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  1. Free, publicly-accessible full text available August 1, 2023
  2. Free, publicly-accessible full text available April 25, 2023
  3. A new pseudopolymorph of berberine, 9,10-dimethoxy-5,6-dihydro-2 H -7λ 5 -[1,3]dioxolo[4,5- g ]isoquinolino[3,2- a ]isoquinolin-7-ylium chloride methanol monosolvate, C 20 H 18 NO 4 + ·Cl − ·CH 3 OH, was obtained during co-crystallization of berberine chloride with malonic acid from methanol. The berberine cations form dimers, which are further packed in stacks. The title structure was compared with other reported solvates of berberine chloride: its dihydrate, tetrahydrate, and ethanol solvate hemihydrate. Hirshfeld analysis was performed to show the intermolecular interactions in the crystal structure of the title compound, and its fingerprint plots were compared with those of the already studiedmore »solvates.« less
    Free, publicly-accessible full text available May 1, 2023
  4. Abstract Background

    Most phages infect free-living bacteria but a few have been identified that infect heritable symbionts of insects or other eukaryotes. Heritable symbionts are usually specialized and isolated from other bacteria with little known about the origins of associated phages.Hamiltonella defensais a heritable bacterial symbiont of aphids that is usually infected by a tailed, double-stranded DNA phage named APSE.

    Methods

    We conducted comparative genomic and phylogenetic studies to determine how APSE is related to other phages and prophages.

    Results

    Each APSE genome was organized into four modules and two predicted functional units. Gene content and order were near-fully conserved in modules 1more »and 2, which encode predicted DNA metabolism genes, and module 4, which encodes predicted virion assembly genes. Gene content of module 3, which contains predicted toxin, holin and lysozyme genes differed among haplotypes. Comparisons to other sequenced phages suggested APSE genomes are mosaics with modules 1 and 2 sharing similarities withBordetella-Bcep-Xylostella fastidiosa-like podoviruses, module 4 sharing similarities with P22-like podoviruses, and module 3 sharing no similarities with known phages. Comparisons to other sequenced bacterial genomes identified APSE-like elements in other heritable insect symbionts (Arsenophonusspp.) and enteric bacteria in the familyMorganellaceae.

    Conclusions

    APSEs are most closely related to phage elements in the genusArsenophonusand other bacteria in theMorganellaceae.

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  5. Abstract Purpose of Review

    A transdisciplinary systems approach to the design of an artificial intelligence (AI) decision support system can more effectively address the limitations of AI systems. By incorporating stakeholder input early in the process, the final product is more likely to improve decision-making and effectively reduce kidney discard.

    Recent Findings

    Kidney discard is a complex problem that will require increased coordination between transplant stakeholders. An AI decision support system has significant potential, but there are challenges associated with overfitting, poor explainability, and inadequate trust. A transdisciplinary approach provides a holistic perspective that incorporates expertise from engineering, social science, and transplantmore »healthcare. A systems approach leverages techniques for visualizing the system architecture to support solution design from multiple perspectives.

    Summary

    Developing a systems-based approach to AI decision support involves engaging in a cycle of documenting the system architecture, identifying pain points, developing prototypes, and validating the system. Early efforts have focused on describing process issues to prioritize tasks that would benefit from AI support.

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  6. Abstract Background

    Mosquito-borne dengue virus (DENV) causes major disease worldwide, impacting 50–100 million people every year, and is spread by the major mosquito vectorAedes aegypti. Understanding mosquito physiology, including antiviral mechanisms, and developing new control strategies have become an important step towards the elimination of DENV disease. In the study reported here, we focused on autophagy, a pathway suggested as having a positive influence on virus replication in humans, as a potential antiviral target in the mosquito.

    Methods

    To understand the role played by autophagy inAe. aegypti, we examined the activation of this pathway in Aag-2 cells, anAe. aegypti-derived cell line, infectedmore »with DENV. Rapamycin and 3-methyladenine, two small molecules that have been shown to affect the function of the autophagy pathway, were used to activate or suppress, respectively, the autophagy pathway.

