ANOVA TEST

Saturday, October 8, 2011


ANOVA (Analysis of variance test)

Groups
Control
Group A
Group 11
Group 111
Group  1v
Total

17
19
18
20
24


21
22
16
23
28


19
25
17
25
29


11
18
13
20
25








Observations
4
4
4
4
4
20(n)







Sigma X
68
84
64
88
106
410  (T)







Mean
17
21
16
22
26.5








Sigma X 2
1212
1794
1038
1954
2826
8824







(Signa X)2 /n
1156
1764
1024
1936
2809
8689








Correction factor   Cf    = T2/N   =  (410) 2  
                                                          ------------    =  8405
                                                              20  
Total sum of squares    =  sigma X2   -  c.f  =  8824 – 8405  = 419
B/N groups sum of squares  = ( sigma X2)/n)   -  c.f  =  8689 – 8405  = 284
                                   
Within groups  =  Total sum of square  - between groups sum of squares
                            =  419 – 284  =  135



Degree of freedom
B/n  groups  =  number of groups  - 1   ,  5-1 =4
Total degree of freedom  =  Total observation of all groups – 1
                                                       20 – 1 = 19
Error (df )  Total df  - between groups df  = 19-4 =15
Mean square(b/n groups)  =   B/n groups sum of squares/degree of
                                                                                                        freedom           
                                                  = 284/4 = 71
                                           
Mean square within groups   = 135/15    =  9

F  =  Between mean squares / within groups mean square

     =   71/9  =  7.89
Referring to F – ration table for (4,15) degrees of freedom we get for F = 7.89 , p greater than  0.01 , hence there is a significant difference between groups
For finding out the differences b/n the groups, error mean square Anova is made use by applying dunnets t test

T test formula
Where s2 is the error mean square obtained from Anova
Dunnets  t test to determine effect of drug against control group

Statistic
A
B
C
D
t
1.886
0.472
2.358
4.481

D.F   = 15
*P less than  0.05  ,          ***P less than 0.001
Therefore drug C and drug D  differ significantly from control , but drug D is highly effective


 Tukeys test



Steps
  1. Calculate an analysis of variance (e.g., One-way between-subjects ANOVA).
  2. Select two means and note the relevant variables (Means, Mean Square Within, and number per condition/group)
  3. Calculate Tukey's test for each mean comparison
  4. Check to see if Tukey's score is statistically significant with Tukey's probability/critical value table taking into account appropriate dfwithin and number of treatments.

Problem: Susan Sound predicts that students will learn most effectively with a constant background sound, as opposed to an unpredictable sound or no sound at all. She randomly divides twenty-four students into three groups of eight. All students study a passage of text for 30 minutes. Those in group 1 study with background sound at a constant volume in the background. Those in group 2 study with noise that changes volume periodically. Those in group 3 study with no sound at all. After studying, all students take a 10 point multiple choice test over the material. She begins by conducting a One-way, between-subjects Analysis of Variance. She finds a significant F score. The relevant variables from her ANOVA table are:
MSwithin =4.18; M1 =6; M2 =4; M3 =3; dfwithin = 21; n = 8


EXAMPLES OF THE NULL HYPOTHESIS
A researcher may postulate a hypothesis:
H1: Tomato plants exhibit a higher rate of growth when planted in compost rather than in soil.
And a null hypothesis:
H0: Tomato plants do not exhibit a higher rate of growth when planted in compost rather than soil.
It is important to carefully select the wording of the null, and ensure that it is as specific as possible. For example, the researcher might postulate a null hypothesis:
H0: Tomato plants show no difference in growth rates when planted in compost rather than soil.
There is a major flaw with this null hypothesis. If the plants actually grow more slowly in compost than in soil, an impasse is reached. H1 is not supported, but neither is H0, because there is a difference in growth rates.
If the null is rejected, with no alternative, the experiment may be invalid. This is the reason why science uses a battery of deductive and inductive processes to ensure that there are no flaws in the hypotheses.
Many scientists neglect the null, assuming that it is merely the opposite of the alternative, but it is good practice to spend a little time creating a sound hypothesis. It is not possible to change any hypothesis retrospectively, including H0.

