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Michigan Technological University

2023

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Articles 1 - 30 of 103

Full-Text Articles in Physical Sciences and Mathematics

Long Oligodeoxynucleotides: Chemical Synthesis, Isolation Via Catching-By-Polymerization, Verification Via Sequencing, And Gene Expression Demonstration, Yipeng Yin, Reed Arneson, Alexander Apostle, Adikari M.D.N. Eriyagama, Komal Chillar, Emily Burke, Martina Jahfetson, Yinan Yuan, Shiyue Fang Dec 2023

Long Oligodeoxynucleotides: Chemical Synthesis, Isolation Via Catching-By-Polymerization, Verification Via Sequencing, And Gene Expression Demonstration, Yipeng Yin, Reed Arneson, Alexander Apostle, Adikari M.D.N. Eriyagama, Komal Chillar, Emily Burke, Martina Jahfetson, Yinan Yuan, Shiyue Fang

Michigan Tech Publications, Part 2

Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex …

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Race: An Efficient Redundancy-Aware Accelerator For Dynamic Graph Neural Network, Hui Yu, Yu Zhang, Jin Zhao, Yujian Liao, Zhiying Huang, Donghao He, Lin Gu, Hai Jin, Xiaofei Liao, Haikun Liu, Bingsheng He, Jianhui Yue Dec 2023

Race: An Efficient Redundancy-Aware Accelerator For Dynamic Graph Neural Network, Hui Yu, Yu Zhang, Jin Zhao, Yujian Liao, Zhiying Huang, Donghao He, Lin Gu, Hai Jin, Xiaofei Liao, Haikun Liu, Bingsheng He, Jianhui Yue

Michigan Tech Publications, Part 2

Dynamic Graph Neural Network (DGNN) has recently attracted a significant amount of research attention from various domains, because most real-world graphs are inherently dynamic. Despite many research efforts, for DGNN, existing hardware/software solutions still suffer significantly from redundant computation and memory access overhead, because they need to irregularly access and recompute all graph data of each graph snapshot. To address these issues, we propose an efficient redundancy-aware accelerator, RACE, which enables energy-efficient execution of DGNN models. Specifically, we propose a redundancy-aware incremental execution approach into the accelerator design for DGNN to instantly achieve the output features of the latest graph …

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Engineering Exosomes To Specifically Target The Mitochondria Of Brain Cells, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi Dec 2023

Engineering Exosomes To Specifically Target The Mitochondria Of Brain Cells, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Michigan Tech Publications, Part 2

Mitochondrial dysfunction is associated with various health conditions, including cardiovascular and neurodegenerative diseases. Mitochondrial-targeting therapy aims to restore or enhance mitochondrial function to treat or alleviate these conditions. Exosomes, small vesicles that cells secrete, containing a variety of biomolecules, are critical in cell-to-cell communication and have been studied as potential therapeutic agents. Exosome-based therapy has the potential to treat both cardiovascular and neurodegenerative diseases. Combining these two approaches involves using exosomes as carriers to transport mitochondrial-targeting agents to dysfunctional or damaged mitochondria within target cells. This article presents a new technique for engineering brain-derived exosomes that target mitochondria and has …

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Engineering Exosomes To Specifically Target The Mitochondria Of Brain Cells, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi Dec 2023

Engineering Exosomes To Specifically Target The Mitochondria Of Brain Cells, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Michigan Tech Publications, Part 2

Mitochondrial dysfunction is associated with various health conditions, including cardiovascular and neurodegenerative diseases. Mitochondrial-targeting therapy aims to restore or enhance mitochondrial function to treat or alleviate these conditions. Exosomes, small vesicles that cells secrete, containing a variety of biomolecules, are critical in cell-to-cell communication and have been studied as potential therapeutic agents. Exosome-based therapy has the potential to treat both cardiovascular and neurodegenerative diseases. Combining these two approaches involves using exosomes as carriers to transport mitochondrial-targeting agents to dysfunctional or damaged mitochondria within target cells. This article presents a new technique for engineering brain-derived exosomes that target mitochondria and has …

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Regulation Of Regeneration In Arabidopsis Thaliana, Md Khairul Islam, Sai Teja Mummadi, Sanzhen Liu, Hairong Wei Nov 2023

Regulation Of Regeneration In Arabidopsis Thaliana, Md Khairul Islam, Sai Teja Mummadi, Sanzhen Liu, Hairong Wei

