sophie7
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Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st :C

Postby sophie7 » Sat Nov 28, 2020 11:50 am

My project is a data analysis project and my question/ topic I'm trying to find out is

"Can serum TDP-43 serve as a biomarker for frontotemporal lobar degeneration"
Is there anyone in science buddies that count help me and guide me through this project especially the data analysis part? I have a mentor but they have been really busy recently and we don't get in contact often.

Here's some of the info about my project and how I came up with it


So basically I came up with this idea at 1 AM when I was watching a random documentary about Clive Wearing, a former British musicologist who loses his memory every 30 seconds or so. He suffers from retrograde amnesia which lead me to do research on memory where I learned more about dementia, so I decided to make that my science fair topic.

I did more digging and discovered FTD, frontotemporal dementia and learned about protein TDP-43, which is normally a transcriptional repressor and it regulates splicing. However, mutations from chromosome 17 caused it to have many genetic causes that contribute to the severity of frontotemporal dementia. From a bit of research and the help of a mentor, my project is "Can serum TDP-43 serve as a biomarker for frontotemporal dementia?" He told me its best not to do an actual experiment since we're in the middle of a pandemic, instead he recommended for me to do a data analysis project but I have no idea how to????? And I'm hoping to make it to my state science fair but I'm not sure if I can if I have no idea how to do this? So here are my questions and I really hope someone can answer them because my project is a complete mess. I'm attaching a few reports where I am getting my data.

1) My "question" or thing I'm trying to solve is literally my project title. Is that fine or do I need to find a new project title? If I do can someone recommend a project title because I'm not creative ;-;
2)I'm in 9th grade, I have no idea how advanced science projects work. I read the science buddies article but is there an example of a good advanced science project somewhere that I can refer to?
3) Where would be a good place to ask about all my questions on the subject Frontotemporal dementia? Does someone on science buddies have time to help me :C
4) What would be my procedures for a data analysis project? I'm planning on getting my data by analyzing 10 papers that include multiple pieces of data.
5) How do I combine these pieces of data into trials? How many trials do I need?
6) My mentor said something about using scatter plots, t-tests, correlations and some sort of software he forgot the name of? Can someone explain these because I don't take statistics?
7) As far as I know I haven't found anything on google scholar where someone has analyzed data from multiple resources to answer the question to my project, but they have done the experiment itself. Does this project have potential if done correctly?
8) How many pages of research should I write? I only did around 3 pages so far.
9) Will all of my questions be miraculously solved if I understand all the reports which I bahaha dont
10) how do I understand all the reports?
11) how long does it take to do a data analysis I have about 7 days in which I have to go to school?
12) I forgot the rest of my questions but if I have more can I post here?

Thank you so much for reading all of this and I really hope you can answer these questions :C

Here's two of the reports I'm using
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789307/
https://link.springer.com/article/10.10 ... 007-0315-5

MadelineB
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby MadelineB » Sat Nov 28, 2020 4:09 pm

Hello Sophie,

This is an interesting approach to a science project! It seems to me that the best way to answer your question "Can serum TDP-43 serve as a biomarker for frontotemporal lobar degeneration" would be to conduct a meta-analysis. Here is a link to a published paper on Meta-analysis in medical research. This paper gives a good description of the process:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049418/

As you can see, this would be a serious undertaking. Since you are in the 9th grade, you might work with your mentor and consider a smaller analysis for this year, with the idea of preparing for a more complete analysis for your 10th grade project.

In preparation for the smaller analysis, I suggest that you search the medical literature to get more background information on serum TDP-43 and frontotemporal lobar degeneration. In your background research, it will be helpful to see whether other researches have already conducted a meta-analysis or a systemic review. In addition, one area where you will need more information is whether TDP-43 is involve in other types of degeneration. The first reference that you give in your post suggests that there are other types of degeneration:

"TDP-43 is also being recognised increasingly as a variable component of inclusions of other neurodegenerative diseases including Alzheimer’s disease (AD) (Amador-Ortiz et al. 2007), ... ".

