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ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
Volume 2, Issue 4, April 2013
1330
www.ijarcet.org
A Review of Soft Computing Advance in Genetics & Laser Biomedical
Instrumentation
1
Dr.
Tryambak A. Hiwarkar, 2
Sridhar Iyer
1
Asso Prof, Computer Science and Engineering, MBITM, Dongargarh (C.G.)
2
Research Scholar, Computer Science, CMJ University, Shillong
ABSTRACT
Soft computing refers to a collection of
computational techniques in computer
science, artificial intelligence, machine
learning, medical instrumentation which
attempt to study, model and analyze very
complex phenomena. The principal
constituents of Soft Computing (SC) are
Neural Networks, Fuzzy Systems,
Evolutionary Computation, Machine
Learning and Probabilistic Reasoning. The
paper studies the biological background of
cells, nucleic acids and terminologies in
genetic algorithms and also uric acid
metabolism with chemical tests and finally
laser lithotripsy procedure.
Keywords:
DNA, RNA, SC, Laser, Genes, Chromosomes,
Lithotripsy
I. INTRODUCTION:
Soft computing is a term applied to a field
within computer science which is
characterized by the use of inexact solutions
to computationally hard tasks such as the
solution of NP complete problems for which
there is no known algorithm that can
compute an exact solution in polynomial
time and is tolerant of imprecision,
uncertainty, partial truth and approximation
and role model for soft computing is the
human mind.
The evolutionary computing algorithms can
be considered global optimization methods
with a met heuristic or stochastic
optimization character and are mostly
applied for black box problems and uses
iterative progress such as growth or
development in a population and is selected
in guided random search using parallel
processing to achieve the desired end and
processes are often inspired by biological
mechanisms of evolution which produces
highly optimized processes and networks it
has many applications in computer science.
1.1 Extents
The soft computing approach provides
problem solving techniques in genetics,
biochemistry, genetic algorithms and neural
networks. The nucleic acids studies DNA
and RNA and genetic algorithms analyzes
various algorithmic approaches in computer
science. The uric acid metabolism and its
chemical examination in kidney stone
expanded for complex procedures. The laser
lithotripsy is a surgical removal of kidney
stones and powerful medical equipments are
available.
1.2 Biological Environment
The science that deals with the mechanisms
responsible for similarities and differences
in a species is called genetics.
1.3 Terminologies Cell
Every animal / human cell is a complex of
many small factories that work together. The
center of all this is the cell nucleus. The
genetic information is contained in the cell
nucleus.
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
Volume 2, Issue 4, April 2013
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Fig.1 Terminologies Cell
II. CHROMOSOMES
All the genetic information gets stored in the
chromosomes. Each chromosome is build of
deoxyribonucleic acid (DNA). In humans
the chromosomes exist in 23 pairs.
The chromosomes are divided into several
parts called genes. Genes code the properties
of species, i.e. the characteristics of an
individual. The possibilities of combination
of the genes for one property are called
alleles and a gene can take different alleles.
The size of the gene pool helps in
determining the diversity of the individuals
in the population and the set of all genes of a
specific species is called genome. Each and
every gene has a unique position on the
genome called locus. The most living
organisms store their genome on several
chromosomes but in the GA all the genes are
usually stored on the same chromosomes.
Thus chromosomes and genomes are
synonyms with one other in GA.
Fig .2 Chromosome
III. GENETICS
For a particular individual the entire
combination of genes is called genotype.
The phenotype describes the physical aspect
of decoding a genotype to produce the
phenotype also selection is always done on
the phenotype whereas the reproduction
recombines genotype.
Thus morphogenesis plays a key role
between selection and reproduction. In
higher life forms chromosomes contain two
sets of genes. These are known as diploids.
In the case of conflicts between two values
of the same pair of genes the dominant one
will determine the phenotype whereas the
other one called recessive will still be
present and can be passed on to the
offspring.
Diploid allows a wider diversity of alleles.
This provides a useful memory mechanism
in changing or noisy environment. The most
GA concentrates on haploid chromosomes
because they are much simple to construct.
In haploid representation only one set of
each gene is stored thus the process of
determining which allele should be
dominant and which one should be recessive
is avoided.
Fig.3 genes
3.1 REPRODUCTION
Reproduction of species via genetic
information is carried out by the following
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
Volume 2, Issue 4, April 2013
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3.2 MITOSIS
In Mitosis the same genetic information is
copied to new offspring. There is no
exchange of information. This is a normal
way of growing of multi cell structures such
as organs.
3.3 MEIOSIS
Meiosis forms the basis of sexual
reproduction. When meiotic division takes
place two gametes appear in the process.
Ehen reproduction occur these two gametes
conjugate to a zygote which becomes the
new individual. Thus in this case the genetic
information is shared between the parents in
order to create new offspring.
NATURAL
EVOLUTION
GENETIC
ALGORITHM
Chromosome
Gene
Allele
Locus
Genotype
Phenotype
String
Feature or
character
Feature value
String position
Structure or Coded
String
Parameter Set &
Decoded Structure
3.4 NATURAL SELECTION
The origin of species is based on
Preservation of favorable variations and
rejection of unfavorable variations. The
variation refers to the differences shown by
the individual of a species and also by
offspring’s of the same parents. There are
more individuals born than can survive so
there is a continuous struggle for the
individuals with an advantage have a greater
chance of survival i.e. the survival of the
fittest.
Fig. 4 Nature Selection
IV. NUCLEIC ACID
Nucleic acids fall into two principal classes
according to the nature of the sugar they
contain the deoxyribonucleic acids (DNA)
and the ribose containing nucleic acids
(RNA). DNA is found primarily in cell
nuclei and certain viruses but it also occurs
in other portions of cells such as
mitochondria. It is associated with the
storage and expression of genetic
information and the primary processes of
heredity.
