Physical Sciences and Mathematics Commons^™

Design, Synthesis And Evaluation Of Molecules With Selective And Poly-Pharmacological Actions At D1r, D3r And Sigma Receptors, Pierpaolo Cordone

Dissertations, Theses, and Capstone Projects

The dopamine D3 receptor (D3R) is one of the most studied receptors involved in drug addiction. One of the most common strategies to treat substance use disorders is via D3R antagonism. The majority of the D3R antagonists synthesized so far have poor pharmacokinetic properties and/or lack selectivity toward D3R. In this thesis, the design, synthesis and biological evaluation of novel molecules that target the dopamine D1 receptor (D1R), D3R and the serendipitous discovery of molecules that target s receptors will be described.

Chapter 1 presents a survey of the fundamental pharmacology of D1R, D3R and s receptors and the therapeutic …

Synthetic And Biological Studies On Benzazepine Derivatives As Dopamine Receptor Ligands, Rajan Giri

Dissertations, Theses, and Capstone Projects

Dopamine (DA) receptors, members of the G-protein coupled receptors (GPCRs) family, are divided in two groups based on their transmembrane structural homology domains: D1R-like (D1R, D5R sub-types) and D2R-like DA receptors (D2R, D3R and D4R sub-types). Disturbances in dopaminergic neurotransmission are associated with several CNS disorders. Hence, DA receptor selective ligands have been sought as pharmacological agents to normalize perturbations in the dopaminergic system. Despite several notable efforts, the discovery of highly selective ligands for dopamine receptor sub-types has proved challenging due to close transmembrane structural similarity, especially between DA receptor sub-types within the same group.

The 1-phenylbenzazepine scaffold is …

Learn Biologically Meaningful Representation With Transfer Learning, Di He

Dissertations, Theses, and Capstone Projects

Machine learning has made significant contributions to bioinformatics and computational biol­ogy. In particular, supervised learning approaches have been widely used in solving problems such as bio­marker identification, drug response prediction, and so on. However, because of the limited availability of comprehensively labeled and clean data, constructing predictive models in super­ vised settings is not always desirable or possible, especially when using data­hunger, red­hot learning paradigms such as deep learning methods. Hence, there are urgent needs to develop new approaches that could leverage more readily available unlabeled data in driving successful machine learning ap­ plications in this area.

In my dissertation, …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

Towards Automated Software Evolution Of Data-Intensive Applications, Yiming Tang

Dissertations, Theses, and Capstone Projects

Recent years have witnessed an explosion of work on Big Data. Data-intensive applications analyze and produce large volumes of data typically terabyte and petabyte in size. Many techniques for facilitating data processing are integrated into data-intensive applications. API is a software interface that allows two applications to communicate with each other. Streaming APIs are widely used in today's Object-Oriented programming development that can support parallel processing. In this dissertation, an approach that automatically suggests stream code run in parallel or sequentially is proposed. However, using streams efficiently and properly needs many subtle considerations. The use and misuse patterns for stream …

Photosensitization And Analytical Study On Reactive Oxygen Intermediates: Self-Sorting Surface Radicals And “On-Off” Sensitizer Function Mechanisms, Sarah J. Belh

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters which are detailed below. Chapter 1 is an introductory chapter, which lays out the background and purpose of the research.

Chapter 2 describes a study of the mobility of alkoxy radicals on a surface by detection of their recombination product. A novel method called symmetrical product recombination (SRP) utilizes an unsymmetrical peroxide that upon sensitized homolysis recombines to a symmetrical product [R'OOR → R'O•↑ + •OR → ROOR]. This allows for self-sorting of the radical to enhance the recombination path to a symmetrical product, which has been used to deduce surface migratory aptitude. SPR …

A Consistent Model Of Terrestrial Planet Magnetospheres And Rotations In Our Solar System, Fred J. Cadieu

Publications and Research

The Sun comprises 99.9% of the solar system mass so it is expected that Sun terrestrial planet interactions can influence the motion as well as the rotation of the terrestrial planets.Gravity affects the planet orbital motions while the changing magnetic fields of the Sun can influence the planet rotations. Planets that manifest a magnetic field dominate any weaker magnetic fields from the Sun, but the rotation of terrestrial planets without a magnetic field interacts with the changing Sun’s field dependent on the electrical conductivity of the core region. It is determined that the average planet density becomes a useful quantity …

An Empirical Study Of Refactorings And Technical Debt In Machine Learning Systems, Yiming Tang, Raffi T. Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja

