Hello World!

We are the Science Writers of RIT

Visual Communications: The Eye as a Window

This piece is intended as a handout to biology and photography students, high school seniors and beginning undergrads especially, who are trying to decide on a career path. It is one of many to choose from, but it is important for seniors to be exposed to every possibility. It includes not only a career description of ophthalmic photography, but also some intriguing facts about the eye, and the practice in general, to spur interest and exploration. Even if not a single student who reads it chooses this rout, I will consider it a success should they at least become curious about the field and want to learn more. As a high school student I know I would love to have been exposed to this sooner. For this reason, I seek to reach out to students like myself.

Communications is a field that is often overlooked, but is a fundamental part of every single workplace. Communications professionals are everywhere, be it visually based or language based. Behind every scientist and doctor there’s a technician; behind every journalist there’s a photographer; behind every celebrity there’s a PR specialist. As communicators, it is our job to not just bridge the gap between audiences, but do so in a way that upholds integrity and understanding.

Ophthalmic photography is a particularly interesting and useful skill set. It falls under the category of visual communication. There are many subcategories of this, but among the most important is diagnostic communication—and that’s where we come in. The doctor performs the diagnosis, and prescribes the treatment—but under the radar, we provide the necessary information for him or her to make a sound decision.

It is important to preface the discussion with a look at what’s called descriptive interpretation. This is a fundamental principle that ophthalmic photographers live by. The doctor may be administering the diagnosis, but it’s our job to provide initial observations and interpretation. It is important to view every retinal photograph as a scientist observes an experiment. Do not draw conclusions right away; take time to make important observations about what may (or may not!) be important for the diagnosis, as compared to what’s considered normal. What color is the retina? How dark or light is it? Do you notice any artifacts? Is there anything unusual about the image? As a communicator, supplying only the image is doing half the job—we must make these key observations. Some of them may even lead to more photographs—images that explore in greater detail what we suspect to be important indicators within the retina.

In this way, the eye can act as a window into the human body—both figuratively and literally. Many people don’t realize, but when you look into someone’s eyes, you’re literally looking into them! The pupil is a hole, around which the iris contracts or relaxes to allow in more or less light, much like the aperture of a camera. If you were to shine a light into the pupil as you peer in, you would see the back of their eyeball—the retina. This is exactly what ophthalmic photography does. Using a special light that shines directly through the lens of a camera system and into the pupil, we get a glimpse of what’s inside the human eye. The image of the retina is reflected back through the lens and onto a film plane or sensor, and thus, a fundus (retinal) photograph is born (right). It’s important to note just what makes the retina so incredible and useful: it is literally the only way to observe blood vessels and nerves without surgery. Not only that, but no incisions whatsoever, no x-rays, no ultrasound, no CAT scans; just a light and a camera. This makes the retina an invaluable diagnostic tool.

Observations of someone’s retina can tell a lot about an individual. Did you know that you could tell someone’s ethnicity by the pigmentation of his or her retina? African-Americans and Asians both tend to have darker retinas, as they have a greater amount of pigment. Europeans, especially blond-haired, have very little pigment and so the retina will be very light.

But more importantly, the retina can be used to identify potential diseases. Take glaucoma, for example. It’s the second most common cause of blindness in the Unites States. The front of the eye is filled with a clear fluid called the aqueous humor; glaucoma occurs when something slows or blocks the flow of this liquid out of the eye, causing an increase in pressure. Excessive eye pressure can eventually cause damage to the optic nerve, which transmits signals from the eye to the brain for sight. Eyesight loss is irreversible, unfortunately; the goal of every ophthalmologist is to slow or stop the loss in its tracks, as that is currently the most anyone can do. There is no cure for glaucoma, but catching it early enough and administering medication can slow the loss of vision enough for someone to live the rest of their life without ever going completely blind.

Eye diseases aren’t the only types that can be diagnosed this way, though; since the retina provides a sampling of blood vessels, observing their behavior can indicate other diseases. Diabetes is a disease in which there are excess levels of glucose in the blood, and it affects 8.3 percent of the United States. 80 percent of patients who have diabetes for ten years or more experience retinopothy—or damage to the retina. It is common for some to see signs of this even earlier, and it often occurs with little or no warning signs. The patient may not be able to tell light from dark in one or both eyes.

Some common observations to search for as indicators of diabetes in the retina include leaking and hemorrhaging blood vessels; they will appear as black splotches on the fundus. Some retinal swelling is also common, and occasionally white, fatty deposits will be observed. Due to the sub-par blood flow, nerve tissue may be damaged, and over a period of time changes to the blood vessels can be observed, often including disappearance and re-growth as the body attempts to deliver oxygen to dying areas of the retina.

