Megan Gabruk, Entry #8, A Wonderful Week Besides My First Goodbye

This past week has been wonderful along with all of the others. On Monday, I attended my weekly meeting for the BABIES project. Recruitment had been a little slow over the weekend, so the other high school student and I emailed the mothers’ groups again. Many of the participants are too young to be part of the study yet since they need to be six months, but the project coordinator did schedule many more participants for August, when they would be old enough.

            On Tuesday, Kate and I went over some statistics for different variables for her chapter on the Bucharest Early Intervention Project. I also went to the weekly RA meeting in which one of the postdocs presented on clinical assessments. We did an activity in which one person acted as the assessor and the other acted as the participant. The participant had to draw a path from number to number, counting up.

            On Wednesday, I finished working on the two E-Prime tasks. One is a dot probe task and the other is a morphing faces task. Both are most likely going to be added to the BABIES study in one of the sessions. I also attended Kate’s weekly RA meeting. We shared our highs and lows as well as talked about possible career options. The two best routes seemed to be a Ph.D. in clinical psychology and an M.D. possibly in psychiatry. With a Ph.D. in clinical psychology, people can be a clinical psychologist or a researcher, which both are interesting paths. Kate also suggested quantitative psychology because there are many job openings in that field.

            On Thursday, I worked on the Horvath clock project and put up more flyers. On Friday, I tested out the E-Prime tasks on the laptop the mothers in the BABIES study will be using, and it worked successfully. I also went out to lunch with the project coordinator and the other high school student. The project coordinator graduated from Stanford with a major award and is currently applying to medical schools. She is very nice and gives great advice. The other high school student’s last day was on Friday which was very sad because we had become good friends over the summer. Outside of the lab, I have been exploring Stanford’s campus even more and went up to the top of Hoover tower which has a great view of the campus.

David Alvarez, Entry #3: Weeks 4-5

Each week here is getting more enjoyable, yet sadly goes by faster as well. I've been paired with the other high school student here, Rodda, to run a series of experiments on a WebRTC test setup. These are similar to the experiments I ran by myself before, except that now we have a third machine acting as a monitor and capturing packets in the stream between the sender and the receiver machines. The data is collected by two different pieces of software; a built-in upload option on the test setup, as well as Wireshark. The data that we get from here we then plot in several charts by two different means. The first is using a built-in graph generator on the test setup that we helped create. This plots five different metrics for both the sender and receiver; data rate, resolution, framewidth, packet loss, and round-trip time (RTT).

The key components of our experiments; a sender (out of camera), monitor machine, router, and receiver machine.

Rodda and I also created a Python script that can generate graphs for some of the other metrics that we couldn't get from the built-in tool; throughput, retransmission rates, and packet length. We also have to save the .pcap traces from Wireshark that show all of the packets captured during the experiment as well as all of their properties, which are found under the RadioTap Header. Over the weekend, I added a feature to the script that can generate .xml files, just in case Bart or Varun want better plots and want to modify the code themselves. We've also added another feature so that cumulative distribution function (CDF) graphs can be generated as well. In essence, most of what Rodda and I have been doing for the past two weeks can be boiled down to doing about a dozen trials, then plotting the data from it and putting it into a folder for Bart and Varun to analyze.

Examples of the types of graphs generated

Outside of the work being done, everything's been good. A visiting professor from the Netherlands is leaving us today, so we had a celebratory dinner for him yesterday. Dr. Venanzi visited me last week and got to meet Varun and learn about what exactly I'm doing in the lab, and I got to have lunch with her, Will, Sharanya, and Alex. It was nice to see everyone and catch up with what they were up to. I'm officially on the home stretch, with my last day being only two weeks from today. I'm excited to wrap up whatever work I can and hopefully finish my time here on a high note!

Joe Yuan @ The Mason Lab: Post #4: Fütball

Oh god I'm only on my 4th post?

So, remember when the Euros where happening?

Well, maybe it wasn't the most memorable UEFA Euro Cup ever, but my experience of celebrating football (yes. it is football.) with my lab was one of the memorable bonding moments of my internship at the Mason Lab.

Since England was an embarrassment and got destroyed early on, and Wales managed to conserve their way to the semis, Dr. Mason, with her English and Welsh heritage, decided to take us all to see the game at 3pm in the afternoon, at a bar.

Here we see Dr. Nikki Mason in her standard dress code.

We were all excited and ready for Wales to kick Portugal and C. Ronaldo's butt, and the grad students were all over the Belgian beer at City Tap House. 

So. We lost. 

Oh well, the game was "Rubbish", and I guess the finals maybe more exciting with Ronaldo and the Portuguese squad. (Turns out CR gets his ankle twisted, and has to sit on the side lines. Thats what he gets for winning against the great nation of Wales.) 

But yes, back to the Lab. It was a slow week, with me doing more maxi preps of cCD19 plasmid and other important backbones that will hopefully last the lab the rest of the summer. And since it was a slow week, I deiced to stay another week to truly experience the frustration of research. Yep, so there goes my summer. 

Anyways here's some DNA concentration and purity data:

The computer software that shows your the nano drop readings.

The way this works is, you add your sample to the Nanodrop machine, and it analyzes said data, and gives your a purity reading in 260/280, and 260/230. These two values will tell you if your DNA or RNA sample is contaminated. And the ng/uL is obviously the DNA Concentration in your solution. So that's exciting that there's DNA in this one. 

And to add on to my last post, the cCD19 virus has been transduced into K562 canine cells, and now we are trying to determine if the CD19 protein is being presented on the surface of the K562s. The issue now is that the original plasmid we generated was missing a section of the cCD19 sequence because fellow lab member who is no longer here decided that region was problematic and cut it out. But now we don't know wether if that caused the proteins produced now to be non functional and not present on the surface of the cell. 

So we ran the K562s through flow cytometry:

Very interesting.

So, our results were fascinating. Because it seems our controls of K562 without CD19 actually bound better to our secondary than the K562 cells with CD19. It could be that the cells aren't functioning very well since they were just transduced. We are going to have to run this experiment a few more times with different variables to see what the actual problem is. But this is a great example of what excitement research can bring. It really is strange, and we're going to have to figure out why this binding situation is happening. 

But I believe, that we will get lucky. 

