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Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria
Article describes how, since the discovery of the second chromosome in the Rhodobacter spaeroides 2.4.1 in 1989 and the revelation of gene sequences, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. In this study, the authors have attempted to leverage machine learning as a means to identify the genetic factors that underlie the differentiation of bacteria with multipartite and unipartite genomes.
Date:
November 13, 2023
Creator:
Almalki, Fatemah; Sunuwar, Janak & Azad, Rajeev K.
Object Type:
Article
System:
The UNT Digital Library
Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement
Article describes how, although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. In this work, the authors combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement.
Date:
June 19, 2023
Creator:
Arias, Cintia Lucía; García Navarrete, Leidy Tatiana; Mukundi, Eric; Swanson, Tyler; Yang, Fan; Hernandez, Jonathan et al.
Object Type:
Article
System:
The UNT Digital Library
Two legume fatty acid amide hydrolase isoforms with distinct preferences for microbial- and plant-derived acylamides
Article describes how analysis of FAAHs from multiple angiosperm species, which revealed two conserved phylogenetic groups that differed in key conserved residues in the substrate binding pocket. The authors combined computational and biochemical approaches to compare the structural and enzymatic properties of two FAAH isoforms in the legume Medicago truncatula designated MtFAAH1 MtFAAH2a.
Date:
May 9, 2023
Creator:
Arias-Gaguancela, Omar; Herrell, Emily; Aziz, Mina & Chapman, Kent Dean
Object Type:
Article
System:
The UNT Digital Library
Formation of cotton bast fiber as a means to modulate carbon capture and increase bio-product utilization
Data management plan for the grant "Formation of cotton bast fiber as a means to modulate carbon capture and increase bio-product utilization."
Date:
2023-05-01/2026-04-30
Creator:
Ayre, Brian G.
Object Type:
Text
System:
The UNT Digital Library
A Laser Microdissection System to Enhance Agricultural and Food Research in the North Texas and Southern Oklahoma Region
Data management plan for the grant, "A Laser Microdissection System to Enhance Agricultural and Food Research in the North Texas and Southern Oklahoma Region."
Date:
2023-09-01/2027-08-31
Creator:
Ayre, Brian G.
Object Type:
Text
System:
The UNT Digital Library
Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice
Article describes how genetic variation accounts for much of the risk for developing a substance use disorder, but the underlying genetic factors and their genetic effector mechanisms are mostly unknown. To test their genetic hypothesis, the authors generated and characterized Nav1 knockout mice.
Date:
October 18, 2023
Creator:
Bagley, Jared R.; Tan, Yalun; Zhu, Wan; Cheng, Zhuanfen; Takeda, Saori; Fang, Zhouqing et al.
Object Type:
Article
System:
The UNT Digital Library
Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light
Article describes how induction of high photosynthetic capacity is a key acclimation response to high light for many herbaceous dicot plants. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions.
Date:
October 17, 2023
Creator:
Baker, Christopher R.; Cocuron, Jean-Christophe; Alonso, Ana Paula & Niyogi, Krishna K.
Object Type:
Article
System:
The UNT Digital Library
Biophotons: New Experimental Data and Analysis
Article describes how biophotons are an ultra-weak emission of photons in the visible energy range from living matter. The authors study the emission from germinating seeds using an experimental technique designed to detect light of extremely small intensity.
Date:
October 10, 2023
Creator:
Benfatto, Maurizio; Pace, Elisabetta; Davoli, Ivan; Francini, Roberto; Matteis, Fabio De; Scordo, Alessandro et al.
Object Type:
Article
System:
The UNT Digital Library
A Highly Contiguous and Annotated Genome Assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus)
Article asserts that the Lesser Prairie-Chicken (Tympanuchus pallidicinctus; LEPC) is an iconic North American prairie grouse, renowned for ornate and spectacular breeding season displays, a species that has been declining in population across much of its historical range, with corresponding precipitous declines in contemporary population abundance, largely due to climatic and anthropogenic factors. The authors describe an annotated reference genome that was generated from a LEPC sample collected from the southern DPS.
Date:
March 17, 2023
Creator:
Black, Andrew N.; Bondo, Kristin J.; Mularo, Andrew; Hernandez, Alvaro; Yu, Yachi; Stein, Carleigh M. et al.
