DEEP LEARNING SERIES- PART 10

This is the last article in this series. This article is about another pre-trained CNN known as the ResNet along with an output visualization parameter known as the confusion matrix.

ResNet

This is also known as a residual network. It has three variations 51,101,151. They used a simple technique to achieve this high number of layers.

Credit – Xiaozhu0429/ Wikimedia Commons / CC-BY-SA-4.0

The problem in using many layers is that the input information gets changed in accordance with each layer and subsequently, the information will become completely morphed. So to prevent this, the input information is sent in again like a recurrent for every two steps so that the layers don’t forget the original information. Using this simple technique they achieved about 100+ layers.

ResNet these are the three fundamentals used throughout the network.

  (conv1): Conv2d (3, 64, kernel_size= (7, 7), stride= (2, 2), padding= (3, 3))

  (relu): ReLU

  (maxpool): MaxPool2d(kernel_size=3, stride=2, padding=1)

These are the layers found within a single bottleneck of the ResNet.

    (0): Bottleneck

  1    (conv1): Conv2d(64, 64, kernel_size=(1, 1), stride=(1, 1))

  2    (conv2): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))     

  3    (conv3): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1))    

      (relu): ReLU(inplace=True)

   Down sampling   

   Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1))

    (1): Bottleneck

  4    (conv1): Conv2d(256, 64, kernel_size=(1, 1), stride=(1, 1))

  5    (conv2): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))     

  6   (conv3): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1))     

      (relu): ReLU(inplace=True)

    )

    (2): Bottleneck

  7    (conv1): Conv2d(256, 64, kernel_size=(1, 1), stride=(1, 1))

  8    (conv2): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))

  9   (conv3): Conv2d(64, 256, kernel_size=(1, 1), stride=(1, 1))

   (relu): ReLU

There are many bottlenecks like these throughout the network. Hence by this, the ResNet is able to perform well and produce good accuracy. As a matter of fact, the ResNet is the model which won the ImageNet task competition.

There are 4 layers in this architecture. Each layer has a bottleneck which comprises convolution followed by relu activation function. There are 46 convolutions, 2 pooling, 2 FC layers.

TypeNo of layers
7*7 convolution1
1*1, k=64 + 3*3, k=64+1*1, k=256 convolution9
1*1, k=128+ 3*3, k=128+1*1, k=512  convolution10
1*1, k=256+ 3*3, k=256 + 1*1, k=1024 convolution16
1 * 1, k=512+3 * 3, k=512+1 * 1, k=2048 convolution9
Pooling and FC4
Total50

There is a particular aspect apart from the accuracy which is used to evaluate the model, especially in research papers. That method is known as the confusion matrix. It is seen in a lot of places and in the medical field it can be seen in test results. The terms used in the confusion matrix have become popularized in the anti-PCR test for COVID.

The four terms used in a confusion matrix are True Positive, True Negative, and False positive, and false negative. This is known as the confusion matrix.

True positive- both the truth and prediction are positive

True negative- both the truth and prediction are negative

False-positive- the truth is negative but the prediction is positive

False-negative- the truth is positive but the prediction is false

Out of these the false positive is dangerous and has to be ensured that this value is minimal.

We have now come to the end of the series. Hope that you have got some knowledge in this field of science. Deep learning is a very interesting field since we can do a variety of projects using the artificial brain which we have with ourselves. Also, the technology present nowadays makes these implementations so easy. So I recommend all to study and do projects using these concepts. Till then,

HAPPY LEARNING!!!

DEEP LEARNING SERIES- PART 9

This article is about one of the pre-trained CNN models known as the VGG-16. The process of using a pretrained CNN is known as transfer learning. In this case, we need not build a CNN instead we can use this with a modification. The modifications are:-

  • Removing the top (input) and bottom (output) layers
  • Adding input layer with size equal to the dimension of the image
  • Adding output layer with size equal to number of classes
  • Adding additional layers (if needed)

The pre-trained model explained in this article is called the VGGNet. This model was developed by the Oxford University researchers as a solution to the ImageNet task. The ImageNet data consists of 10 classes with 1000 images each leading to 10000 images in total.

VGGNet

I/p 1     2   3     4     5        6       7         8      9          10     11            12       13   o/p

Credit: – Nshafiei neural network in Machine learning  Creative Commons Attribution-ShareAlike 4.0 License.

This is the architecture for VGGNet. This has been found for the CIFAR-10 dataset, a standard dataset containing 1000 classes. This was used for multiclass classification. Some modifications are made before using it for detecting OA. The output dimension is changed into 1*1*2 and the given images must be reshaped to 224*224 since this dimension is compatible with VGGNet. The dimensions and other terms like padding, stride, number of filters, dimension of filter are chosen by researchers and found optimal. In general, any number can be used in this place.

The numbers given below the figure correspond to the layer number. So the VGGNet is 13 layered and is CNN till layer 10 and the rest are FNN.

Colour indexName
GreyConvolution
RedPooling
BlueFFN

Computations and parameters for each layer

Input

224*224 images are converted into a vector whose dimension is 224*224*3 based on the RGB value.

Layer 1-C1

This is the first convolutional layer. Here 64 filters are used.

Wi =224, P=1, S=1, K=64, f=3*3

Wo =224 (this is the input Wi for the next layer)

Dim= 224*224*64

Parameter= 64*3*3= 576

Layer 2-P1

This is the first pooling layer

 Wi =224, S=2, P=1, f=3

Wo=112 (this is the input Wi for the next layer)

Dim= 112*112*3

Parameter= 0

Layer 3-C2C3

Here two convolutions are applied. 128 filters are used.

Wi =112, P=1, S=1, K=64, f=3

Wo=112 (this is the input Wi for the next layer)

Dim= 112*112*128

Parameter= 128*3*3=1152

Layer 4- P2

Second pooling layer

Wi =112, P=1, S=2, f=3*3

Wo =56 (this is the input Wi for the next layer)

Dim= 56*56*3

Parameter= 0

Layer 5- C4C5C6

Combination of three convolutions

Wi =56, P=1, S=1, K=256, f=3*3

Wo = 56 (this is the input Wi for the next layer)

Dim= 224*224*64

Parameter= 64*3*3= 576

Layer 6-P3

Third pooling layer

Wi =56, P=1, S=2, f=3*3

Wo =28 (this is the input Wi for the next layer)

Dim= 28*28*3

Parameter= 0

Layer 7-C7C8C9

Combination of three convolutions

Wi =28, P=1, S=1, K=512, f=3*3

Wo =28 (this is the input Wi for the next layer)

Dim= 28*28*512

Parameter= 512*3*3= 4608

Layer 8-P4

Fourth pooling layer

Wi =28, P=1, S=2, f=3*3

Wo =14 (this is the input Wi for the next layer)

Dim= 14*14*3

Parameter= 0

Layer 9-C10C11C12

Last convolution layer, Combination of three convolutions

Wi =14, P=1, S=1, K=512, f=3*3

Wo =14 (this is the input Wi for the next layer)

Dim= 14*14*512

Parameter= 512*3*3= 4608

Layer 10-P5

Last pooling layer and last layer in CNN

Wi =14, P=1, S=2, f=3*3

Wo =7 (this is the input Wi for the next layer)

Dim= 7*7*3

Parameter= 512*3*3= 4608

With here the CNN gets over. So a complex 224*224*3 boil down to 7*7*3

Trends in CNN

As the layer number increases,

  1. The dimension decreases.
  2. The filter number increases.
  3. Filter dimension is constant.

In convolution

Padding of 1 and stride of 1 to transfer original dimensions to output

In pooling

Padding of 1 and stride of 2 are used in order to half the dimensions.

Layer 11- FF1

4096 neurons

Parameter= 512*7*7*4096=102M

Wo= 4096

Layer 12- FF2

4096 neurons

Wo= 4096

Parameter= 4096*4096= 16M

Output layer

2 classes

  • non-osteoarthritic
  • osteoarthritic

Parameter= 4096*2= 8192

Parameters

LayerValue of parameters
Convolution16M
FF1102M
FF216M
Total134M

It takes a very large amount of time nearly hours for a machine on CPU to learn all the parameters. Hence they came with speed enhancers like faster processors known as GPU Graphic Processing Unit which may finish the work up to 85% faster than CPU.

HAPPY LEARNING!!

DEEP LEARNING SERIES- PART 8

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The previous article was about the padding, stride, and parameters of CNN. This article is about the pooling and the procedure to build an image classifier.

Pooling

This is another aspect of CNN. There are different types of pooling like min pooling, max pooling, avg pooling, etc. the process is the same as before i.e. the kernel vector slides over the input vector and does computations on the dot product. If a 3*3 kernel is considered then it is applied over a 3*3 region inside the vector, it finds the dot product in the case of convolution. The same in pooling finds a particular value and substitutes that value in the output vector. The kernel value decides the type of pooling. The following table shows the operation done by the pooling.

Type of poolingThe value seen in the output layer
Max poolingMaximum of all considered cells
Min poolingMinimum of all considered cells
Avg poolingAverage of all considered cells



The considered cells are bounded within the kernel dimensions.

This image has an empty alt attribute; its file name is image-8.png

The pictorial representation of average pooling is shown above. The number of parameters in pooling is zero.

Convolution and pooling are the basis for feature extraction. The vector obtained from this step is fed into an FFN which then does the required task on the image.

Features of CNN

  1. Sparse connectivity
  2. Weight sharing.



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    Feature extraction-CNN              classifier-FNN

In general, CNN is first then FFN is later. But the order or number or types of convolution and pooling can vary based on the complexity and choice of the user.

Already there are a lot of models like VGGNet, AlexNet, GoogleNet, and ResNet. These models are made standard and their architecture has been already defined by researchers. We have to reshape our images in accordance with the dimensions of the model.

General procedure to build an image classifier using CNN

  1. Obtain the data in the form of image datasets.
  2. Set the output classes for the model to perform the classification on.
  3. Transform or in specific reshape the dimension of the images compatible to the model. The image size maybe 20*20 but the model accepts only 200*200 images; then we must reshape them to that size.
  4. Split the given data into training data and evaluation data. This is done by creating new datasets for both training and validation. More images are required for training.
  5. Define the model used for this task.
  6. Roughly sketch the architecture of the network.
  7. Determine the number of convolutions, pooling etc. and their order
  8. Determine the dimensions for the first layer, padding, stride, number of filters and dimensions of filter.
  9. Apply the formula and find the output dimensions for the next layer.
  10. Repeat 5d till the last layer in CNN.
  11. Determine the number of layers and number of neurons per layer and parameters in FNN.
  12. Sketch the architecture with the parameters and dimension.
  13. Incorporate these details into the machine.
  14. Or import a predefined model.  In that case the classes in the last layer in the FNN must be replaced with ‘1’ for binary classification or with the number of classes. This is known as transfer learning.
  15. Train the model using the training dataset and calculate the loss function for periodic steps in the training.
  16. Check if the machine has performed correctly by comparing the true output with model prediction and hence compute the training accuracy.
  17. Test the machine with the evaluation data and verify the performance on that data and compute the validation accuracy.
  18.   If both the accuracies are satisfactory then the machine is complete.

HAPPY LEARNING!!



DEEP LEARNING SERIES- PART 7

The previous article was about the process of convolution and its implementation. This article is about the padding, stride and the parameters involved in a CNN.

We have seen that there is a reduction of dimension in the output vector. A technique known as padding is done to preserve the original dimensions in the output vector. The only change in this process is that we add a boundary of ‘0s’ over the input vector and then do the convolution process.

Procedure to implement padding

  1. To get n*n output use a (n+2*n+2) input
  2. To get 7*7 output use 9*9 input
  3. In that 9*9 input fill the first row, first column, last row and last column with zero.
  4. Now do the convolution operation on it using a filter.
  5. Observe that the output has the same dimensions as of the input.

Zero is used since it is insignificant so as to keep the output dimension without affecting the results

Here all the elements in the input vector have been transferred to the output. Hence using padding we can preserve the originality of the input. Padding is denoted using P. If P=1 then one layer of zeroes is added and so on.

It is not necessary that the filter or kernel must be applied to all the cells. The pattern of applying the kernel onto the input vector is determined using the stride. It determines the shift or gaps in the cells where the filter has to be applied.-

S=1 means no gap is created. The filter is applied to all the cells.

S=2 means gap of 1. The filter is applied to alternative cells. This halves the dimensions on the output vector.

This diagram shows the movement of filter on a vector with stride of 1 and 2. With a stride of 2; alternative columns are accessed and hence the number of computations per row decreases by 2. Hence the output dimensions reduce while use stride.