SIGNIFICANCE TESTS
If significance tests generate 95% or 99% likelihood that the results do not fit the null hypothesis, then it is rejected, in favor of the alternative.
Otherwise, the null is accepted. These are the only correct assumptions, and it is incorrect to reject, or accept, H1.
Accepting the null hypothesis does not mean that it is true. It is still a hypothesis, and must conform to the principle of falsifiability, in the same way that rejecting the null does not prove the alternative. 

PERCEIVED PROBLEMS WITH THE NULL
The major problem with the null hypothesis is that many researchers, and reviewers, see accepting the null as a failure of the experiment. This is very poor science, as accepting or rejecting any hypothesis is a positive result.
Even if the null is not refuted, the world of science has learned something new. Strictly speaking, the term ‘failure’, should only apply to errors in the experimental design, or incorrect initial assumptions. 

DEVELOPMENT OF THE NULL
The Flat Earth model was common in ancient times, such as in the civilizations of the Bronze Age or Iron Age. This may be thought of as the null hypothesis, H0, at the time.
H0: World is Flat
Many of the Ancient Greek philosophers assumed that the sun, moon and other objects in the universe circled around the Earth. Hellenistic astronomy established the spherical shape of the earth around 300 BC.
H0: The Geocentric Model: Earth is the centre of the Universe and it is Spherical
Copernicus had an alternative hypothesis, H1 that the world actually circled around the sun, thus being the center of the universe. Eventually, people got convinced and accepted it as the null, H0.
H0: The Heliocentric Model: Sun is the centre of the universe
Later someone proposed an alternative hypothesis that the sun itself also circled around the something within the galaxy, thus creating a new null hypothesis. This is how research works - the null hypothesis gets closer to the reality each time, even if it isn't correct, it is better than the last null hypothesis.


Gluconeogenesis

Sunday, July 24, 2011


TRANSDUCTION MECHANISMS







Type 1: ligand-gated ion channels:- (also known as ionotropic receptors). These are membrane proteins with a similar structure to other ion channels, and incorporate a ligand-binding (receptor) site, usually in the extracellular domain. Typically, these are the receptors on which fast neurotransmitters act. Examples include the nicotinic acetylcholine receptor (nAChR); GABAA receptor  and glutamate receptors of the NMDA, AMPA and kainate types

The nicotinic acetylcholine receptor, the first to be cloned, It is assembled from
four different types of subunit, termed α, β, γ and δ.The pentameric structure
2, β, γ, δ) possesses two acetylcholine binding sites, each lying at the interface
between one of the two α subunits and its neighbour. Both must bind
acetylcholine molecules in order for the receptor to be activated.

THE GATING MECHANISM
Receptors of this type control the fastest synaptic events in the nervous system,
in which a neurotransmitter acts on the postsynaptic membrane of a nerve or
muscle cell and transiently increases its permeability to particular ions.
Most excitatory neurotransmitters, such as acetylcholine at the neuromuscular
 Junction or glutamate in the central nervous system, cause an increase in
Na+ and K+s permeability. This results in a net inward current carried mainly by
Na+, which depolarises the cell and increases the probability that it will generate
an action potential. The action of the transmitter reaches a peak in a fraction of
a millisecond,and usually decays within a few milliseconds. The sheer speed
of this response implies that the coupling between the receptor and the ionic
channel is a direct one, and the molecular structure of the receptor-channel
complex agrees with this.In contrast to other receptor families, no intermediate
 biochemical steps are involved in the transduction process.

