Digital Commons Network^™

Getting Digital Tools Into Students' And Researchers' Workflows, Oliver Renn, Jozica Dolenc, Joachim Schnabl

Proceedings of the IATUL Conferences

No abstract provided.

Modeling Neural Behavior And Pain During Bladder Distention Using An Agent-Based Model Of The Central Nucleus Of The Amygdala, Joshua Baktay, Rachael Miller Neilan, Marissa Behun, Neal Mcquaid, Benedict Kolber

Spora: A Journal of Biomathematics

Chronic bladder pain evokes asymmetric behavior in neurons across the left and right hemispheres of the amygdala. An agent-based computational model was created to simulate the firing of neurons over time and in response to painful bladder stimulation. Each agent represents one neuron and is characterized by its location in the amygdala and response type (excited or inhibited). At each time step, the firing rates (Hz) of all neurons are stochastically updated from probability distributions estimated from data collected in laboratory experiments. A damage accumulation model tracks the damage accrued by neurons during long-term, painful bladder stimulation. Emergent model output …

Modeling And Simulation On Entities’ Belief In Cyberspace, Jiuyang Tao, Wu Lin, Xiaoyuan He, Rong Ming

Journal of System Simulation

Abstract: Of all cyber-attacks, 'fabrication' which is aimed at impacting one’s awareness is becoming the common means, so it is of great importance to explore ways so as to defend such attacks. An attack can success or not always rely on the entities’ belief of certain events. In this paper, two different ways of 'fabrication' attack are put forward, and three essential conditions for 'fabrication' attack are analyzed. Second, a cyberspace belief model in terms of the Dempster-Shafer framework based on situation awareness theory is built to study the evolution of the cyber entities’ belief under the 'fabrication' attack. In …

Puckett, Dillon Huette "D. Hugh," 1929-2010 (Mss 658), Manuscripts & Folklife Archives

Manuscript Collection Finding Aids

Finding aid only for Manuscripts Collection 658. Lewis family genealogy collected by Dr. Dillon Huette Puckett covering descendants in Virginia, North Carolina, Kentucky and Missouri. Allied family files (those found in Box 4) are available in digital format only in TopSCHOLAR.

Pdx Finder: A Portal For Patient-Derived Tumor Xenograft Model Discovery., Nathalie Conte, Jeremy C Mason, Csaba Halmagyi, Steven Neuhauser, Abayomi Mosaku, Galabina Yordanova, Aikaterini Chatzipli, Dale A. Begley, Debra M Krupke, Helen Parkinson, Terrence F Meehan, Carol J Bult

Faculty Research 2019

Patient-derived tumor xenograft (PDX) mouse models are a versatile oncology research platform for studying tumor biology and for testing chemotherapeutic approaches tailored to genomic characteristics of individual patients' tumors. PDX models are generated and distributed by a diverse group of academic labs, multi-institution consortia and contract research organizations. The distributed nature of PDX repositories and the use of different metadata standards for describing model characteristics presents a significant challenge to identifying PDX models relevant to specific cancer research questions. The Jackson Laboratory and EMBL-EBI are addressing these challenges by co-developing PDX Finder, a comprehensive open global catalog of PDX models …

Expansion Of The Human Phenotype Ontology (Hpo) Knowledge Base And Resources., Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A Mcmurry, David Osumi-Sutherland, Valentina Cipriani, James P Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh Dawkins, Michael Segal, Anna C Jansen, Ahmed Muaz, Willie H Chang, Jenna Bergerson, Stanley J F Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F Freeman, Panagiotis I Sergouniotis, Daniel Durkin, Andrea L Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T Wheeler, Renske Oegema, Halima Lourghi, Maria G Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin A Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia Smith, Joshua D Milner, Dorothée Leroux, Cornelius F Boerkoel, Amy Klion, Melody C Carter, Tudor Groza, Damian Smedley, Melissa A Haendel, Chris Mungall, Peter N Robinson

Faculty Research 2019

The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the …

The Mouse Gene Expression Database (Gxd): 2019 Update., Constance M. Smith, Terry F. Hayamizu, Jacqueline H. Finger, Susan M. Bello, Ingeborg J. Mccright, Jingxia Xu, Richard M. Baldarelli, Jonathan S Beal, Jeffrey Campbell, Lori E. Corbani, Pete J. Frost, Jill R Lewis, Sharon C Giannatto, Dave Miers, David R. Shaw, James A. Kadin, Joel E Richardson, Cynthia Smith, Martin Ringwald