The padding and stride are some features used in CNN.

Parameters in a convolution layer

The following are the terms needed for calculating the parameter for a convolution layer.

Input layer

Width Wi – width of input image

Height Hi – height of input image

Depth Di – 3 since they follow RGB

We saw that 7*7 inputs without padding and stride along with 3*3 kernels gave a 5*5 output. It can be verified using this calculation.

The role of padding can also be verified using this calculation.

The f is known as filter size. It can be a 1*1, 3*3 and so on. It is a 1-D value so the first value is taken. There is another term K which refers to the number of kernels used. This value is fixed by user.

These values are similar to those of w and b. The machine learns the ideal value for these parameters for high efficiency. The significance of partial connection or CNN can be easily understood through the parameters.

Consider the same example of (30*30*3) vector. The parameter for CNN by using 10 kernels will be 2.7 million. This is a large number. But if the same is done using FNN then the parameters will be at least 100 million. This is almost 50 times that of before. This is significantly larger than CNN. The reason for this large number is due to the full connectivity. 

                                                 

Parameter= 30*30*3*3*10= 2.7M

HAPPY READING!!

DEEP LEARNING SERIES- PART 6

The previous article was about the procedure to develop a deep learning network and introduction to CNN. This article concentrates on the process of convolution which is the process of taking in two images and doing a transformation to produce an output image. This process is common in mathematics and signals analysis also. The CNN’s are mainly used to work with images.

In the CNN partial connection is observed. Hence all the neurons are not connected to those in the next layer. So the number of parameters reduces leading to lesser computations.

Sample connection is seen in CNN.

Convolution in mathematics refers to the process of combining two different functions. With respect to CNN, convolution occurs between the image and the filter or kernel. Convolution itself is one of the processes done on the image.

Here also the operation is mathematical. It is a kind of operation on two vectors. The input image gets converted into a vector-based on color and dimension. The kernel or filter is a predefined vector with fixed values to perform various functions onto the image.

Process of convolution

The kernel or filter is chosen in order of 1*1, 3*3, 5*5, 7*7, and so on. The given filter vector slides over the image and performs dot product over the image vector and produces an output vector with the result of each 3*3 dot product over the 7*7 vector.

A 3*3 kernel slides over the 7*7 input vector to produce a 5*5 output image vector. The reason for the reduction in the dimension is that the kernel has to do dot product operation on the input vector-only with the same dimension. I.e. the kernel slides for every three rows in the seven rows. The kernel must perfectly fit into the input vector. All the cells in the kernel must superimpose onto the vector. No cells must be left open. There are only 5 ways to keep a 3-row filter in a 7-row vector.    

This pictorial representation can help to understand even better. These colors might seem confusing, but follow these steps to analyze them.

  1. View at the first row.
  2. Analyse and number the different colours used in that row
  3. Each colour represents a 3*3 kernel.
  4. In the first row the different colours are red, orange, light green, dark green and blue.
  5. They count up to five.
  6. Hence there are five ways to keep a 3 row filter over a 7 row vector.
  7. Repeat this analysis for all rows
  8. 35 different colours will be used. The math is that in each row there will be 5 combinations. For 7 rows there will be 35 combinations.
  9. The colour does not go beyond the 7 rows signifying that kernel cannot go beyond the dimension of input vector.

These are the 35 different ways to keep a 3*3 filter over a 7*7 image vector. From this diagram, we can analyse each row has five different colours. All the nine cells in the kernel must fit inside the vector. This is the reason for the reduction in the dimension of output vector.

Procedure to implement convolution

  1. Take the input image with given dimensions.
  2. Flatten it into 1-D vector. This is the input vector whose values represent the colour of a pixel in the image.
  3. Decide the dimension, quantity and values for filter. The value in a filter is based on the function needed like blurring, fadening, sharpening etc. the quantity and dimension is determined by the user.
  4. Take the filter and keep it over the input vector from the first cell. Assume a 3*3 filter kept over a 7*7 vector.
  5. Perform the following computations on them.

5a. take the values in the first cell of the filter and the vector.

5b. multiply them.

5c. take the values in the second cell of the filter and the vector.

5d. multiply them.

5e. repeat the procedure till the last cell.

5f. take the sum for all the nine values.

  • Place this value in the output vector.
  • Using the formula mentioned later, find the dimensions of the output vector.

HAPPY LEARNING!!

DEEP LEARNING SERIES- PART 5

The previous article was on algorithm and hyper-parameter tuning. This article is about the general steps for building a deep learning model and also the steps to improve its accuracy along with the second type of network known as CNN.

General procedure to build an AI machine

  1. Obtain the data in the form of excel sheets, csv (comma separated variables) or image datasets.
  2. Perform some pre-processing onto the data like normalisation, binarisation etc. (apply principles of statistics)
  3. Split the given data into training data and testing data. Give more preference to training data since more training can give better accuracy. Standard train test split ratio is 75:25.
  4. Define the class for the model. Class includes the initialisation, network architecture, regularisation, activation functions, loss function, learning algorithm and prediction.
  5. Plot the loss function and interpret the results.
  6. Compute the accuracy for both training and testing data and check onto the steps to improve it.

Steps to improve the accuracy

  1. Increase the training and testing data. More data can increase the accuracy since the machine learns better.
  2. Reduce the learning rate. High learning rate often affects the loss plot and accuracy.
  3. Increase the number of iterations (epochs). Training for more epochs can increase the accuracy
  4. Hyper parameter tuning. One of the efficient methods to improve the accuracy.
  5. Pre-processing of data. It becomes hard for the machine to work on data with different ranges. Hence it is recommended to standardise the data within a range of 0 to 1 for easy working.

These are some of the processes used to construct a network. Only basics have been provided on the concepts and it is recommended to learn more about these concepts. 

Implementation of FFN in detecting OSTEOARTHRITIS (OA)

Advancements in the detection of OA have occurred through AI. Technology has developed where machines are created to detect OA using the X-ray images from the patient. Since the input given is in the form of images, optimum performance can be obtained using CNN’s. Since the output is binary, the task is binary classification. A combination of CNN and FFN is used. CNN handles feature extraction i.e. converting the image into a form that is accepted by the FFN without changing the values. FFN is used to classify the image into two classes.

CNN-convolutional neural network

The convolutional neural network mainly works on image data. It is used for feature extraction from the image. This is a partially connected neural network. Image can be interpreted by us but not by machines. Hence they interpret images as a vector whose values represent the color intensity of the image. Every color can be expressed as a vector of 3-D known as RGB- Red Green Blue. The size of the vector is equal to the dimensions of the image.

                                                  

This type of input is fed into the CNN. There are several processing done to the image before classifying it. The combination of CNN and FNN serves a purpose for image classification.

Problems are seen in using FFN for image

  • We have seen earlier that the gradients are chain rule of gradient at different layers. For image data, large number of layers in order of thousands may require. It can result in millions of parameters. It is very tedious to find the gradient for the millions of these parameters.
  • Using FFN for image data can often overfit the data. This may be due to the large layers and large number of parameters.

The CNN can overcome the problems seen in FFN.

HAPPY LEARNING!!!

DEEP LEARNING SERIES- PART 4

The previous article dealt with the networks and the backpropagation algorithm. This article is about the mathematical implementation of the algorithm in FFN followed by an important concept called hyper-parameter tuning.

In this FFN we apply the backpropagation to find the partial derivative of the loss function with respect to w1 so as to update w1.

Hence using backpropagation the algorithm determines the update required in the parameters so as to match the predicted output with the true output. The algorithm which performs this is known as Vanilla Gradient Descent.

The way of reading the input is determined using the strategy.

StrategyMeaning
StochasticOne by one
BatchSplitting entire input into batches
Mini-batchSplitting batch into batches

The sigmoid here is one of the types of the activation function. It is defined as the function pertaining to the transformation of input to output in a particular neuron. Differentiating the activation function gives the respective terms in the gradients.

There are two common phenomena seen in training networks. They are

  1. Under fitting
  2. Over fitting

If the model is too simple to learn the data then the model can underfit the data. In that case, complex models and algorithms must be used.

If the model is too complex to learn the data then the model can overfit the data. This can be visualized by seeing the differences in the training and testing loss function curves. The method adopted to change this is known as regularisation. Overfit and underfit can be visualized by plotting the graph of testing and training accuracies over the iterations. Perfect fit represents the overlapping of both curves.

Regularisation is the procedure to prevent the overfitting of data. Indirectly, it helps in increasing the accuracy of the model. It is either done by

  1. Adding noises to input to affect and reduce the output.
  2. To find the optimum iterations by early stopping
  3. By normalising the data (applying normal distribution to input)
  4. By forming subsets of a network and training them using dropout.

So far we have seen a lot of examples for a lot of procedures. There will be confusion arising at this point on what combination of items to use in the network for maximum optimization. There is a process known as hyper-parameter tuning. With the help of this, we can find the combination of items for maximum efficiency. The following items can be selected using this method.

  1. Network architecture
  2. Number of layers
  3. Number of neurons in each layer
  4. Learning algorithm
  5. Vanilla Gradient Descent
  6. Momentum based GD
  7. Nesterov accelerated gradient
  8. AdaGrad
  9. RMSProp
  10. Adam
  11. Initialisation
  12. Zero
  13. He
  14. Xavier
  15. Activation functions
  16. Sigmoid
  17. Tanh
  18. Relu
  19. Leaky relu
  20. Softmax
  21. Strategy
  22. Batch
  23. Mini-batch
  24. Stochastic
  25. Regularisation
  26. L2 norm
  27. Early stopping
  28. Addition of noise
  29. Normalisation
  30. Drop-out

 All these six categories are essential in building a network and improving its accuracy. Hyperparameter tuning can be done in two ways

  1. Based on the knowledge of task
  2. Random combination

The first method involves determining the items based on the knowledge of the task to be performed. For example, if classification is considered then

  • Activation function- softmax in o/p and sigmoid for rest
  • Initialisation- zero or Xavier
  • Strategy- stochastic
  • Algorithm- vanilla GD

The second method involves the random combination of these items and finding the best combination for which the loss function is minimum and accuracy is high.

Hyperparameter tuning would already be done by researchers who finally report the correct combination of items for maximum accuracy.

HAPPY READING!!!

DEEP LEARNING SERIES- PART 3

The previous article gave some introduction to the networks used in deep learning. This article provides more information on the different types of neural networks.

In a feed-forward neural network (FFN) all the neurons in one layer are connected to the next layer. The advantage is that all the information processed from the previous neurons is fed to the next layer hence getting clarity in the process. But the number of weights and biases significantly increases when there is a large number of input. This method is best used for text data.

In a convolutional neural network (CNN), some of the neurons are only connected to the next layer i.e. connection is partial. Batch-wise information is fed into the next layer. The advantage is that the number of parameters significantly reduces when compared to FFN. This method is best used for image data since there will be thousands of inputs.

In recurrent neural networks, the output of one neuron is fed back as an input to the neuron in the previous layer. A feed-forward and a feedback connection are established between the neurons. The advantage is that the neuron in the previous layer can perform efficiently and can update based on the output from the next neuron. This concept is similar to reinforcement learning in the brain. The brain learns an action based on punishment or reward given as feedback to the neuron corresponding to that action.

Once the final output is computed by the network, it is then compared with the original value, and their difference is taken in different forms like the difference of squares, etc. this term is known as loss function.

It will be better to explain the role of the learning algorithms here. The learning algorithm is the one that tries to find the relation between the input and output. In the case of neural networks, the output is indirectly related to input since there are some hidden layers in between them. This learning algorithm works in such a way so as to find the optimum w and b values for the loss function is minimum or ideally zero.

The algorithm in neural networks do this using a method called backpropagation. In this method, the algorithm starts tracing from the output. It then computes the values for the parameters corresponding to the neuron in that layer. It then goes back to the previous layer does the computations for the parameters of the neurons in that layer. This procedure is done till it encounters the inputs. In this way, we can find the optimum values for the parameters.

The computations made by the algorithm are based on the type of the algorithm. Most of the algorithms find the derivative of a parameter in one layer with respect to the loss function using backpropagation. This derivative is then subtracted from the original value.

Where lr is the learning rate; provided by the user. The lesser the learning rate, the better will be the results but more the time is taken. The starting value for w and b is determined using the initialization.

MethodMeaning
ZeroW and b are set to zero
Xavierw and b indirectly proportional to root n
He w and b indirectly proportional to root n/2

 Where n; refers to the number of neurons in a layer. These depend on the activation function used.

