Showing posts with label Physics. Show all posts
Showing posts with label Physics. Show all posts

February 07, 2014

Revisiting the Sternocleidomastoids: Accessory Muscles of Respiration


We know that sternocleidomastoids (strap muscles of the neck), scalene muscles and alae nasi are considered accessory muscles of breathing, although some controversy exists. If you saw an asthmatic individual in his desperate attempts at breathing or an agitated person or a person exercising vigorously, you could watch these muscles in action. However, that wasn't exactly what I had in mind while I was doing this experiment. I was really thrilled to chance upon it. Kind of a serendipitous discovery in its own right. You too can figure this out easily. The placement of the surface leads were as shown on the right. Red dots were for the reference and recording electrodes whereas the blue dot represents the ground (as usual). 

The neck muscles of each side were tested one at a time. For example, This wav file (open it Audacity or BYB neuron recorder) was obtained from EMG recording from the right sternocleidomastoid; the leads were placed on the right side and the ground lead on the manubrium. The head was at mid-line (neutral position) to start with. Next, it was turned to the right, then midline again, then to the left (without any external resistance applied), then against resistance applied by the left hand. The muscle of the right side moves the head to the left. Finally, the head was again restored in its neutral position. An improvised notation could be N to R to N to L to L+ to N (Legend: N=neutral, R = right, L=left, L+ = left against resistance). 

Similarly, the left side was tested in a likewise manner (N to L to N to R to R+ to N). And this is the waveform obtained. The surprise awaited me, I was in for an ambush!

While the leads were still on the strap muscles of the left side of my neck, I observed the EMG waveform in real-time. I noticed that as I was taking a deep breath, the EMG activity increased significantly. I didn't have to turn to my head to the right anymore! I then maintained this position by holding my breath. The activity continued. Here's the recorded .wav file. The associated camera recording will speak for it (see below: Youtube). Yes, it proved that it was indeed an accessory muscle called in to address forceful inhalation. I then did a forceful exhalation, but no increase in EMG activity was observed, buttressing my observation. 



As you may have noticed that I have used the terms inhalation and exhalation, in lieu of, inspiration and expiration. Well, inspiration, it definitely is! Expiration? No way!
Further analysis still awaits.
Spikerbox recordings may also possibly illustrate simultaneous EMG activities in protagonist and antagonist muscles. More of these later.

To be continued............
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Making a Human Interface Device Using SpikerBox

Q said to Bond: It's activated by nerve impulses from the wrist muscles. This dialog from the 1979 James Bond movie, Moonraker, seems to fit into place when we talk about interfacing biosignals (surface EMG, in this case) with an actuator. [Watch a clip from the movie below]




In order to achieve this human-machine interface using our good not-so-old spikerbox, we need to estimate the output signal amplitude coming from the extensors of the wrist (around 5 mV), amplify the signal by some 300 times by cascading two LM 386 IC (or any opamp taking care that the device doesn't go into saturation) to about 1500 mV. We can then connect the output from pin 5 of the IC via the 250 MFD to a *1K resistor (* = value to be experimented with) to ground. Next we connect a wire from negative terminal of the electrolytic capacitor to pin 13 of CD 4066, a quad bilateral switch IC. The Boolean output (on/off logic) signal may then be driven into terminals of a 'laser pointer', whose push button terminals will have to be replaced by the output from pins 1 and 2 of CD4016/4066. A sketch of it is shown below. Pardon my bad drawing 'skill'! Interfacing should not be a problem as the power supply is 5V and CMOS ICs are happy with that.






Output level of LM386 is at half the supply voltage level (i.e. at 2.5 V). At +5mV signal level, voltage at pin 5 becomes + 4.0 V [2.5 + (5*300*10^-3)], making the control pin of 4066 go logic high. A low resistance (250 ohm) path is established between pin 1 and 2 of this IC, hopefully switching the laser on. We better not play with darts at this moment!

Another idea is to hook up an optical mouse in such a way that its internal potentiometer is swapped with a twin light-dependent resistor (LDR) as shown below. The picture at the left/top panel shows the component side of the mouse and the soldered side at the right. The three leads in the rectangle 'marked' in the right/bottom picture panel on the soldered side may be replaced by the new pot using a twin LDR, as shown in the middle panel (its middle two leads connected to form the central/common lead of the new three terminal pot as shown in red arrows). 











The input maybe obtained preferably in stereo from the sternocleidomastoids of both sides. And the output amplified and fed into two LEDs separated by a window which communicate in a 'line of sight' with the 'twin LDR' setup. This would couple the two circuits (the SpikerBox setup and the laptop via the 'doctored' mouse) optically. The scrolling function (up/down) may then be undertaken by moving the neck sideways. The experimental setup may be as per this link. Details to be updated at a later date. You too may contribute.

Disclaimer: This circuit is a mere prototype, liable to have errors. I will check it at a later date, got to hone my electronic skill a little and get out of any further procrastination.

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This work by Amiya Sarkar is licensed under a Creative Commons Attribution 4.0 International License.

Last modified: Apr20, 2014
Reference: hyper-links, unless specifically mentioned

Surface EMG from Thumb: Strongly 'Opposed' ?

Lead placement for the experiment, as shown on the right.
As I have already mentioned, the ground electrode sits atop
the manubrium sterni, on the upper chest (breastbone).

The camera recording is shown below. You can see the Piezoelectric crystal's spark and also hear its sound on snapping. However, I haven't yet had time to analyze if the spark did contribute some 'useful' static on the trace (open & watch this .wav file in BYB software).






Method: Pressing on a piezo crytal (from a cigarette lighter) by 'opposing' the thumb against the base of the little finger (as shown by the figure). Electrode placement shown in red & green markings [the ground electrode sits atop manubrium sterni]. Muscle (mainly) contracting is "opponens pollicis", a small, triangular muscle in the hand, which functions to oppose the thumb. [Strictly speaking, opposition of the thumb refers to the tip of the thumb touching the tips of other fingers. But that way, generating enough force without creating an unnecessary torque that topples the piezo is quite a challenge! After all, I had no assistant, and had to hold the camera too with the other hand]

Concept: A fixed and constant amount of force is necessary each time before the spring yields and the piezo fires. This end point is supposed to be caught in the trace 1) as a sharp spike after the surface EMG pattern or, 2) can be 'used' as a 'static'.