Publications and Research

Machine Learning (ML), including Deep Learning (DL), systems, i.e., those with ML capabilities, are pervasive in today’s data-driven society. Such systems are complex; they are comprised of ML models and many subsystems that support learning processes. As with other complex systems, ML systems are prone to classic technical debt issues, especially when such systems are long-lived, but they also exhibit debt specific to these systems. Unfortunately, there is a gap of knowledge in how ML systems actually evolve and are maintained. In this paper, we fill this gap by studying refactorings, i.e., source-to-source semantics-preserving program transformations, performed in real-world, open-source …

An Empirical Study Of Refactorings And Technical Debt In Machine Learning Systems, Yiming Tang, Raffi T. Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja

Publications and Research

Machine Learning (ML), including Deep Learning (DL), systems, i.e., those with ML capabilities, are pervasive in today’s data-driven society. Such systems are complex; they are comprised of ML models and many subsystems that support learning processes. As with other complex systems, ML systems are prone to classic technical debt issues, especially when such systems are long-lived, but they also exhibit debt specific to these systems. Unfortunately, there is a gap in knowledge of how ML systems evolve and are maintained. In this paper, we fill this gap by studying refactorings, i.e., source-to-source semantics-preserving program transformations, performed in real-world, open-source software, …

Deep Learning Predicts Chromosomal Instability From Histopathology Images, Zhuoran Xu, Akanksha Verma, Uska Naveed, Samuel F. Bakhoum, Pegah Khosravi, Olivier Elemento

Publications and Research

Chromosomal instability (CIN) is a hallmark of human cancer yet not readily testable for patients with cancer in routine clinical setting. In this study, we sought to explore whether CIN status can be predicted using ubiquitously available hematoxylin and eosin histology through a deep learning-based model. When applied to a cohort of 1,010 patients with breast cancer (Training set: n = 858, Test set: n = 152) from The Cancer Genome Atlas where 485 patients have high CIN status, our model accurately classified CIN status, achieving an area under the curve of 0.822 with 81.2% sensitivity and 68.7% specificity in …

Dom Degradation By Light And Microbes Along The Yukon River‑Coastal Ocean Continuum, Brice K. Grunert, Maria Tzortziou, Patrick Neale, Alana Menendez, Peter Hernes

Publications and Research

The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure …

Luminescence Properties Of Hexagonal Boron Nitride Powders Probed By Deep Uv Photoluminescence Spectroscopy, Nikesh Maharjan, Mim Lal Nakarmi

Publications and Research

Deep ultraviolet (UV) photoluminescence (PL) spectroscopy was employed to study the luminescence properties of hexagonal boron nitride (h-BN) crystal powders after annealing the samples at different temperatures in the range of 100–900 ÅãC for 1 h in ambient air. The PL spectrum from the h-BN powder samples annealed around 700 ÅãC showed strong luminescence intensity at 5.49 eV along with enhanced phonon-assisted band-edge emission at 5.90 eV. Additionally, it revealed sharp atomic-like emission lines in UV region at 4.10, 4.12, 4.14, and 4.16 eV with line widths less than 1 nm from the annealed samples which were not present in …

Intangible Cultural Heritage: A Benefit To Climate-Displaced And Host Communities, Gül Aktürk, Martha B. Lerski

Publications and Research

Climate change is borderless, and its impacts are not shared equally by all communities. It causes an imbalance between people by creating a more desirable living environment for some societies while erasing settlements and shelters of some others. Due to floods, sea level rise, destructive storms, drought, and slow-onset factors such as salinization of water and soil, people lose their lands, homes, and natural resources. Catastrophic events force people to move voluntarily or involuntarily. The relocation of communities is a debatable climate adaptation measure which requires utmost care with human rights, ethics, and psychological well-being of individuals upon the issues …

Estimation Of The Planetary Boundary Layer Height: Part 1: Global Radar Wind Profiler Network Data; Part 2: A Comparison To Ceilometer Data, Holly Josephs

Theses and Dissertations

Two methods for estimating the planetary boundary layer, an algorithm to identify a maximum in the backscatter and a covariance wavelet transform method, are explored and applied to global radar wind profiler network data and ceilometer data respectively. The objective of the study is to establish that the data sources and algorithms can be used to estimate planetary boundary layer heights so that global studies can make use of these estimates. Data from the global network of wind profilers required significant restructuring and quality control in order to be used for the present study. The maximum backscatter identification algorithm was …

Investigating Water Usage Patterns Tied To California State Water Project, Xiaoqing Wu

