Jaime's Senior Project

Monday, April 30, 2012

Blog 25: Service Learning

1. LIA Response to blog:
Literal

Log of specific hours with a total and a description of your duties: Forensic Science Academy Club Log
Contact Name & Number: Ashlee Enriquez & 1(323) 365-8826

Interpretive
What is the most important thing you gained from this experience? Why?

The most important thing I have gained from this experience was being able to placed in an applied real-life simulation of what it is to be a Forensic Anthropologist. I am surrounded by individuals who are in their adult years and this continues to fuel how I am young and so well-interested in this particular field of science. So I would say that the most importance thing I have gained from this experience was being appreciated for my work because I am making doctorate (Ph.D) credentialed professionals, who actually work in the field that I want, ooh-ing and ahh-ing to the presentations and comments that I have to say. The knowledge I have gained is never going to be forgotten, I continue to read articles in the Economist and the Financial Times that feature Anthropology-based interviews, international spotlights, or crime mysteries that I have been able to interpret and understand. For my hard work, I was even given the privilege to use a National Institute of Justice software program known as the Visualization Science Group VSG.

"Hello,

I just wanted to touch base with you to see if there was anything I can do to help with your evaluation of the VSG software that you are using for Forensic Anthropology purposes, please let me know.

We have offered you Beta and Pre-Alpha licenses so you can try our software. By offering this service, we feel that we reducing any risks that may be associated with the purchase.

We want be able to demonstrate to you that our software will work with your data and provide you with the results you desire.

If needed, please contact Ming Lei at Ming.Lei@vsg3d.com for any technical assistance you may need.

We have found that with over 5,000 VSG software licenses in use all around the world, you have become our biggest asset in spreading the word about our applications. We hope hear from you soon!

Best regards,
Bill Henderson
Account Manager, Academic & Government
V S G - Visualization Sciences Group "

Applied
How did what you did help you answer your EQ? Please explain.

What the Forensic Science Academy Club offered allowed me to answer my essential question of, "What is the most important factor of a skeletal remain in a criminal investigation" by implementing hands-on individuals to facilitate simulations, group work with other forensic potential scientists, giving me resources that were government established for my use, field trips to the Los Angeles Coroners Office and Museum of Death, and allowing me to express my knowledge through presentations in front of my peers.

For example, my first answer was "determining if the skeletal remains are in fact of forensic significance based on the presence of trauma." The Forensic Science Academy Club challenged me by taking away that assumption that as soon as I see a bone or a remain I will automatically thing that it is human and try to name or locate where in the human skeletal system it belongs. It was more of a scientific practice to determine the locomotion of the presented remain and being able to draw conclusion by what has been presented to me. It helped me answer my EQ since determine if the bone or remain was of forensic importance would be the most importance factors of a criminal investigation, since after all it is what starts the establishment of an investigation to actually occur! We don't want anyone to get away with it!

Finally, my third answer was "matching a weapon or natural component that was left as a striation of the remains because of the fact that DNA or lethal vectors need to match to an object used to succeed in the cause of death and match trauma-mortem." Now altought this was a tough one, the Forensic Science Academy took me to field trips to the Museum of Death, Los Angeles Coroner's Office, which allowed me to have expert source analysis that determined that this was the most importance factor of a skeletal remain in a criminal investigation. The hands-on application such as the Technology National Institute of Justice Forensic Anthropology Week that allowed me to study, review, and apply matching a weapon or natural component that was left as a striation of the remains because of the fact that DNA or lethal vectors need to match to an object used to succeed in the cause of death and match trauma-mortem and part of the forensics workshop had a lesson about "Tissue & Bone Measurements" and "Forensic Resource Reference on Genetics (FROG) Demonstration and Hands-on Exercise" which allowed me to use impressive government-funded software programs that allowed me to input measurements of bone structures, I applied it with my Service Learning Cranial Reconstruction Project that allowed me to have a computerized version of what I was simulating. Tissue & Bone Measurements program allowed me to know exactly how to measure and be able to apply it in mathematical formulas in order to compute stature and ancestral background, whereas FROG software allowed me to compare skeletal structure caused by DNA in order to compile it with an ancestral background or native origin of the individual I was identifying throughout the entire program.

