Life Sciences Commons^™

Analysis Of Complex Vertebrate Genomes: Computational Challenges And Solutions, Jeramiah J. Smith

Commonwealth Computational Summit

No abstract provided.

Adversarial Discriminative Domain Adaptation For Extracting Protein-Protein Interactions From Text, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu

Commonwealth Computational Summit

Relation extraction is the process of extracting structured information from unstructured text. Recently, neural networks (NNs) have produced state-of-art results in extracting protein-protein interactions (PPIs) from text. While multiple corpora have been created to extract PPIs from text, most methods have shown poor cross-corpora generalization. In other words, models trained on one dataset perform poorly on other datasets for the same task. In the case of PPI, the F1 has been shown to vary by as much as 30% between different datasets. In this work, we utilize adversarial discriminative domain adaptation (ADDA) to improve the generalization between the source and …

Discovery Of Sex-Specific Regions In A Salamander Genome, Nataliya Y. Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith

Commonwealth Computational Summit

Biological Aspects:

Salamander (Ambystoma mexicanum) has a gigantic genome: ~32,000,000,000 bases (10X of size of human genome)

Sex is determined by a pair of morphologically identical chromosomes:

• ZZ in male
• ZW in female

Object:

• Find (if there are any) genomic differences between chromosomes W and Z

Workflow:

1. Sequencing and de novo assembly of the reference salamander genome
2. Alignment of short sequences from male and female genomes to the reference
3. Coverage analysis

Registration And Grouping Algorithms In Protein Nmr Derived Peak Lists And Their Application In Protein Nmr Reference Correction, Andrey Smelter, Xi Chen, Eric C. Rouchka, Hunter N. B. Moseley

Commonwealth Computational Summit

Nuclear magnetic resonance spectroscopy of proteins (protein NMR) is a powerful analytical technique for studying structure and dynamics of proteins. Almost all aspects of protein NMR have been accelerated by the development of software tools that enable the analysis of NMR spectral data and its utilization in studying protein structure and dynamics. This includes software for raw NMR processing, spectral visualization, protein resonance assignment, and structure determination. However, full automation of protein NMR data analysis is still a work in progress and data analysis still requires an expert NMR spectroscopist utilizing an array of software tools.

While manual resonance assignment …

The Lamprey Genome: Illuminating Genomic Change Across Eons And Embryogenesis, Jeramiah J. Smith, Courtney K. M. Waterbury, Melissa C. Keinath, Cody B. Saraceno, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya

Commonwealth Computational Summit

The lamprey genome provides unique insights into both the deep evolutionary history of vertebrate genomes and the maintenance of genome structure/integrity over development. The lamprey lineage diverged from all other vertebrates approximately 500 million years ago. As such, comparisons between lamprey and other vertebrates permit reconstruction of ancient duplication and rearrangement events that defined the fundamental architecture and gene content of all extant vertebrate genomes. Lamprey also undergoes programmatic changes genome structure that result in the physical elimination of ~20% of its genomic DNA (~0.5Gb from a ~2 Gb genome) from all somatic cell lineages during early embryonic development. Here, …

Aberrant Coordination Geometries Discovered In Most Abundant Metalloproteins, Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N. B. Moseley

Commonwealth Computational Summit

Metalloproteins play crucial biochemical roles in our body and are essential across all domains of life. The structural environment around a metal ion, especially the coordination geometry (CG), is both sequentially and functionally relevant. Studies of the metalloprotein’s CG will greatly help alleviate the imbalance between the ample sequence data available and the insufficient knowledge on protein functions. Current methodologies in characterizing metalloproteins’ CG consider only previously reported CG (canonical CG) models based primarily on nonbiological chemical context. Exceptions to these canonical CG models can greatly hamper the ability to characterize metalloproteins both structurally and functionally.

Use Of Hpc To Analyze Changes In Gene Expression During Fruit Fly Spermiogenesis, Sepideh Dadkhah, Douglas A. Harrison, Jeramiah J. Smith

Commonwealth Computational Summit

In the fruit fly, Drosophila melanogaster, JAK/STAT signaling during spermiogenesis is known to play a crucial role in the maintenance of stem cells of the testis. Recent studies in our lab have shown that activation of the JAK/STAT pathway in somatic cyst cells is also required for the later stages of spermiogenesis like individualization.