Object Type:
Article
System:
The UNT Digital Library
Scientists warning on the ecological effects of radioactive leaks on ecosystems
Article describes the devastating effects of nuclear radiation and its long-lasting consequences on Earth’s ecosystems. The authors call upon all scientists to communicate the importance of the environmental impacts of such an event to all life forms on Earth, including humankind.
Date:
January 20, 2023
Creator:
Bonacic, Cristián; Medellin, Rodrigo A.; Ripple, William; Sukumar, Raman; Ganswindt, Andre; Padua, Suzana M. et al.
Object Type:
Article
System:
The UNT Digital Library
Seeing plants as never before
Authors of the article assert that imaging has long supported our ability to understand the inner life of plants, their development, and response to a dynamic environment. The purpose of this review was to provide the scientific community with an overview of current imaging methods, which rely variously on either nuclear magnetic resonance (NMR), mass spectrometry (MS) or infrared (IR) spectroscopy, and to present some examples of their application in order to illustrate their utility.
Date:
March 9, 2023
Creator:
Borisjuk, Ljudmilla; Horn, Patrick J.; Chapman, Kent Dean; Jakob, Peter M.; Gündel, Andre & Rolletschek, Hardy
Object Type:
Article
System:
The UNT Digital Library
POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling
Article presents POSMM, Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. The authors claim that by combining POSMM with ultrafast classifiers such as Kraken2, their complementary strengths can be leveraged to produce higher overall accuracy in metagenomic sequence classification than by either as a standalone classifier. POSMM is a user-friendly and highly adaptable tool designed for broad use by the metagenome scientific community.
Date:
March 8, 2023
Creator:
Burks, David J.; Pusadkar, Vaidehi & Azad, Rajeev K.
Object Type:
Article
System:
The UNT Digital Library
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages
Article asserts that the delivery of consistent and accurate fine-resolution data on biodiversity using metabarcoding promises to improve environmental assessment and research. The authors propose a novel hierarchical approach to recovering abundance information from metabarcoding, and demonstrate this technique using benthic macroinvertebrates.
Date:
March 31, 2023
Creator:
Bush, A.; Compson, Z.; Rideout, N. K.; Levenstein, B.; Kattilakoski, M.; Hajibabaei, M. et al.
Object Type:
Article
System:
The UNT Digital Library
A modified aeroponic system for growing small-seeded legumes and other plants to study root systems
Authors of the article state that various growth systems are available for studying plant root growth and plant–microbe interactions including hydroponics and aeroponics. The aim of their study is to present step-by-step instructions for fabricating an aeroponic system, also called a “caisson,” that has been in use in several legume research labs studying the development of symbiotic nitrogen fixing nodules, but for which detailed directions are not currently available.
Date:
March 3, 2023
Creator:
Cai, Jingya; Veerappan, Vijaykumar; Arildsen, Kate; Sullivan, Catrina; Piechowicz, Megan; Frugoli, Julia et al.
Object Type:
Article
System:
The UNT Digital Library
Correction: A modified aeroponic system for growing small-seeded legumes and other plants to study root systems
This is a correction to an article. The affiliation of the first author was published incorrectly.
Date:
March 25, 2023
Creator:
Cai, Jingya; Veerappan, Vijaykumar; Arildsen, Kate; Sullivan, Catrina; Piehowicz, Megan; Frugoli, Julia et al.
Object Type:
Article
System:
The UNT Digital Library
A metabolomic platform to identify and quantify polyphenols in coffee and related species using liquid chromatography mass spectrometry
Article describes how products of plant secondary metabolism, such as phenolic compounds, flavonoids, alkaloids, and hormones, play an important role in plant growth, development, stress resistance. The authors state that the overall goal of this study was to develop a high-throughput workflow to identify and quantify plant polyphenols.
Date:
January 6, 2023
Creator:
Castro-Moretti, Fernanda R.; Cocuron, Jean-Christophe; Castillo-Gonzalez, Humberto; Escudero-Leyva, Efrain; Chaverri, Priscila; Guerreiro-Filho, Oliveiro et al.
