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Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria

Description: 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.
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Partner: UNT College of Science
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Silicon versus Superbug: Assessing Machine Learning's Role in the Fight against Antimicrobial Resistance

Description: 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.
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Partner: UNT College of Science
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A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1

Description: 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.
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Partner: UNT College of Science
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Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light

Description: 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.
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Partner: UNT College of Science
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Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data

Description: Article describes how taxonomic profiling of ancient metagenomic samples is challenging due to the accumulation of specific damage patterns on DNA over time. The authors performed a comprehensive evaluation on simulated metagenomes representing human dental calculus microbiome, with the level of DNA damage successively raised to mimic modern to ancient metagenomes.
Date: October 2, 2023
Creator: Pusadkar, Vaidehi & Azad, Rajeev K.
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Partner: UNT College of Science
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Dry blood spot samples to monitor immune-associated mRNA expression in intervention studies: Impact of Baker's yeast beta glucan

Description: Article describes how monitoring immunological response to physical stressors in a field setting is challenging because existing methods require a laboratory visit and traditional blood collection via venipuncture. The purpose of this study was to determine if our optimized dry blood spot (DBS) methodology yields sufficient total RNA to quantify the effect of Baker's Yeast Beta Glucan supplementation on post-exercise mRNA expression.
Date: September 22, 2023
Creator: McFarlin, Brian K.; Bridgeman, Elizabeth A.; Vingren, Jakob L. & Will, David W.
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Partner: UNT College of Science
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Silicon supply promotes differences in growth and C:N:P stoichiometry between bamboo and tree saplings

Description: Article describes how silicon can be important for the growth, functioning, and stoichiometric regulation of nutrients for high-Si-accumulating bamboo. The authors demonstrated that silicon supply can decrease the ratio of C:Si in bamboo leaves and increase the ratio of N:P without altering nutrient status or the N:P ratio of tree spalings.
Date: September 21, 2023
Creator: Liu, Xiaoyu; Tang, Xinghao; Compson, Zacchaeus Greg; Huang, Dongmei; Zou, Guiwu; Luan, Fenggang et al.
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Partner: UNT College of Science
open access

Analysis of Pectin-derived Monosaccharides from Arabidopsis Using GC–MS

Description: Article describes how pectin is a complex polysaccharide present in the plant cell wall, whose composition is constantly remodeled to adapt to environmental or developmental changes. Here, authors describe a quick and efficient gas chromatography–mass spectrometry (GC–MS)-based method that allows the differential analysis of pectin monosaccharide composition in plants under different conditions or between mutant plants and their respective wild types.
Date: August 20, 2023
Creator: Scholz, Patricia; Chapman, Kent Dean; Ischebeck, Till & Guzha, Athanas
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Partner: UNT College of Science
open access

Quantification of Botrytis cinerea Growth in Arabidopsis thaliana

Description: Article describes how yield losses attributed to plant pathogens pose a serious threat to plant productivity and food security. Here, the authors describe two methods to quantify B. cinerea development in Arabidopsis thaliana genotypes through measurements of lesion development and quantification of fungal genomic DNA in infected tissues.
Date: August 20, 2023
Creator: Scholz, Patricia; Chapman, Kent Dean; Ischebeck, Till & Guzha, Athanas
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Partner: UNT College of Science
open access

Bibliometric Analysis of Integrated Pest Management Practices

Description: Article discusses how integrated pest management (IPM) is a wide-ranging strategy that involves tactics for the structural control of pests and diseases, also known as integrated pest control (IPC). The authors' prime aim of this study is to explore global scientific publications regarding integrated pest management and map the recent global trends in this innovative research domain, thereby providing future research directions based on dynamic observations.
Date: July 26, 2023
Creator: Zhou, Xi; Yang, Chongxi; Yesmin, Sabina; Islam, Md Ashraful & Sarkar, Apurbo
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Partner: UNT College of Science
open access

Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies

Description: Article describes how, in efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The authors used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies.
Date: July 20, 2023
Creator: Johnson, Jeff A.; Athrey, Giridhar; Anderson, Clifford M.; Bell, Douglas A.; Dixon, Andrew; Kumazawa, Yoshinori et al.
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Partner: UNT College of Science
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DNA metabarcoding captures different macroinvertebrate biodiversity than morphological identification approaches across a continental scale

Description: Article describes how DNA-based aquatic biomonitoring methods show promise to provide rapid, standardized, and efficient biodiversity assessment to supplement and in some cases replace current morphology-based approaches that are often less efficient and can produce inconsistent results. The authors present a comparison of DNA metabarcoding and morphological identification, leveraging national-scale, open-source, ecological datasets from the National Ecological Observatory Network.
Date: July 19, 2023
Creator: Emmons, Sean C.; Compson, Zacchaeus Greg; Malish, Megan C.; Busch, Michelle H.; Saenz, Veronica; Higgins, Kierstyn T. et al.
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Partner: UNT College of Science
open access

Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar

Description: Article describes how the conversion of lignocellulosic feedstocks to fermentable sugar for biofuel production is inefficient, and most strategies to enhance efficiency directly target lignin biosynthesis, with associated negative growth impacts. The authors demonstrate, for both laboratory-and field-grown plants, that expression of Pag-miR408 in poplar significantly enhances saccharification, with no requirement for acid-pretreatment, while promoting plant growth.
Date: July 18, 2023
Creator: Guo, Yayu; Wang, Shufang; Yu, Keji; Wang, Hou-Ling; Xu, Huimin; Song, Chengwei et al.
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Partner: UNT College of Science
open access

