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 …

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 …

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 …

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 …

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 …

A Machine Learning Approach To Post-Market Surveillance Of Medical Devices, Jonathan Bates, Shu-Xia Li, Craig Parzynski, Ronald Coifman, Harlan Krumholz, Joseph Ross

Yale Day of Data

Post-market surveillance is a collection of processes and activities used by product manufacturers and regulators, such as the U.S. Food and Drug Administration (FDA) to monitor the safety and effectiveness of medical devices once they are available for use “on the market”. These activities are designed to generate information to identify poorly performing devices and other safety problems, accurately characterize real-world device performance and clinical outcomes, and facilitate the development of new devices, or new uses for existing devices. Typically, a device is monitored by comparing adverse events in the exposed population to a matched unexposed population. This research considers …

K-Mer Analysis On Developmental And Housekeeping Enhancer Peaks, Yunsi Yang, Anurag Sethi, Mark Gerstein

Yale Day of Data

The regulation of gene expression involves interaction between transcriptional enhancers and core promoters. However, the separation between developmental and housekeeping gene regulation remains unknown. Here, we present a method to detect if different core promoters exhibit specificity to certain enhancers within massively parallel assays for enhancer detection. We use k-mers of various length (3-8bp) as sequence features and compare k-mer frequencies between developmental and housekeeping enhancers. This method shows promoter specificity of enhancers in D. melanogaster.

Incorporating Satellite Derived Cloud Climatologies To Improve High Resolution Interpolation Of Daily Precipitation., Adam M. Wilson, Benoit Parmentier, Brian Mcgill, Rob Guralnick, Walter Jetz

Yale Day of Data

Conservation of biodiversity demands comprehension of evolutionary and ecological patterns and processes that occur over vast spatial and temporal scales. A central goal of ecology is to understand the factors that control the spatial distribution of species and this has become even more important in the face of climate change. However, at global scales there can be enormous uncertainty in environmental data used to model species distributions. Even ‘simple’ metrics such as mean annual precipitation are difficult to estimate in areas with few weather stations and available data sets do not quantify uncertainty in these surfaces. We are developing a …

From Debate To Design: Issues In Clean Energy And Climate Change Law And Policy, Leslie Parker, Jennifer Ronk, Rachel Maxwell, Bradford Gentry, Marijn Wilder, James Cameron

Yale School of the Environment Publications Series

A report on the work of the REIL Network 2007-2008

El Mundo Entero Es Nuestro Bosque: Política Forestal Y Cooperación Internacional, Pablo Martínez De Anguita

Yale School of the Environment Bulletin Series

No abstract provided.

Human Population And Freshwater Resources: U.S. Cases And International Perspectives, Karin M. Krchnak, Victoria Dompka Markham, Nancy Thorne

Yale School of the Environment Bulletin Series

No abstract provided.

Developing Industrial Ecosystems: Approaches, Cases, And Tools, Marian Chertow, Michelle Portlock

Yale School of the Environment Bulletin Series

No abstract provided.

Species And Ecosystem Conservation: An Interdisciplinary Approach, Tim W. Clark, Michael J. Stevenson, Kim Ziegelmayer

Yale School of the Environment Bulletin Series

No abstract provided.

Developing Sustainable Management Policy For The National Elk Refuge, Wyoming, Tim W. Clark, Denise Casey, Anders Halverson

Yale School of the Environment Bulletin Series

No abstract provided.

Transformations Of Middle Eastern Natural Environments: Legacies And Lessons, Jeff Albert, Magnus Bernhardsson, Roger Kenna

Yale School of the Environment Bulletin Series

No abstract provided.

Resource Use In The Trinational Sangha River Region Of Equatorial Africa: Histories, Knowledge Forms, And Institutions, Heather E. Eves, Rebecca Hardin, Stephanie Rupp

Yale School of the Environment Bulletin Series

This volume is based on an international conference, “Natural Resource Use Relations in the Trinational Sangha River Region of the Northwest Congo Basin,” held at Yale University in September 1997. In recognition of the bilingual context in which conservation occurs in the three countries of the Sangha region — Cameroon, Central African Republic, and Congo — all sessions of the conference were conducted simultaneously in French and English. This publication, which is a complete rendering of the conference papers and discussion sessions, is available in its entirety in both French and English.

Restoration Of An Urban Salt Marsh: An Interdisciplinary Approach, David G. Casagrande

Yale School of the Environment Bulletin Series

No abstract provided.

Bridges To Sustainability: Business And Government Working Together For A Better Environment, Luis Gomez-Echeverri

Yale School of the Environment Bulletin Series

No abstract provided.

The Ecotourism Equation: Measuring The Impacts, Elizabeth Malek-Zadeh

Yale School of the Environment Bulletin Series

No abstract provided.

Local Heritage In The Changing Tropics: Innovative Strategies For Natural Resource Management And Control, Greg Dicum

Yale School of the Environment Bulletin Series

No abstract provided.

A Simulation Model For The Management Of Sandhill Cranes, Richard S. Miller, George S. Hochbaum, Daniel B. Botkin

Yale School of the Environment Bulletin Series

No abstract provided.

Chemical Analyses Of Plant Tissues From The Hubbard Brook Ecosystem In New Hampshire, Gene E. Likens, F. Herbert Bormann

Yale School of the Environment Bulletin Series

No abstract provided.

Natural Variation In Susceptibility Of Pinus To Neodiprion Sawflies As A Basis For The Development Of A Breeding Scheme For Resistant Trees, Walter R. Henson, Louis C. O'Neil, Francois Mergen

Yale School of the Environment Bulletin Series

No abstract provided.

Man And His Environment: The Ecological Limits Of Optimism, R. S. Miller, G. M. Woodwell, W. R. Burch, P. A. Jordan, R. L. Means

Yale School of the Environment Bulletin Series

No abstract provided.

Supplying Wood Products For More People - A Challenge To The Forest Industry, John A. Segur, F. Bruce Lamb, Basil E. Allen

Yale School of the Environment Bulletin Series

No abstract provided.

Simulation Of The Growth Of Even-Aged Stands Of White Spruce, Kenneth J. Mitchell

Yale School of the Environment Bulletin Series

No abstract provided.

Wood Formation And The Concept Of Wood Quality, Philip R. Larson

Yale School of the Environment Bulletin Series

No abstract provided.

On Temperature And Heat Flow In Tree Stems, Lee Pierce Herrington

Yale School of the Environment Bulletin Series

No abstract provided.