In order to aid in the diagnosis, a method called OCT (Optical Coherence Tomography) is often used, which takes traditional retinal photography a level further. This method uses interference technology, analogous to ultrasound, to produce a cross-section of the retina (above). This enables the doctor to observe its thickness, as well as any swelling or leaking beneath the visible surface.

The perfect view of blood vessels can aid in the indication of other health problems as well, such as high blood pressure. When it affects the retina, it’s called “hypertensive retinopothy,” and has similar observations to diabetes. Damaged or leaking blood vessels are common, as well as bubbling of veins and arteries due to the increase in pressure. Additionally, due to poor blood flow, damage to nerves is common. Occasionally swelling may also occur, particularly to the optic nerve and the macula (the center of vision).

When you hear someone say, “The eye is a window,” it’s not just a metaphor; it’s a true, literal fact. This window provides a useful tool for doctors, and it’s the job of communicators like us to utilize this tool and gather the necessary visual information. Ophthalmic photography is a realm of endlessly intriguing discoveries, and is a fairly young field of study—there’s yet more to discover, if only you take the time to look!

Sources:

Face-to-Face Interview. Sisson, Christye. Ophthalmic Photography professor.

http://www.ncbi.nlm.nih.gov/

Ophthalmic Photography: Retinal Photography, Angiography, and Electronic

Imaging. Second edition. Saine, Patrick. Tyler, Marshall. 2002.

Don't Send Her Flowers, She Just Wants the Pollen

This summer, while working as an intern at University of California in San Francisco at one of the light microscopy imaging cores there, I received the largest bouquet of flowers I’ve ever gotten. It had been probably a month and a half since I left Rochester, New York to take the internship and my presence was beginning to be missed. I called my boyfriend and thanked him and proceeded to spend the rest of the afternoon pulling apart one of each type of flower to make slides of their pollen. I mentioned it to him later and I could tell he was shaking his head, “You are just unreal,” he said with a giggle.

Perhaps it sounds a little nerdy, and cruel (I only pulled apart about an eighth of the bouquet, I promise) but the images of the pollen at about 100x magnification were just as gorgeous as the flowers themselves. The pollen grains were far too small to be photographed using brightfield microscopes, which are just the typical lab bench instruments most people are familiar with that simply shine a light through an objective lens to magnify the image. Luckily, pollen grains are autofluorescent meaning they absorb one specific wavelength of light and reemit light at a longer wavelength. A few modifications to the lab bench microscope enable us to create images of the emitted light without background brightness obscuring the image.

The light source is sent through an excitation filter, which passes only a specific wavelength of light, which will excite the subject. The light then reaches a beam splitter, a dichroic mirror, which selectively passes a particular wavelength of light while reflecting another. The beam splitter will pass the excitation light through to the objective lens and to the subject. The beam splitter reflects the light emitted by the subject at a longer wavelength directing it through the emission filter, which only allows light at the longer, emission wavelength to pass to the sensor, usually simply a modified CCD camera. It is important that the excitation and emission filters are mutually exclusive, that they do not allow any of the same light to pass so that no stray light makes it to the detector (Figure 1).

Figure 1 Widefield fluorescent light path

Although pollen can be viewed simply by mounting it on a slide and placing it in a fluorescence imaging system, most subjects of interest to biological research are not autofluorescent and must be stained. Green fluorescent protein (GFP) is protein produced by jellyfish that makes them glow green. It has ushered in a new era in microscopy and research. The gene that produces GFP can be inserted into organisms to make certain structures fluoresce green when subjected to blue light. The fluorphore, which generates the light, may also be attached to an antibody that will in turn attach to a protein of interest in the subject. Since the discovery of GFP, many other fluorescent stains have been created based on the same principle, making it possible to stain a single subject for several structures. To image a sample with multiple stains, the excitation and emission filters as well as the beam splitter are rapidly changed out to match the wavelength requirements of the different stains, making a single picture of the light emitted by each stain. These images are then combined into a single image, like the cells in Figure 2.

Figure 2 Bovine pulmonary artery cells, triple stained

Certain subjects, particularly thick samples, begin to present issues for this type of widefield, or modified lab bench microscope system because the objectives used to create magnification have a limited depth of field. As magnification increases, smaller and smaller slices of the subject are in focus, more and more features of the sample become obscured by out of focus light coming from different depths that are above or below the focal plane, as seen in Figure 3. With 100x magnification, which is really necessary to see a pollen grain in detail, that pollen grain is far too thick to be entirely in focus.