~ Joe

Final Week, Cait Barrett, Entry #6

 For my last week Ben’s undergraduate student came into lab. Her name is Karen and she is an undergrad at Penn. We had a lot to do so Ben had me helping to train Karen with certain things, like running PCR and HRM. Having Karen allowed for things to go much faster, and we got a lot done. In order to check our Nog1-CRISPR mutants we did a DNA precipitation. This process required us to “wash” the DNA by taking the liquid in which the DNA pellet was suspended and adding ethanol, and then other alcohols. These washes were done in order to break down free floating nucleotides and proteins that could cause our gel to be messy.

The first gel we ran.

 After this precipitation we ran the gel. Running the gel started with having to make the actual gel, and that included measuring out Agarose and 5xTBE buffer. To get the gel hot enough we had to microwave it, and then pour the mixture into the mold. Loading the gel took a short amount of time because both Karen and I were working at the same time. The results of the gel were not very promising, as bands that should have been the largest were faint, and ones meant to have little DNA were very bright. In order to deal with this we redid the precipitation. This was on my last day so I did not get to see the results, but what we were looking for in a successful gel was a split in the bands. If the bands had two bright bands they would be mutants. That is because these two bands would show that the DNA was cut. If only one bright band, the DNA would be wild type.

For my last week my lab had a goodbye celebration for me, mixed with a birthday celebration for a few of the lab members. There were four cakes, as the lab’s tradition is that you make a cake for the person whose birthday is before yours. I had an amazing time at my lab and was so sad to leave, but many of my lab members promised to stay in touch. 

The Birthday note written on the board.

The many really good cakes made. 

Danny Kim, Entry #5, Final Week at UCLA

This week was mostly focused on working on my small project with the eye tracking using MATLAB. The data I used to input were collected from patients our lab had. I myself went to many of these sessions and tests. We changed the raw data file of eye tracking into excel file in order for it to be able to be inputted into MATLAB. But before that, we only extracted the data we want which are the gaze point coordinates x and y. And to do that we created another folder in the excel file. Using diary, we kept the data that we got from running in the MATLAB and made a excel sheet for them. When on_screen data is too low, we disregarded the whole data from the child because, if the child is looking on screen for a short amount of time, other data are skewed. All the data were evaluated and recorded in one master sheet, which is used to create a visualization- a graph. 

While I thought analyzing and creating graphs were the easiest part of the project, it proved me wrong. I had to edit and revise over and over again. At one point, I was getting very tired of revisions and was starting to get agitated. Then, Scott told me how scientists must be careful and cautious of what they present. He told me that it was essential to be picky about even the smallest mistakes or changes that could be made. It was a moment I learned a valuable lesson as a possible future scientist. I worked on Saturday also for a final checkup for the presentation on Monday for the lab meeting, which unfortunately I had to miss.

Looking back at the six weeks, it passed much faster than I anticipated. I have learned so much over these weeks at Jeste Lab, not only about autism and eye tracking

but also about genetic disorders like Dup15q syndrome, MATLAB, and the attitude as a scientist. It's been a valuable and memorable experience, and I want to thank Dr. Peretz, Dr. Venanzi, and Scott for this great experience. 

Tanvi Dange, Entry #2, Plots on Plots on Plots

For the week of July 18-22, I did multiple things such as conducting another AFST on S. cerevisiae and shadow Lizzie on the flow cytometer, but the most engaging task this week was learning how to make a Job's plot. The purpose of the Job's plot is to determine the reaction stoichiometry for the formation of a metal ion complex between a metal and a ligand. For this week's Job's plots, I was studying the stoichiometry of Copper and Flu- TSCZ, which is one of Lizzie's analogues.

For the first Job's plot for Cu and Flu-TSCZ, we decided to make the highest concentration of metal/ligand 15 uM. That plot ended up looking excellent, but the concentration's were too low for drawing any conclusions, so the next day Lizzie and I decided to try again at higher concentrations.

This is what a Job's Plot should roughly look like: a pointy  mountain

The next day Lizzie and I decided to make the highest concentrations 60 uM in hopes of some data that we could use. But unfortunately, we were just having one of those days where nothing goes right. The point that was suppose to be the peak of our plot (The 5:5) just wouldn't fit the trend of our graph. We tried everything: we made multiple samples, made multiple blanks and switched machines but the point still didn't fit the data. There were still many other things to do in the lab that day, so we decided we would remake all the samples the next day and try again.

notice that one of these points is not like the others...

Finally on Friday, we scanned our new 60uM samples in the UV-vis machine and made a much more normal looking Job's plot. The Job's Plots taught me a very important lesson this week: science involves a lot of trial and error, and while it might seem frustrating to, for example, make the same plot over and over again, it's important to have patience because all of the work you do is important for the project, and the lab, as a whole.

Jessica Cha, Entry #3, Sweaty Mornings

My fourth week at the farm has come to a close, and I am already dreading the day I have to leave. I have begun to look forward to waking up at 6:30 and heading to the pastures to greet the horses and my PI. On the good days, the heat doesn’t really hit until around 10, so it is really peaceful and calming to work out on the grass.

These past two weeks have been a mixture of identifying plants, collecting herbage mass, caring for the horses, and chasing after geese to get them off the pastures. I have gotten better at differentiating between Kentucky Bluegrass, Tall Fescue, and Orchardgrass, although I am still working on identifying the other types. I am hoping that in the next few days, the grass will grow out more (it had been recently mowed), and it will be easier to pick out the certain characteristics that mark each type of grass. This past week, I also found out that the horses in each group have developed a hierarchy. I made the mistake of trying to groom the horse at the bottom of the totem pole first, which caused the lead mare to throw a slight tantrum. She also proceeded to continuously knock over the bucket containing all the brushes and picks. I found this amusing, but the horses seem to take the hierarchy very seriously (which I am now trying to respect).

In the upcoming days, we will try to gather grass samples from each pasture. We were supposed to finish this today, but the grass was too wet from the rain. If the hot weather persists, we will also hose down some of the mares to keep them cool. Normally, they stay cool in the shade, but the temperatures reached the high 90's one afternoon, and one of the larger mares was pouring down sweat. I am looking forward to the next two weeks at the farm!

