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Full-Text Articles in Physical Sciences and Mathematics

Assessing The Impact Of Hurricane Fiona On The Coast Of Pei National Park And Implications For The Effectiveness Of Beach-Dune Management Policies, Robin Davidson-Arnott, Jeff Ollerhead, Elizabeth George, Chris Houser, Bernard Bauer, Patrick Hesp, Ian Walker, Irene Delagado-Fernandez, Danika Van Proosdij Jun 2024

Assessing The Impact Of Hurricane Fiona On The Coast Of Pei National Park And Implications For The Effectiveness Of Beach-Dune Management Policies, Robin Davidson-Arnott, Jeff Ollerhead, Elizabeth George, Chris Houser, Bernard Bauer, Patrick Hesp, Ian Walker, Irene Delagado-Fernandez, Danika Van Proosdij

Earth & Environmental Sciences Publications

The impact of waves, storm surge, and aeolian transport associated with Post-tropical Storm Fiona (offshore significant wave height ∽ 8 m, storm surge up to 2 m) on the sandy beaches and foredunes of the north shore of Prince Edward Island National Park (PEINP), Canada, are assessed. Management policies and practices, as they apply to sandy beach systems within PEINP, are reviewed in the context of the shoreline changes attributed to Fiona. The effectiveness of these policies and practices are evaluated to inform the potential performance of beach-foredune systems as natural protection measures that mitigate the impacts of large-magnitude storms …

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Expanding Analytical Capabilities In Intrusion Detection Through Ensemble-Based Multi-Label Classification, Ehsan Hallaji, Roozbeh Razavi-Far, Mehrdad Saif Apr 2024

Expanding Analytical Capabilities In Intrusion Detection Through Ensemble-Based Multi-Label Classification, Ehsan Hallaji, Roozbeh Razavi-Far, Mehrdad Saif

Electrical and Computer Engineering Publications

Intrusion detection systems are primarily designed to flag security breaches upon their occurrence. These systems operate under the assumption of single-label data, where each instance is assigned to a single category. However, when dealing with complex data, such as malware triage, the information provided by the IDS is limited. Consequently, additional analysis becomes necessary, leading to delays and incurring additional computational costs. Existing solutions to this problem typically merge these steps by considering a unified, but large, label set encompassing both intrusion and analytical labels, which adversely affects efficiency and performance. To address these challenges, this paper presents a novel …

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Single-Stage Few-Cycle Pulse Amplification, Sagnik Ghosh, Nathan G. Drouillard, Tj Hammond Jan 2024

Single-Stage Few-Cycle Pulse Amplification, Sagnik Ghosh, Nathan G. Drouillard, Tj Hammond

Physics Publications

Kerr instability can be exploited to amplify visible, near-infrared, and midinfrared ultrashort pulses. We use the results of Kerr instability amplification theory to inform our simulations amplifying few-cycle pulses. We show that the amplification angle dependence is simplified to the phase-matching condition of four-wave mixing when the intense pump is considered. Seeding with few-cycle pulses near the pump leads to broadband amplification without spatial chirp, while longer pulses undergo compression through amplification. Pumping in the midinfrared leads to multioctave spanning amplified pulses with single-cycle duration not previously predicted. We discuss limitations of the amplification process and optimizing pump and seed …

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Phase Dependence Of Kerr-Based Parametric Amplification, Nathan G. Drouillard, Tj Hammond Jan 2024

Phase Dependence Of Kerr-Based Parametric Amplification, Nathan G. Drouillard, Tj Hammond

Physics Publications

Kerr instability amplification can amplify over an octave of spectrum, a broad bandwidth supporting few-cycle pulses. However, dispersion management in this regime is crucial, and we explore the parameters required to maintain the ultrashort pulse undergoing amplification. At low pump intensities, we experimentally observe an interference between the strongly chirped supercontinuum seed and weakly amplified pulse, reproduced in our model by manipulating the seed dispersion. Extending our model to cases of high gain, our simulation predicts the dispersion is near zero, and the phase can be compensated preamplification to generate near-transform-limited amplified few-cycle pulses.We discuss chirping the seed pulse to …

