Documenti di Didattica
Documenti di Professioni
Documenti di Cultura
B I O LO G Y
F O RU M
107 · 1-2/2014
PISA · ROMA
FABRIZIO SERRA EDITORE
MMXIV
Autorizzazione del Tribunale di Pisa n. 13 del 14 maggio 2012.
Già registrata presso il Tribunale di Genova: registrazione n. 22/96 del 2 maggio 1996.
Direttore responsabile: Fabrizio Serra
*
Amministrazione e abbonamenti
Fabrizio Serra editore ®
Casella postale n. 1, succursale n. 8, I 56123 Pisa
Uffici di Pisa: Via Santa Bibbiana 28, I 56127 Pisa,
tel. +39 050542332, fax +39 050574888, fse@libraweb.net
Uffici di Roma: Via Carlo Emanuele I, I 00185 Roma,
tel. +39 0670493456, fax +39 0670476605, fse.roma@libraweb.net
*
I prezzi ufficiali di abbonamento cartaceo e/o Online sono consultabili
presso il sito Internet della casa editrice www.libraweb.net.
Print and/or Online official subscription rates are available at Publisher’s website www.libraweb.net.
I pagamenti possono essere effettuati tramite versamento su c.c.p. n. 17154550 indirizzato a:
Fabrizio Serra editore ® o tramite carta di credito (American Express, Eurocard, Mastercard, Visa).
Suscriptions should be paid by cheque/international money order to
Fabrizio Serra editore, casella postale 1, succ. 8, I, 56123 Pisa, or by Bank transfer
(Monte dei Paschi di Siena, iban it 90g 0103014009000000012660, swift code pascitm 1y 71),
or by credit card (American Express, Eurocard, Mastercard, Visa).
*
Proprietà riservata · All rights reserved
© Copyright 2014 by Fabrizio Serra editore, Pisa · Roma.
Fabrizio Serra editore incorporates the Imprints Accademia editoriale,
Edizioni dell’Ateneo, Fabrizio Serra editore, Giardini editori e stampatori in Pisa,
Gruppo editoriale internazionale and Istituti editoriali e poligrafici internazionali.
www.libraweb.net
A norma del codice civile italiano, è vietata la riproduzione, totale o parziale
(compresi estratti, ecc.), di questa pubblicazione in qualsiasi forma e versione
(comprese bozze, ecc.), originale o derivata, e con qualsiasi mezzo a stampa o internet
(compresi siti web personali e istituzionali, academia.edu, ecc.), elettronico, digitale,
meccanico, per mezzo di fotocopie, pdf, microfilm, film, scanner o altro,
senza il permesso scritto della casa editrice.
Under Italian civil law this publication cannot be reproduced, wholly or in part (included offprints, etc.),
in any form (included proofs, etc.), original or derived, or by any means: print, internet
(included personal and institutional web sites, academia.edu, etc.), electronic, digital, mechanical,
including photocopy, pdf, microfilm, film, scanner or any other medium,
without permission in writing from the publisher.
