Digital Commons Network^™

The Future Of The Northeast Atlantic Benthic Flora In A High Co2 World, Juliet Brodie, Christopher J. Williamson, Dan A. Smale, Nicholas A. Kamenos, Nova Mieszkowska, Rui Santos, Michael Cunliffe, Michael Steinke, Christopher Yesson, Kathryn M. Anderson, Valentina Asnaghi, Colin Brownlee, Heidi L. Burdett, Michael T. Burrows, Sinead Collins, Penelope J.C. Donohue, Ben Harvey, Andrew Foggo, Fanny Noisette, Joana Nunes, Federica Ragazzola, John A. Raven, Daniela N. Schmidt, David Suggett, Mirta Teichberg, Jason M. Hall-Spencer

School of Biological and Marine Sciences

Seaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will …

Traversing Swanton Road, 16th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Targeting The Wnt/Β-Catenin Signaling Pathway In Liver Cancer Stem Cells And Hepatocellular Carcinoma Cell Lines With Fh535, Roberto Gedaly, Roberto Galuppo, Michael F. Daily, Malay B. Shah, Erin Colleen Maynard, Changguo Chen, Xiping Zhang, Karyn A. Esser, Donald A. Cohen, B. Mark Evers, Jieyun Jiang, Brett T. Spear

Surgery Faculty Publications

Activation of the Wnt/β-catenin pathway has been observed in at least 1/3 of hepatocellular carcinomas (HCC), and a significant number of these have mutations in the β-catenin gene. Therefore, effective inhibition of this pathway could provide a novel method to treat HCC. The purposed of this study was to determine whether FH535, which was previously shown to block the β-catenin pathway, could inhibit β-catenin activation of target genes and inhibit proliferation of Liver Cancer Stem Cells (LCSC) and HCC cell lines. Using β-catenin responsive reporter genes, our data indicates that FH535 can inhibit target gene activation by endogenous and exogenously …

Skpa Restrains Synaptic Terminal Growth During Development And Promotes Axonal Degeneration Following Injury, E. J. Brace, Chunlai Wu, Vera Valakh, Aaron Diantonio

Open Access Publications

The Wallenda (Wnd)/dual leucine zipper kinase (DLK)-Jnk pathway is an evolutionarily conserved MAPK signaling pathway that functions during neuronal development and following axonal injury. Improper pathway activation causes defects in axonal guidance and synaptic growth, whereas loss-of-function mutations in pathway components impairs axonal regeneration and degeneration after injury. Regulation of this pathway is in part through the E3 ubiquitin ligase Highwire (Hiw), which targets Wnd/DLK for degradation to limit MAPK signaling. To explore mechanisms controlling Wnd/DLK signaling, we performed a large-scale genetic screen in Drosophila to identify negative regulators of the pathway. Here we describe the identification and characterization of …

The Bg News June 18, 2014, Bowling Green State University

BG News (Student Newspaper)

The BGSU campus student newspaper. June 18, 2014. Volume 93-Issue 104.

Insights Into The Epitaxial Relationships Between One-Dimensional Nanomaterials And Metal Catalyst Surfaces Using Density Functional Theory Calculations, Debosruti Dutta

USF Tampa Graduate Theses and Dissertations

This dissertation involves the study of epitaxial behavior of one-dimensional nanomaterials like single-walled carbon nanotubes and Indium Arsenide nanowires grown on metallic catalyst surfaces. It has been previously observed in our novel microplasma based CVD growth of SWCNTs on Ni-Fe bimetallic nanoparticles that changes in the metal catalyst composition was accompanied by variations in the average metal-metal bond lengths of the nanoparticle and that in turn, affected nanotube chirality distributions. In this dissertation, we have developed a very simplistic model of the metal catalyst in order to explain the nanotube growth of specific nanotube chiralities on various Ni-Fe catalyst surfaces. …

Development And Assessment Of Self-Explaining Skills In College Chemistry Instruction, Adrian Villalta-Cerdas

USF Tampa Graduate Theses and Dissertations

The prevalent trend in chemistry instruction relies on what has been described as the classroom game. In this model, students take a passive role and the instructor does all the explaining (thinking), and learning is trivialized to knowing the correct answers (memorizing) and being able to produce them when prompted (regurgitating). The generation of explanations is central to scientific and technological development. In the process of figuring out explanations, the generation of inferences relies on the application of skills associated with scientific behaviors (e.g., analytical reasoning and critical thinking). The process of explanation generation causes a deeper analysis and revision …

