Cait, Entry #2, Massacring Fish

This past week I learned how to fin clip fish. This procedure is done by using a razor blade in order to remove the tail from the back of the fish. Keys to fin clipping are to make sure the fish is fully anesthetized (using a solution of a chemical called Tricane which the fish swim in until they fall asleep), because if they are not completely knocked out they will squirm and jump as you attempt the first part of the cut. I learned this the hard way when my first fish began to wriggle after I had only chopped half of his tail. Another key to fin clipping, is to make sure the fish do not die, either by sleeping for too long in the Tricane or by chopping to far up the tail to where you cause the fish to bleed out. I felt morally wrong chopping of the tails of fish who had done no wrong to me, but I learned that a zebra-fish tail has the ability to grow back, and many compare fin clipping to clipping your nails. Also, the results of fin clipping provide a great amount of information in the project my grad student and I are working on.

These fin clips contain DNA from the adult fish. We extracted the DNA by placing the fins in ethanol and then using an enzyme called proteinase to break down the fins. After we extracted the DNA, we performed an HRM analysis on it. HRM stands for High Melt Resolution, and it works by having two different fluorescent binding proteins. One protein when bound to Wild Type DNA shines red, while the other protein binds to mutant DNA and shines green. When the fish are Heterozygous a mixture of the proteins bind causing a fluorescent yellow. The HRM machine looks to see when these fluorescence tags stop shining, and that allows the machine to identify when the DNA has begun to denature. These results allow us to figure out which fish are carrying for mutant alleles.

Another skill I learned in the lab this week was that zebra-fish must die twice in order for it to be humane. Fish are killed for many reasons, they are sick, taking up too much space, or are too old. Ben and I had to clear out tank space in order to raise new fish and this caused me to become very familiar with the fish death method. The first death is done by placing the fish in ice cold water, causing them to freeze. The second death is then placing those fish into bags and putting them in the freezer to freeze more.

Death #1Death #2                                

Aisha Kumar Entry #3 Staining, staining, staining!

This week i stained more mouse brain cells, but looked for different parts of the brain. We stained for dendrites, neurons, pericytes, astrocyters, blood vessels, and microglia. We used about eight different anytibodies (primary and secondary) in the process. In monday, Amy taught me how to use the microscope they have to find good images of the parts of the brain we were looking for, and to capture the images. She taught me how to recognize the hippocampus, and helped me understand what each antibody stained for. I had to present my findings to my PI at the lab meeting, so Amy helped me put together a power point with all of the images and the information. Below are some of the best images we got. The first image is focused on the hippocampus. The second shows neurons and astrocytes, and the third one shows neurons and axons.

The second set of staining i did did not turn out well because we stained the vessls and dendrites in the same color, so it was hard to tell them apart. One of the anytibodies also did not seem to work, because we could not seem to decipher any tubules that we stained for. I am most likely going to try to do this staining again.
I was also able to look at and disect a sheep brain that they had in the lab in order to visualize different parts of the brain. They helped me cut around it to find the hippocampus.

Next week i hope to do more staining, and look at different parts of the mouse brain. I will also hopefully start to cut more of the brains on the cryostat

"Hello" is Ugandan for "Hello"

"What? Where's he doing it?"

Hello everyone! This will be my first entry for the first week of my internship to Uganda (don't know where that is? That's totally fine, I didn't either. Just see my location!)

"Wait what's he doing?"

      So, my internship over the summer (2 months) isn't exactly "hard" scientific research, as some may have known. I'm working of an American NGO called PVI, which works mostly in Uganda. Their work centers around the concepts of media advocacy and "media innovation". From the general theme of "media innovation", the NGO divides into roughly three separate-but-connected parts: distribution, production, and research. Dr. Paul Falzone is the founder and director of PVI, and over four years he has worked to expand all three arms of the NGO. Thus, PVI now has dozens of different projects, in all three arms, running all at once. Since my official internship is to be Dr. Falzone's assistant, I'm spending the next 8 weeks shadowing, learning the ropes, and working in all three arms of the NGO.

My first week...

