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Transcriptomic profiling of miR-203a inhibitor and miR-34b-injected zebrafish (Danio rerio) validates oil-induced neurological, cardiovascular and eye toxicity response pathways (open access)

Transcriptomic profiling of miR-203a inhibitor and miR-34b-injected zebrafish (Danio rerio) validates oil-induced neurological, cardiovascular and eye toxicity response pathways

Article discusses how the global sequencing of microRNA (miRNA; miR) and integration to downstream mRNA expression profiles in early life stages (ELS) of fish following exposure to crude oil determined consistently dysregulated miRNAs regardless of the oil source or fish species. The overlay of differentially expressed miRNAs and mRNAs into in silico software determined that the key roles of these miRNAs were predicted to be involved in cardiovascular, neurological and visually-mediated pathways.
Date: November 21, 2022
Creator: Maguson, Jason T.; Leads, Rachel R.; McGruer, Victoria; Qian, Le; Tanabe, Philip; Roberts, Aaron P. et al.
System: The UNT Digital Library
Long-range current-induced spin accumulation in chiral crystals (open access)

Long-range current-induced spin accumulation in chiral crystals

Article states that chiral materials, similarly to human hands, have distinguishable right-handed and left-handed enantiomers which may behave differently in response to external stimuli, so for the first time the authors use an approach based on the density functional theory (DFT)+PAOFLOW calculations to quantitatively estimate the so-called collinear Rashba–Edelstein effect (REE) that generates spin accumulation parallel to charge current and can manifest as chirality-dependent charge-to-spin conversion in chiral crystals. The authors reveal that the spin accumulation induced in the bulk by an electric current is intrinsically protected by the quasi-persistent spin helix arising from the crystal symmetries present in chiral systems with the Weyl spin–orbit coupling.
Date: November 18, 2022
Creator: Roy, Arunesh; Cerasoli, Frank T.; Jayaraj, Anooja; Tenzin, Karma; Buongiorno Nardelli, Marco & Sławińska, Jagoda
System: The UNT Digital Library
The protein conformational basis of isoflavone biosynthesis (open access)

The protein conformational basis of isoflavone biosynthesis

Authors of the article assert that isoflavonoids play important roles in plant defense and also exhibit a range of mammalian health-promoting activities. They emphasize that understanding the structural basis of isoflavone biosynthesis will facilitate the engineering of new bioactive isoflavonoids.
Date: November 15, 2022
Creator: Wang, Xiaoqiang; Pan, Haiyun; Sagurthi, Someswar; Paris, Vincent; Zhuo, Chunliu & Dixon, R. A.
System: The UNT Digital Library
The Shadow Effect on Surface Biophysical Variables Derived from Remote Sensing: A Review (open access)

The Shadow Effect on Surface Biophysical Variables Derived from Remote Sensing: A Review

Article states that the main objective of this study was to review the recent literature on the shadow effect in remote sensing. An overview of the proposed methods for identifying and removing the shadow effect is presented.
Date: November 12, 2022
Creator: Alavipanah, Seyed Kazem; Firozjaei, Mohammad Karimi; Sedighi, Amir; Fathololoumi, Solmaz; Naghadehi, Saeid Zare; Saleh, Samiraalsadat et al.
System: The UNT Digital Library
Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations (open access)

Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations

Article provides a general reweighting framework based on anisotropic diffusion maps for manifold learning that takes into account that the learning data set is sampled from a biased probability distribution. The authors show that their proposed framework can be used in many manifold learning techniques on data from both standard and enhanced sampling simulations.
Date: November 11, 2022
Creator: Rydzewski, Jakub; Chen, Ming; Ghosh, Tushar K. & Valsson, Omar
System: The UNT Digital Library
A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense) (open access)

A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense)

Article describes a stepwise targeted lipidomics approach to characterize the polar and non-polar lipid classes using complementary LC-MS methods. This lipidomics workflow was applied to developing, mature, and germinated pennycress seeds/seedlings and found unexpected changes among several lipid molecular species.
Date: November 9, 2022
Creator: Romsdahl, Trevor B.; Cocuron, Jean-Christophe; Pearson, Mackenzie J.; Alonso, Ana Paula & Chapman, Kent Dean
System: The UNT Digital Library
Growth of Highly-Ordered Metal Nanoparticle Arrays in the Dimpled Pores of an Anodic Aluminum Oxide Template (open access)

