Life Sciences Commons^™

Toward A Synthesis Of Conservation And Animal Welfare Science, David Fraser

David Fraser, PhD

Conservation biology and animal welfare science are multidisciplinary fields of research that address social concerns about animals. Conservation biology focuses on wild animals, works at the level of populations, ecological systems and genetic types, and deals with threats to biodiversity and ecological integrity. Animal welfare science typically focuses on captive (often domestic) animals, works at the level of individuals and groups, and deals with threats to the animals’ health and quality of life. However, there are many areas of existing or potential overlap: (i) many real-life problems, such as environmental contamination, urban development and transportation, create problems for animals that …

Rating Harms To Wildlife: A Survey Showing Convergence Between Conservation And Animal Welfare Views, S. Dubois, D. Fraser

David Fraser, PhD

Human activities may cause conservation concerns when animal populations or ecosystems are harmed and animal welfare concerns when individuals are harmed. In general, people are concerned with one or the other, as the concepts may be regarded as separate or even at odds. An online purposive survey of 339 British Columbians explored differences between groups that varied by gender, residency, wildlife engagement level and value orientation (conservation-oriented or animal welfare-oriented), to see how they rated the level of harm to wildlife caused by different human activities. Women, urban residents, those with low wildlife engagement, and welfare-orientated participants generally scored activities …

Harnessing Wastewater For Renewable Energy (2013-2), Aaron Adalja, Chalida U-Tapao

Aaron Adalja

This case study explores the options for using wastewater to produce renewable energy in the context of a public wastewater treatment plant. It provides an opportunity for students to synthesize knowledge from resource economics, engineering, environmental science, agriculture, and public policy to develop a transdisciplinary approach to a socio-environmental issue. The case is designed for upper division undergraduate courses in resource economics or environmental engineering, but several modifications are provided graduate course applications. Students assume the role of a newly hired analyst at a consulting firm in Washington, DC, that specializes in renewable energy solutions. They are charged with proposing …

Factors Affecting Individual Foraging Specialization And Temporal Diet Stability Across The Range Of A Large “Generalist” Apex Predator, Adam E. Rosenblatt, James C. Nifong, Michael R. Heithaus, Frank J. Mazzotti, Michael S. Cherkiss, Brian M. Jeffery, Ruth M. Elsey, Rachel A. Decker, Brian R. Silliman, Louis J. Guillette Jr., Russell H. Lowers, Justin C. Larson

Adam Rosenblatt

Individual niche specialization (INS) is increasingly recognized as an important component of ecological and evolutionary dynamics. However, most studies that have investigated INS have focused on the effects of niche width and inter- and intraspecific competition on INS in small-bodied species for short time periods, with less attention paid to INS in large-bodied reptilian predators and the effects of available prey types on INS. We investigated the prevalence, causes, and consequences of INS in foraging behaviors across different populations of American alligators (Alligator mississippiensis), the dominant aquatic apex predator across the southeast US, using stomach contents and stable isotopes. Gut …

300-X-250-7.Jpg, Susunqq Online

susunqq

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulous, Konstantin Läufer, George K. Thiruvathukal, Catherine Putonti

Konstantin Läufer

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Konstantin Läufer

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

First-Principles And Model Simulation Of All-Optical Spin Reversal, Thomas F. George, G.P. Zhang, Z. Babyak, Y. Xue, Y. H. Bai

Thomas George

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Catherine Putonti

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulous, Konstantin Läufer, George K. Thiruvathukal, Catherine Putonti

Catherine Putonti

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Catherine Putonti

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Vetcompass Australia: A National Big Data Collection System For Veterinary Science, Paul Mcgreevy, Peter Thomson, Navneet K. Dhand, David Raubenheimer, Sophie Masters, Caroline S. Mansfield, Timothy Baldwin, Ricardo J. Soares Magalhaes, Jacquie Rand, Peter Hill, Anne Peaston, James Gilkerson, Martin Combs, Shane Raidal, Peter Irwin, Peter Irons, Richard Squires, David Brodbelt, Jeremy Hammond

Paul McGreevy, PhD

Notes On Eryx, Omega, And Ata, Victor Fet

Victor Fet

Observations on several Nabokov’s works (Pale Fire, Lolita) where geographic or zoological names provide sources for puns and hidden parallels.