        Kampala (that's Uganda's capital) was pretty hectic and definitely not for the faint-hearted. There were motorbikes (boda) and cars driving everywhere (not to mention they drive on the left!), which makes it all the more thrilling to walk outside. Thankfully, my humble abode is only about 20 minute of walking to the office so I can go back and forth pretty quickly. Every morning for the first week, I went to work at 10am, and left whenever I was finished with my work (about 5-6pm). And for the first week, I was tasked with mostly smaller stuff (fixing reports going through legal documents, reading up on PVI's current research project), but I also had a taste of most of the things going on at PVI. PVI itself is a small operation; the office is actually in a residential compound, which actually gives it, very much, a start-up-like feel (we have 4 rabbits and a tortoise as pets).
       My first day, about an hour into the job, I shadowed a meeting with Dr. Falzone and the research team. PVI was chosen by Planned Parenthood Global (PPG) to carry out preliminary research, concept design, and concept testings for a future youth sexual reproductive health campaign that PPG and the Bloomberg foundation is launching in Uganda and other African countries. I didn't know about the project beforehand, and was totally caught off guard when research jargon and acronyms were flying across the room at an unimaginable pace. The research manager, Dr. Rachel Clad, sensed my dumbfounded-ness and tried to go slower and decode the acronyms for me (unsuccessfully, though.) So that was my ice-breaker with the research arm. Over the week, I asked Dr. Clad for more reports and reading on the PPG project. She also gladly gave me a one-on-one run through of the project which certainly helped a lot. I still only shadow research meetings, for now, but I have a much better understanding of the project and where it's headed. One particular meeting that stuck on my mind was when the team spent a lot of time going back-and-forth on the semantics of their surveys. And the talk that came with that, about word perception, connotations, charge (positive/negative), was very interesting.
    My second day of the job, I was a production assistant for PVI's news program "Newz Beat". I got to work with the talents, see how production worked, and set up the brand-new teleprompter system. Newz Beat is a youth-oriented, "rap news" program where the rappers raps out international and domestic news stories. Newz Beat is aired on a popular free-to-air channel, NTV, during prime weekend slots, and has recently received 2 Telly Awards from the US.
  So my first week was comparatively light, though there was always work to be done. On the weekend I went on a motorbike tour of the city (the city center, let just say, is a lot different than my expat-filled neighborhood), Stay tune for next week (for those who are reading all of these posts)

Kampala city center (The "Taxi park", great place to survey random people for research, really!)

Alex Larson, Entry #2, Time to Work

  Commuting in to New York everyday has really started to take a toll on me. Every morning I wake up at 6:20 to make a 6:55 train which brings me into Newark at 8. From there I have to take another 30 to 40 minute long path train to get to Greenwich Village. So in essence I have a two hour long commute once walking is factored in. The first week I didn’t mind it that much, the hustle and bustle of Newark and New York was almost fun, now it has become more and more boring. Still, being in New York, the hectic city shows you something new every day and being in the city is a very worthwhile experience in and of itself. I am also one of the first ones to get to the lab every morning. I would be very glad to come in later; only problem is that after the 6:55 train there isn’t another one until 9:15, which I did take one time and by the time I got to New York I was the last one into the lab, which was not fun.

            Right now we are just about wrapping up my mini-project on the different types of buffers. We were able to correctly predict several things from our hypothesis but there were other areas that were not correct. For example, the Sodium Borate buffer is able to withstand much higher voltages without heating up, however, when SB was ran parallel to TAE buffer there was no increase in the speed of band migration across the gel. Also, in general, the bands of most of the ladders and samples we tested came back more pronounced and sharper in the Sodium Borate buffer. As for Lithium borate, the first test proved that the solution heats up very fast under high voltage and therefore is not going to satisfy our lab’s demand for quick and accurate gel electrophoresis. We also tried staining the gels using SYBR gold, a ‘cousin’ of SYBR safe used in biotech, through washing it onto and over the gel after being run, and loading it into the solutions on each well before it was run. The better approach was by far loading it into each solution first, and then loading that solution into the wells. From this method, we were able to reduce background staining while providing sharper clearer bands to read overall. I might actually be presenting this to the lab at our next lab meeting, wish me luck.