The derivative of the loss function determines the updating of the parameters.

Value of derivativeConsequence
-veIncreases
0No change
+veDecreases

The derivative of the loss function with respect to the weight or bias in a particular layer can be determined using the chain rule used in calculus.

HAPPY READING!!

DEEP LEARNING- PART 2

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The previous article gave a brief introduction to deep learning. This article deals with the networks used in deep learning. This network is known as a neural network. As the name suggests the network is made up of neurons

The networks used in artificial intelligence are a combination of blocks arranged in layers. These blocks are called an artificial neurons. They mimic the properties of a natural neuron. One of the neurons is the sigmoid neuron.

This is in general the formula for the sigmoid function. Every neural network consists of weights and biases.

Weights- The scalar quantities which get multiplied to the input

Biases- the threshold quantity above which a neuron fires

NotationMeaning
XInput
YOutput
WWeight
BBias

Working of a neuron

This is the simple representation of a neuron. This is similar to the biological neuron. In this neuron, the inputs are given along with some priority known as weights. The higher the value of the weights, the more prioritized is that input. This is the reason for our brain to choose one activity over the other. Activity is done only if the neuron fires. A similar situation is seen here. The particular activity is forwarded to the next layer only if this particular neuron fires. That is the output must be produced from the neuron.

Condition for the neuron to fire

The neuron will produce an output only if the inputs follow the condition.

As mentioned before, the bias is the threshold value and the neuron will fire only when the value crosses this bias. Thus the weighted sum for all the inputs must be greater than the bias in order to produce an output.

Classification of networks

Every neural network consists of three layers majorly: –

  1. Input layer
    1. Hidden layer
    1. Output layer

Input layer

The input layer consists of inputs in the form of vectors. Images are converted into 1-D vectors. Input can be of any form like audio, text, video, image, etc. which get converted into vectors.

Hidden layer

This is the layer in which all the computations occur. This is generally not visible to the user hence termed as a hidden layer. This layer may be single or multiple based on the complexity of the task to be performed. Each layer processes a part of the task and it is sent to the next layer. Vectors get multiplied with the weight matrix of correct dimensions and this vector gets passed onto the next layer.

Output layer

The output layer gets information from the last layer of the hidden layer. This is the last stage in the network. This stage depends upon the task given by the user. The output will be a 1-D vector. In the case of classification, the vector will have a value high for a particular class. In the case of regression, the output vector will have numbers representing the answer to those questions posed by the user.

The next article is about the feed-forward neural network.

HAPPY LEARNING!!

DEEP LEARNING SERIES- PART 1

Have you ever wondered how the brain works? One way of understanding it is by cutting open the brain and analyzing the structures present inside it. This however can be done by researchers and doctors. Another method is by using electricity to stimulate several regions of the brain. But what if I say that it is possible to analyze and mimic the brain in our computers? Sounds quite interesting right! This particular technology is known as deep learning.

Deep learning is the technique of producing networks that process unstructured data and gives output. With the help of deep learning, it is possible to produce and use brain-like networks for various tasks in our systems. It is like using the brain without taking it out.  Deep learning is advanced than machine learning and imitates the brain better than machine learning and also the networks built using deep learning consists of parts known as neurons which is similar to biological neurons. Artificial intelligence has attracted researchers in every domain for the past two decades especially in the medical field; AI is used to detect several diseases in healthcare.

Sl.noNameDescriptionExamples
1DataType of data provided to inputBinary(0,1) Real
2TaskThe operation required to do on the inputClassification(binary or multi) Regression(prediction)
3ModelThe mathematical relation between input and output. This varies based on the task and complexityMP neuron(Y=x+b) Perceptron(Y=wx+b) Sigmoid or logistic(Y=1/1+exp(wx+b)) *w and b are parameters corresponding to the model
4Loss functionKind of a compiler that finds errors between the output and input (how much the o/p leads or lags the i/p).Square error= square of the difference between the predicted and actual output.  
5AlgorithmA kind of learning procedure that tries to reduce the error computed beforeGradient descent
NAG
AdaGrad
Adam
RMSProp
6EvaluationFinding how good the model has performedAccuracy
Mean accuracy

Every model in this deep learning can be easily understood through these six domains. Or in other words, these six domains play an important role in the construction of any model. As we require cement, sand, pebbles, and bricks to construct a house we require these six domains to construct a network.

 Now it will be more understandable to tell about the general procedure for networks.

  1. Take in the data (inputs and their corresponding outputs) from the user.
  2. Perform the task as mentioned by the user.
  3. Apply the specific relation to the input to compute the predicted output as declared by the user in the form of model by assigning values to parameters in the model.
  4.  Find the loss the model has made through computing the difference between the predicted and actual output.
  5. Use a suitable learning algorithm so as to minimize the loss by finding the optimum value for parameters in the network
  6. Run the model and evaluate its performance in order to find its efficiency and enhance it if found less.

By following these steps correctly, one can develop their own machine. In order to learn better on this, pursuing AI either through courses or opting as a major is highly recommended. The reason is that understanding those concepts requires various divisions in mathematics like statistics, probability, calculus, vectors and matrices apart from programming. 

       

HAPPY READING!!

IMMUNOLOGY SERIES- PART 9- VACCINES

The previous article was all about the process of inflammation. This article is about vaccines.

The vaccines fall under the type of artificial active acquired immunity. This is artificial because we are giving the vaccine externally and this is active because the body is generating the antibodies/response and it is acquired because we are getting the immunity and it is not present by birth. You must have known what immunity is at least by now.

A vaccine is a biological preparation that provides active acquired immunity to a particular infectious disease. A vaccine typically contains an agent that resembles a disease-causing microorganism and is often made from weakened or killed forms of the microbe, its toxins, or one of its surface proteins (antigens). So these vaccines are nothing but the pathogen itself but it cannot cause any disease, instead, it triggers the immune system.

This is a quick recap of the principle of working on vaccines. The vaccine contains the pathogens as a whole or the surface antigens only. These antigens stimulate the immune system. If the immune system had a memory about this antigen, then it would immediately produce an antibody, and phagocytosis of the antigen occurs by the macrophage aided by the antibody. In this scenario, the antigen is new and there is no memory, therefore the immune system struggles and takes time to produce the antibody.

So the antigen reign over the body and this can lead to inflammation. As a result, some of the symptoms of inflammation like fever, heat, pain in the area of application, and swelling may appear. The chances of them are rare and also severity is less (last for a few hours/days) since the pathogen is attenuated.

Once the immune system produces the correct antibody, phagocytosis of the antigen occurs and hence the causative agent is eliminated from the body (primary response). So if the same or similar pathogen which has disease-causing ability enters into the body, the memory triggers the immune system to produce the correct antibody. So a heightened and rapid response is generated in order to kick away the pathogen quickly (secondary response).

There are three types of vaccines:-

Live- infection is caused without any harm – measles & polio

Dead- doesn’t last long, requires booster dose- cholera

Microbial products- involves non-infectious pathogen, capsule and toxoid- anthrax, diptheria

Hence using the vaccine as a stimulus, the body is able to generate a response that is stored and can be useful for preventing the disease caused by the pathogen.

There might be an idea to generate vaccines for all diseases so that all humans are protected. But there are some difficulties in this which are listed below:-

There are new microbes being discovered every day and no one knows which microbe can cause disease. There can be multiple microbes causing the same or similar disease. So being immune to one microbe doesn’t mean being immune to the disease

The disease-causing microbe can undergo mutation meaning that there can be changes in the genetic material and hence the antigen can change. In this case, the antibody which was stimulated by the vaccine won’t work. A suitable example is a common cold, it is impossible to produce a vaccine that covers all mutants of viruses

The pathogen has to be genetically modified so as to remove its disease-causing ability which is easy to say but difficult to implement

Also, it is important that the antigen chose for the vaccine must be close to that of the original causative agent of the disease. If the original pathogen is not so close to that of the vaccine, then it will not work

Hence all these above points explain the difficulties in producing a vaccine. Despite these many research organizations in many countries have produced vaccines especially for the pandemic and dreadful diseases like the COVID-19, hepatitis, polio, etc. in which some vaccines provide lifetime immunity to some of the diseases. We must take a minute to appreciate those who have done immense work and their contribution is stopping some of the dreadful diseases.

With this, we come to the end of the series. I hope that all the concepts explained in this were simple and clear and also would have inculcated an interest in immunology. By now, it would be clear how the immune system protects us from several microbes and diseases.

HAPPY LEARNING!!

IMMUNOLOGY SERIES- PART 8- INFLAMMATION

The previous article dealt with the types and functions of immunoglobulin. This article provides a complete explanation of the process of inflammation.

Inflammation is the process of protection which was seen as one of the six mechanisms of innate immunity.

Inflammation is one of the body’s responses to the invasion of foreign particles. This is an important process in the human body that occurs to drive away from the pathogen. Inflammation is one of the stages seen in healing. Some of the changes that can be seen in the target site are:-

  • Changes in blood flow (mostly blood loss)
  • Increase in platelets (to plug the damaged vessel)
  • Increase in immune cells
  • Supply of nutrients

The word inflammation refers to a burning sensation. Hence there are five cardinal signs in inflammation namely:-

  • Rubor (redness)
  • Tumor (swelling)
  • Calor (heat)
  • Dolor (pain)
  • Functioleasia (loss of function)

These cardinal signs as well as the changes occur due to some mediators which are basically chemicals and also due to the action of various immune cells.

Mediator nameIt’s effect
Bradykinin, histamine, serotoninIncrease permeability
ProstaglandinDecreases blood pressure
CytokinesProduce fever
Toxic metabolitesDamage tissue

This inflammation can be either acute or chronic. As seen earlier, acute stays for a shorter time but produces more vigorous pain whereas chronic stays for a longer time with less vigorous pain. If the causative agent has been driven away then healing occurs either by complete restoration or scar formation. There are chances that the acute inflammation can become chronic which can be worse. It can lead to several diseases and complications.

The pathogen in order to establish its supremacy in the human body, it has to pass through the epidermis which is the outermost layer of the human body. This is known as SALT skin-associated lymphoid tissues. Hence T and B lymphocytes are prominent in the skin. Most of the pathogens get destroyed in this stage. Let us assume that our pathogen is strong and it had passed through it. The next layer it encounters is the dermis. As we go deep inside the skin, more and more immune cells get involved. In the dermis the following immune cells are seen:-

immunity in the skin
  • Macrophage
  • NK cells
  • Mast cell – produce histamine and serotonin
  • T helper cells – it provides help to other immune cells

The next stage is the hypodermis which has a large number of macrophages and neutrophils that phagocytosis the pathogen. Hence these following processes help in defending against the pathogens.

When a particular pathogen say a virus enters the cell, the immune system will get alerted through signals and they immediately send the correct immune cell to the target site. This occurs since either the immune system gets information naturally or artificially through previous infection or vaccine. This leads to the classification of immunity in humans.

So now we will consider a new and strong pathogen that has not been recognized by the immune system and has dodged those barriers and has entered inside the skin. Now it multiplies at a rapid rate and colonizes that particular area. Hence the cells in that area start to die and they release several signals like TNF, cytokines, interleukins. This gets combined with other signals like histamine, serotonin released from immune cells. Some of these signals produce direct effects on the target site as seen in the table.

An array of these signals triggers the immune system and it, in turn, starts the inflammation process and the cardinal signs are observed. This process lasts for some time and as it occurs; the pathogens decrease in number through phagocytosis and subsequently vanishes from the body. This can be observed by a decrease in the signs. After this process, the targeted site starts to heal and the immune system learns how to defend the pathogen when it enters the next time.

Now the damage caused by the pathogen has to be repaired by the process of healing.

  1. Haemostasis
  2. Inflammation
  3. Proliferation
  4. Maturation/Remodelling

The pathogen will rupture and damage the outer layer of blood vessels known as endothelium resulting in blood loss. Hence the blood vessels start to contract to prevent further loss. Also, a plug is formed at the site of leakage by the platelets. Then the process of inflammation occurs; clearing out the dead cells and the pathogen. In the proliferative stage, new blood cells are formed by a process known as neovascularisation and the new epithelium is formed. In the last phase, the newly formed cells become stronger and flexible. Hence the combination of these steps brings the affected area back to normal.

Hence the inflammation is an essential process in the immune system and it has to occur to prevent the conspiracy of the microbes. The next article is about vaccines and their principle of working.

HAPPY READING!!!

