Physical Sciences and Mathematics Commons^™

An Assessment Of Geographic And Taxonomic Biases In Research On Climate Change-Related Range Shifts, Evan J. Parker

Library Map Prize

Geographic and taxonomic biases in ecological literature inhibit the ability of research to be generalized or translated to other systems. This is particularly true with research on climate change-related range shifts, where a diverse and representative set of observations is needed to understand the significant heterogeneity of range shifts and improve models. A literature review was conducted and biases were assessed by examining the geographic location of study areas, the taxonomic makeup of study species, and the location of study areas within species ranges. A substantial geographic skew towards terrestrial, mid-latitude North America and Europe was observed. However, taxonomic coverage …

Strong Inclination Pacing Of Climate In Late Triassic Low Latitudes Revealed By The Earth-Saturn Tilt Cycle, Miranda Margulis-Ohnuma, Jessica Whiteside, Paul Olsen

The Yale Undergraduate Research Journal

Gravitational interactions among masses in the solar system are recorded in Earth’s paleoclimate history because variations in the geometry of Earth’s orbit and axial orientation modulate insolation. However, astronomical models are unreliable before ~50 Ma due to the chaotic nature of the solar system and therefore must be constrained using geological observations. Here, we use environmental proxies from paleo-tropical Late Triassic lake deposits of the Newark Rift Basin to identify and tune to previously undescribed strong variations in orbital inclination. Tuning to the 173 kyr Earth-Saturn inclination cycle, theoretically stable due to the high mass of Saturn, reveals both other …

Analysis Of The Electronic Effects And Reactivity Of Benzhydrols In The Formation Of Benzhydryl Ethers, Katherine Quesada, Daniel Chabeda, Jaeger Johnson, Alex Shore

The Yale Undergraduate Research Journal

Benzhydryl ethers were synthesized through the use of microwave irradiation in a proto-ionic liquid solvent. The resulting products were separated from the reaction mixture by vacuum filtration with a silica gel plug. The products were analyzed using GCMS and 1 H NMR techniques to identify and quantify products. Analysis of the resultant data indicated the syntheses of the desired benzhydryl products were successful for 4,4-dimethoxybenzhydrol (conversion: 83% (1-propyl ether), 11% (2-propyl ether), 11% (menthyl ether)) and 4,4-dimethylbenzhydrol (conversion to desired product: 100% (1-propyl ether), 100% (2-propyl ether), 26% (menthyl ether)). However, the syntheses were unsuccessful for reactant 4,4-difluorobenzhydrol and benzhydrol. …

A Dispersive Force Model Of Caribbean Island Biogeography, Anthony Sarkiss

The Yale Undergraduate Research Journal

Framework-based models serve as an important tool to describe, predict and manage ecological systems. In this paper I construct one such model, a dispersive force model based on MacArthur and Wilson’s (1963) theory of island biogeography, in order to assess island species richness with varying climatic patterns. Specifically, I use island–mainland distance (d), insular area (A), a climatic dispersal parameter (f), and a climatic disturbance parameter (h) to calculate the insular species richness ratio at equilibrium. To test this model through hurricane impact on marine islands, it was executed with data from islands of the Dutch Caribbean. Future climatic conditions …

Incomplete? Or Indefinite? Intuitionism On Gödel’S First Incompleteness Theorem, Quinn Crawford

The Yale Undergraduate Research Journal

This paper analyzes two natural-looking arguments that seek to leverage Gödel’s first incompleteness theorem for and against intuitionism, concluding in both cases that the argument is unsound because it equivocates on the meaning of “proof,” which differs between formalism and intuitionism. I argue that this difference explains why “proof” has definite extension for the formalist but not for the intuitionist. Sections 1-3 summarize various philosophies of mathematics and Gödel’s result. Section 4 argues that, because the Gödel sentence of a formal system is provable to the intuitionist, they are neither aided nor attacked by Gödel’s first incompleteness theorem. Section 5 …

Sounding The Alarm: Down-Ballot Setback For The Democrats In 2020, Yaakov Huba

The Yale Undergraduate Research Journal

The 2020 general election turned out more American voters than any other election, its monumental stakes commanding the attention of the world. While the focus in the race’s aftermath has primarily been the top of the ticket, the rebuke of President Trump’s time in office, the equally important down-ballot races have been largely passed over. Many major political analysts like the Cook Political Report predicted that Democrats would expand their House majority by 5-10 seats. Yet, the Democratic Party ended up losing 10 seats1. During the certification of election results, I collected data on incumbents in the US House of …