Survival rates in the world's southernmost forest bird community

Description: Article asserts that the Magellanic sub-Antarctic Forest is home to the world's southernmost avian community and is the only Southern Hemisphere analogue to Northern Hemisphere temperate forests at this latitude. Authors describe annual survival patterns and their association with climate variables using a 20-year mark–recapture data set of five forest bird species in the Cape Horn Biosphere Reserve.
Date: June 20, 2023
Creator: Sandvig, Erik M.; Quilodrán, Claudio S.; Altamirano, Tomás A.; Aguirre, Francisco; Barroso, Omar; Rivero de Aguilar, Juan et al.
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Partner: UNT College of Science
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Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement

Description: 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.
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Partner: UNT College of Science
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Systematic approaches to C-lignin engineering in Medicago truncatula

Description: Article describes how C-lignin is a homopolymer of caffeyl alcohol present in the seed coats of a variety of plant species including vanilla orchid, various cacti, and the ornamental plant Cleome hassleriana. The authors used information from a transcriptomic analysis of developing C. hassleriana seed coats to suggest strategies for engineering C-lignin in a heterologous system, using hairy roots of the model legume Medicago truncatula.
Date: June 12, 2023
Creator: Ha, Chan Man; Escamilla-Treviño, Luis; Zhuo, Chunliu; Pu, Yunqiao; Bryant, Nathan; Ragauskas, Arthur J. (Arthur Jonas), 1957- et al.
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Partner: UNT College of Science
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Histological features of non-alcoholic fatty liver disease revealed in response to mixed vehicle emission exposure and consumption of a high-fat diet in wildtype C57Bl/6 male mice

Description: Article describes how non-alcoholic fatty liver disease (NAFLD) is currently plaguing the population at pandemic proportions and is expected to become more prevalent over the next decade. The authors investigated the hypothesis that exposure to a mixture of gasoline and diesel engine emissions (MVE), coupled with the concurrent consumption of a HF diet, promotes the development of a NAFLD phenotype within the liver.
Date: June 6, 2023
Creator: Schneider, Leah J.; Santiago, Isabella; Johnson, Bailee; Stanley, Analana Hays; Penaredondo, Bea & Lund, Amie K.
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Partner: UNT College of Science
open access

Sibling Aggression, Feeding Rates, and Hatch Rank of Nestling Red-Shouldered Hawks (Buteo lineatus)

Description: Article describes how, in many raptor species, hatching asynchrony results in a size hierarchy among nestlings, which may facilitate brood reduction by means of sibling aggression-induced mortality, especially in times of low food resources. The authors studied the influence of hatch rank, brood size, and brood age on aggression and feeding rates among Red-shouldered Hawk (Buteo lineatus) nestlings in suburban southwestern Ohio.
Date: May 25, 2023
Creator: Miller, Sara J.; Dykstra, Cheryl R.; Rolland, Virginie; Simon, Melinda M.; Hays, Jeffrey L. & Bednarz, James C.
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Partner: UNT College of Science
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A multiscale approach reveals elaborate circulatory system and intermittent heartbeat in velvet worms (Onychophora)

Description: Article describes how an antagonistic hemolymph-muscular system is essential for soft-bodied invertebrates. The authors analyzed the entire circulatory system of the peripatopsid Euperipatoides rowelli and claimed they discovered a surprisingly elaborate organization.
Date: April 28, 2023
Creator: Jahn, Henry; Hammel, Jörg U.; Göpel, Torben; Wirkner, Christian S. & Mayer, Georg
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Partner: UNT College of Science
open access

Biocultural Calendars Across Four Ethnolinguistic Communities in Southwestern South America

Description: Article describes how, since the mid-20th century, the so-called Great Acceleration has amplified processes of ecosystem degradation, extinction of biological species, displacement of local peoples, losses of languages, and cultural diversity. The authors examine cultural practices and socio-environmental changes across four contrasting ethnolinguistic communities in southwestern South America, from southern to northern Chile along a marked climatic gradient to show the broad application of the… more
Date: April 20, 2023
Creator: Rozzi, Ricardo, 1960-; Álvarez, Ricardo; Castro, Victoria; Núñez, David; Ojeda, Jaime & Tauro, Alejandra
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Partner: UNT College of Science
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Exposure to diesel exhaust particulates and desert sand dust generates microvesicle particles and platelet-activating factor agonists

Description: The authors address the editor in their article, stating that the majority of the general population, particularly, servicemen and women deployed across the globe are exposed to various airborne hazards, including diesel exhaust particulate (DEP) and desert sand dust (DSD). Studies, including the author's study, have shown that exposure to ROS-generating pro-oxidative stressors ranging from environmental carcinogens to pollutants, including cigarette smoke, produces a class of potent phospholip… more
Date: April 8, 2023
Creator: Thyagarajan, Anita; Rapp, Christine M.; Schneider, Leah; Lund, Amie K.; Travers, Jeffrey B. & Sahu, Ravi P.
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Partner: UNT College of Science
open access

Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages

Description: 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.
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Partner: UNT College of Science
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

Description: 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.
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Partner: UNT College of Science
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