(Print out of the Gel results: Left LB buffer, Right TAE buffer)

            I am also in the beginning stages for my real summer project. We are working on a new technique called DASH or Depletion of Abundant Sequences through Hybridization. It is very good for sequencing the RNA of specific strains of flu as well as for characterizing the other types of microorganisms (specifically in the respiratory and digestive tracts) during periods of influenza infection and periods without it. For example, if our lab wants to determine what species of bacteria live in a healthy human respiratory system, DASH is very helpful. We know that we can determine the organism by looking at the variable regions in the DNA gene that codes for ribosomal rRNA. We can do this because that gene is conserved throughout basically all organisms, and most of that DNA (16S gene in prokaryotes) is the same across all organisms except for small regions called variable regions, which functionally do not do a whole lot. We can use DASH (through usage of restriction enzymes and/or CRISPR/Cas9) to eliminate all the DNA that is constant, leaving just the variable regions. We then amplify the variable regions using PCR and sequence them. We can then compare them across databases and determine what species of bacteria were present. In short, DASH specifically is very good at making sure we are not amplifying the wrong regions of DNA/RNA and allow us to more accurately isolate the genetic material we want.

(Basic Diagram of DASH)

  

Nicole Trovato, Entry #4, Starting Over

Slides that did not work :(

Today is officially the halfway point of my time at the lab, and unfortunately it is also the day I restart my project! After looking at my slides with the ConFocal microscope, it appears that the staining with CGRP and synaptophysin did not work properly. This could be for a number of reasons, but for now I am going to redo the same process with 5 micron slices instead of 60, and with 17 and 21 week old lungs instead of the 15, 16, 17, and 18 week old slides. Hopefully after these new slides are done it will become clear what the issue with the original slides was.

Cooling the new slides

Aside from the first slides not working out, things have been great! I have been reading a lot of articles in my free time on neuroendocrine cells in lungs and have also been watching Emma take pictures of her slides. Her most recent slides look really great under the florescent microscope! Denise has also had her two twin boys with her in the lab, so it's been fun to have them around :)

Nicholas Massenburg, Entry #2, Non Stop Quantification

Things have picked up a lot since last week.

My Post Doc Dan's health has finally picked up considerably, and he has been able to mentor me much more efficiently. He was able to explain the significance of our project to me in deeper detail, and I am very excited about where our results might take us in the field of Biology and Medicine. Dan and Cagla, the second in command at our lab, have made considerable gains in their research using Cinnabarinic Acid as a protective agent against HIV induced neurodegeneration, and from those gains, I have been tasked with quantifying the data received to see what it's significance is. I have also been tasked with a series of RNA extraction jobs (something many research scientists never approach because of its difficulty and the sensitivity of results) and PCR of DNA extract to amplify it for further results. These have involved the STC-2 gene I mentioned in my last entry, which we hypothesize increases in expression in times of cell stress due to the increased presence of Cinnabarinic Acid (also as a result of cell stress). In other words, we believe the amount of STC-2 gene expression that occurs, the protein product of which we have observed increases cellular protection, is dependent on the presence of Cinnabarinic Acid.

I, specifically, have been using cell imaging computer programs to create Macro templates from cell culture images, images which include astrocytes, specifically the presence of the GFAP proteins characteristic of astrocytes which are stained in red, MAP2 which is stained green to identify whole neurons, and Dapi, which is stained blue to identify nuclei. In deducing the quality of the image, large blotches of red indicate Astrocytosis, a prcocess that occurs in response to high levels of cell stress to induce combative mechanisms. The presence of these large red blotches in imaging may indicate a culture that has been exposed to toxic agents during experimentation. Other indicators of toxic exposure include large patches of blue dots not coalesced with surrounding green. This indicates death of the cell due, leaving behind only remnants of the nucleus and other undetected organelles.

My lab bench, where I do most of my bio technical work everyday. The computer for imaging is on the other side.

