Caroline Casey - Week 8 - Complex Systems Group: Finding the Distribution of Interference Values and Looking at Plateaus - University of Pennsylvania

This week was eventful and exciting, as every week is! I did some back-tracking with my project this week in order to be sure I can prove why I completed certain steps in the paper. After speaking with Scott and Nicholas last week, Dr. Bassett and I had new ideas for how to move forward with my project.

On Monday, I finished looking at the distributions of the interference values using the two different sets of interference values. Last week, I combined the interference values (from the ANOVA) into two sessions in order to have 40 subjects and then divide the 40 subjects into 2 groups based on having interference or not having interference. I completed that step by using a significance test. However, Dr. Bassett wasn't sure that it was the right method, she thought that I might need to use a median split. So, in order to be sure, I emailed Scott and Nicholas a PowerPoint of what I completed and asked what they suggested. They thought using a significance test would be the best option. They especially wanted me to use the interference values from the difference between pre and post movement time because it seemed to follow a normal distribution. Dr. Bassett and I were now certain that the results from Friday were correct. 

I then decided to make the community structure I identified two weeks earlier clearer by coloring the nodes on the brain plots more distinct colors, so the difference between the communities was more obvious. I also colored all nodes that were the only node assigned to that community (singletons) grey, so as to get a better understanding of the larger communities. It took me a while to figure out how to threshold the singletons to make them all grey and how to make the communities more distinct colors, but I figured it out in the end. We also had our weekly lab meeting on Monday where a post-doc in the lab, Marcelo spoke about his research.

This is the brain plot for one scenario (edges from the correlation of interference session 2 and scan 1) with the nodes colored more distinctly. Grey nodes (hard to see) are the singleton nodes.

Nicholas, one of the researchers I spoke with last Friday sent an email on Tuesday about the plateau results for the motor learning experiment. We decided it would be a good idea to identify whether subjects did or did not have interference when they reached the movement time plateau (no change in movement time greater than 0.25 ms) in order to identify if there was a trend. Attached to the email was a paper, which is not published yet, about the experiment and how the plateau results were found. Nicholas also attached the results from the plateau, including when subjects reached the plateau (which scanning session), which was the most important information in the data he provided. I spent Tuesday reading the paper, looking at the data, and analyzing the results.

On Wednesday, I continued looking at the plateau results and compared those results to whether or not a given subject did or did not have interference. I used the difference between pre and post movement times as the interference values to compare to the plateau results because when looking at the distribution of the interference values, those values gave the most normal distribution. No trend was noticed, there was a mix and the results seemed inconclusive. 

The next steps involved looking at the community structure between the two groups in order to see if the structure was different. I completed this step in order to justify that there truly is a difference between the two groups (interference and no interference), it was a necessary step to prove in the paper that the structures are different. Dr. Bassett wanted me to use the interference values from the ANOVA because it more accurately combined the two sequences and found interference values. I worked on going through all the steps: correlation, finding significant edges, permutation test, creating a network, completing 100 optimizations of the community assignments, modular allegiance matrices, and finally consensus partitions for the two groups. I completed these steps the rest of Wednesday and into Thursday.

I had the consensus partitions of the two groups completed by Thursday afternoon, and there seemed to be a difference in the community structures of the two groups (which is a good sign). Dr. Bassett then sent me the movement times of each subject for the two sequences for before each scanning session, during each scanning session, and after each scanning session. The ultimate goal was to analyze the distribution of the interference values for four scenarios, which are described below. I spent the rest of Thursday thinking through how to manipulate all the data. First, I had to find the interference values for the four scenarios for each subject. The four scenarios involved an ANOVA between: pre-scanning session 2 and within scan 2, within scan 2 with post-scanning session 2, pre-scanning session 3 and within scan 3, within scan 3 and post-scanning session 3. I then needed to separate the data for each subject, each sequence so as to make it compatible for the ANOVA. Next, I needed to complete a repeated measures ANOVA for the four scenarios for each subject. This is very tedious, but necessary work. I spent all of Friday working through these steps. 

Although I have been here for many weeks, I feel like there is still so much that needs to be done in order to truly have a complete understanding of what causes interference and in order to identify a sub-network that can predict who is susceptible to the interference effect. I hope that within the next two weeks I will be able to accomplish a lot more in moving my project forward. I find this research very exciting and interesting and I am learning so much in the process! I am particularly excited about all the applications my research has like the military, test-taking, and sports. The military is a good example because someone could perform well in practice, but in battle, if that person is susceptible to the interference effect, his/her performance could drop dramatically, which is dangerous for the individual as well as the group. I have developed a deep appreciation for network science and really enjoy the discovery that is involved in research!

