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  • Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus

    Adegbola, Raphael O; Keith, Cory V; Gutierrez, Osman; Goenaga, Ricardo; Brown, Judith K; School of Plant Sciences, The University of Arizona (Springer, 2024-03-23)
    The complete genome sequence of cacao leafroll virus (CaLRV; family Solemoviridae, genus Polerovirus) was determined by high-throughput sequencing of total RNA isolated from symptomatic cacao Theobroma cacao L. plants (n = 4). The CaLRV genome sequences ranged from 5,976 to 5,997 nucleotides (nt) in length and contained seven open reading frames (ORFs). Nucleotide and amino acid (aa) sequence comparisons showed that, among selected well-characterized poleroviruses, the CaLRV genome shared the highest nt sequence identity of 62% with that of potato leafroll virus (PLRV, NC_076505). A comparison of the predicted aa sequence of the CaLRV coat protein indicated that cotton leafroll dwarf virus (CLRDV, NC_014545) and melon aphid-borne yellows virus (MABYV, NC_010809) were the closest relatives, sharing 57% aa sequence identity. Bayesian phylogenetic analysis based on complete genome sequences showed that CaLRV grouped with well-characterized poleroviruses that cause diseases of cereal and vegetable crops. During the course of publishing this work, the nearly complete genome sequence of a member of the same polerovirus species, referred to as “cacao polerovirus” (OR605721), with which CaLRV shares 99% nt sequence identity, was reported.
  • Insight into glacio-hydrologicalprocesses using explainable machine-learning (XAI) models

    Hao, Huiqing; Hao, Yonghong; Li, Zhongqin; Qi, Cuiting; Wang, Qi; Zhang, Ming; Liu, Yan; Liu, Qi; Jim Yeh, Tian-Chyi; Department of Hydrology and Atmospheric Sciences, The University of Arizona (Elsevier BV, 2024-03-11)
    The glacio-hydrological process is essential in the global water cycle but is complex and poorly understood. In this study, we couple the deep Shapley additive explanation (SHAP) with a long short-term memory (LSTM) model to construct a machine-learning (XAI) framework that describes the glacio-hydrological process in Urumqi Glacier No. 1, China. The XAI framework reveals 1) the dominant hydro-meteorological factors have a five-month lead time, and each factor has its own active time and degree of contribution; 2) the temperature and precipitation within the lead time dominate the process; 3) identifiable combination of the factors, instead of extreme events themselves, creates the extreme glacio-hydrological phenomena. Generally, the glacial meltwater replenishes the glacial stream runoff, which is influenced by many environmental factors. In particular, the runoff responds to the change in the glacier mass balance with hysteresis within five months. Overall, the temperature and precipitation within the lead time (4–5 months) dominate the runoff processes. This study quantifies the Contribution of each input in the glacio-hydrological process and provides valuable insight into the interaction of various hydro-meteorological factors.
  • The quality of teaching behaviors in learning environments of DHH students

    Rivera, M Christina; Catalano, Jennifer A; Branum-Martin, Lee; Lederberg, Amy R; Antia, Shirin D; Department of Disability and Psychoeducational Studies, University of Arizona (Oxford University Press, 2023-11-17)
    Classrooms are complex learning environments, with instruction, climate, and teacher–student interactions playing important roles in students’ academic progress. To investigate the learning environments of deaf and hard-of-hearing (DHH) students, we developed a new observational tool called the Quality of the Learning Environment-DHH rating scale (QLE-DHH) and rated 98 teachers of DHH students being educated in a range of classroom environments. The present study sought to (1) determine if the items on the QLE-DHH are good indicators of theoretically meaningful dimensions of classroom quality; (2) determine to what extent these dimensions predicted language and reading outcomes of DHH students; and (3) examine how teachers of DHH students were rated on the indicators of classroom quality. The findings suggested that the QLE-DHH has excellent structural validity. Ratings predicted student reading outcomes. Finally, the QLE-DHH was able to capture teachers’ strengths and skills in need of improvement. The QLE-DHH appears to hold promise for use in both research and teacher preparation programs.
  • Astrobiological Potential of Venus Atmosphere Chemical Anomalies and Other Unexplained Cloud Properties

    Petkowski, Janusz J.; Seager, Sara; Grinspoon, David H.; Bains, William; Ranjan, Sukrit; Rimmer, Paul B.; Buchanan, Weston P.; Agrawal, Rachana; Mogul, Rakesh; Carr, Christopher E.; et al. (Mary Ann Liebert Inc, 2024-04-10)
    Long-standing unexplained Venus atmosphere observations and chemical anomalies point to unknown chemistry but also leave room for the possibility of life. The unexplained observations include several gases out of thermodynamic equilibrium (e.g., tens of ppm O2, the possible presence of PH3 and NH3, SO2 and H2O vertical abundance profiles), an unknown composition of large, lower cloud particles, and the ''unknown absorber(s).'' Here we first review relevant properties of the venusian atmosphere and then describe the atmospheric chemical anomalies and how they motivate future astrobiology missions to Venus.
  • Simultaneous Drawing of Layered Trees

    Katheder, Julia; Kobourov, Stephen G.; Kuckuk, Axel; Pfister, Maximilian; Zink, Johannes; Department of Computer Science, University of Arizona (Springer Nature Singapore, 2024-02-29)
    We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to permute the vertices on the other layers (respecting the given tree embeddings) in order to minimize the number of crossings. While this problem is known to be NP-hard for multiple trees even on just two layers, we describe a dynamic program running in polynomial time for the restricted case of two trees. If there are more than two trees, we restrict the number of layers to three, which allows for a reduction to a shortest-path problem. This way, we achieve XP-time in the number of trees.

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