Physical Sciences and Mathematics Commons^™

Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang

Capstones

As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.

https://lucy-huang-9tge.squarespace.com/

Of Rats And Men, Thomas S. Walsh

Capstones

This capstone is a data-driven investigation into New York City's rat problem. By using publicly available government data to map rat activity in NYC, I identified several socio-economic variables that correlate with rat populations at the community district, borough, and city-scale. I used these findings (mainly that rat problems are linked to lower incomes) as the basis of an investigation, which includes interviews with residents, experts, and city officials. Prof. Bobby Corrigan, urban rodentologist and formerly with the NYC Department of Health criticizes the city's efforts for the first time on the record.

https://thomasseiyawalsh.wixsite.com/ratstone

Study Of Self-Similarity In Brain Data, Jennifer Holst

Student Theses

In the area of computer science, past research has found that the concept of self-similarity is present in local and Internet-based network traffic. This study considers the possibility that data traveling through the neuronal network in the human brain is also self-similar. By analyzing publicly available raw EEG data and estimating its Hurst parameter, we find indications that brain data traffic may in fact be self-similar.

Efficient Air Desulfurization Catalysts Derived From Pig Manure Liquefaction Char, Rajiv Wallace, Sundaramurthy Suresh, Elham H. Fini, Teresa Bandosz

Publications and Research

Biochar from the liquefaction of pig manure was used as a precursor of H2S desulfurization adsorbents. In its inorganic matter, it contains marked quantities of calcium, magnesium and iron, which are known as hydrogen sulfide oxidation catalysts. The char was used either as-received or mixed with 10% nanographite. The latter was added to increase both the content of the carbon phase and conductivity. ZnCl2 in two different ratios of char to an activation agent (1:1 and 1:2) was used to create the porosity in the carbon phase. The content of the later was between 18–45%. The activated samples adsorbed 144 …

Synthesis, Crystal Structure, And Photoluminescent Properties Of 3,3′,4,4′-Tetraethyl-5,5′-Divinyl-2,2′-Bipyrrole Derivatives, Toru Okawara, Reo Kawano, Hiroya Morita, Alan Finkelstein, Renjiro Toyofuku, Kanako Matsumoto, Kenji Takehara, Toshihiko Nagamura, Seiji Iwasa, Sanjai Kumar

Publications and Research

Photoluminescent divinylbipyrroles were synthesized from 3,3′,4,4′-tetraetyl-2,2′-bipyrrole-5,5′-dicarboxaldehyde and activated methylene compounds via aldol condensation.For mechanistic clarity, molecular structures of Meldrum’s acid- and 1,3-dimethylbarbituricacid-derived divinylbipyrroles were determined by single-crystal X-ray diffraction. Photoluminescentproperties of the synthesized divinylbipyrroles in dichloromethane were found to be dependent onthe presence of electron withdrawing groups at the vinylic terminal. The divinylbipyrroles derivedfrom malononitrile, Meldrum’s acid, and 1,3-dimethylbarbituric acid showed fluorescent peaks at553, 576, and 602 nm respectively. Computational studies indicated that the alkyl substituents on thebipyrrole 3 and 3′positions increased energy level of the highest occupied molecular orbital (HOMO)compared to the unsubstituted derivatives and provided rationale for the …

Ligand Modulation Of Sidechain Dynamics In A Wild-Type Human Gpcr, Lindsay D. Clark, Igor Dikiy, Karen Chapman, Karin Ej Rodstrom, James Aramini, Michael V. Levine, George Khelashvili, Soren Gf Rasmussen, Kevin H. Gardner, Daniel M. Rosenbaum

Publications and Research

GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A2AR) that are deuterated apart from 1H/13C NMR probes at isoleucine d1 methyl groups, which facilitated 1H/13C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na+] is required to allow large agonist-induced structural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and …

Learning About Women In Stem For First-Year Students [Liberal Arts: Math And Science], Reem Jaafar, Ian Alberts

Open Educational Resources

This assignment was designed for students in the first year seminar and aligns with the Inquiry and Problem Solving core competency, with a focus on “framing the issues” (identifies and/or addresses questions problems and/or hypothesis informed by knowledge of context) and “evidence gathering” (assembles, reviews and synthesizes evidence from diverse sources of relevant knowledge). Both assignments rely on writing and one may include an oral component. In writing, the focus is on “Content Development and Organization,” as well as “Control of Language, Syntax, and Mechanics.”

