. Analysis of lung cytokine and chemokine profiles points to their capacity to block the production of CXCL-1 and further amplification of IL-1β, IL-17 and neutrophilic extracellular trap formation, all of which are essential for TB progression. These data highlight the key role of cording formation in the induction of active TB.

scholarly journals Geometric Morphometric Analyses Support Incorporating the Goshen Point Type into Plainview

2019 ◽  
Vol 85 (1) ◽  
pp. 171-181 ◽  
Author(s):  
Briggs Buchanan ◽  
Mark Collard ◽  
Michael J. O'Brien
Keyword(s):  
Recent Work ◽  
Social Dynamics ◽  
Spatiotemporal Variation ◽  
Single Type ◽  
Geometric Morphometric ◽  
Morphometric Analyses ◽  
Morphometric Methods ◽  
Point Type

Recent work has demonstrated that Goshen points overlap in time with another group of unfluted lanceolate points from the Plains, Plainview points. This has raised the question of whether the two types should be kept separate or consolidated into a single type. We sought to resolve this issue by applying geometric morphometric methods to a sample of points from well-documented Goshen and Plainview assemblages. We found that their shapes were statistically indistinguishable, which indicates that Goshen and Plainview points should be assigned to the same type. Because Plainview points were recognized before Goshen points, it is the latter type name that should be dropped. Sinking Goshen into Plainview allows us to move beyond taxonomic issues and toward understanding both the spatiotemporal variation that exists among Plainview assemblages and what it can tell us about the adaptations and social dynamics of Plainview groups.

scholarly journals Candida albicans forms biofilms on the vaginal mucosa

Microbiology ◽  
2010 ◽  
Vol 156 (12) ◽  
pp. 3635-3644 ◽  
Author(s):  
M. M. Harriott ◽  
E. A. Lilly ◽  
T. E. Rodriguez ◽  
P. L. Fidel ◽  
M. C. Noverr
Keyword(s):  
Biofilm Formation ◽  
Ex Vivo ◽  
Microscopic Analysis ◽  
Vaginal Mucosa ◽  
First Time ◽  
Established Role ◽  
Type Strains

Current understanding of resistance and susceptibility to vulvovaginal candidiasis challenges existing paradigms of host defence against fungal infection. While abiotic biofilm formation has a clearly established role during systemic Candida infections, it is not known whether C. albicans forms biofilms on the vaginal mucosa and the possible role of biofilms in disease. In vivo and ex vivo murine vaginitis models were employed to examine biofilm formation by scanning electron and confocal microscopy. C. albicans strains included 3153A (lab strain), DAY185 (parental control strain), and mutants defective in morphogenesis and/or biofilm formation in vitro (efg1/efg1 and bcr1/bcr1). Both 3153A and DAY815 formed biofilms on the vaginal mucosa in vivo and ex vivo as indicated by high fungal burden and microscopic analysis demonstrating typical biofilm architecture and presence of extracellular matrix (ECM) co-localized with the presence of fungi. In contrast, efg1/efg1 and bcr1/bcr1 mutant strains exhibited weak or no biofilm formation/ECM production in both models compared to wild-type strains and complemented mutants despite comparable colonization levels. These data show for the first time that C. albicans forms biofilms in vivo on vaginal epithelium, and that in vivo biotic biofilm formation requires regulators of biofilm formation (BCR1) and morphogenesis (EFG1).

Development of SFEM-Pre: A Novel Preprocessor for Model Creation for the Smoothed Finite Element Method

2019 ◽  
Vol 17 (02) ◽  
pp. 1845002 ◽  
Author(s):  
J. F. Zhang ◽  
R. P. Niu ◽  
Y. F. Zhang ◽  
C. Q. Wang ◽  
M. Li ◽  
...  
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Complex Geometry ◽  
Three Dimensional ◽  
Efficient Computation ◽  
Practical Engineering ◽  
Smoothed Finite Element Method ◽  
2D And 3D ◽  
First Time ◽  
Element Method

Smoothed finite element method (S-FEM) is a new general numerical method which has been applied to solve various practical engineering problems. It combines standard finite element method (FEM) and meshfree techniques based on the weaken-weak (W2) formulation. This project, for the first time, develops a preprocessor software package SFEM-Pre for creating types of two-dimensional (2D) and three-dimensional (3D) S-FEM models following strictly the S-FEM theory. Because the software architecture of our 3D processor is the same as our 2D preprocessor, we will mainly introduce the 2D preprocessor in terms of software design for easier description, but the examples will include both 2D and 3D cases to fully demonstrate and validate the whole preprocessor of S-FEM. Our 2D preprocessor package is equipped with a graphical user interface (GUI) for easy use, and with a connectivity database for efficient computation. Schemes are developed for not only automatically meshes the problem domains using our GUI, but also accepts various geometry files made available from some existing commercial software packages, such as ABAQUS®and HyperMesh®. In order to improve the efficiency of our preprocessor, a parallel triangulation mesh generator has also been developed based on the advancing front technique (AFT) to create triangular meshes for complex geometry, and at the same time to create six types of connectivity needed for various S-FEM models. In addition, a database is implemented in our code to record all these connectivity to avoid duplicated calculation. Finally, intensive numerical experiments are conducted to validate the efficiency, accuracy and stability of our preprocessor codes. It is shown that with our preprocessor, an S-FEM can be created automatically without much human intervention for geometry of arbitrary complexity.

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