Type 2: G-protein-coupled receptors (GPCRs):- These are also known as metabotropic receptors or 7-transmembrane-spanning (heptahelical) receptors. They are membrane receptors that are coupled to intracellular effector systems via a G-protein (see below). They constitute the largest family,5 and include receptors for many hormones and slow transmitters, for example the muscarinic acetylcholine receptor (mAChR), adrenergic receptors and chemokine receptors
G-proteins and their role
G-proteins comprise a family of membrane-resident proteins whose function is to recognise activated GPCRs and pass on the message to the effector systems that generate a cellular response
They are the go-between proteins, but were actually called G-proteins because of their interaction with the guanine nucleotides, GTP and GDP. G-proteins consist of three subunits: α, β and γ. Guanine nucleotides bind to the α subunit, which has enzymic activity, catalysing the conversion of GTP to GDP. The β and γ subunits remain together as a βγ complex. G-proteins appear to be freely diffusible in the plane of the membrane, so a single pool of G-protein in a cell can interact with several different receptors and effectors.In the 'resting' state, the G-protein exists as an unattached αβγ trimer, with GDP occupying the site on the α subunit. When a GPCR is activated by an agonist molecule, a conformational change occurs, involving the cytoplasmic domain of the receptor, causing it to acquire high affinity for αβγ. Association of αβγ with the receptor causes the bound GDP to dissociate and to be replaced with GTP (GDP-GTP exchange), which in turn causes dissociation of the G-protein trimer, releasing α-GTP and βγ subunits; these are the 'active' forms of the G-protein, which diffuse in the membrane and can associate with various enzymes and ion channels, causing activation of the target.


Signalling is terminated when the hydrolysis of GTP to GDP occurs through the GTPase activity of the α subunit. The resulting α-GDP then dissociates from the effector, and reunites with βγ, completing the cycle.

TARGETS FOR G-PROTEINS


The main targets for G-proteins, through which GPCRs control different aspects of cell function
cAMP is a nucleotide synthesised within the cell from ATP by the action of a membrane-bound enzyme, adenylyl cyclase. It is produced continuously and inactivated by hydrolysis to 5´-AMP, by the action of a family of enzymes known as phosphodiesterases (PDEs). Many different drugs, hormones and neurotransmitters act on GPCRs and produce their effects by increasing or decreasing the catalytic activity of adenylyl cyclase, thus raising or lowering the concentration of cAMP within the cell.
Cyclic AMP regulates many aspects of cellular function including, for example, enzymes involved in energy metabolism, cell division and cell differentiation, ion transport, ion channels, and the contractile proteins in smooth muscle. These varied effects are, however, all brought about by a common mechanism, namely the activation of protein kinases by cAMP. Protein kinases regulate the function of many different cellular proteins by controlling protein phosphorylation.
Examples
1.       Increased cAMP production in response to β-adrenoceptor activation affects enzymes involved in glycogen and fat metabolism in liver, fat and muscle cells. The result is a coordinated response in which stored energy in the form of glycogen and fat is made available as glucose to fuel muscle contraction.
2.       Other examples of regulation by cAMP-dependent protein kinases include the increased activity of voltage-activated calcium channels in heart muscle cells. Phosphorylation of these channels increases the amount of Ca2+ entering the cell during the action potential, and thus increases the force of contraction of the heart.
3.       In smooth muscle, cAMP-dependent protein kinase phosphorylates (thereby inactivating) another enzyme, myosin-light-chain kinase, which is required for contraction. This accounts for the smooth muscle relaxation produced by many drugs that increase cAMP production in smooth muscle
4.       include certain types of mAChR (e.g. the M2 receptor of cardiac muscle; see, α2-adrenoceptors in smooth muscle, and opioid receptors

The phospholipase C/inositol phosphate system
The phosphoinositide system, an important intracellular second messenger system.
PIP2 is the substrate for a membrane-bound enzyme, phospholipase Cβ (PLCβ), which splits it into DAG and inositol (1,4,5) trisphosphate (IP3), both of which function as second messengers. The activation of PLCβ by various agonists is mediated through a G-protein. After cleavage of PIP2, the status quo is restored. DAG being phosphorylated to form phosphatidic acid (PA), while the IP3 is dephosphorylated and then recoupled with PA to form PIP2 once again.
Inositol phosphates and intracellular calcium
Inositol (1,4,5) trisphosphate is a water-soluble mediator that is released into the cytosol and acts on a specific receptor-the IP3 receptor-which is a ligand-gated calcium channel present on the membrane of the endoplasmic reticulum. The main role of IP3, is to control the release of Ca2+ from intracellular stores. Because many drug and hormone effects involve intracellular Ca2+, this pathway is particularly important. IP3 is converted inside the cell to the (1,3,4,5) tetraphosphate, IP4, by a specific kinase. The exact role of IP4 remains unclear, but there is evidence that it too is involved in Ca2+ signalling. One possibility is that it facilitates Ca2+ entry through the plasma membrane, thus avoiding depletion of the intracellular stores as a result of the action of IP3.
Diacylglycerol and protein kinase C
Diacylglycerol is produced as well as IP3 whenever receptor-induced PI hydrolysis occurs. The main effect of DAG is to activate a membrane-bound protein kinase, protein kinase C (PKC), which catalyses the phosphorylation of a variety of intracellular proteins. DAG, unlike the inositol phosphates, is highly lipophilic and remains within the membrane. It binds to a specific site on the PKC molecule, which migrates from the cytosol to the cell membrane in the presence of DAG, thereby becoming activated.
Ion channels as targets for G-proteins


