Life Sciences Commons^™

Identifying Barriers To Data Use On U.S. Beef Cow-Calf Operations And Developing Solutions To Improve Cow-Calf Record-Keeping, William Isaac Jumper

Theses and Dissertations

Cattle health and production records (CHPR) are data collected by cattle producers and veterinarians in the form of measurements, observations, counts of events over time, and physiologic attributes that describe individual and group-level health and production. These data are useful to both veterinarians and cattle producers for making evidence-based decisions on cow-calf operations. Currently, there are no uniform, industry-wide methods of capturing and recording CHPR in the U.S. cow-calf industry. Although many cow-calf producers in the U.S. are thought to collect some form of CHPR, it is believed that relatively few are doing so in an electronic manner that facilitates …

Data Curation For Modeling Tall Fescue Biomass Dynamics With Dssat-Csm, M. B. Hanson, P. D. Alderman, T. J. Butler, A. Caldeira Rocateli

IGC Proceedings (1997-2023)

While models for predicting forage production are available to aid management decisions for some forage crops, there is limited research for a yield model designed specifically for tall fescue (Schedonorus arundinaceus). Therefore, our objective was to adapt an existing perennial forage model, the Decision Support System for Agrotechnology Transfer Cropping Systems Model (DSSAT-CSM) for predicting forage biomass of tall fescue in the southern Great Plains. To evaluate model performance, there must first be a high level of data manipulation and cleaning. In this project, a cohesive dataset combining biomass, weather, soil, and management data were structured into DSSAT …

Visualizing Diversity: Spatial Data As A Resource Enabling Extension To Better Engage Communities, Justin Krohn, Jacqueline Davis-Manigaulte, Christopher Fulcher, Jennifer Sarah Tiffany

Journal of Human Sciences and Extension

Effective Extension programming relies on engaging people of all races, ethnicities, and cultures. Extension educators sometimes struggle with how best to engage communities that are not “traditional” program audiences. Centering data visualization on the strength of Black, Latino/Hispanic, Asian, Native American, and other potentially marginalized communities can assist Extension’s work to engage diverse staff, program participants, and advisory board members. For example, using maps to understand what languages people speak at home strengthens the connections between Extension programs and community participants and can inform staff recruitment and advisory board composition. However, maps of aggregated areas like counties can mask socioeconomic …

Annual Report 2022 - Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program, Gina M. Ralph, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Jameson Gregg, Robert J. Latour

Reports

The threats affecting living marine resources are diverse, including overfishing, climate change, and pollution. In response to long-term challenges in fisheries management, a more holistic evaluation of the natural and anthropogenic drivers of populations sizes is needed. Ecosystem management (EM), a suite of strategies that incorporate ecosystem considerations into fisheries and ecosystem management, can be difficult to implement in practice. In the Mid-Atlantic, efforts to implement EM are ongoing; one output has been the annual ‘State of the Ecosystem Report’ for the region, synthesizes available data on a variety of environmental, ecological, and socioeconomic factors. Historically, the data needed for …

Annual Report - 2021 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Historically, fisheries management has been based on the results of single-species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on …

Ecology Of Texas Zebra Mussels, Heather Arterburn

Biology Datasets

Data analyzing the zebra mussel population dynamics in three Texas reservoirs over a period of 3-5 years. Data includes shell length of adult and planktonic larvae samples collected monthly, growth rates, reproductive periods, and settlement patterns. Additionally, water quality parameters are included for correlational analysis.

“Data Architecture For Pharmaceutical Product Development At Alkermes”, Peter Couture, Damon Warnock, Marcus O'Mahony

Level 3

This paper describes how Alkermes built a data architecture for efficient management of non-GXP and R&D data. Using a ‘Create’, ‘Store’, Describe’ ‘Access’ stepwise model, the ingredients to making the journey a success are described.

