Digital Commons Network^™

Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman

Publications and Research

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …

The Effect Of Deep Oceanic Flushing On Water Properties And Ecosystem Functioning Within Atolls In The British Indian Ocean Territory, Emma V. Sheehan, Phil Hosegood, Chloe A. Game, Martin J. Attrill, David Tickler, Marianne Wootton, David G. Johns, Jessica J. Meeuwig

School of Biological and Marine Sciences

No abstract provided.

The Influence Of Neighborhood Landscape Characteristics On Native Bird Communities: Implications For Increasing Biodiversity In Our Yards, Michael E. Vermeulen

Dissertations and Theses

Avian communities, because of their potential high diversity, are ideal for studying the response to potential quantity of resources provided by local and regional habitat. Urban neighborhoods vary in types and magnitudes of anthropogenic stressors they experience, resulting in a continuum of anthropogenic disturbance, often referred to as a gradient of urbanization. The aim of this study was to investigate anthropogenic drivers of urban bird communities in three Portland, OR neighborhoods (Hillsdale, Lents, and Pearl). The three major questions of this study were: 1) What are the significant landscape traits that characterize the neighborhoods? 2) Is there evidence that the …

Ohio University Receives $1.7 Million Grant To Study Potential Prevention And Treatment For Non-Melanoma Skin Cancers (August 20, 2019), University Communications And Marketing

OHIO News Articles Archive

No abstract provided.

Ohio Professor Saw-Wai Hla Develops Robust Molecular Propeller That Enables Unidirectional Rotations (August 20, 2019), University Communications And Marketing

OHIO News Articles Archive

No abstract provided.

Supervised Walking Exercise Therapy Improves Gait Biomechanics In Patients With Peripheral Artery Diseas, Molly Schieber, Iraklis Pipinos, Jason M. Johanning, George P. Casale, Mark A. Williams, Holly Despiegelaere, Ben Senderling, Sara A. Myers

Journal Articles

Objective

Methods

Seskuiterpenoid Prostanterol Dari Kulit Batang Dysoxylum Excelsum, Tri Mayanti, Achmad Zainuddin, Sylvia Rachmawati Meilanie, Euis Julaeha, Jamaluddin Al Anshori

Chimica et Natura Acta

Dysoxylummerupakan genus besar dari Famili Meliaceae yang terdistribusi di Indonesia. Beberapa spesies Dysoxylum telah dilaporkan mengandung senyawa seskuiterpenoid. Pada penelitian ini, satu senyawa seskuiterpenoid trisiklik, prostanterol (1) telah diisolasi kulit batang Dysoxylum excelsum. Senyawa 1 untuk pertama kali diisolasi dari tumbuhan tersebut. Struktur molekul senyawa 1 ditentukan melalui spektroskopi NMR 1D dan 2D yang dibandingkan terhadap data yang telah dilaporkan sebelumnya.

Prospects For The Sustainable Management Of Public Oyster Resources, Thomas M. Soniat, Nathan A. Cooper, Eric N. Powell

Faculty Publications

Common-pool resources such as public oyster grounds are especially vulnerable to overexploitation and habitat loss. Like those elsewhere, oyster populations and habitat of Louisiana public grounds are in decline. To maintain reef habitat and increase oyster abundance, a sustainable harvest model is applied, which allows harvest above that required to maintain reef cultch stasis. The model is restrained to promote shell gain by limiting fishing by area, type (sack versus seed), effort, and season. Harvest quotas and cultch removal rates derived from shell-budget–based modeling are a foundation for sustainable management of public oyster resources.

Development Of Functionalized Imidazoles As Potential Therapeutical Agents, Drew Christopher Morgan

Theses and Dissertations

Imidazoles are heterocyclic small molecules that play a major role in medicinal chemistry and drug discovery. There are several drugs in the market which contain imidazoles as the pharmacophore. Metronidazole, an imidazole containing compound, is a prominent antibiotic and antiprotozoal medication used for the treatment of a variety of infections such as amoebiasis, trichomoniasis, bacterial vaginosis, etc. The current work involves the synthesis of small molecule libraries of imidazoles derived from metronidazole using Baylis-Hillman (BH) reaction. BH reaction is a carbon-carbon bond forming reaction and involves the coupling of aldehydes or imines with activated alkenes such as acrylates, acrolein, or …

Efficacy And Safety Of Intravenous Golimumab Plus Methotrexate In Patients With Rheumatoid Arthritis Aged < 65 Years And Those ≥ 65 Years Of Age., John Tesser, Shelly Kafka, Raphael J. Dehoratius, Stephen Xu, Elizabeth C Hsia, Anthony Turkiewicz

Department of Pharmacology and Experimental Therapeutics Faculty Papers

OBJECTIVE: To evaluate the safety and efficacy of intravenous golimumab + methotrexate (MTX) in patients with active rheumatoid arthritis (RA) aged < 65 years and those ≥ 65 years who were enrolled in the GO-FURTHER study.

