DIMACS 2006 High School Student Research Conference

April 22, 2006
DIMACS Center, CoRE Bldg, Rutgers University

Fred S. Roberts, DIMACS, Rutgers University, froberts@dimacs.rutgers.edu


Steve Andenmatten, Tucker Anderson, Nick Carlson, Greg Gniadek, Ned Grant, Keelynn Harris, Noah Kirsch, Anna-Lucia Lister, Ethan Seaman, Jess Yarmosky, Monument Mountain Regional High School, Great Barrington, MA

Title: Waksman Challenge
Under the supervision of Kristina Farina and Celeste Drumm

This presentation will focus on molecular suggestions for preventing insecticide resistance in mosquitoes. Iodine replacement, sodium carbonate and organophosphates are some of the proposed solutions to be addressed.

Ceyhun Arslan, Ceren Yalniz, Levent Tuzun, Robert College, Turkey

Title: The Genealogical Connection of Turks to Western Asia and Europe (DVD Presentation)
Under the supervision of Andrew Tingleff and Ipek Tingleff

The aim of this project is to examine and compare the similarity of mitochondrial DNA (mtDNA) of Turks with the mitochondrial DNAs of some nations from Europe and Asia. By doing this, we can have an idea about the genealogical connection of Turks to Western Asia and Europe. In our study, we used the mitochondrial DNA which has a high mutation rate and is inherited from the mother without recombination. We specifically chose the hypervariable control region I of each mtDNA to compare all the sequences with precision and accuracy. We focused on the mitochondrial DNA control region I of four Turks and we compared these sequences with the other mitochondrial DNAs control region I from other nations, which are China, Slovenia, Hungary, Morocco, Britain, Egypt and Israel. Since China is geographically far away from Turkey, we used Chinese mitochondrial DNAs as control sequences in our experiment. We took four mitochondrial DNAs from each nation and compared all those thirty-two sequences in terms of their proximity to each other. We did this by aligning these sequences and translating the distance matrix to the rooted and unrooted phylogenetic trees by neighbor joining. Our results confirmed our hypothesis. With our results, we concluded that Turks are close to Near Eastern and European nations and Turkish mitochondrial DNAs are closest to Near Eastern mitochondrial DNAs. This strengthens the notion that the people in Anatolia came from the Near East. However, it is important to note that we looked at only four sequences from each nation and these results cannot represent all of these nations and that was the main limitation in our project.

Alanna Astion, Matt Dellea, Keelynn Harris, Drew Mintz, Monument Mountain Regional High School, Great Barrington, MA

Title: Reverso
Under the supervision of Kathy Erickson

Numbers arranged in a random sequence can be transformed into the identity sequence by flipping smaller sections of numbers. This talk will explore optimal values when the numbers involved are always positive and when flipping causes a number to change sign. The mathematics relates to the comparison of protein strands among species.

Alden Barbieri, Anna Lucia Lister, Elyse Yarmosky, Monument Mountain Regional High School, Great Barrington, MA

Title: RNA Reconstruction
Under the supervision of Kathy Erickson

This presentation of RNA construction will cover the biological background of RNA reconstruction, as well as fragmenting, Euler paths, and how to work backwards to recover the original RNA chain. The possibility of multiple paths and circuits will also be discussed.

Gary Benson, Boston University

Title: The Human Genome: What's In It and How Do We Know?

The first draft of the human genome was officially completed in 2001 and the work of filling in gaps and correcting mistakes continues to this day. This has been a monumental accomplishment, but having the genome sequence is a far cry from knowing what's in it and how what's there affects human health. These questions are not fully answered and investigating them has required an unprecedented integration of computational and mathematical analysis with laboratory experimentation. In this talk, I will discuss what we know about the contents of the human genome, including protein genes, RNA genes, regulatory regions, repeats (tandem, inverted, transposon), single nucleotide polymorphisms (SNPs), haplotypes, deletions and copy number polymorphisms. I will also discuss some of the mathematical methods used to find these components, with an emphasis on the discovery and analysis of repeats.