IMMUNOLOGY SERIES- PART 7- TYPES OF IMMUNOGLOBULIN

The previous article dealt in detail with immunoglobulin and how they help in phagocytosis. This article is about the types of immunoglobulins, their functions.

The types of immunoglobulins are based on the types of light and heavy chains. There are two types of light chains namely the kappa and the lambda. An immunoglobulin contains either kappa (K-K) or lambda (L-L) but does not have a mixture of both (K-L not possible). About 60% of the immunoglobulins in humans have kappa chains.

So, the classes of immunoglobulins are based on the heavy chain. So based on this condition, there are five classes of immunoglobulins namely:-

  • Immunoglobulin G (IgG) – gamma
  • Immunoglobulin M (IgM) – mu
  • Immunoglobulin A (IgA) – alpha
  • Immunoglobulin D (IgD) – delta
  • Immunoglobulin E (IgE) – epsilon

These immunoglobulins have certain configurations and play different roles in the human body. The immunoglobulin G is present the most. It constitutes about 80% of the total immunoglobulin. These are mostly present in the blood, plasma, and other body fluids. This immunoglobulin has the lowest carbohydrate content when compared to the rest. This immunoglobulin has a half-life of 23 days which is the longest of all. Some of the unique features and functions of this immunoglobulin:-

  • This is the only immunoglobulin which can cross the placenta (this is a unique feature because this immunoglobulin provides immunity to the foetus inside the womb and also after birth for some months. Presence of others may indicate infection)
  • This helps in killing bacteria and viruses by opsonisation (the process of covering the pathogen with a protein coat such that the pathogens become more presentable to the immune cells)
  • Neutralize toxins
  • Activate complement by classical pathway (The complement system, also known as complement cascade, is a part of the immune system that enhances the ability of antibodies and phagocytic cells to clear microbes and damaged cells from an organism, promote inflammation, and attack the pathogen’s cell membrane)
  • Unique catabolism (breaking down of molecules) based on concentration
  • There are four sub classes (G1, G2, G3 and G4) out of which 1,3 and 4 cross the placenta and offer immunity
  • Also involves in the Rh immunization (there are two types’ Rh+ve and Rh-ve based on the presence of Rh factor in blood). The mother being Rh+ve and child the opposite is not a problem in the first pregnancy but can be fatal in second, killing the foetus.

The immunoglobulin M constitutes about 5-10% of total proteins. This is a pentamer structure with a J chain. This weighs about 900000-1000000 and is the heaviest of all. They have 5 days of half-life. Some of its features-

  • Presence in newborn indicate congenital infection as they don’t cross placenta
  • Short lived, so their presence indicates recent infection
  • First Ig to participate in primary response
  • Opsonisation
  • classical pathway
  • bacteria agglutination
  • Play an important role in ABO blood grouping (discovered by Landsteiner). There are 8 types of blood groups based on antigen, antibody and Rh factor

Immunoglobulin A is also known as the secretory immunoglobulin and is mostly present in body secretions (tear, saliva, sebum, mucous, and milk) in which they are dimer and are monomer in blood. They constitute 10-15% of the proteins. They also have a J chain and secretory piece. Their half-life is 6-8 days.

  • The secretory piece protects the Ig from enzymes and juices
  • Complement activation by alternate pathway
  • Promote phagocytosis
  • Intracellular microorganism killing
  • First line of defense against some microbes

Immunoglobulin E is a dimer similar to IgG. This is present in low concentrations (about 0.3) and has the weight of about 1,90,000. These have a half-life of about 2 days and can become inactivated at 56 C.

  • Present extra-cellularly
  • Associated with allergic reactions like asthma, hay fever and anaphylactic shock
  • Bind with the Fc of mast cells and basophils resulting in degranulation and release histamine which causes allergy
  • Mediate the some immunity reactions
  • No complement activation
  • Provide immunity against helminthes

The last is immunoglobulin D.  It is present in low concentrations and on the surface of B lymphocytes. They constitute 0.2% of proteins. They have a half-life of 3 days. The IgM and IgD bind on the B lymphocyte to help in antigen identification.

Hence these were the different types of immunoglobulins and the mechanisms by which they help with immunity. The next article is about the process of inflammation.

HAPPY READING!!

IMMUNOLOGY SERIES- PART 6- IMMUNOGLOBULIN

The previous article was about the different types of immune cells. This article is about a special molecule in immunity known as immunoglobulin.

There might be a question that what is so special about this immunoglobulin. There is a reason for this. These molecules play an important and inevitable role in the phagocytosis of pathogens. To understand this, it is essential to know about immunoglobulins.

The immunoglobulin is a gamma globulin, a specialized group of proteins (glycoprotein) produced in response to pathogens. It is produced by the plasma cells (a globulin protein present in the plasma). These constitute 25-30% of the blood proteins.

There are two important terms that are more commonly known by the most, they are the antigen and the antibody. The antigen is the molecule present on the surface of the pathogen and can stimulate an immune response. There is a small part of the antigen called the epitope which interacts with the antibody.  The epitope is known as the antigen determinant site. An antigen can have unlimited epitopes.

On the contrary, the antibody is the molecule produced in response to the antigen in order to kick it away. The part of the antibody which interacts with the antigen is called a paratope. An antibody must have at least 2 paratopes. These antibodies belong to the immunoglobulins. All antibodies are immunoglobulins but not immunoglobulins are antibodies. To understand how the antibody helps in immunity, it is essential to understand the structure of an antibody/immunoglobulin. The image below shows the general structure of an immunoglobulin:-

There are two chains in an immunoglobulin namely the light chain and heavy chain. The light chain has 212 amino acids (the building block of protein) and the heavy chain has 450 amino acids. Each chain has two types namely the constant and variable. These regions are based on the amino acid sequences. Half of the light chain (1 out of 2) is constant and the rest is variable. A quarter of the heavy chain (1 out of 4) is variable and the rest is constant. These are linked by two types of sulfide bonds namely the intra (H-H AND L-L) and inter (H-L). These molecules contain carbohydrates (CHO) hence these are called as glycoproteins.

The tip of the variable regions of the heavy and light chain is hypervariable in nature and these constitute the antigen-binding site (Fab). These are hyper-variable because they have to produce amino acid sequences complementary to that of the antigen so that they can interact together. The other site is called a crystallizable region (Fc).

Having known all this, now it will be convenient to explain the process by which the antibody plays in the prevention of infections.

There are millions of substances that pass through the blood every day. So there must be a criterion/substance to identify them whether they are pathogenic. This is where antigen comes to play. These antigens present on the surface of the pathogens alert the immune system which then identifies this as a pathogen. So in response to the antigen, a suitable antibody is secreted and deployed to the target site. On reaching the antigen, the Fab region binds with the antigen.

The ultimate aim of the immune system is to abolish the pathogen and one way is by phagocytosing them. This is done by the macrophages. But it is essential for them to identify the substance before engulfing it. This is where the antibody comes to play. The Fc region of the antibody combines with the receptor of the macrophage. This facilitates the process of phagocytosis.

Hence the antibody acts like a bridge between the source (antigen) and the destination (macrophage) aiding in phagocytosis. This is essential because in most of the cases the macrophages, it is difficult to identify the non-self-objects and this is where antibody helps.

In the case of the new pathogen, the antigen is new, and therefore their might not be a suitable antibody. In that case, the macrophage cannot phagocytocise the pathogen and it reigns in the body causing infection and disease.

The next article is about the types of immunoglobulins.

HAPPY LEARNING!!

IMMUNOLOGY SERIES-PART 5- INTRODUCTION TO THE IMMUNE CELLS

The previous article was about the acquired immunity. This article is all about the immune cells, the warriors of the human body.

These cells play a major role in protecting the body from infections. Some of them contribute directly and some contribute indirectly. Despite the methods, all of them are required in optimum amounts so as to live a healthy life.

All of these cells are derived from a specific type of cell found in the blood. The blood is a freely flowing interstitial fluid that transports oxygen, nutrients, etc. to the cells of the body. There are two components in the blood in which the first one is called plasma. The plasma is the liquid carrying water, salts, enzymes, and proteins. There are three specialized proteins in the plasma-

Albumin- to maintain water balance

Globulin- for immunity (it is a part of immunoglobulin)

Fibrinogen- for clotting

Hence the plasma also contributes to immunity. This plasma constitutes about 55% of the blood. The rest 45% of the blood is constituted by the formed elements or corpuscles. There are three elements in it namely-

Erythrocyte or Red Blood Corpuscle- transport of oxygen

Leucocyte or White Blood Corpuscle- fight infections

Thrombocyte or platelets- for clotting

Out of these, the WBC is the one primarily contributing to immunity. A healthy person must have a WBC count from 4000-11000. Count less than 4000 means leukopenia meaning that the immune system is weak. If the count is more than 11000 then it means the condition of autoimmunity known as leucocytosis. There are some further classifications in the WBC which are displayed through the flowchart below.

There are two types of cells in the WBC namely the granulocytes and agranulocytes.

The granulocytes, as the name specifies have granules in their cytoplasm. There are three different cells in this.

The neutrophil constitutes to about 55-70% of the total WBC and they are ones involved in most of the fights against the infections. These defend against bacterial and fungal infections. These cells are mostly found in the epidermal regions and are in the first line of defense.  These cells engulf the pathogens by the process of phagocytosis. These cells have multiple nuclei hence these are also known as PMN (Poly Morpho Neutrophils). Neutrophils help prevent infections by blocking, disabling, and digesting off invading particles and microorganisms. They also communicate with other cells to help them repair cells and mount a proper immune response. The death of these cells often results in the formation of pus (suppuration).

neutrophil

The eosinophil constitutes about 2-4% of the total WBC. These cells are very little in the body but can increase in the case of allergic reactions, parasite infection, and so on. The functions of the eosinophil include movement to inflamed areas, trapping substances, killing cells, anti-parasitic and bactericidal activity, participating in immediate allergic reactions, and modulating inflammatory responses.

eosinophil

The basophil is present in the least concentration of all (0.2%) in total WBC. These cells play an important role in allergic reactions in which their count can increase. The basophil contains inflammatory mediators like histamine and heparin. The release of the compounds results in dilation of the blood vessels. Hence these cells regulate the inflammation process.

The agranulocytes are those which lack granules in their cytoplasm. There are two types in this. The lymphocyte can be called as the memory of the immune system. There are two types of lymphocytes namely T and B lymphocytes. These lymphocytes recognize the incoming pathogens and based on their memory it produces a suitable response in a short amount of time. These cells are involved in the secondary response in the acquired immunity.

B cells make antibodies that can bind to pathogens, block pathogen invasion, activate the complement system, and enhance pathogen destruction. The T cells mostly known as CD4+ T helper cells produce the cytokines (proteins in cell signaling) and coordinate with the immune system. There is another form called CD8+ cytotoxic T cells which is opposite to the previous type, they help in the destruction of tumors and pathogens.

The monocyte is the largest of all the cells in WBC. They function similarly to that of the neutrophils (phagocytosis of the pathogens). These cells present the pathogen to the memory cells upon which a response is generated. Once they leave the blood, they turn into macrophages which help in clearing cell debris and killing pathogens. These are known as the vacuum cleaners of immunity.

Hence all these cells work in different mechanisms and they coordinate together to make sure that we do not fall prey to the disease-causing microorganisms.

HAPPY LEARNING!!

DEBATE CONCEPTS IN OSTEOARTHRITIS

This article deals with some of the concepts related to the progression of osteoarthritis. These statements were given by prominent researchers and resulted in a debate between two prominent groups of researchers against each other. All of these took place actively in the 19th century where the publications of research scholars were opposed to that of the scholars in the other group.

William Bauer told that mechanical trauma can result in OA directly or indirectly. By the 20th century ideologies were majorly split into two ‘inflammation’ and ‘no inflammation’. Henry Fuller and Robert Todd suggested that OA occurred due to disruption to nutrients required for knee development and doesn’t occur through inflammation. On the other hand, Garrod and others stated that OA is partly degenerative and partly inflammative. Hence the study for OA continued under these two domains and each group of scientists trying to prove the other is false. But this situation can be compared to two sides of a coin where both the situations cannot be neglected. Hence both the domains of OA cannot be neglected.

Some others say that OA is a neurogenic immune homeostatic disorder. Garrod in 1988 stated that OA is associated with lesions in CNS in a peculiar manner. CNS refers to the central nervous system which constitutes the brain and spinal cord. The brain is the mastermind of the body which generates electrochemical signals to simulate several neurons in the body. The spinal cord is known as a warehouse of reflexes. Reflex is an involuntary (cannot be controlled by conscience) rapid sequence of actions. Reflex can be best explained by several experiments.