G-protein-coupled receptors can control ion channel function directly by mechanisms that do not involve second messengers such as cAMP or inositol phosphates. This was first shown for cardiac muscle, but it now appears that direct G-protein-channel interaction may be quite general . In cardiac muscle, for example, mAChRs are known to enhance K+ permeability (thus hyperpolarising the cells and inhibiting electrical activity. Similar mechanisms operate in neurons, where many inhibitory drugs such as opiate analgesics reduce excitability by opening potassium channels.
Type 3: kinase-linked and related receptors:- This is a large and heterogeneous group of membrane receptors responding mainly to protein mediators. They comprise an extracellular ligand-binding domain linked to an intracellular domain by a single transmembrane helix. In many cases, the intracellular domain is enzymic in nature (with protein kinase or guanylyl cyclase activity). Type 3 receptors include those for insulin and for various cytokines and growth factors the receptor for atrial natriuretic factor (ANF), is the main example of the guanylyl cyclase type. The two kinds are very similar structurally, even though their transduction mechanisms differ.
KINASE-LINKED AND RELATED RECEPTORS
These membrane receptors are quite different in structure and function from either the ligand-gated channels or the GPCRs. They mediate the actions of a wide variety of protein mediators, including growth factors and cytokines, and hormones such as insulin and leptin, whose effects are exerted mainly at the level of gene transcription.
They play a major role in controlling cell division, growth, differentiation, inflammation, tissue repair, apoptosis and immune responses,
The main types are as follow

  • Receptor tyrosine kinases (RTKs). These receptors have the basic structure, incorporating a tyrosine kinase moiety in the intracellular region. They include receptors for many growth factors, such as epidermal growth factor and nerve growth factor, and also the group of Toll-like receptors that recognise bacterial lipopolysaccarides and play an important role in the body's reaction to infection. The insulin receptor also belongs to the RTK class, although it has a more complex dimeric structure.
  • Serine/threonine kinases. This smaller class is similar in structure to RTKs but phosphorylate serine and/or threonine residues rather than tyrosine. The main example is the receptor for transforming growth factor (TGF).
  • Cytokine receptors. These receptors lack intrinsic enzyme activity. When occupied, they associate with, and activate, a cytosolic tyrosine kinase, such as Jak (the Janus kinase) or other kinases. Ligands for these receptors include cytokines such as interferons and colony-stimulating factors involved in immunological responses.
  • Guanylyl cyclase-linked receptors. These are similar in structure to RTKs, but the enzymic moiety is guanylyl cyclase and they exert their effects by stimulating cGMP formation. The main example is the receptor for ANF.
In many cases, ligand binding to the receptor leads to dimerisation. The association of the two intracellular kinase domains allows a mutual autophosphorylation of intracellular tyrosine residues to occur. The phosphorylated tyrosine residues then serve as high-affinity docking sites for other intracellular proteins that form the next stage in the signal transduction cascade. One important group of such 'adapter' proteins is known as the SH2 domain proteins (standing for Src homology, because it was first identified in the Src oncogene product).