Ionic Liquid Extraction Unveils Previously Occluded Humic-Bound Iron In Peat Soil Pore Water, Timothy J. Veverica, Evan S. Kane, Amy Marcarelli, Sarah A. Green

Amy Marcarelli

Globally, peatland ecosystems store tremendous amounts of C relative to their extent on the landscape, largely owing to saturated soils which limit decomposition. While there is still considerable uncertainty regarding CO2 production potential below the water table in peatland ecosystems, extracellular Fe reduction has been suggested as a dominant pathway for anaerobic metabolism. However, colorimetric methods commonly used to quantitate Fe and partition between redox species are known to be unreliable in the presence of complex humic substances, which are common in peatland pore water. We evaluated both the standard o-phenanthroline (o-P) Method and an ionic liquid extraction (ILE) Method …

Grnsight: A Web Application And Service For Visualizing Models Of Small- To Medium-Scale Gene Regulatory Networks, Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi

Ben G. Fitzpatrick

GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of …

Biophysical And Computational Studies Of The Vcci:Vmip-Ii Complex, Anna Nguyen, Nai-Wei Kuo, Laura Showalter, Ricardo Ramos, Cynthia Dupureur, Michael Colvin, Patricia Liwang

Cynthia Dupureur

Nitrogen Fertilizer Rate Effects On Soil Organic Carbon In Iowa Continuous Corn And Corn-Soybean Systems, Hanna J. Poffenbarger, Daniel W. Barker, Matthew J. Helmers, Fernando E. Miguez, John E. Sawyer, Johan Six, Michael J. Castellano

John E. Sawyer

Nitrogen fertilizer rate is a key factor affecting soil organic C (SOC) in corn-based cropping systems. The objective of this study was to determine the change in SOC in response to long-term N rates for continuous corn and corn-soybean cropping systems at two sites in Iowa. Soil samples were collected to a depth of 15 cm in 1999 and again in 2014 after 15 years of corn N rate treatments ranging from 0 to 269 kg ha^-1. The soil samples were analyzed for total C and N concentrations. For continuous corn at both sites, the average annual change …

New Genera And Species Of Fossil Marine Amioid Fishes (Actinopterygii, Holostei) From The Late Cretaceous Agoult Locality In Southeastern Morocco, Mark V. H. Wilson, Alison M. Murray, Terry C. Grande

Terry Grande

No abstract provided.

Jessicahlawrencemastersportfolio.Pdf, Jessicah Lawrence

Jessicah Lawrence

No abstract provided.

Adoption Of Switchgrass Cultivation For Biofuel Under Uncertainty: A Discrete-Time Modeling Approach, Pralhad Burli, Eric Forgoston, Pankaj Lal, Lora Billings, Bernabas Wolde

Lora Billings

Adoption Of Switchgrass Cultivation For Biofuel Under Uncertainty: A Discrete-Time Modeling Approach, Pralhad Burli, Eric Forgoston, Pankaj Lal, Lora Billings, Bernabas Wolde

Eric Forgoston

Adoption Of Switchgrass Cultivation For Biofuel Under Uncertainty: A Discrete-Time Modeling Approach, Pralhad Burli, Eric Forgoston, Pankaj Lal, Lora Billings, Bernabas Wolde

Pankaj Lal

Dengue Virus Ns2b/Ns3 Protease Inhibitors Exploiting The Prime Side, Kuan-Hung Lin, Akbar Ali, Linah Rusere, Djade I. Soumana, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein …

