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Articles 1 - 8 of 8
Full-Text Articles in Physical Sciences and Mathematics
De Novo Drug Design Using Transformer-Based Machine Translation And Reinforcement Learning Of An Adaptive Monte Carlo Tree Search, Dony Ang, Cyril Rakovski, Hagop S. Atamian
De Novo Drug Design Using Transformer-Based Machine Translation And Reinforcement Learning Of An Adaptive Monte Carlo Tree Search, Dony Ang, Cyril Rakovski, Hagop S. Atamian
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The discovery of novel therapeutic compounds through de novo drug design represents a critical challenge in the field of pharmaceutical research. Traditional drug discovery approaches are often resource intensive and time consuming, leading researchers to explore innovative methods that harness the power of deep learning and reinforcement learning techniques. Here, we introduce a novel drug design approach called drugAI that leverages the Encoder–Decoder Transformer architecture in tandem with Reinforcement Learning via a Monte Carlo Tree Search (RL-MCTS) to expedite the process of drug discovery while ensuring the production of valid small molecules with drug-like characteristics and strong binding affinities towards …
Open Hardware In Science: The Benefits Of Open Electronics, Michael Oellermann, Jolle W. Jolles, Diego Ortiz, Rui Seabra, Tobias Wenzel, Hannah Wilson, Richelle L. Tanner
Open Hardware In Science: The Benefits Of Open Electronics, Michael Oellermann, Jolle W. Jolles, Diego Ortiz, Rui Seabra, Tobias Wenzel, Hannah Wilson, Richelle L. Tanner
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; …
Functional Morphology Of Gliding Flight Ii. Morphology Follows Predictions Of Gliding Performance, Jonathan Rader, Tyson L. Hedrick, Yanyan He, Lindsay D. Waldrop
Functional Morphology Of Gliding Flight Ii. Morphology Follows Predictions Of Gliding Performance, Jonathan Rader, Tyson L. Hedrick, Yanyan He, Lindsay D. Waldrop
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The evolution of wing morphology among birds, and its functional consequences, remains an open question, despite much attention. This is in part because the connection between form and function is difficult to test directly. To address this deficit, in prior work we used computational modeling and sensitivity analysis to interrogate the impact of altering wing aspect ratio, camber, and Reynolds number on aerodynamic performance, revealing the performance landscapes that avian evolution has explored. In the present work, we used a dataset of three-dimensionally scanned bird wings coupled with the performance landscapes to test two hypotheses regarding the evolutionary diversification of …
Functional Morphology Of Gliding Flight I. Modeling Reveals Distinct Performance Landscapes Based On Soaring Strategies, Lindsay D. Waldrop, Yanyan He, Tyson L. Hedrick, Jonathan Rader
Functional Morphology Of Gliding Flight I. Modeling Reveals Distinct Performance Landscapes Based On Soaring Strategies, Lindsay D. Waldrop, Yanyan He, Tyson L. Hedrick, Jonathan Rader
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The physics of flight influences the morphology of bird wings through natural selection on flight performance. The connection between wing morphology and performance is unclear due to the complex relationships between various parameters of flight. In order to better understand this connection, we present a holistic analysis of gliding flight that preserves complex relationships between parameters. We use a computational model of gliding flight, along with analysis by uncertainty quantification, to 1) create performance landscapes of gliding based on output metrics (maximum lift-to-drag ratio, minimum gliding angle, minimum sinking speed, lift coefficient at minimum sinking speed); and 2) predict what …
De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian
De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology …
1h And 13c Nmr Assignments For (N-Methyl)-(−)-(Α)-Isosparteinium Iodide And (N-Methyl)-(−)-Sparteinium Iodide, Kavoos Kolahdouzan, O. Maduka Ogba, Daniel J. O'Leary
1h And 13c Nmr Assignments For (N-Methyl)-(−)-(Α)-Isosparteinium Iodide And (N-Methyl)-(−)-Sparteinium Iodide, Kavoos Kolahdouzan, O. Maduka Ogba, Daniel J. O'Leary
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
(‒)-Sparteine (1) and (–)-(α)-isosparteine (2) are members of the lupine alkaloid family.[1-2] Sparteine has found extensive use in asymmetric organic transformations, including lithiations[3] and Pd-catalyzed oxidations.[4-7] (α)-Isosparteine, which can be made from sparteine, has been utilized as a chiral ligand for a limited number of stereoselective reactions.[8-9] The two compounds differ in that 1 displays an exo-endo arrangement of the bridgehead hydrogens at C-11 and C-6, respectively, while 2 retains an exo-exo arrangement of these atoms (Figure 1). This study is focused on assigning 1H chemical shifts and coupling constants and 13C chemical shifts for N-methyl …
Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich
Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO® ChromaTOF® software and facilitates selection of analytes of interest based on peak area …
Improving The Efficacy Of Web-Based Educational Outreach In Ecology, Gregory R. Goldsmith, Andrew D. Fulton, Colin D. Witherill, Javier F. Espeleta
Improving The Efficacy Of Web-Based Educational Outreach In Ecology, Gregory R. Goldsmith, Andrew D. Fulton, Colin D. Witherill, Javier F. Espeleta
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Scientists are increasingly engaging the web to provide formal and informal science education opportunities. Despite the prolific growth of web-based resources, systematic evaluation and assessment of their efficacy remains limited. We used clickstream analytics, a widely available method for tracking website visitors and their behavior, to evaluate 60,000 visits over three years to an educational website focused on ecology. Visits originating from search engine queries were a small proportion of the traffic, suggesting the need to actively promote websites to drive visitation. However, the number of visits referred to the website per social media post varied depending on the social …