Using all of that complicated information, we hope to create a feasible track for the future of the project to developing a potential medication using STC-2 or Cinnabarinic Acid, which would be tested on animal subjects before moving to trials in human HIV-associated neurocognitive disorder patients in the next 5 years to a decade. Though I will have long left the lab by then, I am really excited that I will have been able to push such an important project in the right direction.

My lab is also very social, and I have made a lot of great friends, especially with the undergraduate students who are doing similar work. We often times go out to lunch as a lab, and have made it a tradition to pick a neat restaurant in the area and treat ourselves on Fridays. We've also planned a lot of other cool bonding activities like Karaoke and bowling int he next few weeks. I did not expect to come to the lab and develop friendships, but I now realize this will become a very important part of my summer experience. Because everyone remains focused together on the same goal of eradicating the existence of HAND, and potentially HIV, when it is time for us to have fun, we are always ready to socialize and remain a tight knit community.

Another great part of the lab experience has been our hour to two hour lab meetings every Thursday evening from 3-5. Here, I am able to listen to practiced and renowned Pathologist and Neuroscientists who do not work in my lab discuss their expertise. This is also the place where I have been able to show off some of my own Biology chops, however rudimentary in comparison. My associates have been very helpful in giving me a better understanding of the other areas of research that are presented. I have often times found myself giving people feedback on their presentations, constructive or otherwise, which I hope has been helpful. I plan to give a lecture of my own in a few weeks on my work with CA and STC-2, which will be presented before the chair of the Pathology Department (My PI) and the chair of the Neuroscience department.

Things continue to be great for me, and I cannot wait to see what the rest of the summer has in store.

Daisy Fang, Entry #3, Pick up the phone!!

After the third week, I have gotten much closer with the undergraduate RAs in the lab. In the beginning, I was worried that I wouldn't get to know the lab members as well because everyone is on their own schedule. People bring their own lunch and eat whenever they have come to a good stopping point. However, soon I realized that the worrying was completely unnecessary.

I have been going to a lot of children's houses for testing appointments lately, usually with an undergraduate RA. Although the car rides are often longer than 30 min, they also give me a chance to get to know the undergrads individually. We talk about college life, the classes they enjoyed taking, good restaurants and shopping areas in Boston, and a lot of random topics.

I made most of the calls in a small room so I wouldn't disturb other lab members as they worked

Last week was a bit hectic for me, as Jill and Alessandra, the only two other people working on the El Sistema project, were both on vacation. My job was to go through a long list to recruit parents into the study through calling and emailing, and schedule testing appointments. Color coding the list and leaving notes after each call is crucial because we would normally go through the list at least twice to make sure we get a response from each family. We want to maximize the number of participants that we can recruit, while not annoying the uninterested parents. Although calling and leaving voice mails sounds could get tedious, it is a really rewarding experience. We did end up recruiting a lot of families, which the cohort 2 control group desperately needed. It was also really cool that I had a chance to do what normally would be my undergrad RA's job, and I was really glad to help in the recruiting process.

Boston Public Garden

The past weekend I also got to explore the city a little more. It's so hard to believe that I have already passed the half way point!

Danny Kim, Entry #2, Third Week and MATLAB

Hellos fellow Peddie EXP students,

My third week in the lab went rather quickly, and I started to feel more comfortable working in the lab. On Monday, Mrs. Terhaar visited my lab, and I had to abandon her for over an hour because of the lab meeting in the morning. I got a little shout out from my research coordinator for finishing the data entry for the Dup15q syndrome in the national database.

Until then, I really did not have a substantial project that I was working on. Luckily, Mrs. Terhaar came in clutch because we had a meeting with my research coordinator, Scott and my PI, Dr. Jeste. I decided to work on eye tracking, which is a process to measure eye positions and movements, for the diagnosis of autism. This would require me to learn MATLAB, which is an essential program in many areas, so I'm killing two birds with one stone (yay!).

Starting from Tuesday, I was working with Carly, a college student who was also working in the lab, to learn MATLAB. We had this handy book that instructed us through different methods. And currently, I am working my ways through the program to master it.