Pieter de Buck - Week 6 - Duke University

Hi everyone, my name is Pieter and this is my 6th week at Duke.

This week I have started using my own data with my processing scripts. I did this because that meant that I was able to set my own simulation parameters such as beam energy, projectile and target particle and something called the impact parameter. This can be a single number or a certain range of numbers, and it defines the separation of the centers of the two nuclei in femtometers. In the picture below the with of the orange blob is the impact parameter. For my data I used a range from 0.5 to 3.75. I set the input parameters such that they corresponded with the conditions for this RHIC experiment.

I chose to use a fairly large sample size for my purposes, I simulated about 4000 collision events, which took at least 16 hours even on the powerful computer that Duke provided me with. When my research group wants to simulate data for use in scientific papers, they run the simulation in parallel on many different computers, to gain as much precision as possible. I then adapted my scripts to be able to read from multiple files and stitch everything together. This was quite straightforward and allowed me to work on the interpretation of the data very quickly.

Since Dr. Bass left for a trip, I started working with Dr. Nahrgang again. She told me that because of my script she found out that she should not have decreased the precision of the simulation in order to save disk space. In the data it would sometimes occur that two numbers were rounded too early, and thus result in division-by-zero errors. We have started working on new ways to interpret the data, and I will be able to talk about that next week.

I have increased the user-friendliness of my scripts. I added thorough comments, explaining each part of the program. Also the program now reads from an input file, instead of having to define all the parameters inside the program, much like the actual collision software, and allowing for automated running of the script. My research group also created an online repository for each of our scripts, allowing for easy troubleshooting and sharing. Think of it as google docs for programs.

Pieter

Chris Oh Week 4 - Gabrieli Lab, MIT

To start the week off, I had a meeting with Zhenhan on Monday to discuss the data analysis.  She showed me the programs on Python I would use and explained to me some statistical terms that would help me plot graphs.  She also recommended a course on Statstical Analysis on Coursera.  She asked me to plot graphs using the data I have collected (Average response time per each subject and per each syllable group) and data of out-of-scanner phonetic test scores of the subjects, which she sent to me briefly after the meeting.
For the rest of Monday and all of Tuesday, I looked through the Internet researching on differnet ways to plot graphs using Python as well as listening to some of the lectures on Coursera.
On Wednesday morning, I was able to graph a boxplot of the average response time for each syllable group with error bars.  At noon, I attended the weekly reading group for undergraduates and high school students.  Due to low attendence (there were only 3 students including me), Sara, the speaker, and the three of us had informal discussions on the papers she sent out the week before.  The papers she assigned to us were ones that were getting media attention this summer.  There were three papers: one about dogs, one about TV and one about food.  The paper about dogs was about an ongoing experiment where the researchers were able to train some dogs to go into the fMRI machine for brain scans.  A striking finding in the experiment was that the caudate nucleus in dogs was very similar in function and structure to the one in humans.  In humans, the caudate plays a key role in anticipation of things that we enjoy or desire.  In dogs, according to the experiment, the caudate activation was increased in response to hand signals indicating food and smell of familiar people.  The second article was about TV, where researchers used EEG and later fMRI to observe the neural response to TV shows and Superbowl commercials.  According to the paper, the researchers were able to use their subjects' neural response to predict the response of mass audience.  They used Twitter activity and Nielson ratings to measure the response of the general audience.  The last article was about food cravings.  It talked about how some people have more trouble resisting food desires due to low activation in the Inferior Frontal Gyrus, mostly in charge of self-control.  After the discussion, we were supposed to go to the fMRI room for fMRI demonstration, but the other two students who were there had other committments, so the demonstration was postponed.
On Thursday, I was able to plot scatter plot and best line of fit using the out-of-scanner behavioral data that Zhenghan sent me to see the relationship between average duration and phonetic abilities.
On Friday, I looked through the links that Zhenghan had sent the previous day to help me with data analysis, and attended the undergraduates' poster session.  Some of them were almost impossible for me to understand with my background, but many of them were very interesting.  For example, one of the presenter's research was similar to the poster I made for the spring poster session.  She was looking to isolate a part of the brain that is activated when presented a familiar word. When she was pointing at the figures showing the areas that were shown to activate when the subjects' saw a familar word and I pointed out that the area was left inferior prefrontal cortex near Broca's area (the area of the brain which was the main focus of my proposal and poster), she was surprised by my observation and was even more stunned when I told her that I was only a high school student with almost no background in Neuroscience.  I stayed for the full two hours had was able to have chats with almost all of the presenters.
I have also scheduled a meeting on Monday with Zhenghan to discussd further analysis of the data.