The major types of nucleic acid are
1. Nuclear Deoxyribonucleic Acids
2. Messenger Ribonucleic Acids
3. Transfer or Soluble Ribonucleic
Acids
4. Ribosomal Ribonucleic Acids
5. Vital Nucleic Acids
6.
4.1 DNA (DEOXYRIBONUCLEIC
ACIDS)
DNA (a double stranded molecule) is
present in the nucleus of eukaryotic
organisms and it is also found in the
mitochondria and chloroplasts. DNA is the
chemical basis of heredity and may be
regarded as the reserve source of genetic
information.
DNA is exclusively responsible for
maintaining the identity of different species
of organisms. Every aspect of cellular
function is under the control of DNA. Gene
is a unit of heredity and it does not have
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
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independent existence but it is a stretch of
DNA.
4.2 Nucleotides
Nucleotides are composed of a nitrogenous
base, a pentose sugar and a phosphate.
4.3 Nucleosides
Nucleosides are composed of a nitrogenous
base and a pentose sugar.
4.4 Nitrogenous Bases
Nitrogenous bases are mainly Purines and
Pyrimidines found in nucleic acid.
Purines are Adenine (A) and Guanine (G)
Pyrimidines are Cytosine (C), Thymine (T)
and Uracil (U)
The two sugars are D - Ribose and 2 –
Deoxy – D – Ribose
V. DEOXYRIBOSE SUGAR:
The deoxyribose sugar of the DNA
backbone has 5 carbons and 3 oxygen. The
carbon atoms are numbered 1', 2', 3', 4' and
5' to distinguish from the numbering of the
atoms of the purines and pyrimidines rings.
The hydroxyl groups on the 5'- and 3'-
carbons link to the phosphate groups to form
the DNA backbone. Deoxyribose lacks
hydroxyl group at the 2'-position when
compared to ribose and sugar component of
RNA
5.1 PURINES
Purine is a heterocyclic aromatic organic
compound. It consists of a pyrimidine ring
fused to an imidazole ring. Purines including
substituted purines and their tautomers are
the most widely occurring nitrogen
containing heterocycle in nature.
Purines and Pyrimidines make up the two
groups of nitrogenous bases including the
two groups of nucleotide bases. Two of the
four de-oxyribonucleotides and two of the
four ribo nucleotides, the respective building
blocks of DNA and RNA are pureness.
There are many naturally occurring purines
and two of the four bases in nucleic acids
are Adenine and Guanine which are
purines. In DNA these bases form hydrogen
bonds with their complementary pyrimidines
like thymine and cytosine. This is called
complementary base pairing. In RNA the
complement of adenine is uracil instead of
thymine. The other notable purines are
Hypoxanthine, Xathine, Theobromine,
Caffeine, Uric acid and Isoguanine
5.2 ADENINE
Adenine is a nucleobase (a purine
derivative) with a variety of roles in
biochemistry including cellular respiration
in the form of both the energy rich
adenosine triphosphate (ATP) and the
cofactors nicotinamide adenine dinucleotide
(NAD) and flavin adenine dinucleotide
(FAD) and protein synthesis as a chemical
component of DNA and RNA. Adenine is
one of the two purine nucleobases (guanine)
used in forming nucleotides of the nucleic
acids. In DNA adenine binds to thymine via
two hydrogen bonds to assist in stabilizing
the nucleic acid structures and RNA which
is used for protein synthesis and also binds
to uracil Adenine formed adenosine, a
nucleoside when attached to ribose and
deoxyadenosine when attached to
deoxyribose. It forms adenosine
triphosphate (ATP), nucleotide when three
phosphate groups are added to adenosine.
Adenosine triphosphate is used in cellular
metabolism as one of the basic methods of
transferring chemical energy between
chemical reactions.
The shape of adenine is complementary to
either thymine in DNA or uracil in RNA.
5.3 GUANINE
Guanine is one of the four main nucleobase
found in the nucleic acids DNA and RNA
also the others being adenine, cytosine and
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
Volume 2, Issue 4, April 2013
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thymine (uracil in RNA). In DNA guanine is
paired with cytosine. With the formula
C5H5N5O, guanine is a derivative of purine
consisting of a fused pyrimidine imidazole
ring system with conjugated double bonds.
Being unsaturated the bicyclic molecule is
planar. The guanine nucleoside is called
guanosine.
The 9 atoms that make up the fused rings (5
carbons, 4 nitrogen) are numbered 1-9. All
rings Atoms lie in the same plane.
5.4 PYRIMIDINE
Pyrimidine is an aromatic heterocyclic
organic compound similar to pyridine. One
of the three diazines (6 membered
heterocyclics with two nitrogen atoms in the
ring) as it has the nitrogen at positions 1 and
3 in the ring. The other diazines are pyrazine
(nitrogens 1 and 4) and pyridazine
(nitrogens 1 and 2).
5.5 CYTOSINE
Cytosine is one of the four main bases found
in DNA and RNA along with adenine,
guanine and thymine (uracil in RNA). It is a
pyrimidine derivative with a heterocyclic
aromatic ring and two substituent attached
(an amine group at position 4 and a keto
group at position 2). The nucleoside of
cytosine is cytidine.
5.6 THYMINE
Thymine is one of the four nucleobase in the
nucleic acid of DNA that are represented by
the letters G–C–A–T. The others are
adenine, guanine and cytosine. Thymine is
also known as 5-methyluracil a pyrimidine
nucleobase.
The thymine may be derived by methylation
of uracil at the 5th carbon. In RNA thymine
is replaced with uracil in most cases. In
DNA thymine (T) binds to adenine (A) via
two hydrogen bonds thus stabilizing the
nucleic acid structures
Cytosine and thymine are pyrimidines. The
6 atoms (4 carbons, 2 nitrogen) are
numbered 1-6. Like purines all pyrimidines
ring atoms lie in the same plane.