When someone comes to hit you; you will either duck or catch his hand spontaneously and this is known as a reflex and the spinal cord or vertebral column is responsible for this.

The reflex of the knee is tested by the doctor who takes a rubber mallet and taps it on the knee and what interestingly happens is that the knee starts to retract and the patient can feel the pain. In case of OA or any knee-related diseases, the patient cannot experience any pain and hence the doctor understands that there is some abnormality in the knee. Hence we can understand that there is a connection between the knee’s ability and CNS and an interruption in this connection can lead to knee diseases.

We have to understand that this is a basic relation and there are other complex associations between them and require more complex methods like electrophysiology and pharmacology to understand them. Later it was proposed that changes in the sympathetic nervous system can also lead to OA.

The sympathetic nervous system is a part of the autonomic nervous system. This can be correlated to the word ‘increase’. The sympathetic nervous system works in response to stimuli like emotions and increases some parameters of the human body like heart rate, eye dilation, blood sugar, blood pressure, etc. this proposal paved the way for using micro-circuitry to correct it.

There is also another field on which the world is divided into two namely ‘nociceptive’ and ‘neuropathic’ where nociceptive refers to pain resulted due to receptors. These are present at target and send signals to the brain via the spine more or less like the reflex. On the other hand neuropathic refers to the condition where pain occurs due to nerves. The following table shows the difference between these two. 

NociceptiveNeuropathic
Receptor-mediated painNerve mediated pain
Doesn’t affect nervesAffects the nerves
Due to painful stimuliDue to inflammation

However, some of the debate topics have not been resolved even till now but a lot of research articles about the progression of the disease and its underlying phenomena have been published. This is one of the cases in which a debate has done some good to the field of science!

HAPPY READING!!

OSTEOARTHRITIS GRADING SYSTEM

Osteoarthritis can be mainly classified into two. They are primary and secondary. The criterion for this classification is based on the different types of risk factors. Primary OA is mainly due to age where the reason for cartilage breakdown is not known or maybe due to genetics. Secondary OA is due to direct injury through sports or trauma, stress, inflammation, or other metabolic diseases. In this case, the cause may localize.

OA grading

Grading is the process of classifying the disease based on its extent or severity. OA has been graded into 5 from grade 0 to grade 4

Stage numberCondition
 0Normal
1Minor
2Mild
3Moderate
4Severe

This was proposed by Kellgren and Lawrence and it is known as KL grading. The five grades have been proposed based on radiographic analysis of subjects. This was accepted as a standard measure by WHO in 1961. The grading has been done based on the narrowing of joint space and the formation of osteophytes.

  • grade 0 (normal): no changes in knee x-ray
  • grade 1 (minor): minimalistic joint space narrowing with possible osteophyte lipping
  • grade 2 (mild): definite osteophytes and  joint space narrowing
  • grade 3 (moderate): multiple osteophytes, definite narrowing of joint space and some sclerosis and possible deformity of bone ends
  • grade 4 (severe): large osteophytes, marked narrowing of joint space, severe sclerosis and definite deformity of bone ends

Grade 0

Grade 0 is considered normal. The subject will not exhibit any features for OA. The x-ray image from this grade is taken as a standard and the other grades are compared with this grade.

Credit:- Häggström, M (2014). “Medical gallery of Mikael Häggström 2014“. WikiJournal of Medicine 1 (2). doi:10.15347/wjm/2014.008. ISSN 2002-4436. Creative Commons CC0 1.0 Universal Public Domain Dedication
X-ray of a healthy knee 
Credit:- Häggström, M (2014). “Medical gallery of Mikael Häggström 2014“. WikiJournal of Medicine 1 (2). doi:10.15347/wjm/2014.008. ISSN 2002-4436. Creative Commons CC0 1.0 Universal Public Domain Dedication
This is the joint space which is observed in healthy patients.

Grade 1

Grade 1 is known as the minor. It can be considered as the initial grade. The joint space has just started to decrease. Osteophyte refers to excess bone growth. It is also known as bone spurs since spur refers to kind to sharp material. This bone growth can be observed as sharp spikes. Here there is very minimal growth of excess bone. Bone spurs occur only at the bones adjacent to the joint. There will be very minor loss of cartilage but this does not contribute to the narrowing of the joint space. Subject in this stage is not confirmed with osteoarthritis. However, subjects having any of the risk factors become more prone to the disease

Grade 2

Grade 2 is known as mild. In this grade, the narrowing of the joint space is more and is visible through the x-ray. There will be also more formation of osteophytes. This grade can be considered as the precursor to many complications like bone dislocation and rubbing. None of these complications are seen in this grade but these complications are soon to occur. The subject in this grade is confirmed with osteoarthritis. Special care has to be taken by those in this grade and through proper medications, they can prevent those further complications.

Grade 3

Grade 3 is known as moderate. Obvious damage occurs to the cartilage and the joint space narrows even at a faster rate. Swelling of the joints starts to occur in this stage. Erosion of cartilage becomes prominent in this stage. The joints become rougher due to spurs leading to stiffness. Inflammation occurs at regular intervals. Subjects can experience popping sounds from the knee.

Grade 4

Grade 4 is known as severe. It is the worst and highest grade of all. The changes become prominent and occur at larger scales. There will be no gap literally meaning the joint is absent. The bones start to rub over each other causing pain. The joint becomes stiff like a rock. The cartilage wears down and maximum growth of osteophyte is seen. Various cytokines are released at cartilage resulting in further death. Life would be dreadful for those in this grade. The arrow in the given X-ray indicates the bones are touching each other and there is no gap in between them.

Grade 4 osteoarthritis
Courtesy: – James Heilman, MD Osteoarthritis of the left knee. Note the osteophytes, narrowing of
 the joint space (arrow), and increased subchondral bone density (arrow). the joint space (arrow), and increased subchondral bone density (arrow). Creative Commons Attribution-Share Alike 3.0

HAPPY READING!!

THE DREADFUL DISEASE FOR THE AGED- THE OSTEOARTHRITIS

Osteoarthritis is the most well-known type of joint pain, influencing a huge number of individuals in the world. It occurs as a result of the wearing down of the cartilage that cushions the ends of your bone over time. It is a complex disease that integrates biomechanics and biochemistry associated with the knee. This is the standard way of defining OA which will be difficult to understand. Hence let us try to understand what OA is. The best way is by splitting the word and analyzing it part by part

Osteo- bone

Arth- joint                        

It is- inflammation    

Knee, Old, Care, Injury, Pain, Knee Pain
x-ray of the osteoarthritic knee joint

                      

As mentioned earlier, the unit of bone is called osteon and any word ending with itis refers to inflammation. Also, arthro term refers to joints in general. Hence the combination of the terms corresponds to inflammation of bones in the joint. This rather sounds simplified. The previous definition had complex terms like biomechanics and biochemistry. Biomechanics refers to the study of movement in living beings. Biochemistry refers to the study of the reactions occurring in living things. So in short, osteoarthritis is such a disease that results in inflammation of joints that occur due to wearing down of the bones surrounding the joint hence affecting the movement and chemical reactions which used to occur properly during normal conditions.

Osteoarthritis can occur in any joint in the human body like elbows, hips, knees, etc. Since our primary focus is on the knee, we will take a deep dive into it. In view of its expectancy and the tolerance that goes with sickness in the knee osteoarthritis represents more prevalence with daily activities like climbing steps and walking when compared to other diseases. Osteoarthritis is the most standardized reason for total knee replacement. As a result of the frequency of this disease especially in middle-aged people, osteoarthritis can act as an extensive barrier towards work and can lead to early retirement.

Coining of OA

Many say that the term osteoarthritis was coined by the British physician John Kent Spender but it was Richard Von Volkmann who tried to separate it from rheumatoid arthritis. The other names which were offered to this disease were ‘chronical rheumatism’

‘senile arthritis’

‘hypertrophic arthritis’

‘arthritis deformans’.

Effect of age

Osteoarthritis can affect people of any age group but it majorly affects old age people. National Library of Medicine suggests that people with an age greater than 70 have more risk to get osteoarthritis. The reason lies in the definition of osteoarthritis. The definition says that disease occurs due to the wearing down of bones. So the bones don’t get worn down the next instant a baby is born. Every process requires time to occur. A mother has to wait for a minimum of 9 months to give birth to a healthy baby. A student must wait for 4 years to get a degree from college. Similarly, it takes time for the bones in the knee to get worn down.

This disease has always troubled old aged people in their lives. Living with osteoarthritis is dreadful. Even climbing the stairs will be a difficult task for them. Hence it is worth knowing about the disease.

HAPPY READING!!

INTRODUCTION TO THE KNEE DISORDERS

When there are some imbalances within the knee then it can lead to disorders which can be indicated by deviation of the knee in terms of function. Most of these disorders occur due to some conditions imposed onto the structures present inside the knee.

BURSITIS: – inflammation (burning sensation) of the bursa causes pain.

(TIP- a word ending with itis refers to inflammation)

FAT PAD IMPINGEMENT: – the fat pad gets swollen heavily and can burst due to over-expansion.

TENDINITIS: – inflammation of a tendon

TORN MENISCUS: – a sudden twist of the knee can tear the rubbery cartilage leading to serious issues.

FRACTURE: – the bones surrounding the joint may get broken especially the patella is viable to damage in the case of accidents.

DISLOCATION: – the knee bone slips and comes out from its original location leading to excruciating pain.

ACL AND PCL INJURY: – the anterior and posterior cruciate ligament gets torn which may occur when there are a lot of instantaneous turns. However, this occurs rarely since these are very strong ligaments naturally. 

OSGOOD-SCHLATTER DISEASE: – this is the swelling of the tendon between the tibia and patellar muscles.

STRAIN AND SPRAIN: – both are injuries but strain occurs in ligaments whereas sprain occurs in tendons.

These are some of the common disorders occurring to the knee. All of these disorders have something in common….PAIN but the intensity can vary based on time and severity of the disorder

ARTHRITIS                                                      

Arthritis is a commonly used word referring to the inflammation of joints. In fact, many people have an intuition that severe pain in the knee corresponds to arthritis mainly in old age groups. This is potentially a dreadful disease and can mainly affect the old aged. Most arthritis occurs over time but some can occur suddenly. Old-aged persons are more prone to this disease. This disease is likely to affect all age groups. This disease is more prevalent in women rather than men since their joints are weaker and more susceptible to motion when compared to men.

differences between normal and arthritic knee joint

  

In the case of arthritis, the bones start to wear down, the ligaments can tear, inflammation and swelling can occur, and also lead to internal bleeding (hematoma). There are about 100+ types of arthritis with different causes and symptoms.

comparisons between some of the arthritis

The different types of arthritis have symptoms different from each other. But arthritis, in general, shows some symptoms irrespective of the type.

Joint pain, stiffness in joints, red swollen mass, deranged and irregular motion is some of the common symptoms exhibited during arthritis. These symptoms are easy to identify by a common man and hence one can consult a medical practitioner known as a rheumatologist. The study of joints is known as arthrology and it is recommended to consult such a person.

As mentioned earlier cartilage is the one that protects the bones and also acts as a shock absorber. In the case of Osteoarthritis, this cartilage starts to vanish slowly. In the case of rheumatoid arthritis, the synovial fluid gets attacked by its own antibodies!!! This phenomenon in medicine is known as autoimmune disease and occurs due to error in the programming of these cells leading to the attack on their own cells.

In the case of gouty arthritis, there is a deposition of sodium urate crystals in the joints. It can lead to redness, pain, and heat around the joint. Uric acid which is generated in our body gets converted to purines (an essential component in DNA). Increased uric acid levels can lead to its deposition in the form of crystals. The best way is to remove the synovial fluid.

So these are the different types of disorders that can be seen in the knee. Proper diet and exercise and a healthy lifestyle can prevent most of them. So it is essential to be healthy to prevent the occurrence of these diseases.

HAPPY READING!!

INTRODUCTION TO THE BONES AND JOINTS

Our human body can be compared to a machine in terms of its functioning, but the magnanimous human can perform extremely better than a machine. As there are many nuts and bolts to connect many parts in a machine, there are too some bolts and nuts in our body which join several parts of the body like arms and legs. The so-called nuts and bolts of the human body are known as JOINTS. A joint in general is the articulation that is present in between two bones. This sounds a bit complex. So joint in the English language refers to the association. So the joints in the human body associate something. The something defined previously is bones. In order to understand this, we have to know about the structure of bone in detail.