ISSN 2282-2593
ISSN ELETTRONICO 1825-6538
CONTENTS
Editorial 9
articles
Pieranna Fietta, Elvira Costa, Giovanni Delsante, Interleukins (ILS),
a Fascinating Family of Cytokines. Part I: ILS from IL-1 to IL-19 13
Katell Guizien, Lorenzo Bramanti, Modelling Ecological Complexity for
Marine Species Conservation: the Effect of Variable Connectivity on Species
Spatial Distribution and Age-structure 47
Gianluca Martelloni, Alisa Santarlasci, Franco Bagnoli, Giacomo
Santini, Modeling Ant Battles by Means of a Diffusion-Limited Gillespie Algo-
rithm 57
Giulia Menichetti, Daniel Remondini, Entropy of a Network Ensemble:
Definitions and Applications to Genomic Data 77
Marco Pellegrini, Giuseppe Pirillo, On the Dinucleotide Circular Codes of
Maximum Cardinality 89
Sergio Pennazio, Elements of Plant Physiology in Theophrastus’ Botany 97
Dušan Ristanović, Bratislav D. Stefanović, Nela Puškaš, Fractal
Analysis of Dendrite Morphology of Rotated Neuronal Pictures: The Modified
Box Counting Method 109
Alessia Rossi, Simone Panigada, Massimo Arrigoni, Margherita Za-
nardelli, Cristina Cimmino, Luigi Marangi, Piero Manfredi, Gio-
vanni Santangelo, Demography and Conservation of the Mediterranean Fin
Whale (Balaenoptera physalus): What Clues can be obtained from Photo-Identifi-
cation Data 123
Sureyya Mert Selimoglu, Conscience Dilemma: to become a Bioengineer or to
survive as a Biologist 143
Masomeh Taherian, Megerdich Toomanian, Mohammadreza Molaei,
A Dynamical Model for Influenza under Seasonal Variables 151
Armando Bazzani, Paolo Freguglia, Dynamics on Genes Network Struc-
tures. An Ago-Antagonist Approach 163
Abstract: The fractal dimension of a non-stel- position of a picture on the computer’s screen. A
late neuron changes continuously with rotation dispersion of the box dimension values of a sam-
of the neuronal picture. For a stellate neuron ple is generally rather large so that their mean
such changes cannot be noticed. During prepro- value is with larger standard deviation. Modi-
cessing for the box counting, non-stellate neurons fied box counting method partly diminishes these
should be arranged so that the major diameters findings. To improve a dependence on neuronal
of their dendrite fields are parallel. It was shown rotation for the box counting dimension of non-
that a non-stellate neuronal picture had the stellate neurons, prior to applying the box count-
smallest box dimension when the angle between ing, the non-stellate neurons should be arranged
the horizontal or vertical axis and its major di- so that the major diameters of their dendrite
ameter was about 45°.The box counting method fields are parallel.
which uses ImageJ software does not consider the
1. Introduction
Fig. 1. Sixteen representative examples of pyramidal neurons. Neurons are selected within fron-
toparietal cortex being dorsally and dorso-laterally positioned in the coronal sections of the rat
forebrain and of cerebral cortex hemispheres. All apical primary dendrites are oriented vertically.
The cortical layers are denoted by Roman numerals. Scale bar: 50 Ìm.
2. 2. Statistics
2. 2. 1. Testing small samples for normality
In order to use a Chi-square distribution to test a population for normality, a fairy
large sample from the population is necessary. In the case of small samples, where
the number of variates is 30 or less [19], we have adopted the criteria for normality
of data distribution offered by Smirnov and Barkovskiy [20]. The method is related
to estimating the third (m3) and fourth (m4) empirical moment about the mean. The
moment of the order k is
n
∑ (X − X
i =1
i av )k
(1)
mk =
n
where Xi is the variate i of the variable X, Xav is the sample mean and n is the num-
ber of variates.
One of the measures describing the asymmetry of a distribution about its maxi-
mum is called the skewness (A), and a measure of the degree of the kurtosis (m4) of
the distribution is called the excess (E). They are given, respectively, as
m3 m
A= 3
E = 44 − 3 (2)
s s
where s is the empirical standard deviation (known as the best estimate of the stan-
dard deviation of the population) which is given by
n
∑ (X − X
i =1
i av )2
(3)
s=
n −1
The value of the skewness for a perfectly symmetrical distribution of data is zero
and the excess for the normal curve has also the value equals zero. In the case of an
experimental normal distribution these parameters should be very small (close to
zero). The degree of how much they should be small to enable the distribution nor-
mality can be estimated by dividing the corresponding mean standard deviations of
asymmetry and excess
6( n − 1) 24n( n − 2)( n − 3)
σ3 = , σ4 = (4)
( n + 1)( n + 3) ( n − 1) 2 ( n + 3)( n + 5)
by the values given by Eq. (2), where n is the number of variates in the sample. If
σ3 σ4
≤ 2.0 ≤ 2.0 (5)
A E
there are grounds for strong believing that the data are normally distributed [20].
fractal analysis of dendride morphology 113
∑ (d − d )
2
i av
i =1 (6)
SE =
n( n − 1)
where n is the number of pairs.