EMG amplitude and rate of spikes will need to be analyzed in short, discrete time intervals by simple counting.

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February 06, 2014

Interpreting Rate Coding Data: Counting Spikes in a Tracing & Consequent Plotting of Firing Rate Versus Time

We acquire data by using the following device configuration (the green laptop cable will go to the laptop mic input, running on battery power) as shown below. Please see this link to learn about the anatomy of a coaxial cable, so that you can make a ground connection off a coaxial cable.

You can also take the ground off the reference point used for the Faraday cage clip, if you'd like. Incoming analog signals from the spikerbox will go into the internal ADC (Analog to Digital Converter) of the Conexant HD audio port of the laptop, whence the signal will be digitally processed. After a signal has been stored either in Audacity or in the BYB neuron recorder, we can open the'.aup' or the '.wav' file respectively later.

Here, I am attaching a typical wav file captured by striking the quadriceps tendon with a percussion hammer (knee jerk). This is a deep (tendon) reflex. I'll post more on this later. You need to open it using either of the two softwares listed. I am posting a screenshot on the right.
You can see three large spikes in the tracing. These spikes are actually not single/solitary, as they might innocuously suggest, but they are a conglomeration of many individual ones.

The below tutorial explains how to interpret these raw data.



By the way, there's no simple way to count spikes! First, we need to define spikes. We can fix an arbitrary threshold, beyond which we will label them as one. Here are some very rudimentary thoughts on counting:
  • Coupling/buffering the output from the laptop audio-out port via ICs like ULN 2004 Darlington transistor arrays to drive filament lamps [these filament lamps are a modest way to an integrator as the heat takes time to dissipate off]. The more the spike rates, greater will be the brightness. Then pick-up this optical signal by an LDR (Light Dependent Resistor) and then noting the resistance change [precalibration is necessary]. We can use capacitors too (using their exponential charging/discharging equations) or a linear optocoupler like MOC5010.
  • Software: writing some code snippets to Matlab/Python programs 
  • Using a Foster-Seeley phase discriminator: However, a new algorithm should be developed.
  • Converting the electrical signals to mechanical tracings on a rotating Kymograph [speed adjusted] may make it easier to read and count
  • Allowing only signals above a certain 'predefined' threshold voltage to pass through. We may use diodes for this cut-off estimation. Next, employ a CD 4520, a dual 4 BIT binary up counter that advances from LOW to High transition on clock input '0' (CK0) when CK1 is high, after the signal has been "gate"d . We can use an appropriate crystal to this counting purpose. Many optically based circuits are available on the net.
  • We can think of using a frequency to voltage converter IC like LM 2907
  • But presently, i'll be counting them manually. My time limitations and fading electronic experiences precludes any pursuits of above kind.
After we have successfully counted the 'rates' of 'action potential's, we can plot their number/spikes vs time plot in a linear or logarithmic scale. 


Here's where I positioned the ground electrode, on the manubrium sterni, on the upper chest (breastbone). The overlying hairs had been shaved and cleaned with spirit to reduce the input impedance. In all the spikerbox experiments the placement of the ground remained the same unless otherwise stated. 

To be continued....

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This work by Amiya Sarkar is licensed under a Creative Commons Attribution 4.0 International License.

Basic Concepts and some 'Assumptions' in SpikerBox Biopotential Experiments

Exploring signals of very low amplitude, as is usual in most bioelectrical signaling, is not an easy job. In many instances the power line hum often drowns these weak electromagnetic dialects. In fact, our body acts as an antenna in receiving these wayward disturbances. We can curb these interference by the following means:

  • Opting for battery operated power for the sensing device (the bio-instrumentation amplifier) as well as the data acquisition inputs, for example, a laptop that runs on battery. The brightness of the laptop display maybe set to maximum, as some laptops may emit significant stray noise when brightness is not saturated.
  • Switching off any fluorescent lights
  • By proper Earthing of the equipment
  • Using differential op-amp configuration for adequate noise suppression by eliminating common mode signals
  • Using a preamplifier; and coupler gels that reduce electrical impedance (resistance) between the electrode (lead) and the body surface
  • Choosing an operational amplifier having a high CMRR (common mode rejection ratio)
  • By using a unity gain amplifier (voltage follower) configuration that has a very high input impedance
  • Employing a noise cancelling mechanism like the 'right leg driver'
  • Using a Farady Cage for effective 'shielding' from electromagnetic interference (static)
  • Employing a hardware filter (band stop or Notch filter) or a software program to eliminate/reject a particular frequency band (e.g. 50 Hertz or 60 Hz cycle frequencies)
There's many more options to tackle the undesirable gatecrasher, the 'hum'. Yet it is so difficult to achieve. Easier said than done!

To probe a physiological or pathophysiological response, a stimulus requires that it be precise/ accurate in timing, amplitude, reproducible, relatively less damaging and that it leaves a 'desirable' stimulus artifact so that we can calculate the delay in response in the tracing. Of the various types of stimuli available we generally prefer electrical stimulation over others; such as, mechanical, thermal and chemical, for the above reasons. 

Yet, we sometimes need to take recourse to other forms; as I was kinda forced to use mechanical stimulation to elicit a 'knee jerk' or that I had to abandon an interesting project (Hoffmann's reflex) as the TENS (Transcutaneous Electrical Nerve Stimulation) unit would invariably inject more than enough electromagnetic static into the waveform to render it useless. Marking the exact instant of an applied mechanical stimulus is bothering. I tried to circumvent this by making an "induction circuit", the makeshift switch of which
would be placed on the patellar tendon and 'close' on tapping by a hammer, thus sending an intended static. Also tried to sandwich a piece of piezoelectric material between the percussion hammer and the quadriceps tendon. But none worked so far. I had to remain contented by recording with a camera simultaneously, so that it picked up the sound of patellar impact!

The experiments I have done so far were mostly on obtaining 'surface Electromyography (EMG)' and nerve conduction velocity studies (NCV or NCS). The signals were fed into the SpikerBox input through coaxial cables into its RCA jack inputs, where it was amplified by an integrated circuit (IC) INA 2126P, an Instrumentation Amplifier. There was also a provision for rendering the electrical impulses 'audible' following amplification of the signal by LM 386, which was set at its default gain of 20. [For a more complete detail, please visit "Backyard Brains Wiki"] Thus, we could hear the action potentials and also interface the output with a laptop or a smartphone by softwares such as Audacity, Backyard brains neuron recorder (my own personal favorite) etc for real-time viewing, as well as, for recording for later storage, retrieval and analysis. 