Michigan Tech Publications, Part 2

We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. …

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Multi-View Information Fusion Using Multi-View Variational Autoencoder To Predict Proximal Femoral Fracture Load, Chen Zhao, Joyce H. Keyak, Xuewei Cao, Qiuying Sha, Li Wu, Zhe Luo, Lan Juan Zhao, Qing Tian, Michael Serou, Chuan Qiu, Kuan Jui Su, Hui Shen, Hong Wen Deng, Weihua Zhou Nov 2023

Multi-View Information Fusion Using Multi-View Variational Autoencoder To Predict Proximal Femoral Fracture Load, Chen Zhao, Joyce H. Keyak, Xuewei Cao, Qiuying Sha, Li Wu, Zhe Luo, Lan Juan Zhao, Qing Tian, Michael Serou, Chuan Qiu, Kuan Jui Su, Hui Shen, Hong Wen Deng, Weihua Zhou

Michigan Tech Publications, Part 2

Background: Hip fracture occurs when an applied force exceeds the force that the proximal femur can support (the fracture load or “strength”) and can have devastating consequences with poor functional outcomes. Proximal femoral strengths for specific loading conditions can be computed by subject-specific finite element analysis (FEA) using quantitative computerized tomography (QCT) images. However, the radiation and availability of QCT limit its clinical usability. Alternative low-dose and widely available measurements, such as dual energy X-ray absorptiometry (DXA) and genetic factors, would be preferable for bone strength assessment. The aim of this paper is to design a deep learning-based model to …

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Integrating Embeddings From Multiple Protein Language Models To Improve Protein O-Glcnac Site Prediction, Suresh Pokharel, Pawel Pratyush, Hamid D. Ismail, Junfeng Ma, Dukka Kc Nov 2023

Integrating Embeddings From Multiple Protein Language Models To Improve Protein O-Glcnac Site Prediction, Suresh Pokharel, Pawel Pratyush, Hamid D. Ismail, Junfeng Ma, Dukka Kc

Michigan Tech Publications, Part 2

O-linked β-N-acetylglucosamine (O-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. O-GlcNAc modification (i.e., O-GlcNAcylation) is involved in the regulation of diverse cellular processes, including transcription, epigenetic modifications, and cell signaling. Despite the great progress in experimentally mapping O-GlcNAc sites, there is an unmet need to develop robust prediction tools that can effectively locate the presence of O-GlcNAc sites in protein sequences of interest. In this work, we performed a comprehensive evaluation of a framework for prediction of protein O-GlcNAc sites using embeddings from pre-trained protein language models. In particular, we …

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Identification Of Selected Persistent Organic Pollutants In Agricultural Land By Carbon Nitride (C3n5) Based Nano Sensors, Puspamitra Panigrahi, P. S. Anuroop, Hoonkyung Lee, Hyeonhu Bae, Thanayut Kaewmaraya, Ravindra Pandey, Tanveer Hussain, Akshaya Panigrahi Nov 2023

Identification Of Selected Persistent Organic Pollutants In Agricultural Land By Carbon Nitride (C3n5) Based Nano Sensors, Puspamitra Panigrahi, P. S. Anuroop, Hoonkyung Lee, Hyeonhu Bae, Thanayut Kaewmaraya, Ravindra Pandey, Tanveer Hussain, Akshaya Panigrahi

Michigan Tech Publications, Part 2

Efficient detection of selected persistent organic pollutants (POPs) is extremely important for the safety of humans and for the moderation of agriculture. This calls for the design of versatile nanosensors capable of sensing toxic POPs with high sensitivity and selectivity. Inspired by this, the sensing characteristics of carbon nitride (C3N5) monolayers toward selected POPs are reported, such as Dichlorodiphenyltrichloroethane (DDT), Methoxychlor (DMDT), Fenthion (FT), Fenitrothion (FNT), and Rennol (RL), employing density functional theory calculations. Analysis of results predicts adsorption energies of −0.93, −1.55, −1.44, −0.98, and −1.15 eV for DDT, DMDT, FT, FNT, and RM, respectively, on C3N5 monolayers. Significant …

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S-Net: A Multiple Cross Aggregation Convolutional Architecture For Automatic Segmentation Of Small/Thin Structures For Cardiovascular Applications, Nan Mu, Zonghan Lyu, Mostafa Rezaeitaleshmahalleh, Cassie Bonifas, Jordan Gosnell, Marcus Haw, Joseph Vettukattil, Jingfeng Jiang Nov 2023

