Ján Dupej | Charles University, Prague (original) (raw)

Talks by Ján Dupej

It is generally assumed that only a few full-size Old Kingdom copper tools for working stone and ... more It is generally assumed that only a few full-size Old Kingdom copper tools for working stone and wood have been preserved. The assumption led to the marginalization of this artefact category in the study of so-called “Pyramid Age” of Ancient Egypt (ca 27th-22nd century BC). The paper reviews the evidence and questions this assumption. The archaeological contexts in which these full-size tools have been found are evaluated and the tool’s morphology and chronology are examined in detail, by means of the traditional approaches and also with the aid of morphometry. A comparison with hundreds of Old Kingdom model copper tools helps to define the characteristics and differences of both artefact categories. Model tools represent full-size toolkits used by stonemasons and carpenters. Questions about the alloys used to produce full-size tools and artefacts in the Old Kingdom will be also addressed.

Papers by Ján Dupej

American Journal of Physical Anthropology, 2017

The understanding of locomotor patterns, activity schemes, and biological variations has been enh... more The understanding of locomotor patterns, activity schemes, and biological variations has been enhanced by the study of the geometrical properties and cortical bone thickness of the long bones measured using CT scan cross-sections. With the development of scanning procedures, the internal architecture of the long bones can be explored along the entire diaphysis. Recently, several methods that map cortical thickness along the whole femoral diaphysis have been developed. Precise homology is vital for statistical examination of the data; however, the repeatability of these methods is unknown and some do not account for the curvature of the bones. We have designed a semiautomatic workflow that improves the morphometric analysis of cortical thickness, including robust data acquisition with minimal user interaction and considering the bone curvature. The proposed algorithm also performs automatic landmark refinement and rigid registration on the extracted morphometric maps of the cortical thickness. Because our algorithm automatically resli-ces the diaphysis into 100 cross-sections along the medial axis and uses an adaptive thresholding method, it is usable on CT scans that contain soft tissues as well as on bones that have not been oriented specifically prior to scanning. Our approach exhibits considerable robustness to error in user-supplied landmarks, suppresses distortion caused by the curvature of the bones, and calculates the curvature of the medial axis.

PeerJ, 2017

Background. Estimating volumes and masses of total body components is important for the study and... more Background. Estimating volumes and masses of total body components is important for the study and treatment monitoring of nutrition and nutrition-related disorders, cancer, joint replacement, energy-expenditure and exercise physiology. While several equations have been offered for estimating total body components from MRI slices, no reliable and tested method exists for CT scans. For the first time, body composition data was derived from 41 high-resolution whole-body CT scans. From these data, we defined equations for estimating volumes and masses of total body AT and LT from corresponding tissue areas measured in selected CT scan slices. Methods. We present a new semi-automatic approach to defining the density cutoff between adipose tissue (AT) and lean tissue (LT) in such material. An intra-class correlation coefficient (ICC) was used to validate the method. The equations for estimating the whole-body composition volume and mass from areas measured in selected slices were modeled with ordinary least squares (OLS) linear regressions and support vector machine regression (SVMR). Results and Discussion. The best predictive equation for total body AT volume was based on the AT area of a single slice located between the 4th and 5th lumbar vertebrae (L4-L5) and produced lower prediction errors (|PE| = 1.86 liters, %PE = 8.77) than previous equations also based on CT scans. The LT area of the mid-thigh provided the lowest prediction errors (|PE| = 2.52 liters, %PE = 7.08) for estimating whole-body LT volume. We also present equations to predict total body AT and LT masses from a slice located at L4-L5 that resulted in reduced error compared with the previously published equations based on CT scans. The multislice SVMR predictor gave the theoretical upper limit for prediction precision of volumes and cross-validated the results.

New techniques of capturing shape geometry for the purpose of studying asymmetry in biological ob... more New techniques of capturing shape geometry for the purpose of studying asymmetry in biological objects bring the need to develop new methods of analyzing such data. In this paper we propose a method of mesh asymmetry analysis and decomposition intended for use in geometric morphometry. In geometric morphometry the individual bilateral asymmetry is captured by aligning a specimen with its mirror image and analyzing the difference. This involves the construction of a dense correspondence mapping between the meshes. We tested our algorithm on real data consisting of a sample of 102 human faces as well as on artificially altered meshes to successfully prove its validity. The resulting algorithm is an important methodological improvement which has a potential to be widely used in a wide variety of morphological studies.