A Brief Review On Leading Big Data Models, Sugam Sharma, Udoyara S. Tim, Johnny S. Wong, Shashi Gadia, Subhash Sharma

Sugam Sharma

Today, science is passing through an era of transformation, where the inundation of data, dubbed data deluge is influencing the decision making process. The science is driven by the data and is being termed as data science. In this internet age, the volume of the data has grown up to petabytes, and this large, complex, structured or unstructured, and heterogeneous data in the form of “Big Data” has gained significant attention. The rapid pace of data growth through various disparate sources, especially social media such as Facebook, has seriously challenged the data analytic capabilities of traditional relational databases. The velocity …

Contextual Motivation In Physical Activity By Means Of Association Rule Mining, Sugam Sharma, Udoyara Sunday Tim, Marinelle Payton, Hari Cohly, Shashi Gadia, Johnny Wong, Sudharshanam Karakala

Sugam Sharma

The primary thrust of this work is to demonstrate the applicability of association rule mining in public health domain, focusing on physical activity and exercising. In this paper, the concept of association rule mining is shown assisting to promote the physical exercise as regular human activity. Specifically, similar to the prototypical example of association rule mining, market basket analysis, our proposed novel approach considers two events – exercise (sporadic) and sleep (regular) as the two items of the frequent set; and associating the former, exercise event, with latter, the daily occurring activity sleep at night, helps strengthening the frequency of …

Interdependence Of Inhibitor Recognition In Hiv-1 Protease, Janet L. Paulsen, Florian Leidner, Debra A. Ragland, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1' and S2' subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. …

Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha

Robyn Lutz

We propose an extension of van Lamsweerde's goal-oriented requirements engineering to the domain of programmable DNA nanotechnology. This is a domain in which individual devices (agents) are at most a few dozen nanometers in diameter. These devices are programmed to assemble themselves from molecular components and perform their assigned tasks. The devices carry out their tasks in the probabilistic world of chemical kinetics, so they are individually error-prone. However, the number of devices deployed is roughly on the order of a nanomole (a 6 followed by fourteen 0s), and some goals are achieved when enough of these agents achieve their …

A Smartphone-Based Device For Measuring Soil Organic Matter, Meng Lu

Meng Lu

The project evaluated the potential of utilizing a smartphone-based system for the in-field analysis of Soil Organic Matter. Although it demonstrated that the performance of the smartphone-based spectrometer can be comparable to commercial spectrometers, the results suggest that it is challenging to identify the spectral “signatures” of the SOM due to the morphology and moisture variation of soil samples.

The Potential Of Three Computer-Based Communication Activities For Supporting Older Adult Independent Living, Melinda Heinz, Jinmyoung Cho, Norene Kelly, Peter Martin, Johnny Wong, Warren Franke, Wen-Hua Hsieh, Joan Blaser

Johnny Wong

Technology has become an increasingly integral part of life. For example, technology allows individuals to stay in touch with loved ones, obtain medical services through telehealthcare, and enjoy an overall higher quality of life. Particularly for older adults, using technology increases the likelihood that they will maintain their independence and autonomy. Long-distance caregiving has recently become a feasible option where caregivers for older adults can access reports and information about their loved one’s patterns that day (e.g., food and medication intake). Technology may be able to offset age-related challenges (e.g., caregiving, accessing healthcare, decreased social networks) by applying technology to …

A Brief Review On Leading Big Data Models, Sugam Sharma, Udoyara S. Tim, Johnny S. Wong, Shashi Gadia, Subhash Sharma

Johnny Wong

Today, science is passing through an era of transformation, where the inundation of data, dubbed data deluge is influencing the decision making process. The science is driven by the data and is being termed as data science. In this internet age, the volume of the data has grown up to petabytes, and this large, complex, structured or unstructured, and heterogeneous data in the form of “Big Data” has gained significant attention. The rapid pace of data growth through various disparate sources, especially social media such as Facebook, has seriously challenged the data analytic capabilities of traditional relational databases. The velocity …