METHODS: In the phase III, double-blind, randomized, placebo-controlled GO-FURTHER trial, patients with active RA were randomized to intravenous (IV) golimumab 2 mg/kg + MTX or placebo + MTX at weeks 0 and 4, then every 8 weeks thereafter (with crossover to golimumab at week 16 [early escape] or week 24 [per-protocol]). The final golimumab infusion was at week 100. Assessments included American College of Rheumatology (ACR) 20/50/70 response criteria. Efficacy and adverse events (AEs) were monitored through 2 years. …

Such News Of The Land: U.S. Women Nature Writers, Thomas S. Edwards, Elizabeth A. Dewolfe

History Faculty Books

This pathbreaking collection, which contains 19 essays from scholars in a variety of fields, illuminates the work of two centuries of American women nature writers. Some discuss traditional nature writers such as Susan Fenimore Cooper, Mary Austin, Gene Stratton Porter, and Annie Dillard. Others examine the work of Zora Neale Hurston, Gloria Anzaldua, and Leslie Marmon Silko, writers not often associated with this genre. Essays on germinal texts such as Marjory Stoneman Douglas's The Everglades: River of Grass stand alongside examinations of market bulletins and women's gardens, showing how the rich diversity of women's nature writing has shaped and expanded …

Engineered Fgf Compositions And Methods Of Use Thereof, Thallapuranam Krishnaswamy Suresh Kumar, David A. Zaharoff, Srinivas Jayanthi, Bhanuprasanth Koppolu, Rebecca Kerr, Kartik Balachandran, David S. Mcnabb

Patents Granted

The present invention relates to the development of stable mutants of FGF-1 and FGF-2. In particular, it relates to novel engineered FGF-1 and FGF-2 polypeptides as well as polynucleotides, DNA constructs, and vectors encoding such polypeptides. In another aspect, pharmaceutical compositions and hydrogels including the disclosed polypeptides, polynucleotides, DNA constructs, and vectors are provided. In a still further aspect, methods of treating conditions using the compositions disclosed herein are provided.

Texture-Based Deep Neural Network For Histopathology Cancer Whole Slide Image (Wsi) Classification, Nelson Zange Tsaku

Master of Science in Computer Science Theses

Automatic histopathological Whole Slide Image (WSI) analysis for cancer classification has been highlighted along with the advancements in microscopic imaging techniques. However, manual examination and diagnosis with WSIs is time-consuming and tiresome. Recently, deep convolutional neural networks have succeeded in histopathological image analysis. In this paper, we propose a novel cancer texture-based deep neural network (CAT-Net) that learns scalable texture features from histopathological WSIs. The innovation of CAT-Net is twofold: (1) capturing invariant spatial patterns by dilated convolutional layers and (2) Reducing model complexity while improving performance. Moreover, CAT-Net can provide discriminative texture patterns formed on cancerous regions of histopathological …

Blood Leukocyte Dna Methylation Predicts Risk Of Future Myocardial Infarction And Coronary Heart Disease, Golareh Agha, Michael M Mendelson, Cavin K Ward-Caviness, Roby Joehanes, Tianxiao Huan, Rahul Gondalia, Elias Salfati, Jennifer A Brody, Giovanni Fiorito, Jan Bressler, Brian H Chen, Symen Ligthart, Simonetta Guarrera, Elena Colicino, Allan C Just, Simone Wahl, Christian Gieger, Amy R Vandiver, Toshiko Tanaka, Dena G Hernandez, Luke C Pilling, Andrew B Singleton, Carlotta Sacerdote, Vittorio Krogh, Salvatore Panico, Rosario Tumino, Yun Li, Guosheng Zhang, James D Stewart, James S Floyd, Kerri L Wiggins, Jerome I Rotter, Michael Multhaup, Kelly Bakulski, Steven Horvath, Philip S Tsao, Devin M Absher, Pantel Vokonas, Joel Hirschhorn, M Daniele Fallin, Chunyu Liu, Stefania Bandinelli, Eric Boerwinkle, Abbas Dehghan, Joel D Schwartz, Bruce M Psaty, Andrew P Feinberg, Lifang Hou, Luigi Ferrucci, Nona Sotoodehnia, Giuseppe Matullo, Annette Peters, Myriam Fornage, Themistocles L Assimes, Eric A Whitsel, Daniel Levy, Andrea A Baccarelli

Faculty, Staff and Student Publications

BACKGROUND: DNA methylation is implicated in coronary heart disease (CHD), but current evidence is based on small, cross-sectional studies. We examined blood DNA methylation in relation to incident CHD across multiple prospective cohorts.