American Journal of Physical Anthropology

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics ... more The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Autónoma de México, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% wa...

%án wupej -Nx Václav 9rajíček -%ana Velemínská x %osef Pelikán -zaculty of =athematics and Physic... more %án wupej -Nx Václav 9rajíček -%ana Velemínská x %osef Pelikán -zaculty of =athematics and PhysicsN 8harles University in Prague x zaculty of ScienceN 8harles University in Prague Vertex-Point Matching TPS on 4=s 8Pw ])]-]

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics ... more The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Aut onoma de M exico, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% was achieved for a pooled sample using Fourier coefficient and Legendre polynomial methods. The success rate of our classification was influenced by the number of semilandmarks or coefficients and was only slightly affected by GSN marginal point positions. The intrapopulation variability of the female GSN shape was significantly lower compared with the male variability, possibly as a consequence of the intense selection pressure associated with reproduction. Males were misclassified more often than females. Our results show that by using a suitable GSN curve representation, a GM approach, and SVM analysis, it is possible to obtain a robust separation between the sexes that is stable for a multipopulation sample. Am J Phys Anthropol 152:558-565,

The analysis of shape represented as surface meshes is an important tool in anthropology and biom... more The analysis of shape represented as surface meshes is an important tool in anthropology and biomedicine for the study of aging, post-treatment development or sexual dimorphism. Most approaches rely on nonrigid registration using manually placed homologous landmarks, it is however often the case that some regions cannot be landmarked due to the lack of clear anatomical features. We therefore present a method of analyzing and visualizing the variability of a set of surface models that does not rely on landmarks for feature matching and uses coherent point drift (CPD), a nonrigid registration algorithm, instead. Our approach is based on the topology transfer of one arbitrarily selected base mesh to all other meshes with the use of CPD. The procedure ensures the identical meanings of corresponding vertices across the sample and allows the use of multivariate statistics even with shapes that would be difficult to process with methods that rely on landmarks for feature-matching.

Pattern Recognition Letters, 2015

Coherent point drift (CPD) is a powerful non-rigid point cloud registration algorithm. A speed-up... more Coherent point drift (CPD) is a powerful non-rigid point cloud registration algorithm. A speed-up technique that allows it to operate on large sets in reasonable time, however depends on efficient low-rank decomposition of a large affinity matrix. The originally used algorithm for finding eigenvectors in this case is based on Arnoldi's iteration which, though very precise, requires the calculation of numerous large matrix-vector products, which even with further speed-up techniques is computationally intensive. We use a different method of finding that approximation, based on Nyström sampling and design a modification that significantly accelerates the preprocessing stage of CPD. We test our modifications on a variety of situations, including different point counts, added Gaussian noise, outliers and deformation of the registered clouds. The results indicate that using our proposed approximation technique the desirable qualities of CPD such as robustness and precision are only minimally affected, while the preprocessing times are lowered considerably.

Forensic science international, Jan 13, 2014

Dealing with the increasing number of long-term missing children and juveniles requires more prec... more Dealing with the increasing number of long-term missing children and juveniles requires more precise and objective age progression techniques for the prediction of their current appearance. Our contribution includes detailed and real facial growth information used for modelling age progression during adolescence. This study was based on an evaluation of the overall 180 three-dimensional (3D) facial scans of Czech children (23 boys, 22 girls), which were longitudinally studied from 12 to 15 years of age and thus revealed the real growth-related changes. The boys underwent more marked changes compared with the girls, especially in the regions of the eyebrow ridges, nose and chin. Using modern geometric morphometric methods, together with their applications, we modelled the ageing and allometric trajectories for both sexes and simulated the age-progressed effects on facial scans. The facial parts that are important for facial recognition (eyes, nose, mouth and chin) all deviated less t...

American Journal of Physical Anthropology, 2013

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics ... more The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Autónoma de México, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% was achieved for a pooled sample using Fourier coefficient and Legendre polynomial methods. The success rate of our classification was influenced by the number of semilandmarks or coefficients and was only slightly affected by GSN marginal point positions. The intrapopulation variability of the female GSN shape was significantly lower compared with the male variability, possibly as a consequence of the intense selection pressure associated with reproduction. Males were misclassified more often than females. Our results show that by using a suitable GSN curve representation, a GM approach, and SVM analysis, it is possible to obtain a robust separation between the sexes that is stable for a multipopulation sample.

