Emmy Wang, Entry #3, Back to the Lab

This week I came back to my lab in Trondheim after taking month off while everyone went on holiday (and my PI went to China for a conference). The weather has become 200% more rainy and the temperature has dropped about 10 degrees as autumn quickly arrives. Today Dr. Berg, the new postdoc Dr. Xi, and I went to the confocal microscope with my 13 preparations. Dr. Xi has just joined the lab so she is learning most things from the beginning, and sometimes she'll ask me about the method of staining or fixing or how to care for the insects.

Preparations

We scanned two preparations, one stained from the antenna and showing the sensory neurons, and one stained from the antennal lobe showing the secondary neurons. I was a bit nervous about how successful the second one would be, since when I was staining directly into the antennal lobe I really was not sure whether I had actually located the brain or if I was just pushing dye into some random muscle tissue, but the scan came out quite nicely.

Grabbing a snack while waiting for a scan

It took a while for each scan so it was a chance for us to get caught up and to eat some pancakes. The confocal microscope scans the brain in slices, and it is very convenient to use insect brains since they are so small that they do not need to be physically sliced up.  We were able to see the neurons coming from the antenna and into glomeruli in the first scan, and the neurons along the tracts going into the higher processing regions in the second. Every preparation gives a unique image so there is always something new to be seen, and there are so many things going on in the image that I could watch it for hours.

One slice of the first scan

Above is the scan of the first preparation with the glomeruli. I somehow managed to accidentally delete the second scan off my USB within like 10 minutes of playing around with it so we have to copy it again when we go back to the microscope next week. They also have a new confocal microscope so my PI is hoping we can go back and become familiar with how to use it, and practice on some of my preparations next week. The new masters students, as well as a guest researcher and another PhD candidate, should be arriving soon, which I am looking forward to!

Trevor Russo, Week #7: An Internship in Review

Now I am not writing this from Pittsburgh, but rather back at home on the couch while the Olympics are on. I am writing this last blog entry more as a retrospective on my whole time, since the blog itself only encompasses 3 days. Now to get to those three days. On Wednesday I was greeted at noon by Chris Fu and his family, who were visiting CMU. I took them to the Union Grill, where Chris tried and succeeded to eat the massive burger they famously had. On the coding side, after writing the masking program, the next step for me was to write a program that applies a white balance to the photos, to presumably make them look better for modeling. This was a lot more difficult than I or Venkat had anticipated, as he assumed that OpenCV, a library for image manipulation, would contain tools for this, but the only such tool was a cpp file called white_balance.cpp. So I did what every reasonable programmer would do and ripped the code straight from the file, making sure to include the right header files, before compiling. Unfortunately, I got the worst error of all from the compiler: the dreaded Segmentation Error. The reason that this is the worst kind of error is because it doesn't even tell you what line of code caused the error. And since it was my last day, I didn't want to spend it debugging. So I told Venkat the problem, and he agreed that it would be something that I could work on afterwards. So instead, I focused on writing a report which would allow any future interns or Venkat to make their own models. And finally, my last task at the lab involved hooking up a USB camera to the computer and testing out my Kinect capture program. It worked, but with the added caveat of not being able to save the photos in the folder I wanted them to be saved in. After that little problem, and with the added fact that my dad would be arriving in a few minutes to the house, I decided to pack it up. I backed up all my code to GitHub, and said my goodbyes to Venkat and Karthik, who were the only two people in the lab at that point. I made sure to get pictures too, and just before leaving, I wrote a message on the whiteboard thanking everyone for all they had done for me.