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Supercontinuum Amplification By Kerr Instability, Sagnik Ghosh, Nathan G. Drouillard, Tj Hammond Jan 2024

Supercontinuum Amplification By Kerr Instability, Sagnik Ghosh, Nathan G. Drouillard, Tj Hammond

Physics Publications

The versatility of optical parametric amplifiers makes them excellent sources for ultrashort visible and infrared pulses that drive strong-field physics experiments. We extend four-wave optical parametric amplification to the strong-field regime, known as Kerr instability amplification, and experimentally verify the modified noncollinear conditions for optimum amplification. We confirm that Kerr instability amplification can be used to amplify spectra that span nearly an octave in a single beam. We also amplify the near-infrared portion of the spectrum to generate the third harmonic downstream.

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Detection And Diagnosis Of Bacterial Pathogens In Blood Using Laser-Induced Breakdown Spectroscopy, E J. Blanchette, E A. Tracey, A Baughan, G E. Johnson, H Malik, C N. Alionte, I G. Arthur, M E. Pontoni, Steven Rehse Jan 2024

Detection And Diagnosis Of Bacterial Pathogens In Blood Using Laser-Induced Breakdown Spectroscopy, E J. Blanchette, E A. Tracey, A Baughan, G E. Johnson, H Malik, C N. Alionte, I G. Arthur, M E. Pontoni, Steven Rehse

Physics Publications

The ability to rapidly and accurately detect and identify pathogenic bacteria in clinically-obtained blood specimens with laser-induced breakdown spectroscopy (LIBS) is evaluated. Samples of blood obtained from five patients in a local hospital were confirmed to be negative for the presence of bacteria by the pathology department and were then tested with LIBS. Specimens of blood were tested as obtained from the hospital with no other alteration as control samples and were also intentionally spiked with known aliquots of Escherichia coli, Staphylococcus aureus, Enterobacter cloacae, and Pseudomonas aeruginosa to simulate blood infections. LIBS spectra were acquired from blood deposited on …

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Detection And Diagnosis Of Bacterial Pathogens In Urine Using Laser-Induced Breakdown Spectroscopy, E J. Blanchette, E A. Tracey, A Baughan, G E. Johnson, H Malik, C N. Alionte, I G. Arthur, M E. Potoni, Steven Rehse Jan 2024

Detection And Diagnosis Of Bacterial Pathogens In Urine Using Laser-Induced Breakdown Spectroscopy, E J. Blanchette, E A. Tracey, A Baughan, G E. Johnson, H Malik, C N. Alionte, I G. Arthur, M E. Potoni, Steven Rehse

Physics Publications

The presence of bacterial cells from three species has been detected in clinical specimens of human urine using laser-induced breakdown spectroscopy (LIBS) by using a partial least squares discriminant analysis (PLS-DA) of 360 spectra obtained from 12 specimens of infected urine and 239 spectra obtained from eight specimens of sterile urine. Nominally sterile urine specimens obtained from four patients at a local hospital after being screened negative for the presence of bacterial pathogens were spiked with known aliquots of Escherichia coli, Staphylococcus aureus, and Enterobacter cloacae to simulate clinical urinary tract infections. Fifteen emission line intensities measured from the LIBS …

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A Survey And Taxonomy Of Sequential Recommender Systems For E-Commerce Product Recommendation, Mahreen Nasir, C. I. Ezeife Nov 2023

A Survey And Taxonomy Of Sequential Recommender Systems For E-Commerce Product Recommendation, Mahreen Nasir, C. I. Ezeife

Computer Science Publications

E-commerce recommendation systems facilitate customers’ purchase decision by recommending products or services of interest (e.g., Amazon). Designing a recommender system tailored toward an individual customer’s need is crucial for retailers to increase revenue and retain customers’ loyalty. As users’ interests and preferences change with time, the time stamp of a user interaction (click, view or purchase event) is an important characteristic to learn sequential patterns from these user interactions and, hence, understand users’ long- and short-term preferences to predict the next item(s) for recommendation. This paper presents a taxonomy of sequential recommendation systems (SRecSys) with a focus on e-commerce product …