Faculty Research 2019

The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD's gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and …

Career Corner: Community Food Initiatives Looking For Interns, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

Bishydrazone-Based Antifungal Agents, Sylvie Garneau-Tsodikova, David S. Watt

Pharmaceutical Sciences Faculty Patents

Hydrazone compounds and pharmaceutical compositions including same are disclosed as having antifungal activity. Such compounds are useful for treating or preventing fungal conditions in a subject in need thereof by administering same.

Dachshund Depletion Disrupts Mammary Gland Development And Diverts The Composition Of The Mammary Gland Progenitor Pool., Xuanmao Jiao, Zhiping Li, Min Wang, Sanjay Katiyar, Gabriele Di Sante, Mehdi Farshchian, Andrew P. South, Cinzia Cocola, Daniele Colombo, Rolland Reinbold, Ileana Zucchi, Kongming Wu, Ira Tabas, Benjamin T. Spike, Richard G. Pestell

Department of Dermatology and Cutaneous Biology Faculty Papers

DACH1 abundance is reduced in human malignancies, including breast cancer. Herein DACH1 was detected among multipotent fetal mammary stem cells in the embryo, among mixed lineage precursors, and in adult basal cells and (ERα⁺) luminal progenitors. Dach1 gene deletion at 6 weeks in transgenic mice reduced ductal branching, reduced the proportion of mammary basal cells (Lin⁻ CD24^med CD29^high) and reduced abundance of basal cytokeratin 5, whereas DACH1 overexpression induced ductal branching, increased Gata3 and Notch1, and expanded mammosphere formation in LA-7 breast cells. Mammary gland-transforming growth factor β (TGF-β) activity, known to reduce ductal …

Mouse Genome Database (Mgd) 2019., Carol J Bult, Judith A. Blake, Cynthia Smith, James A. Kadin, Joel E Richardson, Mouse Genome Database Group

Faculty Research 2019

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the …

The Gene Ontology Resource: 20 Years And Still Going Strong., Gene Ontology Consortium

Faculty Research 2019

The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities …

A Botanist's Take On The Fruits Of The Spirit, Jeff Ploegstra

Faculty Work Comprehensive List

"Love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, and self-control are all signs of a vital and thriving relationship with Christ, but at the heart of these fruits lies a seed."

Posting about living out Christ-like virtues from In All Things - an online journal for critical reflection on faith, culture, art, and every ordinary-yet-graced square inch of God’s creation.

https://inallthings.org/a-botanists-take-on-the-fruits-of-the-spirit/

Plasmodium Para-Aminobenzoate Synthesis And Salvage Resolve Avoidance Of Folate Competition And Adaptation To Host Diet, Joachim Michael Matz, Mutsumi Watanabe, Mofolusho Falade, Takayuki Tohge, Rainer Hoefgen, Kai Matuschewski

Pharmaceutical Sciences Faculty Publications

Folate metabolism is essential for DNA synthesis and a validated drug target in fast-growing cell populations, including tumors and malaria parasites. Genome data suggest that Plasmodium has retained its capacity to generate folates de novo. However, the metabolic plasticity of folate uptake and biosynthesis by the malaria parasite remains unresolved. Here, we demonstrate that Plasmodium uses an aminodeoxychorismate synthase and an aminodeoxychorismate lyase to promote the biogenesis of the central folate precursor para-aminobenzoate (pABA) in the cytoplasm. We show that the parasite depends on de novo folate synthesis only when dietary intake of pABA by …

Vampire Venom: Vasodilatory Mechanisms Of Vampire Bat (Desmodus Rotundus) Blood Feeding, Rahini Kakumanu, Wayne C. Hodgson, Ravi Ravina