This internship has honestly been one of the best experiences I have ever had. I've made some great friends and met some of the most exceptional people in the field of robotics. Professor Likhachev is an absolute genius who can think up planning algorithms on a whim, and Venkat's knowledge of complex machine learning systems kept me in awe in every presentation, even if I was more focused on appearing like I understood his lectures than actually understanding them. And Andrew the software engineer would answer any questions I had about C++ syntax, and though they were few and far between, I still enjoyed our late night Overwatch games. Although we didn't get to know each other that well, I still valued the great help that Karthik gave me. And finally my two greatest friends in Pittsburgh, Joe and Shivam, shared many wonderful moments with me, the tortellini dinner still standing as the best though. To talk about Pittsburgh, it was the best college city I could have imagined; small, but not too suburby, and there was always enough good food and interesting things to do. If it weren't for all the hills, I probably would have been able to accomplish that daily run I set out to do and never did. CMU was great too, with good food at the University Center, a beautiful campus, and a quality gym. Additionally, I feel like I've been able to grow not only as a programmer, but also as a person. Living by myself was one of the most rewarding things that I could have had, as I had the freedom to go eat when I wanted, manage a house, and also manage my own schedule. On the programming side, I now feel like I can manage a Linux system and write code in C++ and bash easily. I really feel confident in my abilities, unlike before when I was really confused. Ultimately, this was a great experience and made all the struggling of the past weeks really worth it. I can't be more grateful to the SBPL for teaching me everything and having the patience to take on a high school student for three years straight. Hopefully I'll get this opportunity somewhere else. And now for some more pictures:

 Dr. Likhachev and I sharing a photo after our last meeting

 A nighttime view of the Tower of Learning at UPitt

 My ID Card

 Venkat and I before my departure

 Last day in the office with Karthik

 Probably the toughest goodbye: the PR2

 Me hard at work on my KinectCapture program

A better view of the lab with Joe in the corner

 A view of Newell-Simon before biking home

 My Apartment before hitting the road back to Princeton

Mr. Corica and I after he came to Pittsburgh

Thanks again to CMU, SBPL, Mr. Corica, Dr. Peretz and Dr. Venanzi and my parents for this incredible experience.

Megan Gabruk, Entry #9, Approaching My Last Week

As I approach my last week, I am thinking about all I have learned through this amazing experience. From experimental design coding to writing letter of inquiries to reference management and many other tasks, I really appreciate this opportunity. On Monday, I read over two peer review articles. A new high school student came to the lab, and I told her about what I had been working on. She has not really been at the lab too much, so I still have to work alone much of the time. However, I now go out to lunch with the project coordinator some days. She is very smart and nice, so it is really great to be able to talk to her about her goals and get advice about my future.

            On Tuesday, I read over two more peer review articles. I also figured out how to read the output files for E-Prime. I had identified a problem on the morphing task that was shared with us, so I had to look at the output files to make sure they actually made a mistake. There was a column in E-Prime that was supposed to be sad faces, but showed happy faces instead. So, I fixed the problem, and we let the group that shared the morphing faces task know about the error.

On Wednesday, I went over the E-Prime output files with Kate and confirmed that there no problem with the version of task that I had fixed. To do this, I ran through the task and made sure I identified all of the images correctly and that the output files matched this which they did, so the task was coded correctly. Also, I put up flyers at some child care centers and other places where new mothers would be in the area. At Kate’s RA meeting, we talked about peer reviewing articles and went over the ones I read. Next week, at Kate’s RA meeting, I will be presenting on Mendeley, the reference management program I have been working with this summer.

On Thursday, I finished filling out the Horvath clock spreadsheet with all of the literature I had identified. Also, I attempted to identify new stimuli for the dot probe task, so that we can use different baby images for the dot probe task and the morphing faces task. Luckily, only eight of the twenty two babies in the dot probe task overlap with the morphing task, so we can still use the current stimuli we have. However, I am still looking for other stimuli sources.

On Friday, I worked on finding a way to put our two tasks on Mechanical Turk which is a program that pays people a little amount of money to do the task, so we can get a lot of data. However, E-Prime files cannot be used on computer that do not have E-Prime, so I am looking into computer programs that allows our tasks to be shared with others once coded.

Outside of the lab, I hiked The Dish. Also, I attended a dinner at Kate’s house on Friday night which was a really great experience and nice to get to know everyone better.