So hopefully you can talk with your mentor to clarify if TDP-43 is specifically a biomarker for frontotemporal lobar degeneration, or if it has more general effects.

I hope this helps. Let us know if you have more questions.

Madeline

BTW, the link to your second reference is broken. Perhaps you could provide that again. Thanks!

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Sun Nov 29, 2020 12:16 pm

Thank you! This helps a lot and here's the link

https://link.springer.com/article/10.10 ... 007-0315-5

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Thu Dec 31, 2020 8:44 am

Hi, I have another question I'm hoping someone can answer. I've recently been trying to collect data, I've looked through 100+ literature reports and I haven't found anything that fits what I'm looking for. Without data, I can't do my meta-analysis therefore my project is currently failing. X_X

Should I keep looking? Am I using the wrong words when searching? (I'm using PubMed and google scholar btw)

If there really is no data, should I switch to another topic? I was thinking of maybe switching to "Can TDP-43 serve as a biomarker for amyotrophic lateral sclerosis" because there is data for that topic but someone has already done a meta-analysis on it and has proven that TDP-43 CAN serve as a biomarker for ALS, and I was hoping to do something original.

MadelineB
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby MadelineB » Thu Dec 31, 2020 3:16 pm

Hello Sophie,

One of the important steps in preparing to do a meta-analysis is to define the criteria for the research papers to include in your analysis (see the reference I gave to you previously).

You've looked at 100+ research papers ... what criteria did you use to decide to look at those papers?

Hopefully, your mentor can help you refine your criteria and select your search terms.

You might also study the methods used in the meta-analysis report you found which showed an association between serum TDP-43 and ALS. One way to double-check your search methods would be to see if you can find the research papers which were included in that meta-analysis.

That finding raises the question whether serum TDP-43 can serve as a biomarker for both frontotemporal dementia and ALS. What is the research that would describe, given subjects with serum TDP-43, how to distinguish which subjects would have (develop) frontotemporal dementia versus those who would have (develop) ALS?

Looking at those research papers might help you select the criteria for your search for whether serum TDP-43 can serve as a biomarker for frontotemporal dementia.

Let us know if any of these suggestions help!

Madeline

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Thu Dec 31, 2020 4:01 pm

When I was looking at the papers, I went through the results google scholar and PubMed provided, and I was hoping to find reports that would include amounts/percentages of that showed the presence of tdp-43, such as the percentages of nuclear-tdp-43 depleted neurons in a sample size from someone's brain as well as any symptoms/ diagnosis of which stage the patient was in something like that. I'm going to re-read the research papers and hopefully find better criteria! Thank you for the advice and happy new years eve!!!!

MadelineB
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby MadelineB » Fri Jan 01, 2021 4:25 pm

Hi Sophie,

Two questions for you:
(1) Are you using some key words to search the PubMed site or are you reading each individual research paper to find your topic?

I suggest that you use the first option in order to limit the number research papers you need to read.

If you haven't reviewed this handing Science Buddies resource "Resources for Finding and Accessing Scientific Papers", I think this will be helpful, particularly the PubMed tutorial:

https://www.sciencebuddies.org/science- ... fic-papers

(2) Are these separate diseases? Frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS)

If you haven't reviewed this paper, I suggest you do. These researchers suggest that FTD and ALS might be 2 diseases on the same spectrum and perhaps TDP-43 is a biomarker for both.

https://pubmed.ncbi.nlm.nih.gov/29954341/

This is probably something to consider when you are doing your literature search and defining your meta-analysis plan.

Let us know what you find and if you have more questions.

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Sun Jan 17, 2021 11:14 pm

Hi Mrs. Madeline!