Intrinsic Innate Immunity Fails To Control Herpes Simplex Virus And Vesicular Stomatitis Virus Replication In Sensory Neurons And Fibroblasts, Pamela C. Rosato, David A. Leib

Dartmouth Scholarship

Herpes simplex virus 1 (HSV-1) establishes lifelong latent infections in the sensory neurons of the trigeminal ganglia (TG), wherein it retains the capacity to reactivate. The interferon (IFN)-driven antiviral response is critical for the control of HSV-1 acute replication. We therefore sought to further investigate this response in TG neurons cultured from adult mice deficient in a variety of IFN signaling components. Parallel experiments were also performed in fibroblasts isolated concurrently. We showed that HSV-1 replication was comparable in wild-type (WT) and IFN signaling-deficient neurons and fibroblasts. Unexpectedly, a similar pattern was observed for the IFN-sensitive vesicular stomatitis virus (VSV). …

A Hybrid, Integrated Iedds For The Management Of Sequencing Batch Reactors, Davide Sottara, Stefano Bragaglia, Dalila Pulcini, Paola Mello, Luca Luccarini

International Congress on Environmental Modelling and Software

A Sequencing Batch Reactor (SBR) is a particular kind of wastewater treatment plant (WWTP), where all treatment processes take place in a single reactor tank, according to a fixed temporal sequence. SBR offers several advantages in terms of reduced costs, minor impact and greater flexibility with respect to traditional WWTPs. However, an optimal cost/performance ratio can only be achieved if the treatment processes are continuously monitored and controlled. In this paper, we present a hybrid, distributed, knowledge-based (Intelligent) Environmental Decision Support System (IEDSS) specifically dedicated to the management of SBRs. The IEDSS is responsible for verifying, ensuring and enforcing the …

Modeling And Implementation Of A Geospatial Database For Environmental Niches And Potential Geographic Distributions, Gerardo José Zárate, Jugurta Lisboa-Filho, Carlos Frankl Sperber, Flavia Maria Da Silva Carmo

International Congress on Environmental Modelling and Software

The ecological niche of a species is defined by an array of biotic and abiotic requirements that allow organisms to live and reproduce in a geographic region. Abiotic data from the ecological niche in combination with occurrence data can be used to predict the potential geographic distribution of a species in different regions. Potential geographic distributions are useful in predicting the extent of invasive species, predict distributions as preparation for climate change and find appropriate regions for endangered species, among others. Geographic entities and environmental variables can be represented with a high-level abstraction in diagrams using formalism dedicated to model …

Evolutionary Computation And Case-Based Reasoning Interoperation In Iedss Through Gesconda, Miquel Sànchez-Marrè, Gibert Karina, Radha K. Vinayagam, Beatriz Sevilla-Villanueva

International Congress on Environmental Modelling and Software

Interoperability of Intelligent Environmental Decision Support Systems (IEDSS) is one open challenge in the IEDSS field. This paper shows the interoperability of Evolutionary Computation, concretely Genetic Algorithms (GA), and Case-Based Reasoning (CBR) in IEDSS through the GESCONDA tool. GESCONDA is a tool for the deployment of Intelligent Decision Support Systems. This interoperability has been tested with several domains with different purposes like classification tasks, predictive tasks, etc. In the paper, the application in one environmental domain is described and analysed. The experimentation results indicate that this interoperation of both methods can improve the results of the application of one single …

Overstepping Digital Boundaries: An Exploration Of Ownership In 3-D Virtual Worlds, Shoshana Altshuller, Donald R. Moscato

Communications of the IIMA

Ownership in virtual worlds is somewhat of an enigma. (If it is not clear that you "exist," how can you have property? If it is not clear that things "exist" how can you own them?) Still, the interconnectedness between real and virtual worlds creates real legal and ethical quandaries about virtual ownership, similar to the issues that have been addressed regarding intellectual property in the real world. While the relationship between virtual world activities and real-world laws has yet to be clearly defined, we identify three categories of intellectual property violations that can take place in virtual worlds : in-world …

Fda’S Quality Systems Methodology At Pharmaceutical Manufacturing Sites, Warren Adis

Communications of the IIMA

This research details the FDA's quality systems methodology used in its inspection of biopharmaceutical manufacturers in the time period between 2003 and 2009. It analyzes the violations specified in FDA site inspection warning letters, reviewing their frequency and specificity. This analysis is an exploration into FDA activity in this sector, focusing particularly on finished pharmaceuticals, and serves as an initial evaluation of the FDA’s performance. In addition, the study pays particular attention to whether the FDA’s risk methodology has enhanced the overall inspection process and increased its quality assurance.

