Digital Commons Network^™

Deep Learning Based Models For Drug-Target Interactions, Ali K. Abdul Raheem, Ban N. Dhannoon

Baghdad Science Journal

The typical drug development approach is slow, costly, and fraught with failure - scientists examine millions of compounds, but only a few make it to preclinical or clinical testing. Machine learning (ML), a subset of AI, is a fast-expanding subject many pharmaceutical businesses increasingly utilize. Incorporating machine learning technologies into the drug development process can aid in automating repetitive data processing and analysis processes. ML techniques may be used at several stages of drug development, including drug property prediction, drug-target interaction (DTI) prediction, and De Novo drug design. DTIs are a critical component of the drug development process. When a …

An Emerging Multi-Omic Understanding Of The Genetics Of Opioid Addiction., Eric O Johnson, Heidi S Fisher, Kyle A Sullivan, Olivia Corradin, Sandra Sanchez-Roige, Nathan C Gaddis, Yasmine N Sami, Alice Townsend, Erica Teixeira Prates, Mirko Pavicic, Peter Kruse, Elissa J Chesler, Abraham A Palmer, Vanessa Troiani, Jason A. Bubier, Daniel A Jacobson, Brion S Maher

Faculty Research 2024

Opioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene …

Back Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

Front Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter, Maryland Birdlife

Maryland Birdlife

No abstract provided.

End Matter (Index), Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter (Index), Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter (Index), Maryland Birdlife

Maryland Birdlife

No abstract provided.

Back Matter (Index), Maryland Birdlife

Maryland Birdlife

No abstract provided.

Discovering Therapeutic Strategies In Colorectal Cancer Via Synthetic Lethal Genetic Screens On Patient-Derived Organoid Models, Sana Khalili

Theses and Dissertations

Precision medicine is a revolutionary approach of targeting genetic alterations that are present only in tumor cells to find vulnerabilities that can be targeted with therapy. Identifying genetic dependencies in human colon cancer could help identify effective treatment strategies. Genome-wide CRISPR-Cas9 dropout screens can reveal all genetic dependencies, some of which could be exploited as therapeutic targets using existing drugs.

In this dissertation, I comprehensively characterized genetic dependencies present in a colon cancer organoid avatar, and validated tumor-specific selectivity of select pharmacologic agents. I identified all somatic mutations, all expressed genes, and conducted a genome-wide CRISPR dropout screen to elucidate …

Leptospirosis In The Platypus (Ornithorhynchus Anatinus) In Australia: Who Is Infecting Whom?, Richard J. Whittington, Thomas R. Grant, Jarrad Mckercher, Monica Suann, Keith Hart, Kathrine A. Handasyde, James Macgregor, Mark E. Westman, Joanne H. Connolly

Research outputs 2022 to 2026

The platypus (Ornithorhynchus anatinus) is an amphibious, egg-laying mammal of high conservation value that is found only in Australia. The zoonotic bacterium Leptospira interrogans serovar Hardjo was discovered in platypuses in prior studies, but little is known about its epidemiology. Samples in the Platypus Serum Bank were tested in 2023 and the results were combined with historical records. Antibodies against L. interrogans serovar Hardjo were found in 50% of 464 serum samples from 411 platypuses collected from 14 river basins in southeastern Australia between 1981 and 2012; prevalence remained high over three decades in the Shoalhaven River population. Seroprevalence increased …

Breakdown Of Boltzmann-Type Models For The Alignment Of Self-Propelled Rods, Patrick Murphy, Misha Perepelitsa, Ilya Timofeyev, Matan Lieber-Kotz, Brandon Islas, Oleg A. Igoshin

Faculty Research, Scholarly, and Creative Activity

Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann's “molecular chaos” hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of …

