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Author |
Shi, P.; Gielis, J.; Quinn, B.K.; Niklas, K.J.; Ratkowsky, D.A.; Schrader, J.; Ruan, H.; Wang, L.; Niinemets, Ü.; Niinennets, U. |
![goto web page (via DOI) doi](http://nano.uantwerpen.be/nanorefs/img/doi.gif)
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Title |
‘biogeom’ : an R package for simulating and fitting natural shapes |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Annals of the New York Academy of Sciences |
Abbreviated Journal |
Ann Ny Acad Sci |
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Volume |
1516 |
Issue |
1 |
Pages |
123-134 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Many natural objects exhibit radial or axial symmetry in a single plane. However, a universal tool for simulating and fitting the shapes of such objects is lacking. Herein, we present an R package called 'biogeom' that simulates and fits many shapes found in nature. The package incorporates novel universal parametric equations that generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings, and three growth-rate equations that generate the profiles of ovate leaves and the ontogenetic growth curves of animals and plants. 'biogeom' includes several empirical datasets comprising the boundary coordinates of bird eggs, fruits, lanceolate and ovate leaves, tree rings, seeds, and sea stars. The package can also be applied to other kinds of natural shapes similar to those in the datasets. In addition, the package includes sigmoid curves derived from the three growth-rate equations, which can be used to model animal and plant growth trajectories and predict the times associated with maximum growth rate. 'biogeom' can quantify the intra- or interspecific similarity of natural outlines, and it provides quantitative information of shape and ontogenetic modification of shape with important ecological and evolutionary implications for the growth and form of the living world. |
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Wos |
000829772300001 |
Publication Date |
2022-07-26 |
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Series Issue |
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Edition |
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ISSN |
0077-8923; 1749-6632 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.2 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 5.2 |
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Call Number |
UA @ admin @ c:irua:189314 |
Serial |
7131 |
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Permanent link to this record |
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Author |
Li, Y.; Niklas, K.J.; Gielis, J.; Niinemets, Ü.; Schrader, J.; Wang, R.; Shi, P. |
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Title |
An elliptical blade is not a true ellipse, but a superellipse : evidence from two Michelia species |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Journal of forestry research |
Abbreviated Journal |
J Forestry Res |
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Volume |
33 |
Issue |
4 |
Pages |
1341-1348 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
The shape of leaf laminae exhibits considerable diversity and complexity that reflects adaptations to environmental factors such as ambient light and precipitation as well as phyletic legacy. Many leaves appear to be elliptical which may represent a ‘default’ developmental condition. However, whether their geometry truly conforms to the ellipse equation (EE), i.e., (x/a)2 + (y/b)2 = 1, remains conjectural. One alternative is described by the superellipse equation (SE), a generalized version of EE, i.e., |x/a|n +|y/b|n = 1. To test the efficacy of EE versus SE to describe leaf geometry, the leaf shapes of two Michelia species (i.e., M. cavaleriei var. platypetala, and M. maudiae), were investigated using 60 leaves from each species. Analysis shows that the majority of leaves (118 out of 120) had adjusted root-mean-square errors of < 0.05 for the nonlinear fitting of SE to leaf geometry, i.e., the mean absolute deviation from the polar point to leaf marginal points was smaller than 5% of the radius of a hypothesized circle with its area equaling leaf area. The estimates of n for the two species were ˂ 2, indicating that all sampled leaves conformed to SE and not to EE. This study confirms the existence of SE in leaves, linking this to its potential functional advantages, particularly the possible influence of leaf shape on hydraulic conductance. |
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Wos |
000695118600001 |
Publication Date |
2021-09-12 |
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Edition |
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ISSN |
1007-662x; 1993-0607 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3 |
Times cited |
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Open Access |
OpenAccess |
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Approved |
Most recent IF: 3 |
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Call Number |
UA @ admin @ c:irua:180967 |
Serial |
7152 |
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Author |
Li, Y.; Quinn, B.K.; Niinemets, Ü.; Schrader, J.; Gielis, J.; Liu, M.; Shi, P. |
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Title |
Ellipticalness index : a simple measure of the complexity of oval leaf shape |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Pakistan journal of botany : An official publication of pakistan botanical society |
Abbreviated Journal |
Pak J Bot |
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Volume |
54 |
Issue |
6 |
Pages |
1-8 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Plants have diverse leaf shapes that have evolved to adapt to the environments they have experienced over their evolutionary history. Leaf shape and leaf size can greatly influence the growth rate, competitive ability, and productivity of plants. However, researchers have long struggled to decide how to properly quantify the complexity of leaf shape. Prior studies recommended the leaf roundness index (RI = 4πA/P2) or dissection index (DI = ), where P is leaf perimeter and A is leaf area. However, these two indices merely measure the extent of the deviation of leaf shape from a circle, which is usually invalid as leaves are seldom circular. In this study, we proposed a simple measure, named the ellipticalness index (EI), for quantifying the complexity of leaf shape based on the hypothesis that the shape of any oval leaf can be regarded as a variation from a standard ellipse. 2220 leaves from nine species of Magnoliaceae were sampled to check the validity of the EI. We also tested the validity of the Montgomery equation (ME), which assumes a proportional relationship between leaf area and the product of leaf length and width, because the EI actually comes from the proportionality coefficient of the ME. We also compared the ME with five other models of leaf area. The ME was found to be the best model for calculating leaf area based on consideration of the trade-off between model fit vs. complexity, which strongly supported the robustness of the EI for describing oval leaf shape. The new index can account for both leaf shape and size, and we conclude that it is a promising method for quantifying and comparing oval leaf shapes across species in future studies. |
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Wos |
000814279700028 |
Publication Date |
2022-05-23 |
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Series Volume |
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Edition |
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ISSN |
0556-3321 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
1.2 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 1.2 |
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Call Number |
UA @ admin @ c:irua:188469 |
Serial |
7153 |
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Permanent link to this record |
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Author |