Tanvi Dange, Entry #3, Weeks 3 & 4- Busiest Weeks Yet!

The weeks of July 25-29 and August 1-5 were super busy in the Franz lab because on August 5, 2016, the undergraduates participating in the Summer Fellowship Program (and me!) were presentation posters at the 2016 Summer Symposium and Poster Session. So the week prior to the session, Lizzie and I spent every second in the lab collecting data for my poster. The main data I was collecting that week was from Antifungal Assays and a Checkerboard Assay all on the brand new S. cerevisiae strains I got from Duke's Magwene Lab. The Magwene lab was so generous to give us 5 different Saccharomyces strains since our Baker's yeast from the store was too resistant to the drugs. So the strain I tested that week was S288c, a  laboratory strain. I made three Antifungal Assays against the S288c: one with Fluconazole +/- CuCl2, Fenpropidin +/- CuCl2, and Flu-TSCZ +/- CuCl2. I also made one checkerboard assay with different concentrations of Fluconazole with different concentrations of CuCl2 against the fungus.

Me preparing my plates-- probably serially diluting 100uM of Fluconazole

 I worked up some of the data over the weekend and the rest on Monday morning. The results themselves were interesting, and I was definitely able to it on my poster, so after all the data was worked up, I started making my poster on Monday, August 1, 2016.

Closer look at the Dose Response I worked up for Flu-TSCZ

During the craziness of making the poster during week four of the lab, Dr. Venanzi came for a visit! This was a really special visit because my PI Dr. Franz was also Dr. V's PI in graduate school-- I'm in her old lab! Dr. Franz and Dr. V both had a chance to catch up, and I showed Dr. V where I work in the lab and how my research is going so far. Then, the entire Franz lab all went out for a group lunch.

Franz lab + Dr. V at Tobacco Road Sports Cafe

For the rest of that week, it was long hours in the lab preparing for the poster presentation, which finally came together the night before the session. Finally the day came, and it was time for the undergraduates and I to present our posters in front of members of the Duke Chemistry Department and others who wished to attend the session. I had an excellent time presenting my poster. I felt a lot of pressure being the youngest one there, but because of my experience presenting at EXP's spring Science Night, I quickly adjusted and had a great time sharing my research with those who were interested. :)

My poster and I

 

David Alvarez, Entry #4: Week 6

The past week has been really fast-paced and busy, which is always a good thing because that means progress. On the WebRTC analysis experiments, Rodda and I have begun to do a lot more complex experiments. The setup now has three machines involved; one sender, one receiver, and one monitor in order to quantify the physical data rate. We've also started having a YouTube video be streamed on a fourth machine that is on the same channel as the other three machines, in order to simulate real-world traffic and interference. Wireshark runs on all three machines, and the .pcap traces from them are used to create data sets, and therefore plots in order to see if any noticeable trends are appearing. Aside from the PHY data rate, the other metrics are throughput, packet loss, time delta, and packet size. We also began including cumulative distribution function (CDF) graphs more.

Examples of the plots we are generating through the Python script.

Varun has also been giving us some reading to do so that we may better understand what exactly WebRTC is doing. They haven't been directly relevant to the API definition, but rather to Google Congestion Control (GCC), which has been proposed for WebRTC. Also, I took some screen capture videos of the trials we conducted, and he sent me a guide to a video analysis software used by another professor working on the project. It's called BVQM, and essentially how it works is that it takes the original clip sent out, and compares it to the processed clip seen by the receiver. From here, it can gather more data to compile, as well as provide a more visual aid to go along with the graphs we've made. There have been some compatibility issues simply because the software hasn't been so friendly with my Peddie laptop, but I've still managed to extract some useful information. I've also begun work on my poster, and after the traumatic experience of reading through how wrong I was on my poster in the spring, I've begun to make some progress.