Sharanya Entry #4-Week #5

It's hard to believe that I only have a week left at the Goes lab. This past week has definitely been the busiest and gone by the fastest. I may have mentioned this before, but there are two separate experiments happening at the same time and on Monday, my partner and I had to help the other group with their experiment since Monday is their sampling day and Thursday is ours. From 9 AM to 6 PM, I was filtering fifty samples of culture, each with one of the four different trace metals in order to collect chlorophyll measurements. My partner was busy using the FIRe to measure fluorescence. Something that I may not have mentioned before is that my PI gave us questions to answer for homework over the course of the experiment and finally we all had a little Q&A session where he asked us what the answer to those questions were. Some of them were pretty straightforward while others were a bit more challenging. Tuesday was also a bit busy since our group had to do cell counts five times for each bottle in duplicates. We found that the counts significantly increased for two of the four prey species. The "50 Noctiluca+Peridinium's" numbers jincreased from an average of 34 and 51 cells per 3mL of culture to an average of to an average of 53.6 and 63.4 while the "50 Noctiluca+Tricornutum's" bottle increased from 34 and 24 cells to 48.6 and 51 cells.

Cell Counts 7/19/2016

Cell Counts on 7/21/16

This increase shows that the Noctiluca cells actually have a preference for the Peridinium prey species which is also a dinoflagellate, and for the Tricornutum, which is a diatom species. This was different from what I thought would happen. I thought that the cells would prefer the Pyramimonas prey species since they are chlorophytes meaning they contain high amounts of chlorophyll. Wednesday was probably the least busiest day since all our group had to do was make seawater and prepare the labels for the next day's sampling. However Dr. Crider visited my lab and I had the pleasure of introducing her to my lab group and my PI. I also explained to her what my project was in the lab and also showed her some of the equipment that we used to calculate things like chlorophyll, ammonia, and fluorescence. We then Ubered our way back to city and met up with David, Will, and Alex for lunch at the Community Restaurant on 116th Street. 

Finally, Thursday was our sampling day. However this time we had to label forty-eight bottles for ammonia and another forty-eight for nutrients. So instead of only doing ninety-six bottles for samples, we actually had to sample double that amount! Initially, I was overwhelmed with the amount of work we had that day and was wondering whether we would finish all 196 bottles in time to catch the shuttle back to NYC. The first two duplicates of bottles contained Peridinium and Tricornutum respectively so we spent a lot of time (two hours) trying to get through those and not make any mistakes that might compromise our results. Fortunately, my partner and I realized that after the first two bottles, the rest were pretty easy since there weren't as many cells inside and they were significantly easier to sample. The easiest to sample was definitely the Pyramimonas culture since the cells were larger than most and also contained more endosymbionts. They were easier to spot during cell counts and were also easier to pick with the pipette. Concurrently, as my partner and I were sampling the other group was helping us by filtering our chlorophyll samples and operating the FIRe machine. Basically, we use the FIRe to measure fluorescence by measuring both MT and ALS measurements and adjusting the GAIN values. Normally, most of our samples fluctuate around a GAIN of 2,000. Those that contain the media (blanks) would have different GAIN's due to the lack of Noctiluca cells. For these values, we would only measure the MT value and ignore the ALS value on the monitor. In the end, we were surprised to finish only an hour late and were able to catch the 6 o'clock shuttle. 

Sadly, this week was the last week for doing any hands-on work and Thursday was our third and final sampling day. I have really enjoyed learning about and how to operate all of the different methods. This upcoming week will mostly be analyzing and organizing our data for our research paper and posters. While I will miss the hands-on experience of experimenting, I am looking forward to fully understanding and synthesizing the details of our data so that it is ready to be presented.

Trevor Russo, Week #5, 3D Modeling Time

This week was a little more frustrating than I thought it would be, but it also was a lot sadder than I thought. On Monday and Tuesday, not much happened, except for the ineptness of the software I was using. Insight3D, which was the OpenSource tool that was supposed to create 3D models on Linux. However, after spending days uploading image after image, only to see it fail after a 5 hour upload, I decided to choose only 20 select pictures. The software took this to mean that no common points could be found, and it once again failed miserably. Angered, I went to Venkat to ask if he knew of some other software that I could use, and he recommended Autodesk's Remake. This software had two benefits to it. Firstly, it was completely free, granted I sign up with a student license, and it additionally created full 3D models with texture and everything else I needed. After fiddling around with the software through Wednesday and Thursday, I was confident that coming in on Friday I would be able to create a full 3D model of a book easily. I left my computer on overnight to analyze the pictures, and went home. When I arrived to work on Friday, I found out that the windows partition of my computer, where I had been using Remake, was going through a system update. Ok, I thought, this seems pretty routine, so I'll just wait until it finishes. I'll put in a disclaimer here. My computer, in order to switch between Windows and Linux, is on a partition system. That means that whenever I boot up the computer, I can choose which operating system I want. The hard drive space is divided accordingly, and it usually is supposed to work. What I had found was that after the update, the Windows partition had somehow unallocated all the data on my Linux partition, effectively deleting it. I had essentially lost all the work I had done in the past five weeks. Luckily, the software genius Andrew had just gotten into the lab and we were able to rescue my Kinect Picture node with a flash drive and some downloaded software.

On the other side of things, this was the last week that Shivam, the intern from India, would be at the lab. Joe and I decided to make it an incredible week for him. We went out to dinner, got waffles and pizza and heaps of nachos every night after work, and on Thursday I threw for the two of them a tortellini bash. Basically we just made tortellini and curry and watched a bad movie. Another day, we went up to the top of the learning tower at Pitt and took pictures. And finally on his last day, we went out to the park to get sugar waffles and play catch before the park workers told us to stop. It was both really fun and really sad at the same time to know that one of my closest friends in Pittsburgh would no longer be working at the lab. When we returned to the lab, I said goodbye and departed home to watch baseball. Over the weekend my dad came over, and we watched a Pirates-Phillies game, with the Pirates winning 7-4. We also went out for some food and got a tour of the campus, which is about 10 times smaller than Pitt's. Hopefully next week will build on what has been an incredible time in this city.

Christopher Fu Entry #6: Pen(n)ultimate Week

This week was composed of a lot of data collection to form a database for the ridge regression analysis. We used bulk lead titanate (PbTiO3) and incremented the Z position of the titanium atom by 0.1 bohr, and performed DFT calculations on the system. We then plotted the change in total energy, total force, force along the Z axis, pressures, and charges of each atom in the system.

Charges

Z Forces

This coming week--my final week, sadly--I plan to work with Rob to create a set of data for random changes of position of each atom in the PbTiO3 structure. This way, we can use a regression on a more complex set of data to predict the charge density and other variables of  any possible orientation of atoms.

I'm pretty sad that I'm coming onto my final week in the group, but I plan on talking with my PI and seeing if I could continue to have access to the supercomputers; since the only tool needed to do the research in the lab is a computer, I can continue research on my project as long as I really want. So hopefully, this may not be the last week after all--I'll be able to continue my research from anywhere I want.