2d Hydrodynamic Based Logic Modelling Tool For River Restoration Decision Analysis: A Quantitative Approach To Project Prioritization, David J. Bandrowski, Yong G. Lai, D. Nathan Bradley, Josh Murauskas, Dave Gauman

International Congress on Environmental Modelling and Software

In the field of river restoration sciences there is a growing need for analytical modelling tools and quantitative processes to help identify and prioritize project sites. Two-dimensional (20) hydraulic models have become more common in recent years and with the availability of robust data sets and computing technology, it is now possible to evaluate large river systems at the reach scale. The Trinity River Restoration Program (TRRP) - Bureau of Reclamation in Northern California is now analyzing a 40 mile segment of the Trinity River to determine priority and implementation sequencing for its Phase II channel rehabilitation projects. A comprehensive …

Accept'hydro: A Tool For Evaluating Potential Wetland Areas At Floodplain Scale., Adrien Bonneu, Grégory Espitalier-Nöel, Patrice Torguet, Jean-Pierre Jessel, José-Miguel Sanchez-Pérez, Vervier Philippe, Sabine Sauvage

International Congress on Environmental Modelling and Software

Alluvial wetlands have the functions of hydrological regulation and water purification, but are also of interest for preventing flooding and improving the water quality of the natural environment that serves as a reserve for drinking water and biodiversity.

Delimiting these areas is often difficult because it involves both the physical characteristics (topography, river morphology etc.) and hydrodynamic characteristics of the porous medium (permeability etc.) The proposed tool, Accept’Hydro, includes a hydrodynamic simulation of the river, the alluvial aquifer and their interaction, and produces maps of alluvial wetlands with using hydrological criteria. The tool’s primary step consists …

Extending Existing Models To Capture Vegetation Response To Extreme Weather Events: The Modextreme Project, Gianni Bellocchi, Francisco J. Villalobos, Marcello Donatelli, Ole B. Christensen, Oscar Rojas, Roberto Confalonieri, Ioannis N. Athanasiadis, Irina Carpusca, Claudio O. Stöckle

International Congress on Environmental Modelling and Software

Extreme weather events are combinations of meteorological drivers that exceed certain thresholds and occur with low frequency, negatively impacting human living conditions and economic systems including agriculture. The three-year European project MODEXTREME (started on November 1st, 2013) aims at improving the predictive capability of biophysical crop and grassland simulation models under extreme weather conditions (mainly high/low temperatures and water deficit/excess). Existing modelling solutions can be improved with re-usable software libraries to capture extreme weather impacts. Estimates from existing and new modelling solutions will be compared on a variety of datasets and evaluated with respect to medium-term trajectories of future climate …

Predicting Impact Of Natural Calamities In Era Of Big Data And Data Science, Carol K. Joseph, Sunil Kakade

International Congress on Environmental Modelling and Software

Every year thousands of lives and millions of dollars are lost during natural catastrophic events. Data scientists have recognized the value of employing data mining techniques for evaluating these events to assist in understanding trends, predicting future disasters, and assessing vulnerability of populations. The goal of such analysis is to prepare governments for emergency response and relief efforts as well as to formulate strategies for future disaster mitigation. In addition, increasing pressures from a growing world population further emphasize the need for governments to seek viable solutions for balancing human needs with environmental constraints. Identifying populations vulnerable to environmental calamities …

Graph Clustering Based On Social Network Community Detection Algorithms, Enrique Campbell, David Ayala-Cabrera, Joaquín Izquierdo, Rafael Pérez-García

