Digital Commons Network^™

Icsdb: An Integrated Database Of Crispr Screens., Ahyoung Choi, Insu Jang, Heewon Han, Min-Seo Kim, Jinhyuk Choi, Jieun Lee, Sung-Yup Cho, Yukyung Jun, Charles Lee, Jaesang Kim, Byungwook Lee, Sanghyuk Lee

Faculty Research 2021

High-throughput screening based on CRISPR-Cas9 libraries has become an attractive and powerful technique to identify target genes for functional studies. However, accessibility of public data is limited due to the lack of user-friendly utilities and up-to-date resources covering experiments from third parties. Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS. DepMap portal itself is an integrated database that includes three large-scale projects of CRISPR screening. We additionally aggregated CRISPR screens from BioGRID ORCS that is a collection of screening …

The Human Phenotype Ontology In 2021., Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M Brower, Tiffany J Callahan, Christopher G Chute, Johanna L Est, Peter D Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L Harris, Michael J Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A Mcmurry, Jillian A Miller, Monica C Munoz-Torres, Rebecca L Peters, Christina K Rapp, Ana M Rath, Shahmir A Rind, Avi Z Rosenberg, Michael M Segal, Markus G Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J Mungall, Melissa A Haendel, Peter N Robinson

Faculty Research 2021

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical …

Myc Regulates Ribosome Biogenesis And Mitochondrial Gene Expression Programs Through Its Interaction With Host Cell Factor-1., Tessa M. Popay, Jing Wang, Clare M. Adams, Gregory Caleb Howard, Simona G. Codreanu, Stacy D. Sherrod, John A. Mclean, Lance R. Thomas, Shelly L. Lorey, Yuichi J. Machida, April M. Weissmiller, Christine M. Eischen, Qi Liu, William P. Tansey

Department of Cancer Biology Faculty Papers

The oncoprotein transcription factor MYC is a major driver of malignancy and a highly validated but challenging target for the development of anticancer therapies. Novel strategies to inhibit MYC may come from understanding the co-factors it uses to drive pro-tumorigenic gene expression programs, providing their role in MYC activity is understood. Here we interrogate how one MYC co-factor, host cell factor (HCF)-1, contributes to MYC activity in a human Burkitt lymphoma setting. We identify genes connected to mitochondrial function and ribosome biogenesis as direct MYC/HCF-1 targets and demonstrate how modulation of the MYC-HCF-1 interaction influences cell growth, metabolite profiles, global …

Kg-Covid-19: A Framework To Produce Customized Knowledge Graphs For Covid-19 Response., Justin T Reese, Deepak Unni, Tiffany J Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent A Shefchek, Benjamin M Good, James P Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L Harris, Monica C Munoz-Torres, Melissa A Haendel, Peter N Robinson, Marcin P Joachimiak, Christopher J Mungall

Faculty Research 2021

Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time-consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community vary drastically for different tasks; the optimal data for a machine learning task, for example, is much different from the data used to populate a browsable user interface for clinicians. To address these challenges, we created KG-COVID-19, a flexible …

Partial Inhibition Of Mitochondrial Complex I Ameliorates Alzheimer's Disease Pathology And Cognition In App/Ps1 Female Mice., Andrea Stojakovic, Sergey Trushin, Anthony Sheu, Layla Khalili, Su-Youne Chang, Xing Li, Trace Christensen, Jeffrey L Salisbury, Rachel E Geroux, Benjamin Gateno, Padraig J Flannery, Mrunal Dehankar, Cory C Funk, Jordan Wilkins, Anna Stepanova, Tara O'Hagan, Alexander Galkin, Jarred Nesbitt, Xiujuan Zhu, Utkarsh Tripathi, Slobodan Macura, Tamar Tchkonia, Tamar Pirtskhalava, James L Kirkland, Rachel A Kudgus, Renee A Schoon, Joel M Reid, Yu Yamazaki, Takahisa Kanekiyo, Song Zhang, Emirhan Nemutlu, Petras Dzeja, Adam Jaspersen, Ye In Christopher Kwon, Michael K Lee, Eugenia Trushina

Articles, Abstracts, and Reports

Alzheimer's Disease (AD) is a devastating neurodegenerative disorder without a cure. Here we show that mitochondrial respiratory chain complex I is an important small molecule druggable target in AD. Partial inhibition of complex I triggers the AMP-activated protein kinase-dependent signaling network leading to neuroprotection in symptomatic APP/PS1 female mice, a translational model of AD. Treatment of symptomatic APP/PS1 mice with complex I inhibitor improved energy homeostasis, synaptic activity, long-term potentiation, dendritic spine maturation, cognitive function and proteostasis, and reduced oxidative stress and inflammation in brain and periphery, ultimately blocking the ongoing neurodegeneration. Therapeutic efficacy in vivo was monitored using translational …