Megan Gabruk, Entry #7, Going by too Fast

Another great week has gone by so fast. I have learned even more because of new tasks I took on. On Monday, Kate was nice enough to take the time to drive the other high school student, a college student, and me around to put up flyers and hand out brochures. We went to local child care centers, the YMCA, and libraries. We have been doing better with recruitment because we contacted some mother groups in the area. Hopefully, this trip will help us get even more participants. Also, I made a chart for a book chapter Kate is publishing.

Brochure we handed out.

            On Tuesday, we had our weekly RA meeting and one of the Ph.D students presented on cortisol responses and early life stress. I continue to work on the Horvath clock and DNA methylation project I was given. I have to identify literature that uses the Horvath clock method. Also, Kate gave me four articles about what she studied at her previous lab and had me identify variables as well as make another chart.

            On Wednesday, Kate held her weekly meeting for her RAs. We always share our highs and lows of the week because I suggested it at the first meeting. We also discussed what irritability was (an emotion, mood state, temperament, or disorder). Along with the highs and lows as well as the discussion about irritability, we also went over more statistics, specifically we went over Zagat ratings of restaurants in Los Angeles to demonstrate how to use the program. The high school student and I sorted pictures to prepare for programming the dot probe task. We had to switch all of the adult photos out for baby photos, but we could not just insert the photos. So, we had to code for the photos.

            On Thursday, I coded for all of the photos and tested out the task to make sure it worked. I was successful in this. On Friday, I tested out the dot probe task with different biases and recorded those results. I also continued to identify potential funding sources by their deadline. Outside of the lab, I continue to explore Palo Alto, discovering new spots to run.

Gwyneth Tefft, Entry #5, Last Week :(

I can't believe how fast this experience has gone by! It seems like just last week I was getting moved in and now I'm leaving. Throughout my time here at Berkeley, I have learned more than I ever could have imagined about research and I truly do feel like an ant expert now.
The past few weeks in the lab have been spent working on Brian's project and doing data analysis. I never realized how bad I am with computers until I was asked to make a graph of the results from the desiccation trails on an excel spreadsheet. Of course Brian had to walk me through everything, and even then I got confused, but I eventually figured it out. We also got results from the SPME trials and it was clear that Argentine ants release higher amounts of iridomyrmecin when distressed compared to when no threat is present. This suggests that this compound is an alarm pheromone, but still further research needs to be done in order to prove this.

This chart compares the control SPME trails (non-agitated ants) to the treatments (ants fighting each other) 

I am sad to leave my lab and everyone I've been working with behind. One of the most valuable things about this experience has been being surrounded by such smart, motivated people. From listening to my grad students speak about interesting papers they've read, to discussing their newest projects they're working on, I have learned so much about the world of science! 

Julia Hu, Entry #4 -- My First Perfusion and My First Farewell

I wrote in my last two blog posts that my molecular cloning project is almost finished, but unfortunately, this week Felicia and I got stuck on the final step of the engineering of the construct hSyn-hM3D-2a-smRuby-V5-pA. In order to create this construct, we need to cut the vector, hSyn-ChiEF-2a-Venus, using the enzymes SalI-HF and XbaI in order to remove the ChiEF-2a-Venus and then later ligate the hSyn fragment with the insert, hm3D-2a-smRuby-V5-pA. We attempted but failed the digest of hSyn-ChiEF-2a-Venus twice using the two aforementioned enzymes, so we are currently troubleshooting to find the root cause of this issue. As of now, we have figured out that the problem is not with the enzymes. We think the problem is either 1.) the hSyn-ChiEF-2a-Venus DNA is contaminated or 2.) we are not digesting hSyn-ChiEF-2a-Venus DNA for enough time. Hopefully, we will be able to resolve the issue and complete the construct before I leave. 

This past Thursday, Felicia allowed me to perform my first perfusion under her supervision. As I mentioned in a previous post, a perfusion is the process by which we kill the mouse, inject paraformaldehyde (PFA) into the left ventricle of its heart so the PFA perfuses through the mouse's body and drains the mouse's blood, and extract the brain of the mouse to slice and observe it under an episcope. Although I have already shadowed many perfusions, I never realized how difficult they are as the graduate students and postdocs made the perfusion process seem so easy.

Firstly, I found that the mouse's skin is surprisingly thick and difficult to cut. Additionally, I found it difficult to determine if my needle was injecting PFA into the right part of the mouse's heart since the heart is so small. A perfusion is successful if the mouse's brain turns white because all the blood should be drained. When I cut open my mouse's head to view the brain, my mouse's brain was still a little bit pink, indicating that the perfusion was not entirely successful. Extracting the brain from the mouse's skull was the most difficult part of the perfusion for me. The thick layer surrounding the brain is quite difficult to peel off, and I ended up slightly impaling the brain while trying to remove it with tweezers. Even though it wasn't a completely successful perfusion, I am still glad that I was able to be exposed to a process that is very different from the midi preps, bacterial transformations and molecular cloning techniques that I am used to performing. To be honest, I have wanted to do a perfusion myself for a while, and I am very grateful that Felicia allowed me and helped me to perform one.

In addition to the molecular cloning and the perfusion, I have sliced another two brains this week and performed immunohistochemical staining on slices from both of the brains.

My first perfusion! 

This past Friday, Felicia left for California to spend two weeks at home with her family, so I had to bid her farewell on Friday afternoon. She was kind enough to gift me with a book named Brilliant Blunders: From Darwin to Einstein, as well as a card thanking me for working with her this summer. We have promised each other that we will stay in contact, but I am definitely going to miss being with her in the lab and singing along to christmas carols together in the middle of summer. She has been an amazing mentor and friend to me in these past six weeks. Perhaps I will be able to return next year to work with or simply visit her again!

The book

I still cannot believe that I only have one week left here at the Fuccillo lab. Looking back on the past six weeks, one important lesson I have learned is that instead of being afraid of and beating myself up over my mistakes and failures, it is wiser and more efficient to learn from these blunders and to try my best to solve the dilemmas I run into during my experiments. Even though I walked into the Fuccillo lab telling myself "don't you dare make a mistake", I will walk out of the lab encouraging myself to not fear failure and instead take advantage of and learn from it. 

Nicholas Massenburg, Entry #4, Gaining a sense of independence

The past two weeks in the Jordan-Sciutto lab have been both extremely interesting and rewarding.