Asxl1/Tet2 Genotype-Based Risk Stratification Outperforms Asxl1 Mutational Impact And Is Independent Of Mutant Variant Allele Fractions In Chronic Myelomonocytic Leukemia, Clifford M Csizmar, Mark Gurney, Rashmi Kanagal-Shamanna, Kelly Chien, Danielle Hammond, Terra L Lasho, Christy M Finke, Christopher Dean, Anuya Natu, Abhishek A Mangaonkar, Aref Al-Kali, Naseema Gangat, Ayalew Tefferi, Hassan Alkhateeb, Guillermo Garcia-Manero, Rami S Komrokji, Najla A Ali, Eric Padron, Guillermo Montalban-Bravo, Mrinal M Patnaik

Faculty, Staff and Student Publications

No abstract provided.

Synthesis, Characterization, Industrial And Biological Studies Of Azo Dye Ligand And Their Some Metallic Ions, Abaas Obaid Hussein, Rana Abdulilah Abbas, Jinan M. M. Al-Zinkee, Amerj. Jarad

Baghdad Science Journal

4-((2-hydroxy-3,5-dinitrophenyl)diazenyl)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one was produced through the reaction of diazonium salt from 4-amino antipyrine with 2,4-dinitrophenol. This ligand is examined by (UV-Vis, FTIR,1H,13CNMR, and LC-Mass) spectral techniques and micro elemental analysis (C.H.N.O). Co(II), Ni(II), Cu(II), and Zn(II) complexes were also performed and depicted. Metal chelates were distinguished by utilizing flame atomic absorption, infrared analysis, and elemental, visible, as well as ultraviolet spectroscopy, in addition to conductivity and magnetic quantification. Methods of mole ratio and continuous contrast have been studied to determine the nature of the compounds. Beer's law was followed throughout a condensation reach of about 1×10-4 - 3×10-4 M/L. A higher …

Mixed Ligand Complex: Synthesis, Characterization, And Investigation Of Biomedical Activity, Elaf A. Mousa, Basim I. Al-Abdaly

Baghdad Science Journal

A new complex, CuCl2.2H2O (M), was synthesized to react with melatonin (L1) and one of the amino acids (L-cysteine, L2) in a mole ratio of (1:1:1) (M: L1:L2) to produce the metal complex. The synthesized complex was then characterized using spectral techniques including infrared (FT-IR), thermal analysis (TG), flame atomic absorption (AAS), micro elemental analysis (CHNS), melting point (m.p.) measurement, and determination of chloride. Octahedral geometry was proposed for the complex. The copper complex was paramagnetic and non-electrolyte. The synthesized complex was evaluated as an antibacterial and antifungal agent against Escherchia coli (G-) and Staphylococcus aureus (G+). fungus Candida. The …

Immunohistochemical Expression Of Galectin-3 In Thyroid Neoplasms And Its Correlation With Cd56, Banan Mohammed, Wahda Al.Nuaimy

Iraqi Postgraduate Medical Journal

AbstractBackground: The incidence of thyroid cancer has been increasing significantly since the mid-1990s.Some studies have revealed that in thyroid gland, the galectin-3 plays a role in the pathogenesis of well-differentiated carcinoma. For that, it is may be one of the markers that may help to assist in distinguishing thyroid neoplasms. Objective : To detect the frequency of immunohistochemical expression and diagnostic value of Galectin-3 in different types of thyroid neoplasms.To correlate the expression of galectin-3 findings with immunoprofile data of CD56. To correlate the result of immunohistochemical expression of Galectin-3 with the age and gender of the sampled cases.Patients and …

Sheared Turbulent Flows And Wake Dynamics Of An Idled Floating Tidal Turbine, Lilian Lieber, Shaun Fraser, Danny Coles, Alex Nimmo Smith

School of Biological and Marine Sciences

Ocean energy extraction is on the rise. While tides are the most predictable amongst marine renewable resources, turbulent and complex flows still challenge reliable tidal stream energy extraction and there is also uncertainty in how devices change the natural environment. To ensure the long-term integrity of emergent floating tidal turbine technologies, advances in field measurements are required to capture multiscale, real-world flow interactions. Here we use aerial drones and acoustic profiling transects to quantify the site- and scale-dependent complexities of actual turbulent flows around an idled, utility-scale floating tidal turbine (20 m rotor diameter, D). The combined spatial resolution of …

