Proceedings of 2009

Harlem Children Society Workshop & Lecture Series #1

July 7^th 2009

                                                                                                                Printable pdf.

On Tuesday, July 07, 2009, the first of the seminars in the Harlem Children Society (HCS) Summer Internship Weekly Series was held in Caspary Auditorium of Rockefeller University. The day’s agenda opened with a guest presentation by Ms. Carol Feltes, a Rockefeller University librarian entitled, “Literature Research Basics: World Wide Web and Beyond.” She appropriately began with the Abraham Lincoln quotation, “If we could first know where we are, and whither we are tending, we could then better judge what to do, and how to do it.” Ms. Feltes then provided the pre-summary of topics she would discuss, including: understanding research, the characteristics of research (methodology, control, comprehensiveness), selecting a topic, and available resources (books, databases, journals, et al).

In the first segment, Ms. Feltes discussed the “why” of research. She mentioned first that we perform research to learn, to answer questions, contribute new knowledge, and verify what is known. Ms. Feltes then turned to the characteristics of research. First, it is methodical with results that can be duplicated and verified. Further, research should be controlled, with its limits understood, and variables are known and controlled. Lastly, it is comprehensive, meaning all appropriate and relevant information should be considered. Students were advised that they should be looking at/into all relevant resources and anything pertinent to the topic of consideration.

The third main topic was a discussion of the scientific method. Ms. Feltes began, saying “science” is a way of knowing. It is not limited to the common notion of ‘hard sciences’ like math and physics, but rather applies to all areas of research, and is a structured way of asking questions and learning. Research is transparent and reproducible, and used in library/literature research. 

Further to the discussion of method, the librarian explained that first it is important to formulate one’s question, which may lead to a conclusion either positive or negative. Next, one should design the ‘test’ (experiment) or the plan of investigation. The process then involves conducting the research, followed by recording, analyzing, and describing the results. It is then necessary to discuss the results in light of the original question, and the broader context of one’s topic. Finally, the researcher comes to conclusions. Ms. Feltes added that in scientific research, sometimes one cannot answer a question as a conclusion, and that this in and of itself is an answer.

Ms. Feltes then went into the controls on research. She stated that one must understand the limitations involved in one’s research. It’s important to define what those limitations might be, e.g., language, geography, time period, culture, etc. The researcher must be able to also identify those limitations in connection with his/her controlling the scope and setting the boundaries of the topic. One should ask if there are factors influencing the investigation that must be either eliminated or accounted for. As examples, she cited the effects of temperature or pressure conditions/limitations in terms of physical science, and religious or political climate in terms of social science.

Next, she spoke about being comprehensive. Ms. Feltes stated that within the domain of one’s research, one should strive to consult all of the relevant sources and acknowledge limitations of time and resources. She advised students to select resources that are appropriate and accessible given their age and educational levels.  Some resources are simply not appropriate for all to use based on those and other factors.

Ms. Feltes then turned to selecting a research project. She advised that when selecting a topic area, it is best to select something that intrigues the researcher. “You’ll do a better job, and you’ll have more fun.” Besides this, Ms. Feltes advised students to make sure that their advisor judges the topic to be suitable and do-able.  She continued saying that the topic should be the right scope, the necessary resources should be available, and the research makes a contribution to knowledge.

With regard to resources, Ms. Feltes then discussed evaluating them to ensure they are right and appropriate.  First, one should evaluate content. One should use the resources targeted to one’s topic. She advised students to consult their advisor and library staff to identify databases and other information sources specific to the research. 

Next, Ms. Feltes discussed resource format. She began by saying that not everything is digital, and advised students to look at anything that has the right content. The librarian urged students to go beyond the web,  “Don’t forget that print books still exist, and are not yet available in digital format… Further, anyone can put anything on the web.  Not all sources are authoritative.”

One must evaluate availability of desired resources. Since many high quality resources are costly, not all of the information is available in all libraries. It is important to determine what is available either for free or at one’s library (ies). Ms. Feltes then generously offered the resources of Rockefeller’s Markus Library for HCS students to use.

The Medical librarian then advised students to immediatelye establish a protocol to manage the information one gathers. Again, Ms. Feltes emphasized that it is critical to evaluate the resources used for quality, authority, timeliness, completeness, and comprehension. Those resources could involve a number of things: books, journals, databases, reports, “grey” literature, and patents.

Ms. Feltes delved into the value of each of these types of resources, first mentioning that books are the perfect place to begin since they give one context and synthesize the established facts.  She then furnished a handful of useful online links to book catalogues, and suggested that by looking at available books on a given topic, one discovers and identifies important authors in the field, and this can lead the researcher to look via different avenues perhaps not otherwise considered.

