Physical Sciences and Mathematics Commons^™

Using Fish Population Metrics To Compare The Effects Of Artificial Reef Density, Catheline Y. M. Froehlich, Richard Kline

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Artificial reefs continue to be added as habitat throughout the world, yet questions remain about how reef design affects fish diversity and abundance. In the present study, the effects of reef density were assessed for fish communities and sizes of economically valuable Lutjanus campechanus 13 km off Port Mansfield, Texas, at a reef composed of more than 4000 concrete culverts. The study spanned from May to June in 2013 and 2014, and sites sampled included natural reefs, bare areas, and varying culvert patch density categories, ranging from 1–190 culverts. Abundances of adults and species evenness of juvenile populations differed between …

U.S. Drought Monitor, September 29, 2015, Eric Luebehusen

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for September 29, 2015 (9/29/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

An Evolutionary Vaccination Game In The Modified Activity Driven Network By Considering The Closeness, Dun Han, Mei Sun

Publications and Research

In this paper, we explore an evolutionary vaccination game in the modified activity driven network by considering the closeness. We set a closeness parameter p which is used to describe the way of connection between two individuals. The simulation results show that the closeness p may have an active role in weakening both the spreading of epidemic and the vaccination. Besides, when vaccination is not allowed, the final recovered density increases with the value of the ratio of the infection rate to the recovery rate λ/μ. However, when vaccination is allowed the final density of recovered individual first increases and …

Heterogeneous Oxidation Of Catechol, Elizabeth A. Pillar, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

Natural and anthropogenic emissions of aromatic hydrocarbons from biomass burning, agro-industrial settings, and fossil fuel combustion contribute precursors to secondary aerosol formation (SOA). How these compounds are processed under humid tropospheric conditions is the focus of current attention to understand their environmental fate. This work shows how catechol thin films, a model for oxygenated aromatic hydrocarbons present in biomass burning and combustion aerosols, undergo heterogeneous oxidation at the air–solid interface under variable relative humidity (RH = 0–90%). The maximum reactive uptake coefficient of O₃(g) by catechol γ_O3 = (7.49 ± 0.35) × 10^–6 occurs for …

U.S. Drought Monitor, September 22, 2015, Eric Luebehusen

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for September 22, 2015 (9/22/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

A Scientific Basis For Regulating Deep-Sea Fishing By Depth, Jo Clarke, Rosanna Milligan, David M. Bailey, Francis Neat

Marine & Environmental Sciences Faculty Articles

The deep sea is the world’s largest ecosystem, with high levels of biodiversity and many species that exhibit life-history characteristics thatmake them vulnerable to high levels of exploitation. Many fisheries in the deep sea have a track record of being unsustainable. In the northeast Atlantic, there has been a decline in the abundance of commercial fish species since deep-sea fishing commenced in the 1970s. Current management is by effort restrictions and total allowable catch (TAC), but there remain problems with compliance and high levels of bycatch of vulnerable species such as sharks. The European Union is currently considering new legislation …

U.S. Drought Monitor, September 15, 2015, Chris Fenimore

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for September 15, 2015 (9/15/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

U.S. Drought Monitor, September 8, 2015, Richard Tinker

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for September 8, 2015 (9/8/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

Effect Of Quercetin, Genistein And Kaempferol On Glutathione And Glutathione-Redox Cycle Enzymes In 3t3-L1 Preadipocytes, William Y. Boadi, Paul K. Amartey, Andrew Lo

Chemistry Faculty Research

Context and objective: Many studies have shown that cellular redox potential is largely determined by glutathione (GSH), which accounts for more than 90% of cellular nonprotein thiols. The aim of this study was to delineate the effect of three flavonoids – namely, quercetin, kaempferol and genistein – and exogenous GSH on oxidative damage by the Fenton’s pathway through the GSH and GSH-redox cycle enzymes in 3T3-L1 cells. Materials and methods: 3T3-L1 preadipocytes were exposed to each flavonoid and GSH at concentrations of 0, 5, 10, 15, 20 and 25 µM and then GSH levels and activities of glutathione peroxidase (GSH-Px), …

A Comparison Of The Bioaccumulation Potential Of Mercury And Polychlorinated Biphenyls In Goldfish (Carassius Auratus), Jiajia Li, Ken G. Drouillard, Brian Braunfireun, Douglass G. Haffner