S-Net: A Multiple Cross Aggregation Convolutional Architecture For Automatic Segmentation Of Small/Thin Structures For Cardiovascular Applications, Nan Mu, Zonghan Lyu, Mostafa Rezaeitaleshmahalleh, Cassie Bonifas, Jordan Gosnell, Marcus Haw, Joseph Vettukattil, Jingfeng Jiang

Michigan Tech Publications, Part 2

With the success of U-Net or its variants in automatic medical image segmentation, building a fully convolutional network (FCN) based on an encoder-decoder structure has become an effective end-to-end learning approach. However, the intrinsic property of FCNs is that as the encoder deepens, higher-level features are learned, and the receptive field size of the network increases, which results in unsatisfactory performance for detecting low-level small/thin structures such as atrial walls and small arteries. To address this issue, we propose to keep the different encoding layer features at their original sizes to constrain the receptive field from increasing as the network …

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Hydrogen Peroxide-Dependent Oxidation Of Erk2 Within Its D-Recruitment Site Alters Its Substrate Selection, Anthony E. Postiglione, Laquaundra L. Adams, Ese S. Ekhator, Anuoluwapo E. Odelade, Supriya Patwardhan, Meenal Chaudhari, Avery S. Pardue, Anjali Kumari, William A. Lefever, Olivia P. Tornow, Tamer S. Kaoud, Johnathan Neiswinger, Jun Seop Jeong, Derek Parsonage, Kimberly J. Nelson, Dukka Kc, Cristina M. Furdui, Heng Zhu, Andrew J. Wommack, Kevin N. Dalby, Ming Dong, Leslie B. Poole, Jeremiah D. Keyes, Robert H. Newman Oct 2023

Hydrogen Peroxide-Dependent Oxidation Of Erk2 Within Its D-Recruitment Site Alters Its Substrate Selection, Anthony E. Postiglione, Laquaundra L. Adams, Ese S. Ekhator, Anuoluwapo E. Odelade, Supriya Patwardhan, Meenal Chaudhari, Avery S. Pardue, Anjali Kumari, William A. Lefever, Olivia P. Tornow, Tamer S. Kaoud, Johnathan Neiswinger, Jun Seop Jeong, Derek Parsonage, Kimberly J. Nelson, Dukka Kc, Cristina M. Furdui, Heng Zhu, Andrew J. Wommack, Kevin N. Dalby, Ming Dong, Leslie B. Poole, Jeremiah D. Keyes, Robert H. Newman

Michigan Tech Publications, Part 2

Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are dysregulated in many pervasive diseases. Recently, we discovered that ERK1/2 is oxidized by signal-generated hydrogen peroxide in various cell types. Since the putative sites of oxidation lie within or near ERK1/2’s ligand-binding surfaces, we investigated how oxidation of ERK2 regulates interactions with the model substrates Sub-D and Sub-F. These studies revealed that ERK2 undergoes sulfenylation at C159 on its D-recruitment site surface and that this modification modulates ERK2 activity differentially between substrates. Integrated biochemical, computational, and mutational analyses suggest a plausible mechanism for peroxide-dependent changes in ERK2-substrate interactions. Interestingly, oxidation decreased ERK2’s …

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Fast And Slow Microphysics Regimes In A Minimalist Model Of Cloudy Rayleigh-Bénard Convection, Raymond A. Shaw, Subin Thomas, Prasanth Prabhakaran, Will Cantrell, Mikhail Ovchinnikov, Fan Yang Oct 2023

Fast And Slow Microphysics Regimes In A Minimalist Model Of Cloudy Rayleigh-Bénard Convection, Raymond A. Shaw, Subin Thomas, Prasanth Prabhakaran, Will Cantrell, Mikhail Ovchinnikov, Fan Yang

Michigan Tech Publications, Part 2

A minimalist model of microphysical properties in cloudy Rayleigh-Bénard convection is developed based on mass and number balances for cloud droplets growing by vapor condensation. The model is relevant to a turbulent mixed-layer in which a steady forcing of supersaturation can be defined, e.g., a model of the cloudy boundary layer or a convection-cloud chamber. The model assumes steady injection of aerosol particles that are activated to form cloud droplets, and the removal of cloud droplets through sedimentation. Simplifying assumptions include the consideration of mean properties in steady state, neglect of coalescence growth, and no detailed representation of the droplet …