International Congress on Environmental Modelling and Software

Graph network clustering has been an important field of investigation in recent years with a wide spectrum of applications, including environmental, genetic and engineering studies. There are two main types of applications; their suitability depends of the modeling context. Cases where the number of subdivisions is a priori known are tackled with different techniques than those where such number is not clearly evident. The second falls within the field of community detection, which has been broadly studied by social network scientists. Traditionally, community detection in graphs has been tackled by means of hierarchical clustering, which groups nodes based on their …

Dear: A New Technique For Information Extraction And Context-Dependent Text Mining, Tod Sedbrook, Jay M. Lightfoot

Communications of the IIMA

The desire to store and the need to use electronic data has greatly increased as the power, availability, and connectivity of computers has grown. A large portion of this data is in the form of unstructured text documents. Locating specific information within this amorphous mass of documents is an area of active research. Our contribution to this pursuit is the development of the Document Entity and Resolution (DEAR) system. This system combines semantic similarity matching as provided by the open source WordNet database with the ability to recognize named entities through the OpenCalais system. When used in concert, this provides …

A Graph-Theoretic Approach To Improved Curriculum Structure And Assessment Placement, Jay M. Lightfoot

Communications of the IIMA

Assurance of student learning is an important issue in modern education. Accrediting bodies and government entities alike have begun requiring proof that students actually learn the material taught in the classroom. To comply with this mandate, education programs are actively engaged in incorporating assessment procedures into their curricula. Unfortunately, there are no generally agreed upon methods on how to do this. This paper addresses the issue and answers several key questions concerning where to locate topic coverage, assessment data collection, and corrective action within the curriculum. The approach described and developed in this paper cast the curriculum problem into an …

A Modeling Framework For Oceanic Basins Under Double Exposure, Christian Mullon, Gorka Merino, Jose Fernandez, William Cheung, Manuel Barange

International Congress on Environmental Modelling and Software

Oceans stand under double exposure to global warming and of economic globalization. This generates anxieties and contributes to the need for specific governance. A first expression lies in the needs for integrated representations allowing a collaborative development of scenarios. Main challenge here lies in finding, in these representations, a balance between realism and abstraction admissible by all participants.

In this talk, we present modeling framework that has been designed to build scenarios about the possible futures of an oceanic basin. The principle lies in using a network model in which nodes correspond to fish stocks, specialized fleets, farming systems, trade …

Physiological And Behavioural Responses To Noxious Stimuli In The Atlantic Cod (Gadus Morhua), Jared R. Eckroth, Øyvind Aas-Hansen, Lynne U. Sneddon, Helena Bichão, Kjell B. Døving

Aquaculture Collection

In the present study, our aim was to compare physiological and behavioural responses to different noxious stimuli to those of a standardized innocuous stimulus, to possibly identify aversive responses indicative of injury detection in a commercially important marine teleost fish, the Atlantic cod. Individual fish were administered with a noxious stimulus to the lip under short-term general anaesthesia (MS-222). The noxious treatments included injection of 0.1% or 2% acetic acid, 0.005% or 0.1% capsaicin, or piercing the lip with a commercial fishing hook. Counts of opercular beat rate (OBR) at 10, 30, 60, 90 and 120 min and observations of …

Dissolved And Particulate Nutrient Transport Dynamics Of A Small Irish Catchment: The River Owenabue, S. T. Harrington, Joseph R. Harrington

Publications

The objective of this research was to investigate the relationship between water and sediment discharge on the transport of nutrients: nitrogen and phosphorus. Water discharge, suspended sediment concentration and dissolved and particulate forms of nitrogen and phosphorus were monitored on the 105 km2 River Owenabue catchment in Ireland. Water discharge was found to have an influence on both particulate and dissolved nutrient transport, but more so for particulate nutrients. The particulate portion of N and P in collected samples was found to be 24 and 39 %, respectively. Increased particulate nitrogen concentrations were found at the onset of high discharge …

Cercyonis Pegala Agawamensis (Satyridae): A New Butterfly Subspecies From The Coastal Salt Marshes Of The Northeastern United States Of America, Matthew D. Arey, Alex Grkovich

The Taxonomic Report of the International Lepidoptera Survey

A new subspecies of the Common Wood Nymph (Cercyonis pegala) from the New England coastline in the northeastern region of the United States is described on the basis of phenotype, behavior, habitat, seasonality, flight period, and phenology. Agawamensis is univoltine as in all pegala. The newly described subspecies occurs almost entirely in coastal salt marshes and estuarine meadows, quite atypical as understood for Cercyonis pegala. The newly described subspecies agawamensis predominately prefers and occurs within large open salt marshes but can also be found in similar habitat along smaller tidal rivers, coastal inlets and streams

06-17-2014 Swosu Biology Student Wins National Award, Southwestern Oklahoma State University

THE BARK ARCHIVE 2014

Southwestern Oklahoma State University biology student Lauren Blatzheim of Norman (North) recently won a national first-place award at the recent 2014 Beta Beta Beta national convention that took place in Erie (PA).