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A Survey Of Sequential Pattern Based E-Commerce Recommendation Systems, Christie I. Ezeife, Hemni Karlapalepu Oct 2023

A Survey Of Sequential Pattern Based E-Commerce Recommendation Systems, Christie I. Ezeife, Hemni Karlapalepu

Computer Science Publications

E-commerce recommendation systems usually deal with massive customer sequential databases, such as historical purchase or click stream sequences. Recommendation systems’ accuracy can be improved if complex sequential patterns of user purchase behavior are learned by integrating sequential patterns of customer clicks and/or purchases into the user–item rating matrix input of collaborative filtering. This review focuses on algorithms of existing E-commerce recommendation systems that are sequential pattern-based. It provides a comprehensive and comparative performance analysis of these systems, exposing their methodologies, achievements, limitations, and potential for solving more important problems in this domain. The review shows that integrating sequential pattern mining …

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Structural Mapping Of The Base Stacks Containing Post-Transcriptionally Modified Bases In Rna, Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma Jun 2023

Structural Mapping Of The Base Stacks Containing Post-Transcriptionally Modified Bases In Rna, Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma

Chemistry and Biochemistry Publications

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis …

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Structural Mapping Of The Base Stacks Containing Post-Transcriptionally Modified Bases In Rna, Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma Jun 2023

Structural Mapping Of The Base Stacks Containing Post-Transcriptionally Modified Bases In Rna, Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma

Chemistry and Biochemistry Publications

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis …

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Mitocans Induce Lipid Flip-Flop And Permeabilize The Membrane To Signal Apoptosis, Stuart R. Castillo, Michael H.L. Nguyen, Mitchell Dipasquale, Elizabeth G. Kelley, Drew Marquardt Jun 2023

Mitocans Induce Lipid Flip-Flop And Permeabilize The Membrane To Signal Apoptosis, Stuart R. Castillo, Michael H.L. Nguyen, Mitchell Dipasquale, Elizabeth G. Kelley, Drew Marquardt

Chemistry and Biochemistry Publications

Pancratistatin (PST) and narciclasine (NRC) are natural therapeutic agents that exhibit specificity toward the mitochondria of cancerous cells and initiate apoptosis. Unlike traditional cancer therapeutic agents, PST and NRC are effective, targeted, and have limited adverse effects on neighboring healthy, noncancerous cells. Currently, the mechanistic pathway of action for PST and NRC remains elusive, which in part inhibits PST and NRC from becoming efficacious therapeutic alternatives. Herein, we use neutron and x-ray scattering in combination with calcein leakage assays to characterize the effects of PST, NRC, and tamoxifen (TAM) on a biomimetic model membrane. We report an increase in lipid …

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Boron Neutron Capture Therapy In The New Age Of Accelerator-Based Neutron Production And Preliminary Progress In Canada, Dominik Dziura, Sana Tabbassum, Amanda Macneil, Dalini D. Maharaj, Robert Laxdal, Oliver Kester, Ming Pan, Hiroaki Kumada, Drew Marquardt Jun 2023

Boron Neutron Capture Therapy In The New Age Of Accelerator-Based Neutron Production And Preliminary Progress In Canada, Dominik Dziura, Sana Tabbassum, Amanda Macneil, Dalini D. Maharaj, Robert Laxdal, Oliver Kester, Ming Pan, Hiroaki Kumada, Drew Marquardt

Chemistry and Biochemistry Publications

Each year more than 3000 Canadians are diagnosed with brain cancers like glioblastoma multiforme or recurrent head and neck cancers, which are difficult to treat with conventional radiotherapy techniques. One of the most clinically promising treatments for these cancers is boron neutron capture therapy (BNCT). This procedure involves selectively introducing a boron delivery agent into tumor cells and irradiating them with a neutron beam, which kills the cancer cells due to the high-linear energy transfer radiation produced by the 10B(n,α)7Li capture reaction. The theory of BNCT has been around for a long time since 1936, but has historically been limited …