Priority Areas For Action And Research On Pastoralism And Rangelands In Eastern Africa, M. O. Odhiambo

IGC Proceedings (1997-2023)

There is an element of irony around pastoralism and research in Eastern Africa. While it is one of the most researched production and livelihood systems, pastoralism is also the least understood by policymakers and development actors, with discussions about its importance characterized by significant gaps in knowledge. What is more, policy actors have difficulties accessing empirical data specific to pastoralism and rangelands in a form that allows well-founded decision-making on policy and action. Most available data tend to be out of date and not disaggregated with reference to pastoralism and rangelands. As a result, much of the discourse around pastoralism …

Annual Report - 2020 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Historically, fisheries management has been based on the results of single-species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on …

Agricultural Pesticide Use In The Upper Citarum River Basin: Basic Data For Model-Based Risk Management, Rosetyati R. Utami, Gertjan W. Geerling, Indah R. S. Salami, Suprihanto Notodarmojo, Ad M.J. Ragas

Journal of Environmental Science and Sustainable Development

Since the middle of the 20th century, pesticide use has been a primary foundation of global agricultural development. However, the massive usage of pesticides can have detrimental impacts on human health and the environment, particularly in the aquatic ecosystem. This study determined the use of pesticides in the agricultural area of the Upper Citarum River Basin (UCRB); a crucial water resource on Java Island. A survey of 174 farmers was conducted in eight districts along the basin by using the random walk and quota sampling method. The questionnaire was designed to acquire data about the amount and types of pesticides …

The State Of Outdoor Recreation In Utah 2020, Jordan Smith, Anna B. Miller

All Current Publications

The purpose of this report is to provide a high-level review of the trends that define outdoor recreation within Utah. We do this by distilling data from a variety of sources, focusing on ‘key metrics’ that can be tracked over time, serving as a finger on the pulse on the health of outdoor recreation within Utah. Data on outdoor recreation participation and its benefits and impacts varies considerably across the state depending upon the managing agency collecting the data. This report focuses on statewide data available for outdoor recreation opportunities provided on lands managed by the Bureau of Land Management, …

Methane Emission Estimated From Different Cattle Intake Data In Heifers Grazing A Tropical Pasture, José Augusto Imaz, O. Hernández, D. Dos Santos, A. Radrizzani, J. I. Arroquy

IGC Proceedings (1997-2023)

The quantification of methane (CH₄) from enteric fermentation related to cattle diet is a useful tool to identify strategies to mitigate greenhouse gas emissions. This is even important in tropical and subtropical regions due to the lack of CH₄ estimations in beef cattle, particularly from Bos Indicus breeds grazing tropical grasses (Kurihara et al., 1999). Several modelling approaches have been developed in order to predict CH₄ emission. However, the use of these models has limitations associated with uncertainty information required such as feed intake (FI), composition of the selected diet and animal responses (Gonzalez et …

Annual Report - 2019 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Historically, fisheries management has been based on the results of single-species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on …

Complex Systems Analysis In Selected Domains: Animal Biosecurity & Genetic Expression, Luke Trinity

Graduate College Dissertations and Theses

I first broadly define the study of complex systems, identifying language to describe and characterize mechanisms of such systems which is applicable across disciplines. An overview of methods is provided, including the description of a software development methodology which defines how a combination of computer science, statistics, and mathematics are applied to specified domains. This work describes strategies to facilitate timely completion of robust and adaptable projects which vary in complexity and scope. A biosecurity informatics pipeline is outlined, which is an abstraction useful in organizing the analysis of biological data from cells. This is followed by specific applications of …

Supporting The Essential - Recommendations For The Development Of Accessible And Interoperable Marine Biological Data Products, D. Lear, P. Herman, G. Van Hoey, L. Schepers, N. Tonné, M. Lipizer, F. E. Muller-Karger, W. Appeltans, W. D. Kissling, N. Holdsworth, M. Edwards, E. Pecceu, H. Nygård, G. Canonico, S. Birchenough, G. Graham, K. Deneudt, S. Claus, P. Oset