Outside of all of this, the Wireless and Mobile Networking Lab has continued to be a really great place to work. The structure of work in the lab has left me a lot of freedom to work at whatever pace I'd like, leaving my schedule very flexible. This helps a lot now that I have to start my summer work for all of my classes, as well as the Common App. Everyone I'm working with here has been understanding of that too, which has been even more helpful. Yesterday, we had to say good-bye to an undergraduate student who was here for the summer, Andy, and went out to go get dinner at an Ethiopian food place near the university's main campus. I'd never had it before, and was pleasantly surprised by how much I liked it. 

Time has flown by and I now only have one week left here. I hope to be able to do a lot of work and try to get as close as I can to a good stopping point before my last day. 

Tiffany Budiman, Entry #3, Mice Brains and Fruit Loops

This past week, I felt really comfortable and confident working on the tasks assigned to me. I continued to help Sarah condition the mice and set up the CPP boxes for conditioning and handle the second group of mice. The second group of mice had a surgery on Monday and Reem and I went down to the vivarium with Sarah to assist her. I was tasked to shave the mice and prep them before Sarah performed the surgery. I was amazed when Sarah was able to put the very small and transparent cuff around the nerve of the mice because I could barely see the nerve or the cuff. We also set up a recovery station with heated pads and gave them fruit loops and peanut butter as a treat.

When I wait for the mice to habituate in the room, I help the other people in the lab with the Western blots, watch my other lab mates, or wash up some glassware.

Watching Angeli cut brain slices

Since Sarah and Reem don't come in on Tuesdays, I'm the only one working with the mice and CPP testing on those days. I immediately go down to the vivarium once I arrive and either handle them or set up the boxes. However, during conditioning days, either Chris, an older, more experienced volunteer or Sarah have to inject the mice with the drug since I don't have the training needed to inject the animals with anything. Other than that, I sometimes oversee what Angeli does and help Sid, another high school volunteer, with the Western Blot he and Steve runs. 

On Thursday, once Reem finished the second Von Frey test on her group of mice, Sarah sent Reem and I an excel sheet that our lab uses to analyze the data for the Von Frey tests. We input X's or O's on the sheet depending on how the mice reacted and the algorithms already set up on the excel sheet calculates a score out of 2, 2 being the highest pain threshold. 

The Von Frey data on Reem's group of mice

I also met my PI for the first time today since she just came back from vacation. Next week, my PI wants to talk to me about the poster and the overall goal of the project I'm currently working on.

Joe Yuan @ The Mason Lab: Post #5: The Finale.

So, this two month journey has come to an end.

What started with panic and confusion ended with one final explanation of why CD79 ACP was used in my CD19 flow cytometry stains. Although my projects during my time at the Mason lab were not groundbreakingly successful, I was able to learn more than I ever could in a classroom setting. From creating a plasmid to transducing cells, I had a very comprehensive laboratory experience.

I want to thank everyone who's made this possible:

Dr. Peretz and Dr. Venanzi, whose instruction and guidance enabled me to jump into a research lab and come out without blowing the whole thing up.

My PennVet Grad students, Sri and Meg, whose humorous remarks and friendly spirit made my days with excellent power point presentations and sarcastic comments about maxi prep columns.

My cats and dog diarrhea mentor Martha, whose working spirit and love for the animals is inspiring and unbeatable despite having to deal with Lincoln's butt situation and only surviving on glucose.

The in lab magician and fantastically sarcastic PhD student Kazim, whose guidance and humor saved my summer from catastrophe. And I loved the framed photo of my mega prep, that's going in my dorm room.

And of course, Dr. Nicola Mason, who was kind enough to take me into the world of a clinician scientists and walk me through the process of creating new solutions to some of the most important issues in canine and human medicine today.

I just want to thank you all for being a part of my summer. Thanks Chris for being an amazing roommate and partner in crime for our days in Philly. And I hope everyone else in Philly is having or already had a time as great as I did.

Ala Viva,
Joe Yuan

Bonus Cats: