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  1. Systematic Pan-Cancer Analysis of Somatic Allele Frequency [Download]

    Title: Systematic Pan-Cancer Analysis of Somatic Allele Frequency
    Author: Spurr, Liam
    Description: Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, and can therefore indicate possible driving potential of the underlying genetic variants. To explore the correlation between allele frequency of somatic variants, and total gene expression of their harboring gene, we used the unique data set of matched tumor and normal RNA and DNA sequencing data of 5523 distinct single nucleotide variants in 381 individuals across 10 cancer types obtained from The Cancer Genome Atlas (TCGA). We analyzed the purity-adjusted allele frequency in the context of the variant and gene functional features, and linked it with changes in the total gene expression. We documented higher allele frequency of somatic variants in cancer-implicated genes (Cancer Gene Census, CGC). Furthermore, somatic alleles bearing premature terminating variants (PTVs), when positioned in CGC genes, appeared to be less frequently degraded via nonsense-mediated mRNA decay, indicating possible favoring of truncated proteins by the tumor transcriptome. Among the genes with multiple PTVs with high allele frequency were key cancer genes including ARID1, TP53 and NSD1. Altogether, our analysis suggests that high allele frequency of tumor somatic variants can indicate driving functionality, and can serve to identify potential cancer-implicated genes.
    Keywords: Research Days 2018, Cancer, Genetics, Somatic alleles
    Date Uploaded: 04/28/2018
  2. Understanding Outbound Student Mobility in Lebanon's Sectarian Environment [Download]

    Title: Understanding Outbound Student Mobility in Lebanon's Sectarian Environment
    Author: Sirgi, Youmna
    Description: The multitude of sects in Lebanon, compounded by a decentralized government, has led to a highly fragmented society. Largely influenced by their roles during the state’s historical development, sects maintain different nationalist viewpoints, influencing their political ambitions and decisions. While some argue that Lebanon should form its own national identity, others argue that Lebanon should integrate into the larger Muslim-Arabic fabric of the Middle East. The fragmented government grants each sect more autonomy to dictate its own affairs, including the ability to establish separate school systems and insert divergent nationalist views in schools, limiting the interaction between sects from adolescence onward. However, as students exit the sectarian environment, say to pursue higher education abroad, they are given the independence to reevaluate their bias and articulate their sectarian and nationalist beliefs. This study aims to identify how students’ removal from a sectarian environment influences their biases. Recent scholarship has focused on the impact of sectarianism within Lebanon’s education system. However, in order to determine the depth of students’ sectarian biases, it is important to understand what happens when they are removed from this environment. In order to do so, this study surveys over 75 Lebanese students who are currently attending university in the United States. Questions focus on students’ educational and familial backgrounds, their preexisting notions of sectarianism, and their current perceptions of sectarianism. To fully understand the notion that students’ sectarian and nationalist identities are malleable based on their environment, further research would be required to survey students who have both exited and re-entered Lebanon. That said, the results of this study indicate that sectarian division, which is currently seen as a deep-rooted reality within Lebanon’s society, may be more circumstantial than previously understood.
    Keywords: Research Days 2018, Lebanon, Sectarian division, Middle East
    Date Uploaded: 04/28/2018
  3. Nucleolar Access Is Variable in Leukocytes Depending on Cellular Migration & Adhesion [Download]

    Title: Nucleolar Access Is Variable in Leukocytes Depending on Cellular Migration & Adhesion
    Author: Suchowiecki, Karol
    Description: The nucleolus within eukaryotic nuclei is formed from ribosomal DNA (rDNA) regions of acrocentric chromosomes 13, 14, 15, 21 and 22 in humans. In addition to ribosome biogenesis, the nucleolus has been shown to be important in mRNA splicing, DNA damage responses, and RNA metabolism. Nucleoli provide a link between transcription and translation, making them critical for protein expression. Viruses can alter nucleolar function by targeting viral proteins to this structure. HIV-1 early-expressed proteins Tat and Rev both have highly basic nucleolar localization signals (NoLS) which may cause HIV-induced alterations of mRNA splicing, cytoplasmic transport, and translation. HIV-1 effects showed differences in nucleolar availability by highly-basic NoLS-containing peptides within adherent versus migrating leukocytes. This may suggest HIV-1 Tat and Rev only localize to the nucleolus when the infected cell is adherent.
    Keywords: Research Days 2018, Microbiology, Cellular adhesion and migration, Immunology
    Date Uploaded: 04/28/2018
  4. The Welfare State Across the Green Line: Measuring the Effects of Israeli Economic Policy on the West Bank Settlement Enterprise [Download]

    Title: The Welfare State Across the Green Line: Measuring the Effects of Israeli Economic Policy on the West Bank Settlement Enterprise
    Author: Zand, Hillel
    Description: The Israeli-Palestinian conflict is oft heralded as one of the greatest geopolitical conflicts of our time, yet the discourse surrounding this issue tends to gravitate toward political considerations, and less toward the socioeconomic forces at play. In addition, intra-national tensions are often overlooked for the more eye-catching international disputes and developments. One of these intra-national tensions is the Israeli settlement enterprise, which is often painted in the lens of religious and ideological extremism. In reality, the overwhelming majority of Jews emigrating to West Bank settlements have chosen to do so in search of a lower cost of living and higher standard of living, a seemingly impossible combination that has been made feasible by a high degree of government economic intervention in the occupied territories. The juxtaposition of government economic intervention in the settlements with Israel’s neoliberal and market-oriented economy only complicates the issue further. Through a mixed quantitative and qualitative analysis, this research seeks to contribute a socioeconomic perspective to existing theories on the settlement enterprise and the conflict writ large. Specifically, this research tests the theory of Danny Gutwein (University of Haifa) that argues that settlement growth is directly correlated with the rise of Israeli neoliberal economic policy and privatization.
    Keywords: Research Days 2018, Israeli-Palestinian conflict, West Bank, Geopolitics, Israeli settlement enterprise
    Date Uploaded: 04/28/2018
  5. Geopolitical Relations: Uganda’s Role in the Development and Use of the River Nile [Download]

    Title: Geopolitical Relations: Uganda’s Role in the Development and Use of the River Nile
    Author: Williams, Jordan
    Description: This study examined the geopolitical relations of the Nile Basin by looking at Uganda as a case study, and to analyze Uganda’s use and development of the River Nile. It looks at the history of transboundary politics and treaties in the region and of Uganda’s development projects of the region. The project discusses modern relations and agreements, with a focus on the most recent agreement between the Riparian States, the Cooperative Framework Agreement, and how Uganda fits into them with regards to their interest in hydropower development within their borders on the Nile. It then explores possible future developments on the river and the potential for future conflict in the region, and finishes by making recommendations for the Nile Basin and Uganda. The whole project is looked at using the sustainable development paradigm. This study was conducted over six weeks through primarily document review and eight expert interviews. Documents provided historical information and facts and statistics on the modern development and geopolitical relations of the Nile Basin. Field based interviews served to enhance and further the information gathered in document review. All interviewees were experts in their fields and most worked within the Ugandan Ministry of Foreign Affairs, the Ugandan Ministry of Water and Environment and their directorates. The study was conducted in accordance to ethical considerations and all wishes of interviewees were upheld throughout the paper. The researcher found that modern geopolitics of the region have been greatly influenced by the 1929 and 1959 colonial agreements that gave Egypt power of the Nile. Today geopolitics focus on changing this status quo, despite protests from Egypt. Uganda must balance its position as both an upstream and downstream Riparian state, and could be a key middle ground country for maintaining peace in the region by appealing to both sides of the water sharing debate. Uganda’s primary investment in the river is hydropower, and so they must balance the want to release enough water to generate electricity, and preserving their water catchments to protect the resource for long term use. Other than hydropower, which is a hotspot for international criticism due to environmental and cultural impacts, Uganda has the potential to develop irrigation from the Nile and Lake Victoria that could increase agricultural yields. Uganda’s position in the Nile Basin makes it unique both in its ability to use and regulate the White Nile, and in the political framework of the region.
    Keywords: Research Days 2018, Geopolitics, Nile Basin, Uganda, Egypt
    Date Uploaded: 04/28/2018
  6. Acoustic Vaporization Threshold of Lipid Coated Perfluoropentane Droplets [Download]

    Title: Acoustic Vaporization Threshold of Lipid Coated Perfluoropentane Droplets
    Author: Aliabouzar, Mitra
    Description: Ultrasound has been embraced as a non-invasive, well-understood and relatively inexpensive tool for diagnostic and therapeutic purposes compared to other imaging modalities such as computed tomography, positron emission tomography and magnetic resonance imaging. However, this modality suffers from low sensitivity. To overcome this limitation, ultrasound contrast agents have been introduced which are gas-filled colloidal particles with a size range of 1-7 micrometers. These microbubbles are highly echogenic and therefore they enhance the sensitivity of conventional ultrasound imaging by expansion and contraction in the alternating pressure waves of the ultrasound beam, while tissue is almost incompressible. Currently available microbubbles used for ultrasound imaging and therapeutics are restricted to intravascular space due to their micron size distribution. Recently an interest is developed in designing novel contrast agents with enhanced stability in vivo and a sufficiently small size distribution for extravascular interrogations (Fig.1). Introducing phase-shift droplets which consist of a nanoscale droplet of perfluorocarbons in an encapsulating shell has led to novel ways of approaching ultrasound-based techniques for both diagnostic and therapeutic purposes. These droplets undergo a phase transition to the highly echogenic gaseous state and are convertible to micron-sized bubbles upon the input of sufficient acoustic activation energy which is termed as acoustic droplet vaporization (ADV) [1]-[3]. In this study, we investigated the ADV thresholds and its dependence on excitation pressure and frequency using acoustic recordings. In addition, we have also compared the scattered response from droplets with that of conventional microbubbles at the corresponding excitation pressure and frequency.
    Keywords: Research Days 2018, Ultrasound, Perfluoropentane droplets
    Date Uploaded: 04/28/2018
  7. Overexpressions of Fatty Acid-Related Genes During Neurodevelopment in a FASD Model [Download]

    Title: Overexpressions of Fatty Acid-Related Genes During Neurodevelopment in a FASD Model
    Author: Basha, Aiesha
    Description: Fetal Alcohol Spectrum Disorders (FASD), caused by prenatal alcohol exposure (PAE), is characterized by congenital central nervous system dysfunction resulting in impaired learning and motor skill deficits. FASD affects 2-5% of children in the U.S., with similar or higher rates reported worldwide. Subsequent single-cell RNA-sequencing in cortex of PAE mice showed variable gene expressions of individual neurons that persisted throughout life. Markedly, high expressions of fatty acid elongase 4 (ELOVL4) and fatty acid synthase (FASN), genes involved in fatty acid biosynthesis, were observed in a specific neuronal population in the PAE mouse cortex. FASN encodes a multi-enzyme protein involved in synthesis of palmitate into long-chain saturated fatty acids, and ELOVL4 encodes a membrane-bound protein involved in elongation of very long chain saturated and polyunsaturated fatty acids in the brain. Fatty acids are essential for regulating neuronal structure and function, and interferences in fatty acid metabolism are associated with neurodevelopmental disorders like autism and ADHD. Changes of fatty acid contents suggestively serve as peripheral biomarkers of FASD. However, functions of fatty acids synthesized by ELOVL4 and FASN remain unknown, and pathological mechanisms due to disturbed fatty acid contents in the brain are elusive. Our working hypothesis is that increase of these fatty acid-related gene expressions in the cerebral cortex is involved in the pathophysiology of FASD. To examine this hypothesis, we first tested if the increases of these genes occur at the protein level by performing immunohistochemistry. We further tested the pattern of increases; which types of neuronal cells and cortical regions show the increase, and which subcellular compartments show the increase of the expressions. In this presentation, based on the staining results, we will discuss how the expressions of fatty acid-related genes are altered due to the effects of PAE.
    Keywords: Research Days 2018, Fetal Alcohol Spectrum Disorders, Health sciences, Central nervous system dysfunctions, Immunohistochemistry
    Date Uploaded: 04/28/2018
  8. The Effect of University Belongingness in Anxiety and Depression Among Emerging Adults [Download]