KIP Articles

Animals that specialise in blood feeding have particular challenges in obtaining their meal, whereby they impair blood hemostasis by promoting anticoagulation and vasodilation in order to facilitate feeding. These convergent selection pressures have been studied in a number of lineages, ranging from fleas to leeches. However, the vampire bat (Desmondus rotundus) is unstudied in regards to potential vasodilatory mechanisms of their feeding secretions (which are a type of venom). This is despite the intense investigations of their anticoagulant properties which have demonstrated that D. rotundus venom contains strong anticoagulant and proteolytic activities which delay the formation of blood clots and …

Etoxpred: A Machine Learning-Based Approach To Estimate The Toxicity Of Drug Candidates 11 Medical And Health Sciences 1115 Pharmacology And Pharmaceutical Sciences 03 Chemical Sciences 0305 Organic Chemistry 03 Chemical Sciences 0304 Medicinal And Biomolecular Chemistry, Limeng Pu, Misagh Naderi, Tairan Liu, Hsiao Chun Wu, Supratik Mukhopadhyay, Michal Brylinski

Faculty Publications

© 2019 The Author(s). Background: The efficiency of drug development defined as a number of successfully launched new pharmaceuticals normalized by financial investments has significantly declined. Nonetheless, recent advances in high-throughput experimental techniques and computational modeling promise reductions in the costs and development times required to bring new drugs to market. The prediction of toxicity of drug candidates is one of the important components of modern drug discovery. Results: In this work, we describe eToxPred, a new approach to reliably estimate the toxicity and synthetic accessibility of small organic compounds. eToxPred employs machine learning algorithms trained on molecular fingerprints to …

Afobazole Nanoparticles Formulation For Enhanced Therapeutics, Javier Cuevas, Christopher Katnik, Vijaykumar B. Sutariya

USF Patents

A novel nanoparticle drug composition and method of use thereof is presented herein. The nanoparticle drug composition is comprised of at least one nanoparticle carrier, formed from the conjugation of PLGA and PEG, which encapsulates a drug such as afobazole and its derivatives, in a pharmaceutically acceptable carrier. The nanoparticle drug composition may be used to treat various diseases of the central nervous system involving excessive neuronal activity and inflammation such as stroke, Alzheimer's disease and anxiety.

Role Of The Atchafalaya River Basin In Regulating Export Fluxes Of Dissolved Organic Carbon, Nutrients, And Trace Elements To The Louisiana Shelf, Dongjoo Joung, Laodong Guo, Alan M. Shiller

Faculty Publications

The abundance and fluxes of selected dissolved trace elements (TE), nutrients, and dissolved organic carbon (DOC) were quantified in the Atchafalaya River Basin to better understand its influence on the chemical regime of the Louisiana Shelf, a region where bottom water hypoxia occurs annually during late spring to early fall. Water samples were collected from throughout the entire Atchafalaya River Basin including from the Mississippi and Red Rivers as well as basin swamp waters during April and November 2010, and June 2011, which represent “typical” high and low, and “unusual” high river discharges, respectively. Within the total dissolved (< 0.45 µm) pool, most of the TEs were mainly partitioned to the < 0.02 µm dissolved phase with the exception of Cr, Cs, Fe, Pb and Zn which were dominantly in the colloidal (0.02-0.45 µm) phase. In the Atchafalaya River, seasonal concentration variations in nutrients, DOC and most TEs were similar to those in the Mississippi River, reflecting a major contribution of water from the Mississippi River. Contributions of the Red River to the Atchafalaya River’s DOC and nutrients were estimated to be 1-35%, similar to previous estimates for this system. The Red River contribution to the fluxes of Co, Cr, Cs, Fe, Mn, Pb, Rb, and Zn was generally disproportionally high (>20%), …

Climate Change Within A Biome, Tyone Kruse, Lisa Forcier, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White

iLEARN Teaching Resources

In this iLEARN lesson, students will investigate impacts of climate change on the native plants and animals, as well as the fisheries, agriculture, and forestry, within a biome of their choosing, and then develop and refine a solution for one of the impacts resulting from the climate change.