2. Confirmation of Contact Person, Contact Phone Number, and 50 hours completed

Contact: Ashlee Enriquez & Number: 1(323) 365-8826

Ms. Enriquez was also an interview which has been scanned and placed here for your convenience.

Refer to Forensic Science Academy Club Log along with blog post evidence:

Wednesday, April 25, 2012

Blog 24: Independent Component 2

Click the following link for the Independent Component 2 Calendar Spreadsheet: Advances in Forensic Anthropology Technology Transition Workshop - National Forensic Science Technology Center - NIJ

Literal
(a) Statement saying: “I, Jaime Cervantes, affirm that I completed my independent component which represents 48 hours of work.”
(b) Explanation of what you completed. I have completed 48 hours of work by completing the entire NFSTC FA Workshop. This workshop allowed me to have knowledge in the perspective on human variation based on ancestral background and geographical location, be able to discuss the determination of biological sex in an anthropological atmosphere, have the fundamental values in order to explain the craniometrics and geometric morphometircs, being able to apply segmentation methods for CT images, bone measurements to use the facial reproduction empirical modeling software tool, explain genetic variation in the context of forensics, emphasizing ancestry informative DNA markers, apply likelihood methods of cause and time of death vector qualities, estimate ancestry using advanced computer software programs. Some of these programs were known as 3D-ID, AVIZO Forensic Anthropology Software, STRUCTURE, Forensic Resource Reference on Genetics (FROG), Dental MP Records Acquisition, and Simple/Complex UP. Within each of these lessons, I was provided with live audio visuals, resources, training videos, information sites, computer software programs and hands-on materials.

Interpretive
Defend your work and explain how the significant parts of your component and how it demonstrates 30 hours of work.

I believe my second independent component was rather genius! Having access to Ph.D credentialed resource analysis that I will be able to use within my I-Search, 2 Hour Presentation, Exit Interview, and in a higher education will allow to be more competitive than I initially was when I went to the LA County Science Fair. I believe if I completed the 48 hours of this component at an earlier time I would be able to have a better chance of explaining and executing my knowledge on Forensic Anthropology. The program, lectures, resources, and software are all amazing and well-designed. I am honestly not a computer expert but the software I was provided with allowed me to put in formulas, different cranial measurements in order to simulate a 3D image that I was able to identify with all of the sources. With this I was able to significantly indicate the humanoid establishment of the individual (Homo sapiens sapiens) stature of an individual, ancestral background (cleaner version of the controversial race/ethnicity/etc. sect groups), time of death, and cause of death, bone and tissue deterioration, and craniometrics and geometric morphometirc factors of a skeletal remain!

My answer 1 for my EQ is: determining if the skeletal remains are in fact of forensic significance based on the presence of trauma and part of the workshop had a lesson about "Fundamentals of Traditional Craniometircs and Geometric Morphometrics" which mathematically computed a 3D image of the skull or any type of skeletal remain when the coordinates have been inputted, can recreate the image. With this software program I had the ability to have a closer look and be able to find out to see if there was an entrance wound, a striation in the bone, healed wound, or any discoloration with the bone that I can suggest to be of forensic importance. This workshop had a high amount of resources, a live video lecture, software application, and hands-on experience.

My answer 2 is : determining the horizontal excavation layer in which the remains were found in order to determine the possible time of death and part of the workshop had a lesson about "Segmentation Hands-On" which literally was about my answer: the paleoanthropological aspect of soil time scales and being able to relate them accordingly with my current research aspect and be able to broaden my perspective on what exactly segmentation is used for in the field of Forensic Anthropology and how it continues to create an advancement within the scientific community.

My answer 3 is: Matching a weapon or natural component that was left as a striation of the remains because of the fact that DNA or lethal vectors need to match to an object used to succeed in the cause of death and match trauma-mortem and part of the forensics workshop had a lesson about "Tissue & Bone Measurements" and "Forensic Resource Reference on Genetics (FROG) Demonstration and Hands-on Exercise" which allowed me to use impressive government-funded software programs that allowed me to input measurements of bone structures, I applied it with my Service Learning Cranial Reconstruction Project that allowed me to have a computerized version of what I was simulating. Tissue & Bone Measurements program allowed me to know exactly how to measure and be able to apply it in mathematical formulas in order to compute stature and ancestral background, whereas FROG software allowed me to compare skeletal structure caused by DNA in order to compile it with an ancestral background or native origin of the individual I was identifying throughout the entire program.