Picture of the poster session:

Winston Kung - Week 7 (7/21 - 7/25) - Silverman Lab, Columbia University

Hi there, I'm Winston and this is my EXP Summer Lab Research Experience thus far:

I can't believe my last week is already here.  Time at my lab this summer really did fly by, and I am honestly astonished at how quickly my last day crept up on me.

Every morning of this week I attempted to go to both butcher places and get a rabbit head for the lab member who asked me for one the previous week.  Unfortunately, however, it seemed that every day of the week, both butcher places had something that would not allow me to get a rabbit head.  The second place had run out of rabbits for the entire week on Monday since someone came before I did and bought them all.  The first place was closed for Monday and Tuesday and did not had any on Wednesday and Thursday.  When Friday rolled around, I was simply told not to even make the effort to go again.

On Monday, Tuesday, and Wednesday, I managed to finish analyzing the data for the rest of the four rabbit OCT scans.  By Tuesday or Wednesday, I became much faster and much more efficient with the data analysis program after I learned various different tricks and keyboard shortcuts.  I was able to finish one head per day.  On Thursday, I returned to working on the ultrasound scans and was able to get the majority of them done.  When my last day on Friday rolled around, I was already pretty close to finishing all 200 scans.  My PI, who had returned from his hiatus, had additional requests for me regarding the ultrasound scan data.  The last day (which was only until around 2 PM) was more work than I anticipated it to be.

At around 2, I handed in the key to my lab that I had received during my second week at the lab and certain odds and ends that I had received from them over time (such as a metro card to get rabbit heads).  I guess that's when it really hit me that I was actually going to leave the lab.  I was sad to leave, but also happy that I had been so productive in the time that I was here.  My PI remarked that it was probable that we would be able to make at least one ARVO (Association for Research in Vision and Ophthalmology) abstract that we could present at a national conference sometime within the next year.  Just before we left to go meet my parents for a "farewell lunch" that we had planned earlier, they gave me a Columbia University Medical Center T-Shirt as a souvenir which I really appreciated.  It read "Be nice to me.  I might be your doctor someday."

Perhaps someday!

Winston Kung - Week 6 (7/14 - 7/18) - Silverman Lab, Columbia University

Hi there, I'm Winston and this is my EXP Summer Lab Research Experience thus far:

Because we couldn't get a rabbit on Friday, I tried to get a rabbit again today.  As my luck would have it, the butcher's place was not open for some reason.  Fortunately, however, I was prepared.  I talked to people in my lab and found another butcher's place.  Although it was much farther than the first butcher's place, and much more unsanitary, it got the job done at the end of the day.  I was able to get a white rabbit's head and cross-link the corneas.  This fourth rabbit is going to be the last rabbit I use in my cross-linking procedure.  I've collected enough data for all intents and purposes.  What lies in store for me is to begin analyzing the data I collected from the all the scans I took.  My PI plans to teach me how to do this tomorrow.

As expected, the data analysis phase of this research project is quite repetitive.  Furthermore, we gathered quite a bit of data, so it's a large quantity of repetitiveness to chug through.  Consequently, it's taking me quite a while to get through just one rabbit eye/cornea.  At the rate I'm going at right now, I will probably be able to finish one whole rabbit head in two work days.  Unfortunately, my PI is going away on Wednesday for some sort of conference, and won't be back until Friday of next week, my last day at the lab.  In preparation for this, he taught me how to analyze the ultrasound data that we collected as well.  We took 200 scans per eye for one patient, and he had expressed his hope that I would be able to get at least 200 scans done by the time he got back.  So I have to finish the rabbit OCT scan analysis as well as the ultrasound analysis.  I have my work cut out for me.

On Wednesday, I tried analyzing as much of the ultrasound scan data as I could, since I was less familiar with this process than the OCT scan data analysis process.  This was the second to last day I would see my PI so I wanted to make sure I had everything down before he left.  Luckily, the data analysis process was not too complicated, and I only ran into one problem with the data analysis software coding which my PI soon fixed.