The main goal of this project is to characterize the events downstream of JAK/STAT signaling in spermiogenesis and more specifically to determine the mechanism by which JAK/STAT activation regulates individualization, a later stage in spermiogenesis where 64 individual spermatids are formed from a 64-interconnected spermatid …

Session 1c (Source Water Protection), Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• The Pleasant Grove Spring Non-Point Source Pollution Study: An Underused Data Set, James Currens, Kentucky Geological Survey
• Kentucky’s Source Water Protection Program, Robert Blair, Kentucky Division of Water
• Assistance Program for Source Water Protection: Success in Kentucky, Laura Norris and Allan Shingleton, Kentucky Division of Water

Session 2c (Sediment And Nutrients), Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Real-Time Continuous Monitoring of Nutrients and Biological Parameters in Kentucky’s Rivers and Lakes, Mac Cherry, USGS Indiana-Kentucky Water Science Center
• Sediment Transport Modeling using Dynamic (Dis)connectivity to Assess Sediment Impacts on Water Quality, Tyler Mahoney and others, Dept. of Civil Engineering, University of Kentucky
• Sediment Nitrogen and Nitrate Dynamics of a Fluviokarst System in the Bluegrass Region: Isotopic and Numerical Modeling Investigation, Admin Husic and others, Dept. of Civil Engineering, University of Kentucky

Poster Session 2, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

1. GIS as a Tool to Inform Field Studies and Reduce Human Health Exposure Risks, Evan Willett and others, Dept. of Civil Engineering, University of Kentucky
2. The Use of Environmental DNA to Detect Bacterial Molecular Markers in the Triplett Creek Watershed, Rowan County, Kentucky, Rachel Brown and others, Dept. Biology and Chemistry, Morehead State University
3. Detection of Percopsis ominsomaycus (TROUT-PERCH) using eDNA in Eastern Kentucky Streams, Ben Brammell and others, Dept. of Natural Sciences, Asbury University
4. Seasonal Fluctuations in Salamander eDNA in Central Kentucky Streams, Ronald Sams and others, Dept. Natural Sciences, Asbury University
5. Virtual 3D Septic …

Session 1b (Agriculture And Water), Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Feathered or Four-Legged: Working Together to Manage Manure in Kentucky, Amanda Gumbert and others, College of Agriculture, Food, and Environment, University of Kentucky
• There’s a Purple Cow in My MS4, Steve Higgins, College of Agriculture, Food and Environment, University of Kentucky
• Field Scale Characterization of Soil Hydraulic Conductivity and its Implication for Irrigation Management, Xi Zhang and Ole Wendroth, Dept. Plant and Soil Sciences, University of Kentucky

Session 2b (Biology), Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Microscale Electrokinetics for Phytoplankton Analysis, Stuart Williams, Mechanical Engineering Dept., University of Louisville and Susan Hendricks, Hancock Biological Station, Murray State University
• Selenium Reduction by a Co-Culture of Pantoea vagans strain EWB32213-2 and Shigella fergusonii strain TB42616, Yuxia Ji and Yi-tin Wang, Dept. of Civil Engineering, University of Kentucky
• Effects of Temperature and Macronutrient Ratios (N:P) on Microcystis aeruginosa Toxin Production and Growth, Brandon Yates and Brian Reeder, Dept. of Biology and Chemistry, Morehead State University

Session 1a (Soils And Geology), Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Potential Mechanism Contributing to the Development of Cover Collapse in Kentucky, James Currens, Kentucky Geological Survey
• Preliminary Assessment of the Geothermal Potential of the Alluvial Aquifer Beneath Louisville, Kentucky Created by Rising Groundwater Levels and Temperatures, Mike and K.G. Unthank, USGS Indiana- Kentucky Water Science Center
• Influence of Land Use on Soil Bulk Density, Infiltration, and NRCS Runoff Curve Number, Samuel Austen and others, Dept. of Biosystems and Agricultural Engineering, University of Kentucky