Dina L. G. Borzekowski, presented by April Schindler, Rondout Valley High School, Accord, NY

Title: The 30 Second Effect: An Experiment Revealing the Impact of Television Commercials on Food Preferences of Preschoolers (Poster Presentation)
Under the supervision of Elissa Jury

Nicholas L. Carnagey, Craig A. Anderson, presented by Deven Connelly, Rondout Valley High School, Accord, NY

Title: The Effects of Reward and Punishment in Violent Video Games on Aggressive Affect, Cognition, and Behavior (Poster Presentation)
Under the supervision of Elissa Jury

Kathleen Carter, Villa Maria Academy, Malvern, PA

Title: SLC24A5 and Its Role in Human Pigmentation
Under the supervision of Teresa Friedrichsen

This presentation will examine the SLC24A5 gene and its role in human pigmentation. The presentation will begin with a discussion of the determinants of skin color, the parts of the cell which participate in melanin production and their respective functions. I will then present the molecular details of the SLC24A5 gene, and using various visual models, describe the ways in which it affects pigmentation. Additionally, I will outline the original experiments performed by the Penn State University research team on the golden phenotype zebrafish (Danio rerio), wherein the scientists were able to identify the human SLC24A5 gene as being 69% similar in sequencing to the golden phenotype. Finally, I will conclude with statements on where I believe research on skin color is moving, and I will discuss what is still unknown about the genesis of light skin in European and East Asian peoples.

Chase Chapdelaine, Nate Jones, Billy Kistler, Dylan McKenna, Jessica Platt, Monument Mountain Regional High School, Great Barrington, MA

Title: Won't you be my Neighbor...Joining Project
Under the supervision of Kristina Farina

A distance matrix uses numbers to show relationships between species. The neighbor joining algorithm translates that matrix into a phylogenetic tree. Since the algorithm is computationally intensive, the use of technology greatly enhances the process. This talk will explain the algorithm and show programs created by students.

Haley Garrison, Villa Maria Academy, Malvern, PA

Title: The Influence of WNT16 on Cell Division
Under the supervision of Teresa Friedrichsen

WNT is a family of protiens that, when produced by a cell, induces cell division. This project examines the environmental conditions that cause WNT16 to be produced and its specific effects in cell division, especially during uncontrolled cell division (cancer). WNT16's relationship with B-cells and beta catenin are observed and results of inhibition of WNT16 production are also examined.

Yasemin Gokce, Dilan Mizrakli, Arda Kara, Aycan Nur Sagir, Robert College, Turkey

Title: Avian Influenza Project (DVD Presentation)
Under the supervision of Andrew Tingleff and Ipek Tingleff

The aim of the project is to determine the effect of migratory wildbirds on the spread of the H5N1 avian influenza virus and the possible threat to Turkey. Viral sequences of the hemagglutinin gene from various countries, where H5N1 was isolated and sequenced, were chosen from GenBank. The sequences were aligned and the distance matrix was translated into a rooted and an unrooted phylogenetic tree by neighbor joining. Japanese sequences were our controls, as they were geographically further away from the migratory bird pathways in Asia. Our results confirmed our hypothesis, which stated that the H5N1 virus was transmitted by migratory birds to countries along their flyways. Geographic proximity didn't determine genetic similarity for all the sequences, but an explanation with the migratory bird flyways was possible. According to our results, Novosibirsk, the only sequence from a different flyway than the rest of the places available in GenBank, had been introduced to the virus through birds from central China, which lies on the intersection point between two major bird flyways, the East Asia flyway and the West Asia flyway. Our project had some limitations, mainly the lack of sequences from the route of West Asia flyway and the assumptions underlying our phylogenetic trees. But with our results we concluded that it was likely that the migratory birds carried the epidemic to Turkey and that other countries on the route of the migratory waterbirds were in danger, too.

Daniel F. Huber, Martial Herbert, presented by Andy Eggers, Rondout Valley High School, Accord, NY

Title: A Method for Automatically Registering Multiple Rigid Three Dimensional (3D) Data Sets
Under the supervision of Elissa Jury

This paper presents a method for automatically registering multiple rigid three dimensional (3D) data sets, a process we call multi-view surface matching. Previous approaches required manual registration or relied on specialized hardware to record the sensor position. In contrast, our method does not require any pose measuring hardware or manual intervention. We do not assume any knowledge of initial poses or which data sets overlap. Our multi-view surface matching algorithm begins by converting the input data into surface meshes, which are pair-wise registered using a surface matching engine. The resulting matches are tested for surface consistency, but some incorrect matches may be indistinguishable from correct ones at this local level. A global optimization process searches a graph constructed from the pair-wise matches for a connected sub-graph containing only correct matches, employing a global consistency measure to eliminate incorrect, but locally consistent, matches. From this sub-graph, the rigid-body transforms that register all the views can be computed directly. We apply our algorithm to the problem of 3D digital reconstruction of real-world objects and show results for a collection of automatically digitized objects.