LaGuardia’s Core Competencies and Communication Abilities

Main Course Learning Objectives:

• The LMF course for Liberal …

Computational Investigation Of The Pore Formation Mechanism Of Beta-Hairpin Antimicrobial Peptides, Richard Lipkin

Dissertations, Theses, and Capstone Projects

β-hairpin antimicrobial peptides (AMPs) are small, usually cationic peptides that provide innate biological defenses against multiple agents. They have been proposed as the basis for novel antibiotics, but their pore formation has not been directly observed on a molecular level. We review previous computational studies of peptide-induced membrane pore formation and report several new molecular dynamics simulations of β-hairpin AMPs to elucidate their pore formation mechanism. We simulated β-barrels of various AMPs in anionic implicit membranes, finding that most of the AMPs’ β-barrels were not as stable as those of protegrin. We also performed an optimization study of protegrin β-barrels …

Walking As Ontological Shifter: Thoughts In The Key Of Life, Bibi (Silvina) Calderaro

Dissertations, Theses, and Capstone Projects

With walking as ontological shifter I pursue an alternative to the dominant modernist episteme that offers either/or onto-epistemologies of opposition and their reifying engagements. I propose this type of walking is an intentional turning towards a set of radical positions that, as integrative aesthetic and therapeutic practice, brings multiplicity and synchronicity to experience and being in an expanded sociality. This practice facilitates the conditions of possibility for recurring points of contact between the interiority perceived as ‘body’ and the exteriority perceived as ‘world.’ While making evident the self’s at once incoherence with it-self, it opens to a space beyond the …

A Realization Of Modernity: Case Studies In Connectivity And Time, Mari Gorman

Dissertations, Theses, and Capstone Projects

My stated goal in applying to The Graduate Center was to explore my previous research in diverse fields of study. This research, the result of a formal investigation of acting, was and still is centrally focused on the subject of relationship itself, relationships being what actors create. In pursuit of a greater understanding of the essential nature of relationship in practical terms, a self-organizing complex system that constitutes universal relationship was unexpectedly discovered. As such, this system has been shown to offer solutions to many outstanding problems in diverse areas of study. The Liberal Studies program track, Approaches to Modernity …

A Combinatorial Framework For Multiple Rna Interaction Prediction, Syed Ali Ahmed

Dissertations, Theses, and Capstone Projects

The interaction of two RNA molecules involves a complex interplay between folding and binding that warranted recent developments in RNA-RNA interaction algorithms. However, biological mechanisms in which more than two RNAs take part in an interaction also exist.

A typical algorithmic approach to such problems is to find the minimum energy structure. Often the computationally optimal solution does not represent the biologically correct structure of the interaction. In addition, different biological structures may be observed, depending on several factors. Furthermore, scoring techniques often miss critical details about dependencies within different parts of the structure, which typically leads to lower scores …

Morphogenesis And Growth Driven By Selection Of Dynamical Properties, Yuri Cantor

Dissertations, Theses, and Capstone Projects

Organisms are understood to be complex adaptive systems that evolved to thrive in hostile environments. Though widely studied, the phenomena of organism development and growth, and their relationship to organism dynamics is not well understood. Indeed, the large number of components, their interconnectivity, and complex system interactions all obscure our ability to see, describe, and understand the functioning of biological organisms.

Here we take a synthetic and computational approach to the problem, abstracting the organism as a cellular automaton. Such systems are discrete digital models of real-world environments, making them more accessible and easier to study then their physical world …

Tumor Necrosis Factor Dynamically Regulates The Mrna Stabilome In Rheumatoid Arthritis Fibroblast-Like Synoviocytes, Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Christopher Sohn, Bethany Syracuse, Eugenia G. Giannopoulou, Sung Ho Park, Hyelim Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias

Publications and Research

During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches …

Species Identification Of Necrophagous Insect Eggs Based On Amino Acid Profile Differences Revealed By Direct Analysis In Real Time-High Resolution Mass Spectrometry, Justine E. Giffen, Jennifer Y. Rosati, Cameron M. Longo, Rabi A. Musah

Publications and Research

The colonization of decomposing remains by necrophagous insects such as blow flies is of forensic importance because the progression through the various stages of insect development can be correlated to time of death. The ability to infer this information hinges on accurate determination of the fly species that are associated with the entomological evidence collected. This evidence can include eggs, larvae, pupae, and puparial casings. Determination of the egg’s identity is particularly challenging because the eggs of multiple species are morphologically very similar. We report here that the species identity of fly eggs can be determined from their chemical fingerprint …