METHODS: Nine population-based cohorts from the United States and Europe profiled epigenome-wide blood leukocyte DNA methylation using the Illumina Infinium 450k microarray, and prospectively ascertained CHD events including coronary insufficiency/unstable angina, recognized myocardial infarction, coronary revascularization, and coronary death. Cohorts conducted race-specific analyses adjusted for age, sex, smoking, education, body mass index, blood cell type proportions, and technical variables. We conducted fixed-effect meta-analyses across cohorts.

RESULTS: Among …

Mucosal Infection Rewires Tnfɑ Signaling Dynamics To Skew Susceptibility To Recurrence, Lu Yu, Valerie P. O'Brien, Jonathan Livny, Denise Dorsey, Nirmalya Bandyopadhyay, Marco Colonna, Michael G. Caparon, Elisha D.O. Roberson, Scott J. Hultgren, Thomas Hannan

Open Access Publications

A mucosal infectious disease episode can render the host either more or less susceptible to recurrent infection, but the specific mechanisms that tip the balance remain unclear. We investigated this question in a mouse model of recurrent urinary tract infection and found that a prior bladder infection resulted in an earlier onset of tumor necrosis factor-alpha (TNFɑ)-mediated bladder inflammation upon subsequent bacterial challenge, relative to age-matched naive mice. However, the duration of TNFɑ signaling activation differed according to whether the first infection was chronic (Sensitized) or self-limiting (Resolved). TNFɑ depletion studies revealed that transient early-phase TNFɑ signaling in Resolved mice …

Development Of Predictive Model For Helper T Lymphocyte Epitope Binding To Hladrb1* 01:01, Ari Hardianto, Muhammad Yusuf

Chimica et Natura Acta

Epitopes are essential peptides for immune system stimulation, such as governing helper T lymphocyte (HTL) activation via antigen presentation and recognition. Current predictive models for epitope selection mainly rely on the antigen presentation, although HTLs only recognize 50% of the presented peptides. Thus, we developed a HTL epitope predictor which involves the antigen recognition step. The predictor is specific for epitopes presented by Human Leukocyte Allele (HLA)-DRB1*01:01, which is protective against developing multiple sclerosis and association with autoimmune diseases. As the data set, we used binding register of immunogenic and non-immunogenic HTL peptides related to HLA-DRB1*01:01. The binding registers were …

Pengaruh Persentase Pva-Alginat Beads Terhadap Tingkat Dekolorisasi Pewarna Sintetis Azo Menggunakan Konsorsium Bakteri Amobil, Christina Ekawati Halim, Kezia Abib Yerah Tjandra, Venisa Yosephi, Agustin Krisna Wardani

Chimica et Natura Acta

Pewarna merupakan salah satu komponen dalam industri tekstil yang sangat penting. Salah satu senyawa pewarna seperti pewarna Azo pada limbah cair tekstil memiliki bahan pencemar yang berbahaya bagi lingkungan. Dekolorisasi pewarna menggunakan metode fisik dan kimia membutuhkan biaya yang tinggi dan masih menghasilkan hasil samping yang beracun, sehingga diperlukan pendekatan dekolorisasi menggunakan metode biologis yang lebih ramah lingkungan dengan memanfaatkan konsorsium bakteri seperti Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli dan Bacillus subtilis. Konsorsium bakteri diimobilisasi menggunakan beads dengan variasi perbandingan PVA-alginat 8:1, 10:1, dan 12:1. Pengujian menunjukkan bahwa komposisi PVA dan alginat mempengaruhi kemampuan dekolorisasi pewarna sintetis azo. Parameter yang …

Produksi Dan Pemurnian Human Epidermal Growth Factor (Hegf) Rekombinan Menggunakan Metode Heat Treatment, Fraksionasi Amonium Sulfat Dan Kromatografi Filtrasi Gel, Iman Permana Maksum, Alifa I. Nabila, Sunan M. Alpiansyah, Sriwidodo Sriwidodo, Toto Subroto