The following blog posts can facilitate how my independent component represented 48 hours of work:

Applied
How did it help you answer your EQ? Be specific and use examples.

My independent study component completely relates to my EQ because in this workshop I will have access to professional software and Forensic Anthropology-heavy hands-on activities and work that will give me a new paradigm of how scientific and mathematical this topic is. Based on the NFSTC Forensic Anthropology Workshop, all of the application and literal analysis that I will be able to have a hold of will be able to be well interpreted within my two hour presentation and further research knowledge.

My answer 1 for my EQ is: determining if the skeletal remains are in fact of forensic significance based on the presence of trauma and part of the workshop had a lesson about "Fundamentals of Traditional Craniometircs and Geometric Morphometrics" which mathematically computed a 3D image of the skull or any type of skeletal remain when the coordinates have been inputted, can recreate the image. With this software program I had the ability to have a closer look and be able to find out to see if there was an entrance wound, a striation in the bone, healed wound, or any discoloration with the bone that I can suggest to be of forensic importance. This workshop had a high amount of resources, a live video lecture, software application, and hands-on experience.

Blog 23: Helping 2013

Interview 5

Who did you interview: Jada Hall
What day and time: Thursday, April 26, 2012 Location: Denny's 12:40-13:38

1. What ideas do you have for your senior project and why?

Her answer: I want it to be on Psychiatry specifically on patients who have Autism. I want it to be my senior project because I always enjoyed watching films of people with Autism and I would love to interact and help them out through the field of Psychiatry.
Feedback offered: It's excellent that you have a solid senior topic, the fact that you pin-pointed it to a specific type of Psychiatry and not let it be general is a great idea! The fact that you have been so interested in Psychiatry regardless of how many years of school it would require suggests that you are really interested in the topic and will be able to create a superb product.

2. What do you plan to do to complete the 10 hours of service learning (working with an expert) which is due prior to senior year starting? Note: They also have to complete the 50 hours during the school year.

Her answer: I haven't started looking for a place on Psychiatry, although I do know that I either want to shadow a Psychiatrist or be able to observe group sessions with people with Autism or other mental disorders.
Feedback offered: Make sure to find a place to conduct your service learning as soon as you can, and make sure you have the ability to commute there: either make it near I-Poly or near your home so that it wouldn't be such a hassle. Most importantly, don't give up looking for places because you want to continue to have service learning in a point of interest and not just because you didn't look hard enough. You have a great idea of shadowing one-on-ones and group sessions, although I am not specifically sure if my peers had trouble finding service learning, I know that your interest will allow Psychiatrist to let you into their facility with open arms.

3. What do you hope to see or expect to see when watching the class of 2012 present their two hour presentations?

Her answer: I have high expectations on the Seniors; they have been working on this project for eight months and I expect it to be engaging, interesting, and not boring! Since the dedication and projects and presentations have been happening for a long time I expect to see a great presentation and most importantly learn from the projects and being able to get little pits and pieces to use on my presentation.
Suggestions regarding how they should approach watching the 2 hour presentation: I suggest that Jada would try her best on going to senior projects in the fields of Psychiatry, Psychology, and other mental forms of therapy. Keep all of the hand-outs, take mental or actual notes of how they executed their presentation and method of engaging the students and being able to use it on her own.

4. What questions do they have about senior project? What additional recommendations would you give the 2013 student about senior project? Be specific and note what you told them.

Questions she asked:

Do you get half-days off? Yes! The half-days are designed to allow you to take Young Scholars courses which you should take advantage of and use for an independent component since you are eligible. Also, it allows you to go to service learning and be able to complete your hours with an expert in your field.
Why do I have to start looking for places to interview at and volunteer right now? Although you can't start anything in this current type except the summer component, it is great to start getting involved in service learning in order to get multiple contacts, have access to resources that will be extremely helpful in your senior project?
How many presentations do you have to do? A 5 minute on the reason you want to do your senior project, three 5 minute presentations on your answers for your essential question, a 20 minute presentation with a foundation on your essential question with an activity included, and the beloved 2 hour presentation.
If I have more questions can I ask you later? Sure!