Fig 1.1- structure of a bone 

                     

The above image depicts the structure of a bone in general. Important information to be known is that the unit of a bone is called an osteon. Many osteons combine together to form a bone. Bone-destroying cells are known as osteoclasts and bone-forming cells are known as osteoblasts. The external structure of a bone has two parts namely epiphysis and diaphysis. Physis refers to the growing plate. An increase in the bone’s height corresponding to bone growth. Epi means above and dia means through. Hence diaphysis is found in between two epiphysis which acts as the head and tail to the bone. The point of attachment of muscle in this bone is known as the trochanter. Everything present in the human body has some kind of protection. In the case of bone, that protection is offered by the periosteum. The inner layers can be visualized by peeling off those previous layers hindering them. Next, we have the cartilage which is a rubbery kind of protection to the bone. Hyaline cartilage present in bone is rather glassy in nature. The bone also has nerves and blood vessels since the bone requires nourishment and a proper message for its functioning. Bone marrow is the spongy tissue inside the bones. It contains stem cells. The stem cells can develop into the red blood cells that carry oxygen through your body, the white blood cells that fight infections, and the platelets that help with blood clotting. Bone marrow can be considered the mother of blood cells. This table provides insights on the types.

Type namePrevalenceContent
RedChildrenBlood
YellowAdultsFat

So now we move onto how a joint connects two bones. Consider this situation where there are two pipes and we want to connect them. The best way to connect so as to minimize their loss is by using a junction. There may be other options also, but there is no need to make a fuss about it.

Fig 1.2- the structure of a healthy joint

Hence from all these, we can come to an understanding of the importance of joints in the human body. To be short, the human body is meaningless and fragmented as the face, trunk, hands, and legs are separated without the joints.

HAPPY READING!!

WEIGHT BEARERS OF THE BODY- THE KNEE JOINT

The knee joint is one of the biggest and most important joints in the lower part of the body. The knee plays an important role in distributing the body weight throughout the body. It is worth studying about this joint.

The knee joint is the tibiofemoral synovial hinge joint. This seems a bit complex. This can be easily understood by splitting each term.

  • Tibio- tibia bone
  • Femoral- femur bone
  • Synovial- freely movable joint
  • Hinge- swinging motion

We can consider the knee joint as a castle with the patellar bone as a castle wall protecting it from the front, the femur from top, tibia and fibula from bottom and muscles aiding these bones. In general, the massive structures protect the joint from mechanical damage like banging the knee onto a hard surface etc…

                      the detailed structure of knee joint.
                   Credit:- OpenStax College Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013

The above diagram shows the complete parts of the knee joint. There are some terms that were not explained earlier. Bursa can be compared to a tin of oil or any other lubricant and structurally is like a sac containing fluid to reduce friction. Friction is      

A physical quantity develops when two things come in contact and the lubricant is the one that provides a medium between the two objects thus reducing friction.

Here are the anatomical terms and their meaning:-

  • Anterior-front
  • Posterior-back
  • Supra-upper
  • Infra-lower
  • Cruciate-cross shape
  • Pre-before

The fat pad is the one present beneath the knee bone and acts as a cushion for the joint. Ligaments are the primary elements of the knee joint which connect bone to bone.

There are two types of ligaments namely ACL and PCL. They connect the tibia to the femur as mentioned earlier through the term tibiofemoral. ACL is medial (present more close to centre) than PCL and PCL are lateral (present far from the centre).

NOTE:-Understanding these structures are very important as an imbalance in each structure can lead to a disorder.

The knee is the largest known joint in the human body which performs very complex functions. The various functions are:-

  1. It bears the weight load and prevents the lower legs to take in all the weight.
  2. Acts as a supportive agent to the body.
  3. Provides motion but is limited.
  4. Coordination of the movement of upper and lower legs
  5. Fat present in knee acts as thermal insulator
  6. Bursa reduces friction between the bones
  7. Synovial fluid acts as medium for bones to articulate with.

As mentioned earlier motion is a key aspect amongst the functions of the knee. The following table shows the various movements exhibited directly or indirectly using the knee.

Knee movements are of two types- primary and secondary.

NameMeaning
FlexionDecreasing the angle
ExtensionIncreasing the angle
Medial rotationRotating towards centre
Lateral rotationRotating away from centre
AdductionMoving towards middle
AbductionMoving away from the middle
Anterio-posterior displacementFront and back movement

Flexion, extension, medial and lateral rotations constitute the primary movements. Adduction, abduction and anterio-posterior displacement constitute secondary movements. Hence all these movements can be offered by the knee. In addition to that knee joint also has sensory receptors and produce proprioreceptic information about the position of knee.

The ligaments contribute more towards the stability of the joint as compared to other elements.  The several structures inside the knee must perform perfectly so that the knee functions properly as a whole. The knee joint is hinge type and hence it is more vulnerable to injury (stretching beyond the limit leads to injury). In case of injury, the damaged cells start to heal when the stress is removed but there is a chance of losing their functions as there is a chance of them getting replaced with scars.

It is absolutely worth knowing about the structure and function of the knee joint and how they help to carry ourselves on.

HAPPY LEARNING!!

IMMUNOLOGY SERIES- PART 4- ACQUIRED IMMUNITY

The previous article dealt in detail about innate immunity. This article is about another type of immunity known as the acquired immunity.

The acquired immunity, unlike the innate immunity, is not present from birth. As the name suggests, it is the immunity that we acquire throughout our lives. This immunity is acquired through experience and learning. In order to understand the previous statement, it is essential to know about primary and secondary infections.

The first encounter with the foreign agent is known as the primary infection. Since this pathogen is new to the immune system, it does not know what to do and hence it produces a generalized response through innate immunity. Once the pathogen is driven away from the body, certain information related to this encounter is stored in the memory of the immune system.

If the same or a similar pathogen enters into the body, the memory is triggered and a strong & quick response is generated which kicks away the pathogen faster than before. Hence the immune system has learned to defend from a new pathogen through learning. This is known to be a secondary infection.

These two combine together to form the natural active acquired immunity which is the immunity acquired as a result of diseases. In most of these cases, innate immunity fails and we get sick. During the recovery phase, the immunity is good and the activity is stored. Hence we may not get these diseases for a long period. The following diseases fall into this category:-

  • Polio
  • Chicken pox
  • Measles
  • Influenza
  • Common cold (not effective since there are several strains of viruses)

There are two characteristics in this which are:-

  • Latent period= time in which no response is seen (required for activation)
  • Negative response= time in which there is reduced response

The second type is the artificial active acquired immunity. This is similar to that of the first type with a slight change. In this case, we are artificially introducing pathogens into the body. But these pathogens have undergone a major modification. Their disease-causing ability has been genetically removed. Still, these are non-self for the immune system but they do not cause infections. Hence the immune system produces responses similar to that of natural active. These artificially induced pathogens are called vaccines. These help to induce immunity in our bodies. There are three types of vaccines:-

  1. Live
  2. Dead
  3. Products

I will be writing a separate article regarding vaccines.

The third type is natural passive acquired immunity. This is the immunity that we get from a natural source. You might have the answer. It is indeed the milk from the mother. Breast milk is rich in immunity cells especially immunoglobulins. A better idea will be in the article upon the immunity cells. This can provide immunity to the newborn up to 3 years but after three months it deteriorates since the child starts to develop immunity.

The last type is artificial passive acquired immunity. In this type, we get immunity (immunoglobulin) from an artificial source. These immune cells play a major role in identifying and binding to the pathogens and aid in phagocytosis. Don’t worry this process will be covered in the subsequent articles. There are three types in this namely

  • Hyperimmune sera- from animal or human source
  • Convalescent sera- from a recovering patient
  • Pooled human gamma globulin- from a healthy person

It is important to understand that the word active refers that the body is developing immunity and passive refers that we are providing immunity. The words artificial and natural refer to the source. There is one called combinational immunity (active+passive) in which the passive immunity provides protection until the active immunity activates (latent response).

Till now we have seen several types of immunity, the next article will be on the immune cells, the guys who are behind all these.

HAPPY READING!!!

RUMINOCOCCUS- THE TRUSTABLE BACTERIA

Bacteria, Microbiology, Organism

In general, microbes are known to cause harm to plants, animals, and humans, and so on. In particular, bacteria have caused a lot of problems in humans like tuberculosis, anthrax, cholera, etc. but not all bacteria are pathogenic (disease-causing) in nature. The particular bacteria discussed here is friendly to humans and is completely trustable.

The ruminococcus genus of bacteria falls under the class clostridia. These bacteria are round-shaped, anaerobic (do not need oxygen for survival), and are gram-positive. These bacteria are gut-friendly. More than one type of these bacteria is present in the human’s gut helping in the process of digestion.

The gut of the human which primarily includes the intestines is known as the bacterial fermentation chamber. Most of these bacteria help the human and have a symbiotic relationship.

The symbiotic relationship is a relationship between two organisms in which both of the organisms get benefitted. A suitable example of this is the lichens.

The lichen is a symbiotic association between fungi and algae. The shape of the lichen is purely based on the fungus which is dominant and the green color is due to the presence of algae. The role of the algae is to produce food and the role of the fungi is to provide water from the tree it is in. So the fungus gets food in return for the water it gives to the algae. The lichen is not harmful and it gets converted into the organic matter once dead.

A similar relationship is seen in the intestine of the human. The bacteria help the human in digestion and in return get food. We all know that the human digestive system has HCl acid accompanied by a lot of other digestive enzymes and juices. There is a fact that the stomach acid is able to digest even a bar of steel. So in that case why are there some bacteria helping us out with indigestion?

Monkey, Mammal, Animal, Gorilla
gorilla- a perfect example for an omnivore

The reason is that we humans are omnivorous. So we eat meat and vegetables. There is no problem in digesting the meat. But there is a small concern when digesting the vegetables. The problem is that the cell wall of most of the plants contains a substance called cellulose which is lacking in the animal cell walls.

The enzyme which is used to digest cellulose is known as cellulase. This enzyme is not present in the human but is present in the ruminococcus species. Hence these bacteria present in the gut provide this enzyme in return for the food we give to them. Hence there is a mutualistic behavior seen in the gut. Also, there is an added advantage.

There fecal and genital routes are the most important routes for the transmission of several infectious and deadly diseases and most of these are caused by bacteria. There is a fact that the presence of one species/genus does not allow the presence of other species/genus. So the healthy bacteria present in the gut prevent some deadly infections.

Based on these facts, I think it is appropriate to say that this is a human-friendly bacterium and can be completely trusted.

HAPPY LEARNING!!!

IMMUNOLOGY SERIES- PART 3- MECHANISMS OF INNATE IMMUNITY

A detailed description of innate immunity has been provided in the previous article. This article explains in detail the action of innate immunity. As mentioned earlier, innate immunity is a non-specific immunity that acts as the first line of defence. There are six mechanisms backing innate immunity. They are:-

  1. Epithelial surfaces
  2. Antimicrobial products
  3. Microbial antagonism
  4. Cellular factors
  5. Inflammation
  6. Acute phase proteins

These are the six different mechanisms of innate immunity.

Epithelial surfaces

The epithelial surfaces are those which form the outermost layer of the body. It is pretty obvious that the pathogens gain access into the body through the body openings. Hence it is trivial that the immunity is strong at these places. The following are the body openings where the immunity is present:-

  • Eyes
  • Ears
  • Nose
  • Mouth
  • Skin
  • Genital tracts

Eyes– there is a special fluid called the ‘tear’ generated by the lacrimal apparatus. This tear can flush out the microbes by its mechanical action. Also, the enzyme called lysozyme is present in it which is antibacterial in nature. This particular enzyme splits certain polysaccharide molecules from the cell wall of the bacteria without which it cannot sustain. Hence these are processes that confer immunity to the eyes.

Ears– there is a constant production of wax that entraps the foreign microbes. The cells lining the outer surface of the ear membranes secrete the wax for cleaning and protective purposes. The inner ear is filled with phagocytic cells.