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Evolution Of Glassy Carbon Derived From Pyrolysis Of Furan Resin, Josh Kemppainen, Ivan Gallegos, Aaron Krieg, Jacob R. Gissinger, Kristopher E. Wise, Margaret Kowalik, Julia A. King, S. Gowtham, Adri Van Duin, Gregory Odegard Oct 2023

Evolution Of Glassy Carbon Derived From Pyrolysis Of Furan Resin, Josh Kemppainen, Ivan Gallegos, Aaron Krieg, Jacob R. Gissinger, Kristopher E. Wise, Margaret Kowalik, Julia A. King, S. Gowtham, Adri Van Duin, Gregory Odegard

Michigan Tech Publications, Part 2

Glassy carbon (GC) material derived from pyrolyzed furan resin was modeled by using reactive molecular dynamics (MD) simulations. The MD polymerization simulation protocols to cure the furan resin precursor material are validated via comparison of the predicted density and Young's modulus with experimental values. The MD pyrolysis simulations protocols to pyrolyze the furan resin precursor is validated by comparison of calculated density, Young's modulus, carbon content, sp carbon content, the in-plane crystallite size, out-of-plane crystallite stacking height, and interplanar crystallite spacing with experimental results from the literature for furan resin derived GC. The modeling methodology established in this work can …

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The Influence Of Arm Positions On Mechanical Dyssynchrony Measured By Gated Myocardial Perfusion Imaging, Zhongqiang Zhao, Cheng Wang, Zeyu Peng, Ju Bu, Chunxiang Li, Dianfu Li, Weihua Zhou, Rongsheng Lu, Lijun Tang, Yong Li Oct 2023

The Influence Of Arm Positions On Mechanical Dyssynchrony Measured By Gated Myocardial Perfusion Imaging, Zhongqiang Zhao, Cheng Wang, Zeyu Peng, Ju Bu, Chunxiang Li, Dianfu Li, Weihua Zhou, Rongsheng Lu, Lijun Tang, Yong Li

Michigan Tech Publications, Part 2

Background : In routine procedures, patient's arms are positioned above their heads to avoid potential attenuation artifacts and reduced image quality during gated myocardial perfusion imaging (G-MPI). However, it is difficult to achieve this action in the acute period following pacemaker implantation. This study aimed to explore the influence of arm positioning on myocardial perfusion imaging (MPI) in different types of heart disease. Methods: This study was conducted retrospectively. A total of 123 patients were enrolled and underwent resting G-MPI using a standard protocol with arms positioned above their heads and again with their arms at their sides. All individuals …

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Augerprime Surface Detector Electronics, A. Abdul Halim, P. Abreu, M. Aglietta, P. Allison, I. Allekotte, K. Almeida Cheminant, B. Fick, K. Nguyen, D. Nitz, A. Puyleart, Et Al. Oct 2023

Augerprime Surface Detector Electronics, A. Abdul Halim, P. Abreu, M. Aglietta, P. Allison, I. Allekotte, K. Almeida Cheminant, B. Fick, K. Nguyen, D. Nitz, A. Puyleart, Et Al.

Michigan Tech Publications, Part 2

Operating since 2004, the Pierre Auger Observatory has led to major advances in our understanding of the ultra-high-energy cosmic rays. The latest findings have revealed new insights that led to the upgrade of the Observatory, with the primary goal of obtaining information on the primary mass of the most energetic cosmic rays on a shower-by-shower basis. In the framework of the upgrade, called AugerPrime, the 1660 water-Cherenkov detectors of the surface array are equipped with plastic scintillators and radio antennas, allowing us to enhance the composition sensitivity. To accommodate new detectors and to increase experimental capabilities, the electronics is also …

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A Usability Study Of Nomon: A Flexible Interface For Single-Switch Users, Nicholas Bonaker, Emli Mari Nel, Keith Vertanen, Tamara Broderick Oct 2023

A Usability Study Of Nomon: A Flexible Interface For Single-Switch Users, Nicholas Bonaker, Emli Mari Nel, Keith Vertanen, Tamara Broderick