Optimal Information Design In Two-Sided Trade, Pradhi Aggarwal

The Yale Undergraduate Research Journal

In a two-sided market with a broker, the broker can influence the buyer’s and seller’s optimal trading behaviour through strategic information design. We study the impact of information about waiting times on riders and drivers in a rideshare market. We consider three information regimes: the first in which no information about time is revealed, the second in which true waiting times are communicated, and finally an intermediate regime in which agents are only told whether their waiting time falls within a high or low category. We evaluate the optimality of each information regime by maximizing welfare and revenue for each …

Development And Distribution Of Thermometry Hardware For The Simons Observatory, Samuel Day-Weiss

The Yale Undergraduate Research Journal

The Simons Observatory (SO) is a new cosmic microwave background (CMB) experiment consisting of four telescopes. SO is being constructed at an elevation of 5,190 meters on Cerro Toco in the Atacama Desert in Chile, and is set to begin observation in 2022. SO will employ 60,000 detectors, yielding a sensitivity greater than all previous CMB experiments. To achieve low noise performance the telescope cryostats will be cooled to ~100 mK using low temperature dilution refrigerators. Measuring cryostat temperatures is essential for pre-deployment testing, telescope installation, and telescope monitoring during observation. The purpose of this project is to design, build, …

Transfer Learning For Low-Resource Part-Of-Speech Tagging, Jeffrey Zhou, Neha Verma

The Yale Undergraduate Research Journal

Neural network approaches to Part-of-Speech tagging, like other supervised neural network tasks, benefit from larger quantities of labeled data. However, in the case of low-resource languages, additional methods are necessary to improve the performances of POS taggers. In this paper, we explore transfer learning approaches to improve POS tagging in Afrikaans using a neural network. We investigate the effect of transferring network weights that were originally trained for POS tagging in Dutch. We also test the use of pretrained word embeddings in our POS tagger, both independently and in conjunction with the transferred weights from a Dutch POS tagger. We …

Designing A Microsecond-Long On-Chip Microwave Delay Line Using Srtio3 Dielectricity, Kazemi Adachi, Mingrui Xu, Hong Tang

The Yale Undergraduate Research Journal

The delay line is a fundamental circuit design component which slows down a signal with minimal attenuation to provide delay effects, with applications that include interferometry and signal filtering. Cryogenic superconducting delay lines can be less lossy than their regularly conducting counterparts. Scientists can engineer microwave photos with coherence times of several microseconds (us), longer than current on-chip delays. We utilize the high dielectric constant (>10^4) of strontium titanate at cryogenic temperatures to slow own signal propagation on a coplanar waveguide. Here, we present a design for an on-chip 5 (us) superconducting delay line ad 5 GHz with small …

Applications Of Bayesian Inference For Modelling Dynamic Instability In Neuronal Dendrite Morphogenesis, Daniel Fridman

The Yale Undergraduate Research Journal

Neurons are complex biological systems which develop intricate morphologies and whose dendrites are essential in receiving and integrating input signals from neighboring neurons. While much research has been done on the role of dendrites in neuronal development, a further understanding of dendrite dynamics can provide insight into neural development and the cellular basis of neurological diseases such as schizophrenia, Down’s syndrome, and autism. The Jonathon Howard lab hypothesizes that microtubules are a primary driving force in dendrite dynamics. Since it is known that microtubules display dynamic instability, rapidly transitioning between growth, paused, and shrinking states, the Howard lab proposes a …

The Concept Of Natureculture Document: A Conceptual Exploration Of Seeds, Embodied Information, And Unconventional Records, Marc Kosciejew

Journal of Contemporary Archival Studies

Seedbanks, or so-called archival arks of the apocalypse, are addressing accelerating anthropocentric alterations to the environment by collecting, storing, and preserving seeds. These are specialized archival repositories that approach, frame, and use seeds as documents for agricultural and scientific research, classification and preservation work, and various other archival and administrative purposes. Seedbanks indeed are archives of unconventional records.