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Battery Parameter Analysis Through Electrochemical Impedance Spectroscopy At Different State Of Charge Levels, Yuchao Wu, Sneha Sundaresan, Balakumar Balasingam Jun 2023

Battery Parameter Analysis Through Electrochemical Impedance Spectroscopy At Different State Of Charge Levels, Yuchao Wu, Sneha Sundaresan, Balakumar Balasingam

Computer Science Publications

This paper presents a systematic approach to extract electrical equivalent circuit model (ECM) parameters of the Li-ion battery (LIB) based on electrochemical impedance spectroscopy (EIS). Particularly, the proposed approach is suitable to practical applications where the measurement noise can be significant, resulting in a low signal-to-noise ratio. Given the EIS measurements, the proposed approach can be used to obtain the ECM parameters of a battery. Then, a time domain approach is employed to validate the accuracy of estimated ECM parameters. In order to investigate whether the ECM parameters vary as the battery’s state of charge (SOC) changes, the EIS experiment …

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Investigating The Effect Of Medium Chain Triglycerides On The Elasticity Of Pulmonary Surfactant, Maksymilian Dziura, Stuart R. Castillo, Mitchell Dipasquale, Omotayo Gbadamosi, Piotr Zolnierczuk, Michihiro Nagao, Elizabeth G. Kelley, Drew Marquardt Apr 2023

Investigating The Effect Of Medium Chain Triglycerides On The Elasticity Of Pulmonary Surfactant, Maksymilian Dziura, Stuart R. Castillo, Mitchell Dipasquale, Omotayo Gbadamosi, Piotr Zolnierczuk, Michihiro Nagao, Elizabeth G. Kelley, Drew Marquardt

Chemistry and Biochemistry Publications

In recent years, vaping has increased in both popularity and ease of access. This has led to an outbreak of a relatively new condition known as e-cigarette/vaping-associated lung injury (EVALI). This injury can be caused by physical interactions between the pulmonary surfactant (PS) in the lungs and toxins typically found in vaping solutions, such as medium chain triglycerides (MCT). MCT has been largely used as a carrier agent within many cannabis products commercially available on the market. Pulmonary surfactant ensures proper respiration by maintaining low surface tensions and interface stability throughout each respiratory cycle. Therefore, any impediments to this system …

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“Breaking Bud”: The Effect Of Direct Chemical Modifications Of Phytocannabinoids On Their Bioavailability, Physiological Effects, And Therapeutic Potential, Abhinandan Banerjee, John J. Hayward, John F. Trant Feb 2023

“Breaking Bud”: The Effect Of Direct Chemical Modifications Of Phytocannabinoids On Their Bioavailability, Physiological Effects, And Therapeutic Potential, Abhinandan Banerjee, John J. Hayward, John F. Trant

Chemistry and Biochemistry Publications

Tetrahydrocannabinol (THC) and cannabidiol (CBD) are the two “major cannabinoids”. However, their incorporation into clinical and nutraceutical preparations is challenging, owing to their limited bioavailability, low water solubility, and variable pharmacokinetic profiles. Understanding the organic chemistry of the major cannabinoids provides us with potential avenues to overcome these issues through derivatization. The resulting labile pro-drugs offer ready cannabinoid release in vivo, have augmented bioavailability, or demonstrate interesting pharmacological properties in their own right. This review identifies and discusses a subset of these advanced derivatization strategies for the major cannabinoids, where the starting material is the pure phytocannabinoid itself, and …