I had a day off on Friday because my research coordinator had to go to a conference out of town, so I had a chance to rest a bit and catch up with my parents. All the members in the LA squad had a chance to go to the Venice beach together and enjoy the summer vibe.

I can't believe the third week is already gone, and we met the midpoint of our lab experience. I realize how fast this is going and should value every second more. Have fun guys :).

Jay Swarup, Entry #1, Making tablets!

My first week at the Ramachandran lab at Rutgers University has been hectic, but fun! The lab is a chemical engineering lab on Busch Campus. My first day was a bit uneventful because the lab ordered materials for the experiment we will be doing. But, I got to be familiar with the place and also meet the folks that work in the lab. While I was with the group, they showed around the campus, and we decided to eat lunch in the Busch campus center. Advised by my peers, I chose to eat a great slice of pizza.

                After we went out to eat, I started to ask the graduate students what they were doing for their work. Half of the students were doing experiments and the other half was focused on modeling raw data. Because the parts were still being ordered for the experimenters, I decided to learn what the coders do. Modeling is very different than what I expected. It is mandatory that you know both MATLAB and excel because all the code is written in MATLAB and some computation is done using excel. Because an undergrad who is familiar with MATLAB is also interning in the lab, we decided to try and model a function. It was very difficult, but when we finally got a good curve, it was very satisfying. Obviously the graduate students helped us a lot, but it was still cool to see a finished product. 

                After our parts came in, though, we started doing more experimental work. Professor Ramachandran gave us a project to work on that involves making tablets and measuring the uniformity of the active pharmaceutical ingredient in the tablet. Making tablets was definitely the best part of the experiment. In order to make tablets, one must: sieve the powder, then use a granulette to vacuum a amount of powder to then drop in a tube. After this, the tube which contains the powder is then sent into an instrument with a certain force, and the tablet is extracting from the tube and ready to be used! The tablets I made are below:

  

The instrument used to make the tablets is below.

Our first step was making the tablets, which is complete. Now, we will be finding out the uniformity of the active pharmaceutical ingredient in the tablet. This will be done using the raman spectroscopy. Can’t wait to start!

Emmy Wang, Entry #2, More Preparations

I'm now beginning my third week here at the lab. I've been continuing with the staining but instead of just cutting of the antenna and inserting the dye crystals through there I now cut open the head of the moth and apply the dye directly to the brain. Such a procedure has proven to be quite challenging, especially since the brain is hard to distinguish from the other components of the head and specific regions of the brain are even more difficult to discern. I'm using two different colored dyes on the two antennal lobes which respond to different wavelengths under the light microscope:

Since I will have access to the confocal microscope in August, for now I am trying to get as many preparations done as possible. The procedure is quite demanding since at every step I have to be careful not to destroy the very small brain. This is especially difficult when I am trying to move the brain from a glass bottle of ethanol onto the microscope slide with a toothpick.
Right now I am the only one in the lab working with the moths, so I am also responsible for insect care. This involves transporting the newly hatched moths into cylindrical containers. It is fine for the most part but if the moths are feeling especially excited I'll stick them in the fridge for a bit to calm them down.

The three masters students that were in the lab have all had their exams and left, so right now the lab is quiet, but the new masters students will hopefully be here in August. Last Tuesday Dr. Berg invited us all over for dinner which was fun, especially to be able to talk to the lab members outside of the lab setting. I'm looking forward to the rest of this week and then taking a month off while my lab goes on holiday.

Christopher Fu, Entry #2: Getting Started

"Hello World" on steroids (first half)

After a week of introductory chemistry lectures, I dive straight into the tough work: pseudopotentials for manganese and iridium, and possibly for elements 113+ as well. Granted, it's nothing close to the complexity of what the grad students and postdocs are doing--but since I'm having quite some difficulty absorbing the material, I like to tell myself that it's really hard so I can feel better about myself. With three days and a lot of YouTube tutorials from my boy SlideNerd, I've been able to create a crude code that can iterate through a set of input values into OPIUM, extract the data from the .log (log) and .rpt (report) files, and find the minimized errors within the non-local pseudopotential and transferability configurations. But cutting out all the fancy words, my code basically finds the minimum of polynomials (a technique I refined thanks to Dr. Cags and his Alg. II course). It works well when I tested it against the simple elements-- hydrogen, helium, etc.--but it's quite a bit inefficient when it comes to systems with more valence orbitals due to some issues with ghosts, cutoff energies, and more. Unfortunately, my target pseudopotential, manganese, has three orbitals; I've got quite some work left to do.