5.7 FORMATION OF NUCLEOSID
The pentoses are bound to nitrogenous bases
by Beta – N - glycosidic bounds. The N9 of
a purine ring binds with C1 of a pentose
sugar to form a covalent bold in purine
nucleoside.
VI. FORMATION OF A
NUCLEOTIDE
The hydroxyl group of the pentose of a
nucleotide is esterified with phosphate to
form 5’ monophosphate
6.1 STRUCTURE OF DNA
DNA is a polymer made up of
deoxynucleotides and is composed of
monomeric units. The monomeric
deoxynucleotides in DNA are held together
by 3’, 5’ – phosphodiester bridges. The
DNA is a right handed double helix. It
consists of two anti parallel right handed
double helix in which one strand runs in 5’
to 3’ direction while the other in 3’ to 5’
direction.
The two strands are held together by
hydrogen bonds formed by complementary
base pairs. The A-T pair has 2 hydrogen
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
Volume 2, Issue 4, April 2013
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bonds while G-C pair has 3 hydrogen bonds.
In all the species the DNA has equal
numbers of adenine and thymine residues
(A=T) and equal numbers of guanine and
cytosine residues (G = C). DNA double
helix is the most predominant form under
physiological conditions and known as B –
form.
In a human cell there are 46 chromosomes
(23 pairs) which contain about 100,000
genes. A Total length of DNA per cell of 1 –
2 meters is packed in to a nucleus millions
of times smaller in diameter. An adult
human body has about 1014
cells. Thus the
total length of DNA in the human body is
about 2 x 10 10
km i.e. 20 billion km.
6.2 BASIC TERMINOLOGIES IN
GENETIC ALGORITHM
The two distinct elements in the GA are
individuals and populations. An individual is
a single solution while the population is the
set of individuals currently involved in the
search process.
6.3 INDIVIDUALS
An individual is a single solution and groups
together two forms of solutions. The
chromosome is raw generic information
(genotype) that GA deals and phenotype
which is the expressive of the chromosome
in the terms of the model. A chromosome is
sub divided into genes. A gene is the GA’s
representation of a single factor for a control
factor. Each factor in the solution set
corresponds to a gene in the chromosome.
A chromosome should in some way contain
information about the solution that it
represents. The morphogenesis function
associates each genotype with its phenotype.
It simply means that each chromosome must
define one unique solution but it does not
mean that each solution is encoded by
exactly one chromosome.
The morphogenesis function should at least
be subjective. The candidate solutions of the
problem must correspond to at least one
possible chromosome to be sure that the
whole search space can be explored. Thus
when the morphogenesis function that
associates each chromosome to one solution
is not injective i.e. different chromosomes
can encode the same solution the
representation is said to be degenerated.
A slight degeneracy is not so worrying even
if the space where the algorithm is looking
for the optional solution is inevitably
enlarged. But a too important degeneracy
could be a more serious problem. It can
badly affect the behavior of the GA mostly
because if several chromosomes can
represent the same phenotype the meaning
of each gene will obviously not correspond
to a specific characteristic of the solution. It
may add some kind of confusion in the
search.
6.4 GENES
Genes are the basic instructions for building
a GA. A chromosome is a sequence of
genes. Genes may describe a possible
solution to a problem without actually being
the solution. A gene is a bit string of
arbitrary lengths.
The bit string is a binary representation of
number of intervals from a lower bound. A
gene is the GA’s representation of a single
factor value for a control factor where
control factor must have an upper bound and
a lower bound. This range can be divided
into the number of intervals that can be
expressed by the gene’s bit string. A bit
string of length n can represent (2 – 1)
intervals. The size of the interval would be
(range) / (2 – 1).
The structure of each gene is defined in a
record of phenotype parameters. The
phenotype parameters are instructions for
mapping between genotype and phenotype.
It can also be said as encoding a solution set
in to a chromosome and decoding a
chromosome to a solution set.
The mapping between genotype and
phenotype is necessary to convert solution
sets from the model into a form that the GA
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
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can work with and for converting new
individuals from the GA in to a form that the
model can evaluate.
6.5 FITNESS
The fitness of an individual in a GA is the
value of an objective function for its
phenotype. For calculating fitness the
chromosome has to be first decoded and the
objective function has to be evaluated. The
fitness not only indicates how good the
solution is but also corresponds to how close
the chromosome is to the optimal one.
In the case of multi criterion optimization
the fitness function is definitely more
difficult to determine to multi criterion
optimization problems there is often a
dilemma as how to determine if one solution
is better than another.
6.6 URIC ACID
Dietary nucleic acids are digested in the
small intestine as follows. The enzyme
polynucleotidase acts on nucleic acids to
form nucleotides Nucleotides act on
nucleotides to form nucleosides and
phosphates Nucleosidase splits nucleosides
in to purine or pyrimidines base and ribose
or 2 – Deoxy – D -Ribose molecules After
absorption it is the small intestine where
purine and pyrimidines reach liver through
portal circulation. In liver both exogenous
and endogenous purines are degraded to the
excretory end product uric acid.
6.7 URIC ACID METABOLISM
Uric acid is the end product of purine
metabolism. The two purines found in RNA
& DNA are adenine and guanine. The first
step in the catabolism of purines is their
hydrolytic deamination to form xanthine and
hypoxanthine. These are then oxidized to
uric acid. The chemical reactions involved
in the formation of uric acid are
Adenosine in presence of Adenosine
deaminase gives inosine in presence of
nucleoside phosphorylase gives
hypoxanthine gives xanthine and in presence
of xanthine oxidase produces uric acid. The
guinosine in presence of nucleoside
phosphorylase gives guanine in presence of
guanase gives xanthine and in presence of
xanthine oxidase produces uric acid.