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The “Nitrogen Effect”: Complexation With Macrocycles Potentiates Fused Heterocycles To Form Halogen Bonds In Competitive Solvents, Dr. Kwaku Twum, Sanaz Nadimi, Frank Boateng Osei, Dr. Rakesh Puttreddy, Dr. Yvonne Bessem Ojong, Dr. John J. Hayward, Prof. Kari Rissanen, Prof. John F. Trant, Prof. Ngong Kodiah Beyeh Kodiah Beyeh Jan 2023

The “Nitrogen Effect”: Complexation With Macrocycles Potentiates Fused Heterocycles To Form Halogen Bonds In Competitive Solvents, Dr. Kwaku Twum, Sanaz Nadimi, Frank Boateng Osei, Dr. Rakesh Puttreddy, Dr. Yvonne Bessem Ojong, Dr. John J. Hayward, Prof. Kari Rissanen, Prof. John F. Trant, Prof. Ngong Kodiah Beyeh Kodiah Beyeh

Chemistry and Biochemistry Publications

Weak intermolecular forces are typically very difficult to observe in highly competitive polar protic solvents as they are overwhelmed by the quantity of competing solvent. This is even more challenging for three-component ternary assemblies of pure organic compounds. In this work, we overcome these complications by leveraging the binding of fused aromatic N-heterocycles in an open resorcinarene cavity to template the formation of a three-component halogen-bonded ternary assembly in a protic polar solvent system.

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Structural And Energetic Features Of Base–Base Stacking Contacts In Rna, Zakir Ali, Ambika Goyal, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma Jan 2023

Structural And Energetic Features Of Base–Base Stacking Contacts In Rna, Zakir Ali, Ambika Goyal, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma

Chemistry and Biochemistry Publications

Nucleobase π–π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of …

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Investigating The Cut-Off Effect Of N-Alcohols On Lipid Movement: A Biophysical Study, Michael H.K. Nguyen, Dominik Dziura, Mitchell Dipasquale, Stuart R. Castillo, Elizabeth G. Kelley, Drew Marquardt Jan 2023

Investigating The Cut-Off Effect Of N-Alcohols On Lipid Movement: A Biophysical Study, Michael H.K. Nguyen, Dominik Dziura, Mitchell Dipasquale, Stuart R. Castillo, Elizabeth G. Kelley, Drew Marquardt

Chemistry and Biochemistry Publications

Cellular membranes are responsible for absorbing the effects of external perturbants for the cell’s survival. Such perturbants include small ubiquitous molecules like n-alcohols which were observed to exhibit anesthetic capabilities, with this effect tapering off at a cut-off alcohol chain length. To explain this cut-off effect and complement prior biochemical studies, we investigated a series of nalcohols (with carbon lengths 2-18) and their impact on several bilayer properties, including lipid flip-flop, intervesicular exchange, diffusion, membrane bending rigidity and more. To this end, we employed an array of biophysical techniques such as time-resolved small angle neutron scattering (TRSANS), small angle X-ray …

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Semantic Enhanced Markov Model For Sequential E-Commerce Product Recommendation, Mahreen Nasir, C. I. Ezeife Jan 2023

Semantic Enhanced Markov Model For Sequential E-Commerce Product Recommendation, Mahreen Nasir, C. I. Ezeife

Computer Science Publications

To model sequential relationships between items, Markov Models build a transition probability matrix P of size n× n, where n represents number of states (items) and each matrix entry p(i,j) represents transition probabilities from state i to state j. Existing systems such as factorized personalized Markov chains (FPMC) and fossil either combine sequential information with user preference information or add the high-order Markov chains concept. However, they suffer from (i) model complexity: an increase in Markov Model’s order (number of states) and separation of sequential pattern and user preference matrices, (ii) sparse transition probability matrix: few product purchases from thousands …

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Survey Of Multiple Clouds: Classification, Relationships And Privacy Concerns, Reem Al-Saidi, Ziad. Kobti Jan 2023

Survey Of Multiple Clouds: Classification, Relationships And Privacy Concerns, Reem Al-Saidi, Ziad. Kobti