Books by Ján Dupej

The Old Kingdom of Egypt (Dynasties 4–6, c. 2600–2180 BC) is famous as a period of the builders o... more The Old Kingdom of Egypt (Dynasties 4–6, c. 2600–2180 BC) is famous as a period of the builders of the largest Egyptian pyramids. It is generally accepted that the evidence on the use of copper alloy tools from this era is meagre. Martin Odler gathers the textual, iconographic and palaeographic evidence and examines Old Kingdom artefacts in order to revise this view on the use of copper alloy tools and model tools. Furthermore, he provides updated definitions of tool classes and tool kits, together with the context of their use. Besides rare specimens of full-size tools, the largest corpora of the material have been preserved in the form of model tools in the burial equipment of the Old Kingdom elite and were most probably symbols of their power to commission and fund craftwork. Moreover, the size and elaboration of the model tools were probably connected to the social status of the buried persons. The long-standing division in the Egyptological literature between full-size tools and model tools is questioned. The ancient sources also enable to show that the preservation of material culture from the Old Kingdom was largely dependent on a conscious selection made within the past culture, with completely different settlement and funerary contexts and a conspicuous absence of weapons. The volume is completed by co-authored case studies on archaeometallurgy of selected Old Kingdom artefacts in the collection of the Egyptian Museum of Leipzig University, on morphometry of Old Kingdom adze blades and on the finds of stone and ceramic vessels associated with the findings of so-called Old Kingdom model tools.

The book can be purchased here: http://www.archaeopress.com/Public/displayProductDetail.asp?id=%7BDED38ACF-A714-4454-8448-4C8C91A92F43%7D

Archaeology of Egypt and Sudan by Ján Dupej

Lectures in Slovak by Ján Dupej

Public lecture held in Slovak and Czech, in the Municipal Library of Prague, on 17th January 2017

Conference Presentations by Ján Dupej

American Journal of Physical Anthropology, 2017

The diaphysis of long bones responds to biomechanical loading by remodeling. Thus a quantified de... more The diaphysis of long bones responds to biomechanical loading by remodeling. Thus a quantified description of the geometrical properties of long bones, such as their cortical area (CA) thickness can help improve the understanding of the functional adaptation process, activity patterns and biological variations. Because on these surfaces landmarks are scarce, ordinary geometric morphometrics cannot be directly applied.
Several algorithms have been proposed to extract dense CA profiles from femoral diaphysis. Some disregard bone curvature, or do not take measures to enforce correspondence. Others focus on the creation of finite element models. We present a workflow for morphometric analysis of femoral CA profiles that takes medial axis curvature into account and performs a simple correspondence search. Minimal user interaction is required.
We demonstrate our approach on a sample of 66 CT scans of the lower limb and construct mean CA thickness profiles of the right femur for both sexes. We also identify the areas in which sexual dimorphism is statistically significant. In our sample, males possessed overall thicker cortex with a peak in posterior direction reaching 10 mm. In females, that peak barely exceeded 8 mm. In all orientations, except lateral, that difference was significant. An inspection of normalized profiles suggests that while males generally have a sharper spike of CA thickness in posterior direction, females have a more even distribution of cortical bone around the medial axis.
This work has been supported by Charles University Grant Agency (GAUK) as project 230516.

American Journal of Physical Anthropology, 2017

Body mass estimation methods from the femur provide adequate results for inter-population compari... more Body mass estimation methods from the femur provide adequate results for inter-population comparisons but have not been designed, nor provide reliable information for the purpose of studying inter-individual variability, which is influenced by fat (FM) and fat-free masses (FFM). Hence, our study aimed to evaluate the co-variation of body composition (FM, FFM and body fat percent or BF%) and the femur.
Femoral articular dimensions, typically used to predict inter-population sbody mas, correlate with FFM in males, but not FM or BF% in either sex.
Cortical thickness at specific locations correlates with FM and BF% in females only (R ≥ .6). Cortical thickness correlation with FFM is lower than with fat and weaker in males compared to females.
There is a significant link between robustness (which equals to diaphyseal cortical volume divided by femoral length) and FM, FFM and BF% in females. In males, a significant relationship has been found between robustness and FFM.
Femoral curvature is the only predictor that significantly correlates with BF% and FM but not FFM in both sexes and particularly in females.
Hence, the femoral diaphysis seems to get thicker, straighter, and more robust with the increasing of FM or BF% in females while it solely reduces curvature in males. In contrast, an increase in FFM correlates with femoral articular dimensions in males and with robustness in both sexes. Further research is needed to confirm the results.