Naturally-Derived Molecular Ensembles In Medicine, Materials Science And Evolutionary Biology: An Interdisciplinary Study, Silvio Panettieri

Dissertations, Theses, and Capstone Projects

The first chapter will introduce the work carried out in collaboration with the Govind laboratory at CCNY. Our quest was set forth to investigate the intimate relationship lying between chronic inflammation and tumor development. For at least the last fifteen years much research has been conducted on this topic; yet, the level of complexity arising from exceedingly interwoven biochemical pathways in mammals has resulted in slow advancements in this field. This is why we resorted to a simple yet powerful immunogenetic model organism, the fruit fly Drosophila melanogaster, in combination with the administration of the most common anti-inflammatory drug, …

Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen

Dissertations, Theses, and Capstone Projects

Conservation biology is a scientific discipline that draws on methods from diverse fields to address specific conservation concerns and inform conservation actions. This field is overwhelmingly focused on charismatic animals and vascular plants, often ignoring other diverse and ecologically important groups. This trend is slowly changing in some ways; for example, increasing number of fungal species are being added to the IUCN Red-List. However, a strong taxonomic bias still exists. Here I contribute four research chapters to further the conservation of lichens, one group of frequently overlooked organisms. I address specific conservation concerns in eastern North America using modern methods. …

A Global Study Of Gpp Focusing On Light-Use Efficiency In A Random Forest Regression Model, Suhua Wei, Chuixiang Yi, Wei Fang, George Hendrey

Publications and Research

Light-use efficiency (LUE) is at the core of mechanistic modeling of global gross primary production (GPP). However, most LUE estimates in global models are satellite based and coarsely measured with emphasis on environmental variables. Others are from eddy covariance towers with much greater spatial and temporal data quality and emphasis on mechanistic processes, but in a limited number of sites. In this study, we conducted a comprehensive global study of tower-based LUE from 237 FLUXNET towers, and scaled up LUEs from in situ tower level to global biome level. We integrated the tower-based LUE estimates with key environmental and biological …

Conserved Patterns Of Integrated Developmental Plasticity In A Group Of Polyphenic Tropical Butterflies, Erik Van Bergen, Dave Osbaldeston, Ullasa Kondandaramaiah, Oskar Brattström, Kwaku Aduse-Poku, Paul M. Brakefield

Publications and Research

Background: Developmental plasticity is thought to have profound macro-evolutionary effects, for example, by increasing the probability of establishment in new environments and subsequent divergence into independently evolving lineages. In contrast to plasticity optimized for individual traits, phenotypic integration, which enables a concerted response of plastic traits to environmental variability, may affect the rate of local adaptation by constraining independent responses of traits to selection. Using a comparative framework, this study explores the evolution of reaction norms for a variety of life history and morphological traits across five related species of mycalesine butterflies from the Old World tropics.

Results: Our data …

Impact Of Urbanization On Temperature Variation In Big Cities: Measuring Health Risk While Targeting Vulnerable Population, Maryam E. Karimi

Dissertations, Theses, and Capstone Projects

Densely populated cities are experiencing Urban Heat Island (UHI) effects and localized hotspots. Cities, such as New York can form heat islands all year round. This is primarily due to land surface modifications, radiative trapping in urban canyons and lack of cooling through evapotranspiration caused by displaced trees and vegetation. UHI refers to an increase in air and surface temperature in cities compared to surrounding suburban and rural areas. Large scale environmental forcing can cause subdivisions of UHI throughout a city. The combined of environmental forcing effects lead to the formation of hot pockets within the cities at micro-scale. The …

Evolution Of Complex Target Selex To Identify Aptamers Against Mammalian Cell-Surface Antigens, Prabodhika R. Mallikaratchy

Publications and Research

The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This …

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching …

Enzymatically Active Microspheres For Self-Propelled Colloidal Engines, Jungeun Park

Dissertations and Theses

Micro- and nano-motors have attracted numerous attentions from various scientific areas due to their potential applications. Most studies on self-propelled colloidal engines have exploited catalytic decomposition of hydrogen peroxide to drive the motor. Since the hydrogen peroxide is caustic, it is not suitable to use in biological applications, encouraging people to develop “greener” fuels. The aim of this research is to study a new transduction mechanism for self-propulsion not tied to hydrogen peroxide, and which can in particular be used with biological molecules as fuels. In this study, we focus on making particles with enzymatic activity which can effectively decompose …