Computer Science Publications

When major Cloud Service Providers (CSPs) network with other CSPs, they show a predominant area over cloud computing architecture, each with different roles to serve user demands better. This creates multiple clouds computing environments, which overcome the limitations of cloud computing and bring a wide range of benefits (e.g., avoiding vendor lock-in problem). Numerous applications can use various multiple clouds types depending on their specifications and needs. Deploying multiple clouds under hybrid or public models has introduced various privacy concerns that affect users and their data in a specific application domain. To understand the nuances of these concerns, the present …

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Performance Analysis Of Empirical Open-Circuit Voltage Modeling In Lithium-Ion Batteries, Part-3: Experimental Results, Prarthana Pillai, James Nguyen, Balakumar Balasingam Jan 2023

Performance Analysis Of Empirical Open-Circuit Voltage Modeling In Lithium-Ion Batteries, Part-3: Experimental Results, Prarthana Pillai, James Nguyen, Balakumar Balasingam

Computer Science Publications

This paper is the third part of a series of papers about empirical approaches to open circuit voltage (OCV) modeling of lithium-ion batteries. The first part of the series proposed models to quantify various sources of uncertainties in the OCV models; the second part of the series presented systematic data collection approaches to compute the uncertainties in the OCV to state of charge (SOC) models. This paper uses data collected from 28 OCV characterization experiments, performed according to the data collection plan presented in the second part, to compute and analyze three OCV uncertainty metrics: cell-to-cell variations, C-Rate error, and …

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Biallelic Mutations In P4htm Cause Syndromic Obesity, Sadia Saeed, Lijiao Ning, Alaa Badreddine, Muhammad Usman Mirza, Mathilde Boissel, Roohia Khanam, Jaida Manzoor, Qasim M. Janjua, Waqas I. Khan, Bénédicte Toussaint, Emmanuel Vaillant, Souhila Amanzougarene, Mehdi Derhourhi, John F. Trant, Anna-Maria Siegert, Brian Y.H. Lam, Giles S.H. Yeo, Layachi Chabraoui, Asmae Touzani, Abhishek Kulkarni, I. Sadaf Farooqi, Amélie Bonnefond, Muhammad Arslan, Philippe Froguel Jan 2023

Biallelic Mutations In P4htm Cause Syndromic Obesity, Sadia Saeed, Lijiao Ning, Alaa Badreddine, Muhammad Usman Mirza, Mathilde Boissel, Roohia Khanam, Jaida Manzoor, Qasim M. Janjua, Waqas I. Khan, Bénédicte Toussaint, Emmanuel Vaillant, Souhila Amanzougarene, Mehdi Derhourhi, John F. Trant, Anna-Maria Siegert, Brian Y.H. Lam, Giles S.H. Yeo, Layachi Chabraoui, Asmae Touzani, Abhishek Kulkarni, I. Sadaf Farooqi, Amélie Bonnefond, Muhammad Arslan, Philippe Froguel

Chemistry and Biochemistry Publications

We previously demonstrated that 50% of children with obesity from consanguineous families from Pakistan carry pathogenic variants in known monogenic obesity genes. Here, we have discovered a novel monogenetic recessive form of severe childhood obesity using an in-house computational staged approach. The analysis included whole-exome sequencing data of 366 children with severe obesity, 1,000 individuals of the Pakistan Risk of Myocardial Infarction Study (PROMIS) study, and 200,000 participants of the UK Biobank to prioritize genes harboring rare homozygous variants with putative effect on human obesity. We identified five rare or novel homozygous missense mutations predicted deleterious in five consanguineous families …

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Guanidinium–Amino Acid Hydrogen-Bonding Interactions In Protein Crystal Structures: Implications For Guanidinium-Induced Protein Denaturation, Indu Negi, Raman Jangra, Amit Gharu, John F. Trant, Purshotam Sharma Dec 2022

Guanidinium–Amino Acid Hydrogen-Bonding Interactions In Protein Crystal Structures: Implications For Guanidinium-Induced Protein Denaturation, Indu Negi, Raman Jangra, Amit Gharu, John F. Trant, Purshotam Sharma