Additional recommendations given:

Prepare your summer in managing your time wisely, don't leave anything last minute or procrastinate. You don't want due dates of core-related projects and homework snowballing down on you when you have to also work on senior project.
Try your best to complete all the work on time, the Senior Team follow the NC rule and if you are unable to complete a component you will have to do it as soon as possible or suffer from not walking during graduation, going to prom, or Grad Nite.
Take your time on projects, work on them little by little each day and you will be able to go above-and-beyond the said expectations in order to get the AE. Don't be the person in class who moans and groans when they are told a due date and have not worked on it!
Don't stress yourself out too much, since senior project is something you chose then you should be so engaging on the topic and be able to have a flawless project. I am sure everyone who has said, "and that concludes my final presentation!" will feel extremely accomplished. Make senior year count!

Technical Details on Posterior and Anterior Cranium

According to Mr. Ogden we do not use or apply mathematics in our senior project. So I am here to prove him wrong and apply it directly into Forensic Anthropology. One approach to this problem is to focus on the analysis cranial Cartesian coordinate points instead of the distances or angles they form. This requires some pre-processing of the data whcih are catalogged by a Forensic Anthropological Institution/Laboratory to construct proper shape variables. However, these vectors will retain all geometric information that could be collected from the cranium. That pre-processing step usually involves the registration of the configurations of landmarks for all specimens into a common coordinate system using a least-squares estimation of location and orientation parameters and a reasonable size standardization. This approach, in which data from individual specimens are fit to an iteratively computed mean configuration, is called Generalized Procrustes Analysis.

Traditional measurements of these skulls are based on anatomical landmarks I discussed on a later blog post. Landmarks included are prosthion, nasion, bregma, lambda, inion, opisthion, and basion. The measurements are the distances between the nasion and basion and the angle formed is from three points from the basion. For other noted refernces, let the record know that the anatomical landmark positions are encoded as Cartesian coordinates.

3 Dimentional Identification implements this approach to help characterize human remains by using cranial remains. To do this, the user provides the program with three-dimensional coordinates of a subset of the landmarks described above. A reference database is then processed to extract appropriate reference samples. Then, the unknown is compared to the groups available in the reference sample to estimate group membership. Separate groupings are considered for each sex, but if sex can be determined by other means, the comparisons can be easily restricted to only female or male groups. The details of how this is accomplished follow:

The f function is the probability density function for the unknown and the group specified in the subscript. With unequal sample sizes and estimated means and covariance structures it leads to the second line of equation. On the third equation, v is the dimensionality of the space of the Anthropological data, ni is the size of the ith reference group. Again, the generalized inverse is used by the program to address singularities and avoid instabilities. The second diagnostic measure provided by the program is a “typicality” measure. This is simply the probability of an observation being as far or farther away from the mean as the unknown for a particular group. Typicality measures how likely it is that the unknown came from a particular population at all. For instance, an unknown will always be suggested as belonging to one of the available reference groups, but typicality measures how likely that is to be true for any given population. That is, the unknown could be suggested for membership in one (the closest) population, but still be so different that the probability of actually finding a specimen that different from the population is small. Again in such cases, the suggested assignment should be taken with an appropriate degree of skepticism. Typicality is computed by finding the probability of: for an F distribution with v and nf – v +1 degrees of freedom, F(v, nf – v + 1). In general, then, the program will suggest an assignment to the group whose mean is closest in the Mahalanobis sense to the unknown. Posterior probabilities can be used to assess how strong the evidence is this assignment versus that for assignment to other reference groups. The typicality can be used to assess how likely the unknown is to have come from a particular population regardless of how much closer it is to it than the other populations or how much that difference is similar to other such differences.