This article introduces the concept of natureculture document as a framing device in which to help analyze the documentary status of objects that are not necessarily or usually considered as documents or having documentary characteristics. This concept, coupled with its interdisciplinary theoretical …

Temporally Consistent Urban-Rural Delineations For Global Urban Heat Island Monitoring, Tc Chakraborty

Yale Day of Data

Urbanization leads to local-scale modification of climate, particularly the urban heat island (UHI) effect - the high temperature in cities compared to their surroundings. The UHI effect is generally quantified by measuring the temperature differential between the city and its surrounding rural reference. Choices of both the city and the rural reference are prone to assumptions, which may affect, among other things, temporal variability in UHI intensity. To reduce these uncertainties, I create a global dataset of urban-rural delineations that can be used to better constrain the temporal trends in UHI intensity throughout the globe using the European Space Agency's …

Generating Contextual Text Embeddings For Emergency Department Chief Complaints Using Bert, David Chang

Yale Day of Data

We applied BERT, a state-of-the-art natural language processing model, on chief complaint data from the Yale Emergency Department to map free-text notes to structured chief complaint categories.

Saving Software And Using Emulation To Reproduce Computationally Dependent Research Results, Euan Cochrane, Limor Peer, Ethan Gates, Seth Anderson

Yale Day of Data

Using digital data necessarily involves software. How do institutions think about software in the context of the long-term usability of their data assets? How do they address usability challenges uniquely posed by software such as, license restrictions, legacy software, code rot, and dependencies? These questions are germane to the agenda set forth by the FAIR principles. At Yale University, a team in the Library is looking into the application of a novel approach to emulation as a potential solution. In this presentation, we will outline the work of the Emulation as a Service Infrastructure (EaaSI) program, discuss our plans for …

Renewable Energy Access And Resilience In Urban Developing Areas: Distributed Solar Networks And Peer-To-Peer Energy Trading In Puerto Rico, Pascale Bronder

Harvey M. Applebaum ’59 Award

This senior essay under the Environmental Studies major at Yale University explores the environmental and social benefits of applying innovative technology to the energy sector. Three types of energy networks are analyzed, focusing on the use of distributed energy and peer to peer energy trading on a blockchain platform. The benefits of distributed renewable energy networks can most strongly be applied to locations in need of more reliable, resilient, and cost-effective electricity. Puerto Rico is a case study. Methods include analysis of U.S. Energy Information Administration and Census Bureau data as well as personal interviews with Puerto Rican energy developers. …

Low-Cost 8mm/Super 8 Film Digitization Using A Canon 9000f Ii Flatbed Scanner And Photoshop: A Case Study, Kenneth Eckert

Journal of Contemporary Archival Studies

For some fifty years, 8mm/Super 8 movie film was a widespread format for home movies and amateur hobbyists; yet the films and projection or telecine transfer equipment are now aging and obscure, presenting a difficulty for archivists and filmmakers. Online DIY solutions usually involve photographing the film with a DSLR and macro bellows, requiring a high degree of expertise and expense. This case study examines typical problems and proposes a simpler and low-cost solution involving using a Canon flatbed scanner with a transparency adapter and improvised film holder, and more importantly, describes technical solutions and script code to straighten and …

A Global Database Of Surface Urban Heat Island Intensity, Tc Chakraborty, Xuhui Lee

Yale Day of Data

The urban heat island (UHI) effect - the phenomenon of higher temperatures in urban environments - is one of the most well-known consequences of urbanization on local climate. We develop the simplified urban-extent (SUE) algorithm, a new algorithm to estimate the urban heat island (UHI) intensity at a global scale. This algorithm is implemented on the Google Earth Engine platform and uses satellite-derived images to calculate the surface UHI intensity for over 9500 urban clusters covering 15 years, making this the most comprehensive global UHI database. The data are validated against previous multi-city studies and then used to estimate the …

Gene Co-Expression Networks Analysis Reveal Novel Molecular Endotypes In Alpha-1 Antitrypsin Deficiency, Jen-Hwa Chu, Wenlan Zang

Yale Day of Data

Rationale:Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that predisposes to early onset pulmonary emphysema and airways obstruction. The exact mechanism through which AATD leads to lung disease is incompletely understood.

Objectives: To investigate the effect of AAT genotype and augmentation therapy on bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMC) transcriptome, while examining the link between gene expression profiles, and clinical features of AATD.

Methods: We performed RNA-Seq on RNA extracted from BAL and PBMC on samples obtained from 89 AATD patients enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Differential …

Topovar90m: Global High-Resolution Topographic Variables For Environmental Modeling, Giuseppe Amatulli Dr.