Post-doc Dan, who I have been working with for the past 6 weeks, recently recruited a Dental School student as his school year pupil as I begin to wrap up my work for the summer. Generally, in the beginning, Dan would shadow me in all of my endeavors in the lab in order to ensure that I was doing everything correctly and to promptly answer any questions whenever I had them. With some bumps in the road (including me contaminating a whole batch of RNA extract, the process of which is one of the most difficult in biology laboratory science), I was generally successful with his help. The new student, Ahn, has required a lot of Dan's time to become acclimated to the lab, and he has also enlisted me to help her with some of the laboratory logistics (with experience in medicine, she has required some assistance with laboratory science, which seems to be more my speed). She is extremely nice and easy to talk to, so helping her has been rather easy and enjoyable.

Dan is taking on two new projects, so he is passing on a bulk of our work with Stanniocalcin 2 (STC-2) and it's potential upregulation by Cinnabarinic acid to me for the remainder of my stay. He no longer sits by while I do work at my bench or on the Keyence computer microscope, something that has been scary but liberating at the same time. I find that he has prepared me extremely well to conduct reverse transcription and bulk PCR on my own, and he is still available to answer my questions, but does so much less now. I have also been left to my own whims to tabulate and quantify our results for many of the trials we have done in our experimentation, and I have been privileged to display those results to our lab PI and colleagues in other labs on campus. I plan in my last two weeks to make a presentation in our seminar meetings discussing our results and success with ER stress inducing agents such as hydrogen peroxide, thapsigargan, and most recently ritonavir, an antiretroviral medication used to exhibit the toxicity that medical overdose can cause in HIV-patients, specifically in those with HIV-associated neurocognitive disorders (HAND).

Dr. Venanzi also visited us yesterday, and I got to see some of the Philly EXPers who I don't usually see that often during the week or on weekends. I had a great time with them as well, but unfortunately returned to the lab with a stack of PCR materials waiting for me on my lab bench (thanks Dan :( ).

I have found this experience extremely rewarding, and the independent work I have done over this past week has made my experience all the more challenging, rewarding, and enjoyable. Here's to two more weeks.

Ian Loeb, Entry #5, Wrapping it Up

With my EXP experience coming to a close, I can say I feel a great deal of sorrow and remorse. It was indeed the experience of a lifetime. The independence and overall experience opened my eyes to a lifestyle I have yet to experience, and has given me a taste of one that I could definitely see myself having in the future. Although the work was in no way all fun and games, and sometimes could be tedious beyond measure, it was one of the most enjoyable work experiences I had, mostly because of the gratification, but also because of the overall enjoyment I had every day.

While 6 weeks seemed like ages before I arrived in California, the time passed quicker than I could have ever anticipated. Before I knew it, my project was almost ready for posting, and the ending was in sight. While I was working, I regret not taking the time to appreciate the opportunity I had been given, and not savoring every minute I had. It's not until my experience ended that I truly saw how lucky I was to have this experience. Yet on the upside, I have gained knowledge as to what I enjoy doing, and how I would like to tackle future endeavors, and which direction to point future experiences in.

I would like to thank Dr. Peretz and Dr. Venanzi for giving me this opportunity, and opening my eyes to a world I would not have expected to enjoy, nor would have experienced otherwise. It has truly been a wonderful experience, and I hope to have more like it in the future.

Oliver Crane, Post #4, Almost Done : (

With one week left to go I can’t believe that I am already nearly done with my EXP experience. This past week had a lot of work but fun as well. The lab manager, who I had spent most of my time working with, left for her new job. Because of this I’ve had to figure out a lot of my new responsibilities on my own without much guidance. I spent most of the week renaming sections of mouse brains which had been improperly labelled. This task involves comparing the computer images of each section of the brain with the Allen Brain Atlas (basically a map of every section in the average mouse’s brain). Although it becomes quite tedious having to rename hundreds of brain sections which are very thinly sliced, I enjoy the work because of how challenging it is properly matching up each section.

Mouse Brain Slices Pre-Imaging

The lab is currently working on various projects regarding morphine and heroin but I have been put on one which has priority because it has to be published soon. We are basically feeding two different diets to groups of mice, one group gets regular mouse food, while the other gets the same food mixed with crushed up DHA pills. DHA pills are commonly known as fish oil pills which people take for their high concentrations of OMEGA-3. It’s my job to prepare this food mixture by blending the pills with the food and then feeding the different cages of mice. One cool aspect of this job is that I get to work in the animal room which is filled with hundreds of mice and giant white rats with red eyes (biggest rats I’ve ever seen in my life). On Friday, we had a small party during lunch to say goodbye to the lab manager who is leaving. There was a ton of free food and it was a lot of fun. I also made chocolate chip cookies for the party which everyone enjoyed. Outside of work we got to go to Hollywood Avenue and see all the different stars including Chuck Norris and Bruce Lee! It wasn’t that great though because there were a ton of huge crowds of tourists as well as street performers dressed up in strange costumes asking for money. I also have started working on my exp poster for science night on which I am going to talk about the DHA experiment that I am working on. Danny's parents also visited us from nearby Irvine and took us all out to all you can eat Korean bbq! Although we nearly died ingesting as much red meat as possible within the span of a couple of hours, it was great getting out of the house and getting to meet Danny's parents. Looking forward to my last week in Los Angeles despite it being the end of my exp experience!

Danny Kim '17 and his mother, Mrs. Kim.

Entry #5 Cait Barrett Sorting eggs

This week is mainly about sorting and collecting fish. These fish have been injected with a CRISPR protein that has a target site at the beginning of a gene called NOG and at the end. Our goal is to hopefully remove the whole gene from the fish’s genome. So far this has been a very unsuccessful gene for Ben, as no mutants have been found over the past year. This time we attempted a new target site during injection, as well as increasing the amount we were injecting the fish with. After we injected we allowed the fish to sit in the 55 degree Celsius incubator for about 3 hours in order for the eggs to begin to develop. When we looked at the eggs at 3 hours post fertilization we were just checking to see infertile vs fertile eggs, in order to discard the infertile eggs and also get infertility ratios of the parents. After this we allowed for the eggs to incubate overnight in the 45 degree Celsius incubator. Looking at them 24 hours post fertilization, we hoped to see patterns of ventralization. Ventralizing is when you begin to see more tail than head. There are different levels of ventralization, from wild type which has none to V5 which is an embryo with just a tail crumpled on the yolk. The more seriously ventralized fish won’t survive. We sampled some of these fish taking about 6 of each phenotype from the different clutches, and then performed HRM on them. The HRM results we got back showed that we had indeed made mutants this time around. This was a big step for Ben’s project, as he could not create mutants the previous year. In order to celebrate this we moved Ben’s dial on the lab struggle-meter down a notch.  