With this equation I received the result of:

rs:1904727279 through rs:184877381

H(1)=V(1)S(1)U(1)

H= 0.9948

G(1)=0.9848 G(2)= 0.9924

A=0.3485 G= 0.3505

A= 0.0606 G=0.9394

A=0.0076

G=0.9924

When entered these results onto the cranium software it depicted these images:

What this indicates from my observation is that even mathematical computations will result hand-in-hand with scientific analysis that Forensic Anthropologists come up with. The results I received from comparing cranial deformation and by solving the mathematical formulas I was able to answer the question of who the individual was. In this case a Mesoamerica (possibly of Mexican origin/ancestral background) between the age of his late 30s (39 years old) to early 40s (42 years old). This accuracy can be able to be matched with the missing person and create a scientific phenomena.

Matching and Exclusions Demonstration with FROG Software

FROG Software is Forensic Resource Reference on Genetics. Compiled by Kenneth K. Kidd, Ph.D. North Carolina Physical Anthropologist.

This Forensic Anthropological tool can three functions; two general functions: the ability to enter genotypes of an individual at multiple SNPs and calculate likelihoods of that multisite genotype in each of several populations, and an eye color prediction function specific to a PISNP panel. These functions are possible for three types of SNP panels, IISNPs, AISNPs, and PISNPs.

1) For Individual Identification SNPs (IISNPs) this implementation provides examples and the ability to calculate match probabilities for user-specified genotypes. Two different published panels of IISNPs can be used to determine the probability of the user-specified genotype in each of several populations that have allele frequencies available for all SNPs in the panel.

2) For Ancestry Inference SNPs (AISNPs) this implementation provides examples and ability to calculate relative likelihoods of ancestry from different populations for user-specified genotypes. Two published AISNP panel can be used as well as a provisional panel of 39 SNPs assembled specifically to test this functionality.

3) For Phenotype Informative SNPs (PISNPs) this implementation provides ability to predict eye color for user-specified genotypes. One published PISNP panel can be used to test the eye color prediction functionality which is based on a published formula.

The interpretation of results likelihoods are calculated by maximum likelihood estimates because they are based on the maximum likelihood estimates for allele frequencies for independent loci. However, those allele frequency estimates have associated standard errors that vary inversely as the sample sizes. Thus, there are greater uncertainties for the likelihoods calculated for populations with small sample sizes. One of the results is that rankings among populations with very similar skeletal system structures and formations.

The images above are screenshots of the results of skeletal DNA traits that were compiled from the previous blog posts based on the first case. It is clear that he is a part of the Homo sapiens sapiens humanoid ladder and is a male between the ages of 39.48-39.49 (theoretically 39 years-old). What these images represent is that many of the ancestral backgrounds share common DNA genomes, however, one ancestral background will stand out from the rest. In this case, however, the young male that I was trying to identify contains Mesoamerican characteristics based on the Populations/Samples and genetic detail. This suggests that the young male originated from South of the United States where Mesoamerica is located as well as overlapping over to the country of Mexico and Belize.

The 3D Analysis Software for Scientific Visualization

Case #: 1 The 3D Identification Data Entry Template is from this Excel file: HERE
This is a first case that I had worked on in a simulation on the NFTSC Technology Transition Workshop with Advances in Forensic Anthropology. I used a program known as 3D-ID. This program uses geometric morphometrics in an approach to shape analysis that efficiently and maximally incorporates the geometry of specimens into the analysis of their shapes. Traditional approaches to shape analysis rely on somewhat disparate collections of linear distances, ratios, and angular measurements that generally lose valuable shape information. Most, but not all, geometric morphometric methods focus on the analysis of the two- or three-dimensional coordinates of anatomical points from which any distance or angle defined by those points can be computed. This preserves all geometric information obtainable from the points and creates a direct link from the statistical analysis back into the physical space of the specimen.

3D-ID is a program providing geometric morphometric tools to aid in the assessment of the sex and ancestral affiliation of unknown cranial remains. I simply provide the three-dimensional coordinates of anatomical points available from the subject, and the program constructs comparable reference samples and assigns the subject to one of several groups for which sufficient data are available. Quantitative measures used in the assignment are provided for all tested groups so the investigator can make an informed choice after examining the relative similarity or distinctiveness of the specimen.

Here are the results that I received from computing the work:

Options...
FitMethod: CVA
Include size: false
Determine group and sex: true
Reference Data Set: data/3d_id.mdt

__Assessing group membership...

Using 89 shape dimensions.