Yale Day of Data

Topographical relief involves the vertical and horizontal variation of the Earth's terrain and it drives processes in hydrology, climatology, geography and ecology. Its assessment and characterization is fundamental for various types of modeling and simulation analysis. In this regard, the Multi-Error-Removed Improved Terrain (MERIT) Digital Elevation Model (DEM) currently provides the best high-resolution DEM globally available, at a 3 arc-second resolution (90m), due to the removal of multiple error components from the underlying SRTM3 and AW3D30 DEMs. To depict topographical variations worldwide, we developed a new dataset comprising different terrain features derived from the MERIT-DEM. The fully standardized topographical variables …

Non-Invasive Analysis Of The Sputum Transcriptome Discriminates Clinical Phenotypes Of Asthma, Xiting Yan

Yale Day of Data

Whole transcriptome wide gene expression profiles in the sputum and circulation from 100 asthma patients were measured using the Affymetrix HuGene 1.0ST arrays. Unsupervised clustering analysis based on pathways from KEGG were used to identify TEA clusters of patients from the sputum gene expression profiles. The identified TEA clusters have significantly different pre-bronchodilator FEV1, bronchodilator responsiveness, exhaled nitric oxide levels, history of hospitalization for asthma and history of intubation. Evaluation of TEA clusters in children from Asthma BRIDGE cohort confirmed the identified differences in intubation and hospitalization. Furthermore, evaluation of the TH2 gene signatures suggested a much lower prevalence of …

A Novel Pathway-Based Distance Score Enhances Assessment Of Disease Heterogeneity In Gene Expression, Yunqing Liu, Xiting Yan

Yale Day of Data

Distance-based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and the relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. In this study, we developed a novel computational method to assess the biological differences based on pathways by assuming that ontologically defined biological pathways in biologically similar samples have similar behavior. Application of this distance score results in more accurate, robust, and biologically meaningful clustering results in both …

Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks, Olivier Trottier, Jonathon Howard

Yale Day of Data

In the biological sciences, image analysis software are used to detect, segment or classify a variety of features encountered in living matter. However, the algorithms that accomplish these tasks are often designed for a specific dataset, making them hardly portable to accomplish the same tasks on images of different biological structures. Recently, convolutional neural networks have been used to perform complex image analysis on a multitude of datasets. While applications of these networks abound in the technology industry and computer science, use cases are not as common in the academic sciences. Motivated by the generalizability of neural networks, we aim …

Land Conservation In A Changing Climate:Stewardship Science And Financing, Bradford S. Gentry, Shelley Clark, Colin Kelly, Joshua Morse

Yale School of the Environment Publications Series

Report of the 2016 Berkley Workshop

Held at the Pocantico Center of the Rockefeller Brothers Fund, Tarrytown, NY - July 2016

Yale’S Environmental Performance Index: The Construction And Use Of A Composite Index For Global Sustainability, Zach Wendling

Yale Day of Data

No abstract provided.

Closing The Water Budget In An Experimental Urban Watershed: A Comparative Assessment Of Methods For Measuring Evapotranspiration, Leana M. Weissberg, Gaboury Benoit

Yale Day of Data

No abstract provided.

Extracting Geography From Datasets In Social Sciences, Yuke Li, Tianhao Wu, Nicholas Marshall, Stefan Steinerberger

Yale Day of Data

No abstract provided.

Safer Chemicals Design Diagrams, Longzhu Shen, Fjodor Melnikov, John Roethle, Aditya Gudibanda, Richard Judson, Julie Zimmerman, Paul Anastas

Yale Day of Data

The NRF2-ARE antioxidant pathway is an important biological sensing and regulating system that responds to chemical insults. At minute level, it protects a living species to go through hard environmental conditions. However, when the external disruption exceeds the inherent resilience, cellular damage can occur, eventually leading to cytotoxicity. Therefore, studying the likelihood of a chemical activating the NRF2-ARE pathway is interesting to discovering therapeutic agents and designing safer chemicals. In this research, we engaged a combination of computational chemistry, statistical learning and mechanistic toxicology to estimate the likelihood of a chemical to perturb this critical toxicological pathway and derive a …

Data Collection And Analysis At The Atlas Detector, Savannah Thais

Yale Day of Data

No abstract provided.

Regional Supply Chains: Strengthening Urban-Rural Connections Around The Benefits From Natural Areas, Bradford S. Gentry, Eve Boyce, Abigail Martin, Max Webster, Rachel Weston

Yale School of the Environment Publications Series

Report of the 2017 Berkley Workshop

Held at the Inn at Shelburne Farms, Shelburne, VT - June 2017