Variant Surface Protein Gp60 Contributes To Host Infectivity Of Cryptosporidium Parvum, Muxiao Li, Fuxian Yang, Tianyi Hou, Xiaoqing Gong, Na Li, L David Sibley, Yaoyu Feng, Lihua Xiao, Yaqiong Guo

2020-Current year OA Pubs

Biological studies of the determinants of Cryptosporidium infectivity are lacking despite the fact that cryptosporidiosis is a major public health problem. Recently, the 60-kDa glycoprotein (GP60) has received attention because of its high sequence polymorphism and association with host infectivity of isolates and protection against reinfection. However, studies of GP60 function have been hampered by its heavy O-linked glycosylation. Here, we used advanced genetic tools to investigate the processing, fate, and function of GP60. Endogenous gene tagging showed that the GP60 cleavage products, GP40 and GP15, are both highly expressed on the surface of sporozoites, merozoites and male gametes. During …

Full Issue, Bulletin Of The Texas Ornithological Society

Bulletin of the Texas Ornithological Society

No abstract provided.

Characterization Of Carbon Dots From Fructus Gardeniae (Zhi-Zi) And Gardenia Charcoal (Black Zhi-Zi) Via Microwave-Assisted Extraction, Hung-Wen Tsai, Nelly Fitri Tampubolon, Tsunghsueh Wu, Mei-Yao Wu, Yang-Wei Lin

Journal of Food and Drug Analysis

We employed a straightforward microwave-assisted extraction technique to investigate the presence of carbon dots (CDs) in Chinese herbal extracts derived from fructus gardeniae and gardenia charcoal, designated as CDs-1 and CDs-2, respectively. The found CDs exhibited unique photoluminescence with quantum yields of 0.95% for CDs-1 and 1.81% for CDs-2, indicating significant potential for bioimaging applications. Both CD types maintain approximately 80% of their fluorescence intensity after 120 minutes of continuous 365 nm UV exposure, underscoring their stability and suitability for prolonged biological studies. Moreover, antioxidant activity tests showed that CDs-2 have a higher scavenging capacity, with an SC-50 value of …

Functional Gold Nanoparticles For Analysis And Delivery Of Nucleic Acids, Po-Tsang Huang, Yen-Ling Chen, Yi-Hui Lin, Chun-Chi Wang, Huan-Tsung Chang

Journal of Food and Drug Analysis

Gold nanoparticles (AuNPs) have become the rising stars in the field of nanotechnology and made a revolution in exploiting the profundity of genomics due to their distinguished properties such as stability, ease in preparation and conjugation, biocompatibility, and unique optical properties. These characteristics have greatly expanded their applications such as sensitive and selective quantitation of nucleic acids and as effective carriers for specifically delivering various important molecules/biomolecules to various targets, which are the cornerstone in treating genetic disorders. This review comprehensively discusses the most recent progress in utilization of AuNPs in quantitation and delivery of nucleic acids. The future prospects …

Full Issue, Cleveland Bird Calendar

Cleveland Bird Calendar

No abstract provided.

Biology Department Publications: 2018, Sam Lindgren

Biology Department Bibliographies

This document is a noncomprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2018. It indexes those publications available through major databases, and serves as an archival record of the Department’s robust scholarly contributions.

Phylogenetic Patterns Of Parental Care In Calidridine Sandpipers, Oksana A. Borowik, Deborah A. Mclennan

The Auk

No abstract provided.

Why Do Marbled Murrelets Attend Old-Growth Forest Nesting Areas Year-Round?, Nancy L. Naslund

The Auk

No abstract provided.

Reviews, The Auk

The Auk

No abstract provided.