Figure 3 Immature daphnia eye spot, out of focus light above the focal plane obscures in focus information

Computational deconvolution attempts to reassign the out of focus light to its point of origin. This is possible because the way in which light spreads from its origin is affected by a number of factors which can be roughly estimated by software. Even when experimental values for these factors, such as the quality of the objective or how much the mounting media bends the light, are acquired whenever data must be quantified for research studies the accuracy of the deconvolution algorithms may be called into question.

For this reason, many researchers choose to use confocal imaging systems to image subjects that are thicker than the objective’s depth of field. There are several different types of confocal systems that are widely used in biological research but they all operate on the same principal, preventing out-of-focus light from ever reaching the camera. An aperture is placed in front of the camera and any light that is not in focus at the current focal plane falls outside the aperture, resulting in an image that is made up of only light that is in focus. To image the whole subject a series of images must be taken, moving the focal plane from the bottom of the sample to the top. This results in a sequence of images which are referred to as optical sections that can be realigned in three dimensions. The series of images that my flowers died for, the realigned and stacked images, and the 3D reconstruction can be seen in Figure 4.

Perhaps spending hours a day staring down into microscope eye pieces has warped by view of the larger world: I see it for its pollen rather than its flowers, and for their bits and pieces of transparent invisible cells that we’ve learned to make glow bright, beautiful colors in order to learn about how it is they function to build that larger world.

Supermassive Black Holes

Drew Lierheimer is a 4th year Finance Student in the Saunders College of Business. This piece is aimed to educate students from grade 6-8 about supermassive black holes in a manner that will peak their interest to pursue the topic further.

I. What is a Supermassive Black Hole (SBH):

As we learned in our last lesson, (the life of a star) we discovered that at the end of their life, higher mass stars tend to collapse. This happens due to a characteristic of the star, which exhausts every last resource needed to function. Once this is done, gravity takes over and forces the star to implode. All of the matter in the star condenses into the smallest (densest) size possible. Sometimes stars will get into such a dense size that they will transform into a black hole. A black hole functions similar to a funnel, the dense mass that was created by the collapse of a star has a strong gravitational pull, which is stronger than the speed of light (the fastest speed capable). As a result, once anything is in the gravitational pull of a black hole, there little hope for its escape.

A supermassive black hole has the same characteristics, as a regular black hole, the only difference, is that a SBH is denser. Due to its density, the black hole has a stronger gravitational pull that allows it to swallow up more matter out into space, which will result into the SBH to continue to gain mass.

There are two ways in which a black hole can transform into a supermassive black hole. One way is to have two black holes collide into each other. This collision would cause both black holed to merge together and create a black hole with enough mass to be one hundred thousand times that of the sun. This collision usually causes all matter around the SBH to be ejected out of its gravitational pull, which means that there is no matter for it to continue its growth resulting in a dormant SBH.

The second way happens when a large black hole or a stellar black hole is formed from a large star collapse. This collapse gives the black hole a mass of three to ten times that of the sun. This stellar black hole then pulls all matter around it into its core, until it has become dense enough to be called a SBH.

The following exercise is aimed at visualizing the basic concept of how a supermassive black hole functions in out universe.

Class Exercise #1: Supermassive Black Hole Visual Concept

Supplies Needed:

· Spandex cloth (10ft X 10ft)

· Dense ball 1 in to .5 in diameter (steel/lead)

· (10) Less dense balls greater and smaller in diameter to dense ball (ping-pong ball, tennis ball, gum ball.etc.)

Instructions: (For teacher to explain)

· Have students line up around the spandex cloth, each holding part of the 10X10 piece at chest height until it is stretched flat between the students.

· The teacher will place the dense ball on the spandex and explain to the students that this acts as the supermassive black hole.

· The teacher then rolls less dense balls by the crater that the dense “ supermassive black hole” ball made.

· Students will watch the path of the less dense balls alter, and eventually fall into the “supermassive black hole”

· As more balls fall into the cave, it will become deeper, which signifies the “ supermassive black holes” gravitational pull is stronger and the SBH is denser, meaning it is harder for the balls to ever leave the hole.

· Students can take turns rolling balls past the “ supermassive black hole” so they can have a better understanding of the principles.

A supermassive black hole has an incredibly large amount of mass, in extremely small volume. This means that the particles are packed extremely tight together. To put it into perspective, the sun, which is in the center of our solar system, has a gravitational pull, which keeps 8 planets revolving round it. A supermassive black hole has few as one hundred times the mass of the sun, in something the size of a pinhead. A SBH is typically found in the center of a galaxy floating around waiting for something to run across its path.