Chimica et Natura Acta

Human Epidermal Growth Factor (hEGF) adalah suatu protein yang membantu dalam proses penyembuhan luka, dalam hal proses proliferasi, migrasi dan diferensiasi sel. Protein hEGF dengan tingkat kemurnian tinggi sangat diperlukan agar mencapai aktivitas yang maksimal untuk pengaplikasian sebagai protein terapeutik. Tujuan penelitian ini adalah untuk mengetahui karakteristik hEGF rekombinan setelah pemurnian menggunakan metode heat treatment, fraksionasi amonium sulfat dan kromatografi filtrasi gel, dan menentukan kadar protein hEGF setelah dimurnikan dengan metode ELISA dan Lowry. Metode pertama yang digunakan pada penelitian ini adalah produksi protein hEGF skala fermentor pada sel inang E. coli. Hasil produksi kemudian disentrifugasi. Supernatan hasil ekspresi selanjutnya …

Optimasi Ekspresi Human Epidermal Growth Factor (H-Egf) Rekombinan Dalam Escherichia Coli Bl21(De3) Dengan Variasi Media Dan Konsentrasi Penginduksi, Riyona Desvy Pratiwi

Chimica et Natura Acta

Epidermal growth factor (EGF) merupakan protein yang sangat penting dalam proliferasi, diferensiasi, dan pematangan sel. EGF sintetik atau recombinant human EGF (rh-EGF) telah digunakan secara klinis untuk mengatasi kondisi kekurangan EGF alami seperti mempercepat pemulihan luka pada penderita diabetes dan teravaksin untuk pengobatan kanker paru. Ekspresi rh-EGF dilaporkan tidak mudah karena protein ini sensitif terhadap proteolisis intraselular. Kondisi yang optimal sangat diperlukan untukekpsresi rh-EGF agar diperoleh protein dalam jumlah yang tinggi. Hingga saat ini, sejumlah studi ekspresi rh-EGF telah dilaporkan, namun harus difusi dengan protein peningkat solubilitas. Pada penelitian ini, rh-EGF berhasil diekspresikan, meskipun tanpa protein peningkat solubilitas. Ekspresi rh-EGF …

Editorial: Cancer Ecosystems., Ubaldo E. Martinez-Outshoorn, Mireia Bartrons, Ramon Bartrons

Department of Medical Oncology Faculty Papers

No abstract provided.

Research On Foreign Member System Of The Chinese Academy Of Engineering, Zhu Yu, Zhao Qian, Wu Xiaodong

Bulletin of Chinese Academy of Sciences (Chinese Version)

The foreign member of the Chinese Academy of Engineering (CAE) is an important part of China's talents team building and the influential force in the construction of the think tank. Strengthening the team building of foreign members is an important channel to promote international academic and scientific exchanges, utilize international high-end intellectual resources, and serve the country's scientific and technological development and diplomatic strategy. This study comprehensively analyzes the origin of the foreign member system, and the status quo of the foreign member system of CAE. Through case studies, it has also researched on the working mechanism to ensure the …

Long-Term Monitoring And Field Control Experiments Reveal The Structure, Function And Evolution Of Typical Temperate Forests, Zheng Xingbo, Yu Dapao, Wang Anzhi, Dai Guanhua

Bulletin of Chinese Academy of Sciences (Chinese Version)

The temperate forest ecosystem in China is an important part of the ecological barrier in Northeast China. It not only breeds abundant biodiversity, but also is an important timber resource cultivation base and an important support for China to cope with climate change. Due to unreasonable over-harvesting and utilization, the structure and function of temperate mixed forests have been seriously affected, which has significantly affected the regional ecological security. The Research Station of Changbai Mountain Forest Ecosystem, Chinese Academy of Sciences (Changbai Mountain Station), takes revealing the structure, function, and evolution process of the original broad-leaved Korean pine forest in …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Professor wins Jean Dreyfus Lectureship Grant
• Dr. Wu wins the University Excellence in Research Award 2019-20

Establishing A Monitoring Program To Estimate Urban Parrot Populations In San Diego, Maisy Feeley, Maxwell Johnson

Creative Collaborations: Annual Showcase of Undergraduate Research

Though parrots from Mexico, South and Central America, and other countries have become naturalized in Southern California, their presence is not reflected by ample study or literature. The impacts of these non-native species on their new environment are thus unknown. The urban environments of Southern California serve as residence of at least thirteen parrot species. Given there is no standard protocol for surveys of introduced parrots, we will estimate population size by conducting point-counts with a double-observer dependent approach. This approach will increase detection probability and decrease duplicate or false detections. The primary and secondary observer will alternate between point-counts …

Sediment Grain Size And Organic Matter As Indicators For Benthic Meiofauna Community Composition And Distribution In Mission Bay, San Diego, Leslie Gobel