Prognostic Gene Expression Signatures Of Breast Cancer Are Lacking A Sensible Biological Meaning., Kalifa Manjang, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer, Galina Glazko, Frank Emmert-Streib

Articles, Abstracts, and Reports

The identification of prognostic biomarkers for predicting cancer progression is an important problem for two reasons. First, such biomarkers find practical application in a clinical context for the treatment of patients. Second, interrogation of the biomarkers themselves is assumed to lead to novel insights of disease mechanisms and the underlying molecular processes that cause the pathological behavior. For breast cancer, many signatures based on gene expression values have been reported to be associated with overall survival. Consequently, such signatures have been used for suggesting biological explanations of breast cancer and drug mechanisms. In this paper, we demonstrate for a large …

Gardner-Webb University Prepares To Welcome Students Back To Campus, Office Of University Communications

Gardner-Webb NewsCenter Archive

Gardner-Webb University faculty and staff are preparing to welcome back more than 1,750 residential, undergraduate and graduate students who will attend face-to-face classes on the Boiling Springs campus for the spring semester. Equipped with information learned during the fall, David S. Wacaster, director of operations for GWU Facilities and Maintenance, along with the Daily COVID Team, are implementing new testing requirements and disinfecting procedures before the first day of classes on Jan. 13.

Small Molecule Inhibitors Of The Bacterioferritin (Bfrb)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas Aeruginosa Cells, Anabel Soldano, Huili Yao, Achala N.D. Punchi Hewage, Kevin Meraz, Joel K. Annor-Gyamfi, Richard A. Bunce, Kevin P. Battaile, Scott Lovell, Mario Rivera

Faculty Publications

© 2020 American Chemical Society. Bacteria depend on a well-regulated iron homeostasis to survive adverse environments. A key component of the iron homeostasis machinery is the compartmentalization of Fe3+ in bacterioferritin and its subsequent mobilization as Fe2+ to satisfy metabolic requirements. In Pseudomonas aeruginosa Fe3+ is compartmentalized in bacterioferritin (BfrB), and its mobilization to the cytosol requires binding of a ferredoxin (Bfd) to reduce the stored Fe3+ and release the soluble Fe2+. Blocking the BfrB-Bfd complex in P. aeruginosa by deletion of the bfd gene triggers an irreversible accumulation of Fe3+ in BfrB, concomitant cytosolic iron deficiency and significant impairment …

Trudging Through The Brakes: Mapping River Cane (Arundinaria Gigantea (Walter) Muhl.) And Canebrake Habitat In 19th Century Arkansas, Patrick Solomon

Theses and Dissertations

River cane (A. gigantea) is one of three bamboos native to the North American continent but has been greatly diminished since European colonization. To explore this lost landscape, this paper applies an interdisciplinary approach to examine and interpret the pre-historic, historic, and current status of cane and canebrake habitat in Arkansas. Historic cane data has been collected and used to create an informed map of canebrake habitat in 19th century Arkansas. To examine references in more detail, cane points collected within the five study areas have been examined using a Geographic Information System. Maps of historic cane references have been …

The Mouse Gene Expression Database (Gxd): 2021 Update., Richard M. Baldarelli, Constance M. Smith, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. Mccright, Jingxia Xu, David R. Shaw, Jonathan S Beal, Olin Blodgett, Jeff Campbell, Lori E. Corbani, Pete J. Frost, Sharon C Giannatto, Dave Miers, James A. Kadin, Joel E Richardson, Martin Ringwald

Faculty Research 2021

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded …

The Gene Ontology Resource: Enriching A Gold Mine., Gene Ontology Consortium, Judith A. Blake, Mary E. Dolan, Harold J. Drabkin, David P. Hill

Faculty Research 2021

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles …

Mouse Genome Database (Mgd): Knowledgebase For Mouse-Human Comparative Biology., Judith A. Blake, Richard M. Baldarelli, James A. Kadin, Joel E Richardson, Cynthia Smith, Carol J Bult, Mouse Genome Database Group

Faculty Research 2021

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological reference data related to mouse genes, gene functions, phenotypes and mouse models of human disease. MGD is the primary source for official gene, allele, and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. MGD's biocuration scientists curate information from the biomedical literature and from large and small datasets contributed …

Performance Evaluation And Enhancement Of Medical Imaging Using Plasmonic Gold Nanostars., Kholoud Abdelhady, Hossam El-Din Moustafa, Bedir B. Yousif

Mansoura Engineering Journal

This paper gives insights about examinations of plasmonic nanoparticles (NPs) and particularly gold nanostar as sign enhancer and contrast agent for clinical imaging and the optical properties of (NPs) of different volume and morphology and the encompassing medium were stood out from affirm that the gold nanostars are the best shape that can scatter the light, thusly obtaining better and all the clearest clinical imaging. Stars formed gold nanoparticles have a greater surface comparative with its volume and contact surface cross section than spherical and rods shaped nanoparticles, and accordingly act even more firmly as a radiation enhancer. At that …