The EMG recordings was done when the muscles were at rest, and at exercise: isometric or isotonic. Since I do not have a 'force transducer', a 'dynamometer' or a Mosso's ergograph; I had to invent ways to measure force/'work done' by other ingenious (or ingenuous? only time will tell !) means. Here's some:
  • spring constant (Hooke's Law) of the device maybe obtained by calibrating with a known device and by measuring how far the cylinder moves into the outer barrel (there's a spring inside that snaps hard onto a piezo crystal when force is applied).
    Piezo based cigarette lighter producing high enough voltage causing a spark thus igniting the gas 
  • by coupling it to a linear potentiometer which have also been previously calibrated (see figure), and then displaying the resistance in a multimeter or through a linear dot/bar display using LM 3914 IC.
  • Work done = Force*Distance=m(mass)*g(acceleration due to Gravity)*displacement (see schematic diagram)
Although we would love a stereo output from a 2 channel SpikerBox, the one I have, I do not have a laptop that accepts stereo microphone input.  Stereo signals are more preferable to human interface devices than plain old mono input. A stereo signal 'may' still possibly be 'recorded' by a 
  • Desktop line-in (via Avance AC97 soundcard) input but that would entail 50 Hz hum to pass through as well. 
  • A stereo (tape/CD) recorder running on battery power is a better option. The data can later be played/digitized at a later time. 
  • A stereo FM transmitter or a 3 pin to USB adapter is yet another option. 

Meanwhile, here's some relevant issues regarding Two channel spikerbox:
  • The internal connection pattern of (4 ring TRRS vs 3 ring stereo) 'smartphone'-'laptop' cable foxed me  for some time to realize that the Left & Right channels were only capacitively coupled
  • That my low-cost Penta T-Pad tablet could NOT render waveforms in BYB app while my Samsung GT-S5360 gleefully obliged. However, the screen was way too small to allow any reasonable analysis & that data longer than >=2 seconds could not be saved in the mobile
  • There was significant 'clipping'/distortion of the waveform in my mobile phone [maybe I could have attached a resistor to the ground/common pin to attenuate the signal. But I opted for not modifying the device in any way.]
Hence, I used the other cable coming from Y splitter (audio splitter) for the measurement of output signal amplitude, since I was outsmarted by my smartphone!

My tryst with such experiments is not new. I have previously done amphibian nerve-muscle preparation experiments using Kymograph and Dubois-Reymond induction coils, in medical curriculum. This included studying the effects of external influences like temperature, load, repeated stimuli causing beneficial effect & fatigue etc. on the tissue. I also studied peristalsis & effects of external influences including drugs on Guinea-pig smooth muscle in Dale's tissue organ bath. Also being an electronics enthusiast, I tried to decode the language the heart speaks, in the honest pursuit of making biomedical instrumentation. It's tough! (fun intended)

Lastly, all that has been said above may be modified as we gain more insight and experience. Please feel free to use/modify this work, do your own research, give your feedback or point something wrong in this article. 

N.B.-Remember, electricity kills! Try to have a close friend, preferably a doc, by your side. Check that the 'Earth' outlet is really what it outta be!

Last modified: never
Reference: hyper-links, unless specifically mentioned

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This work by Amiya Sarkar is licensed under a Creative Commons Attribution 4.0 International License.

September 11, 2010

fMRI, BOLD and the Beautiful

ResearchBlogging.orgWhen we want to examine the brain of a person noninvasively by Computed Tomography (CT) or MRI, we get a ‘snapshot’ of the anatomy (or pathology, if any) of the subject’s brain. We are however clueless as to its functional aspect. fMRI or Functional Magnetic Resonant Imaging allows us to do just that. The difference is not unlike a ‘still picture’ versus a ‘video of a moving train’. PET scans, previously described, also can asses the functional state of the brain.

Whenever we do a task, think, dream, memorize, speak or see things, the brain is not activated as a whole; but only certain portions of it are activated. Activation, here, means increased metabolic activity of neurons in certain areas of the brain. Naturally, these ‘metabolically active’ neurons would demand more energy which would power them. The blood supply to these areas increases as a result of this metabolically driven vasodilation. The arteries then bring in glucose and oxygen with them, with Oxygen being transported in the form of Oxyhemoglobin (oxygenated hemoglobin or HbO2). Neurons on the other hand use up the oxygen contained in the blood, thereby reducing it to de-oxyhemoglobin or simply Hb. However, the alteration in tissue perfusion exceeds the extraction of oxygen by the neurons, so the concentration of deoxyhemoglobin within ‘the areas’ decreases. This causes molecular inhomogeneities in the magnetic field.

Oxyhemoglobin is diamagnetic, meaning that they align perpendicularly to magnetic field lines. On the other hand, deoxyhemoglobin is paramagnetic, i.e. it aligns parallely and proportinately with the intensity of the magnetic field. This causes the inhomogeneity within the magnetic field (magnetic susceptibility) in the tissue sampled. This inhomogeneity is exploited in fMRI in terms of decay of transverse magnetization, T2*, with longer T2* values in HbO2 blood and shorter values in Hb (paramagnetic) blood.Since this stems from the oxygen content in blood, fMRI is also known as the BOLD ((blood oxygenation level dependent) effect.

The machine is essentially the same as the MRI machine with echo planar imaging technology that permits faster imaging due to faster gradient switching, improved algorithm and faster CPU processing power. The patient/subject is placed inside the magnetic chamber and MRI signals are acquired, Fourier transformed and corrected for artifacts. Finally the computer reconstructs a 3D fMRI image out of this.

As is obvious, we can learn about the motor areas of a patient by asking him to grasp an object or giving him any motor task and noticing which area(s) of the brain lights up. A neurosurgeon can then be cautious about not hurting these areas. Similarly, the mapping will help spare motor and other vital areas like auditory, visual and language areas from damage in radiotherapy procedures, in addition to neurosurgery. It can also detect occult Alzheimer’s disease and cognitive deficits including those of the autism spectrum and dyslexia (reading disorder).

fMRI can also be employed to ‘read peoples’ minds’, thoughts, intentions including lie detection. Watch the video below which explains how an fMRI scan is done and interpreted.