Nose– the nose and the respiratory pathway are very important to be protected since they involve the exchange of air and microbes can easily enter. So there is tightened defence provided by several mechanisms:-

  • The anatomy of the nose itself prevents the entry of some microorganisms
  • There is mucus lining the entire respiratory pathway which have hairs that can sweep the microbes back to the air
  • There are mucopolysaccharides which are sticky in nature and hence the microbes get stuck to them
  • The alveoli of the lungs are filled with phagocytic cells

Mouth– the mouth and the digestive system are also as important as the nose. The following defence mechanisms can be seen

  • Saliva which is basic in nature kills some of the pathogens
  • The peristalsis movement can kick away some of the microbes
  • The stomach acid which is low in Ph can destroy most of the microbes
  • The digestive juices and secretions like the bile also provide immunity

Skin- the skin is present all over the body and there are 4 mechanisms

  • Long chain fatty acid
  • Salty nature of the sweat
  • Soaps contribution
  • Oils and sebaceous glands

Genital tract- this is also an important opening to be concerned about as there is a large concentration of microbes found here. The urine itself flushes out any incoming pathogens. In males, the sperm protein spermine and zinc are antibacterial. In females, high acidity can kill the microbes.

Antimicrobial products

There are some anti-microbial products present naturally in the bloodstream and other body fluids.

  • Beta lysine- effective against thermostable bacteris
  • Polypeptides- leukin and plakin
  • Lactic acid- muscles
  • Lactoperoxidase- present in breast milk
  • Interferons- effective against virus

Microbial antagonism

Remember the fact in the first article that the foreign microbe has to find a suitable ‘target site’. The reason is that there are already some microbes present inside us. Don’t worry they won’t hurt us. These microbes constitute the normal flora and are resident. They follow symbiotic relationships with us. A suitable example is an e.coli present in the intestine helping indigestion for food.

So the presence of one species of organisms do not allow the presence of similar or different species. So these microbes indirectly furnish immunity to the body. So nice of them!

Cellular factors

These are some cells that are specialised in the function of protecting the body by destroying pathogens. It is done by the process of phagocytosis which is the engulfing of substances. The phagocytising cells engulf the foreign particles in response to the chemical mediators (mediators are certain chemicals released by a special type of immune cell known as mast cell).

There is a special defence for viral infections. In this case, the interferons activate the NK cells (Natural Killer) to undergo phagocytosis. This cell can be called the assassin of the immune system.

Inflammation

Inflammation is one of the body’s responses to the invasion of foreign particles. This is an important process in the human body that occurs to drive away from the pathogen. Inflammation is one of the stages seen in healing. This inflammation can be either acute or chronic. Acute stay for a shorter time but produces more vigorous pain whereas chronic stays for a longer time with less vigorous pain. If the causative agent has been driven away then healing occurs either by complete restoration or scar formation. There are chances that the acute inflammation can become chronic which can be worse. It can lead to several diseases and complications.

Acute-phase proteins

These are certain indicator proteins present in the blood whose increase in the level indicates infections. A group of these proteins constitute the acute phase proteins. They are:-

  • C-reactive protein
  • Mannose binding factor
  • Serum P amyloid component
  • Alpha -1-acid antitrypsin

These proteins enhance the defence and host resistance, prevent tissue injury and aid in damage repairs.  

The next article deals in detail with another type of immunity, the acquired immunity.

HAPPY READING!!!

THE MULTIPURPOSE TREE- A GOD’S GIFT

Bananas, Banana Trees, Banana Plantation

All of us have some purpose in our lives. This can apply to all the living species in this universe. The bees are present to produce honey, the flowers are present to produce nectar and pollen, and the cows are present to produce milk and plants to produce food. It is generally seen in plants that more than one part of them has a purpose. But there is a specific tree in which all its parts are useful and none of them is wasted. This is a tree with several purposes and indeed it is a gift from god. Already some of you would have found it out! It is the banana tree.

Mostly the fruits, vegetables and flowers of a plant are useful. But all the parts in the banana tree have more than one specific purpose. Also, these do not serve a purpose for humankind, but also to a lot of animals. This article mainly highlights the medicinal benefits of each part of the banana tree.

Speciality of banana tree

As we know the portion which is above the ground and which houses the leaves, flowers, fruits etc. is known as the stem. However, in the case of the banana tree, the true stem is found underground and the green part which we see is a ‘pseudo stem’ meaning false stem; the true stem is a rhizome. Even this part is also consumable. If one has decided to cut a banana tree, he can cut it till the pseudostem and a new tree start to grow from the original stem. This depends upon the condition and strength of the root to regenerate one.

Banana fruit

The fruit is the tastiest and delicious part of the tree. An interesting fact which some might know is that the banana tree can produce fruit only once in its lifetime. They say that the banana tree is dead after fruiting because it starts to degrade after fruiting. So the tree is cut down up to the false stem after fruiting.

There are different sizes and colours of bananas which are based on the fruit obtained from the banana tree. Some of the banana varieties known are:-

  • Red banana
  • Nendran
  • Mountain
  • Rasthali
  • Robusta

There is a banana known as the blue java banana which looks blue in colour and tastes like ice cream!!

  • Bananas are a good source of potassium, an ion which takes part in most of the body’s metabolic processes
  • Bananas can aid in weight loss
  • Bananas can make us full (healthy food)
  • Bananas are rich in antioxidants
  • Bananas are rich in fibre essential for proper stool

And there are even more health benefits. It is recommended to eat at least one banana a day.

Banana vegetable

Shrub, Banana, Banana Plant, Fruit

The vegetable cannot be consumed raw as compared to its fruit. This is a bit hard in nature when compared to the fruit. This is mainly used in cooking to make curries, chips etc.

  • The raw bananas are rich in magnesium, a micronutrient essential for the body
  • They can help in regulation of blood sugar levels
  • They are a healthy source of starch
  • They aid in digestion due to high content of fibre
  • They can prevent constipation and other digestive problems

Banana flower

Banana, Banana Tree, Bunch Of Bananas

The flower is said to have an umami profile of taste. Hence this is least preferred by children. Also at the same, this part has the highest medicinal benefits.

  • They are immunity boosters; they prevent infections and add resistance to the body
  • Promote the kidney function in the filtration of the blood
  • They help in regulating diabetes
  • They can reduce anxiety and relax the mind
  • They help in reducing the blood cholesterol and blood pressure levels

Banana leaf

Banana, Leaf, Green, Tropical, Plant

This is the point that separates the banana tree from the rest. The leaves of these trees are also used, apart from the fact that animals eat them. This part of the tree is non-edible for humans. The leaves of the tree have been traditionally used as plates. the following are the reasons for this purpose:-

  • There is a thin coating of wax in the leaves which get melted when hot food is placed, this process results in a release of good aroma and also enhances the flavour
  • These waxes are totally consumable and they contain polyphenols which is required for the immunity to fight off diseases
  • The antimicrobial property of the leaf is exposed when hot food is served, so these properties infuse into the food
  • The leaves are easy to use and are cheap

There is one dish called ‘kizhi parotta’ where the parotta is wrapped in a banana leaf and is steamed. All the flavours of the leaf enter into the food, enhancing its taste.

Banana pseudostem

The false stem is also edible and has a lot of medicinal benefits. It can be cooked to make a lot of dishes or can be consumed raw as juice.

  • Rich in fibre and helps in digestion
  • ‘Kidney-friendly’, in fact it is recommended for kidney stone patients to drink the juice. It aids the kidney in the filtration process
  • Helps in weight loss
  • Rich in potassium and vitamin B, boosts the production of haemoglobin
  • Boosts the production of insulin hence helping in controlling diabetes

Banana root

Even the root of the tree is useful. It can be used to make ropes and sacks. The following are its medicinal purposes.

  • The root can cure tooth pain
  • They are rich in dopamine and can assist the mind in taking decisions
  • They can cure stomach problems

On the whole, the entire banana tree is useful and none of them gets wasted. from the medical point of view, this tree is equivalent to medicine. There is no doubt in calling this tree the ‘GIFT OF GOD’

IMMUNOLOGY SERIES-PART 2- CLASSIFICATION OF IMMUNITY & INNATE IMMUNITY

The previous article gave a brief introduction to immunity, the internal force protecting us from several hazards. This article will be on the classification of immunity.

This is the classification chart for immunity. Immunity can be briefly classified as two, innate immunity and the acquired immunity. Innate immunity also known as natural immunity and native immunity is the one that has been bestowed to us. This type of immunity is present from birth till death. The following are the other names of innate immunity:-

  • Natural immunity
  • Native immunity
  • Non-specific immunity

Innate immunity is the resistance to infections which an individual possesses due to their genetics. Also, there are other factors that can decide native immunity.

Species- the native immunity which is present within everyone is species-specific. The meaning is that humans have resistance to a specific set of infections and the plants have resistance to another specific set of infections. This is the reason for which humans do not get affected by plant diseases and vice versa.

Race- race refers to the group of people from several parts of the world. People in one part of the world may be resistant to a particular disease when compared to others. This can also depend on the environmental conditions and other factors in which people reside. A suitable example for this is a study that shows that the Negroid species (of African origin) in the US are more resistant to tuberculosis when compared to the Caucasian species (European origin).

Individual- people having a similar genetic constitution may have the same resistance/non-resistance to infections. A study shows that twins have the same level of resistance and non-resistance to several diseases.

The innate immunity is long-lasting, non-specific, and has a good memory. The term memory will be explained while introducing the immune cells. Innate immunity forms the first line of defence in our body. This immunity primarily focuses on providing a barrier to the body and destroying the microbes and pathogens, irrespective of their type. Hence the innate immunity is known as non-specific immunity. There are specified cells that perform this activity and the process is known as phagocytosis. More details will be provided in the next article.

The innate immunity can be comprised of four namely. These can be known as the barriers of innate immunity:-

  • Physical
  • Physiological
  • Cellular
  • Cytokine

The physical type includes the mechanical barriers mostly present in the openings of the body (eye, nose, mouth, ears, genitals, and skin) which prevent the entry of microbes through several mechanisms.

The physiologic type includes the secretions of which help in kicking out the pathogens. These include sweat, highly acidic stomach acid, saliva, sebaceous glands, earwax, and mucus, and so on. These secretions mostly trap the pathogens and prevent them from reaching inside.

The cellular type includes some arrangements made to prevent microbe entry. For example, the wall of the blood vessels is tightly attached with each other ensuring that there is no gap hence preventing the entry of microbes.

The last type includes cytokines. The cytokines are a broad group of signaling proteins that take an important part in immunity. These molecules help in regulating the immune response.

The next article deals with the 6 mechanisms of innate immunity. Till that

HAPPY READING!!

IMMUNOLOGY SERIES- PART 1- INTRODUCTION TO IMMUNITY

There are about 1 trillion microbial species which constitutes about only 0.0001% of the entire species. One trillion itself is a huge number and they constitute the number of identified species only. Most of the microbes are packed inside the glaciers and is said that global warming which melts the glaciers can release them! The microbes can be broadly classified into 6:-

  • Bacteria
  • Archaea
  • Fungi
  • Protozoa
  • Virus
  • Algae
some shapes and forms of the microbes

An important thing is that even though there are these many species of microbes, we do not get infected by them so often. To understand this it is trivial to know about the infection. Infection is defined as the invasion of the host’s body tissues by disease-causing microorganisms followed by their multiplication, colonization, reaction with the host, and release of toxic product metabolites. Infection is a complex process in which the harmful organisms enter into the host, finds a suitable and weak target place, establishes themselves well, multiples themselves, react with body cells, and release bad substances. The series of these events constitutes the prevalence of several diseases. The word ‘target site’ is very important since the microbe cannot establish themselves in any place in the human body. A clear-cut idea of this concept will be given in the next article.

Infection by a microbe can be best understood through relationships. A relationship is always exhibited between two organisms. There are three different kinds of relationships namely parasitism, commensalism, and symbiosis.

Commensalism– the relationship in which one of the organisms is benefitted and the other is neutral (neither harmed nor benefitted)

Symbiosis/mutualism– the relationship in which both the organisms help out with each other so that both are benefited

Parasitism– the relationship in which one organism is benefitted and the other is harmed. In this scenario, the harmed one is known as the host and the one causing the harm is the parasite.


Credit- differencebetween.net

The reason for which that all microbes don’t cause disease might be that some of them are cannot cause infection meaning that they are not parasitic. Under those circumstances, there are about 1500+ kinds of microorganisms that particularly target and infect human beings. If so, then we would have got around 1500+ diseases and that is not the case. So there is some inner force that protects/guards us against these microbes. This protective force present in our body is known as immunity.

Immunity is defined as the response generated by the local mammalian in response to the infection caused by the pathogenic microbes and their products (toxins).

As mentioned earlier, the microbe has to enter into the body in order to establish itself. In fact, this is the hardest part for the microorganisms and most of them fail to cross this stage. It is this immunity that prevents most of the microbes to enter the body and cause infections. The immunity identifies and destroys these microbes and prevents their infections.