*      Two well-defined signal transduction pathways are summarised in The Ras/Raf pathway mediates the effect of many growth factors and mitogens. Ras, which is a proto-oncogene product, functions like a G-protein, and conveys the signal (by GDP/GTP exchange) from the SH2 domain protein, Grb, which is phosphorylated by the RTK. Activation of Ras in turn activates Raf, which is the first of a sequence of three serine/threonine kinases, each of which phosphorylates, and activates, the next in line. The last of these, mitogen-activated protein (MAP) kinase, phosphorylates one or more transcription factors that initiate gene expression, resulting in a variety of cellular responses, including cell division.
Many SH2 domain proteins are enzymes, such as protein kinases or phospholipases. Some growth factors activate a specific subtype of phospholipase C (PLCγ), thereby causing phospholipid breakdown, IP3 formation and Ca2+ release. Other SH2-containing proteins couple phosphotyrosine-containing proteins with a variety of other functional proteins, including many that are involved in the control of cell division and differentiation. The end result is to activate or inhibit, by phosphorylation, a variety of transcription factors that migrate to the nucleus and suppress or induce the expression of particular genes.
*      A second pathway, the Jak/Stat pathway is involved in responses to many cytokines. Dimerisation of these receptors occurs when the cytokine binds, and this attracts a cytosolic tyrosine kinase unit (Jak) to associate with, and phosphorylate, the receptor dimer. Jaks belong to a family of proteins, different members having specificity for different cytokine receptors. Among the targets for phosphorylation by Jak are a family of transcription factors (Stats). These are SH2 domain proteins that bind to the phosphotyrosine groups on the receptor-Jak complex, and are themselves phosphorylated. Thus activated, Stat migrates to the nucleus and activates gene expression.
*      The membrane-bound form of guanylyl cyclase, the enzyme responsible for generating the second messenger cGMP in response to the binding of peptides such as atrial natriuretic peptide, resembles the tyrosine kinase family and is activated in a similar way by dimerisation when the agonist is bound.
Type 4: nuclear receptors:- These are receptors that regulate gene transcription. The term nuclear receptors is something of a misnomer, because some are actually located in the cytosol and migrate to the nuclear compartment when a ligand is present. They include receptors for steroid hormones, thyroid hormone, and other agents such as retinoic acid and vitamin D.
NUCLEAR RECEPTORS
Receptors for steroid hormones such as oestrogen and the glucocorticoids were present
in the cytoplasm of cells and translocated into the nucleus after binding with their
steroid partner. Other hormones, such as the thyroid hormone T3 and the fat-soluble
vitamins D and A (retinoic acid) and their derivatives that regulate growth and
development, were found to act in a similar fashion.


Glycolysis





Permanent methods of family planning

Tuesday, July 12, 2011

The Vasectomy Procedure
Vasectomy is a safe, simple and effective birth control method.
One of the most common and popular means for contraception around the world is vasectomy – a brief, surgical procedure used for male sterilization. It is a popular means of birth control for couples that have decided that their family is complete. It is nearly 100% effective and is intended to be permanent.
The procedure starts with the administration of local anesthesia, to numb the genitals. This allows the patient to remain awake and alert during the procedure, but unable to feel the surgery. In some cases, a new technology, the needleless injection, is used to administer the anesthetic in this sensitive area. Your doctor may or may not have this new system available for use during surgery.
Once the genital area is numbed, the area will be shaved and the skin prepared with a solution that kills bacteria on the surface of the skin. Once the solution dries, the surgery begins with 1 or 2 half-inch long incisions on the underside of the scrotum. The vas deferens, the cord that carries sperm, is then located and either cut and tied off or cut and cauterized. Research shows that the use of cautery is the most effective, as it prevents the vas deferens from healing back together. 


The incision is then closed with sutures, which can be removed at the surgeon’s office in a week to ten days.

A vasectomy is chosen by over 600,000 American men annually, and as many as 30 million men worldwide. The vasectomy procedure is uncomplicated, is commonly performed in a doctor’s office and usually takes about 15 to 20 minutes.
All about vasectomy.
The simplest and safest vasectomy method is the No-Scalpel Vasectomy (NSV), which, as the name suggests, requires no scalpel, no incisions (only two tiny punctures in the skin) and no sutures. It is performed with a local anesthetic to numb the area. The No-Scalpel Vasectomy is rapidly becoming the procedure of choice among patients and is also favored by many doctors.
Urologists perform most vasectomies, although up to 30 % are performed each year by family practitioners, depending on the location. Costs range from $500 to over $1,000 and is reimbursed by many health insurance programs.
In Summary:
  • A vasectomy is a safe and simple procedure.
  • It is one of the most common means for permanent contraception.
  • The procedure is over 99 % effective and intended to be permanent.
  • The "No-Scalpel Vasectomy" method is popular with patients and doctors.
  • It is usually performed in the doctor's office in less than 30 minutes.
  • Urologists and general practitioners perform vasectomies.
The cost is low and is often reimbursed by health insurance.