There is a supermassive black hole that resides in the middle of our galaxy (The Milky Way). Its name is Sagittarius A, and it 4 million times denser than the sun. It is a dormant SBH, which means that it is emitting energy that is weaker than SBH’s of comparable mass. Recent studies have shown that Sagittarius A was just as strong as any comparable mass SBH 300 years ago. Scientists don’t know for certain why Sagittarius A has gone dormant, but they assume it is due to a recent (300 years ago) major outburst of energy.

II How We Detect Supermassive Black Holes:

Supermassive black holes can’t be seen since they do not emit the energy inside of them visually. Even though they are “invisible” Scientists believe that they can see a distortion in the visual plane where a SBH is known to be. It is interesting evidence to support the power that a SBH has.

In a more scientific approach, professionals will look at telescope photos of galaxies or areas of high activity and analyze the movement of matter in that activity. Evidence of a swirling effect around a central area is one way of discovering where a SBH is. This swirling effect can create accretion disc & jets (which you will learn about in section IV) Another way scientists find SBH’s is by using an X-ray telescope to measure the amount of energy that a certain area in the universe is emitting. Typically, supermassive areas of energy are correlated to supermassive black holes, since the only think we know that has enough mass to emit such massive amounts of energy is a SBH.

III Inside a Supermassive Black Hole:

Most questions directed towards SBH’s inquire about what is inside. The quick answer is no one knows, and will ever know. What scientists do know is that no light can escape once inside of one. Since their gravitational pull is so strong it distorts the light, which disallows any light to pass through the event horizon.

The event horizon is the point at which there is no return for matter being sucked into a SBH. It is the point at which an outside observer can no longer interact or see any of the matter entering the black hole. At some point the object being pulled into the black hole is brought in at a speed faster than the speed of light, which means light that the object is displaying to an outside observer is not fast enough to “out run” the force pulling against it so it loses “contact” with anything outside the SBH. This being said, to an outside observer, may think they are seeing an actual object on the outside of the SBH, but in actuality it isn’t there. Since light only travels at a certain speed, It will take a while for an outside observer to notice when the matter has been captured by the SBH.

Once an object makes it to the event horizon, it is instantly inside of the SBH. Since the size of the SBH is so small and dense (the size of a pin head) there is nothing to see inside of it. In essence, “there is so much stuff inside a black hole, that there isn’t anything”. This means and everything that enters the event horizon of am SBH does not exist anymore. This is a strange concept to wrap your head around, but if you think of something that can swallow whole galaxies that are millions of light years in size into something the size of a pin, then you can think that there is no room for anything, and that matter must not exist anymore. There is not physical proof that this is what happens, but it is what scientists have calculated should happen inside a black hole.

IV Accretion Discs & Jets:

The pull of some supermassive black holes is so extreme; it rarely pulls any matter into its “core”. Since the SBH acts as a funnel, it is constantly swirling large amounts of matter around at a fast pace towards its small entrance. A combination of theses elements leads to the creation of an accretion disc. This disc is made up of space matter that is trapped in limbo waiting to be lost into a black hole forever. At some points the amount of matter that enters the back hole at one time is too great that the SBH’s “spits” it out back into the universe. This action will be seen as a jet shooting from the center of the SBH (see exhibit 1 in appendix)

The following exercise will help illustrate the concept of an accretion disc and the jets that form around a black hole.

Exercise #2: Accretion Disc & Jets Visualization

Supplies Needed: For Each Student

· 1 inch diameter foam ball

· 2 pieces of 100 lb. card stock

· 1 pair of scissors

· 1 roll of scotch tape

· 1 bottle of Elmer’s liquid glue

· 1 drafting compass

· 1 ruler

Instructions:

· Take the scissors and cut the foam ball into two equal halves.

· Take the compass and draw a 5-inch diameter circle on both sheets of card stock.

· Cut both circles out of the sheet of card stock.

· Take one circle and glue it in between the two halves of foam ball (make sure the flat sides of the halves are on either side in the center of the paper)

· Take the ruler and draw two perpendicular lines through the center of the second circle cut out (so it looks like A big +).

· Cut along the lines that were drawn, to make the circle into 4 separate pieces.

· Take one of the four pieces and curve the two straight sides into each other and fasten them with the scotch tape. (This should look like a cone)

· Repeat previous step with a second cut out.

· Fasten the two cones to each end of the foam ball (the curved side of the ball)

The end result should look like this:

This model should help visualize what happens around a SBH when matter is being attracted. You can see the disc around the ball acting as the accretion disc and the cones on the top and bottom of the foam ball act as the jets that shoot out from either end of the SBH.

V. Function within a universe:

A supermassive black hole can’t be characterized as having a specific purpose, like you would assign to a toothbrush. It can however, teach us lessons about fundamental forces within our universe.