Michigan Tech Publications, Part 2

Many individuals with severe motor impairments communicate via a single switch - which might be activated by a blink, facial movement, or puff of air. These switches are commonly used as input to scanning systems that allow selection from a 2D grid of options. Nomon is an alternative interface that provides a more flexible layout, not confined to a grid. Previous work suggests that, even when options appear in a grid, Nomon may be faster and easier to use than scanning systems. However, previous work primarily tested Nomon with non-motor-impaired individuals, and evaluation with potential end-users was limited to a …

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Molecular And Physical Composition Of Tar Balls In Wildfire Smoke: An Investigation With Complementary Ionisation Methods And 15-Tesla Ft-Icr Mass Spectrometry, Amna Ijaz, William Kew, Zezhen Cheng, Susan Mathai, Nurun Nahar Lata, Libor Kovarik, Simeon Schum, Swarup China, Lynn Mazzoleni Sep 2023

Molecular And Physical Composition Of Tar Balls In Wildfire Smoke: An Investigation With Complementary Ionisation Methods And 15-Tesla Ft-Icr Mass Spectrometry, Amna Ijaz, William Kew, Zezhen Cheng, Susan Mathai, Nurun Nahar Lata, Libor Kovarik, Simeon Schum, Swarup China, Lynn Mazzoleni

Michigan Tech Publications, Part 2

Tar balls (TBs) are a major carbonaceous product of wildfires and other biomass-burning events that often exceed soot or other elemental forms of carbon in number and mass. Being a recalcitrant fraction of organic carbon, TBs are capable of long-range atmospheric transport, and thus, exert influence not only in the vicinity of wildfires but also in remote regions. Here, we characterised ambient atmospheric aerosol samples with varying TB number fractions collected downwind of Pacific Northwest wildfires using a 15-Tesla Fourier transform-ion cyclotron resonance mass spectrometer (15-T FT-ICR MS). Relative to non-TB aerosol, we found 2006 and 851 molecular formulae exclusively …

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Joint Semiparametric Kernel Network Regression, Byung Jun Kim, Inyoung Kim Sep 2023

Joint Semiparametric Kernel Network Regression, Byung Jun Kim, Inyoung Kim

Michigan Tech Publications, Part 2

Variable selection and graphical modeling play essential roles in highly correlated and high-dimensional (HCHD) data analysis. Variable selection methods have been developed under both parametric and nonparametric model settings. However, variable selection for nonadditive, nonparametric regression with high-dimensional variables is challenging due to complications in modeling unknown dependence structures among HCHD variables. Gaussian graphical models are a popular and useful tool for investigating the conditional dependence between variables via estimating sparse precision matrices. For a given class of interest, the estimated precision matrices can be mapped onto networks for visualization. However, the limitation of Gaussian graphical models is that they …

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From Random To Rational: Improving Enzyme Design Through Electric Fields, Second Coordination Sphere Interactions, And Conformational Dynamics, Shobhit S. Chaturvedi, Daniel Bím, Christo Christov, Anastassia N. Alexandrova Sep 2023

From Random To Rational: Improving Enzyme Design Through Electric Fields, Second Coordination Sphere Interactions, And Conformational Dynamics, Shobhit S. Chaturvedi, Daniel Bím, Christo Christov, Anastassia N. Alexandrova

Michigan Tech Publications, Part 2

Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme …

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Hawc Study Of The Very-High-Energy Γ-Ray Spectrum Of Hawc J1844−034, A. Albert, C. Alvarez, D. Avila Rojas, H. A.Ayala Solares, R. Babu, E. Belmont-Moreno, S. Groetsch, D. Huang, P. Huntemeyer, R. Turner, X. Wang, Et Al. Sep 2023

Hawc Study Of The Very-High-Energy Γ-Ray Spectrum Of Hawc J1844−034, A. Albert, C. Alvarez, D. Avila Rojas, H. A.Ayala Solares, R. Babu, E. Belmont-Moreno, S. Groetsch, D. Huang, P. Huntemeyer, R. Turner, X. Wang, Et Al.