Growth of Highly-Ordered Metal Nanoparticle Arrays in the Dimpled Pores of an Anodic Aluminum Oxide Template

Article presents a reliable, scalable, and inexpensive technology for the fabrication of ordered arrays of metal nanoparticles with large areal coverage on various substrates. Using a simple model, the experimental results were interpreted and supported by numerical estimations.
Date: November 8, 2022
Creator: Farmer, Gavin; Abraham, James; Littler, Chris; Syllaios, A. J. & Philipose, Usha
System: The UNT Digital Library
Identification of Novel Antimicrobial Resistance Genes Using Machine Learning, Homology Modeling, and Molecular Docking (open access)

Identification of Novel Antimicrobial Resistance Genes Using Machine Learning, Homology Modeling, and Molecular Docking

Article claims antimicrobial resistance (AMR) threatens the healthcare system worldwide with the rise of emerging drug resistant infectious agents. To infer novel resistance genes, we used complete gene sets of several bacterial strains known to be susceptible or resistant to specific drugs and associated phenotypic information within a machine learning framework that enabled prioritizing genes potentially involved in resistance.
Date: October 23, 2022
Creator: Sunuwar, Janak & Azad, Rajeev K.
System: The UNT Digital Library
MetaLP: An integrative linear programming method for protein inference in metaproteomics (open access)

MetaLP: An integrative linear programming method for protein inference in metaproteomics

Authors of the article discuss how MetaLP was developed here for protein inference in metaproteomics using an integrative linear programming method. Authors claim that MetaLP could substantially improve protein inference for complex metaproteomes by incorporating taxonomic abundance information in a linear programming model.
Date: October 21, 2022
Creator: Feng, Shichao; Ji, Hong-Long; Wang, Huan; Zhang, Bailu; Sterzenbach, Ryan; Pan, Chongle et al.
System: The UNT Digital Library
Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome (open access)

Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome

Article describes how postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The authors perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility.
Date: October 18, 2022
Creator: Neugent, Michael D.; Kumar, Ashwani; Hulyalkar, Neha V.; Lutz, Kevin C.; Nguyen, Vivian H.; Fuentes, Jorge L. et al.
System: The UNT Digital Library
Sustainable nutrition: a spatially explicit modeling approach for urban land use planning (open access)

Sustainable nutrition: a spatially explicit modeling approach for urban land use planning

Article describes how rapid urbanization has influenced the transformation of local and global food systems, altering the availability, access to, and distribution of healthy food. Micronutrient deficiency and hunger have been exacerbated worldwide. The author's research proposes a simulation strategy to evaluate the impact of agricultural land use and crop choices on nutritional production in rapidly growing urban areas.
Date: October 14, 2022
Creator: Torres, Angélica Torres; Tiwari, Chetan & Atkinson, Samuel F.
System: The UNT Digital Library
Unusual Mathematical Approaches Untangle Nervous Dynamics (open access)

Unusual Mathematical Approaches Untangle Nervous Dynamics

Article reports that the massive amount of available neurodata suggests the existence of a mathematical backbone underlying neuronal oscillatory activities. The authors assert that the Monge’s theorem might contribute to our visual ability of depth perception and the brain connectome can be tackled in terms of tunnelling nanotubes.
Date: October 14, 2022
Creator: Tozzi, Arturo & Mariniello, Lucio
System: The UNT Digital Library
Optical in-situ measurements and modeling of post-flame sulfation of NaOH(g) and NaCl(g) (open access)

Optical in-situ measurements and modeling of post-flame sulfation of NaOH(g) and NaCl(g)

Article describes post-flame sulfation of gaseous sodium hydroxide (NaOH) and sodium chloride (NaCl) was investigated with optical in situ measurements at 850 to 1475°C. The combined experimental data, chemical equilibrium calculations and kinetic modeling of the present study support that sulfation of alkali species can occur in the gas phase through homogeneous reactions.
Date: October 13, 2022
Creator: Schmid, Daniel; Weng, Wubin; Li, Shen; Karlström, Oskar; Hupa, Mikko; Li, Zhongshan et al.
System: The UNT Digital Library
Tuning the decay of sound in a viscous metamaterial (open access)