Dopamine D2 Long Receptors Are Critical For Caveolae-Mediated Α-Synuclein Uptake In Cultured Dopaminergic Neurons, Ichiro Kawahata, Tomoki Sekimori, Haoyang Wang, Yanyan Wang, Toshikuni Sasaoka, Luc Bousset, Ronald Melki, Tomohiro Mizobata, Yasushi Kawata, Kohji Fukunaga

Pharmacy Faculty Publications and Presentations

Abstract: α-synuclein accumulation into dopaminergic neurons is a pathological hallmark of Parkinson's disease. We previously demonstrated that fatty acid-binding protein 3 (FABP3) is critical for α-synuclein uptake and propagation to accumulate in dopaminergic neurons. FABP3 is abundant in dopaminergic neurons and interacts with dopamine D2 receptors, specifically the long type (D2L). Here, we investigated the importance of dopamine D2L receptors in the uptake of α-synuclein monomers and their fibrils. We employed mesencephalic neurons derived from dopamine D2L --/--, dopamine D2 receptor null (D2 null), FABP3--/--, and wild type C57BL6 mice, and analyzed the uptake ability of fluorescence-conjugated α-synuclein monomers and …

Floral Color Properties Of Serpentine Seep Assemblages Depend On Community Size And Species Richness, Kathryn A. Lecroy, Gerardo Arceo-Gómez, Matthew H. Koski, Nathan I. Morehouse, Tia L. Ashman

ETSU Faculty Works

Functional traits, particularly those that impact fitness, can shape the ecological and evolutionary relationships among coexisting species of the same trophic level. Thus, examining these traits and properties of their distributions (underdispersion, overdispersion) within communities can provide insights into key ecological interactions (e.g., competition, facilitation) involved in community assembly. For instance, the distribution of floral colors in a community may reflect pollinator-mediated interactions between sympatric plant species, and the phylogenetic distribution of color can inform how evolutionary contingencies can continue to shape extant community assemblages. Additionally, the abundance and species richness of the local habitat may influence the type or …

Fibulin-2: A Novel Biomarker For Differentiating Grade Ii From Grade I Meningiomas, Agbolahan A. Sofela, David A. Hilton, Sylwia Ammoun, Daniele Baiz, Claire L. Adams, Emanuela Ercolano, Michael D. Jenkinson, Kathreena M. Kurian, Mario Teo, Peter C. Whitfield, Felix Sahm, C. Oliver Hanemann

Peninsula Medical School

There is an unmet need for the identification of biomarkers to aid in the diagnosis, clinical management, prognosis and follow-up of meningiomas. There is currently no consensus on the optimum management of WHO grade II meningiomas. In this study, we identified the calcium binding extracellular matrix glycoprotein, Fibulin-2, via mass-spectrometry-based proteomics, assessed its expression in grade I and II meningiomas and explored its potential as a grade II biomarker. A total of 87 grade I and 91 grade II different meningioma cells, tissue and plasma samples were used for the various experimental techniques employed to assess Fibulin-2 expression. The tumours …

Integrated Genetic And Metabolic Landscapes Predict Vulnerabilities Of Temozolomide Resistant Glioblastoma Cells., Selva Rupa Christinal Immanuel, Avinash D Ghanate, Dharmeshkumar S Parmar, Ritu Yadav, Riya Uthup, Venkateswarlu Panchagnula, Anu Raghunathan

Articles, Abstracts, and Reports

Metabolic reprogramming and its molecular underpinnings are critical to unravel the duality of cancer cell function and chemo-resistance. Here, we use a constraints-based integrated approach to delineate the interplay between metabolism and epigenetics, hardwired in the genome, to shape temozolomide (TMZ) resistance. Differential metabolism was identified in response to TMZ at varying concentrations in both the resistant neurospheroidal (NSP) and the susceptible (U87MG) glioblastoma cell-lines. The genetic basis of this metabolic adaptation was characterized by whole exome sequencing that identified mutations in signaling pathway regulators of growth and energy metabolism. Remarkably, our integrated approach identified rewiring in glycolysis, TCA cycle, …

The Dark Kinase Knowledgebase: An Online Compendium Of Knowledge And Experimental Results Of Understudied Kinases, Matthew E. Berginski, Nienke Moret, Changchang Liu, Dennis Goldfarb, Peter K. Sorger, Shawn M. Gomez