She then discussed journals, which feature opinion-based articles, editorials, essays, letters, and expert statements on the state of the art. Though, Ms. Feltes said, one might not choose to necessarily use this information in the research per se, journals help one identify the important people and the most recent developments in the field. Thus, they provide “pointers.” Further, journals provide review articles that illuminate reports of new knowledge, articles, and conference abstracts. 

Ms. Feltes then approached the world of databases, collections of organized, accessible, selected information. She gave examples of what one would expect to find in various databases, including citation information, data, images, etc. Commercial databases are generally high quality, but expensive, whereas government databases are generally high quality, and free. There are academic databases that are highly specific and high quality since they are maintained by institutions. Databases target specific audiences by topical areas and level of expertise. They are structured to reflect the knowledge area, and characteristically implement special vocabularies and data ‘fields.’

The next resource Ms. Feltes highlighted was reports. She first mentioned that federal and state government reports are usually free and mentioned those of the CDC, Bureau of Labor Statistics, Census Department, the EPA and NIH. Further, she went into the value of various other types of reports by industries and association/professional groups. The information features such items as marketing studies, statistical information, and demographical information.

With respect to other resources, Ms. Feltes then spoke about grey literature featuring information that is more difficult to find. This information includes marketing collateral, which provide useful “pointers” to other publications. There are public information bureaus and non-profit organizations, said Ms. Feltes that produce much valuable information of this category. Finally, she pointed the students to information on patents, and provided more useful online links to researching such.

Before closing, Ms. Feltes spoke about ethics. She advised the students to keep excellent records, cite correctly, give credit where it is due, verify facts, be honest, be aware of copyright protections and honor them. She then closed, summarizing her speech by saying that in research, students should seek advice, consult appropriate resources, behave ethically, and above all, “Enjoy the hunt!”.

Following Ms. Feltes’ talk, Dr. Sat approached the podium and added his comments on research before introducing the first student speaker of the day, Ivan Schoop, HCS Class of 2007 and a student at Manhattan Hunter High School. Ivan had prepared his presentation entitled “Mercury-Oxygen Secondary Bonding,” during a previous summer internship with Dr. Artëm E. Masunov at University of Central Florida’s NanoScience Technology Center. Ivan introduced his work first by discussing the structure of Hg₂acet crystals (mercury acetate), and two types of bonds that occur within the crystal structure: covalent bonding of oxygen and carbon and secondary bonding of oxygen and mercury, which is a D/A interaction (nO: (e^- pair) à Hg).

The student’s motivation for this research was to prove the experimental data theoretically, explain experimental trends, and determine the distance affect on the structure. Ivan stated that secondary bonding is helpful to crystallographers, and he had wanted to be able to predict crystal packing so as to determine intermolecular interactions in the body. His goals were to find interaction energies in varying distances between Hg and O (the secondary bond) and find effect on vibration between O and C in the covalent bond.

Ivan’s method was to apply the Density Functional Theory (DFT), which is a quantum mechanical method used in physics and chemistry to investigate the electronic structure of multi-electron systems. He explained the components of the theory in depth. The student then explained the DFT (PBE0 density functional) was used with effective core pseudo potentials and a Gaussian basis set. Geometry and the total energy of the reaction complex were determined with constrained optimization. Ivan further explained how frequency and vibration were measured, and described the bonds as behaving like springs when atoms are in motion. Ivan then went into vibration, which varies depending on bond strength. Infrared light was (IR) passed through the molecular crystal, the light of specific frequencies was absorbed, and the absorption spectrum was recorded. It was determined that most of the light was absorbed in C=O bond. The resulting data reflected the difference in interaction energies and frequency shift.

Ivan concluded that the theory was in general agreement with experiment. As distance increased, the energy of the secondary bond between Hg and O decreased (with both DFT and MP2). As the distance increased, vibrational frequency in the covalent bond between O and C decreased, albeit much slower. The student ended his presentation saying that the DFT is not sufficiently accurate to describe the secondary Hg…O bond.

In the second student presentation of the day, Lena Mei, HCS Class of 2007, of Manhattan Hunter Science High School, Savita Ramlall, HCS Class of 2006, of Clara Barton High School, and Rasheeda Abdullah, HCS Class of 2008, also of Clara Barton High School, presented their summer 2008 work under the mentorship of Dr. Gerry Moore and Paul Harwood at Brooklyn Botanic Garden (BBG) entitled, “BBG: Improving and Editing the Interactive Keys.”