Object Type:
Article
System:
The UNT Digital Library
Assembling Artificial Photosynthetic Models in Water Using β-Cyclodextrin-Conjugated Phthalocyanines as Building Blocks
Article describes how two water-soluble zinc(II) phthalocyanines substituted with two or four permethylated β-cyclodextrin (β-CD) moieties at the α positions have been utilized as building blocks for the construction of artificial photosynthetic models in water. The hydrophilic and bulky β-CD moieties not only can increase the water solubility of the phthalocyanine core and prevent its stacking in water but can also bind with a tetrasulfonated zinc(II) porphyrin (ZnTPPS) and/or sodium 2-anthraquinonesulfonate (AQ) in water through host–guest interactions.
Date:
March 29, 2023
Creator:
Chen, Xiao-Fei; Gobeze, Habtom B.; D'Souza, Francis & Ng, Dennis K. P.
Object Type:
Article
System:
The UNT Digital Library
Tuning excited state electronic structure and charge transport in covalent organic frameworks for enhanced photocatalytic performance
Article describes how covalent organic frameworks (COFs) represent an emerging class of organic photocatalysts. The authors use reticular chemistry to construct a family of isoreticular crystalline hydrazide-based COF photocatalysts, with the optoelectronic properties and local pore characteristics of the COFs modulated using different linkers.
Date:
February 27, 2023
Creator:
Chen, Zhongshan; Wang, Jingyi; Hao, Mengjie; Xie, Yinghui; Liu, Xiaolu; Waterhouse, Geoffrey I. N. et al.
Object Type:
Article
System:
The UNT Digital Library
Quantitative PCR Primer Development for Early Detection of Invasive Species
Data management plan for the grant, "Quantitative PCR Primer Development for Early Detection of Invasive Species."
Date:
2023-09-01/2026-08-31
Creator:
Compson, Zacchaeus Greg
Object Type:
Text
System:
The UNT Digital Library
Southwest Local Algebra Meeting 2023
Data management plan for the grant, "Southwest Local Algebra Meeting 2023." No data will be collected or reported for this grant.
Date:
2023-01-15/2023-12-31
Creator:
Conley, Charles H.
Object Type:
Text
System:
The UNT Digital Library
Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance
Article describes how, in his 1945 Nobel Prize acceptance speech, Sir Alexander Fleming warned of antimicrobial resistance (AMR) if the necessary precautions were not taken diligently. This paper explores the applications of ML in predicting and understanding AMR, highlighting its potential in revolutionizing healthcare practices.
Date:
November 8, 2023
Creator:
Coxe, Tallon & Azad, Rajeev K.
Object Type:
Article
System:
The UNT Digital Library
A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1
Article describes how within the genome of a pathogen is the information regarding factors responsible for its pathogenicity. the authors of the article developed a novel pipeline that uses standard protocol in combination with gene co-expression network of a pathogen constructed using publicly available RNA-Seq data sets.
Date:
November 3, 2023
Creator:
De, Ronika; Whiteley, Marvin & Aza, Rajeev K.
Object Type:
Article
System:
The UNT Digital Library
Duals of Tirilman spaces have unique subsymmetric basic sequences
Article describes how the Tirilman spaces were introduced by Casazza and Shura as variations of the spaces constructed by Tzafriri. We prove that all subsymmetric basic sequences in the dual space are equivalent to its canonical subsymmetic but not symmetric basis.
Date:
September 5, 2023
Creator:
Dilworth, Steven J.; Kutzarova, Denka; Sari, Bünyamin & Stankov, Svetozar
Object Type:
Article
System:
The UNT Digital Library
Gemini Near Infrared Spectrograph–Distant Quasar Survey: Prescriptions for Calibrating UV-based Estimates of Supermassive Black Hole Masses in High-redshift Quasars
Article describes how the most reliable single-epoch supermassive black hole mass (MBH) estimates in quasars are obtained by using the velocity widths of low-ionization emission lines, typically the Hβλ4861 line. The authors find that utilizing both emission lines, where available, reduces the scatter of UV-based MBH estimates by ∼15% when compared to previous studies.
Date:
June 13, 2023
Creator:
Dix, Cooper; Matthews, Brandon; Shemmer, Ohad; Brotherton, Michael S.; Myers, Adam D.; Andruchow, I. et al.
Object Type:
Article
System:
The UNT Digital Library