Great Lakes Institute for Environmental Research Publications

Both mercury (Hg) and polychlorinated biphenyls (PCBs) demonstrate food web biomagnification in aquatic ecosystems, yet their toxicokinetics have not been simultaneously contrasted within a common fish species. This study quantifies uptake and elimination rates of Hg and PCBs in goldfish. Fish were exposed to contaminated food containing PCBs and Hg to determine dietary chemical assimilation efficiencies (AEs) and elimination coefficients (k_tot). To test first-order kinetics, three exposure regimes were established by varying the proportion of contaminated fish incorporated into the food. Dietary AEs were 98 ± 10, 75 ± 12, and 40 ± 9% for MeHg, THg, and …

U.S. Drought Monitor, September 1, 2015, Anthony Artusa

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for September 1, 2015 (9/1/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

Evaluating Sub-Lethal Effects Of Orchard-Applied Pyrethroids Using Video-Tracking Software To Quantify Honey Bee Behaviors, Erin M. Ingram, Julie Augustin, Marion D. Ellis, Blair Siegfried

Department of Entomology: Faculty Publications

Managed honey bee, Apis mellifera L., colonies are contracted to pollinate fruit and nut orchards improving crop quality and yield. Colonies placed in orchards are potentially exposed to pyrethroid insecticides used for broad-spectrum pest control. Pyrethroids have been reported to pose minimal risk to bees due to their low application rates in the field and putative repellent properties. This repellency is believed to alter foraging behavior with the benefit of preventing bees from encountering a lethal dose in the field. However, sub-lethal exposure to pyrethroids may adversely impact bee behavior potentially resulting in social dysfunction or disruption of foraging.

This …

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Bioinformatics Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …

If You've Seen One Worm, Have You Seen Them All? Spatial, Community, And Genetic Variability Of Tubificid Communities In Montana, Nilanjan Lodh, Donna M. Rizzo, Billie L. Kerans, Stephanie Mcginnis, Nikolaos Fytilis, Lori Stevens

College of Engineering and Mathematical Sciences Faculty Publications

Genetic studies are recognized increasingly as important for understanding naturally occurring disease dynamics and are used to predict host genetic diversity and coevolutionary processes and to identify species composition in ecological communities. Tubifex tubifex, the definitive host of the whirling disease parasite Myxobolus cerebralis, comprises 6 known lineages that vary widely in parasite susceptibility. We used 16S ribosomal DNA (16S rDNA) to identify relationships among genetic variability of 3 oligochaete genera (T. tubifex, Rhyacodrilus spp., and Ilyodrilus spp.; Oligochaeta:Tubificidae), oligochaete assemblage composition, and the presence of whirling disease in 9 locations across 4 watersheds in Montana, USA. We assessed genetic …

Sex Allocation And The Emergence Of Helping In Cooperatively Breeding Species., Josh D Dunn, Teodora Vujicic, Geoff Wild

Applied Mathematics Publications

In cooperative breeding systems individuals invest in the reproductive success of others. In this paper, we study the emergence of cooperative breeding systems in which reproductively active breeders receive investment from reproductively non-active helpers. Our goal is to understand how the division of an investment between male and female components of breeder fitness (i.e. the helper sex-allocation strategy) influences the emergence of cooperative breeding itself. Using mathematical models, we arrive at expressions for the inclusive-fitness advantage of helpful behaviour that generalize previous work. These expressions assume an ecologically stable environment, and that breeders make evolutionarily stable sex-allocation decisions. We find …

Prescribed Fire Monitoring Report, Tallgrass Prairie National Preserve 2014 (Iqcs Fire Number 285382, 285383, 266782, 285677), Sherry A. Leis, Sarah E. Hinman

United States National Park Service: Publications

Introduction

In 2014, the preserve’s federal and NGO partners conducted prescribed fires during March, April, and October that encompassed 8129.8 acres of Tallgrass Prairie National Preserve (TAPR). This was a unique burn year in that prescribed burns occurred in the spring, the traditional burn season, and the fall. Fall burns were conducted to support needed archaeological surveys as part of the environmental compliance for a symphony event scheduled for June 2015 at the preserve. Burns at TAPR were coordinated with local US Fish and Wildlife Service (USFWS), The Nature Conservancy (TNC), and various units of the National Park Service.