Thus the legal and forensic implications are obvious. However, in fMRI, correlation doesn't always mean causation. Whatever it may be, it seems that fMRI is very much here to stay, both in the clinics as well as in cognitive neuroscience research. It may also be combined with tractography, MRI or other diagnostic radiologic modalities.

Hardenbergh et al combined Tractography techniques with fMRI, using a technique capable of rendering multiple color-coded functional activation volumes and fiber tract bundles. Many pharmacologically active drugs have effect on memory impairment, which can be seen in ‘telltale’ fMRI scans. Sperling et al studied the effects of lorazepam (a benzodiazepine) and scopolamine (an anticholinergic drug once used as ‘truth serum’ by the CIA) Effect of scopolamine and lorazepam on memory using fMRIon healthy volunteers and found that they did impair memory and their functional coordinates could be reproducively mapped on fMRI scans (see figure on the left). I still shudder at the thought of what happened during my PG exam when I took a benzodiazepine.

Last modified: Mar 09, 2014
Reference: Integrated 3D Visualization of fMRI and DTI tractography
Gore, J. (2003). Principles and practice of functional MRI of the human brain Journal of Clinical Investigation, 112 (1), 4-9 DOI: 10.1172/JCI200319010

September 07, 2010

The World of Tractography Where The White Matter Tracts Appear Colored

The Central Nervous System (CNS) communicates with the exterior (sensory e.g. gets visual, tactile information etc. on the one hand; and motor, performs limb movement, posture regulation etc. on the other) via the peripheral (somatic) nervous system. It also connects with the interior (our viscera or organs) via the Autonomic Nervous System. That is, it does its job in a bidirectional way: by the motor or the actuator arm, and sensory or the receptor arm. For such ‘actions’ to occur, cables of nerve fibers are laid within our body. Wouldn't it be nice if we could visualize these cables, their dispositional anatomy or any pathology that could afflict them?
a neuron showing an axon wrapped by myelin sheath
Schematic of a 'peripheral' myelinated axon 
The brain and spinal cord together constitute the CNS. We also know that there are about a hundred billion neurons in the CNS. Each neuron has a cell body (soma), an axon wrapped by myelin, and many dendrites. (See figure). It is the axon that carries the information in the form of action potential. These cables (bunch of axons, called tracts) are not laid haphazardly. Nature tries to conserve space, length, energy and so on and thus the axons form into tracts in a topologically efficient way. They run up and down (also front-back and sideways) the cord to the brain, the organ that we will now concentrate upon.

Your electrical wiring to your ceiling fan would include a switch and the fan itself. The wire (cable) from the switch would ascend vertically up the wall, make a 90 degree angle, and then reach the fan horizontally up in the ceiling. Likewise, in our brain, which is made up of two hemispheres, would connect. Three broad fiber types are seen: from one hemisphere to the other (commisural fibers), restricted to one hemisphere (front to back or antero-posteriorly are association fibers) and finally vertically (up down orientation go the projection fibers).

Exploring the tracts can now be done in live animals including humans. Improvement in MRI technology has enabled us to see the tracts (tractography). Improved gradient coils, faster processors and superior software have shortened the scanning time, thereby reducing 'blur' due to organ movement (e.g. diaphragm) and patient movement. This procedure called Echo Planar Imaging (EPI) has given birth to Functional Magnetic Resonance Imaging (fMRI), Diffusion Weighted Imaging (DWI), tractography and many other diagnostic and research procedures.

Consider the neuron shown in the above picture. Water molecules in the axon (yellow) are constantly in Brownian (random) motion due to thermal energy within. Hence they tend to diffuse constantly to come to equilibrium. In most of the cerebrospinal fluid spaces these microscopic motions are equal in all directions. This is called isotropic diffusion. But in myelinated neurons, as in the white matter fiber tracts, water motion is constrained due to the fatty nature of the myelin sheath (in blue) which hinders water flow across it. This anisotropic diffusion allows the flow of more water molecules along (parallel) the direction of the nerve fiber. The apparent diffusion coefficient (ADC) is thus more along the nerve fiber. Diffusion Weighted Imaging (DWI) can capture this microscopic water flow and delineate anatomically the orientation of nerve fiber tracts.

Pyogenic abscesses hinder diffusion by virtue of their increased viscosity, a rheological property. In the early stages of acute cerebral infarction there is reduced diffusion too, giving rise to high signal intensity. However, in most pathologies of the brain the ADC is increased. Diffusion Tensor Imaging (DTI), a diffusion MRI technology, tracks fiber orientation by assigning values in ellipsoid voxels (VOlume piXEL). Ellipsoid because unlike isotropic diffusion where molecules diffuse equally in all directions, the anisotropy in the white matter tracts does not permit them to move with equal ease in all directions, and hence the pattern is that of an ellipsoid and not spherical. By connecting the long axes of all the ellipsoids, the trajectory/orientation is deduced.

Colors are added to it with respect to the three principal axes (x, y and z)colorful world of tractography and the result is a stunning tractography! (see left)



The YouTube video below describes the colorful realms of tractography and how they are used.

When fMRI and DTI are combined together, a whole new world emerges. But, I prefer to keep it on hold till I discuss Functional Magnetic Resonance Imaging.

NB: The picture of the neuron/axon shown is not representative of CNS neurons. Oligodendrocytes that form myelin in the CNS does not encircle so many times as the Schwann cells in peripheral neurons do. It has been shown here only for the sake of clarity.

Last modified: Mar 10, 2014
Reference: Diffusion Tensor Tractography: Exploring the Cost-Benefit Ratio of Incorporating CSF Suppression into Fiber Tracing Algorithms

William P. Dillon. Neuroimaging in Neurologic Disorders. In: Harrison's Principles of Internal Medicine, 17th Ed., Volume 2, McGraw Hill; 2008. p. 2491-2497.