The resulting t statistic is determined by
dav
. t= (7)
SE
If ‰ is the difference between the means of the two populations, the hypotheses are:
H0: ‰ = 0 (there is no difference between the populations); H1: ‰ ≠ 0 (there is a dif-
ference between the populations - treatments). We reject the null hypothesis at a sig-
nificance level p if t > ttab, where ttab is the critical value from the Student’s table,
with n – 1 degrees of freedom, where n is the number of pairs. If t < ttab the hy-
pothesis is accepted.
2. 2. 3. Fisher’s F test
For a sample of n variates, X1, X2, X3, …, Xn, whose mean is Xav, the best estimate of
the standard deviation of the population, denoted by s, is given by Eq. (3). The
square of the standard deviation [Eq. (3)] is called the variance. The variance is wide-
ly used as a measure for dispersion of a set of variates about their mean. The vari-
ances of two samples are said to be homogeneous if the populations from which the
two samples are selected, have identical variances (or identical standard deviations).
If X and Y are normally distributed populations with identical standard deviations,
than the ratio of the squares of the best estimates of the standard deviations (the
ratio of the variances), that is,
s x2
F= (8)
s y2
Where
nx ny
∑ (X − X
i =1
i av ) 2
∑ (Y − Y
i =1
i av )2
(9)
s x2 = s y2 =
nx − 1 ny − 1
114 dušan ristanović · bratislav d. stefanović · nela puškaš
Fig. 3. Relations between the fractal (box) dimensions and the rotational angle (A) for the
skeletonized square (the data of each branch are fitted by a general second-degree function, the co-
efficient of correlation being R1 = 0.988), (B) and for the binary square (the data of each branches
are fitted by a general third-degree polynomial, the coefficient of correlation being R2 = 0.959).
Fig. 4. Relations between the fractal (box) dimensions and rotational angle (A) of a skeletonized
neuron 5 selected at random from Fig. 1, (B) and of a binary picture of the same neuron. In both
cases the minima are about 40°. Data points are connected using the spline-B function.
dimension of the square decreases when the angle of the square changes from 0°
to 45°. After that the box dimension increases. Each branch of these data is fitted
using the second-degree polynomial. In Fig. 3B where the square is shown as a bi-
nary image (the width of the lines is 1 pt) a similar result is obtained. The branches
are fitted using the third-degree polynomial.
(2) From Fig. 1 we selected, at random, a neuron (say, neuron 5), chose its api-
cal dendrite and performed with it the same procedure as with the square in the
preceding example. In Fig. 4A it is shown that the fractal dimension of the skele-
tonized neuron also decreases to the value around 40° and that of the binary pic-
ture of the neuron decreases to the value around 45° (Fig. 4B). Small deviations
from 45° are the consequence of some branches of the primary dendrite which
emanate from the apical stem in diverse directions.
116 dušan ristanović · bratislav d. stefanović · nela puškaš
(3) We applied the ImageJ on a non-
stellate binary picture in Fig. 10 [3],
which represents the arbor of a non-
stellate neuron used from a 34-week-old
human fetus (adopted from Schoenen
[17] - with permission). The picture is
continuously rotated from 0° to 90° and
the relation between the fractal dimen-
sion and angle of rotation is presented
in Fig. 5. The graph is similar to that
shown in Fig. 4. From Fig. 5 it is seen
Fig. 5. Relation between the fractal (box)
that the fractal dimension of the picture
dimension and angle of rotation of the binary whose major diameter (see later) is un-
neuron shown in Fig. 2. Data points are der the angle of about 45° is again the
connected using the spline-B function. smallest one.
Fig. 6. Relations between the fractal (box) dimensions and the space-filling capacity
(A) of the skeletonized square (the data are fitted by a general first-degree function,
the coefficient of correlation R1 = 0.988), (B) and of the binary square
(the data are fitted by a general first-degree polynomial, R2 = 0.963).