Publications and Research

California (USA) is the largest agricultural producer and one of the populous states in the United State. As the population and agriculture grows, water consumption patterns become crucial to keep track of especially surface water. In this research project, we studied possible changes in water consumption patterns in different counties and water rights holders who obtain surface water supply from the State Water Project (SWP) in California. We conducted a time series analysis on the California Monthly Diverted Surface Water dataset through two different time series forecasting models. Our analysis indicates that the total diverted surface water presents a periodic …

Interfacial Dynamics And Ionic Transport Of Radiologic Contrast Media In Carbohydrate Matrix: Utility And Limits Of X-Ray Imaging, Lin Mousa, Hayley Sanchez, Subhendra Sarkar, Zoya Vinokur

Publications and Research

Hello, our names are Lin Mousa and Hayley Sanchez, this semester we participated in a research project dedicated to analyzing the interactions of contrast media with the molecular components of fruits to compare how they would react with the human brain. This project involved the injection of fruits with varying contrasts and the imaging of the diffusion and interactions of the contrast within the fruits with X-rays. With setup technical parameters on the x-ray equipment images were taken with identical setups at an hourly rate for several days. The final results of this experiment indicated that contrasts such as Gadolinium …

Flooding Effects On China And Indonesia, Junhao Tan, Yuxuan Zhao, Yujie Li, Denny Caisaguano, Tanvir Hossain, Allan Zhu, Abdou Bah

Publications and Research

As climate change continues affecting the world, the damages and the problems follow by the flooding in certain regions are increasing. The research will be focuses on the impact of flood on two counties. The causes of flooding, the damages of flooding, and the solution developed to prevent and protect the cities.

The Effects Of Late Spring Frost On Forest And Landscape Health And Recovery Of The Black Rock Forest, New York, Caroline Eco, Oliver Imhans, Aaron Davitt, Andrew B. Reinmann

Publications and Research

Projected changes in climate are expected to increase the frequency of late spring frost events in the Northeast US. Such events can be harmful to trees because freezing temperatures that occur after leaf-out can damage or kill young leaves. The resultant defoliation typically forces a second flush of leaves, but delays canopy development, which in turn delays the onset of canopy carbon uptake and alters canopy thermal properties. In this study, we analyzed a recent freeze event that occurred on 8-9 May 2020 (DOY 129-130) at Black Rock Forest (BRF), which is in the Hudson Highlands of southeastern New York …

Application Of Randomness In Finance, Jose Sanchez, Daanial Ahmad, Satyanand Singh

Publications and Research

Brownian Motion which is also considered to be a Wiener process and can be thought of as a random walk. In our project we had briefly discussed the fluctuations of financial indices and related it to Brownian Motion and the modeling of Stock prices.

Downscaling Methodology For Satellite Land Surface Temperatures Over Urban Environments, Naved Khan, Ruben Vecino

Publications and Research

The objective of this study is to develop high spatial and temporal resolution Land Surface Temperature (LST) data using a combination of Landsat 8, infrared satellite sensors such as the Moderate Resolution Imaging Spectroradiometer (MODIS), and the Geostationary Operational Environmental Satellite-R Series (GOES-16). The Landsat 8 Thermal Infrared Sensor (TIRS) provides higher spatial resolution (30 m) estimates of skin temperature every 16 days. MODIS makes daytime and nighttime observations of the Earth’s thermal emission at a coarser spatial resolution (1000 m), while GOES-16, which has lower spatial resolution (2 km), measures the skin temperature at a much higher temporal resolution …

International Migration From The Latin American-Caribbean Region: Taking Environmental Indicators Into Consideration, Chelsea Wepy

Student Theses and Dissertations

International migration, the act of leaving one’s country to permanently settle in another country, is driven by many socio economic/political factors, such as lack of economic opportunity, access to education, governmental corruption, and violence. These factors have proven to be the reason that many citizens within the Latin American-Caribbean region either choose or are forced to relocate internationally. While these factors are important to consider independently; these issues are often exacerbated by changes in the natural environment. The objective of my paper is to highlight the importance of considering changes in the natural environment. In doing so, I hope to …

Species In Vernal Pools: Anova, Lisa Manne

Open Educational Resources

A one-way analysis of variance exercise using data on species diversities from vernal pools.Data are from vernal pools in Willowbrook Park (adjacent to College of Staten Island's campus) in spring.

The typical ANOVA gives a straightforward result (significant anova, easily-interpreted Tukey-Kramer analysis). This data set requires more nuanced interpretation, as the ANOVA is marginally significant, and Tukey-Kramer yields one significant pairwise comparison between groups. Relative lack of variation within groups explains this apparent enigma.