Michigan Tech Publications, Part 2

Recently, the region surrounding eHWC J1842−035 has been studied extensively by γ-ray observatories due to its extended emission reaching up to a few hundred TeV and potential as a hadronic accelerator. In this work, we use 1910 days of cumulative data from the High Altitude Water Cherenkov (HAWC) observatory to carry out a dedicated systematic source search of the eHWC J1842−035 region. During the search, we found three sources in the region, namely, HAWC J1844−034, HAWC J1843−032, and HAWC J1846−025. We have identified HAWC J1844−034 as the extended source that emits photons with energies up to 175 TeV. We compute …

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Establishing Physical And Chemical Mechanisms Of Polymerization And Pyrolysis Of Phenolic Resins For Carbon-Carbon Composites, Ivan Gallegos, Josh Kemppainen, Jacob R. Gissinger, Malgorzata Kowalik, Adri Van Duin, Kristopher E. Wise, S. Gowtham, Gregory Odegard Sep 2023

Establishing Physical And Chemical Mechanisms Of Polymerization And Pyrolysis Of Phenolic Resins For Carbon-Carbon Composites, Ivan Gallegos, Josh Kemppainen, Jacob R. Gissinger, Malgorzata Kowalik, Adri Van Duin, Kristopher E. Wise, S. Gowtham, Gregory Odegard

Michigan Tech Publications, Part 2

The complex structural and chemical changes that occur during polymerization and pyrolysis critically affect material properties but are difficult to characterize in situ. This work presents a novel, experimentally validated methodology for modeling the complete polymerization and pyrolysis processes for phenolic resin using reactive molecular dynamics. The polymerization simulations produced polymerized structures with mass densities of 1.24 ± 0.01 g/cm3 and Young's moduli of 3.50 ± 0.64 GPa, which are in good agreement with experimental values. The structural properties of the subsequently pyrolyzed structures were also found to be in good agreement with experimental X-ray data for the phenolic-derived carbon …

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Reconstructing 42 Years (1979–2020) Of Great Lakes Surface Temperature Through A Deep Learning Approach, Miraj Kayastha, Tao Liu, Daniel Titze, Timothy C. Havens, Chenfu Huang, Pengfei Xue Aug 2023

Reconstructing 42 Years (1979–2020) Of Great Lakes Surface Temperature Through A Deep Learning Approach, Miraj Kayastha, Tao Liu, Daniel Titze, Timothy C. Havens, Chenfu Huang, Pengfei Xue

Michigan Tech Publications, Part 2

Accurate estimates for the lake surface temperature (LST) of the Great Lakes are critical to understanding the regional climate. Dedicated lake models of various complexity have been used to simulate LST but they suffer from noticeable biases and can be computationally expensive. Additionally, the available historical LST datasets are limited by either short temporal coverage (<30 >years) or lower spatial resolution (0.25° × 0.25°). Therefore, in this study, we employed a deep learning model based on Long Short-Term Memory (LSTM) neural networks to produce a daily LST dataset for the Great Lakes that spans an unparalleled 42 years (1979–2020) at …

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A Search For Relativistic Ejecta In A Sample Of Ztf Broad-Lined Type Ic Supernovae, Alessandra Corsi, Anna Y.Q. Ho, S. Bradley Cenko, Shrinivas R. Kulkarni, Shreya Anand, Sheng Yang, Jesper Sollerman, Gokul P. Srinivasaragavan, Conor M.B. Omand, Arvind Balasubramanian, Dale A. Frail, Christoffer Fremling, Daniel A. Perley, Yuhan Yao, Aishwarya S. Dahiwale, Kishalay De, Alison Dugas, Matthew Hankins, Jacob Jencson, Mansi M. Kasliwal, Anastasios Tzanidakis, Eric C. Bellm, Russ R. Laher, Frank J. Masci, Josiah N. Purdum, Nicolas Regnault Aug 2023

A Search For Relativistic Ejecta In A Sample Of Ztf Broad-Lined Type Ic Supernovae, Alessandra Corsi, Anna Y.Q. Ho, S. Bradley Cenko, Shrinivas R. Kulkarni, Shreya Anand, Sheng Yang, Jesper Sollerman, Gokul P. Srinivasaragavan, Conor M.B. Omand, Arvind Balasubramanian, Dale A. Frail, Christoffer Fremling, Daniel A. Perley, Yuhan Yao, Aishwarya S. Dahiwale, Kishalay De, Alison Dugas, Matthew Hankins, Jacob Jencson, Mansi M. Kasliwal, Anastasios Tzanidakis, Eric C. Bellm, Russ R. Laher, Frank J. Masci, Josiah N. Purdum, Nicolas Regnault