The last two days of the week, I spent working on the rabbit OCT scan data analysis.  By the end of this week, I had finished the entire first rabbit head.  I also started the second rabbit head, but the amount that I had completed for the second rabbit head was practically negligible.  Towards the end of the work day on Friday, one of the members of my lab asked me if I could go back to the butcher's shop on Monday to see if I could get a rabbit for one of her experiments.  She said she gets queasy easily and preferred to not go herself if she could help it.   It was totally fine for me and I was glad to be relied upon.

Sophie Kennedy B.I.O.S. week 4

 This week I got to live in one of the dorm rooms at BIOS which was an awesome experience because I finally had the chance to bond with the interns outside of the lab. Monday and Tuesday we made dinner at another intern’s apartment and then Dr. Peretz came to Bermuda on Wednesday!!! Dr. Peretz and I went to the town of Hamilton for dinner. I had hoped to take her to harbor nights (a Wednesday night event in town similar to a street fair) but it turned out to be a stormy night. I really enjoyed showing her our lab and the BIOS facility as both of us dreamed of bringing a group of Peddie kids here. (I’m thinking an EXP field trip?)

 On Tuesday we went out to collect and put back the corals from the patch reef. The corals are put back on the reef by using underwater cement that Lea and I made a few days before. We were supposed to collect the rim reef corals and put some back however the weather was not quite working in our favor this week. On Wednesday the wind was so strong that it snapped the roof of our wet lab in half. So I spent most of the week helping Kevin take pictures and map the growth of the spat (settled planula).  The process of mapping spat growth starts with cleaning each tile: ensuring that each spat is growing on a flat surface, can be photographed, and is circled. In order to obtain the reasonable data, we sometimes need to kill a spat that is growing into another. Then by attaching a lens that extends into the microscope to the camera, I can take pictures of each circled spat. We had a worm infestation one day and found that many spat had been eaten but with thorough washing our tanks are nice and worm free now!

The past few weeks have consisted more of collecting data versus settling the planula or looking for spat. I spent most days taking pictures for the 10 day, 20 day, and 4 week checks for the porites and favia. As tiles are lost and spat are accidently touched our data is messed up. I was shocked at how much human error is present in scientific experiments. In school labs I always mentioned human error as a possible source of error however it wasn’t until my time in Sam’s lab that I truly saw how often it occurs.

I finally made it out on Friday for my two last open water dives. I am now a certified open water SCUBA diver! We dove a shipwreck a couple miles off shore (a rim reef). I was amazed at all the brain coral and sea fans.  I also had the chance to meet a few other interns- one goes to Princeton!

I could not be happier with my choice to work at B.I.O.S. this summer. I never just have to concentrate on my lab work but, with my P.I.'s encouragment, I was able to get my open water certification, help teach a class with her, and get my lionfish spearfishing permit. I do wish that I had my own project that I worked on all summer however I have learned so much with the 5 of us working as a team. Overall it has been an amazing experience and I am torn that I only have a little over a week left here.

Corals at the rim reef dive site. (notice the clarity)

Showing Dr. Peretz our coral lab!

 20 day Favia growth picture from the Y tank. (Low light, high temperature)

Alex Hauschild - Shields Oncology Research Rotation - Week 8 (the final week)

           Back two weeks ago when ABC news came in to interview Dr. Carol, we got to do a couple shots of us in the clinic. I managed to make it into the final cut: http://www.wsoctv.com/news/news/special-reports/9-investigates-cancer-mystery-huntersville/ngpwT/?__federated=1 (at 2:27)

As my great experience learning with the inspiring people of the 14^th floor clinic of Wills Eye Hospital winds to a close, I am at a loss for words. Oddly enough, this is the first time I have ever worked doing anything where I only wish that I could stay longer and do more work. As I look back at all the experiences I had this summer and all the people that I met, I believe I made some powerful connections and managed to find not only one but two welcoming homes in the process: one at Wills and another at the apartment of the Kleinbergs whom I stayed with all summer. I only want to thank all who made this possible including my wonderful mother and astute teachers Drs. Peretz and Crider whose keen guidance helped me find a place with the Shields, the Shields and associates who put up with all the students for two months while we learned all that they had to offer, Teri who opened her home to me and taught me the basics of cooking gourmet food, and of course the med-students who helped me understand everything when I was first starting and helped me write my poster and article. The list goes on as to all the people that I could thank, but one thing is for sure: I will never forget the summer of 2014.

                My final week in review: Monday – nothing new, just the usual retinoblastoma, uveal melanoma, nevi in various shapes and forms, and another sad case of melanoma that required enucleation. Of course research was also done on all days.