Along with sorting these CRIPR Nog fish, Ben and I also sorted embryos that we had injected with 3 different morpholinos for Woods Hole. These injections went very well as with each different morpholinos, mSmad5 a morpholinos that is normally used in mice and disrupts the Smad protein, xbmp7 which is found in xenopus and knocks out the Bmp7 receptor, and Chordin which is a different protein that has to do with ventral formation. For the mSmad5 and xBmp7 we saw dorsalization phenotypes. Dorsalization is when the tail becomes less prominent and these have a scale as well. From wild type to C5. With the Chordin morpholinos we saw a ventralized phenotype as we expected. In all this week has been pretty successful in terms of experiments so far. 

This picture is a chart that shows the different dorsalized levels, and the tail features that identify them from wild type to C5. 

   

This picture is a chart that shows the different ventralized levels, and the tail features that identify them from wild type to V5.

John Bokman, Entry #5, Over But Not Completely Finished

Boston Skyline

The time has passed so quickly and I am already home again. As far as research is concerned I am realizing what a small period of time six weeks is. I feel like, despite the progress I was able to make, there is so much unfinished work left behind. I have been remaining in contact with the friends I made in the lab and continuing to do some work from home. I still have to clean up and send in a commented version of the scoring program I finished writing.  I am also still coordinating with my undergrad as we work online on analyzing the data creating models for the dyslexia intervention study.

In the past week, the undergrad and I had worked quickly on the analysis but had some trouble with the data. The sample size of the study was small to begin with, but an error made by someone during data collection forced us to cut some participates from the analysis.  Despite the difficulties with the data set and later with the modelling, the undergrad and I showed there were significantly better scoring results from the intervention group and were able to present a program that demonstrated the comparison in progress with a visual.

Also, Mrs. Honsel came and visited my lab this Thursday. It was great to show her what I had been working on and introduce her to everyone in my lab. Everyone in the lab was excited to meet her and talk about the research.

I have learned a lot in Boston. In addition to what I read and studied, I also had to figure out how to live by myself, which presented a whole new set of struggles that created some funny moments. Altogether, I really had a lot of fun and I am grateful I had the chance to go. I didn’t expect to become so comfortable and make as many friends inside the lab, especially with the older students. As the weeks passed by, I realized that many of the important things I gained were taught to me by the undergrads and other interns and that making a connection with them is a huge part of the experience. I also saw that when working on a project you learn things faster than you can often teach yourself. Having a situation in which to practice skills, and the pursuit of a goal guiding the acquisition of the skills, makes the process more interesting and quicker.

Jay Swarup, Entry #3, Bad Results :(

Hey all,
        I just finished my fourth week at the Ramachandran Lab studying pharmaceutical tablet manufacturing. In my last post I mentioned that I completed an experiment in which the aim was to increase the size of the granules after performing granulation. Well, unfortunately the size of the granules increased way too much. In fact, the size of the granules increased to a size 3 times of our desire. So, after discovering these results, we had to change a few parameters on the granulator, such as increasing the chopper speed and decreasing the impeller speed. So, after we created the powders and did our experiment on the granulator, we had to measure the particle size distribution. But, something went wrong with the laser diffraction machine that automatically reports us the data in about 2 minutes for each sample. So, we had to think of ways to measure the particle size distribution without this machine. After badly failing at trying to fix the machine, I decided to measure the particle size distribution (PSD) manually. So to do this, we used a method of sieve analysis. With sieve analysis, we sieve the granules into different size sieves. After this we measure the total weight of the granules in each of the sieves. A picture of the machine used to perform sieve analysis is below.

After sieve analysis was performed, I had to go into Excel and manually plot the data. But, after receiving the average amount (D50) of the granules, even this created too big granules for my liking. The reason why I want a certain size for the granules is because an increase in the size of the granules to the size I am trying to get will make the fluidity of the tablet much better when users ingest it. Hopefully this week we will be able to get the desired granule size.
           Also, it appears that the graduate student that I helped out last week also got bad results. Her experiment was trying to use the raman spectroscopy to test the uniformity of the active pharmaceutical ingredient in her tablets. But, after she showed the pictures to the company, they said that the pictures did not show what they wanted to see. In fact, they said that the chemical lost its properties and therefore the machine could not report the correct data. So, she assigned me to research different chemicals and ways that we can make sure the raman analyzes the tablets correctly. After reading articles and talking to her, we decided to decrease the temperature that the tablets were being dried at before ordering new chemicals. This week, after we make and dry the tablets and put it in the raman, we hope to get better results.
       Along with working hard in the lab, I have also been enjoying my summer vacation. This past week I went to the golf course to try and fix my swing. Even in that experiment, unfortunately, I have been getting bad results. But, I have still been enjoying my time on and off the golf course.
      Although I did get bad results, it was still fun being in the lab and performing experiments. I am looking forward to more experimental work!

Sharanya, Entry #3, Week #4-Glowing Cannibals

This week was definitely a lot smoother than the last one, despite us having our second sampling day and using new machinery in the lab. We were able to efficiently sample and filter sixty-three bottles of cells and prey cultures in six hours and I also learned how to use the FIRe (Fluorescence Induction Relaxation sytem) and the chlorophyll filters. On Monday, my lab partner and I went to check on the progress and growth of the Noctiluca cell cultures in the incubators. Some of the bottles demonstrated what we were expecting while others surprised us. Specifically, we noticed certain bottles like the "Noctiluca+Pyramimonas" under light conditions were lacking prey so this shows that the Noctiluca were indeed feeding on these chlorophytes and may even prefer them to other modes of consumption. Since there was light in the cultures, one would think that the Noctiluca are inclined to photosynthesize but this doesn't seem to be the case in this particular culture. The "Noctiluca+Pyramimonas" in the dark surprised us as well, indicating that the Noctiluca were not feeding as much on the prey but were actually participating in photosynthesis. I have attached an image below to show the comparison between the light, dark, and only-prey cultures. 