Picture Dav ± SE t F
(0°) (45°) (20° - 320°) 0° - 45° 0° - (20° - 320°)
Binary 1.357 ± 0.005 1.325±0.006 1.338 ± 0.008 4.301** 3.684* 2.63
Skeletonized 1.139 ± 0.006 1.110 ± 0.004 1.133 ± 0.009 5.821** 3.227* 2.49
* p < 0.01. ** p < 0.001
Tab. 2. Results of statistical analysis of the distribution of box-counting fractal dimensions
for binary and skeletonized pictures of pyramidal neurons. The values of mean fractal
dimensions are given as the means (Dav) and standard errors (SE) when the neurons were
in vertical position 0° (Fig. 1), rotated for 45° and rotated between 20° and 320° (see text).
Parameter t is the Student’s statistic and F is the Fisher’s statistic.
118 dušan ristanović · bratislav d. stefanović · nela puškaš
Fig. 7. The bar graph. The graph represents the box dimensions of 16 binary neurons
in vertical position, as in Fig. 1 (the first bars, in black) and those of the same neurons
rotated for 45° (the second bars in groups of two, in gray).
4. Discussion
Panico and Sterling [9] noticed that for large boxes the box-counting method is sen-
sitive to the position of the figure upon the grid, so they averaged as many as 200
fractal analysis of dendride morphology 119
Fig. 8. The bar graph. The graph represents the box dimensions of 16 skeletonized neurons
in vertical position, as in Fig. 1 (the first bars, in black) and those of the same neurons
rotated for 45° (the second bars, in gray).
trials for each grid size, randomizing the grid position for each trial. We have
reported that if a picture is translated into CorelDraw software and such a new
picture is read into ImageJ software, its fractal dimension remained the same [14].
In the present study we reported that the box dimension measured using ImageJ
depends on the rotating position of the picture.
Panico and Sterling [9] stated that the fractal dimension reflects an average of the
pattern’s interior (whose fractal dimension is 2) and its boundary (whose fractal di-
mension approximates 1). Although these assertions seem attractive, no explicit
proof for them has been offered yet.
Neale et al. [7] claimed that total dendrite length could be obtained by counting
the number of black pixels in the skeletonized image. This can be correct only if
the dendrites of an arbor are horizontal and/or vertical with no axial inflections
which are seldom obtained in experimental data.
Stellate neurons comprise a rather broad class of cells. Stellate cells are found
throughout the brain and spinal cord, and predominate in non-laminated subcorti-
cal nuclei such as the inferior olive, pontine nuclei, striatum, thalamus, etc. [16]. The
box-counting method can be directly applied to these neurons. For the other types
of neurons, the modified box-counting method proposed here is advisable.
The rotation of neurons has been previously used and discussed by some authors
[11, 23, 24]. For example, Montaque and Friedlander [23] were randomly varied the
position and orientation of the overlay drawing relative to the grid. At each partic-
ular box size, this procedure was done 10 times. The number of boxes intersected
120 dušan ristanović · bratislav d. stefanović · nela puškaš
was then averaged. Thus, they calculated the mean fractal dimension for a neuron,
while we calculated this mean but for a sample of neurons.
5. Conclusion
We propose a modification to box-counting methods to address rotational variation
in non-stellate neurons. We recommend arranging pictures of neurons of a given
sample with non-stellate dendritic fields so that, when possible, the major axes of
the fields are parallel (see Fig. 1), prior to applying box-counting methods. This is
likely to reduce spurious effects on the box counting dimension that are attributa-
ble to image orientation and can obscure measures of a pattern’s complexity.
References
1. Mandelbrot BB. The Fractal Geometry of nature. 20th ed. New York: NW Freeman and Co;
2004.
2. Caserta F, Eldred WD, Fernández E, Hausman RE, Stanford LR, Buldyrev SV, et alii.
Determination of fractal dimension of physiologically characterized neurons in two and three
dimensions. J Neurosci Meth. 1995; 56: 133-144.