Yao, W.; Niinemets, Ü.; Yao, W.; Gielis, J.; Schrader, J.; Yu, K.; Shi, P. |
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Title |
Comparison of two simplified versions of the Gielis equation for describing the shape of bamboo leaves |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Plants |
Abbreviated Journal |
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Volume |
11 |
Issue |
22 |
Pages |
3058-11 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
Bamboo is an important component in subtropical and tropical forest communities. The plant has characteristic long lanceolate leaves with parallel venation. Prior studies have shown that the leaf shapes of this plant group can be well described by a simplified version (referred to as SGE-1) of the Gielis equation, a polar coordinate equation extended from the superellipse equation. SGE-1 with only two model parameters is less complex than the original Gielis equation with six parameters. Previous studies have seldom tested whether other simplified versions of the Gielis equation are superior to SGE-1 in fitting empirical leaf shape data. In the present study, we compared a three-parameter Gielis equation (referred to as SGE-2) with the two-parameter SGE-1 using the leaf boundary coordinate data of six bamboo species within the same genus that have representative long lanceolate leaves, with >300 leaves for each species. We sampled 2000 data points at approximately equidistant locations on the boundary of each leaf, and estimated the parameters for the two models. The root–mean–square error (RMSE) between the observed and predicted radii from the polar point to data points on the boundary of each leaf was used as a measure of the model goodness of fit, and the mean percent error between the RMSEs from fitting SGE-1 and SGE-2 was used to examine whether the introduction of an additional parameter in SGE-1 remarkably improves the model’s fitting. We found that the RMSE value of SGE-2 was always smaller than that of SGE-1. The mean percent errors among the two models ranged from 7.5% to 20% across the six species. These results indicate that SGE-2 is superior to SGE-1 and should be used in fitting leaf shapes. We argue that the results of the current study can be potentially extended to other lanceolate leaf shapes. |
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Wos |
000887783400001 |
Publication Date |
2022-11-14 |
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ISSN |
2223-7747 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:191859 |
Serial |
7289 |
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Permanent link to this record |
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Author |
Niklas, K.J.; Shi, P.; Gielis, J.; Schrader, J.; Niinemets, U. |
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Title |
Editorial: leaf functional traits : ecological and evolutionary implications |
Type |
Editorial |
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Year |
2023 |
Publication |
Frontiers in plant science |
Abbreviated Journal |
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Volume |
14 |
Issue |
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Pages |
1169558-5 |
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Keywords |
Editorial; Sustainable Energy, Air and Water Technology (DuEL) |
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Wos |
000964122500001 |
Publication Date |
2023-03-21 |
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Abbreviated Series Title |
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ISSN |
1664-462x |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.6 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 5.6; 2023 IF: 4.298 |
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Call Number |
UA @ admin @ c:irua:196076 |
Serial |
7834 |
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Permanent link to this record |
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Author |
Shi, P.; Liu, M.; Ratkowsky, D.A.; Gielis, J.; Su, J.; Yu, X.; Wang, P.; Zhang, L.; Lin, Z.; Schrader, J. |
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Title |
Leaf area-length allometry and its implications in leaf shape evolution |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Trees: structure and function |
Abbreviated Journal |
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Volume |
33 |
Issue |
4 |
Pages |
1073-1085 |
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Keywords |
A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
According to Thompson’s principle of similarity, the area of an object should be proportional to its length squared. However, leaf area–length data of some plants have been demonstrated not to follow the principle of similarity. We explore the reasons why the leaf area–length allometry deviates from the principle of similarity and examine whether there is a general model describing the relationship among leaf area, width and length. We sampled more than 11,800 leaves from six classes of woody and herbaceous plants and tested the leaf area–length allometry. We compared six mathematical models based on root-mean-square error as the measure of goodness-of-fit. The best supported model described a proportional relationship between leaf area and the product of leaf width and length (i.e., the Montgomery model). We found that the extent to which the leaf area–length allometry deviates from the principle of similarity depends upon the extent of variation of the ratio of leaf width to length. Estimates of the parameter of the Montgomery model ranged between 1/2, which corresponds to a triangular leaf with leaf length as its height and leaf width as its base, and π/4, which corresponds to an elliptical leaf with leaf length as its major axis and leaf width as its minor axis, for the six classes of plants. The narrow range in practice of the Montgomery parameter implies an evolutionary stability for the leaf area of large-leaved plants despite the fact that leaf shapes of these plants are rather different. |
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Wos |
000475992600010 |
Publication Date |
2019-04-04 |
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Edition |
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ISSN |
0931-1890; 1432-2285 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Times cited |
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Open Access |
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Approved |
no |
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Call Number |
UA @ admin @ c:irua:159970 |
Serial |
8170 |
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Permanent link to this record |
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Author |
Shi, P.; Gielis, J.; Niklas, K.J.; Niinemets, Ü.; Schrader, J. |
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Title |
Leaf functional traits : ecological and evolutionary implications |
Type |
ME3 Book as editor |
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Year |
2023 |
Publication |
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Abbreviated Journal |
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Volume |
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Issue |
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Pages |
185 p. |
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Keywords |
ME3 Book as editor; Sustainable Energy, Air and Water Technology (DuEL) |
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Wos |
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Publication Date |
2023-04-14 |
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ISBN |
978-2-8325-2086-4; 1664-8714 |
Additional Links |
UA library record |
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Impact Factor |
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Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:198002 |
Serial |
8894 |
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Permanent link to this record |