Marine Science Faculty Publications

In this paper we outline the stakeholder-led approaches in the development of biological data products to support effective conservation, management and policy development. The requirements of a broad range of stakeholders and iterative, structured processes framed the development of tools, models and maps that support the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. By structuring the resultant data products around the emerging biological Essential Ocean Variables, and through the engagement with a broad range of end-users, the EMODnet (European Marine Observation and Data Network) Biology project has delivered a suite of demonstration data products. These products are presented in the …

What Can We Do? Puzzling Over The Interpretation Of Heredity And Variation From Galton To Genetic Engineering, Peter J. Taylor

Working Papers on Science in a Changing World

First six chapters of a book motivated as follows: When I had mentioned to colleagues that I was exploring some significant issues overlooked by both sides in nature-nurture debates, the typical response was “we know, of course, that nature and nurture are intertwined”; they never asked “which nature-nurture science are you referring to?” It occurred to me that, in the long history of nature-nurture debates, opposing sides had always assumed or implied that these different scientific approaches were speaking to the same issues. If that were the case, then the challenge—something I was already puzzling over—was how best to draw …

Annual Report - 2018 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program., Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Historically, fisheries management has been based on the results of single‐species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on …

Microarray Data Analysis And Classification Of Cancers, Grant Gates

Williams Honors College, Honors Research Projects

When it comes to cancer, there is no standardized approach for identifying new cancer classes nor is there a standardized approach for assigning cancer tumors to existing classes. These two ideas are known as class discovery and class prediction. For a cancer patient to receive proper treatment, it is important that the type of cancer be accurately identified. For my Senior Honors Project, I would like to use this opportunity to research a topic in bioinformatics. Bioinformatics incorporates a few different subjects into one including biology, computer science and statistics. An intricate method for class discovery and class prediction is …

From Data To Decisions: Navigating The “So What?” And “What’S Next?” Conversation Around Nearshore Data, Dawn Spilsbury Pucci

Salish Sea Ecosystem Conference

Ever wonder what happens to all those data being collected? In Island County, we are fortunate to be the focus of a plethora of data collection efforts. We have comprehensive nearshore assessments that describe where our habitats are and how those habitats are built. We have habitat assessments that are a collaborative effort between citizen science groups and state agencies. We have long-term status and trends data sets on intertidal habitats and presence for a few specific species. We have a high resolution shoreline armor dataset and we have a predictive probability model for coastal flood risk. But what do …

Development Of An Interactive Web Map To Visualize A Complex Dataset, Lisa Ferrier

Salish Sea Ecosystem Conference

The Washington State Department of Natural Resources (DNR) is steward to 2.6 million acres of state-owned aquatic lands. As part of its management responsibilities, DNR’s Submerged Vegetation Monitoring Program (SVMP) documents occurrences of seagrass throughout greater Puget Sound. Seagrasses are recognized globally as a sensitive indicator of water quality while providing productive, critical habitat utilized by many fish, bird and invertebrate species. The SVMP has been conducting seagrass surveys in Puget Sound, using underwater video, since 2000. Video is reviewed, classified for presence/absence, and ultimately used to characterize abundance, distribution and change in seagrass at local, regional, and sound-wide scales. …

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

Northeast Area Monitoring And Assessment Program (Neamap) 2016 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In The Mid‐Atlantic: Northeast Area Monitoring And Assessment Program Near Shore Trawl Survey, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Concerns regarding the status of fishery‐independent data collection from continental shelf waters between Cape Hatteras, North Carolina and the U.S. / Canadian border led the Atlantic States Marine Fisheries Commission’s (ASMFC) Management and Science Committee (MSC) to draft a resolution in 1997 calling for the formation of the Northeast Area Monitoring and Assessment Program (NEAMAP) (ASMFC 2002). NEAMAP is a cooperative state‐federal program modeled after the Southeast Area Monitoring and Assessment Program (SEAMAP), which has been coordinating fishery‐independent data collection south of Cape Hatteras since the mid‐ 1980s (Rester 2001). The four main goals of this new program directly address …