Since the discovery of SBH’s, scientists have developed technologies in order to explore more about SBH’s. For example the investigation of gravitational waves, which scientists believe are created due to black holes, has led to the development of a device called an interferometer, whose purpose is to help sense and analyze the structure of gravitational waves.

VI. Conclusion:

Supermassive Black Holes are amazing in their functioning principles. They seem to go against everything that we know about physics, but still the proof of their existence is apparent. Hopefully up and coming scientists like yourselves will uncover the next discovery in supermassive black holes, which will bring us closer to fully understanding what a supermassive black hole is.

Appendix

Exhibit 1: Black hole with accretion disc and jets.

http://www.dailygalaxy.com/my_weblog/2009/01/supermassive-bl.html

The Chips Are Stacked

Chris Lockfort is a fifth year student at the Rochester Institute of Technology studying Applied Networking & Systems Administration and Computer Engineering. This piece about emerging computer chip manufacturing methods is intended for the "gadget-loving-geek" audience, typical to someplace liked Wired or Slashdot for instance.

The Chips Are Stacked

How the Move to 3-D Chip Technology Changes the Processor Game

Chris Lockfort

Smaller, more battery-friendly cell phones. Cooler, more powerful desktop computers. More complex video processors. A gadget revolution is at hand.

Simplified, the computer chips of today are manufactured as a two-dimensional plane of transistors and interconnecting wires, all printed onto a piece of backing material (substrate) via a complex and delicate manufacturing process. This process is reaching its limits in several areas; in order to keep increasing the number of transistors per chip, chip manufacturers have been making smaller and smaller transistors. This has its side benefits; it takes less power to switch these tinier transistors. However, this planar approach has its issues; as the interconnecting wires between these transistors become smaller and smaller (only a few atoms thick in the latest revisions), there is more electrical resistance, and therefore, more heat is created, which can offset any heat savings garnered by needing less power to switch the transistors themselves. With transistors approaching their minimum possible size, it will become increasingly difficult to increase the number of transistors per chip in the future.

The solution is as deceptively simple as it is elegant; thinking three-dimensionally, one can stack multiple planes of transistors on top of each other, and connect them together. This design concept solves many of the problems with the previous architecture.

Some manufacturers are already taking steps into this area; in an early foray into the 3D chip making field, Intel will soon be mass-producing chips with a pseudo-3D architecture; all of the transistor logic will still be on the same two-dimensional slice, but a top layer is added to provide additional interconnect wires, in a bid to reduce heat output through lower electrical resistance. Memory manufacturers have been doing chip stacking (the process of stacking these multiple planes of transistors on top of each other) for some time to achieve the densities required for newer chips’ memory capacity.

While these applications have entered the market, they are not without their issues. The manufacturing process is delicate enough that in each wafer made, a few chips are expected to fail. This problem is compounded when multiple layers are used; if each layer has a chance of failing, then the chance that at least one part of the entire chip will be bad is multiplied, so even relatively high yields (90%+ good layers) can result in three-quarters of the final products having to be thrown out, which is obviously an expensive endeavor. And, while having more transistors per square inch of chip area is a good thing, this means more heat, and less area to dissipate it, requiring additional cooling, and bringing with it a slew of new problems.

There are many problems with this new chip stacking concept, but, pun not intended, the only way to go is up. As unrelated transistor switching problems have required a paradigm shift to CPUs with many slower cores, rather than a single fast CPU, there has arisen an electrical problem with interconnecting on-chip memory between these CPUs so that they may share data. Electrons must take a very arduous stop-and-go path through the huge field of on-die memory, much like a wave overflowing many locks on its way to a town, and by the time it reaches the processor logic, it is full of turbulence and missing most of its original push, an analogue to electrical properties of greatly increased capacitance and inductance.

There are high hopes for the technology going forward, with hopes for applications in creating even lower power chips, both via using multilayer technology for resistance reduction as Intel is currently, and by using the extra vertical space to scatter voltage regulators throughout the chip, the computer engineering equivalent of the plumbing practice of installing pressure regulators every few floors of a high building, so that the pressure required to reach the top floor does not cause poor lower-floor residents with jet-stream sinks and those at the top with barely a dribble. Another hoped future application is for memory much physically closer to the processing pipeline, both reducing the electrical problems described above, as well as reducing the latency required to access this memory, which should result in faster-performing processors.

Works Cited

Edwards, C. "Doing the 3D chip shuffle." Engineering & Technology (17509637) 6.9 (2011): 82-85. Business Source Elite. EBSCO. Web. 25 Oct. 2011.