Bulletins et Mémoires de la Société d'Anthropologie de Paris, 2016

Les méthodes permettant d'estimer le poids uniquement à partir du squelette ont été créées pour e... more Les méthodes permettant d'estimer le poids uniquement à partir du squelette ont été créées pour estimer une masse corporelle " idéale " proportionnelle aux dimensions squelettiques, excluant, de fait, la variation pondérale liée aux tissus mous. Néanmoins, de nombreuses études ont visé à tester leur efficacité sur des populations obèses/ chétives ou sportives. Si les résultats confirment le postulat initial – i.e. ces méthodes estiment raisonnablement le poids moyen d'ensembles d'individus membres d'une même population et/ou d'individus dont le poids se situe dans la moyenne –, elles n'en restent pas moins utilisées et testées pour estimer des poids individuels " réels ". Parallèlement, des recherches suggèrent que l'aire corticale enregistrerait, quant à elle, le poids des tissus mous. Cette étude vise (1) à vérifier que la quantité de tissus mous n'est pas prise en compte par les méthodes " classiques " d'estimation du poids à partir du membre inférieur ; (2) à démontrer que la superficie d'os cortical des diaphyses du membre inférieur est liée à la masse des tissus mous. Des distances ostéométriques et la superficie d'os cortical ont été mesurées sur un échantillon de 55 angioscanners de membres inférieurs. Les masses maigre et grasse ont été évaluées à partir d'une régression estimant la composition corporelle totale et de coupes au niveau L3-L4 et à mi-fémur. Les résultats montrent que (1) les méthodes d'estimation du poids à partir du membre inférieur modélisent la variation pondérale liées aux muscles et organes mieux qu'attendu mais qu'elles fonctionnent, cependant, indépendamment de la quantité de masse grasse ; (2) la superficie d'os cortical est plus clairement influencée par la masse maigre que la masse grasse. Cette recherche constitue le premier pas vers la création d'un modèle qui tiendrait compte du poids " idéal " estimé par les méthodes déjà existantes et y ajouterait la possibilité d'estimer la masse de tissus mous à partir du squelette.

It is generally assumed that only a few full-size Old Kingdom copper tools for working stone and ... more It is generally assumed that only a few full-size Old Kingdom copper tools for working stone and wood have been preserved. The assumption led to the marginalization of this artefact category in the study of so-called “Pyramid Age” of Ancient Egypt (ca 27th-22nd century BC). The paper reviews the evidence and questions this assumption. The archaeological contexts in which these full-size tools have been found are evaluated and the tool’s morphology and chronology are examined in detail, by means of the traditional approaches and also with the aid of morphometry. A comparison with hundreds of Old Kingdom model copper tools helps to define the characteristics and differences of both artefact categories. Model tools represent full-size toolkits used by stonemasons and carpenters. Questions about the alloys used to produce full-size tools and artefacts in the Old Kingdom will be also addressed.

American Journal of Physical Anthropology, 2017

The understanding of locomotor patterns, activity schemes, and biological variations has been enh... more The understanding of locomotor patterns, activity schemes, and biological variations has been enhanced by the study of the geometrical properties and cortical bone thickness of the long bones measured using CT scan cross-sections. With the development of scanning procedures, the internal architecture of the long bones can be explored along the entire diaphysis. Recently, several methods that map cortical thickness along the whole femoral diaphysis have been developed. Precise homology is vital for statistical examination of the data; however, the repeatability of these methods is unknown and some do not account for the curvature of the bones. We have designed a semiautomatic workflow that improves the morphometric analysis of cortical thickness, including robust data acquisition with minimal user interaction and considering the bone curvature. The proposed algorithm also performs automatic landmark refinement and rigid registration on the extracted morphometric maps of the cortical thickness. Because our algorithm automatically resli-ces the diaphysis into 100 cross-sections along the medial axis and uses an adaptive thresholding method, it is usable on CT scans that contain soft tissues as well as on bones that have not been oriented specifically prior to scanning. Our approach exhibits considerable robustness to error in user-supplied landmarks, suppresses distortion caused by the curvature of the bones, and calculates the curvature of the medial axis.