P. Mukherjee,, J.I. Berman,, S.W. Chung,, C.P. Hess, & R.G. Henry (2008). Diffusion Tensor MR Imaging and Fiber Tractography: Theoretic Underpinnings AM J Neuroradiol DOI: 10.3174/ajnr.A1051

July 21, 2010

Relaxation in the Nuclear Microcosm

All of us want to give themselves a hard earned ‘rest’ after a “hard day’s night”, don’t we? So do the protons, perturbed by the destabilizing magnetic component of the radio-frequency pulse [which previously ‘happily’ aligned themselves to the externally applied magnetic field; one way (parallel) or the other (antiparallel)] applied at the Larmor frequency. It is like slapping an individual in a “merry go round” each time he came near a person who is paid just for slapping that person. But, when we call ‘spin’, we do not mean ‘spin’ the way we see them in a classical world. [We’ve given various names to the ‘quarks’: up, down, strange, bottom etc. depending on ‘something’ called ‘flavor’; and red, green and blue depending on ‘something’ called ‘color’.However, spin, flavor, color etc.‘in the quantum world’ have ‘no relevance’ to what we usually attribute to them in our everyday life. Things are a bit crazy in the quantum world, but I will take recourse to some ‘classical world’ analogies to make the description lucid.]

Thus, the already aligned nuclei (parallel or anti-parallel to the applied steady external magnetic field B0), has now been perturbed owing to the ‘knocking’ by the ‘magnetic component’ (B1) of the electromagnetic RF pulse. The nuclei gain energy and sway away from the perpendicular to the horizontal (90 degree) depending on how long the RF pulse is applied. So, now the nuclei behave like ‘punch-drunk’( like a person who’s been reeling due to a strong blow to the head!). magnetization vector resolved into its components horizontal Mxy and a vertical MzRemember, that this new angular momentum is also a vector quantity having magnitude and direction. It can be resolved in terms of a horizontal component (Mxy) and a vertical component Mz. Anyway, the proton does recover from this situation, after some time, once the external RF field has stopped. Typically, Mxy component decays faster than the recovery of Mz.

The excited proton recovers in two ways and both forms occur simultaneously: (1) The excited nuclei which now have been ‘forced’ to lie horizontally (90 degree), ‘re-align’ themselves back to their ‘original position’ as they were before the RF pulse (perpendicularly towards the field of externally applied field B0); and (2) the energized protons dissipate their energies to the surrounding nuclei (horizontally) at their level. The first example, obviously, is called the (spin-lattice, or longitudinal) relaxation; while the second one, transverse relaxation (T2). There is little energy loss due to RF emission.

T1 relaxation, also known as, longitudinal relaxation or spin-lattice relaxation can be best understood if you see the following Youtube video. [The spiral trajectory, in this case, reminds me of the laser experiment I did to satisfy my lesser friends. Analogically, the trajectory would be such, if the power supply were switched off.] In T1 relaxation, the proton loses energy to the surrounding lattice, by interacting with nuclei in the lattice which are in vibrational, translational and rotational motion. Clearly, the surrounding nuclei (lattice) having the same (or nearly same) Larmor frequency will efficiently absorb energy of the excited proton, resulting in a tiny rise of temperature.

T2 relaxation (transverse or spin-spin relaxation) on the other hand, does not involve exchange of energy with the lattice.
The magnetic moments of the protons merely changes phase. Here, the nuclei exchange “quantum states” (kind of, what Einstein called ‘spooky action at a distance’): an excited nucleus (proton) will transfer its energy and relax, while the neighboring nucleus in the lower energy state that absorbs it becomes excited. This loss of phase coherence of spins can be clearly seen in this beautiful video.

It can be understood easily that T1 and T2 values would depend on the surrounding molecular environment (tissues, for example). Hence, the values differ in different tissues. Again, since Mxy decays faster, as described, it may be understood why T1 is greater than T2 (usually, T1=5T2). Both T1 and T2 contribute toward contrast in tissues. T1 relaxation time is the time needed for 63% of protons to return to their previous equilibrium state. Likewise, T2 relaxation time is the time needed for 63% of protons to become dephased owing to their interaction with nearby protons. The contrast, naturally depends on the water content of the tissues. Grey matter has about 10% more water than white matter and this creates a contrast. We can also create contrast by varying TR and TE times.

TR (Repetition Time) refers to the time gap at which consecutive RF pulses are applied; while TE (Echo Time) refers to the time delay between the applied RF pulse and its reception (echo). T1 weighted images (T1W) are produced by keeping TR and TE relatively short, while T2 weighted images (T2W) are produced by keeping TR and TE relatively long. Water molecules being relatively light spins much faster than the Larmor frequency, making energy transfer rather tough (exchanging of packets of energy becomes more efficient as the relative angular velocity narrows). Consequently, water has a long T1 time. Proteins and nucleic acids being rather heavy, spin slowly. They also have problem with energy exchanging, and thus have a long T1. Cholesterol, a medium sized molecule, precesses near the Larmor frequency, efficiently absorbing the energy and giving a small T1 value.Thus (fat) liquid cholesterol in craniopharyngiomas, a benign tumor, appears bright on T1W images (T1 being small, the rate at which RF energy is released is fast. Hence, the signal intensity in NMR is high).

Subacute hemorrhage also has shorter T1, due to the presence of paramagnetic iron in methemoglobin present in the tissue, hence high signal intensity. Cerebrospinal fluid (CSF), edema (collection of fluid in tissue space or ECF) having more water content have both long T1 & T2 relaxation time. They give low signal intensity in T1 (dark) but higher signal intensity (bright) in T2W images. T2W images are superior to their T1 counterparts in case of infarction, edema, demyelination etc. Contrast agents like the heavy metal Gadolinium, a paramagnetic substance, has been used to reduce both T1 and T2 times by introducing inhomogeneity in the magnetic field. Gadolinium is complexed (chelated) with a substance called DTPA to prevent toxic build-up inside body tissues. This gives high signal in T1W but a low signal in T2W. It (the complex) does not cross the blood brain barrier (BBB); but disruption in the BBB or parts of the brain where it is deficient (circumventricular organs), take-up the substance and affects relaxation properties.

Below is an MRI showing changes in Subacute Sclerosing Panencephalitis, a complication of measles. T1 and T2 weighted MRI scansNote: Panels A and C are T1-weighted images; B and D are T2-weighted images. The hypointense (darker) signal on the T1-weighted image (arrow in A) and a hyperintense (bright) signal on the T2-weighted image (arrow in B) can be clearly seen.

Given all these, it can be said that relaxation parameters of nuclei have enabled us in visualizing biological tissues nonivasively, identifying chemicals spectroscopically and a lot more as we shall see later.