Master-Slave Control Method Of Dexterous Hands Based On Data Glove, Kangjun Pan

Journal of System Simulation

Abstract: With the limitations of artificial intelligence, automatic control, and sensor, the dexterous hand in unstructured environments is still very difficult to achieve fully autonomous operation. A master-slave control method of dexterous hands with the combination of data glove and stepper motors is proposed. By the CybergloveII device, human finger joints’ motion data is gathered in real time, then, the motion data are matched to the dexterous hand’ joints respectively. A communication protocol is designed to transfer the motion data between the PC and the ICB. Lastly, the motion data are transferred to the ICB through a serial interface and …

Volume Rendering For Ct Images Based On 3d Gradient Amplitude, Luo Ming, Shuifa Sun, Liwen Wang, Fangmin Dong

Journal of System Simulation

Abstract: In order to maintain the partial shape characteristics of the three-dimensional space of interest in the process of CT images volume rendering, a transfer function method based on the three dimensional gradient amplitude is proposed. Edge detection and denoising segmentation are employed to obtain the complete edge structure of the interested area. The distance between the image sequences pixels and the edge in the body data is calculated, so that the framework can be formed with the distance data brought into the Kindlmann transfer function. Therefore, a new transfer function is achieved. The comparison experiment with semi-automatic transfer function …

Functional And Structural Studies Of Tolloid-Like 1 Mutants Associated With Atrial-Septal Defect 6., Lukasz Sieron, Marta Lesiak, Izabela Schisler, Zofia Drzazga, Andrzej Fertala, Aleksander L. Sieron

Department of Orthopaedic Surgery Faculty Papers

Inactive mammalian tolloid-like 1 (tll1) and mutations detected in tolloid-like 1 (TLL1) have been linked to the lack of the heart septa formation in mice and to a similar human inborn condition called atrial-septal defect 6 (ASD6; OMIM 613087, formerly ASD II). Previously, we reported four point mutations in TLL1 found in approximately 20% of ASD6 patients. Three mutations in the coding sequence were M182L, V238A, and I629V. In this work, we present the effects of these mutations on TLL1 function. Three recombinant cDNA constructs carrying the mutations and one wild-type construct were prepared and then expressed in HT-1080 cells. …

Biological Determinants Of Physical Activity Across The Life Course: A “Determinants Of Diet And Physical Activity” (Dedipac) Umbrella Systematic Literature Review, Katina Aleksovska, Anna Puggina, Luca Giraldi, Christoph Buck, Con Burns, Greet Cardon, Angela Carlin, Simon Chantal, Donatella Ciarapica, Marco Colotto, Giancarlo Condello, Tara Coppinger, Cristina Cortis, Sara D’Haese, Marieke De Craemer, Andrea Di Blasio, Sylvia Hansen, Licia Iacoviello, Johann Issartel, Pascal Izzicupo, Lina Jaeschke, Martina Kanning, Aileen Kennedy, Fiona Ling, Agnes Luzak, Giorgio Napolitano, Julie Anne Nazare, Camille Perchoux, Tobias Pischon, Angela Polito, Alessandra Sannella, Holger Schulz

Publications

Background: Despite the large number of studies and reviews available, the evidence regarding the biological determinants of physical activity (PA) is inconclusive. In this umbrella review, we summarized the current evidence on the biological determinants of PA across the life course, by pooling the results of the available systematic literature reviews (SLRs) and meta-analyses (MAs). Methods: We conducted an online search on MEDLINE, ISI Web of Science, Scopus, and SPORTDiscus databases up to January 2018. SLRs and MAs of observational studies that investigated the association between biological determinants of PA and having PA as outcome were considered eligible. The extracted …

Choline Is An Intracellular Messenger Linking Extracellular Stimuli To Ip3-Evoked Ca2+ Signals Through Sigma-1 Receptors, Eugen Brailoiu, Sumita Chakraborty, G. Cristina Brailoiu, Pingwei Zhao, Jeffrey L. Barr, Marc A. Ilies, Ellen M. Unterwald, Mary E. Abood, Colin W. Taylor

College of Pharmacy Faculty Papers

Sigma-1 receptors (Sig-1Rs) are integral ER membrane proteins. They bind diverse ligands, including psychoactive drugs, and regulate many signaling proteins, including the inositol 1,4,5-trisphosphate receptors (IP₃Rs) that release Ca²⁺ from the ER. The endogenous ligands of Sig-1Rs are unknown. Phospholipase D (PLD) cleaves phosphatidylcholine to choline and phosphatidic acid (PA), with PA assumed to mediate all downstream signaling. We show that choline is also an intracellular messenger. Choline binds to Sig-1Rs, it mimics other Sig-1R agonists by potentiating Ca²⁺ signals evoked by IP₃Rs, and it is deactivated by metabolism. Receptors, by stimulating PLC and …