Creative Collaborations: Annual Showcase of Undergraduate Research

As a prime source of revenue for the tourist industry in San Diego, Mission Bay is a crucial part of the city?s economy. Therefore, it is important to understand how certain factors, both natural and anthropogenic, could alter the ecological health of the bay for both marine organisms and humans. As an extension of an ongoing project studying the benthic composition of Mission Bay, my project focused on how benthic meiofaunal communities vary in abundance and diversity spatially throughout the bay in response to abiotic factors such as organic matter and grain size. Using sediment samples dyed with Rose Bengal, …

The Influence Of Great White Shark Size Behavior Near A Chumming Vessel, Kaitlin Gasper

Creative Collaborations: Annual Showcase of Undergraduate Research

Chumming for Great White Sharks: Investigating how Shark Size Influences Interaction with Chumming Vessels This study was performed through field observation of the white shark population around a Cape Fur Seal colony in Mosselbaai, South Africa. Behavior between different sized great white sharks around a baited vessel was investigated during a two-month period during winter 2018. It was hypothesized that smaller white sharks would interact with a chumming vessel more frequently than larger sharks. Data was collected from a research vessel using bait heads and chum to attract sharks to the boat. Shark interaction was classified by how long the …

A Signal Transduction Pathway To Motility In Rhodospirillum Centenum, Julia Roccato

Creative Collaborations: Annual Showcase of Undergraduate Research

Bacteria cover our Earth in abundance, from any environmental niche right to our human body. Of particular importance are bacteria that can form either vegetative cells or hardy, dormant cyst cells depending upon environmental conditions. This study aims to elucidate more of the signal transduction pathway leading to motility in the bacterial species Rhodospirillum centenum to better understand the complicated genetic basis of encystment and motility. The current model pathway in R. centenum follows a histidine kinase and response regulator pattern, with the phosphorylation of the CtrA protein ultimately promoting motility genes. By studying a related bacterium, Caulobacter crescentus, additional …

Is Metal Toxicity Effect On Ion Regulation Similar To Ph Toxicity In Amazonian Fish?, Jad Shami

Creative Collaborations: Annual Showcase of Undergraduate Research

Metal toxicity was investigated in two pH tolerant species of cichlids, Tapajos cichlids (Geophagussp.) and Oscars (Astronotus ocellatus) from the Rio Negro, an ion-poor acidic blackwater water. We measured rates of Na+uptake and loss during exposure to dissolved copper, and silver. Exposure of Tapajos cichlids to 1000 µg/L Cu2+ inhibited Na+ ?influx by 45.5% and stimulated Na+ efflux by 23.9%. Exposure to 1 µM Ag+completely inhibited Na+ ?influx of Tapajos while increasing efflux threefold, and 200 mg/L Ni2+ increased efflux by 43.8%. These metals and others will be looked at on Astronotus ocellatus. These results indicate cichlids show high resistance …

Ecological Effectiveness Of Protected Areas In Tarangire-Manyara Ecosystem, Northern Tanzania, Francesca Spruiell

Creative Collaborations: Annual Showcase of Undergraduate Research

Protected areas in Tanzania, while plentiful, are not routinely monitored. So, little insight into the areas? successes or failures in the meeting of their goals for animal population maintenance is produced. This study assessed the conservation efforts of protected areas in the Tarangire-Manyara ecosystem through the monitoring of population densities of five species: elephant (Loxodonta africana), giraffe (Giraffa tippelskirchi), zebra (Equus quagga), wildebeest (Connochaetes), impala (Aepyceros melampus). We drove terrestrial line transects seasonally- dry, long rains, and short rains- from 2011 to 2018 in four conservation areas of varying protection levels: Tarangire National Park and Lake Manyara National Park, Manyara …

Selective Serotonin-Reuptake Inhibitors (Ssris): Mechanism For Treatment Of Depression And Relationship With Suicide Risk, Erin Carollo

Creative Collaborations: Annual Showcase of Undergraduate Research

In 2017, suicide was found to be the second leading cause of death for people aged 10 - 34 in the United States. At least 90% of suicides are found to be comorbid with mental illness, most commonly: depression. Research suggests depression develops due to a combination of environmental, psychological, and biological factors. Imbalances in neurotransmitters, specifically serotonin (5-HT), is one of the leading hypotheses for the biochemical basis of depression. On this basis, selective serotonin reuptake inhibitors (SSRIs) are the most commonly prescribed antidepressant and have been shown to be an effective treatment for moderate to severe depression. However, …