PeerJ, 2017

Background. Estimating volumes and masses of total body components is important for the study and... more Background. Estimating volumes and masses of total body components is important for the study and treatment monitoring of nutrition and nutrition-related disorders, cancer, joint replacement, energy-expenditure and exercise physiology. While several equations have been offered for estimating total body components from MRI slices, no reliable and tested method exists for CT scans. For the first time, body composition data was derived from 41 high-resolution whole-body CT scans. From these data, we defined equations for estimating volumes and masses of total body AT and LT from corresponding tissue areas measured in selected CT scan slices. Methods. We present a new semi-automatic approach to defining the density cutoff between adipose tissue (AT) and lean tissue (LT) in such material. An intra-class correlation coefficient (ICC) was used to validate the method. The equations for estimating the whole-body composition volume and mass from areas measured in selected slices were modeled with ordinary least squares (OLS) linear regressions and support vector machine regression (SVMR). Results and Discussion. The best predictive equation for total body AT volume was based on the AT area of a single slice located between the 4th and 5th lumbar vertebrae (L4-L5) and produced lower prediction errors (|PE| = 1.86 liters, %PE = 8.77) than previous equations also based on CT scans. The LT area of the mid-thigh provided the lowest prediction errors (|PE| = 2.52 liters, %PE = 7.08) for estimating whole-body LT volume. We also present equations to predict total body AT and LT masses from a slice located at L4-L5 that resulted in reduced error compared with the previously published equations based on CT scans. The multislice SVMR predictor gave the theoretical upper limit for prediction precision of volumes and cross-validated the results.

New techniques of capturing shape geometry for the purpose of studying asymmetry in biological ob... more New techniques of capturing shape geometry for the purpose of studying asymmetry in biological objects bring the need to develop new methods of analyzing such data. In this paper we propose a method of mesh asymmetry analysis and decomposition intended for use in geometric morphometry. In geometric morphometry the individual bilateral asymmetry is captured by aligning a specimen with its mirror image and analyzing the difference. This involves the construction of a dense correspondence mapping between the meshes. We tested our algorithm on real data consisting of a sample of 102 human faces as well as on artificially altered meshes to successfully prove its validity. The resulting algorithm is an important methodological improvement which has a potential to be widely used in a wide variety of morphological studies.

American Journal of Physical Anthropology

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics ... more The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Autónoma de México, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% wa...

%án wupej -Nx Václav 9rajíček -%ana Velemínská x %osef Pelikán -zaculty of =athematics and Physic... more %án wupej -Nx Václav 9rajíček -%ana Velemínská x %osef Pelikán -zaculty of =athematics and PhysicsN 8harles University in Prague x zaculty of ScienceN 8harles University in Prague Vertex-Point Matching TPS on 4=s 8Pw ])]-]

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics ... more The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Aut onoma de M exico, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% was achieved for a pooled sample using Fourier coefficient and Legendre polynomial methods. The success rate of our classification was influenced by the number of semilandmarks or coefficients and was only slightly affected by GSN marginal point positions. The intrapopulation variability of the female GSN shape was significantly lower compared with the male variability, possibly as a consequence of the intense selection pressure associated with reproduction. Males were misclassified more often than females. Our results show that by using a suitable GSN curve representation, a GM approach, and SVM analysis, it is possible to obtain a robust separation between the sexes that is stable for a multipopulation sample. Am J Phys Anthropol 152:558-565,

The analysis of shape represented as surface meshes is an important tool in anthropology and biom... more The analysis of shape represented as surface meshes is an important tool in anthropology and biomedicine for the study of aging, post-treatment development or sexual dimorphism. Most approaches rely on nonrigid registration using manually placed homologous landmarks, it is however often the case that some regions cannot be landmarked due to the lack of clear anatomical features. We therefore present a method of analyzing and visualizing the variability of a set of surface models that does not rely on landmarks for feature matching and uses coherent point drift (CPD), a nonrigid registration algorithm, instead. Our approach is based on the topology transfer of one arbitrarily selected base mesh to all other meshes with the use of CPD. The procedure ensures the identical meanings of corresponding vertices across the sample and allows the use of multivariate statistics even with shapes that would be difficult to process with methods that rely on landmarks for feature-matching.