Uric Acid is filtered in the glomeruli and
partially reabsorbed by the tubules and then
it is excreted in urine. The quantity
excreted in urine depends to a large extent
on the purine content of the diet and
normally the excretion rate is 0.5 – 2.0 g / 24
hrs. The normal plasma uric acid level is 2.0
– 7.0 mg / dl.
The uric acid concentration in erythrocytes
is lower than in plasma so that the normal
range in whole blood is 1.4 mg / dl. The
plasma uric acid level is little affected by
variation in the purine content of the diet
and maintains a steady state between
endogenous synthesis and urinary excretion.
A raised plasma uric acid may be found in
the following conditions like
Hyperuricemia, Gout,Primary Gout and
Secondary Gout
6.8 CHEMICAL EXAMINATION OF
URIC ACID IN KIDNEY STONE
MUREXIDE TEST
One milligram or more of the powder is
treated with 2 or 3 drops of concentrated
nitric acid in a
Porcelain dish. The mixture is carefully
evaporated to dryness and heating continued
until the colour change is complete. If the
test is carried out on the water bath uric acid
gives first a lemon yellow colour and if
heating is continued for few minutes longer
the colour changes to orange and finally to
scarlet. Now on adding of a drop of
ammonia the uric acid oxidation product
assumes a brilliant purple colour.
6.9 PHOSPHOTUNGSTIC ACID TEST
A pinch of powder is treated with 1 drop of
20 g/dl sodium carbonate and added 2 drops
of phosphotungstic acid reagent. A deep
blue colouration is produced.
ISSN: 2278 – 1323
International Journal of Advanced Research in Computer Engineering & Technology (IJARCET)
Volume 2, Issue 4, April 2013
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VII. LASER LITHOTRIPSY
The urinary system removes a type of waste
called urea from our blood. This urea is
produced when foods containing protein
such as meat, poultry and certain vegetables
are broken down in the body. Urea is carried
in the bloodstream to the kidneys.
The main function of the kidneys is to filter
out impurities and add them to the urine.
These impurities usually dissolve in the
urine and are flushed out naturally.
The urine then trickles down the ureter into
the bladder as shown in figure. The
undissolved waste materials remain in the
kidneys and form small crystals. These
crystals stick together creating kidney
stones. This condition is termed renal stone
disease. The size of a kidney stone may vary
from a few mm to several cm. Many stones
pass naturally through urination however
some stones due to their size remain in
either the kidney or the ureter. Stones that
remain in the ureter are termed ureteral
stones.
If a patient shows symptoms of a urinary
stone the physician will diagnose the
problem using either x ray or ultrasound
imaging. To know the precise size and
location of the stones the doctor may use a
cystoscope to see the inside of the bladder
and urethra. Lithotripsy is a technique for
breaking up these stones. There are several
ways of performing lithotripsy depending
upon the size and location of the stone as
well as patient’s history. The most common
treatment for urinary stones is
extracorporeal shock wave lithotripsy
(ESWL). Extracorporeal means outside the
body. High energy shock waves also called
sound waves pass through the body to the
area on the kidney stones.
The waves break the stones into tiny pieces.
It is easier for smaller pieces to pass out of
the body during urination. This type of
lithotripsy must not be performed during
pregnancy. Moreover not all stones can be
treated using this method and alternative to
ESWL is laser lithotripsy. This treatment too
breaks down kidney stones without making
any incisions.
Laser lithotripsy is generally performed
under general anaesthesia and is considered
minimally invasive. A urologist inserts a
cystoscope into the patient’s urethra either
directly or over a guide wire and proceeds
visually up the urinary tract to locate the
target kidney or bladder stone. To monitor
the procedure an endoscope is used which
has a camera on the end of a long flexible
tube.
The endoscope is inserted into the body
through the urinary tract and advanced to the
location of the stone. Once the stone is
located a thin fibre optic is introduced into
the working channel of the endoscope which
acts as a light guide and advanced until it
comes in contact with the stone.
Light from a holmium laser is directed
through the fibre optic and the stone
disintegrates or fragments. The Holmium
laser fibre can be placed in contact with the
stone or adjacent to it. Short Holmium laser
pulses create a shockwave that causes
fragmentation of the stone. Smaller stones
can be fragmented directly whereas with
larger ones holes are punched in the centre
after which the edges are chiselled away
with the Holmium laser. The Holmium laser
has a wavelength of 2100 nm which is in the
infrared spectrum. This wavelength is ideal
for treating stones.
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The Holmium laser energy is absorbed by
the stone creating cracks within the stone.
This laser energy is sufficient to break even
the hardest stone. The high absorption of the
holmium laser light by the kidney stones
leads to the fragmentation of the stone
regardless of its chemical composition. The
smaller fragments can be removed with a
basket tool or left or flush out with normal
urinary function.
Conclusion:
The soft computing approach solves various
biological aspects of computing and
evolutionary computation uses iterative
progress such as growth or development in a
population. The DNA is unique for each
individual. The qualitative chemical test for
uric acid is normally done for kidney stone
disease and laser lithotripsy is the procedure
for surgical removal of kidney stones in
medical instrumentation.