    Title: The Effect of University Belongingness in Anxiety and Depression Among Emerging Adults
    Author: Adom, Kelvin
    Description: Introduction: Emerging adulthood is a stage of life characterized by notable personal development across several domains, including social identity. Many emerging adults attend colleges and universities, a context in which substantial social identity growth occurs. James Cameron's three-factor model proposes that social identity is comprised of Centrality, Ingroup Affect, and Ingroup Ties. Centrality refers to the amount of time spent thinking about being a group member. Ingroup Affect refers to the emotions associated with membership in the group. Lastly, Ingroup Ties are the perceptions of similarity, bonds, and belongingness with other group members. Studies have shown that a lack of bonds with social groups predicts negative mental health outcomes, while development of strong social ties predicts positive psychological adjustment to college and lower rates of anxiety and depression. Furthermore, strong social ties to the university have been shown to be associated with lower rates of anxiety and depression. This is particularly important given rates of such internalizing disorders have been increasing in college students, where 21.8% and 13.5% report impairment in functioning from anxiety and depressive symptoms, respectively. The present study hypothesized inverse relationships between social ties to one's university and both anxiety and depression in college students. Methods: Undergraduate students (n = 341) attending a private urban university completed self-report matures. These measures included the Penn State Worry Questionnaire, the Beck Anxiety Inventory, and the Patient Health Questionnaire-9. Participants also completed the Three Dimensional Strength of Group Identification Scale to measure aspects of their social identity as students of a university. Results: Bivariate correlational analysis revealed a significant inverse relationship between overall social identification with the university and depressive symptoms (r = -.16, p < .05). Ingroup Affect also had a significant inverse relationship with depressive symptoms (r = -.18, p < .05) and with worry symptoms (r = -.16, p < .05). Ingroup Ties had a significant inverse relationship with depressive symptoms (r=-0.24, p<.0001), worry symptoms (r=-.12, p<.05) and panic symptoms (r=-.14, p <.05). Discussion: The findings of the present study support prior research which claim that an emerging adult's connection to their educational institutions may be critical for their psychological well being. The importance of these findings could contribute to lower instances of reported depression and anxiety cases on university campuses. Universities can use these findings to develop programs which foster a sense of community; which could ultimately promote more positive mental health on campus and a strong sense of school spirit among college students.
    Keywords: Social Identity, Social Belongingness, Emerging Adulthood, Research Days 2018
    Date Uploaded: 04/26/2018
  9. Socio-Economic Status as a Predictor of Sexual Behaviors Among Latino Immigrant MSM and Their Sexual Partners [Download]