Open Access Publications

Kinases form the backbone of numerous cell signaling pathways, with their dysfunction similarly implicated in multiple pathologies. Further facilitated by their druggability, kinases are a major focus of therapeutic development efforts in diseases such as cancer, infectious disease and autoimmune disorders. While their importance is clear, the role or biological function of nearly one-third of kinases is largely unknown. Here, we describe a data resource, the Dark Kinase Knowledgebase (DKK; https://darkkinome.org), that is specifically focused on providing data and reagents for these understudied kinases to the broader research community. Supported through NIH's Illuminating the Druggable Genome (IDG) Program, the DKK …

Development Of Artificial Neural Network Models For Predicting Lipid Profile Using Smartmf Electrical Parameters, Ahmad Zulkhairi Zulkefl

Student Works (2020-2029)

This research project aims in the development of artificial neural network (ANN) to classify lipid profile parameters; total cholesterol (TC), triglycerides (TG), high density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) by utilizing a non-invasive bioelectrical impedance analysis (BIA) device (SmartMF). Data were obtained from volunteer patients requiring lipid profile testing at the primary care department of University Malaya Medical Centre (UMMC). The data were divided into two categories for each lipid profile parameters, normal and abnormal. Statistical analysis including T-Test and logistic regression analysis for the bioelectrical parameters were employed to understand the data and determine suitable predictors …

Assessment Of Monochloramine Toxicity On Three Small Coastal Organisms, Ashley K. Le

All HCAS Student Capstones, Theses, and Dissertations

Monochloramine ( is a secondary disinfectant used by water treatment facilities to eliminate lingering bacteria in basins, filters, and pipelines. While an effective disinfectant, monochloramine can have negative effects on aquatic organisms. Organis ms affected by the chemical can include species whose environment is near to effluent sites and aquaculture facilities that use tap water lines or has water intake pipes near to effluent sites. Three species commonly found in south Florida that are lik ely exposed to MCA by effluent sites or aquaculture facilities are mosquitofish Gambusia affinis pink shrimp Farfantepenaeus duorarum and the hard clam Mercenaria mercenaria These …

An Evaluation Of The Indian Chemical Science Research Publications Output Of The Last Two Decades (2000 – 2019), Mahadevi Nyamagoudar, Gavisiddappa Anandhalli

Library Philosophy and Practice (e-journal)

This study evaluates the Indian chemical science research output of the last two decades (2000 to 2019). We have made a scientometric analysis of contributions from India in leading chemical science journals over 20 years period 2000 – 2019. We have compared India’s performance with that of the USA. The data was sourced from the Scopus database during 2000 – 19. The study finds that the research output of the world in chemical science research was 76, 08,260 publications and it was 469,689 publications by India, accounting for 6.1% global publications share in a 20 years window covering the period …

Simultaneous Determination Of Purine Derivatives And Creatinine In Ruminant Urine By Hplc, F. L. Yang, Ruijun Long, H. C. Wang, X. P. Li

IGC Proceedings (1977-2023)

No abstract provided.

Suitable Grazing Methods For The Stipa Bungeana Grassland In Southern Ningxia Foothills, Jinhua Wang, Binyu Zhang, Chengjiang Dai, Shouding Shi

IGC Proceedings (1977-2023)

No abstract provided.

The Role Of Functional Plant In Sheep Foraging, Ling Wang, Guowei Chen, Xiao Shun, Deli Wang

IGC Proceedings (1977-2023)

No abstract provided.

Chronic Traumatic Encephalopathy: Mental Disease Or Defect That Can Trigger A Successful Criminal Defense, Thomas Mosczczynski

Journal of Civil Rights and Economic Development

(Excerpt)

When he was a child, he was called kind, gentle and even sweet. He started playing football at a young age that ripened into a successful high school career that lasted from 2004 to 2007. He was a dominant force on the gridiron under the Friday night lights as he played both offense and defense—rarely missing a play. College scouts took notice, and suddenly, the world was his oyster. A small-town kid from Bristol, Connecticut became the talk of college recruiters across the country. In 2007, a year after the death of his father, the quiet kid from Bristol …

Navigating Surrogacy Law In The Non-United States: Why All States Should Adopt A Uniform Surrogacy Statute, Stephanie Canner

Journal of Civil Rights and Economic Development

(Excerpt)

“My water broke; the baby is coming! Come now!” Normally, a woman in labor makes this frantic phone call to her partner, who would immediately drop whatever they were doing to be by her side at the local hospital and be present to welcome their child into the world. However, this scenario is not the reality for many couples across the United States. For example, there is a New York couple who have a different story to tell their daughter about her birth. Brad Hoylman and David Sigal received a phone call a month before their baby’s due date …

Creativity And Covid-19, Sarah Moss

The Voice

No abstract provided.

Dordt Records Fall Enrollment High Despite Uncertain Times, Sarah Moss

The Voice

No abstract provided.

The Perfect Puff, Briana Williams

CLAMANTIS: The MALS Journal

No abstract provided.

Queer Timelines For Justice, Sarah Koppelkam

CLAMANTIS: The MALS Journal

No abstract provided.