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POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling (open access)

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.
System: The UNT Digital Library
Assembling Artificial Photosynthetic Models in Water Using β-Cyclodextrin-Conjugated Phthalocyanines as Building Blocks (open access)

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.
System: The UNT Digital Library
Effects of cultivar and nitrogen application rate on lint, seed, oil, and protein yields of field-grown cotton (open access)

Effects of cultivar and nitrogen application rate on lint, seed, oil, and protein yields of field-grown cotton

Article describes how the objective of this study was to evaluate the lint, seed, oil, and protein yield responses of cultivars with different seed mass and composition to N application rates (0–168 kg N ha−1) for field-grown cotton. The authors conclude that variability in the distribution of photosynthates to fiber and seed as well as seed oil and protein composition can significantly alter trends in fiber, seed, and seed component yields in response to cultivar or N application rates for field-grown cotton.
Date: March 9, 2023
Creator: Parkash, Ved; Snider, John L.; Bruce, Aaron; Ermanis, Alessandro; Virk, Gurpreet; Kaur, Navneet et al.
System: The UNT Digital Library
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages (open access)

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.
System: The UNT Digital Library
A modified aeroponic system for growing small-seeded legumes and other plants to study root systems (open access)

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.
System: The UNT Digital Library
Genetic Differentiation of the South Florida Red-Shouldered Hawk (Buteo lineatus extimus) from the Nominate Subspecies (Buteo lineatus lineatus) (open access)

Genetic Differentiation of the South Florida Red-Shouldered Hawk (Buteo lineatus extimus) from the Nominate Subspecies (Buteo lineatus lineatus)

Article discusses how the south Florida subspecies of the Red-shouldered Hawk (Buteo lineatus extimus) is distinctly paler and smaller than other subspecies, reproduces at a lower rate, and can occupy very different habitats such as open marshes and grasslands with only scattered trees. The authors evaluated population differentiation between the south Florida population of Red-shouldered Hawks and two populations of eastern Red-shouldered Hawks (B. l. lineatus) in suburban (Cincinnati) and rural (Hocking Hills) environments in southern Ohio.
Date: March 1, 2023
Creator: Dykstra, Madeline A.; Marain, Donna M.; Wrona, Anna M.; Dysktra, Cheryl R.; Farrington, Heather L.; Johnson, Jeff A. et al.
System: The UNT Digital Library
FERONIA and wall-associated kinases coordinate defense induced by lignin modification in plant cell walls (open access)

FERONIA and wall-associated kinases coordinate defense induced by lignin modification in plant cell walls

Article discusses authors' findings that through genetic screening for suppressors of defense gene induction in the low lignin ccr1-3 mutant of Arabidopsis thaliana, we found that loss of function of the receptor-like kinase FERONIA, although not restoring growth, affected cell wall remodeling and blocked release of elicitor-active pectic polysaccharides as a result of the ccr1-3 mutation. They determine that engineering plant cell walls will require development of ways to bypass endogenous pectin signaling pathways.
Date: March 10, 2023
Creator: Liu, Chang; Yu, Hasi; Voxeur, Aline; Rao, Xiaolan & Dixon, R. A.
System: The UNT Digital Library
Preferential Solvation Study of Rosuvastatin in the {PEG400 (1) + Water (2)} Cosolvent Mixture and GastroPlus Software-Based In Vivo Predictions (open access)

Preferential Solvation Study of Rosuvastatin in the {PEG400 (1) + Water (2)} Cosolvent Mixture and GastroPlus Software-Based In Vivo Predictions

Article claims that rosuvastatin (RST) is a poorly water-soluble drug responsible for limited in vivo dissolution and subsequently low oral systemic absorption (poor bioavailability). The results of inverse Kirkwood–Buff integrals showed the PS of RST by PEG400 as observed in all studied ratios of the binary mixture.
Date: March 28, 2023
Creator: Hussain, Afzal; Afzal, Obaid; Yasmin, Sabina; Haider, Nazima; Alfawaz Altamimi, Abdulmalik Saleh; Martínez, Fleming et al.
System: The UNT Digital Library
Urinary Glycosaminoglycans Are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women (open access)