Tuesday – other than the typical scarring and loss of vision because of radioactive plaque treatment and other secondary problems associated with treatment, we managed to see some paving stone retinal degeneration which was very cool.

Wednesday – In the morning, I went around with Dr. Jerry Shields seeing patients and saw some pretty interesting stuff. One patient we saw had a multifocal melanocytosis of the uveal tract with multiple melanocytomas very interesting but luckily completely benign. Another was a highly unusual variant of hyperplastic limbal epithelium which presented as a small white elevated mass on the edge of the cornea. The final case that was of interest was one of only four patients in the entire system of patients that the Shields treat whose cancer is unclassifiable. “This tumor just defies diagnosis” said Dr. Jerry Shields. Needless to say that it is beyond rare to have the Shields come up empty handed, period. I went down for some time in the OR after that to watch some EUAs. Just the normal stuff really, typical retinoblastoma cases that are either new or are coming in for a follow up to be sure that everything is fine.

Thursday I started the day by bringing in some donuts from the best donut shop in Philadelphia – Federal donuts all of the students pitched in to get some stuff for the clinic staff and doctors. We even brought some down to the break room in the OR so that the doctors could snack on them as well. In Dr. Jerry’s OR (which I started in) I saw a removal of a conjunctival lesion and a very long removal of a lacrimal gland cyst. After watching a plaque with Dr. Carol, she decided that she would introduce us to some of the other surgeons and lend a few of us out. I had the opportunity to watch Dr. Maguire of the Wills retina service perform some surgeries in his OR. The first was to fix a macular hole. The surgery went something like this: first a vitrectomy was done to remove all the vitreous from the posterior chamber and replace it with balanced solution (similar in molecular composition to the vitreous). Kenelog is then injected into the posterior chamber to help visualize the hyaloid membrane adhering to the macula. This membrane is then carefully removed and suctioned up. Indocyanine green (ICG) is then injected to stain the internal limiting membrane (ILM) which is then carefully removed. After removal of the ILM, the solution in the posterior camber is replaced with high pressure air forcing the macula back together. The air is then replaced with SF₆ gas to preserve the anatomy of the eye and help it heal. While the gas is in the eye, the patient will not be able to see, but this will resolve in 2 weeks time when the vitreous starts to return. I then went back to Dr. Carol’s OR to see an aspiration of an iris cyst – kind of self-explanatory. I left just as the enucleation was beginning and returned to Dr. Maguire’s OR to watch another macular hole surgery.  Once the surgery was completed I thanked him for letting me observe and went back to Dr. Carol’s enucleation and made it just as they were pulling out the eye. We all crowded around a small prep-table as the doctors opened up the eye to harvest tissue samples from the tumor. It was quite a sight: 17 people crowded around one table with nothing on it but a very out of place looking eye. It should be noted that the table was no bigger than a common student’s desk. Shortly after that, I counted 21 people in that room. To say that this was an exciting day would be an understatement.

Friday was my final day. I spent the morning helping the fellows with research (mostly pulling charts and entering data). I left to have lunch with Teri, the nice graduated-resident-of-Wills that I was staying with for the summer. I came back to do some more work before a few of the remaining students suggested that we all get our eyes dilated and have a full workup by the photography department. Just a few of the photos taken:

Apparently I have a spot of pigment on my right iris...

The back of my right eye

The retina (as shown by the cake like layering), the fovea (the little dip in the middle), the Choroid (the bulging sponge like mass under it), the orbit under that, and the optic nerve to the far right. This is the macula of my right eye.

 We took our last photos as a group with the Drs. Shields and said our goodbyes. Dr. Carol gave me some great advice on applying to her alma mater: The University of Notre Dame. Exciting things including the strongly implied fact that all of the students who worked on the massive project would be given author status on the publication once it goes to print in about a year or so. She also said that any EXP-ers would be welcome to spend the summer doing something similar and I would be welcome back anytime… She actually said that she expects me to come back for another summer sometime again. Something tells me that my experiences in medicine are only just beginning…

Dr. Carol (center) and the students, 5 not pictured.

                As I finished writing this, I was actually offered another research job by Dr. Levin in the pediatrics department working on redefining convergence insufficiency. For reference, the study that I was working on for most of the summer had 1200 patients in it, and with 20 people working on it for 4 hours per day, it got done in about 2 months. In truth, it still has more work to be done on it. Comparatively, my the pediatric study is fairly large, encompassing some 800+ patients and with only 3 people working on it, something tells me that it will take a very long time to complete...