Chemistry and Biochemistry Publications

In the present work, 86 available high resolution X-ray structures of proteins that contain one or more guanidinium ions (Gdm+) are analyzed for the distribution and nature of noncovalent interactions between Gdm+ and amino-acid residues. A total of 1044 hydrogen-bonding interactions were identified, of which 1039 are N–H⋯O, and five are N–H⋯N. Acidic amino acids are more likely to interact with Gdm+ (46% of interactions, 26% Asp and 20% Glu), followed by Pro (19% of interactions). DFT calculations on the identified Gdm+–amino acid hydrogen-bonded pairs reveal that although Gdm+ interacts primarily with the backbone amides of nonpolar amino acids, Gdm+ …

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A Nanodiamond Chemotherapeutic Folate Receptor-Targeting Prodrug With Triggerable Drug Release, Jiangtao Wu, Xiangbin Du, Dongmei Zhang, Jicheng Cui, Xiaoxia Zhang, Xine Duan, John F. Trant, Yingqi Li Nov 2022

A Nanodiamond Chemotherapeutic Folate Receptor-Targeting Prodrug With Triggerable Drug Release, Jiangtao Wu, Xiangbin Du, Dongmei Zhang, Jicheng Cui, Xiaoxia Zhang, Xine Duan, John F. Trant, Yingqi Li

Chemistry and Biochemistry Publications

No abstract provided.

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Vitamin E Does Not Disturb Polyunsaturated Fatty Acid Lipid Domains, Mitchell Dipasquale, Michael H.L. Nguyen, Stuart R. Castillo, Isabelle J. Dib, Elizabeth G. Kelley, Drew Marquardt Nov 2022

Vitamin E Does Not Disturb Polyunsaturated Fatty Acid Lipid Domains, Mitchell Dipasquale, Michael H.L. Nguyen, Stuart R. Castillo, Isabelle J. Dib, Elizabeth G. Kelley, Drew Marquardt

Chemistry and Biochemistry Publications

The function of vitamin E in biomembranes remains a prominent topic of discussion. As its limitations as an antioxidant persist and novel functions are discovered, our understanding of the role of vitamin E becomes increasingly enigmatic. As a group of lipophilic molecules (tocopherols and tocotrienols), vitamin E has been shown to influence the properties of its host membrane, and a wealth of research has connected vitamin E to polyunsaturated fatty acid (PUFA) lipids. Here, we use contrast-matched small-angle neutron scattering and differential scanning calorimetry to integrate these fields by examining the influence of vitamin E on lipid domain stability in …

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Partial Volumes Of Phosphatidylcholines And Vitamin E: Α-Tocopherol Prefers Disordered Membranes, Mitchell Dipasquale, Michael H.L. Nguyen, Georg Pabst, Drew Marquardt Sep 2022

Partial Volumes Of Phosphatidylcholines And Vitamin E: Α-Tocopherol Prefers Disordered Membranes, Mitchell Dipasquale, Michael H.L. Nguyen, Georg Pabst, Drew Marquardt

Chemistry and Biochemistry Publications

Despite its discovery over 95 years ago, the biological and nutritional roles of vitamin E remain subjects of much controversy. Though it is known to possess antioxidant properties, recent assertions have implied that vitamin E may not be limited to this function in living systems. Through densitometry measurements and small-angle X-ray scattering we observe favorable interactions between α-tocopherol and unsaturated phospholipids, with more favorable interactions correlating to an increase in lipid chain unsaturation. Our data provide evidence that vitamin E may preferentially associate with oxygen sensitive lipids-an association that is considered innate for a viable membrane antioxidant.