Burns …

Student Fellows 2015-2016, Place

PLACE Historical Documents

This document provides biographies of PLACE student fellows at Linfield College for 2015-2016.

Faculty Fellows 2015-2016, Place

PLACE Historical Documents

This document provides biographies of PLACE faculty fellows at Linfield College for 2015-2016.

Air, Water, Earth, And Fire: The Ancient Elements On A Changing Planet, Place

PLACE Historical Documents

This document explains the PLACE theme at Linfield College for 2015-2016 (Air, Water, Earth, and Fire: The Ancient Elements on a Changing Planet).

An Allosteric Interaction Links Usp7 To Deubiquitination And Chromatin Targeting Of Uhrf1, Zhi-Min Zhang, Scott B. Rothbart, David F. Allison, Qian Cai, Joseph S. Harrison, Lin Li, Yinsheng Wang, Brian D. Strahl, Gang Greg Wang, Jikui Song

College of the Pacific Faculty Articles

The protein stability and chromatin functions of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) are regulated in a cell-cycle-dependent manner. We report a structural characterization of the complex between UHRF1 and the deubiquitinase USP7. The first two UBL domains of USP7 bind to the polybasic region (PBR) of UHRF1, and this interaction is required for the USP7-mediated deubiquitination of UHRF1. Importantly, we find that the USP7-binding site of the UHRF1 PBR overlaps with the region engaging in an intramolecular interaction with the N-terminal tandem Tudor domain (TTD). We show that the USP7-UHRF1 interaction perturbs the TTD-PBR interaction of …

An Analytical Method For Detecting Toxic Metal Cations Using Cyclotriveratrylene Derivative Capped Gold Nanoparticles, Zachary R. Osner, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Cyclotriveratrylene-oxime (CTV-oxime) derivatives that terminate with a dithiolate linker were synthesized enabling the supramolecular scaffold to adhere to gold nanoparticles (AuNPs) with the bowl-shaped cavity of the CTV scaffold exposed for utilization in host–guest chemistry. Exposure of these CTV functionalized AuNPs to varying concentrations of di- and trivalent metal cations resulted in the formation of large CTV-AuNP polymeric clusters and an accompanying a shift in the plasmon resonance. These interactions between the CTV-AuNPs and the metal cations in solution provides proof-of-concept that supramolecular functionalized AuNPs can be used as a simple and straightforward, on-site detection system for toxic metal cations …

Automatic Emotion Identification From Text, Wenbo Wang

Kno.e.sis Publications

Emotions are both prevalent in and essential to most aspects of our lives. They in- fluence our decision-making, affect our social relationships and shape our daily behavior. With the rapid growth of emotion-rich textual content, such as microblog posts, blog posts, and forum discussions, there is a growing need to develop algorithms and techniques for identifying people’s emotions expressed in text. It has valuable implications for the studies of suicide prevention, employee productivity, well-being of people, customer relationship management, etc. However, emotion identification is quite challenging partly due to the following reasons: i) It is a multi-class classification problem that …

Evaluating Recruitment Of American Eel, Anguilla Rostrata, In The Potomac River (Spring 2015), Troy D. Tuckey, Mary C. Fabrizio

Reports

The Atlantic States Marine Fisheries Commission (ASMFC) adopted the Interstate Fishery Management Plan (FMP) for the American Eel in November 1999. The FMP focuses on increasing coastal states’ efforts to collect American Eel data through both fishery‐dependent and fishery‐independent studies. Consequently, member jurisdictions agreed to implement an annual survey for young‐of‐year (YOY) American Eels. The survey is intended to “…characterize trends in annual recruitment of the YOY eels over time [to produce a] qualitative appraisal of the annual recruitment of American Eel to the U.S. Atlantic Coast” (ASMFC 2000). The development of these surveys began in 2000 with full implementation …

Coastal Sediment Elevation Change Following Anthropogenic Mangrove Clearing, Heather Lyn Hayden, Elise F. Granek