The students prefaced their research discussion by recapping their initial presentation of their summer 2007 work. They had previously detailed expanding the work being done on a plant classification computer program with identification and synopsizing capabilities known as interactive keys. Their particular mission had been to add pictures of plant specimens to the interactive keys to enhance identification function. 

They also recapped their prior work in the BBG Herbarium, a cold room that preserves dried plant specimens from The New York Metropolitan area and plants from around the world.  Their work had been focused on collecting specimens, recording relevant data (locality, date, collector, etc.), drying and mounting them on heavy acid free paper, and then freezing them (to destroy insects and other pests).  Then they put specimens in the Herbarium to preserve them as archives to be checked periodically for insect damage and reorganization. Additionally, they had worked on a seed index, involving a worldwide seed exchange.

The students’ 2008 work involved invasive protocol, and transferring related plant information from older format into a more current format in the database. The students carefully transferred the information to ensure the integrity of the data on invasive plant species and the area where they had been found/ identified. This information was to be added to the interactive keys, which would expand the data to include herbaceous plants as well as woody plants.

Lena, Savita, and Rasheeda also spoke about their research related to the rubus species, aka, blackberry plants.  The students collected information, which involved going through each species of the genus, and assembled distribution maps for their mentor, Dr. Gerry Moore, who is writing about rubus for “Flora of North America,” a research project that seeks to describe all plant species in North America. This summer, the students plan to further expand the interactive keys to include invasive species and all rubus species.

At this point in the program, Prof. D. Jeanne Ross, HCS Special Projects Coordinator, provided a detailed explanation for each item listed on a student handout entitled, “Getting a Perfect Score,” which had been distributed to students. Her discussion included both suggested paper format and a break-out of the grading system, so as to establish HCS standards and expectations for students’ weekly seminar paper submissions, and so that they could have the guidelines available for easy reference throughout the summer. During this segment of the agenda, students were also given an opportunity to pose their questions on writing papers.

Ms. Vicki Javier, HCS Class of 2005, and a senior at Dartmouth University in anthropology and public policy, next presented her talk, “Obesity and the Hypothalamus.” Vicki did her summer 2006 research under the mentorship of Dr. Solen Gorkhan and Dr. Volkan Granit in the Neurology Department of Albert Einstein College of Medicine. She began her discussion by describing the mechanism and function of the hypothalamus. Vicki worked with a colony of mice to study the hypothalamus and its relationship to obesity and diabetes.

The student went into a discussion on the central nervous system (CNS), composed of the brain and spinal cord. She discussed the peripheral nervous system (PNS), and differentiated the somatic from the autonomic, and further drilled down to the somatic and voluntary systems of the autonomic PNS. She explained that the autonomic PNS is also composed of sympathetic system (“fight & flight”) and parasympathetic system (“rest & digest”). Vicki further went into background on the hypothalamus, and displayed a cross-section of the lateral hypothalamus demonstrating hunger, and the ventromedial hypothalamus indicating the sensation of “full.”

In her experiment, Vicki deleted/knocked out the MASH1 gene, performed perfusion, isolated the DNA, and genotyped it. Next, MASH1 & NEO were amplified via Polymerase Chain Reaction (PCR). Using NEO as an indicator, she performed immuno-histochemistry (IHC). The tools Vicki used in the experiment were PCR, mouse perfusion & IHC. In the future, the student expressed she would like to cross-heterozygous mice with wild-type (WT) mice to get a bigger colony. She would like to examine the progression of obesity in transgenic mice and compare with WT mice.

Dr. Sat then approached the podium and spoke about genes, and the “knocking out” and mutations of such. He then introduced the next student presenters of the day. Littin Kandoth, HCS Class of 2005, and Kenneth D’silva, HCS Class of 2008, and a student at High School for Math, Science and Engineering at City College, presented their work, “Improving the Aerodynamics of a Side Channel Blower“. They had done their project in summer 2008 under the mentorship of Dr. Chang-Hwon Choi at the Stevens Institute of Technology.

They first defined a side channel blower as a pump that transfers gas contents. Introduced in 1996, with a design similar to a turbine, it is used in agriculture, barge unloading, propane bulk transfer, etc. It operates with a rotating impeller, such that when air is sucked in, the pressure difference in the blower pushes the air out.  The pressure at the exit point is much lower so the velocity of the air is much greater.

The students also discussed the various principles of physics in connection with side channel blower, including centrifugal force (created by the rotation of the shaft) accelerating the liquid and pushing it out, and impeller speed that increases the amount of liquid that exits. They added that velocity and pressure are inversely proportional, and entrained gas/air pressure increases the efficiency of the pump.