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Ijarcet vol-2-issue-4-1330-1338

  • 1. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1330 www.ijarcet.org A Review of Soft Computing Advance in Genetics & Laser Biomedical Instrumentation 1 Dr. Tryambak A. Hiwarkar, 2 Sridhar Iyer 1 Asso Prof, Computer Science and Engineering, MBITM, Dongargarh (C.G.) 2 Research Scholar, Computer Science, CMJ University, Shillong ABSTRACT Soft computing refers to a collection of computational techniques in computer science, artificial intelligence, machine learning, medical instrumentation which attempt to study, model and analyze very complex phenomena. The principal constituents of Soft Computing (SC) are Neural Networks, Fuzzy Systems, Evolutionary Computation, Machine Learning and Probabilistic Reasoning. The paper studies the biological background of cells, nucleic acids and terminologies in genetic algorithms and also uric acid metabolism with chemical tests and finally laser lithotripsy procedure. Keywords: DNA, RNA, SC, Laser, Genes, Chromosomes, Lithotripsy I. INTRODUCTION: Soft computing is a term applied to a field within computer science which is characterized by the use of inexact solutions to computationally hard tasks such as the solution of NP complete problems for which there is no known algorithm that can compute an exact solution in polynomial time and is tolerant of imprecision, uncertainty, partial truth and approximation and role model for soft computing is the human mind. The evolutionary computing algorithms can be considered global optimization methods with a met heuristic or stochastic optimization character and are mostly applied for black box problems and uses iterative progress such as growth or development in a population and is selected in guided random search using parallel processing to achieve the desired end and processes are often inspired by biological mechanisms of evolution which produces highly optimized processes and networks it has many applications in computer science. 1.1 Extents The soft computing approach provides problem solving techniques in genetics, biochemistry, genetic algorithms and neural networks. The nucleic acids studies DNA and RNA and genetic algorithms analyzes various algorithmic approaches in computer science. The uric acid metabolism and its chemical examination in kidney stone expanded for complex procedures. The laser lithotripsy is a surgical removal of kidney stones and powerful medical equipments are available. 1.2 Biological Environment The science that deals with the mechanisms responsible for similarities and differences in a species is called genetics. 1.3 Terminologies Cell Every animal / human cell is a complex of many small factories that work together. The center of all this is the cell nucleus. The genetic information is contained in the cell nucleus.
  • 2. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1331 www.ijarcet.org Fig.1 Terminologies Cell II. CHROMOSOMES All the genetic information gets stored in the chromosomes. Each chromosome is build of deoxyribonucleic acid (DNA). In humans the chromosomes exist in 23 pairs. The chromosomes are divided into several parts called genes. Genes code the properties of species, i.e. the characteristics of an individual. The possibilities of combination of the genes for one property are called alleles and a gene can take different alleles. The size of the gene pool helps in determining the diversity of the individuals in the population and the set of all genes of a specific species is called genome. Each and every gene has a unique position on the genome called locus. The most living organisms store their genome on several chromosomes but in the GA all the genes are usually stored on the same chromosomes. Thus chromosomes and genomes are synonyms with one other in GA. Fig .2 Chromosome III. GENETICS For a particular individual the entire combination of genes is called genotype. The phenotype describes the physical aspect of decoding a genotype to produce the phenotype also selection is always done on the phenotype whereas the reproduction recombines genotype. Thus morphogenesis plays a key role between selection and reproduction. In higher life forms chromosomes contain two sets of genes. These are known as diploids. In the case of conflicts between two values of the same pair of genes the dominant one will determine the phenotype whereas the other one called recessive will still be present and can be passed on to the offspring. Diploid allows a wider diversity of alleles. This provides a useful memory mechanism in changing or noisy environment. The most GA concentrates on haploid chromosomes because they are much simple to construct. In haploid representation only one set of each gene is stored thus the process of determining which allele should be dominant and which one should be recessive is avoided. Fig.3 genes 3.1 REPRODUCTION Reproduction of species via genetic information is carried out by the following
  • 3. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1332 www.ijarcet.org 3.2 MITOSIS In Mitosis the same genetic information is copied to new offspring. There is no exchange of information. This is a normal way of growing of multi cell structures such as organs. 3.3 MEIOSIS Meiosis forms the basis of sexual reproduction. When meiotic division takes place two gametes appear in the process. Ehen reproduction occur these two gametes conjugate to a zygote which becomes the new individual. Thus in this case the genetic information is shared between the parents in order to create new offspring. NATURAL EVOLUTION GENETIC ALGORITHM Chromosome Gene Allele Locus Genotype Phenotype String Feature or character Feature value String position Structure or Coded String Parameter Set & Decoded Structure 3.4 NATURAL SELECTION The origin of species is based on Preservation of favorable variations and rejection of unfavorable variations. The variation refers to the differences shown by the individual of a species and also by offspring’s of the same parents. There are more individuals born than can survive so there is a continuous struggle for the individuals with an advantage have a greater chance of survival i.e. the survival of the fittest. Fig. 4 Nature Selection IV. NUCLEIC ACID Nucleic acids fall into two principal classes according to the nature of the sugar they contain the deoxyribonucleic acids (DNA) and the ribose containing nucleic acids (RNA). DNA is found primarily in cell nuclei and certain viruses but it also occurs in other portions of cells such as mitochondria. It is associated with the storage and expression of genetic information and the primary processes of heredity. The major types of nucleic acid are 1. Nuclear Deoxyribonucleic Acids 2. Messenger Ribonucleic Acids 3. Transfer or Soluble Ribonucleic Acids 4. Ribosomal Ribonucleic Acids 5. Vital Nucleic Acids 6. 4.1 DNA (DEOXYRIBONUCLEIC ACIDS) DNA (a double stranded molecule) is present in the nucleus of eukaryotic organisms and it is also found in the mitochondria and chloroplasts. DNA is the chemical basis of heredity and may be regarded as the reserve source of genetic information. DNA is exclusively responsible for maintaining the identity of different species of organisms. Every aspect of cellular function is under the control of DNA. Gene is a unit of heredity and it does not have