Tubectomy
Tubal Sterilization is a permanent method of contraception where the fallopian tubes are blocked so that the ova or eggs are prevented from traveling to the uterus from the ovary.
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and laparoscopic surgeons perform tubectomy.
The Fallopian Tubes are two in number and are attached on either side of the uterus at one end and the other end is open in the abdomen. The length of each Fallopian tube is about 10cm.When the ovum or egg is released from the ovary, it is picked up by Fallopian tube through which it moves into the uterus. If sperms are present in the Fallopian tubes, the ovum is fertilized and the resulting embryo is transmitted to the uterus where it is embedded. In short, we can say that Fallopian tubes are channels through which the eggs from the ovaries travel to the uterus. In Tubectomy the tubes are blocked or divided to prevent the eggs from entering the uterus. This prevents any future pregnancies to occur after the surgical procedure. 

The preferred method that is used commonly is to use a laparoscopic approach to identify the fallopian tubes on both the sides and apply plastic clips.

There are different surgical approaches for the tubal sterilization operations are

1. Laparoscopy
2. Microlaparoscopy
3. Laparotomy (concurrent with cesarean delivery)
4. Minilaparotomy
5. Hysteroscopy
6. Vaginal approaches.


Laparoscopy

The most popular is using a laparoscope; where the patient has just a couple of small scars and is discharged home the same day.

If laparoscopy is not available an open surgical operation may be required. Here the tubes are completely divided and a section is excised.

Local anesthesia is used for more than 75% of sterilizations worldwide. Laparoscopic sterilization in performed under general anesthesia. Spinal anesthesia is preferred for procedures done immediately after delivery of the baby
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Local anesthesia is the standard for the hysteroscopic approach, and it may be supplemented by oral or IV sedation if needed.

The actual procedure is done in an operating room, either in a hospital or a surgical center.

Currently, Laparoscopy is the most popular method of female sterilization in nonpregnant women. It is performed under General Anesthesia. The surgery takes about half an hour.

1. In the Laparoscopy procedure, the abdomen is filled with carbon dioxide gas by introducing a needle so that the abdominal wall balloons away from the uterus and tubes.

2. The surgeon makes a small cut just below the navel and inserts a laparoscope, a small telescope-like instrument.

3. A second incision is made just above the pubic hairline to allow the entrance of another small instrument that can help with closure of the fallopian tubes.

4. Usually Falope rings or Filshie clips are placed on the fallopian tubes to block the tubes. Sometimes the tubes are cut and clipped

5. The skin incision is then closed with one stitch or a tape. The patient may feel well enough to go home from the outpatient surgery center in a few hours.


Advantages include small incisions, rapid access to the fallopian tubes and rapid recovery.

Disadvantages include the need for general anesthesia, the risks of injury to internal organs with needle insufflations. Difficulty associated with Laparoscopy in patients who are obese.

Micro-laparoscopy
Micro-laparoscopy involves use of micro endoscopes of smaller diameter with 5 to 7 mm suprapubic incisions being made. This surgery is possible because of improved technology in light transmission and fiber optic bundles.

There are some theoretical advantages such as even smaller scars, less pain, less cost, and faster patient recovery. However the difference is so marginal that it has never become very popular despite being available for almost 20 years.


Contraindications

1. The patient should make the request herself, be of sound mind, and not act under external duress.

2. During delivery of the baby some women opt for sterilization; however this should be deferred if maternal or infant complications are anticipated.

3. Surgery is contraindicated in patients with active infections like Pelvic Inflammatory Disease (PID)

4. The laparoscopic approach is also contraindicated in patients with severe heart or lung problems.

5. Surgery is deferred in patients with suspected pregnancy
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