Discovering Kepler’S Third Law From Planetary Data, Boyan Kostadinov, Satyanand Singh

Publications and Research

In this data-inspired project, we illustrate how Kepler’s Third Law of Planetary Motion can be discovered from fitting a power model to real planetary data obtained from NASA, using regression modeling. The power model can be linearized, thus we can use linear regression to fit the model parameters to the data, but we also show how a non-linear regression can be implemented, using the R programming language. Our work also illustrates how the linear least squares used for fitting the power model can be implemented in Desmos, which could serve as the computational foundation for this project at a lower …

Shedding Light On Dark Patterns: A Case Study On Digital Harms, Noreen Y. Whysel

Publications and Research

You’ve been there before. You thought you could trust someone with a secret. You thought it would be safe, but found out later that they blabbed to everyone. Or maybe they didn’t share it, but the way they used it felt manipulative. You gave more than you got and it didn’t feel fair. But now that it’s out there, do you even have control anymore?

Ok. Now imagine that person was your supermarket. Or your bank. Or your boss.

As designers of digital spaces for consumer products and services, how often do we consider the relationship we have with our …

Factoring: Difference Of Squares, Thomas Lauria

Open Educational Resources

This lesson plan will explain how to factor basic difference of squares problems

Enhanced Nonlinear Interaction Of Polaritons Via Excitonic Rydberg States In Monolayer Wse2, Jie Gu, Valentin Walther, Lutz Waldecker, Daniel Rhodes, Archana Raja, James C. Hone, Tony F. Heinz, Stéphane Kéna-Cohen, Thomas Pohl, Vinod M. Menon

Publications and Research

Strong optical nonlinearities play a central role in realizing quantum photonic technologies. Exciton-polaritons, which result from the hybridization of material excitations and cavity photons, are an attractive candidate to realize such nonlinearities. While the interaction between ground state excitons generates a notable optical nonlinearity, the strength of such interactions is generally not sufficient to reach the regime of quantum nonlinear optics. Excited states, however, feature enhanced interactions and therefore hold promise for accessing the quantum domain of single-photon nonlinearities. Here we demonstrate the formation of exciton-polaritons using excited excitonic states in monolayer tungsten diselenide (WSe₂) embedded in a …

Automated Evolution Of Feature Logging Statement Levels Using Git Histories And Degree Of Interest, Yiming Tang, Allan Spektor, Raffi Khatchadourian, Mehdi Bagherzadeh

Publications and Research

Logging—used for system events and security breaches to more informational yet essential aspects of software features—is pervasive. Given the high transactionality of today’s software, logging effectiveness can be reduced by information overload. Log levels help alleviate this problem by correlating a priority to logs that can be later filtered. As software evolves, however, levels of logs documenting surrounding feature implementations may also require modification as features once deemed important may have decreased in urgency and vice-versa. We present an automated approach that assists developers in evolving levels of such (feature) logs. The approach, based on mining Git histories and manipulating …

Human Ace2‑Functionalized Gold “Virus‑Trap” Nanostructures For Accurate Capture Of Sars‑Cov‑2 And Single‑Virus Sers Detection, Yong Yang, Yusi Peng, Chenglong Lin, Li Long, Jingying Hu, Jun He, Hui Zeng, Zhengren Huang, Zhi-Yuan Li, Masaki Tanemura, Jianlin Shi, John R. Lombardi, Xiaoying Luo

Publications and Research

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold “virus traps” nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106- fold virus enrichment originating from high-affinity of ACE2 with S protein as well as “virus-traps” composed of oblique gold nanoneedles, and 109- fold enhancement of Raman signals originating from multicomponent SERS effects. Furthermore, the identification standard of virus …

Eas 201: Nature Of New York, Cuny School Of Professional Studies

Open Educational Resources

Provides an introduction to ecological reasoning through study of New York City’s geologic origins and transformations over time: natural and man-made environments, cultural history, biological diversity, habitats, and invasive species. Lectures, discussion, virtual labs and field experiences show how various elements have combined over time to form the current urban metropolis. Students will formulate testable hypothesis, collect and analyze field data, create well-developed laboratory reports.

Eas 250: Oceanography, Cuny School Of Professional Studies

Open Educational Resources

Oceanography is an interdisciplinary field studying the processes and interrelationships of geology, chemistry, geography, geophysics, meteorology, and biology. This course focuses on how scientific processes and scientific understanding are applied to questions such as: Which factors control life in the ocean? How do we know what we know about the ocean? What's at the bottom of the ocean? How does the water in the ocean move? How are human activities and climate change altering the ocean? Oceanographic data is used to understand the ocean and its interactions with the rest of the planet.

This course is based in part upon …