Outside of working on projects, the Rappe group holds weekly hour/two-hour meetings where members present their progress and plans for the next week. Although everyone is focusing on theoretical chemistry work, there are a lot of different branches--it's very interesting to sit in and listen to all the cutting-edge science that everyone is pursuing at the lab.

Outside of the lab, Joe and I have started to cook. Our first meal was fried eggs with tomatoes and steak stir-fry with tomatoes and onions. We plan on making a quinoa salad, steak, and butter chicken curry sometime soon. The weather here has been phenomenal, and Joe and I plan to take advantage of it with afternoon distance runs so we don't enter preseason out of shape ("The more we sweat in peace, the less we bleed in war" --Vijaya Lakshmi Pandit) .

Anyways, that's enough about me. I'm glad that everyone's having a good time, and keep up the good work!

--Chris

William Ma Entry #3, Getting started on my individual project

Three weeks really flew by. Half way through the lab, I have learned a lot from my projects. For the Meta-analysis, I have screened 35 articles and identified about 75 measures of self regulation so far. There are 15 people who are working on the same part of the project (identifying measures of self-regulation) with me. As you can see in the picture below, our productivity has increased drastically over the past couple of weeks. (The Cumulative Total is the number of papers we need to screen and the bar on top is the total number of papers). With this rate, we will be able to finish this stage of the meta-analysis project in three weeks, which is the time I leave. I'm proud of being on this wonderful team and I am also proud of what we have accomplished.

  

One thing that I didn't mention before about the meta-analysis project is that each paper is screened by two people. The answers are then compared to ensure validity. Any disagreements are settled through communications between the two coders and Dr. Sulik himself. If each paper was only screened by one coder, we would've finished this stage by now, but that would sacrifice the validity of the project, which is crucial in scientific research.

For CSRP, I am still learning data cleaning by watching a lot of youtube videos. I also spent some time last week looking for a website/app to allow assessors of CSRP videochat and sharescreen with participants who have left Chicago. Skype would not work since we are trying to make this as simple as possible for both the assessors and the participants (many assessors are the elderly who are not great with technology). After going through a couple of websites, I found one that's called Zoom that's free and easy to use. I then made a manual for both the assessors and the participants.

Now, my individual project. After discussing with Dr. Sulik, I have decided to research the ways that we can measure our neighborhoods' impact on us. As someone who has moved a lot and lived in many neighborhoods, I have always been interested in the characteristics of neighborhoods and how different neighborhood's can impact people differently. Therefore, in the next three weeks, I will set aside the meta-analysis and work on a literature review of the way people have measured neighborhoods as well as things worth noting when doing so.

John Bokman, Entry #2, Settled in

My desk in the Gabrieli lab

      These last two weeks have been great as I am finding my place in the lab and I am really starting to love it in Boston the more time I spend here. The weather is beautiful almost every day and the Charles river carries a much needed breeze right though the city. I am also beginning to adjust to city life and living by myself. Running in the local area has allowed me to scout out nearby restaurants and other stores fairly easily.

     Last week, the undergrads in the lab organized a reading group with weekly meetings and presentations. I was invited to join and in doing so I have met many of the members of the lab I rarely see otherwise. With over 15 undergrads and interns working under many grad students, and on countless projects, the lab can often feel disunified. The reading meets are a great way to bring everyone together and recognize our common goals in our research.