The problem that the students wanted to address has to do with the mechanism body/casing of the blower, which doesn’t have an evenly spaced passageway. Hence, as the area decreases, the velocity of gas inside the blower increases. Littin and Kenneth wanted to optimize the design, making changes in the existing design to improve the volume of air/gas moved per minute. As well, they wanted to get a higher rate of airflow without increasing the speed of rotation of the shaft and thereby increase efficiency with less energy. They wanted to also achieve an increase in power range, i.e., increase the impeller speed and air pressure, and improve the use of centrifugal force. 

To achieve their intended goals, the students used a Pro Engineer interface to model a design, Ansys CFX, a simulation program, to analyze the design, and a Siemens Elmo Side Channel Pump (G_200 series) to create and modify a model. They changed the design of the impeller, the outer body of the blower, and the positioning of the inlet and outlet of the airflow using Pro Engineer.  Littin and Kenneth concluded by displaying models and diagrams of their work.

Dr. Sat returned to the podium and mentioned that, while the current presentations represented previous research by more seasoned HCS students, newer students would soon be expected to begin presenting their current research.  He continued saying that they would likely not yet have results, but could still describe their work and discuss what they might expect to achieve or find.  Dr. Sat then explored the notion of getting “unexpected” results, and that this is not a sign of failure, but often is the seed of great discoveries.

Next on the program, Pratyush Narayan, HCS Class of 2006, and a student at Manhattan Center for Science and Math, discussed his 2008 summer research, “The Micronucleus Formation in Total Body Irradiation (TBI) Study Samples,” under the mentorship of Dr. Helen Turner and Dr. David J. Brenner, at Columbia University.

Pratyush first defined total body irradiation (TBI) as procedure using a megavoltage photon beam most commonly used as part of the conditioning region for bone marrow transplantation. It is used in the treatment of a variety of diseases such as leukemia, lymphoma, aplastic anemia, and multiple myeloma and typically in conjunction with high dose chemotherapy. He also discussed micronucleus assay, an in-vitro cytokinesis-block micronucleus (CBMN) assay to measure micronucleus frequency in human lymphocytes.  HPBL refers to Human Peripheral Blood Lymphocyte. Micronuclei (MNi) formation refers to radiation exposure that induces micronuclei formation in HPBL cells. MNi originate from chromosome fragments or whole chromosomes that lag behind during nuclear division. These micronuclei are counted to assess the extent of damage caused by genotoxic agents including radiation. The higher the frequency of the micronuclei the greater is the DNA damage. Finally, he defined gray (Gy), which is the measurement of a dose of radiation. 1Gy of radiation is defined as the absorption of one joule of ionizing radiation by 1Kg of matter¹. The machine used by Pratyush in this study emits 0.86 Gy of gamma rays per minute.

The student’s objective was to determine the effect of radiation induced DNA damage in HPBLs by counting micronuclei. The micronuclei were counted after irradiating HPBL’s with 5 and 6 Gy Gamma Rays. The goal was to make a dose-response curve to examine the frequency of MNi formation in human lymphocytes exposed to different doses of gamma radiation (0 to 8 Gy). The assessment of DNA damage and the presence of MNi formation were done in TBI blood samples provided by the Memorial Sloan-Kettering Cancer Center.

Pratyush’s materials included a cell system (HPBLs). He also used the chemicals, PHA, RPMI 1640 Medium, FBS, Cytochalasin B, KCl, Fixative (3:1 methanol: acetic acid), Cell Mask Orange, and DAPI. His equipment included light and fluorescence microscopes, T-25 flasks, 15ml centrifuge tubes, Gamma-chamber, pipettes, beakers, slides, cover slips, water bath, coupling jar, incubator, humidifying chamber, fridge, freezer, centrifuge, computer.

Pratyush’s procedure first involved collecting blood from an irradiated patient. The blood was then cultured and PHA was added to induce cell division. Forty-four hours later, Cytochalasin B was added to inhibit cell division. The lymphocytes were harvested and 0.56% KCl was added to burst the cell membrane. A fixative was then added, and the lymphocytes were placed on a slide. The slide was then washed with 1X PBS, and 1.25 and 2.25μL per ml of blood and 50μL of Vectashield Mounting Medium with DAPI were added to it. A cover slip was placed on the slide and sealed with transparent nail polish. The slides were scored for micronuclei and the data was recorded. Via fluorescent microscopy, he was able to observe the results, which he then described.