Tuning the decay of sound in a viscous metamaterial

Authors of the article use analytical results for viscous dissipation in phononic crystals to calculate the decay coefficient of a sound wave propagating at low frequencies through a two-dimensional phononic crystal with a viscous fluid background. They claim that the decay coefficient exhibits dependence on the direction of propagation; that is, a homogenized phononic crystal behaves like an anisotropic viscous fluid.
Date: October 10, 2022
Creator: Ibarias, M.; Doporto, J.; Krokhin, Arkadii A. & Arriaga, J.
System: The UNT Digital Library
A covalently linked nickel(II) porphyrin–ruthenium(II) tris(bipyridyl) dyad for efficient photocatalytic water oxidation (open access)

A covalently linked nickel(II) porphyrin–ruthenium(II) tris(bipyridyl) dyad for efficient photocatalytic water oxidation

Article describes how photocatalytic water splitting into H2 and O2 has attracted significant scientific interest for solar energy conversion applications during the last two decades. Authors of the article further elaborate that One of the half-reactions of this process, water oxidation, is known to be the key step in natural and artificial photosynthesis to convert and store solar energy.
Date: October 5, 2022
Creator: Nikoloudakis, Emmanouil; Alsaleh, Ajyal Z.; Charalambidis, Georgios; Coutsolelos, Athanassios G. & D'Souza, Francis
System: The UNT Digital Library
Corrosion Inhibition Effect of Pyridine-2-Thiol for Brass in An Acidic Environment (open access)

Corrosion Inhibition Effect of Pyridine-2-Thiol for Brass in An Acidic Environment

Article states that the inhibitive performance of pyridine-2-thiol added to a corrosive solution was investigated for brass using potentiodynamic polarization, electrochemical impedance spectroscopy, and X-ray photoelectron spectroscopy. Scanning electron microscopy showed defect free and less scale formation for the inhibited surface but the bare brass surface had larger amounts of scale formation. X-ray photoelectron spectroscopy and UV-vis spectroscopy was used to investigate surface chemical composition and inhibitor structural changes over time.
Date: October 3, 2022
Creator: Karunarathne, Darshan Jayasinghe; Aminifazl, Alireza; Abel, Tori E.; Quepons, Karen L. & Golden, Teresa Diane, 1963-
System: The UNT Digital Library
Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification associated pleiotropic effects (open access)

Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification associated pleiotropic effects

Article discusses how a bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon.
Date: September 28, 2022
Creator: Shrestha, Him K.; Fichman, Yosef; Engle, Nancy L.; Tschaplinski, Timothy J.; Mittler, Ron; Dixon, R. A. et al.
System: The UNT Digital Library
Urban edge trees: Urban form and meteorology drive elemental carbon deposition to canopies and soils (open access)

Urban edge trees: Urban form and meteorology drive elemental carbon deposition to canopies and soils

Article asserts that urban tree canopies are a significant sink for atmospheric elemental carbon (EC)--and air pollutant that is a powerful climate-forcing agent and threat to human health. The authors' findings indicate that complex configurations of roads, buildings, and vegetation produce “urban edge trees” that contribute to heterogeneous EC deposition patterns across urban systems, with implications for greenspace planning.
Date: September 27, 2022
Creator: Ponette-González, Alexandra G.; Chen, Dongmei; Elderbrock, Evan; Rindy, Jenna E.; Barrett, Tate E.; Luce, Brett W. et al.
System: The UNT Digital Library
Habitat amount or landscape configuration: Emerging HotSpot analysis reveals the importance of habitat amount for a grassland bird in South Dakota (open access)

Habitat amount or landscape configuration: Emerging HotSpot analysis reveals the importance of habitat amount for a grassland bird in South Dakota