Environmental Science and Management Faculty Publications and Presentations

Coastal mangrove forests along tropical shorelines serve as an important interface between land and sea. They provide a physical buffer protecting the coastline from erosion and act as sediment “traps” catching terrestrial sediment, thus preventing smothering of subtidal coral reefs. Coastal development that removes mangrove habitat may impact adjacent nearshore coral reefs through sedimentation and nutrient loading. We examined differences in sediment elevation change between patches of open-coast intact and anthropogenically cleared red mangroves (Rhizophora mangle) on the east side of Turneffe Atoll, Belize, to quantify changes following mangrove clearing. Samples were collected over a 24 month period at five …

Climate-Suitable Planting As A Strategy For Maintaining Forest Productivity And Functional Diversity, Matthew Joshua Duveneck, Robert M. Scheller

Environmental Science and Management Faculty Publications and Presentations

Within the time frame of the longevity of tree species, climate change will change faster than the ability of natural tree migration. Migration lags may result in reduced productivity and reduced diversity in forests under current management and climate change. We evaluated the efficacy of planting climate-suitable tree species (CSP), those tree species with current or historic distributions immediately south of a focal landscape, to maintain or increase aboveground biomass, productivity, and species and functional diversity. We modeled forest change with the LANDIS-II forest simulation model for 100 years (2000–2100) at a 2-ha cell resolution and five-year time steps within …

Managing Precision Dairy Farming Technologies, Barbara Alice Wadsworth, Amanda Stone, Lauren M. Mayo, Nicky Tsai, Jeffrey M. Bewley

Agriculture and Natural Resources Publications

Precision dairy farming is the use of technologies to measure physiological, behavioral, and production indicators of individual animals to improve management strategies and farm performance. These systems have the potential to detect disease and estrus and to evaluate cow comfort by monitoring activity, feeding time, lying time, mounting activity, real-time location, reticulorumen pH, rumination time, and body temperature.

The data provided by a precision dairy farming device is only valuable if it records the data properly for the right cow and is used by the producer. This factsheet will describe problems that researchers at the University of Kentucky have experienced …

Intrinsic Fluctuations And Driven Response Of Insect Swarms, Rui Ni, James G. Puckett, Eric R. Dufresne, Nicholas T. Ouellette

Physics and Astronomy Faculty Publications

Animals of all sizes form groups, as acting together can convey advantages over acting alone; thus, collective animal behavior has been identified as a promising template for designing engineered systems. However, models and observations have focused predominantly on characterizing the overall group morphology, and often focus on highly ordered groups such as bird flocks. We instead study a disorganized aggregation (an insect mating swarm), and compare its natural fluctuations with the group-level response to an external stimulus. We quantify the swarm’s frequency-dependent linear response and its spectrum of intrinsic fluctuations, and show that the ratio of these two quantities has …

Groundwater Chemistry Of The Weaber Plain (Goomig Farmlands): Baseline Results 2010–13, Adam Lillicrap, Richard J. George Dr, Arjen Ryder, D L. Bennett

Resource management technical reports

The Ord River Irrigation Area (ORIA) is located in the north-east of the Kimberley region of Western Australia, near the town of Kununurra. The irrigation area was established in 1963 and over time developed to the current extent of 14 000 hectares (ha). The Weaber Plain (Goomig Farmlands) area is located north-north-east of the existing irrigation area, 30km from Kununurra, and has been identified as being suitable for irrigated agriculture for many decades. However, it was not until 2009, with state government support, that the 7400ha project commenced, with construction starting in 2010. State and Australian government environmental approvals required …

Southeast Florida Coral Reef Fishery-Independent Baseline Assessment, Kirk Kilfoyle, Brian K. Walker, Dana P. Fisco, Steven G. Smith, Richard E. Spieler

Marine & Environmental Sciences Faculty Reports

Reef fishes are important biologic, ecologic, and economic resources of the marine ecosystem which must be managed for sustainability. Until recently, there was no long-term monitoring program in place to assess the condition of reef fish resources of the northern Florida Reef Tract (FRT) (northern Miami-Dade, Broward, Palm Beach, and Martin counties). An assessment/monitoring plan for the northern portion of the Florida reef tract was designed through a joint cooperative effort by scientists at the University of Miami, Rosenstiel School of Marine and Atmospheric Science (RSMAS), National Oceanic and Atmospheric Administration (NOAA)-Southeast Fisheries Science Center (SEFSC) and Nova Southeastern University …

U.S. Drought Monitor, August 25, 2015, Anthony Artusa

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for August 25, 2015 (8/25/15) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.