     As far as my work goes I have just started a new project in the past week. My mentor Kelly, a physco-evaluator for the lab, introduced me to one of her colleagues who needed someone to help debug a program that one of the past research assistants had written. The program was intended to sort and analyze survey data and then return it in a spreadsheet. I had to quickly adjust to Python so that I could start working with the program, which was beautifully written but contained a few major errors. I updated the code to new Python and I am almost finished filling in the holes in the code and cleaning the output up. I will be presenting the new program to my mentor on Tuesday and I hope she will assign me to more projects like this one during my remaining time in the lab.

Megan Gabruk, Entry #3, Third Week - Getting Even Better

This week was very fun inside and outside of the lab. Inside of the lab, I learned even more such as how to write a good CV. That was really helpful because it allowed me to organize what I have accomplished so far during my high school career. Also, I learned how to make a Facebook ad. It was more complicated than I expected, but I managed to understand how to create the ad. Along with that, one of the full-time RA’s taught the other high school student and me how to upload the data from the LENA device. The device records everything the mother says to its baby in order for the lab to be able to analyze every factor that is part of the study. My work continues to be focused on recruiting participants, finding funding opportunities, and finding references for a book chapter my postdoc is working on.

I continue to make more friends in the lab. It is very nice to have another high school student in the lab, so we can help each other with any problems that we encounter. We go out to lunch every day at the business school with another RA who is in college. At the business school cafeteria, we seem to be the only people in high school there. The RA in college is very kind and gives good advice on college. She goes to the University Chicago and gave me her honest opinion about the different aspects of the school.

President Obama was at Stanford later in the week. Unfortunately, the closest I came to seeing him was passing by the building he was talking in.

Outside of the lab, I have had a lot of fun also. Last weekend I went with my aunt who was visiting me to San Francisco and Pebble Beach where saw the 18^th hole. It was pretty cool even though I don’t play golf.

18^th hole at Pebble Beach

This weekend I met up with two friends, Gwyneth and Aditi in San Francisco. It was really nice to see some familiar faces. I felt very independent when riding the train in by myself. Once I figured out the schedule, it went pretty smoothly from there.

The Golden Gate Bridge

Oliver Crane, Entry # 2, Second Week - More Work, More Fun

My second week was far busier and generally harder than my first week here. My day to day schedule this week usually went  like this. Wake up at 8 and bike to my lab (usually takes 20 minutes) while trying not to get hit by car in LA traffic or take the bus (it takes a lot longer). After arriving at my lab, I would ask my post-doc whether there were any little jobs she needed done. These tasks ranged from cleaning the mouse droppings out of the operant chambers (the special chambers used in experiments that have levers which the mice press for drugs) to helping sort data on the computer. I then would take a short lunch break to enjoy my yummy homemade pb&j sandwich before helping my PI setup for an outreach program she is running for a short time which provides high schoolers an exposure to neuroscience. Helping out this past week with the program has been really helpful with refreshing my memory about all the various lab techniques we learned in biotech and with preparing me to do more in depth work in my lab. During the program (which ran from 1-4 pm) we reviewed pcr, qPCR, and other techniques while analyzing mouse brain tissue with massive amounts of CAG repeats (an indicator of Huntington's disease). Following the end of this program I would then take the bus home or bike back and then figure out what to do about dinner which Danny, Ian, and I have been taking turns handling.

Santa Monica Pier

There was definitely an increase in work during my second week however it was still quite enjoyable working in the lab. I have also become good friends with my post-doc, an Armenian woman named Ani, who graduated from UCLA a few years ago. On the weekend, Danny, Ian, and I went to the beach which was really nice and rode a few rides at the Santa Monica pier. The funnel cake I bought there was a huge highlight as was winning my first carnival game ever!

Eating Lunch at the local In-n-Out

Ian Loeb, Entry #2, The Grind

As my lab experience continues to further, I feel the increase in both workload and difficulty. Not only have I installed and began to get familiar with MatLab, but I am also currently trying to integrate the correct individual 3D brain images so that they highlight only the individual region being hovered over. Dr. Kutch has also asked me to begin to look at user interface, for example having a single click rotate the 3D image and a double click open the wikipedia link can be confusing, as if you click too quickly the wikipedia link will accidentally pop up. As a solution I've started looking into a click-hold or keyboard event that could trigger the wikipedia link. The updated chord chart, with live data and the correct individual 3D diagram is shown below:

As seen in the picture above, when the region is highlighted, there is no longer a place-holder image with every single connection mapped out, rather the correct connection pertaining the the individual region being hovered over.