Pattern Recognition Letters, 2015

Coherent point drift (CPD) is a powerful non-rigid point cloud registration algorithm. A speed-up... more Coherent point drift (CPD) is a powerful non-rigid point cloud registration algorithm. A speed-up technique that allows it to operate on large sets in reasonable time, however depends on efficient low-rank decomposition of a large affinity matrix. The originally used algorithm for finding eigenvectors in this case is based on Arnoldi's iteration which, though very precise, requires the calculation of numerous large matrix-vector products, which even with further speed-up techniques is computationally intensive. We use a different method of finding that approximation, based on Nyström sampling and design a modification that significantly accelerates the preprocessing stage of CPD. We test our modifications on a variety of situations, including different point counts, added Gaussian noise, outliers and deformation of the registered clouds. The results indicate that using our proposed approximation technique the desirable qualities of CPD such as robustness and precision are only minimally affected, while the preprocessing times are lowered considerably.

Forensic science international, Jan 13, 2014

Dealing with the increasing number of long-term missing children and juveniles requires more prec... more Dealing with the increasing number of long-term missing children and juveniles requires more precise and objective age progression techniques for the prediction of their current appearance. Our contribution includes detailed and real facial growth information used for modelling age progression during adolescence. This study was based on an evaluation of the overall 180 three-dimensional (3D) facial scans of Czech children (23 boys, 22 girls), which were longitudinally studied from 12 to 15 years of age and thus revealed the real growth-related changes. The boys underwent more marked changes compared with the girls, especially in the regions of the eyebrow ridges, nose and chin. Using modern geometric morphometric methods, together with their applications, we modelled the ageing and allometric trajectories for both sexes and simulated the age-progressed effects on facial scans. The facial parts that are important for facial recognition (eyes, nose, mouth and chin) all deviated less t...

American Journal of Physical Anthropology, 2013

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics ... more The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Autónoma de México, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% was achieved for a pooled sample using Fourier coefficient and Legendre polynomial methods. The success rate of our classification was influenced by the number of semilandmarks or coefficients and was only slightly affected by GSN marginal point positions. The intrapopulation variability of the female GSN shape was significantly lower compared with the male variability, possibly as a consequence of the intense selection pressure associated with reproduction. Males were misclassified more often than females. Our results show that by using a suitable GSN curve representation, a GM approach, and SVM analysis, it is possible to obtain a robust separation between the sexes that is stable for a multipopulation sample.

The Old Kingdom of Egypt (Dynasties 4–6, c. 2600–2180 BC) is famous as a period of the builders o... more The Old Kingdom of Egypt (Dynasties 4–6, c. 2600–2180 BC) is famous as a period of the builders of the largest Egyptian pyramids. It is generally accepted that the evidence on the use of copper alloy tools from this era is meagre. Martin Odler gathers the textual, iconographic and palaeographic evidence and examines Old Kingdom artefacts in order to revise this view on the use of copper alloy tools and model tools. Furthermore, he provides updated definitions of tool classes and tool kits, together with the context of their use. Besides rare specimens of full-size tools, the largest corpora of the material have been preserved in the form of model tools in the burial equipment of the Old Kingdom elite and were most probably symbols of their power to commission and fund craftwork. Moreover, the size and elaboration of the model tools were probably connected to the social status of the buried persons. The long-standing division in the Egyptological literature between full-size tools and model tools is questioned. The ancient sources also enable to show that the preservation of material culture from the Old Kingdom was largely dependent on a conscious selection made within the past culture, with completely different settlement and funerary contexts and a conspicuous absence of weapons. The volume is completed by co-authored case studies on archaeometallurgy of selected Old Kingdom artefacts in the collection of the Egyptian Museum of Leipzig University, on morphometry of Old Kingdom adze blades and on the finds of stone and ceramic vessels associated with the findings of so-called Old Kingdom model tools.

The book can be purchased here: http://www.archaeopress.com/Public/displayProductDetail.asp?id=%7BDED38ACF-A714-4454-8448-4C8C91A92F43%7D

Public lecture held in Slovak and Czech, in the Municipal Library of Prague, on 17th January 2017