  • 4. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1333 www.ijarcet.org independent existence but it is a stretch of DNA. 4.2 Nucleotides Nucleotides are composed of a nitrogenous base, a pentose sugar and a phosphate. 4.3 Nucleosides Nucleosides are composed of a nitrogenous base and a pentose sugar. 4.4 Nitrogenous Bases Nitrogenous bases are mainly Purines and Pyrimidines found in nucleic acid. Purines are Adenine (A) and Guanine (G) Pyrimidines are Cytosine (C), Thymine (T) and Uracil (U) The two sugars are D - Ribose and 2 – Deoxy – D – Ribose V. DEOXYRIBOSE SUGAR: The deoxyribose sugar of the DNA backbone has 5 carbons and 3 oxygen. The carbon atoms are numbered 1', 2', 3', 4' and 5' to distinguish from the numbering of the atoms of the purines and pyrimidines rings. The hydroxyl groups on the 5'- and 3'- carbons link to the phosphate groups to form the DNA backbone. Deoxyribose lacks hydroxyl group at the 2'-position when compared to ribose and sugar component of RNA 5.1 PURINES Purine is a heterocyclic aromatic organic compound. It consists of a pyrimidine ring fused to an imidazole ring. Purines including substituted purines and their tautomers are the most widely occurring nitrogen containing heterocycle in nature. Purines and Pyrimidines make up the two groups of nitrogenous bases including the two groups of nucleotide bases. Two of the four de-oxyribonucleotides and two of the four ribo nucleotides, the respective building blocks of DNA and RNA are pureness. There are many naturally occurring purines and two of the four bases in nucleic acids are Adenine and Guanine which are purines. In DNA these bases form hydrogen bonds with their complementary pyrimidines like thymine and cytosine. This is called complementary base pairing. In RNA the complement of adenine is uracil instead of thymine. The other notable purines are Hypoxanthine, Xathine, Theobromine, Caffeine, Uric acid and Isoguanine 5.2 ADENINE Adenine is a nucleobase (a purine derivative) with a variety of roles in biochemistry including cellular respiration in the form of both the energy rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD) and protein synthesis as a chemical component of DNA and RNA. Adenine is one of the two purine nucleobases (guanine) used in forming nucleotides of the nucleic acids. In DNA adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures and RNA which is used for protein synthesis and also binds to uracil Adenine formed adenosine, a nucleoside when attached to ribose and deoxyadenosine when attached to deoxyribose. It forms adenosine triphosphate (ATP), nucleotide when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the basic methods of transferring chemical energy between chemical reactions. The shape of adenine is complementary to either thymine in DNA or uracil in RNA. 5.3 GUANINE Guanine is one of the four main nucleobase found in the nucleic acids DNA and RNA also the others being adenine, cytosine and
  • 5. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1334 www.ijarcet.org thymine (uracil in RNA). In DNA guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine consisting of a fused pyrimidine imidazole ring system with conjugated double bonds. Being unsaturated the bicyclic molecule is planar. The guanine nucleoside is called guanosine. The 9 atoms that make up the fused rings (5 carbons, 4 nitrogen) are numbered 1-9. All rings Atoms lie in the same plane. 5.4 PYRIMIDINE Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. One of the three diazines (6 membered heterocyclics with two nitrogen atoms in the ring) as it has the nitrogen at positions 1 and 3 in the ring. The other diazines are pyrazine (nitrogens 1 and 4) and pyridazine (nitrogens 1 and 2). 5.5 CYTOSINE Cytosine is one of the four main bases found in DNA and RNA along with adenine, guanine and thymine (uracil in RNA). It is a pyrimidine derivative with a heterocyclic aromatic ring and two substituent attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine. 5.6 THYMINE Thymine is one of the four nucleobase in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine and cytosine. Thymine is also known as 5-methyluracil a pyrimidine nucleobase. The thymine may be derived by methylation of uracil at the 5th carbon. In RNA thymine is replaced with uracil in most cases. In DNA thymine (T) binds to adenine (A) via two hydrogen bonds thus stabilizing the nucleic acid structures Cytosine and thymine are pyrimidines. The 6 atoms (4 carbons, 2 nitrogen) are numbered 1-6. Like purines all pyrimidines ring atoms lie in the same plane. 5.7 FORMATION OF NUCLEOSID The pentoses are bound to nitrogenous bases by Beta – N - glycosidic bounds. The N9 of a purine ring binds with C1 of a pentose sugar to form a covalent bold in purine nucleoside. VI. FORMATION OF A NUCLEOTIDE The hydroxyl group of the pentose of a nucleotide is esterified with phosphate to form 5’ monophosphate 6.1 STRUCTURE OF DNA DNA is a polymer made up of deoxynucleotides and is composed of monomeric units. The monomeric deoxynucleotides in DNA are held together by 3’, 5’ – phosphodiester bridges. The DNA is a right handed double helix. It consists of two anti parallel right handed double helix in which one strand runs in 5’ to 3’ direction while the other in 3’ to 5’ direction. The two strands are held together by hydrogen bonds formed by complementary base pairs. The A-T pair has 2 hydrogen