3. Ristanović D, Milošević NT. Fractal analysis: methodologies for biomedical research. Theor.
Biol Forum. 2012; 105(2): 99-108.
4. Losa GA. The fractal geometry of life. Riv Biol. 2009; 102(1): 29-59.
5. Morigiwa K, Tauchi M, Fukuda Y. Fractal analysis of ganglion cell dendritic branching
patterns of the rat and cat retinae. Neurosci Res. 1989; 10: S131-S140.
6. Smith TG, Marks WB, Lange DG, Sheriff WH, Neale EA. A fractal analysis of cell images.
J Neurosci Meth. 1989; 27: 173-180.
7. Neale EA, Bowers LM, Smith TG. Early dendrite development in spinal cord cell cultures: a
quantitative study. J Neurosci Res. 1993; 34: 54-66.
8. Smith TG, Lange DG, Marks WB. Fractal methods and results in cellular morphology -
dimensions, lacunarity and multifractals. J Neurosci Meth. 1996; 69: 123-136.
9. Panico J, Sterling P. Retinal neurons and vessels are not fractal but space-filling. J. Comp
Neurol. 1995; 36: 479-490.
10. Voss RF. Random fractal forgeries. In: Earhsghow RA, editor. Fundamental Algorithms for
Computer Graphics. NATO ASI Berlin: Springer; Series, Vol. F17, 1985: 805-835.
11. Fernández E, Jelinek HF. Use of fractal theory in neuroscience: methods, advantages, and
potential problems. Methods. 2001; 24: 309-321.
12. Jelinek HF, Ristanović D, Milošević NT. The morphology and classification of alpha ganglion
cells in the rat retinae: a fractal analysis study. J Neurosci. Meth. 2011; 201: 281-287.
13. Ristanović D, Krstonošić B, Milošević NT, Gudović R. Mathematical modelling of
transformations of asymmetrically distributed biological data: an application to a quantitative
classification of spiny neurons of the human putamen. J Theor Biol. 2012; 302: 81-88.
14. Ristanović D, Stefanović BD, Puškaš N. Fractal analysis of dendrites morphology using
modified Richardson’s and box-counting method. Theor. Biol. Forum. 2013; 1-2: 157-168.
15. Schneider CA, Rasband WS, Eliceir KW. NIH Image to ImageJ: 25 years of image analysis,
Nature Methods. 2012; 9: 671-685.
16. Fiala JC, Harris KM. Dendrite structure. In: Stuar G, Spruston N, Häustorn M, editors.
Dendrites. Oxford: Oxford Univ Press; 2002; 1-34.
17. Schoenen J. The dendritic organization of the human spinal cord: the dorsal horn. Neuro-
science 1982; 7: 2057-2087.
fractal analysis of dendride morphology 121
18. Milošević NT, Ristanović D, Stanković JB. Fractal analysis of the laminar organization of
spinal cord neurons. J Neurosci Meth. 2005; 146: 198-204.
19. Alder HL, Roessler EB. Introduction to Probability and Statistics. San Francisco: W.H. Free-
man and Co; 1972.
20. Kurickiy BY, Mathematical Methods in Physiology (in Russian). Leningrad: Nauka; 1969.
21. Dodge Y. The Concise Encyclopedia of Statistics. Berlin: Springer; 2008.
22. Milošević NT, Ristanović D, Jeline HF, Rajković K. Quantitative analysis of dendritic
morphology of the alpha and delta retinal ganglion cells in the rat: a cell classification study. J
Threor Biol. 2009; 259: 142-150.
23. Montague PR, Friedlander MJ. Expression of an intrinsic growth strategy by mammalian
retinal neurons. Proc Natl Acad Sci USA. 1989; 86: 7223-7227.
24. Montague PR, Friedlander MJ, Morphogenesis and territorial coverage by isolated
mammalian retinal ganglion cells. J Neurosci. 1991; 11(5): 1440-1457.
set in dante monotype by
fabrizio serr a editore, pisa · roma.
printed and bound by
tipo gr afia di agnano, agnano pisano (pisa).
*
December 2014
(cz 2 · fg 21)