American Journal of Physical Anthropology, 2017

The diaphysis of long bones responds to biomechanical loading by remodeling. Thus a quantified de... more The diaphysis of long bones responds to biomechanical loading by remodeling. Thus a quantified description of the geometrical properties of long bones, such as their cortical area (CA) thickness can help improve the understanding of the functional adaptation process, activity patterns and biological variations. Because on these surfaces landmarks are scarce, ordinary geometric morphometrics cannot be directly applied.
Several algorithms have been proposed to extract dense CA profiles from femoral diaphysis. Some disregard bone curvature, or do not take measures to enforce correspondence. Others focus on the creation of finite element models. We present a workflow for morphometric analysis of femoral CA profiles that takes medial axis curvature into account and performs a simple correspondence search. Minimal user interaction is required.
We demonstrate our approach on a sample of 66 CT scans of the lower limb and construct mean CA thickness profiles of the right femur for both sexes. We also identify the areas in which sexual dimorphism is statistically significant. In our sample, males possessed overall thicker cortex with a peak in posterior direction reaching 10 mm. In females, that peak barely exceeded 8 mm. In all orientations, except lateral, that difference was significant. An inspection of normalized profiles suggests that while males generally have a sharper spike of CA thickness in posterior direction, females have a more even distribution of cortical bone around the medial axis.
This work has been supported by Charles University Grant Agency (GAUK) as project 230516.

American Journal of Physical Anthropology, 2017

Body mass estimation methods from the femur provide adequate results for inter-population compari... more Body mass estimation methods from the femur provide adequate results for inter-population comparisons but have not been designed, nor provide reliable information for the purpose of studying inter-individual variability, which is influenced by fat (FM) and fat-free masses (FFM). Hence, our study aimed to evaluate the co-variation of body composition (FM, FFM and body fat percent or BF%) and the femur.
Femoral articular dimensions, typically used to predict inter-population sbody mas, correlate with FFM in males, but not FM or BF% in either sex.
Cortical thickness at specific locations correlates with FM and BF% in females only (R ≥ .6). Cortical thickness correlation with FFM is lower than with fat and weaker in males compared to females.
There is a significant link between robustness (which equals to diaphyseal cortical volume divided by femoral length) and FM, FFM and BF% in females. In males, a significant relationship has been found between robustness and FFM.
Femoral curvature is the only predictor that significantly correlates with BF% and FM but not FFM in both sexes and particularly in females.
Hence, the femoral diaphysis seems to get thicker, straighter, and more robust with the increasing of FM or BF% in females while it solely reduces curvature in males. In contrast, an increase in FFM correlates with femoral articular dimensions in males and with robustness in both sexes. Further research is needed to confirm the results.

Bulletins et Mémoires de la Société d'Anthropologie de Paris, 2016

Les méthodes permettant d'estimer le poids uniquement à partir du squelette ont été créées pour e... more Les méthodes permettant d'estimer le poids uniquement à partir du squelette ont été créées pour estimer une masse corporelle " idéale " proportionnelle aux dimensions squelettiques, excluant, de fait, la variation pondérale liée aux tissus mous. Néanmoins, de nombreuses études ont visé à tester leur efficacité sur des populations obèses/ chétives ou sportives. Si les résultats confirment le postulat initial – i.e. ces méthodes estiment raisonnablement le poids moyen d'ensembles d'individus membres d'une même population et/ou d'individus dont le poids se situe dans la moyenne –, elles n'en restent pas moins utilisées et testées pour estimer des poids individuels " réels ". Parallèlement, des recherches suggèrent que l'aire corticale enregistrerait, quant à elle, le poids des tissus mous. Cette étude vise (1) à vérifier que la quantité de tissus mous n'est pas prise en compte par les méthodes " classiques " d'estimation du poids à partir du membre inférieur ; (2) à démontrer que la superficie d'os cortical des diaphyses du membre inférieur est liée à la masse des tissus mous. Des distances ostéométriques et la superficie d'os cortical ont été mesurées sur un échantillon de 55 angioscanners de membres inférieurs. Les masses maigre et grasse ont été évaluées à partir d'une régression estimant la composition corporelle totale et de coupes au niveau L3-L4 et à mi-fémur. Les résultats montrent que (1) les méthodes d'estimation du poids à partir du membre inférieur modélisent la variation pondérale liées aux muscles et organes mieux qu'attendu mais qu'elles fonctionnent, cependant, indépendamment de la quantité de masse grasse ; (2) la superficie d'os cortical est plus clairement influencée par la masse maigre que la masse grasse. Cette recherche constitue le premier pas vers la création d'un modèle qui tiendrait compte du poids " idéal " estimé par les méthodes déjà existantes et y ajouterait la possibilité d'estimer la masse de tissus mous à partir du squelette.