    Title: Socio-Economic Status as a Predictor of Sexual Behaviors Among Latino Immigrant MSM and Their Sexual Partners
    Author: Parchem, Ben
    Description: Background: Sexual risk for HIV is stratified by sexual role and activities, particularly presenting a higher risk for receptive partners due to biological vulnerabilities. Sexual role-based identity among Latino men who have sex with men (MSM) often coincides with assumptions regarding power dynamics between sexual partners. Latino MSM often associate pasivo (receptive) roles with less power in the dyad whereas activo (insertive) roles are associated with more power. A more granular understanding of the role socio-economic status (SES) plays in power dynamics, and thus HIV risk, is warranted given the identity-based oppression faced by Latino MSM. Our study aimed to explore the implications of SES for sexual activities among Latino immigrant MSM. Methods: Our sample included 350 Brazilian, Colombian, and Dominican immigrant MSM residing in New York City. We estimated SES differential using participants’ responses on questions gauging their sex partner’s education and income compared to their own. We categorized SES as favoring the participant, the partner, or equal between partners. Participants also reported their participation in a series of sexual activities during the most recent sexual encounter with a single partner. Results: Regarding SES differentials, 24% of participants had a higher SES than their partner, 40.9% had a lower SES, and 35.1% reported equal SES. A series of logistic regressions revealed that, as compared to participants with higher or equal SES, participants with lower SES than their sexual partner were more likely to receive oral sex and manual stimulation of their penis and anus by their sexual partner. They were also less likely to penetrate or ejaculate in their partner’s anus. They were not more or less likely to receive anal penetration or ejaculation in their anus from their sexual partner. Conclusions: Although participants with lower SES were more likely to receive oral and manual stimulation, it did not confer an increased risk of HIV through receptive anal intercourse. The conceptualization of dyadic power between activo and pasivo partners was not aligned with SES. To minimize the influence of SES on HIV risk, user-controlled forms of protection such as PrEP may be more of an acceptable option for Latino immigrant MSM.
    Keywords: Research Days 2018, Psychology, HIV, Sexual behavior, Latino studies
    Date Uploaded: 04/21/2018
  10. Pulsatile flows in a Curved Artery Model [Download]

    Title: Pulsatile flows in a Curved Artery Model
    Author: Najjari, Mohammad Reza
    Description: Due to the importance of understanding behavior of blood flow in curved arteries, we experimentally modeled the flow of blood analog fluids through curved vessels. The curvature deviates the primary flow and causes the formation of helical motions inside the vessels, i.e. vortices. These vortices play important roles in hemodynamics and can affect mixing of different blood components and wall shear stress inside the artery. Therefore, understanding of the dynamics of these vortices is important. There are some characteristics that can affect the vortices in vessels e.g. rheological properties of the blood analog, vessel wall properties (rigid/elastic), and geometry of vessel. We investigate the morphology of vortical structures inside curved vessels under different conditions and aim to portray a complete picture of their evolution in 3D space. In order to investigate the effect of different parameters on vortices we used a canonical 180˚ curved vessel geometry. The rigid models were machined from an acrylic block. To fabricate the more complex elastic models we developed an injection molding method to produce optically clear elastic vessels from silicone. Our working blood-analog fluid is a mixture of water and glycerin to match the viscosity of blood. Viscoelastic and shear-thinning properties of blood were simulated by adding Xanthan gum. The refractive index was perfectly matched to that of the vessel to minimize distortion for imaging with our optical diagnostics. To produce the required variable pulsatile flow rates, an adaptive feedback PID controller was developed that automatically adjusts the input to the pump to match the desired flow rate waveform. Particle image velocimetry (PIV) was used in all experiments to measure the velocity fields inside the curved vessel. After obtaining the velocity data, vortices were detected using the d2 vortex identification method with an in-house Fortran code and vortex circulation analysis was performed. Our findings have resolved conflicting viewpoints in the scientific literature concerning the effects of complex fluids and effect of vessel wall elasticity. Our published results provide justification for using simple Newtonian fluids in rigid geometries as opposed to using more complex fluids in elastic vessels. These simpler models capture all the relevant flow physics and are simpler to construct, and are more amenable to optically-based measurements. Also, we showed that the effects of local elasticity on morphology of vortices are less important compared to dominant effect of geometry and torsion. Therefore, this justifies the use of simple rigid models with realistic geometry.
    Keywords: Research Days 2018, Mechanical and Aerospace Engineering, Blood flow, Biology
    Date Uploaded: 04/21/2018