The authors of the article used pheasants (Phasianus colchicus) across South Dakota, USA as a model species to identify environmental factors driving spatiotemporal variation in population productivity. They found that the amount of grassland at a local spatial scale was the primary factor influencing an area being a HotSpot.
Date: September 26, 2022
Creator: Harsh, Sprih; Lonsinger, Robert C. & Gregory, Andrew
System: The UNT Digital Library
Object-Oriented Canopy Gap Extraction from UAV Images Based on Edge Enhancement (open access)

Object-Oriented Canopy Gap Extraction from UAV Images Based on Edge Enhancement

Article describes the efficient and accurate identification of canopy gaps is the basis of forest ecosystem research, which is of great significance to further forest monitoring and management. One major limitation of the traditional methods of remote sensing to map canopy gaps is that they cannot finely extract the complex edges of canopy gaps in mountainous areas. The authors proposed an object-oriented classification method that integrates multi-source information.
Date: September 23, 2022
Creator: Xia, Jisheng; Wang, Yutong; Dong, Pinliang; He, Shijun; Zhao, Fei & Luan, Guize
System: The UNT Digital Library
Complete Genome Sequences of the Novel Cluster BP Phages Infecting Streptomyces sanglieri, AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra (open access)

Complete Genome Sequences of the Novel Cluster BP Phages Infecting Streptomyces sanglieri, AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra

Article describes the Streptomyces sanglieri bacteriophages AxeJC, Cumberbatch, Eastland,Eklok, HFrancette, Ignacio, Piccadilly, and Vondra form a novel actinobacteriophage cluster,BP. These siphoviruses have circularly permuted genomes with an average size of 37,700 bp and a GC content of 71%. Each genome contains approximately 58 protein-coding genes, with no tRNAs.
Date: September 14, 2022
Creator: Nath, Sreemoye; Sulaiman, Ahmad; Maneekul, Jindanuch; Bhuiyan, Swapan; Layton, Sonya R.; Menchaca, Carolina et al.
System: The UNT Digital Library
Metal-organic framework nanocrystal-derived hollow porousmaterials: Synthetic strategies and emerging applications (open access)

Metal-organic framework nanocrystal-derived hollow porousmaterials: Synthetic strategies and emerging applications

Article discusses how the fascinating, functional properties and applications of MOF-derived hollow porous materials primarily lie in their chemical composition, hollow character, and unique porous structure. The authors discuss a comprehensive overview of the synthetic strategies and emerging applications of hollow porous materials derived from MOF-based templates and/or precursors.
Date: September 13, 2022
Creator: Lui, Xiaolu; Verma, Guarav; Chen, Zhongshan; Hu, Baowei; Huang, Qifei; Yang, Hui et al.
System: The UNT Digital Library
Evaluation of pathways to the C-glycosyl isoflavone puerarin in roots of kudzu (Pueraria montana lobata) (open access)

Evaluation of pathways to the C-glycosyl isoflavone puerarin in roots of kudzu (Pueraria montana lobata)

Article describes how kudzu produces both O- and C-glycosylated isoflavones, with puerarin (C-glucosyl daidzein) as an important bioactive compound. The authors go on to explain how expression of recombinant UGTs in Escherichia coli and candidate C-glycosyltransferases in Medicago truncatula were used to explore substrate specificities, and gene silencing of UGT and key isoflavone biosynthetic genes in kudzu hairy roots employed to test hypotheses concerning the substrate(s) for C-glycosylation.
Date: September 2, 2022
Creator: Adolfo, Laci M.; Burks, David J.; Rao, Xiaolan; Alvarez-Hernandez, Anislay & Dixon, R. A.
System: The UNT Digital Library
Stereochemical and Biosynthetic Rationalisation of the Tropolone Sesquiterpenoids (open access)

Stereochemical and Biosynthetic Rationalisation of the Tropolone Sesquiterpenoids

Article summarises the known structures, biological activities, and biosynthetic pathways of the tropolone sesquiterpenoid family of fungal secondary metabolites. Synthesis of this knowledge allows likely structural and stereochemical misassignments to be revised and shows how the compounds can be divided into three main biosynthetic classes based on the stereochemistry of key biosynthetic steps.
Date: August 31, 2022
Creator: Li, Lei & Cox, Russell, J.
System: The UNT Digital Library