  • 6. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1335 www.ijarcet.org bonds while G-C pair has 3 hydrogen bonds. In all the species the DNA has equal numbers of adenine and thymine residues (A=T) and equal numbers of guanine and cytosine residues (G = C). DNA double helix is the most predominant form under physiological conditions and known as B – form. In a human cell there are 46 chromosomes (23 pairs) which contain about 100,000 genes. A Total length of DNA per cell of 1 – 2 meters is packed in to a nucleus millions of times smaller in diameter. An adult human body has about 1014 cells. Thus the total length of DNA in the human body is about 2 x 10 10 km i.e. 20 billion km. 6.2 BASIC TERMINOLOGIES IN GENETIC ALGORITHM The two distinct elements in the GA are individuals and populations. An individual is a single solution while the population is the set of individuals currently involved in the search process. 6.3 INDIVIDUALS An individual is a single solution and groups together two forms of solutions. The chromosome is raw generic information (genotype) that GA deals and phenotype which is the expressive of the chromosome in the terms of the model. A chromosome is sub divided into genes. A gene is the GA’s representation of a single factor for a control factor. Each factor in the solution set corresponds to a gene in the chromosome. A chromosome should in some way contain information about the solution that it represents. The morphogenesis function associates each genotype with its phenotype. It simply means that each chromosome must define one unique solution but it does not mean that each solution is encoded by exactly one chromosome. The morphogenesis function should at least be subjective. The candidate solutions of the problem must correspond to at least one possible chromosome to be sure that the whole search space can be explored. Thus when the morphogenesis function that associates each chromosome to one solution is not injective i.e. different chromosomes can encode the same solution the representation is said to be degenerated. A slight degeneracy is not so worrying even if the space where the algorithm is looking for the optional solution is inevitably enlarged. But a too important degeneracy could be a more serious problem. It can badly affect the behavior of the GA mostly because if several chromosomes can represent the same phenotype the meaning of each gene will obviously not correspond to a specific characteristic of the solution. It may add some kind of confusion in the search. 6.4 GENES Genes are the basic instructions for building a GA. A chromosome is a sequence of genes. Genes may describe a possible solution to a problem without actually being the solution. A gene is a bit string of arbitrary lengths. The bit string is a binary representation of number of intervals from a lower bound. A gene is the GA’s representation of a single factor value for a control factor where control factor must have an upper bound and a lower bound. This range can be divided into the number of intervals that can be expressed by the gene’s bit string. A bit string of length n can represent (2 – 1) intervals. The size of the interval would be (range) / (2 – 1). The structure of each gene is defined in a record of phenotype parameters. The phenotype parameters are instructions for mapping between genotype and phenotype. It can also be said as encoding a solution set in to a chromosome and decoding a chromosome to a solution set. The mapping between genotype and phenotype is necessary to convert solution sets from the model into a form that the GA
  • 7. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1336 www.ijarcet.org can work with and for converting new individuals from the GA in to a form that the model can evaluate. 6.5 FITNESS The fitness of an individual in a GA is the value of an objective function for its phenotype. For calculating fitness the chromosome has to be first decoded and the objective function has to be evaluated. The fitness not only indicates how good the solution is but also corresponds to how close the chromosome is to the optimal one. In the case of multi criterion optimization the fitness function is definitely more difficult to determine to multi criterion optimization problems there is often a dilemma as how to determine if one solution is better than another. 6.6 URIC ACID Dietary nucleic acids are digested in the small intestine as follows. The enzyme polynucleotidase acts on nucleic acids to form nucleotides Nucleotides act on nucleotides to form nucleosides and phosphates Nucleosidase splits nucleosides in to purine or pyrimidines base and ribose or 2 – Deoxy – D -Ribose molecules After absorption it is the small intestine where purine and pyrimidines reach liver through portal circulation. In liver both exogenous and endogenous purines are degraded to the excretory end product uric acid. 6.7 URIC ACID METABOLISM Uric acid is the end product of purine metabolism. The two purines found in RNA & DNA are adenine and guanine. The first step in the catabolism of purines is their hydrolytic deamination to form xanthine and hypoxanthine. These are then oxidized to uric acid. The chemical reactions involved in the formation of uric acid are Adenosine in presence of Adenosine deaminase gives inosine in presence of nucleoside phosphorylase gives hypoxanthine gives xanthine and in presence of xanthine oxidase produces uric acid. The guinosine in presence of nucleoside phosphorylase gives guanine in presence of guanase gives xanthine and in presence of xanthine oxidase produces uric acid. Uric Acid is filtered in the glomeruli and partially reabsorbed by the tubules and then it is excreted in urine. The quantity excreted in urine depends to a large extent on the purine content of the diet and normally the excretion rate is 0.5 – 2.0 g / 24 hrs. The normal plasma uric acid level is 2.0 – 7.0 mg / dl. The uric acid concentration in erythrocytes is lower than in plasma so that the normal range in whole blood is 1.4 mg / dl. The plasma uric acid level is little affected by variation in the purine content of the diet and maintains a steady state between endogenous synthesis and urinary excretion. A raised plasma uric acid may be found in the following conditions like Hyperuricemia, Gout,Primary Gout and Secondary Gout 6.8 CHEMICAL EXAMINATION OF URIC ACID IN KIDNEY STONE MUREXIDE TEST One milligram or more of the powder is treated with 2 or 3 drops of concentrated nitric acid in a Porcelain dish. The mixture is carefully evaporated to dryness and heating continued until the colour change is complete. If the test is carried out on the water bath uric acid gives first a lemon yellow colour and if heating is continued for few minutes longer the colour changes to orange and finally to scarlet. Now on adding of a drop of ammonia the uric acid oxidation product assumes a brilliant purple colour. 6.9 PHOSPHOTUNGSTIC ACID TEST A pinch of powder is treated with 1 drop of 20 g/dl sodium carbonate and added 2 drops of phosphotungstic acid reagent. A deep blue colouration is produced.