Session 2a (Climate Change/Data Platform), Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Assessing Climate Change and Impacts on Future Water Availability and Droughts in the Kentucky River Basin, Som Chattopadhyay and Dwayne Edwards, Dept. of Biosystems and Agricultural Engineering, University of Kentucky
• Variance Decomposition of Maxima Extreme Streamflow Forecasted with Global Climate Models, Nabil Al Aamery and Jimmy Fox, Dept. of Civil Engineering, University of Kentucky
• Aquavit: A HUBzero-Based Collaboration Portal for the AFI and SENSE Projects, Jack Smith and Justin Chapman, Marshall University

Poster Session 1, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

1. Sensing and Educating the Nexus to Sustain Ecosystems (SENSE): A Kentucky-West Virginia Partnership, Susan Hendricks and others, Hancock Biological Station, Murray State University
2. Using OpenNSPECT to Model Riparian Buffer Effectiveness for Mitigating Sediment Accumulation in Small Order Agricultural Streams, Lee Moser, College of Agriculture, Food and Environment, University of Kentucky
3. The Benefits of Staying Local – the Kentucky Section of the American Society of Agricultural and Biological Engineers, Carmen Agouridis and Michael Sama, Dept. of Biosystems and Agricultural Engineering, University of Kentucky
4. Overview of Groundwater Sampling Conducted in an Unconventional Oil and Gas Play Area of eastern …

Plenary Session, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

• Assessing Public Drinking Water Systems in Kentucky, Caroline Chan and Russell Neal, Kentucky Division of Water
• Bankfull Regional Curves and Hydraulic Geometry Curves for the Eastern Kentucky Coalfields, Ashlan Berry and Carmen Agrouridis, Dept. Biosystems and Agricultural Engineering, University of Kentucky
• Quasi-Three-Dimensional Hydrodynamic Model Development for Two-Phase Flow Applied to Geyser Phenomena in Urban Storm Sewers, Richard Shook and others, Dept. of Civil Engineering, University of Kentucky
• Curve Numbers for Urban Watersheds: A Problem and an Interim Solution, Robert Peterson and Lindell Ormsbee, Dept. of Civil Engineering, University of Kentucky

Proceedings Of 2017 Kentucky Water Resources Annual Symposium, Kentucky Water Resources Research Institute, University Of Kentucky

Kentucky Water Resources Annual Symposium

This symposium was planned and conducted as a part of the state water resources research institute annual program that is supported by Grant/Cooperative Agreement Number G16AP00055 from the United States Geological Survey. The contents of this proceedings document and the views and conclusions presented at the symposium are solely the responsibility of the individual authors and presenters and do not necessarily represent the official views of the USGS or of the symposium organizers and sponsors. This publication is produced with the understanding that the United States Government is authorized to reproduce and distribute reprints for government purposes. Mention of trade …

Kentucky Alfalfa Awards History, Kentucky Alfalfa And Stored Forages Conference

Kentucky Alfalfa and Stored Forage Conference

The Kentucky Alfalfa Awards Program was initiated in 2000 at the 20th Anniversary of the Kentucky Alfalfa Conference. The Awards Program is funded annually from revenues generated each year for the Silent Auction during the Annual Conference.

Photo Highlights Of The 36th Kentucky Alfalfa And Stored Forages Conference, Kentucky Alfalfa And Stored Forages Conference

Kentucky Alfalfa and Stored Forage Conference

No abstract provided.

Alfalfa Conference Speakers From The Beginning, Kentucky Alfalfa And Stored Forages Conference

Kentucky Alfalfa and Stored Forage Conference

No abstract provided.

Save The Date! [Announcement], S. Ray Smith, Krista Lea

Kentucky Alfalfa and Stored Forage Conference

This is an announcement of upcoming events.

Selecting Summer Annual Varieties Using Yield And Digestibility, Christopher D. Teutsch

Kentucky Alfalfa and Stored Forage Conference

Although cool-season grasses can provide ample and high quality forage for grazing livestock in the spring and fall, forage growth during the summer months is often restricted by high temperatures (Figure 1). In contrast warm-season annual grasses are most productive during the summer months and do not reach peak growth until temperatures approach 90 degrees Fahrenheit. Summer annual grasses such as forage sorghum (Sorghum bicolor (L.) Moench), sudangrass (Sorghum bicolor (L.) Moench), sorghum-sudangrass hybrids, and pearl millet (Pennisetum americanum (L.) Leeke) can provide high quality summer grazing for ruminant livestock in many regions of the United States.