Last Modified: Aug 19, 2010

October 13, 2009

Atomic Force Microscopy: Feels The Atoms, Sees The Bonds

When it comes to viewing things on the atomic scale, one has to be very careful and innovative. To understand how an atomic force microscope works, we should better discuss a bit about its predecessor: the scanning tunneling microscope (STM). STM was invented by Binnig and Rohrer for which they got the Nobel Prize in Physics. Binnig and colleagues later went on to develop the first Atomic Force Microscope (AFM). Both AFM and STM are types of Scanning Probe Microscopy, which employs a probe that scans the sample.

STM consists of a sharp probe tip, which scans over the specimen as the adjoining picture shows. Diagrammatic representation of Scanning Tunneling MicroscopeFirst, the probe tip is brought near the sample manually, and then the finer adjustment of maintaining probe sample distance (height) is done by piezoelectric control. A voltage applied between the tip and the sample causes electrons to tunnel from the tip to the sample. As we have seen in Ohm’s law, the tunneling current will depend on the applied potential difference (voltage bias); and the height of tip-sample separation and the local density of states (factors determining ‘resistance’). If we know two of the three unknowns, we can calculate the other, which is actually done by the computer by data acquisition.

We can do STM in two ways. We can keep the tip position (height) fixed as it scans the specimen topography (constant height mode). Here the voltage and height are both held constant, while the tunneling current varies. In constant current mode, the tip is always at a specific height over the specimen. That is, as the tip hovers over the rugged terrain of the sample surface and comes close to a raised spot, the tunneling current will increase. The increased current will be sensed, amplified and passed to the feedback electronic circuitry which will ‘lift’ the probe-tip by applying a voltage to the piezo crystal. Hence the electronic servomechanism maintains a constant tip sample distance in constant current mode. Piezoelectric crystals translate pressure changes into electricity (and vice versa) as we see in oven gas lighters and in mobile phone speakers.

But STM has its inherent drawback: the sample has to be a conductor or a semiconductor, in order for tunneling to occur. Hence, biological tissues, non conducting polymers can not be imaged. So, the need for atomic force microscopy arose. Here again, Gerd Binnig played a pivotal role.

Atomic Force Microscopy operates on a similar principle. First, let’s discuss how the music on gramophone record grooves is translated. Scanning Tunneling Microscopy is like a blind man walking with a stickThe stylus (which overlies a piezo crystal) feels the groovy surface of the vinyl LP disc which revolves on a turntable. The mechanical vibration sets in a voltage in the piezo via the stylus. We get the surface topology in the form of music. Another great way of viewing how the AFM scans and interprets a sample is how a blind person ‘feels’ a surface by using a stick (see picture).

In AFM, a very sharp tip (made of silicon or silicon nitride) is scanned over a surface with similar feedback mechanisms that maintain the tip at a constant force (to get height information), or height (to obtain force information) above the sample surface. This sharp tip is mounted on a cantilever, a rod like structure whose other end is fixed and unmovable. As the probe tip raster scans (i.e. scans in a zigzag fashion as done in TV scanning) the surface of the sample, a laser light is made to fall on the back of the cantilever. The light gets reflected off from this side and is detected by one of a dual photodiode. The cantilever ‘tilts’ as it slopes ‘down a bump’, causing another reflection that hits the other of the dual photodiode. A differential amplifier then calculates the difference output between the two light intensities and this is proportional to the cantilever deflection. We can calculate the force (acting between the cantilever tip and the sample) using Hooke’s law (F=-kx), where F is force, k is constant for a particular cantilever, and x is the deflection of the cantilever. The amplifier difference output may be used to keep the tip in either at a constant force or at a constant height above the sample, through piezoelectric servo mechanism (feedback).

AFM is very versatile and allows many user specific modifications. It can be done in contact mode, where the tip remains in contact with the surface as it scans over the specimen. In tapping mode, the cantilever oscillates over the sample, touching the surface intermittently. Interatomic forces like van der Waals forces and electrostatic forces cause a deflection of the cantilever when the tip comes closer to the sample. In the non contact mode, the cantilever does not touch the sample, and is oscillated at slightly above its natural resonance frequency. Any long range force like van der Waals force will decrease the frequency of the vibrating cantilever, when the tip approaches the sample. There are many other variants of AFM and combination of AFM with other imaging modalities like optical microscopy, Raman spectroscopy and so on.

But Leo Gross and colleagues at IBM Research Zurich wanted another, so they went on to develop another variant of AFM. They used a tuning fork like probe. One end of the probe was near, while the other end was away from the sample. When the fork was vibrated, the prong next to the sample experienced a minute shift in frequency due to forces acting upon it. This frequency drift when compared to the other prong, gives the molecular picture.

To get the finer detail of a molecule, one had to use a sharp AFM probe tip. They Pentacene Molecule's AFM image showing bondslinked a molecule of carbon monoxide to the tip in such a way so that the lone oxygen atom became the de facto tip. It gave the structure of pentacene in unprecedented detail. You can clearly see even the bonds between carbon atoms, just as we read in our textbooks. However, the experiment must be vibration free, thermal noise free (at a very low temperature), and should be done in vacuum.

References: Scanning tunneling microscope (Wikipedia), Atomic Force Microscope (Wikipedia),
Single molecule's stunning image (BBC)

Last modified: never
Reference: hyper-links, unless specifically mentioned

March 30, 2009

Build Yourself a DIY AM Radio Transmitter

diagram of a very simple, miniature medium wave amplitude modulation radio transmitterIntroduction: Understanding the fundamental principles of radio waves, their generation, propagation and reception is essential not only for the electronic enthusiasts, but also in other disciplines of science which employ radio-frequency (RF) in scientific investigation and even in medical imaging and treatment. Here, the construction of a cheap and simple DIY (do-it-yourself) transmitter (Tx) circuit is described and its operations explained in simple terms.

Materials you'll need: A microphone, a transistor (ask your friends to help with the emitter, base and collector terminals. Alternatively, look up the web), a radio frequency coil (choke, RFC), a variable capacitor (365 or 500 pF; pF = pico farad), 2 resistors, 3 condensers , an aerial (antenna), a soldering iron, solder wire, a stripboard (also known as veroboard) and a power supply (9V).