Annual Report - 2016 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Historically, fisheries management has been based on the results of single‐species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on …

Loon Project Database, Walter H. Piper

Biology, Chemistry, and Environmental Sciences Faculty Data Sets

Data collected since 1993 in Oneida County, Wisconsin, on the breeding and territorial behavior of the common loon, Gavia immer. This study population is marked with USGS metal bands and colored leg bands for individual identification. It includes many individuals banded as chicks, whose life histories are known thoroughly. Data are collected from April through August of most years on this migratory species.

Supporting Biomedical Research In The Era Of Omics And Precision Medicine, Rolando Garcia-Milian, Denise Hersey, Nathan Rupp

Rolando Garcia-Milian

Ifly: Code Development For An App To Support Automating Entomological Data Collection, Michael P. Cosentino, Trevor Stamper

The Summer Undergraduate Research Fellowship (SURF) Symposium

We are developing a prototype entomological data-collection application called "iFly," which runs on a field-capable iPad device. In this phase, we tackled refining screens and introducing a database manager to streamline operations as info is entered, stored, retrieved and delivered. We used SQLite3 database in Apple's Xcode Integrated Development Environment (IDE). Xcode gives mixed programming results. Apple's iOS environment ensures functional and fairly error-free apps can be built. But the sophisticated Xcode IDE requires specialist developers and valuable project time is spent as new programmers learn key techniques. The iFly prototype was advanced with improved database integration; however, more work …

Northeast Area Monitoring And Assessment Program (Neamap) 2015 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In The Mid‐Atlantic: Northeast Area Monitoring And Assessment Program Near Shore Trawl Survey Annual Report, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Concerns regarding the status of fishery‐independent data collection from continental shelf waters between Cape Hatteras, North Carolina and the U.S. / Canadian border led the Atlantic States Marine Fisheries Commission’s (ASMFC) Management and Science Committee (MSC) to draft a resolution in 1997 calling for the formation of the Northeast Area Monitoring and Assessment Program (NEAMAP) (ASMFC 2002). NEAMAP is a cooperative state‐federal program modeled after the Southeast Area Monitoring and Assessment Program (SEAMAP), which has been coordinating fishery‐independent data collection south of Cape Hatteras since the mid‐ 1980s (Rester 2001). The four main goals of this new program directly address …

Slides: Rivers And People In The Neotropics: Social And Ecological Science For Environmental Flows, Elizabeth P. Anderson

Coping with Water Scarcity in River Basins Worldwide: Lessons Learned from Shared Experiences (Martz Summer Conference, June 9-10)

Presenter: Elizabeth P. Anderson, Florida International University

38 slides

Calculating The Predictability Of Climate Change: The Effect Of Climate Change On Moth Species In The Pacific Northwest Varies Among Functional Groups., Julie Maurer

Scholars Week

Climate change has driven shifts in phenology and distribution for many species. These effects are often idiosyncratic and it remains unclear whether they vary consistently among functional groups, limiting our ability to draw broad conclusions about how climate change affects species. Previous studies have indicated that Lepidoptera (butterflies and moths) are sensitive to climate change. We analyzed a large database of moth specimen records from the Pacific Northwest (PNW) to examine climate change responses over more than 100 years for a suite of 241 functionally diverse species, including spring and fall active species as well as dietary generalists and specialists. …

Annual Report - 2015 Data Collection And Analysis In Support Of Single And Multispecies Stock Assessments In Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring And Assessment Program Chesmmap, Christopher F. Bonzek, James Gartland, Debra J. Gauthier, Robert J. Latour

Reports

Historically, fisheries management has been based on the results of single‐species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on …