A Comparison of the Light, Prey-only, and Dark cultures of N+Pyramimonas (Left to right)

Additionally, I also learned how to use the chlorophyll filters (image directly below) to extract the Noctiluca/prey cultures from the solutions. Basically, I am filtering the cells and other "organic material" onto small, circular, combustible filters and then placing those filters into tubes of acetone. This had to be done in the dark since the photosynthetic cultures are light-sensitive. This would cause the cells to rupture (die) and would give us the inner contents including chlorophyll, ammonia, and endosymbionts. We then removed these filters from the acetone 'culture' and placed the samples into the FIRe. This is probably one of my favorite things that I have done in the lab so far because as I was transferring the cultures onto the filters, I was able to see cells from some of the cultures glow as they made contact with the filters. I tried attached a video of the fluorescence (below the image of the filters), though it's easy to miss unless you focus on the center of the screen.:)

Chlorophyll filter =D

Finally, we also observed that our control cultures, which only contain fifty Noctiluca cells without any prey, were somehow thriving on their own without photosynthesizing. We deduced this because of the lack of chlorophyll and endosymbionts within each individual cell. But somehow they were thriving. I remember my PI saying a few moments later, "I think they are either cannibals or are feeding on their own endosymbionts, since there is no prey and they are not photosynthesizing." This possibility is something that hasn't been discussed within the marine biology community, but we were all definitely excited to have had such profound results.

It's been a great week and I can't believe my time here is almost over! I am looking forward to these next two weeks and will update you all soon!

Alex Larson, Entry #4, Feeling ever more comfortable

So on Thursday afternoon of last week our Primers finally came in. Unfortunately, since they came in a small cardboard envelope they were easily misplaced and Adam and I had to run all over the building that afternoon to try to find it. Turns out that a member of our lab took it over to her bench because she thought it was for her. On Friday Adam taught me how to rehydrate the primers since they are shipped in a form without water. Earlier in the week we were supposed to go over to the old building and grab some fresh A549 cells (adenocarcinomic human alveolar basal epithelial cells) for DNA extraction to use as the template for PCR. We use A549 cells because our lab has a ton of these cells since they provide good mediums for which we can grow the influenza virus, plus the 45S gene we are looking for is still present and functioning in those cells. It wasn’t until Friday, however, that we were able to get those cells so instead of rushing the extraction, Adam decided to dig through the freezer and find some old A549 DNA and use that instead. Adam later left me in charge of picking the polymerase and the settings for the thermal cycler. After a little research on my own (Adam let me be in charge here), I decided to use the Q5 High-Fidelity Mastermix because it contained basically every component necessary except the primers and template while also being 100 times for accurate than Taq polymerase. So after a lot of tedious benchwork, we were able to create 45S PCR amplicons.

            We later ran our amplicons on a gel, and the amplicons that turned up with bands were subsequently sent off for sequencing. In total, 14 amplicons (though some were of the same amplicon, just a different primer) were sent off, and of those 14, none were sequenced successfully. A lot of the results did have partial sequences though, so when we ran the sequences by NCBI, in virtually all instances where there was a sequence to use, the resulting region of genomic DNA was somewhere in the 45S gene. So while a lot of red color might have turned up on the results page of the sequencing website, we were able to confirm that the region of DNA sequenced was the same region we wanted to sequence. To get full readings and better results, Adam and I are looking into different parameters for PCR and perhaps a different method of sequencing. This is very specific to our overarching DASH project. Our next step is to use this sequence information and amplicons to design single-guideRNA for CRISPR/CAS9 which should snip out the regions within the 18S, 5.8S, and 28S Genes that are not variable leaving us with the ability to see how the variable regions within the entire 45S gene on a whole function.

            On a side note, Dr. Ghedin has been out of the lab on vacation for the past 2 weeks so our entire lab decided to play hooky and go hiking Bull Hill in Cold Spring, New York last Wednesday (7-13). Adam was the one who orchestrated everything because he grew up in Rockland County. We all met at Grand Central and took MetroNorth up to Cold Spring. From there, the 12 of us who went embarked on a 4 hour hike up and down this very steep mountain that had gorgeous views of the Hudson Valley. It was nice to be able to finally get to see members of my lab whom I only occasionally talk to anyway outside the laboratory setting. Plus we were all able to bond about the tortures of walking uphill under a bright sun in high 80 degree temperature. The views certainly made the hike worthwhile though, and I did have the best shower and sleep of my life when I got home that night.     

(Results of our 45S PCR amplicons on a gel)

(Top of Bull Hill)

Daisy Fang, Entry #5, It's A Wrap!

It is still hard to believe that I finished my last day in the Arts and Mind Lab. I have been very busy the last two weeks of my time here as we dived into data analysis. While we continued to recruit and test the Bridge Boston control group, data collection for cohort one after a year of music training was officially concluded. In order to prepare for data analysis, I spent a few days watching Khan Academy videos to familiarize myself with the basics of statistics. Furthermore, Alessandra and I cleaned and organized the cohort one data into an excel spreadsheet which compares the first and second testing scores of each measures so that the data was ready to be entered into SPSS.

On Monday, Jill, Alessandra and I met with Dr. Winner to begin the long-awaited process of data analysis. During the meeting, Dr. Winner patiently explained to me that we were going to run a repeated measure ANOVA analysis, since each participant was tested with the same measures between two time points. We were interested in seeing the interaction of time point and group, as we hypothesized the control group score to stay the same while the treatment group score improves over time. It was really nice of Dr. Winner to spend time and walk us through the detailed the process of using SPSS using one of the six measures as an example. After the meeting, I was able to run the complete analyses on all measures and create a summary of the results. 

Summary of tests of within-subject contrasts of the Dot Counting task. Timepoint*GroupCvT is the interaction we are interested in, but unfortunately the significance level is not high enough.

Mean score graph of the Dot Counting task

In the repeated measure ANOVA that we performed, group (treatment and control) was identified as the between subject factor, and time point (K2 and 1^st grade) the within subject factor. Although the mean of each group changed in the expected direction for some of the measures, some changed in direction contrary to the hypothesis. No interaction between group and time point significant enough was shown, as the significance level of all measures were above 0.05 which indicates a 95% confidence interval. The graph shown above is the analysis of the Dot Counting task, testing working memory as a measure of executive functioning.

Initially, I was frustrated that after all the hard work, analyses showed that the data turned out to support the null hypothesis. But then I realized that we only analyzed the data for one cohort (half of the sample size) and after only one year of treatment. Dr. Winner pointed out that it is difficult for transfer studies to show results. She also taught me that null findings are also extremely important because it defies what is assumed to be true. Although many people claim that music education helps children improve executive functioning, the argument is false as concluded by the study so far. 