Assembly: Clean the leads (wire terminals) free of oxides/ enamel coatings by rubbing with fine grained sandpaper. Next, in accordance with the accompanying diagram, wire the components together in one of the following ways:
1. Connect the components directly and cover these joints by insulating tapes such as black tapes, cello tapes or scotch tapes (it is said that the scotch tape emits X-rays when pulled off, well it's unimportant here) . This will prevent accidental shorting with similar joints.
2. Or use a breadboard and press-fit the leads in the slots. The breadboard has prewired connections within it, which will take care of the rest. Make sure that these prefixed connection layouts are followed. You may need to make some extra connections by using external hook-up wires/jumpers.
3. Or use a stripboard/veroboard: Put the components into the drilled holes according to the circuit layout. Now, solder the leads using a 20 watt soldering iron. It is the best option among the three mentioned.

When the iron is sufficiently hot, apply the hot tip to the component lead (not to the solder wire!) to be soldered, and bring the solder wire near it. Within a few seconds, solder will melt and flow evenly around the joint. Withdraw the iron (take as little time as possible).
Check with the circuit again. Cut any extra strip of copper track which might act as a potential short. You may need to make some extra connections by using external hook-up wires/jumpers.

Turn on your radio: Set your radio receiver to any empty slot on the medium wave frequency band. Switch on your newly assembled wireless Tx. Turn the spindle of the variable condenser of 'your set'. At some point you'll hear a 'smooth hissing carrier tone' on the receiver. Keep the variable capacitor there. You're almost done! Speak on the mike, you'll hear the same on the radio receiver. If you press the mike on your left chest, you will hear your heart sounds on the receiver set. You can make a 'phonocardiogram' too this way.

How it works: The Tank oscillator produces the carrier frequency (freq = 1/{2*pi*sqrt.[LC]}; L= inductance of the coil in Henry, C = capacitance in Farad, as dictated by the variable capacitor). To see an animation of how a 'tank circuit' works visit this page. The amplitude of the freq. of the carrier wave is modulated by the input from the microphone. As we speak on to the microphone, the diaphragm vibrates. This makes a coil of copper, wound around a powerful magnet, vibrate too, making induced current in the coil, the magnitude and frequency of which depends on the loudness and frequency of the speech/audio signal. The mike is connected to the base of the transistor via a capacitor. This capacitor allows AC (alternating currents) to pass, but blocks any DC component. The second feature thus, does not let the microphone change the bias voltage conditions of the transistor. The biasing of the NPN type transistor is done by one or two fixed resistor networks (one in this case).
When some audio signal is present, collector current will increase. Since it is the tank circuit at the collector load, the amplitude of the 'carrier frequency' will thus be modified. Amplitude Modulation has been achieved! You will notice that one end of the output capacitor has been connected to the antenna, while the other end is connected to the ground (earth, ground of your wall power outlet, or safer still the traditional lead water pipe). This arrangement makes the capacitor plates look like, as if, they are placed far apart; earth and sky! This causes dissipation of the energy in the form of electromagnetic waves.
Frequency Modulation (FM) transmission is better, since the static (electrical noise from man made appliances, lightnings etc) is almost absent and stereo signal can be transmitted, to name a few.

Experiments and lessons on it:
1. Move a magnet at the back of the radio receiver (where the RFC choke is located) with the receiver tuned to the short wave band. You'll notice that the frequency changes: many different stations come in (without even having to turn the tuner knob!). This happens as the magnet alters the local oscillator of the receiver.
2. Put the radio inside a metal container and try to catch a station. You won't succeed. This is 'shielding'; the metal does not allow electromagnetic wave to pass in. Co-axial cables exploit this phenomenon to avoid noisy interferences. Sensitive instruments used in medicine (e.g. EEG) or radioastronomy were often built underground. This phenomenon is exploited in a Faraday cage.
3. Just touch two different metals in front of the radio receiver: the radio will make noise. This is due to passage of free electrons between the metals.
4. Short two ends of a battery (cathode and anode), the radio hisses and makes noise. Obviously, electromagnetic fields are created.
5. The telltale undulations heard in shortwave, is due to the reflection (actually total internal reflection, a type of refraction) of radio waves from the Kennely-Heaviside layer of the ionosphere, a charged layer in the higher atmosphere, that frequently changes its altitude. If you put a laser beam or any light on the ground and put a mirror higher up, you would get a reflection. Moving the mirror up and down will put the reflected beam closer or further away (light is also an electromagnetic wave). This layer is absent in night time and Appleton layer still higher up reflects then. This is why SW broadcasting stations are best heard at different frequencies during different parts of the daytime.
6. You can listen to cosmic noise, falling meteors (by their 'heated' ionization trail) etc.
7. Take a radio and tune it to a station. Now take a second radio and turn the tuner knob till that same radio station is obtained. You'll notice a drop in volume of the former radio (and vice versa). This illustrates energy transfer by resonance.

Uses of Radio waves: Telecommunications, radar, radioastronomy, medical investigations such as MRI (NMR), medical therapies (radio frequency ablation in ectopic pacemakers of the heart (electrophysiology), short-wave diathermy, research procedures such as thought broadcasting etc.

N.B. : 1. This is a very simple, low cost transmitter, but many countries might have legal restrictions on it. A crystal controlled version of the set is more likely to be approved, as the bandwidth is less.
2. Other forms of electromagnetic waves may be broadcast in much the same way e.g. our good old TV remote uses infrared waves.

Last modified: Mar10, 2014
Reference: hyper-links, unless specifically mentioned

January 19, 2009

Phase Alignment of Neocortical Gamma Oscillations by Hippocampal Theta Waves

An empty brain is the devil’s workshop, goes the proverb. Actually, the brain is never empty. Even in our deepest slumber, the brain continues to weave waves of electrical rhythms that can be seen with the aid of electroencephalogram or EEG. When we place electrodes on the scalp or on the cortex (inside the skull), and amplify the faint signals via bioinstrumentation amplifier, we can lay our hands on these fluctuating rhythms. (More on the electronics of EEG may be found at the OpenEEG project site).

We have as many as 100 billion neurons in the brain. In the superficial layers of the cortex, the neurons have numerous dendrites branching out from the soma or cell body (shown in grey oval in this picture).diagrammatic representation of cortical dipole with dendritic treesThese neurons have been compared to a forest of trees where the branches are the dendrites and the trunk the axon. These dendrites make extensive connections among each other. They also get connections from the axon collaterals of neighboring axons (i.e. the 'trunks' of other trees connect to these 'twigs' by offshoot from the trunks). Since there are a lot of axons converging on the dendrites of each neuron, and given the fact that these axons can be excitatory (red) or inhibitory (green) depending on the neurotransmitter, the sum of input may be either negative or positive (with respect to the cell body). Thus an alternating current (cortical dipole) will flow between the shifting dendrites and the soma. This along with thalamocortical oscillations produces the EEG waves.