Sorry I just now saw this, I just finished my midterms (still waiting for results D:)
I used to read individual papers that I found from google scholar and I would read the sources that those papers cited, but after looking through some of the resources you previously sent, I started using keyword searches :D

I think ALS and FTD are two separate neurodegenerative diseases but they do overlap a lot. ALS mostly causes patients to lose their movement abilities (including swallowing, breathing) over time while FTD causes cognitive decline and behavioral problems in patients. I watched a video that said TDP-43 was the accumulating disease protein in almost all ALS cases and more than 50% of FTD cases.
There's been a lot of papers that mention TDP-43 as a possible biomarker for FTD, but that's only mentioned alongside other diseases such as Alzheimer's, FTLD, ALS.

There's still no biomarker for FTD which makes it hard for medical professionals to diagnose people since the only way they can get a confirmed diagnosis is through an autopsy.
https://health.usnews.com/health-care/p ... 0diagnosis.

I've started choosing papers where I can extract data from, but I've only found around 30-40 ish FTD patients so far and a lot more controls. They're more related to my project though, and I've started looking at the data they got from plasma and cerebrospinalfluid. I'm planning on extracting the genders, ages of onset/death/age, disease duration, mean absorbance, any MMSE scores. I'm trying to find a positive correlation between TDP-43 and FTD, but I'm not sure how I can do that without any behavioral symptoms and neuronal damage. I'm hoping to use the disease duration instead, but disease duration might not depend entirely on TDP-43? I'm also thinking of maybe comparing TDP-43 levels in FTD with TDP-43 levels in other neurodegenerative diseases such as Alzheimer's and Parkinson's but I'm not sure. What other data should I extract? Here are some of the papers:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2464623/
https://www.hilarispublisher.com/open-a ... uction.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2809136/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690860/

Thank you so much for helping me with my project and I'm really sorry you have to read this mess
-Sophie

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Sun Jan 17, 2021 11:34 pm

Hi, Mrs/Ms/Miss Madeline! Sorry, one more question
Instead of comparing FTD with Parkinson's and Alzheimer's and other neurodegenerative diseases, should I consider looking at TDP-43 levels in variants of FTD?
(Behavioral variant frontotemporal dementia (bvFTD)
Semantic variant primary progressive aphasia (svPPA)
Non-fluent/agrammatic variant primary progressive aphasia (nfvPPA)
thank you so much again-sophie

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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby MadelineB » Mon Jan 18, 2021 3:45 pm

Hello Sophie,

Congratulations on surviving your exams! Thank you for the links to the references. Due to other commitments, I will need a couple of days before I have time to look at those. In the meantime, thank you for your patience.

Madeline

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Mon Jan 18, 2021 4:41 pm

Of course!

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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby MadelineB » Thu Jan 21, 2021 4:12 pm

Hello Sophie and thank you for your patience!

You are studying an important area and thank you for providing the links to the research papers. I do need to emphasize that I am not a physician. I am a biostatistician and data scientist. Although I have collaborated with medical researchers in other areas of medical research, I have no experience in the areas you are studying. Hopefully your mentor has experience in these areas.

I do have several questions after reading these papers. These are the types of questions to ask your mentor!

If I understand the results, TDP-43 is found in plasma (peripheral blood) and Cerebrospinal Fluid (CSF) is associated with both ALS and FTLD, although it is suggested that higher levels of TDP-43 are more likely to be associated with patients with FTLD.

Your original question is whether TDP-43 can be used as a biomarker for FTD. If TDP-43 is associated with FTD, Alzheimer's and ALS, it looks like you will need to consider how levels of TDP-43 might be useful to distinguish between these diagnoses.

These are some of the data items you will need to record for each paper in your literature search. Your background research will be useful to learn what other patient characteristics (age, symptoms, laboratory tests, etc), if any, are thought to be useful in distinguishing among ALS, AD and FTD. It looks like some of the studies use patients with clinical diagnoses and others are studying patients for whom the diagnosis was made at autopsy.

When researchers report that higher levels of TDP-43 are more likely to be associated with patients with FTD, it is important to see if the patients in the study had similar patient characteristics and if the TDP-43 was measured at the same time during the course of the disorder for each patient, for example, at the time of the initial diagnosis.