The first step is known as recognition which is an important characteristic of the immune system. It is the ability that the immune system destroys the objects which are foreign or not present in the body (non-self) and do not affect the body cells (self). An error occurs in this and as a result, the immune system is unable to differentiate both and starts to destroy their own body cells. This condition is known as autoimmunity.

A brief introduction to immunity has been provided, the next article discusses the classification of immunity.

HAPPY LEARNING!!

CAUTION TO THE DEEP SEA DIVERS- DECOMPRESSION SICKNESS

Have you experienced pain in you legs and hands after a good session of deep sea diving? This blog explains about this particular problem which is experienced by most of the deep sea divers. A particular aspect of this problem is based on the affinity for the nitrogen by the fatty tissues. It is recommended to read the previous blog (CRACKING OF FINGERS-GOOD OR NOT) to get a clear idea on the affinity of nitrogen by the fatty tissues.

The particular problem which can affect the deep sea divers is known as decompression sickness. It can be classified as one of the forms of embolism. Embolism refers to the obstruction caused by any mass carried in the circulation. The human body is known to have a closed system of vascular system unlike cockroaches which have open type where the fluids freely flow throughout the body.

Human Body, Circulatory System, Circulation, Blood
the representation of closed system of vasculation in the human body

In the case of human beings, there are vessels which carry the blood throughout the body. They can be broadly classified as three namely the arteries (carry oxygenated blood), the veins (carry deoxygenated blood) and capillaries (the mix of two). A vessel is like a cylindrical tube and there are high chances for it to be obstructed. This is known as embolism and the substance causing it is known as emboli. The following list shows the various possible emboli:-

  • Thromboemboli
  • Tumour cell
  • Athermatous plaque (fat)
  • Tissue fragments
  • Parasites
  • Foreign bodies
  • Amniotic fluid
  • Bone marrow
  • Air/gases
an example of fat emboli which obstructs the artery

As a result, these substances which initially obstruct the blood vessel; slowing cover the blood vessel and finally block them. So the oxygen and nutrient rich blood cannot be delivered to the target which leads to the death of cells from lack of oxygen and nutrients (infarction in medical terminologies)

The primary concern for us is the gas/air. Air or gas embolism can occur when the air or gas is introduced into the vasculature. Air emboli is seen in common while using invasive biomedical equipment (invasive refers to penetration into the body). This can be seen while using injections, IV supplementation, catheter usage etc.

If gases enter into the body and cause embolism then it is known as gas embolism. The particular concern for the divers is decompression sickness. The decompression sickness or generalised barotrauma (baro- pressure trauma-sickness) is a medical condition which results in injuries due to release of several gas bubbles as a result of rapid decrease in the pressure in the surroundings.

The rapid decrease can occur in two cases. The first case is descending from higher altitude to normal altitude and the second case is descending from normal altitude to lower altitude. In both these cases, there is a rapid decline in the atmospheric pressure. There are two situations to analyse right here.

credit-facebook

Situation-1

This occurs during the descent. As we go deep into the ocean, the pressure increases. So the gases that are present in the ocean diffuses into the blood and tissues. The primary gases which diffuse are nitrogen, oxygen and carbon-di-oxide.

Situation-2

This occurs when returning to original (ascent) quickly. As we go towards the surface of the ocean, the pressure decreases. So the gases which got diffused into blood, form bubbles and they are released from the blood. We already know that the fatty tissues have great affinity for nitrogen and hence they accept them. If the level of absorbed nitrogen is too much, then it can cause severe pain in the muscles and joints. Also these bubbles can block the blood vessels in any part of the body and can be fatal in areas like lung, brain etc.

The following are the consequences of the decompression sickness:-

Bends– acute pain in the skeletal muscles, joints and ligaments due to the accumulation of nitrogen bubbles

Chokes– accumulation of nitrogen bubbles in the lungs causing shortness of breath

Cerebral effects– stroke, vertigo, coma and even death

The severity of the consequences of decompression sickness depends on the following factors:-

  • Depth reached
  • Duration under the deep sea
  • Rate of ascent/descent (quick ascent after long descent can lead to this problem)
  • Condition of the individual

The chronic condition is known to as Caisson’s disease which can lead to the formation of gas emboli in the head of several bones like the tibia, femur and humerus and so on. The disease is named because it was seen primarily in deep sea divers who drill underwater tunnels. They are referred to as caissons (diving bell).

Man Left Looking Like Popeye After Diving Accident
the condition of bends seen in a peruvian diver suffering with decompression sickness

Hence it is important to understand that the decompression sickness is mostly rare but dangerous. It can become fatal if not treated soon. It is trivial that the condition arises with a quick ascent after a deep descent. The following are some of the steps that can be followed to prevent decompression sickness:-

  1. Take a safety stop or pauses in the ascent; this is done to make sure that there are gradual changes in the pressure
  2. Drinking lots of water
  3. Spending less time under the sea, this can reduce the concentration of nitrogen
  4. Avoiding air travel after diving
  5. keep nitroglycerin sublingual doses it can immediately cure the bends

Scuba and deep sea diving are indeed fun and interesting activities. It is recommended to enjoy and experience them at least once in a lifetime. But be aware of this problem that can occur while diving and take the precautionary measures responsively!!

HAPPY READING!!!

COOL AND HEALTHY

It is around summer, and you have come home from an intense gym session/casual cricket match with your friends. You take a bottle of ice-cold water or any chilled beverage from the refrigerator and chug it at once. You can feel the immense amount of pleasure you get from this just by reading this. But what if I say that your body hates this even though you like it? This article brings upon the ill-effects of drinking ice water and a sustainable solution/alternative to that.  

Ice water has some of its own benefits like ice water stimulates thirst enabling further consumption of water. Hence ice water can keep you hydrated. Also, ice water can keep one mentally active and awake. Research says that athletes who consume cold water are able to exercise or perform longer.

However, the benefits of ice water are countable and limited. On the other hand, there are many ill-effects of consuming ice water. Consumption of ice water and any chilled products can lead to “brain freeze”- an intense headache that is seen within few seconds of consumption of a chilled product. It is a principle that cold produces vasoconstriction (contraction of blood vessels) and this sudden experience of cold can make the blood vessels in the brain contract.

cartoonic representation of brain freeze

Hence there is limited blood and oxygen supply to the brain. This in medical conditions is known as shock. So in order to balance this more blood is supplied to the brain and hence the vessels swell. This can be considered as a mechanism of the brain in order to avoid consuming the cold substance. Hence this can be the reason for children not eating the ice cream after getting brain freeze. It is a natural defensive process and is not dangerous when it goes away within seconds but can be detrimental if prolonged. Repeated consumption can lead to migraines (heavy headache accompanied by nausea).

Also, ice water can disrupt the process of digestion. According to Ayurveda, there is a fire (jatharagni) inside us that helps in the process of digestion. This can be compared to the digestive enzymes and juices which aid in digestion. There must be an appropriate temperature for the digestive organs to work. This has also been proven scientifically which says that a minimum of 38’C of core body temperature is required. The ice water can disrupt the internal heat environment and can prolong digestion. This is not advisable in the long run.

a pictorial representation of inner fire- jatharagni

The entire process of digestion is prolonged especially in the regions of the stomach and intestine. Ice water can affect the absorption of nutrients in the small intestine. The intestine contract as a result and there can be chances that the stool becomes too hard. So it can lead to constipation. The worst time to drink ice water is after a meal. The reason is that the body raises the core temperature so as to start the process of digestion and ice can disrupt it. There are even more ill effects like a decrease in heart rate, improper fat metabolism, and throat irritation, and so on.

So a solution to all these problems is to avoid drinking ice cold water. But if we do so, we cannot rejoice in the pleasure we get from it. So we have to find an alternative method/source of ice water which is healthy for us. The answer lies with our ancestors. Years ago, there were no refrigerators then how was it possible for them to have cold water? They used earthen pots to get chilled water.

Earthen pots or Matka have been used for many years. They produce chilled water by the process of evaporative cooling. The pores present in the pot release the heat out by capillary action hence making the water ‘cool’. It is important to understand that the water is cool and is not cold.

This water provides the benefits of refrigerated ice water and rules out all its ill effects. The pot water does not only affects digestion problems but also enhances digestion. The minerals that are present in the water help in digestion and create a balance in the Ph. The minerals in pot water make it alkaline which balances the acidic Ph of the stomach. This can prevent a lot of digestive problems which can be caused due to excess acidic Ph.

Pot water does not irritate the throat and does not cause sore throat. Also, it refreshes the body with mineral-rich water and prevents dehydration and sunstroke in summer. The pot water also boosts metabolism. The earthen pots act as natural filters and remove the toxins. Apart from that, earthen pots are sustainable, eco-friendly, and also cheap to use. The fridges release chlorofluorocarbons (CFC) which is an important cause of ozone depletion. No such problems are seen in earthen pots.

earthen pots with water kept during summer to quench the thirst of several passerby’s
source- twitter

On the whole, the earthen pots have produced the benefits of refrigerated water and on the contrary, they have no ill effects as compared to refrigerated water. And the important point is that we can get these benefits at minimal cost and do not harm Mother Nature. So from here afterward, chug upon a pot full of Matka water after an intense gym session or long and tiring sports match. This time, your body also enjoys the water along with you.

HAPPY READING !!!

CRACKING OF JOINTS- GOOD OR NOT

written by Sairam Adithya

The cracking of the joints is often a common habit seen in a lot of people. This is especially seen in the joints of the fingers in the hand and legs (medically known as phalanges). Many people say that this is a very bad habit and can degrade your joints. However, to confirm this, it is essential to find the reason for the sound. Then, based on the cause we can come to a conclusion that whether the habit is good or not. This would be an appropriate and better approach.

In order to understand the noise, it is essential to understand joints. Joints can be called the nuts and bolts of the body. The joints are a medium of connection between several bones. There are about 360 joints and all of them fall into three main categories and have some subcategories. The table below well represents the classification.

Type Other namesMobility Constituent Example 
FibrousSynarthroses ImmovableHyaline(denser)Skull
Cartilaginous SynchondrosisSlightly movableHyaline cartilageSternum
SynovialDiarthrosesMovableArticular cartilage covered with synovial membraneKnee 

Out of these the synovial joints are of our importance. The prominent examples of a synovial joint include the knee, the hip and the forearms. There are six types of synovial joints which are tabulated below:-

Typedescription/analogyExample
Ball and socketThe tail of bone attached to the head of other boneShoulder
HingeHinge present between the doorKnee
PivotAction of turningNeck
CondyloidTwo plane motionWrist
SaddleLooks like a seat in horseThumb
Gliding Bones pass over each otherWrist
pictorial representation of different synovial joints in human body

Hence it is to be understood that the freely moving joints (synovial joints) are those which are capable of producing the cracking sound. Also, not all of them can do so, it is the phalanges of the hands and legs, the elbow, the neck, and sometimes the knee which can produce the cracking sounds.

The important characteristic of synovial joints is the presence of synovial fluid and a fatty layer. There are two specific functions for the fat layer. An important feature of fat is that it has the highest affinity for nitrogen. Affinity can be known as “chemical love”. Like it can be considered that nitrogen is a drug for the fat in our joints which has an irresistible addiction towards it (just for analogy, please don’t even think about drugs….).

i)       To provide protection from mechanical damage; For instance, banging the fingers/knee onto a wall

ii)     To trap the heat; heat is required for internal mechanisms to occur, so it is essential that fat (adipose tissue) encapsulates the heat

There are two important facts that have to be known relevant to this phenomenon. The first is the atmosphere; it is a collection of enormous amounts of gases, liquids, and lots more. What is trivial is that nitrogen constitutes about 78% of the total atmosphere. Phew! That is indeed huge. Another aspect is the process of diffusion. Diffusion is a passive method of gas transportation that moves from a higher concentration to a lower concentration.

a visualisation of diffusion between oxygen and hydrogen molecules

So what happens is that the nitrogen diffuses from the atmosphere (high concentration) to the fat present in the joint (low concentration). As a result of this process, nitrogen bubbles get accumulated in the gaps in the synovial fluid. As we press the joints or do any movements, the bubbles inside the gaps are forced to be released out. This process is known as capitation and as a result, a popping/cracking sound is developed.

To conclude, the release of the nitrogen bubbles are the ones responsible for the popping sound and this activity has nothing related to the health of the joints. You can pop the joints and this is not a bad habit (in the sense of health). Make sure that you don’t disturb others in the process!!

HAPPY READING!!!