Other than working, we've been going to the beach on the weekends, having numerous divine dinners, and just in general enjoying the California life. Danny and I even made a new friend, who you can see a picture of on Danny's first blog post. We regularly grab lunch together, and talk about our work and what we do each day. Mrs. Terhaar's visit was also lovely. She came around our individual labs and although it was a bit hard to communicate since I accidentally gave her the wrong number, we were able to coordinate and found her alright. I showed her around my lab, and introduced her to Dr. Kutch. She then took us out to a much appreciated free dinner with all the LA EXPers, which was very enjoyable. All in all, my experience has only gotten better, and more memorable.

Trevor Russo, Entry #1, Learning (with difficulty) about Point Clouds

            My first week at Carnegie Mellon University has been a mix of failure and adjustment. On the first day, I grabbed my bike, my laptop and some other supplies and rode over to CMU’s Newell-Simon Hall, home of the Robotics Institute. However, upon arrival I discovered that I was early by at least 2 hours, so I decided to read some papers that my grad student Venkat had sent to me. Of course, most of it was written in really complex robotics terms, so I made the best I could of it before I ventured down to my lab. After some time, I was joined by two fellow interns, Joe and Shivam, both college students. We went out to lunch, and after that I was ready to begin work. Venkat had given me the task of familiarizing myself in the Point Cloud Library, or PCL for short. This software allows for 3D object manipulation by breaking it up in to a collection of dots, or a point cloud. I worked for 6 hours reading overviews of the software, and then I attempted to create my own program through the tutorial. Unfortunately, the second challenge on the website was too hard for the initial go, so I had to learn how to use software called CMake, which creates crucial files that allow for said software to run. After a long day of asking many questions and progress, I headed home. 

 

My Workstation

The next few days were much more difficult than I expected. Being good at computers and knowing secret commands on Windows is one thing. However, the tutorials that I had been attempting got increasingly difficult, as I was asked to accomplish tasks that I had never encountered on a system that I have rarely used. The system that I use, known as Ubuntu, doesn’t run through applications. Instead, I have to type commands through a really complicated terminal system. Often, I would try and run the code that I had written or modified and instead of seeing the success indicator, some stupid error would pop up and I would groan in disgust. Other times, I would see something, not understand what it meant, and spend 2 hours learning about it so that I could. Coding is much more difficult than I had expected. To help smooth the process out though, Venkat has told me to write a summary of the PCL tutorials that I had been learning about so that he can check whether I am knowledgeable enough to proceed on the creation and manipulation of point clouds.

The AI Secretary in the Entrance of the Robotics Institute

In between this work, I’ve attended a couple of talks. The talks are incredibly complicated and thus difficult to understand the meaning behind them, but they have taught me a valuable lesson: that not all research is good research. The first talk I saw was presented by a British fellow at the Imperial College of London. The presenter talked about deep learning, which is when a machine uses data and trials in order to “learn” how to better accomplish a task. Unfortunately, his research applied it to picking up blocks with a robot arm, and in the middle of the talk one of the professors called him out for it. The professor explained that to throw out a process like deep learning for such an easy task was preposterous. Instead of breaking into a prestigious field of robotics by being one of the first to introduce deep learning to robotics, the man instead stood up there looking foolish.

Working with Point Clouds

Even though I haven't been able to explore next, Pittsburgh is still an incredible city. There's the Pirates, a beautiful park, 5 museums and of course lots of good food. So far, my favorite place to eat has been the Rose Tea Cafe, which is a takeout Taiwanese place about a minute's walk from my apartment. The beef and broccoli there is incredible, although I'm sure there's a catch to that somewhere. The nice thing about the city is that everything is within reach of a 5 minute bike ride, so getting to work and back is extremely easy. Now that I've settled in after my first week, I finally feel that my next week will be much smoother, both in coding and getting to do things around the city.