Another thing to look for in your background research, is whether the levels of plasma and/or CSF TDP-43 increase over time, perhaps suggesting the patient's disorder is getting more severe.

Your references are from 2008 and 2009. It would be useful to see if there are more recent publications, 2019, 2020. Perhaps there has been some progress in the understanding of the association between TDP-43 and these disorders. If you haven't already, you might also check the website for the National Institutes of Neurological Disorders and Stroke (NINDS) at NIH. https://www.ninds.nih.gov/Disorders/All ... ation-Page

I realize I am mostly asking questions, not answering yours. Hopefully your mentor can help you with the medical aspects.
Madeline

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Wed Mar 03, 2021 6:22 pm

Hi Madeline!

I'm so sorry I haven't been able to check science buddies in a while since my project date was coming up. A lot happened in February so I wasn't able to check. My school fair happened, and I won first so I was able to progress to regionals. Then my regionals fair happened really soon and I wasn't able to make any edits but I somehow won (idk how oof) that two so now I get to progress to state and I couldn't have done it without you!

For the data, I decided to collect the age, their symptoms, the tests used to determine tdp-43 levels, sample sizes, absorbance values, medical diagnosis, and MMSE scores! I really wish I had checked science buddies before because that link you sent really helped me understand the standing of where scientists are on biomarkers for FTD.

I ended up calculating the effect sizes, finding the p values, measures of error, measures of dispersion, variance, and standard deviation. I didn't include the data for all of them on my poster, and with this kind of wacky science fair year, I don't have a chance to really present these numbers.

In the end, I also calculated the relative values of tdp-43 levels in patients without ftd and patients with ftd. It was hard to find data, and even my mentor couldn't really find anything else because he doesn't have access to some papers either so I just ended up analyzing 5 papers with a total of 281 patients. I had to combine non-FTD patients all together (a couple cases of Parkinsons, a couple of alzheimers, a lot of control) because their numbers weren't sufficient alone.(Spoiler: in the end, patients with FTD had a higher relative value by 0.93 compared to non-FTD patients so that was cool) I did the best I could, but I'm not really confident with my data and its too late for me to change it because its just been fair after fair and my state fair is 3/7.

For my state fair, we need to have a 2-3 minute recording explaining our projects. We aren't going to be able to personally present to the judges over zoom or answer any questions which makes me sad.

I'm planning on introducing myself and my project first (cuz that's required) for 25 secs, then I'm going to spend maybe 50 seconds explaining the topic with the research I did, then I'm going to talk about the procedures and materials I used for 35 secs, then explaining results for 35 seconds, then the final 35 seconds talking about future applications and how this is relevant to society or whatever.

Do you have any suggestions on making my video as good as I possibly can? I can't change anything right now so how would u recommend presenting my sad data with confidence?

Thanks ,sophie

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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby MadelineB » Wed Mar 03, 2021 9:20 pm

Wow Sophie7! That's amazing!

I think about the only suggestion I might have relative to the time on each section of your video ... think about the questions the judges asked, particularly at the regional: if their questions were mainly about the results, you might be sure to allow time for the results. On the other hand, if they focused on your methods and procedures, then maybe move 5 seconds there.

The other way to allocate your time for the video is to visualize how you allocated the different sections on your poster. It seems hard to argue with how you arranged your poster since you've won first place locally and regionally!

Finally, for sure, talking about the future applications and relevance to society.

I also wonder if you know if the other students are just talking to the camera? or are they showing a powerpoint slide show with your head shot off in the corner? At this point though, I think you will be best to just do what ever you've been doing!

Best of luck with your video ... work on that presentation until you appear and sound really comfortable.

I'm excited for you! Best wishes!

sophie7
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Re: Need help with data analysis project- I have a lot of questions and theres a lot to read pls answer by december 1st

Postby sophie7 » Fri Mar 12, 2021 6:44 pm

Thank you!!!!!!!!!!!!!!!!!


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