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Novel Quinoline-Derived Chemosensors: Synthesis, Anion Recognition, Spectroscopic, And Computational Study†, Tahira Saleem, Samra Khan, Muhammad Yaqub, Muhammad Khalid, Muhammad Islam, Muhammad Yousaf Ur Rehman, Muhammad Rashid, Iqra Shafiq, Ataualpa A. C. Braga, Asad Syed, Ali H. Bahkali, John F. Trant, Zahid Shafiq Aug 2022

Novel Quinoline-Derived Chemosensors: Synthesis, Anion Recognition, Spectroscopic, And Computational Study†, Tahira Saleem, Samra Khan, Muhammad Yaqub, Muhammad Khalid, Muhammad Islam, Muhammad Yousaf Ur Rehman, Muhammad Rashid, Iqra Shafiq, Ataualpa A. C. Braga, Asad Syed, Ali H. Bahkali, John F. Trant, Zahid Shafiq

Chemistry and Biochemistry Publications

Fluorescent-small molecules offer an excellent source of chemosensors when optimized for detection of anions with sensitivity and selectivity, low-cost and robust synthesis. In the present study we synthesized new quinoline-based chemosensors (4a–e) via the one-pot multi component reaction and confirmed their potential for chemosensory via cyclic voltammetry. 4a–e were tested for ligand–anion interaction against F−, OAc−, Br−, ClO3, I−, HSO4−, CN−, ClO4− and SCN-ions, by using UV-visible, colorimetry and Fluorescence. The NH deprotonation was observed as the mechanism of anion interaction via FTIR and H1NMR spectroscopies. Benesi–Hildebrand plot was drawn to calculate binding constants and limit of detection was also …

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A Revised Synthesis Of 6-Alkoxy-2-Aminopurines With Late-Stage Convergence Allowing For Increased Molecular Complexity†, Lavleen Mader, John J. Hayward, Lisa A. Porter, John F. Trant Aug 2022

A Revised Synthesis Of 6-Alkoxy-2-Aminopurines With Late-Stage Convergence Allowing For Increased Molecular Complexity†, Lavleen Mader, John J. Hayward, Lisa A. Porter, John F. Trant

Chemistry and Biochemistry Publications

6-Alkoxy-2-aminopurine derivatives are potent inhibitors of Cyclin Dependent Kinases (CDKs), with some selectivity towards CDK2 and thus have potential as cancer therapeutics. Development of these inhibitors for targeting CDK2-cyclin A/E complexes has previously involved a thorough investigation of structure activity relationships of the C-2 amine moiety. However, the established synthesis of these compounds, which uses the alcohol reagent as solvent, limits the complexity of the O-6 functionality which is required for more selective targeting. Herein we report an improved and refocused synthesis of a model CDK2 inhibitor (NU6247), affording convenient access to inhibitors with O-6 substituents whose parent alcohol is …

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The Interaction Of Deep Eutectic Solvents With Pristine Carbon Nanotubes And Their Associated Defects: A Density Functional Theory Study, Hamid Reza Ghenaatian, Mehdi Shakourian-Fard, Ganesh Kamath, John F. Trant, Farouq S. Mjalli Jul 2022

The Interaction Of Deep Eutectic Solvents With Pristine Carbon Nanotubes And Their Associated Defects: A Density Functional Theory Study, Hamid Reza Ghenaatian, Mehdi Shakourian-Fard, Ganesh Kamath, John F. Trant, Farouq S. Mjalli

Chemistry and Biochemistry Publications

In this study, the interaction of four deep eutectic solvents (DESs): [Choline chloride][Urea] ([ChCl][U]), [Choline chloride][Ethylene glycol] ([ChCl][EG]), [Choline chloride][Glycerol] ([ChCl][Gly]) and [Choline chloride][Benzoic acid] ([ChCl][BA]), with pristine carbon nanotube (CNT) and its defects: double-vacancy and Stone–Wales structures (CNT-DV and CNT-SW) is investigated using density functional theory (DFT) calculations. The geometry optimization, electronic property calculations, noncovalent interaction analysis and optical properties of the DES@nanotube complexes were carried out at the M06-2X/cc-pVDZ level of theory. The adsorption energy (Eads) calculations show that the presence of the DV and SW defects on the CNT increases the adsorption strength of the DESs, DES@CNT-SW …

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