  • 8. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1337 www.ijarcet.org VII. LASER LITHOTRIPSY The urinary system removes a type of waste called urea from our blood. This urea is produced when foods containing protein such as meat, poultry and certain vegetables are broken down in the body. Urea is carried in the bloodstream to the kidneys. The main function of the kidneys is to filter out impurities and add them to the urine. These impurities usually dissolve in the urine and are flushed out naturally. The urine then trickles down the ureter into the bladder as shown in figure. The undissolved waste materials remain in the kidneys and form small crystals. These crystals stick together creating kidney stones. This condition is termed renal stone disease. The size of a kidney stone may vary from a few mm to several cm. Many stones pass naturally through urination however some stones due to their size remain in either the kidney or the ureter. Stones that remain in the ureter are termed ureteral stones. If a patient shows symptoms of a urinary stone the physician will diagnose the problem using either x ray or ultrasound imaging. To know the precise size and location of the stones the doctor may use a cystoscope to see the inside of the bladder and urethra. Lithotripsy is a technique for breaking up these stones. There are several ways of performing lithotripsy depending upon the size and location of the stone as well as patient’s history. The most common treatment for urinary stones is extracorporeal shock wave lithotripsy (ESWL). Extracorporeal means outside the body. High energy shock waves also called sound waves pass through the body to the area on the kidney stones. The waves break the stones into tiny pieces. It is easier for smaller pieces to pass out of the body during urination. This type of lithotripsy must not be performed during pregnancy. Moreover not all stones can be treated using this method and alternative to ESWL is laser lithotripsy. This treatment too breaks down kidney stones without making any incisions. Laser lithotripsy is generally performed under general anaesthesia and is considered minimally invasive. A urologist inserts a cystoscope into the patient’s urethra either directly or over a guide wire and proceeds visually up the urinary tract to locate the target kidney or bladder stone. To monitor the procedure an endoscope is used which has a camera on the end of a long flexible tube. The endoscope is inserted into the body through the urinary tract and advanced to the location of the stone. Once the stone is located a thin fibre optic is introduced into the working channel of the endoscope which acts as a light guide and advanced until it comes in contact with the stone. Light from a holmium laser is directed through the fibre optic and the stone disintegrates or fragments. The Holmium laser fibre can be placed in contact with the stone or adjacent to it. Short Holmium laser pulses create a shockwave that causes fragmentation of the stone. Smaller stones can be fragmented directly whereas with larger ones holes are punched in the centre after which the edges are chiselled away with the Holmium laser. The Holmium laser has a wavelength of 2100 nm which is in the infrared spectrum. This wavelength is ideal for treating stones.
  • 9. ISSN: 2278 – 1323 International Journal of Advanced Research in Computer Engineering & Technology (IJARCET) Volume 2, Issue 4, April 2013 1338 www.ijarcet.org The Holmium laser energy is absorbed by the stone creating cracks within the stone. This laser energy is sufficient to break even the hardest stone. The high absorption of the holmium laser light by the kidney stones leads to the fragmentation of the stone regardless of its chemical composition. The smaller fragments can be removed with a basket tool or left or flush out with normal urinary function. Conclusion: The soft computing approach solves various biological aspects of computing and evolutionary computation uses iterative progress such as growth or development in a population. The DNA is unique for each individual. The qualitative chemical test for uric acid is normally done for kidney stone disease and laser lithotripsy is the procedure for surgical removal of kidney stones in medical instrumentation. REFERENCES 1. Pal, S.K. (1998, January-April) Soft computing tools and pattern recognition IETE Journal of Research, 44 (1-2), 61-87. 2. S.N. Sivanandam, S.N. Deepa, Principles of Soft Computing, Wiley India Publications 3. Davis, L. (1991) Handbook of Genetic Algorithms, Van Nostrand Reinhold, New York. 4. Maynard Smith, J. (1989) Evolutionary Genetics, Oxford University Press, Oxford. 5. Koza, J. (1992) Genetic Programming, MIT Press, Cambridge, MA. 6. Bronzino, Joseph D., Biomedical Engineering Fundamentals, CRC Press, Taylor and Francis Group, Boca Ration FL. 2006 7. Carr, Joseph J. and John M. Brown, Introduction to Biomedical Equipment Technology, Pearson Education, Delhi 2003. 8. Mandeep Singh, Introduction to Biomedical Instrumentation, PHI Learning Private Limited 9. Webster, John G. Bioinstrumentation, John Wiley & Sons, Singapore, 2004. 10. Enderle, John D. Bioinstrumentation, Morgan and Claypool, 2005. 11. Wells, P.N. T., 1977, Biomedical Ultrasonics, Acad. Press, London 446. 12. Kochevar, R.E., 1992, Biological effects of excimer laser radiation, Proc. IEEE, 80, 6,833. 13. Cayton, M. M. 1983, Nursing responsibilities in laser surgery, Med. Inst., 17, 419. 14. www.genetic-programming.com 15. Praful B. Ghodkar, Darshan P. Ghodkar, Textbook of Medical Laboratory Technology, Bhalani Publishing House 16. Coleman, A.J., J.E. Saunders and E.L. H. Palfrey, 1987. The destruction of renal calculi by external shock-waves; Practical operation and initial results with the Dornier lithotriptor, Jr. of Medical Engg. And Technology 11, 1, 4 17. Tompkins, W.J., 1980, Modular design of microcomputer-based medical instruments, Med.Instru.,14, 315. 18. Dixon , M., and Webb, E.C.: Enzymes, 2nd ed. Academic Press, New York, 1964: p. 627 19. Caraway, W.T. (1963). Standard Methods of Clinical Chemistry edited by Seligson, D., Academic Press, New York and London, 4.239. 20. Remp, D.G. (1970), Standard Methods of Clinical Chemistry edited Macdonald R.P. Academic Press, 61. 21. Enzymatic test : Klose S;, et al, Boehringer Manmheim GmBH, personal comm. 22. Luke R.G. , “Uremia and the BUN”, N. Engl. J. Med, 1981, 305: 1213-5 (editorial) 23. Fearon, W.R. (1939), Biochem. J., 33, 902. 24. R.S. Khandpur, Handbook of Biomedical Instrumentation, Tata McGraw Hill Education Private Limited 25. Taurog, A., and Chaikoff, I.L.: J. Biol. Chem., 165, 217, 1946. 26. Chaikoff, I.L., and Taurog, A.: Ann. N.Y. Acad.Sci. , 50, 377, 1949. 27. Geddes, L.A. and L.E. Baker 1968, Principles of Applied Biomedical Instrumentation, John Wiley and Sons, New York, 411. 28. Reichenberger, H., 1988, Lithotriptor Systems, Proc. IEEE 76, 9, 1236. 29. Engel, L.L., and Langer, L.L.: Ann. Rev. Biochem. 30, 499, 1961. 30. Edward Staunton West, Wilbert R. Todd, Howard S. Mason, John T. Van Bruggen, Textbook of Biochemistry, Oxford and IBH Publishing Private Limited