Tissue Specific Isolation Of Nucleosomes In Caenorhabditis Elegans, Hyrum Shumway, Dr. Steven Johnson

Journal of Undergraduate Research

Hershey and Chase proved DNA to be the genetic material of life in 1952. The structure of DNA largely eluded investigators until Watson and Crick discovered it a year later. These two landmark experiments laid a foundation so that questions in transcription, translation, gene regulation, and inheritance could be answered.

A 2-Step Penalized Regression Method For Family-Based Next-Generation Sequencing Association Studies, Xiuhua Ding, Shaoyong Su, Kannabiran Nandakumar, Xiaoling Wang, David W. Fardo

Biostatistics Faculty Publications

Large-scale genetic studies are often composed of related participants, and utilizing familial relationships can be cumbersome and computationally challenging. We present an approach to efficiently handle sequencing data from complex pedigrees that incorporates information from rare variants as well as common variants. Our method employs a 2-step procedure that sequentially regresses out correlation from familial relatedness and then uses the resulting phenotypic residuals in a penalized regression framework to test for associations with variants within genetic units. The operating characteristics of this approach are detailed using simulation data based on a large, multigenerational cohort.

Modeling Of Multivariate Longitudinal Phenotypes In Family Genetic Studies With Bayesian Multiplicity Adjustment, Lili Ding, Brad G. Kurowski, Hua He, Eileen S. Alexander, Tesfaye B. Mersha, David Fardo, Xue Zhang, Valentina V. Pilipenko, Leah Kottyan, Lisa J. Martin

Biostatistics Faculty Publications

Genetic studies often collect data on multiple traits. Most genetic association analyses, however, consider traits separately and ignore potential correlation among traits, partially because of difficulties in statistical modeling of multivariate outcomes. When multiple traits are measured in a pedigree longitudinally, additional challenges arise because in addition to correlation between traits, a trait is often correlated with its own measures over time and with measurements of other family members. We developed a Bayesian model for analysis of bivariate quantitative traits measured longitudinally in family genetic studies. For a given trait, family-specific and subject-specific random effects account for correlation among family …

Evaluation Of The Power And Type 1 Error Of Recently Proposed Family-Based Tests Of Assocations For Rare Variants, Allison Hainline, Carolina Alvarez, Alexander Luedtke, Brian Greco, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Until very recently, few methods existed to analyze rare-variant association with binary phenotypes in complex pedigrees. We consider a set of recently proposed methods applied to the simulated and real hypertension phenotype as part of the Genetic Analysis Workshop 18. Minimal power of the methods is observed for genes containing variants with weak effects on the phenotype. Application of the methods to the real hypertension phenotype yielded no genes meeting a strict Bonferroni cutoff of significance. Some prior literature connects 3 of the 5 most associated genes (p <1 × 10−4) to hypertension or related phenotypes. Further methodological development is needed to extend these methods to handle covariates, and to explore more powerful test alternatives.

Impedimetric Detection Of Mutant P53 Biomarker-Driven Metastatic Breast Cancers Under Hyposmotic Pressure, Menglu Shi, Nataly Shtraizent, Alla Polotskaia, Jill Bargonetti, Hiroshi Matsui

Publications and Research

In cancer cells, the oncogenic mutant p53 (mtp53) protein is present at high levels and gain-of-function (GOF) activities with more expression of mtp53 proteins contribute to tumor growth and metastasis. Robust analytical approaches that probe the degree of metastasis of cancer cells in connection with the mtp53 activity will be extremely useful not only for establishing a better cancer prognosis but also understanding the fundamental mechanism of mtp53 oncogenic action. Here we assessed the influence of mtp53 in breast cancers to the mechanical property of breast cancer cells. Recently, ovarian and kidney cancer cell lines have been shown to have …