Christoph Kohler, Ulrich Ebert, Karlheinz Baumann, and Hannsjorg Schroder, presented by Sonia Narvaez, Rondout Valley High School, Accord, NY

Title: Alzheimer's Disease-like Neuropathology of Gene-targetednext Term APP-SLxPS1mut Mice Expressing the Amyloid Precursor Protein at Endogenous Levels (Poster Presentation)
Under the supervision of Elissa Jury

Most transgenic mice used for preclinical evaluation of potential disease-modifying treatments of previous termAlzheimer'snext term disease develop major histopathological features of this disease by several-fold overexpression of the human amyloid precursor protein. We studied the phenotype of three different strains of previous termgene-targetednext term mice which express the amyloid precursor protein at endogenous levels. Only further crossing with transgenic mice overexpressing mutant human presenilin1 led to the deposition of extracellular amyloid, accompanied by the deposition of apolipoprotein E, an astrocyte and microglia reaction, and the occurrence of dilated cholinergic terminals in the cortex. Features of neurodegeneration, however, were absent. The pattern of plaque development and deposition in these mice was similar to that of amyloid precursor protein overproducing strains if crossed to presenilin1-transgenics. However, plaque development started much later and developed slowly until the age of 18 months but then increased more rapidly.

Adam Laud and Gerald DeJong, presented by Leif Tokle, Rondout Valley High School, Accord, NY

Title: Reinforcement Learning and Shaping: Encouraging Intended Behaviors (Poster Presentation)
Under the supervision of Elissa Jury

We explore dynamic shaping to integrate our prior beliefs of the final policy into a convential reinforcement learning system. Shaping provides a positive or negative artificial increment to the native task rewards inorder to encourage or discourage behaviors. Previously, shaping functions have been static: the additional rewards do not vary with experience. But some prior knowledge cannot be expressed as static shaping. We take an explanation-based approach in which the specific shaping function emerges from initial experiences with the world. We compared no shaping, static shaping, and dynamic shaping in the task of learning bipedal-walking on a simulator. We empirically evaluate the convergence rate and final performance among these conditions while varying the accuracy of the prior knowledge. We conclude that in the appropriate context, dynamic shaping can greatly improve the learning of action policies.

Danqing Li, Rondout Valley High School, Accord, NY

Title: The Interaction of TOG within the Cytoskeletal Complex in Immature Oligodendrocytes
Under the supervision of Elissa Jury
Mentors: Elisa Barbarese Ph.D. and Linda Kosturko Ph.D. at the University of Connecticut Health Center

TOG, a microtubule-associated protein, is involved in the transport of mRNA necessary for protein synthesis in distant cell compartments. The purpose of this study is to determine if TOG plays a role in the proper morphological development of oligodendrocytes which involves elaborating long processes. We explored the interaction of TOG with the cytoskeletal complex in immature cells. The native association of TOG with microfilaments and microtubules was probed using drugs, Latrunculin and nocodazole, that disrupt each of these elements, respectively. Fluorescence microscopy of drug-treated and immunostained cells revealed that TOG was co-localized with microfilaments as well as with microtubules. Both antimicrotubule and antimicrofilament drugs compromised the abundance and distribution of TOG. The re-appearance of TOG after treatment with Latrunculin however, was much greater than the re-appearance of the protein after treatment with nocodazole. These results suggest a novel association of TOG with microfilaments that may be a prerequisite to its further association with microtubules. The localization of TOG at the growing tips of immature cell processes suggests further that TOG is necessary for oligodendrocyte development.

Zane Martin, Lauren Stephenson, Cindy Schmelkin, Emily Ury, Monument Mountain Regional High School, Great Barrington, MA

Title: Rodents and Humans and Cows (Oh My!)
Under the supervision of Celeste Drumm

This presentation compares and contrasts the structure of proteins related to collagen, T-cells and immunoglobulin between humans and other animals. Work was done with the Biology Student Workbench, a tool which allows users to access and compare proteins from numerous species.