The Economics Of Hay Quality, Madeline L. Dant, Kenneth H. Burdine, Brandon Sears

Kentucky Alfalfa and Stored Forage Conference

Hay quality is often discussed when one considers the viability of cash hay operations. A great deal is known about how production impacts quality and how quality impacts animal performance. This knowledge certainly has economic implications, but the economics of hay quality has primarily been evaluated from the animal performance perspective. Analyzing the economics of hay quality from the cash hay producer’s prospective becomes more difficult due to data limitations.

There are approximately 2.5 million acres of hay produced in Kentucky annually. The vast majority of this hay is grass type hay that is produced and fed on beef cattle …

What Is New In Seed Coatings, Bill Talley

Kentucky Alfalfa and Stored Forage Conference

Seed Coatings started many centuries ago when the Chinese wrapped their rice seed in a mud ball when planting their rice fields. The ball would keep the seed from floating to the top when they flooded their fields. Seed treatment of Alfalfa first began with preinoculation of the seed to make it more convenient to plant. The farmer did not have to go through the process of inoculating the seed himself, and this was a great improvement at the time. In 1975 Ramsey Seed in California acquired technology from a New Zealand company to begin coating seed with a buildup …

Western Hay Production Vs. Eastern Hay Production, Tom Keene

Kentucky Alfalfa and Stored Forage Conference

Early in the history of mankind, man was nomadic and moved from location to location in order to gather and find sustenance for themselves as well as their livestock. At some point in time, man decided that rather than keep moving, they would establish a community in one location, usually near running water (or fresh water of some kind), and would begin to sustain themselves with production agricultural practices.

Planting and harvesting soon took the place of packing up and moving every time the current resources had been depleted. Each year a new crop would be planted; livestock also became …

Why Is Intake Reduced When Cattle Are Fed Tall Fescue?, James L. Klotz

Kentucky Alfalfa and Stored Forage Conference

A major problem for the cattle producer that utilizes tall fescue forage is the unrealized or reduced gains in body weight in growing animals. This result has been reproduced across numerous studies evaluating cattle performance on tall fescue (Hoveland et al., 1983; Boling, 1985; Schmidt et al., 1986; Goetsch et al., 1987). Cattle have gained from 30 to 100% less consuming toxic endophyte-infected tall fescue compared to consumption of an endophyte-free tall fescue (Paterson et al., 1995). This effect of reduced gain is a consequence of a fungal endophyte present within the grass that produces toxins called ergot alkaloids. Fungal …

Understanding And Improving Fermentation In Alfalfa And Grass Baleage, Dennis Hancock

Kentucky Alfalfa and Stored Forage Conference

The ancient Egyptian and Carthaginians are believed to be the first conserve forage by ensiling it in the absence of oxygen. Though the technique has been refined in the 3500 years since, the basic fermentation process has not changed. Populations of naturally-occurring bacteria on the plant surface can consume some of the readily available carbohydrates and produce organic acids. These organic acids lower the pH of the forage material and prevent fungal deterioration of the product. Fermentation has been used for millennia as a natural method for preserving food. Similar bacterial fermentation occurs when one makes yogurt, sour cream, or …

Hay Making Weather In Kentucky: How To Get Good Information, Matthew Dixon, Tom Priddy

Kentucky Alfalfa and Stored Forage Conference

The UK Agricultural Weather Center, housed within the Department of Biosystems and Agricultural Engineering, was developed in 1978. As part of the Cooperative Extension Service, the goal of the Ag Weather Center is to minimize weather and climate related surprise for Kentucky residents and their agricultural needs, ultimately for profitable and sustainable production. In doing so, numerous tools and models have been developed throughout the years to further help farmers and producers in management and production related decisions.

Foreword Of Kentucky Alfalfa And Stored Forages Conference [2017], S. Ray Smith, Krista Lea

Kentucky Alfalfa and Stored Forage Conference

This is the front matter of the proceedings.

Moderator Biographies, Heart Of America Grazing Conference

Kentucky Grazing Conference

No abstract provided.