Characterization Of Chromatin Interaction In Mammalian Cells, Jufen Zhu

Doctoral Dissertations

Higher-order chromatin organization in cell nucleus is mysterious. Microscopy and high-throughput sequencing technologies have been applied to reveal the connections between genome structure and gene transcription, which is the main topic of my thesis. Higher-order chromatin organization differs across cell types and species, giving an insight into disease genesis and tumorigenesis. Despite an enormous progress has been made recently in epigenomic study, lots of things remain unknown.

My dissertation reviews the current understanding of epigenomics, characterizes chromatin interaction in mammalian cells using different technologies, investigates chromatin reorganization in breast cancer cells, analyzes integrated genomic and epigenomic data in breast cancer …

Data Discovery Paradigms: User Requirements And Recommendations For Data Repositories, Mingfang Wu, Fotis Psomopoulos, Siri Jodha Khalsa, Anita De Waard

Copyright, Fair Use, Scholarly Communication, etc.

As data repositories make more data openly available it becomes challenging for researchers to find what they need either from a repository or through web search engines. This study attempts to investigate data users’ requirements and the role that data repositories can play in supporting data discoverability by meeting those requirements. We collected 79 data discovery use cases (or data search scenarios), from which we derived nine functional requirements for data repositories through qualitative analysis. We then applied usability heuristic evaluation and expert review methods to identify best practices that data repositories can implement to meet each functional requirement. We …

Review Of 3d Facial Expression Acquisition And Modeling Technology, Wang Shan, Xukun Shen, Qinping Zhao

Journal of System Simulation

Abstract: Face is an important biological feature of human. High-fidelity 3D face construction is widely applied and has attracted the attention of researchers for a long time. Now the mature 3D model acquisition still depends on the expensive hardware and controlled lighting environment in the lab. However, academic focus has gradually transformed to researches based on daily living environment and low cost equipment. According to the source of input data, the existing works are divided into two categories: works under controlled environment and uncontrolled environment. Methods are summarized and classified based on the categories. Existing problems and future research directions …

Modeling Of Wheat Ears Growth Based On Bezier Surface, Junxiao Xue, Chenyang Sun, Mingliang Xu, Yin Hui, Haiyu Yu

Journal of System Simulation

Abstract: Simulation model of wheat growth has important theoretical significance and application value for wheat growth regulation and management. Study the growth of wheat ears from heading to maturity. We propose an unified modeling method for the grain, lemma and palea of wheat ears based on Bezier surface. Meanwhile, all the models are re-polygonized so that it can be easier to detect the collision. The method can simulate the growth of wheat ear with relatively high modeling efficiency. Experiment results show that the proposed method has very good modeling effect and the modeling of wheat ear at different growth stages …

Research Of Nonlinear Time Series Prediction Method For Motion Capture, Tianyu Huang, Yunying Guo

Journal of System Simulation

Abstract: In this paper, we study the nonlinear time series prediction method for action capture. A prediction method based on the capture data is studied and implemented by analyzing human motion data to solve the data loss and correction problem caused by sensor failure. Based on this research purpose, the simulation experiment assumes that a sensor in the sequence of actions fails, then uses eight kinds of machine learning methods, and evaluates them with six indexes. The prediction results of different methods are compared and the predicted motions are visualized. Through the experiments, data prediction accuracy by random forest, decision …

Stability Analysis Of Post-Fault Power Angle Based On Relevance Vector Machine, Haiying Li, Zhuocheng Xue

Journal of System Simulation

Abstract: Energy interconnection has become a hot topic in the current research.With the large-scale of new energy into the grid, the safe operation of power system is facing new challenges. On line fast stability analysis is one of the effective ways to solve this problem. Traditional power system transient safety analysis method is difficult to adapt to the on-line analysis, and the further development of large data processing and machine learning provides a new way of thinking. The classification model of relevance vector machine (RVM) based on Bayesian framework is used to design a kind of power angle classification strategy. …