Sarah Prehn, Rondout Valley High School, Accord, NY

Title: Coliform Testing at a Wastewater Treatment Plant After Flooding in the Town of Ulster, NY
Under the supervision of Elissa Jury

When flooding occurs, water levels at wastewater treatment plants become unbalanced, therefore creating a possible hazardous situation for the surrounding environment. In spring 2005, coliform counts at a local wastewater treatment plant were assessed after a large flood to find if levels were problematic and to discover if counts decreased as water levels decreased. For the experiment, the membrane filter method and fecal coliform membrane filter procedures were performed with samples taken from primary influent, effluent, upstream and downstream sites and diluted to gain a statistically accurate range of colonies. Two Petri dishes per test at each site were performed to ensure accuracy. Results showed that, with the exception of the two weeks directly after the flood, the plant effectively disinfected the water and stream levels were within safe ranges of coliforms. In the creek, the upstream and downstream samples were different by negligible amounts in the upstream and downstream site because simultaneous increases in the volume of water and coliform counts kept levels proportionate in the natural environment.

Lesley J. Rogers, presented by Kristen Lamastro, Rondout Valley High School, Accord, NY

Title: Evolution of Hemispheric Specialization: Advantages and Disadvantages (Poster Presentation)
Under the supervision of Elissa Jury

Paulette Schatz and Kuzvinetsa P. Dzvimbo, presented by Colleen Kruppa, Rondout Valley High School, Accord, NY

Title: The Adolescent Sexual World and AIDS Prevention: A Democratic Approach to Programme Design in Zimbabwe (Poster Presentation)
Under the supervision of Elissa Jury

April Schindler, Rondout Valley High School, Accord, NY

Title: Marketing Advertisement and the Strong Link with the Obesity of Children in Today's Society
Under the supervision of Elissa Jury

Marketing advertisement has a strong link with the obesity of children in today's society. This is a study and experiment about the constant advertising images portrayed to children how they may be effected by it. Obesity in children today is a very big concern among parents, relatives, neighbors, friends, and the children themselves. Each year the statistics get uglier and uglier as the obesity in children get higher and higher, affecting more children who are younger every year. There has been alot of worry and blame going around as to what is causing such an obese epidemic among our children, but perhaps the answer lies not in just the television many children like to stare at, but marketing everywhere.

Future research may be able to prove this even more by conducting other experiments with children about how they feel when they eat and explain when and why they eat and compare results. Future research would hopefully be able to convince the public or hopefully the government that there is too much marketing and the people would be better off without it.

Sam Stewart, Rondout Valley High School, Accord, NY

Title: An Underlying Cause of Hyperthyroidism in Felines; Is Diet a Demon?
Under the supervision of Elissa Jury

Hyperthyroidism is becoming an all too common problem in cats today. The numbers of positive cases is believed to have well exceeded the old prediction of 33% infected. Hyperthyroidism is a disorder in which there is an over-production of the circulating thyroid hormone. This can lead to kidney and liver failure, muscle damage, excessive heart rates, and a significant decrease in weight. The purpose of this study is to look into causes of increased hyperthyroidism. My study will consist of a questionnaire given with an informed consent form to owners of cats in the Hudson Valley Area. The owners will be asked questions on the food they feed their cats, as well as the type of water they give them. There is also a question asking about litter box use, because that is another suspected cause of hyperthyroidism. The collected data will be broken down into sub-groups of positive and negative cats, and then will be examined as far as the ingredients in the food and water. If there is a suspected chemical found in any of the foods or water, a blood sample will be taken from the positive cats and sent off to a lab to be tested for the amount of that substance in the cats system. The negative case cats will be used as a control group. This study will not analyze genetic factors.

Sophia Wagner-Serrano, Rondout Valley High School, Accord, NY

Title: The Effect of Music on Auditory Acuity
Under the supervision of Elissa Jury
Mentor: Dr. Robert E. Remez, Barnard College

Previous studies have shown that musicians are more able to identify pitch changes in speech with higher accuracy than non-musicians. The purpose of this study was to evaluate the differences of musicians' ability to perceive spoken words with background noise in a Speech Perception in Noise (SPIN) test to the ability of non-musicians'. The study also examined the relationship between the Self-Rated Music Survey (SRMS), which evaluated music exposure, and the Selmer Music Guidance Survey (SMGS), which evaluated music ability. On the first day 14 musicians and 11 non-musicians took the SRMS and SMGS. The next day, 14 musicians and 11 non-musicians took the SPIN test. The SRMS and SMGS had a direct relationship, where the more music exposure a subject had, the higher the subject would score on the music ability test (Pearson function showed that r = .63). Both the music exposure and musical ability had a very weak relationship to performance on the SPIN tests (r = -.28, r=.23). These results show that there is no effect of music on this particular aspect of speech perception, but future studies will look at other variables and different parts of speech perception.

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Document last modified on April 21, 2006.