Looking back on the six weeks I spent at the Arts and Mind Lab, I have learned so much more than just how to collect and analyze data. The long data collection period may get tedious, but it is crucial in ensuring the validity of the results. I also realized that the essence of science research is not trying to prove the hypothesis correct, but to thoroughly explore the question with an open mind. I will miss working with the undergrads and grad students every day, and I hope to come back and visit in the future!

Danny Kim, Entry #4, Fourth week at the lab

This week has been the busiest week for sure, but it was also the most exciting week of all. I actually felt like I was useful. For the first half of the week, I continued on learning how to use MATLAB and helped with the sessions with the patients, mostly children with Dup15q syndromeor autism spectrum disorder. My research coordinator, Scott told me to pay attention to the eye tracking part of the session. The patients were shown different videos - some with socialization and some with no socialization between the people. And the results from the eye tracking of these children were going to be the ones I would input and use to analyze.

And finally, on Wednesday, college student from France came back, and we worked together to change the results into analyzable data using coding. But, it was more like her writing a code and then explaining to me how and why she wrote it. We had many errors and had to revise several times. For example, we were trying to get the percentage of time when the patient was focused on the faces on the screen and the number of fixations. But then, we would get very high percentage of time on faces but very low number of fixations, which contradicted themselves. We tested many results from the patients and finally got it to work. Next week, we would spend time inputing all the data and make graphs to visualize and analyze them. I feel quite nervous, as we would most likely need to present this in front of the whole lab in a lab meeting.

This weekend, my parents came to LA and took us all to a Korean BBQ place. The food was great and it was good to see my parents once in a while.

Chris Fu, Entry #5: Machine Learning

Last week, I began work on machine learning code. My task is to create a network of data regarding positions of atoms in 3D. Each time, an angle and bond length will be slightly changed, and we will measure the distribution of charge within the system. Once we've developed enough data points, we will then use statistics to determine the charge distribution of other structures using the data as a baseline. To do so, my grad student and I are preparing a python code that can store a matrix of the data, then perform ridge regression to predict other values.

Other than that, there's not much to talk about. I made myself dinner a few times, and Joe, Nick and I met for dinner. The Schulykill trail and Franklin Field are fantastic places to go on runs. I plan on visiting some of the libraries on campus this week, and hopefully seeing a few more museums while I'm here. Have a nice day everyone.

Masa, Entry#5, The Finish Line

With a heavy heart I recently completed my final day at the lab. Over the past six weeks, I have truly learned so much not only about science, but also about working and living alone in a city. At the Hussaini lab I was able to watch cutting edge technique used to learn more about a devastating disease, as well as do my part in furthering the research. By being in a lab for such a long time, I have begun to realize just how tedious yet rewarding science can be. Papers can take months and years to write, only to be criticized and turned back by editors. Experiments can takes ages to set up and complete, only to yield insignificant results. No matter how time consuming, however, the end result is always positive for science and humanity as we increase our knowledge and ability to combat horrible diseases that blight our world.

I would like to thank everyone at the lab, especially Eden, Gus, Matt, and Dr. Hussaini for being there whenever I needed to teach me a new skill or give me some tips on my work. Thanks also for giving me the opportunity to watch different procedures done and answering any questions that I had, as well as taking a chance on letting me work at the lab. I hope that I have been able to contribute something towards the lab's research, and that we can perhaps work together again in the future.

Trevor Russo, Weeks 3 and 4, Finishing My First Node

When I started off the third week of my time at CMU, I felt like I was a long way off from learning how to code and accomplish my goal of creating a program for taking pictures and turning them into 3D Models. By the start of the fourth week I had already created a program that would subscribe to a camera and take pictures with a user's input and save them to a folder. This progress was possible due to a few factors. When Venkat and Dr. Likhachev came back from Berlin, they thought that the daunting task of three programs in one would be a rude awakening. Instead, Venkat decided to change my project to a simple ROS node, that wouldn't require me to use any of the Point Cloud Library that I had been preparing me for. This ROS node would subscribe to a camera, for example a Kinect, and ask the user if they would like to take a picture. Then a picture would be taken, displayed on the screen and saved in a folder for later use. I was able to write the User Interface pretty quickly, but the taking of the picture and the subscribing of the camera was a lot more difficult than I had expected. Fortunately, after some interrogation of the other interns in the lab, I was able to learn about callback functions, which are special functions that are designed to wait until the user calls upon them. Still, I felt like I was having some trouble, so I asked Shivam, another intern in the lab, for some advice, and as I outlined my code on the whiteboard, he told me that I had already basically finished. That got me to realize that my biggest barrier was not actually my level of skill, but that they were mental ones instead.

My ROS node displaying the UI and pictures that I had taken

After finally finishing my first project, my next task was to turn these many pictures into 3D models. Thankfully, I didn't have to create this program, but rather find some software on the internet that would help me accomplish my goal. The one I wanted to use, Autodesk 123D Catch, unfortunately doesn't work on a Linux computer, so I had to find another free solution. After a lot of searching, I settled on Insight3D, but only because it was the only program that didn't cost 200 dollars or ask me to install 7 different programs on top of compiling the main one. Unfortunately, it hadn't received an update in 5 years, so compilation proved to be a nightmare, with bugs popping up every time I told the computer to finish compiling. Fortunately, after some extended help from Venkat, I was able to finally install the program and test it out on some sample pictures of buildings. It will be a while until I can actually take photos with my program, as the PR2 robot is currently being updated by Venkat and our Software Engineer, Andrew.

Outside of the lab, I've been spending a lot of time with the two other interns, Joe and Shivam. They are both a part of a special program called the RISS, which is an 11-week paid internship in one of the robotics labs in the Robotics Institute. These past couple of weeks I've gone out to lunch and dinner with the two of them a lot. In addition, I spent the 4th of July at Joe's house, where we had some Chinese food and waffles in town and spent the evening shooting cups with a Nerf gun. And last weekend, I was talking to Shivam, who is from India, and he told me that he had never gone to a baseball game, to which I suggested that we go see the Pirates play the Cubs on Sunday. It was awesome to get to explain all the rules to someone who had never gone, and I even got to chat with some fellow Red Sox fans (I didn't have any other things to wear, so I wore my David Ortiz jersey). 

Top: Our view of PNC Park; Bottom: Shivam and I enjoying the game

Although my time at CMU got off to a slow start, I've really enjoyed my time here, and I'm somewhat sad that I only have 3 more weeks left. Being in a city by myself has been really fun and the real-life coding experience that I have received is probably going to be really valuable in the future. I hope everyone else's time at their labs has been going as great, as its been weird to see people finishing their time up while I am still working.