Michigan Tech Publications, Part 2

The dividing line between gamma-ray bursts (GRBs) and ordinary stripped-envelope core-collapse supernovae (SNe) is yet to be fully understood. Observationally mapping the variety of ejecta outcomes (ultrarelativistic, mildly relativistic, or nonrelativistic) in SNe of Type Ic with broad lines (Ic - BL) can provide a key test to stellar explosion models. However, this requires large samples of the rare SN Ic - BL events with follow-up observations in the radio, where fast ejecta can be probed largely free of geometry and viewing angle effects. Here, we present the results of a radio (and X-ray) follow-up campaign of 16 SNe Ic …

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Cytochrome P450 Gene Families: Role In Plant Secondary Metabolites Production And Plant Defense, Panchali Chakraborty, Ashok Biswas, Susmita Dey, Tuli Bhattacharjee, Swapan Chakrabarty Jul 2023

Cytochrome P450 Gene Families: Role In Plant Secondary Metabolites Production And Plant Defense, Panchali Chakraborty, Ashok Biswas, Susmita Dey, Tuli Bhattacharjee, Swapan Chakrabarty

Michigan Tech Publications, Part 2

Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by …

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Biological Formation Of Ethylene, Robert P. Hausinger, Simahudeen Bathir Jaber Sathik Rifayee, Midhun George Thomas, Shramana Chatterjee, Jian Hu, Christo Christov Jul 2023

Biological Formation Of Ethylene, Robert P. Hausinger, Simahudeen Bathir Jaber Sathik Rifayee, Midhun George Thomas, Shramana Chatterjee, Jian Hu, Christo Christov

Michigan Tech Publications, Part 2

This review summarizes the structures, biochemical properties, and mechanisms of two major biological sources of ethylene, the ethylene-forming enzyme (EFE) and 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACCO). EFE is found in selected bacteria and fungi where it catalyzes two reactions: (1) the oxygen-dependent conversion of 2-oxoglutarate (2OG) to ethylene plus three molecules of CO2/bicarbonate and (2) the oxidative decarboxylation of 2OG while transforming l-arginine to guanidine and l-Δ1-pyrroline-5-carboxylic acid. ACCO is present in plants where it makes the plant hormone by transforming ACC, O2, and an external reductant to ethylene, HCN, CO2, and water. Despite catalyzing distinct chemical reactions, EFE and …

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Deep Learning-Based Diagnosis Of Disease Activity In Patients With Graves’ Orbitopathy Using Orbital Spect/Ct, Ni Yao, Longxi Li, Zhengyuan Gao, Chen Zhao, Yanting Li, Chuang Han, Jiaofen Nan, Zelin Zhu, Yi Xiao, Fubao Zhu, Min Zhao, Weihua Zhou Jul 2023

Deep Learning-Based Diagnosis Of Disease Activity In Patients With Graves’ Orbitopathy Using Orbital Spect/Ct, Ni Yao, Longxi Li, Zhengyuan Gao, Chen Zhao, Yanting Li, Chuang Han, Jiaofen Nan, Zelin Zhu, Yi Xiao, Fubao Zhu, Min Zhao, Weihua Zhou

Michigan Tech Publications

Purpose: Orbital [99mTc]TcDTPA orbital single-photon emission computed tomography (SPECT)/CT is an important method for assessing inflammatory activity in patients with Graves’ orbitopathy (GO). However, interpreting the results requires substantial physician workload. We aim to propose an automated method called GO-Net to detect inflammatory activity in patients with GO. Materials and methods: GO-Net had two stages: (1) a semantic V-Net segmentation network (SV-Net) that extracts extraocular muscles (EOMs) in orbital CT images and (2) a convolutional neural network (CNN) that uses SPECT/CT images and the segmentation results to classify inflammatory activity. A total of 956 eyes from 478 patients with GO …

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Identification Of Dialect For Eastern And Southwestern Ojibwe Words Using A Small Corpus, Kalvin Hartwig, Evan Lucas, Timothy C. Havens Jul 2023

Identification Of Dialect For Eastern And Southwestern Ojibwe Words Using A Small Corpus, Kalvin Hartwig, Evan Lucas, Timothy C. Havens

Michigan Tech Publications, Part 2

The Ojibwe language has several dialects that vary to some degree in both spoken and written form. We present a method of using support vector machines to classify two different dialects (Eastern and Southwestern Ojibwe) using a very small corpus of text. Classification accuracy at the sentence level is 90% across a five-fold cross validation and 72% when the sentence-trained model is applied to a data set of individual words. Our code and the word level data set are released openly at https://github.com/evanperson/OjibweDialect.