MNi were identified as round in shape and clearly separated from the main nucleus; exhibiting similar staining characteristics as the main nucleus, and found to be within the same cytoplasm. At least 500-1000 DAPI stained binucleated lymphocytes per dose were manually and systematically scored for micronuclei. The dose-response curve revealed a linear increase in MNi frequency with increased exposure to γ-rays. He found that there was a significant (p = < 0.05) induction of MN formation following the first fraction of radiation. Furthermore, the results showed that the MN formation was cumulative and evidenced by an observably significant increase of MN formation following the second round of radiation 24 hours later. 

Pratyush concluded that TBI induces MNi formation and that increasing the dosage of radiation increases the number of MNi. He found that the higher the dosage of radiation given to a patient during TBI, the higher the frequency of micronuclei in the patient’s cells. His results indicated that the frequency of micronuclei could be used as an index of the radiation exposure, and that this assay could be useful in regulating the dose of radiation given to cancer patients.

Dr. Sat once again took the podium and added his comments on micronuclei. He then introduced HCS staffer, and nutrition group mentor, Brandon Burton. The HCS President provided an introduction to Brandon’s overview of the upcoming summer work entitled “Nutrition and Healthy Living.”

Brandon first provided a bit of background on the project. He described the work HCS students had done in summer 2008. Harlem Children Society had teamed up with Columbia University’s CHALK program (Choosing Healthy & Active Lifestyles for Kids) to assess the price and quality of produce sold at Farmers’ Markets (in the New York City Greenmarket program) and supermarkets in Harlem and Manhattan. The students had hypothesized that the price of produce sold at supermarkets is lower than that of farmers’ markets, and that the quality of produce sold at supermarkets is lower than that of produce found at farmers’ markets. Their results had showed that produce sold at farmers’ markets was cheaper than that sold in supermarkets both in Harlem and Manhattan. They had also concluded that there was little quality difference in produce sold at both types of markets. However, there were significant statistical results that showed the color of produce was better at Manhattan locations than at Harlem locations.

Brandon then set out the purpose of this summer’s nutrition group work to evaluate the quality and availability of specific foods at farmers’ markets, grocery stores and corner stores in various locations throughout the five boroughs of New York City. The students also intend to identify food-related health problems, define the characteristics of a given area, and draw conclusions based on the correlation between various factors.

Next, Brandon outlined the methodology for the summer’s work, which is essentially the basic form of scientific method. The groups would be defining the specific question, gathering information and resources, forming a hypothesis, performing the experiment and collecting data. Next, they would analyze the data, interpret it, and draw conclusions that would serve as a starting point for a new hypothesis. Brandon’s students would also publish the results. Retesting (by others) would also be on the drawing board.

The project was then set out in three phases, the first of which was to collect data involving field research. This would entail students collecting information from various sites and observing their own surroundings/environments. It would also involve researching various databases, looking into available statistical data on demographics, economics of a given area, and prevailing health conditions.

Phase II would involve data transformation. The students would be rendering a visual representation of the collected data. Once a given area was properly defined, students would then be mapping and graphing the data to assist in their interpretation of such.

In Phase III, the students would be analyzing and interpreting the information. They would be looking at various graphs and charts, and maps of the sites visited. Once the students developed a clear understanding of what the data revealed, they would then test their hypothesis with our findings. The resulting research would then be compiled and students would write a report on the study.

Brandon next discussed skills that would be developed through the study. Students would be engaged in research and hone their ability to use the tools at their disposal to properly find information. Students’ analytical skills would be sharpened by looking at data sets and properly identifying existing patterns and trends. Moreover, they would be gaining a broader sense and appreciation of the subject of geography as they received introductory training in GIS (Global Information System).

By the end of the project, Brandon stated, students would gain a better understanding of nutritional health, different socioeconomic characteristics, and get hands on experience with this field of science. Furthermore, students would be able to suggest possible solutions for the health problems that affect local communities throughout New York City. With the conclusion of Brandon’s presentation, the seminar broke for lunch. 

Upon recommencement of activities, Ms. Caty Santos first announced the names of all HCS group leaders. She was followed by HCS’s IT Coordinator, Alejandro Naranjo, who discussed online forms. All students were instructed to complete three online documents, including Confidential Information Preparation, Student Survey, and Knowledge Assessment forms. Alejandro then walked students through registration on to use the HCS online Forum, profile setup, and instructions on submission of student weekly seminar written reports. 

In the remaining time left, the IT staff met with HCS students on individual problems and questions about all things technological. The first seminar of the HCS 2009 summer program was then effectively concluded, and the meeting was adjourned.

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