The brain doesn’t churn out the rhythm just like that. Had the neurons fired randomly the oscillations would have cancelled out.EEG showing alpha, beta and other brainwavesEEG waves occur due to synchronous discharge of neurons producing the alpha, beta, theta, gamma and other telltale waves. Like all other electrical waves, they too have a frequency and amplitude. Alpha waves, for example, have a frequency of 8-12 Hz (cycles per second) and an amplitude ranging from 50-100 microvolt when recorded from the scalp, and it is found when a person is resting comfortably with eyes closed and the mind wandering. On the other hand, gamma rhythm has a frequency of 30-80 Hz, and it is found when a person is deeply engrossed on some work.

It was known for a long time that the hippocampus exerted a role in learning by fostering long term potentiation (LTP) by aligning the neocortex, where memories are stored. The mechanisms behind this are now emerging. Sirota et al and Siapas et al have analyzed rat brains and found out that there were many localized gamma oscillators within the brain that gave rise to neocortical gamma bursts. These oscillators had varying frequencies but they phase aligned themselves with the arrival of hippocampal theta waves. A large fraction of pyramidal cells and interneurons too were phase aligned to the hippocampal theta rhythm.Bar magnet showing lines of forceThis is similar to a bar magnet aligning iron dust or other ferromagnetic materials by virtue of its magnetic field. Apart from the cerebral cortex, the cerebellar cortex and the hippocampus too can generate brain waves. Such a mechanism may explain the orchestration of many parts of the cortex (and hence the memory engrams they contain); and data synchronization and downloading to the hippocampus for memory retrieval. It also shows how hippocampus does the ‘indexing’ of cortical contents. These experiments throw light on neuronal plasticity and information flow, and may be someday they could help clinicians in fighting memory loss as it occurs in neurodegenerative diseases like Alzheimer’s disease.

Last modified: never
References:
Prefrontal Phase Locking to Hippocampal Theta Oscillations
Athanassios G. Siapas, Evgueniy V. Lubenov and Matthew A. Wilson. doi:10.1016/j.neuron.2005.02.028
ResearchBlogging.orgA SIROTA, S MONTGOMERY, S FUJISAWA, Y ISOMURA, M ZUGARO, G BUZSAKI (2008). Entrainment of Neocortical Neurons and Gamma Oscillations by the Hippocampal Theta Rhythm Neuron, 60 (4), 683-697 DOI: 10.1016/j.neuron.2008.09.014

December 05, 2008

PET Scan: Particle Physics And Electronics in Medical Imaging

Numerous imaging modalities are there to view anatomical structures in our body. They include X rays, Ultrasound imaging, MRI and many other procedures where we can see normal or diseased tissues in our body. They tell us ‘the location’ (position) in the body the image corresponds to. If we wanted to see what were happening in these locations, we would then need to perform functional imaging techniques like PET scan or fMRI.

In Positron Emission Tomography or PET, a radioactive isotope that decays by positron emission is introduced into the body. Positron emitting radioisotopes are prepared by bombarding stable atomic nuclei by protons. Protons are speeded up in a particle accelerator called cyclotron which then impinge upon the stable nuclei, and knocks out one neutron from its nucleus. The proton now occupies the position where the ousted neutron once stayed. But this atomic configuration is unstable, so the proton now decays. It decays by emitting positron, a particle resembling an electron in all aspects except that the charge is positive and not negative. In other words, a positron is an antimatter: an anti-electron.

positron annihilation and formation of two collinear gamma ray photonsMany different radioisotopes are there, such as Fluorine18, Oxygen15, and Carbon11. 18F is the most commonly used isotope. It replaces hydroxyl (OH) group in molecules of interest. We can use 18F Fluorodeoxyglucose (18FDG) an analog of glucose for probing the activity of brain. Our brain uses glucose for its metabolism, so when it encounters 18FDG, it stores them. The FDG in the brain begins emitting positrons. These particles travel only a short distance before they meet nearby electrons and annihilate. Two gamma ray photons, each having 511 keV of energy are produced--- Photons because they are electromagnetic waves, and gamma ray because the frequencies correspond to the gamma ray spectrum of electromagnetic waves.

So by detecting these photons, we can find out where they came from, since we know that these photons are emitted back to back, 180 degrees apart. (They aren’t exactly collinear as their initial velocity is not zero, and some computational error always creeps in). For the detection part, we need a detection array which will convert these photons into electrons. This is done by scintillators. Bismuth germanate, Luterium oxyorthosilicate (LSO) are some of them. Photons which are incident on them produce electrons by photoelectric effect. These electrons are then guided through a vacuum tube, which has many positive electrodes (dynodes) held at successively higher voltages. These dynodes of this photomultiplier tube accelerate these electrons, which in turn knock-off more electrons from the dynode plates. Thus we get more electrons than what we started with. The signal has now been amplified and we now have a measurable current.

With advancement in detection technology, silicon avalanche photodiodes (silicon APD) has now shown promise to replace the vacuum technology (photomultiplier tube). As the name suggests, APDs work in a similar way an avalanche gains its momentum as it descends from the mountain-avalanche effect. Detecting photons aren’t sufficient. We need to detect only co-linear (coincident) photons. Each collinear photon pair (i.e. 180 degrees apart) will constitute an event. All other photons (noise) must be rejected. About 10^7 to 10^8 or more ‘events’ must be registered in order to have a good signal to noise ratio. Image faithfulness varies proportionally with the square root of the number of events.

By acquiring a large number of events, the computer software is able to determine exactly where these radioactive tracers are located. This, in our case, means the locations where the neurons are accumulating (accumulation is a function of utilization of glucose) 18FDG. Thus we get a functional map. In order to know ‘what’ these structure were, we need to combine anatomical imaging like MRI or CT with PET. This combined PET-CT or PET-MRI let us know what structures are doing how much.

PET scan is very useful in neuroscience researches, clinical diagnoses like cancer detection, receptor analyses and even watching gene expression in molecular biology.

References: A good site with animation: PET animation
Physicsworld

Last Mod: 10 Mar, 2014