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Single-Mode Quasi Pt-Symmetric Laser With High Power Emission, Enes Şeker, Babak Olyaeefar, Khalil Dadashi, Serdar Şengül, Mohammad Hosain Teimourpour, Ramy El-Ganainy, Abdullah Demir Jun 2023

Single-Mode Quasi Pt-Symmetric Laser With High Power Emission, Enes Şeker, Babak Olyaeefar, Khalil Dadashi, Serdar Şengül, Mohammad Hosain Teimourpour, Ramy El-Ganainy, Abdullah Demir

Michigan Tech Publications

Large-area lasers are practical for generating high output powers. However, this often comes at the expense of lower beam quality due to the introduction of higher-order modes. Here, we experimentally demonstrate a new type of electrically pumped, large-area edge-emitting lasers that exhibit a high power emission (∼ 0.4 W) and a high-quality beam (M ∼ 1.25). These favorable operational characteristics are enabled by establishing a quasi PT-symmetry between the second-order mode of a large area two-mode laser cavity and that of a single-mode auxiliary partner cavity, i.e., by implementing a partial isospectrality between the two coupled cavities. This in turn …

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Limits On Leptonic Tev Emission From The Cygnus Cocoon With Swift-Xrt, David Guevel, Andrew Beardmore, Kim L. Page, Amy Lien, Ke Fang, Luigi Tibaldo, Sabrina Casanova, Petra Huentemeyer Jun 2023

Limits On Leptonic Tev Emission From The Cygnus Cocoon With Swift-Xrt, David Guevel, Andrew Beardmore, Kim L. Page, Amy Lien, Ke Fang, Luigi Tibaldo, Sabrina Casanova, Petra Huentemeyer

Michigan Tech Publications

3-ray observations of the Cygnus Cocoon, an extended source surrounding the Cygnus X star-forming region, suggest the presence of a cosmic-ray accelerator reaching energies up to a few PeV. The very-high-energy (VHE, 0.1-100 TeV) 3-ray emission may be explained by the interaction of cosmic-ray hadrons with matter inside the Cocoon, but an origin of inverse Compton radiation by relativistic electrons cannot be ruled out. Inverse Compton 3-rays at VHE are accompanied by synchrotron radiation peaked in X-rays. Hence, X-ray observations may probe the electron population and magnetic field of the source. We observed 11 fields in or near the Cygnus …

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Coordinating Tethered Autonomous Underwater Vehicles Towards Entanglement-Free Navigation, Abhishek Patil, Myoungkuk Park, Jungyun Bae Jun 2023

Coordinating Tethered Autonomous Underwater Vehicles Towards Entanglement-Free Navigation, Abhishek Patil, Myoungkuk Park, Jungyun Bae

Michigan Tech Publications

This paper proposes an algorithm that provides operational strategies for multiple tethered autonomous underwater vehicle (T-AUV) systems for entanglement-free navigation. T-AUVs can perform underwater tasks under reliable communication and power supply, which is the most substantial benefit of their operation. Thus, if one can overcome the entanglement issues while utilizing multiple tethered vehicles, the potential applications of the system increase including ecosystem exploration, infrastructure inspection, maintenance, search and rescue, underwater construction, and surveillance. In this study, we focus on developing strategies for task allocation, path planning, and scheduling that ensure entanglement-free operations while considering workload balancing among the vehicles. We …

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Learning Neutrino Effects In Cosmology With Convolutional Neural Network, Elena Giusarma, Mauricio Reyes, Francisco Villaescusa-Navarro, Siyu He, Shirley Ho, Chang Hoon Hahn Jun 2023

Learning Neutrino Effects In Cosmology With Convolutional Neural Network, Elena Giusarma, Mauricio Reyes, Francisco Villaescusa-Navarro, Siyu He, Shirley Ho, Chang Hoon Hahn

Michigan Tech Publications

Measuring the sum of the three active neutrino masses, M ν , is one of the most important challenges in modern cosmology. Massive neutrinos imprint characteristic signatures on several cosmological observables, in particular, on the large-scale structure of the universe. In order to maximize the information that can be retrieved from galaxy surveys, accurate theoretical predictions in the nonlinear regime are needed. Currently, one way to achieve those predictions is by running cosmological numerical simulations. Unfortunately, producing those simulations requires high computational resources—several hundred to thousand core hours for each neutrino mass case. In this work, we propose a new …

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