Physical Sciences and Mathematics Commons^™

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 …

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 …