Summary...
========== D2 Posterior Typicality
African - female (3): 153.9654 0.0000 0.3782
African - male (4): 120.7248 0.0000 0.7729
African_American - female (96): 94.6922 0.0009 0.8220
African_American - male (121): 104.0255 0.0000 0.6412
Circumcaribbean - female (1): 284.4074 0.0000 0.0556
Circumcaribbean - male (3): 110.8446 0.0000 0.9459
East_Asian - male (6): 140.9908 0.0000 0.2789
European - female (18): 131.4788 0.0000 0.2204
European - male (24): 145.2291 0.0000 0.0710
European_American - female (61): 124.4696 0.0000 0.2524
European_American - male (96): 125.6240 0.0000 0.2238
Mesoamerican - female (4): 114.2442 0.0000 0.8571
Mesoamerican - male (21): 76.9341 0.9990 0.9892 <===
South_American - female (4): 163.9665 0.0000 0.1380
South_American - male (9): 139.2772 0.0000 0.2091
==========
*** PROCESSING COMPLETE ***

To maximize the number of specimens in the reference set, all available material is included regardless
of the presence of missing data. Some points (especially, for historical reasons, right orbital landmarks)
are missing in quite a few specimens.The following list will helps identify points you may wish to exclude from your assignment. This information will be incorporated into the documentation upon the next release.

This were the quantifiable data that I have inputted into the Excel file linked above.

m=number missing
n=total in data set
pro=m/n
Points:
# m n pro
1 left_asterion 15 1086 0.01
2 right_asterion 17 1086 0.02
3 basion 16 1086 0.01
4 bregma 6 1086 0.01
5 left_dacryon 6 1086 0.01
6 right_dacryon 6 1086 0.01
7 left_ectomalare 391 1086 0.36
8 right_ectomalare 424 1086 0.39
9 left_ectoconchion 18 1086 0.02
10 right_ectoconchion 11 1086 0.01
11 left_frontomalare_anterior 14 1086 0.01
12 right_frontomalare_anterior 8 1086 0.01
13 left_frontomalare_temporale 12 1086 0.01
14 right_frontomalare_temporale 8 1086 0.01
15 glabella 2 1086 0.00
16 lambda 13 1086 0.01
17 left_mastoidale 28 1086 0.03
18 right_mastoidale 26 1086 0.02
19 nasion 2 1086 0.00
20 inferior_nasal_border 13 1086 0.01 //hidden on screen
21 left_lower_orbital_border 19 1086 0.02 20 <- screen position
22 right_lower_orbital_border 738 1086 0.68 21
23 left_upper_orbital_border 22 1086 0.02 22
24 right_upper_orbital_border 739 1086 0.68 23
25 opisthion 18 1086 0.02 24
26 prosthion 274 1086 0.25 25
27 subspinale 27 1086 0.02 26
28 left_nasomaxillary_suture_pinch 15 1086 0.01 27
29 right_nasomaxillary_suture_pinch 14 1086 0.01 28
30 left_zygion 55 1086 0.05 29
31 left_zygomaxillare 18 1086 0.02 30
32 right_zygomaxillare 11 1086 0.01 31
33 left_zygoorbitale 19 1086 0.02 32
34 right_zygoorbitale 14 1086 0.01 33
35 right_zygion 40 1086 0.04 34

Improving Forensic Facial Reproduction Using Empirical Modeling & Forensic Resource Reference on Genetics

With this program in the Advancement in Forensic Anthropology seminar technological precision I learned of an approach for forensic facial reproduction that uses empirical modeling during this session. The process of using a portion of the known landmarks traditionally accessed or facial reconstruction prediction, while also incorporating the effect of body mass index (BMI) in the empirical model, will be described. Unlike current forensic facial reconstruction techniques that use average facial tissue depths from a population sample of individuals, the technique applied during the workshop session will use a non-parametric empirical model to predict facial tissue depths that are unique to each cranium. This technique also has potential to predict facial features like the eyes, nose, and ears. The purpose will be to learn to use this technique to generate more accurate facial reconstructions, thus improving forensic facial reconstruction by enhancing the accuracy of soft tissue thickness prediction.

The image I have inserted is an easy approach of how to understand the biological genetically modified aspect of how to better understand the skeletal remain-DNA compilation as well as how to easily use the DNA genome database.