Urinary Glycosaminoglycans Are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women

Article asserts that glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides composed of repeating disaccharide units of uronic acid and amino sugars. To investigate the relationship between GAGs and recurrent urinary tract infection (rUTI), the authors profiled urinary GAGs in a controlled cohort of postmenopausal women.
Date: March 21, 2023
Creator: Neugent, Michael L.; Hulyalkar, Neha V.; Kumar, Ashwani; Xing, Chao; Zimmern, Philippe E.; Shulaev, Vladimir et al.
System: The UNT Digital Library
A Highly Contiguous and Annotated Genome Assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) (open access)

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.
System: The UNT Digital Library
Seeing plants as never before (open access)

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
System: The UNT Digital Library
Correction: Vu et al. Specific Changes in Arabidopsis thaliana Rosette Lipids during Freezing Can Be Associated with Freezing Tolerance. Metabolites 2022, 12, 385 (open access)

Correction: Vu et al. Specific Changes in Arabidopsis thaliana Rosette Lipids during Freezing Can Be Associated with Freezing Tolerance. Metabolites 2022, 12, 385

Article is a correction to an error in the original publication. The enzymatic step catalyzed by oxophytodienoic acid reductase 3 was misstated. A correction has been made to Section 2. Results and Discussion, Subsection 2.13. Lipids of Plants with Mutations in Lipid-Related Genes, Paragraph 1.
Date: March 30, 2023
Creator: Vu, Hieu Sy; Shiva, Sunitha; Samarakoon, Thilani; Li, Maoyin; Sarowar, Sujon; Roth, Mary R. et al.
System: The UNT Digital Library
Correction: A modified aeroponic system for growing small-seeded legumes and other plants to study root systems (open access)

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.
System: The UNT Digital Library
Measurement of the Intramolecular Hydrogen-Shift Rate Coefficient for the CH3SCH2OO Radical Between 314 and 433 K (open access)

Measurement of the Intramolecular Hydrogen-Shift Rate Coefficient for the CH3SCH2OO Radical Between 314 and 433 K

Article describes how the intramolecular hydrogen-shift rate coefficient of the CH3SCH2O2 (methylthiomethylperoxy, MSP) radical, a product formed in the oxidation of dimethyl sulfide (DMS), was measured using a pulsed laser photolysis flow tube reactor coupled to a high-resolution time-of-flight chemical ionization mass spectrometer that measured the formation of the DMS degradation end product HOOCH2SCHO. Measurements performed over the temperature range of 314–433 K yielded a hydrogen-shift rate coefficient of k1(T) = (2.39 ± 0.7) × 109 exp(−(7278 ± 99)/T) s–1 Arrhenius expression and a value extrapolated to 298 K of 0.06 s–1.
Date: March 2, 2023
Creator: Assaf, Emmanuel; Finewax, Zachary; Marshall, Paul; Veres, Patrick R.; Neuman, Andrew & Burkholder, James B. (James Bart), 1954-
System: The UNT Digital Library
Probing High-Temperature Amine Chemistry: Is the Reaction NH3 + NH2 ⇄ N2H3 + H2 Important? (open access)

Probing High-Temperature Amine Chemistry: Is the Reaction NH3 + NH2 ⇄ N2H3 + H2 Important?

Article describes how the reaction NH3 + NH2 ⇄ N2H3 + H2 (R1) has been identified as a key step to explain experimental results for pyrolysis and oxidation of ammonia. In the present work, the reaction was studied by ab initio theory and by reinterpretation of experimental data.
Date: March 14, 2023
Creator: Marshall, Paul & Glarborg, Peter
System: The UNT Digital Library