    Results

    At 1-day post-DENV infection in Aag-2 cells, transcript levels of both the microtubule-associated protein light chain 3-phosphatidylethanolamine conjugate (LC3-II) and autophagy-related protein 1 (ATG1) increased. Rapamycin treatment activated the autophagy pathway as early as 1-h post-treatment, and the virus titer had decreased in the Aag-2 cells at 2 days post-infection; in contrast, the 3-methyladenine treatment did not significantly affect the DENV titer. Treatment with these small molecules also impacted the ATG12 transcript levels in DENV-infected cells.

    Conclusions

    Our studies revealed that activation of the autophagy pathway through rapamycin treatment altered DENV infection in the mosquito cells, suggesting that this pathway could be a possible antiviral mechanism in the mosquito system. Here we provide fundamental information needed to proceed with future experiments and to improve our understanding of the mosquito’s immune response against DENV.

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  7. Abstract Background

    Innovation in STEM (science, technology, engineering, and math) fields in the U.S. is threatened by a lack of diversity. Social identity threat research finds messages in the academic environment devalue women and underrepresented groups in STEM, creating a chilly and hostile environment. Research has focused on the mechanisms that contribute to STEM engagement and interest at the K-12 and undergraduate level, but the mechanisms that predict sustained engagement at the graduate level have not been studied.

    Results

    In a longitudinal study of doctoral students in STEM disciplines, we demonstrate that students’ beliefs that their STEM colleagues believe intelligence is amore »fixed (vs. malleable) trait undermine women’s engagement in STEM. Specifically, perceiving a fixed ability environment predicts greater perceptions of sexism, which erode women’s self-efficacy and sense of belongingness and lead women to consider dropping out of their STEM career.

    Conclusion

    These findings identify one potential pathway by which women leave their STEM fields, perpetuating gender disparities in STEM.

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  8. Abstract Background

    The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.

    Results

    Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.

    Conclusions

    The PGV software can be installed via conda or downloaded fromhttps://github.com/ucrbioinfo/PGV. The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracksmore »available from the GitHub page.

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  9. Abstract Background

    As biomedical knowledge is rapidly evolving, concept enrichment of biomedical terminologies is an active research area involving automatic identification of missing or new concepts. Previously, we prototyped a lexical-based formal concept analysis (FCA) approach in which concepts were derived by intersecting bags of words, to identify potentially missing concepts in the National Cancer Institute (NCI) Thesaurus. However, this prototype did not handle concept naming and positioning. In this paper, we introduce a sequenced-based FCA approach to identify potentially missing concepts, supporting concept naming and positioning.

    Methods

    We consider the concept name sequences as FCA attributes to construct the formal context.more »The concept-forming process is performed by computing the longest common substrings of concept name sequences. After new concepts are formalized, we further predict their potential positions in the original hierarchy by identifying their supertypes and subtypes from original concepts. Automated validation via external terminologies in the Unified Medical Language System (UMLS) and biomedical literature in PubMed is performed to evaluate the effectiveness of our approach.

    Results

    We applied our sequenced-based FCA approach to all the sub-hierarchies underDisease or Disorderin the NCI Thesaurus (19.08d version) and five sub-hierarchies underClinical FindingandProcedurein the SNOMED CT (US Edition, March 2020 release). In total, 1397 potentially missing concepts were identified in the NCI Thesaurus and 7223 in the SNOMED CT. For NCI Thesaurus, 85 potentially missing concepts were found in external terminologies and 315 of the remaining 1312 appeared in biomedical literature. For SNOMED CT, 576 were found in external terminologies and 1159 out of the remaining 6647 were found in biomedical literature.

    Conclusion

    Our sequence-based FCA approach has shown the promise for identifying potentially missing concepts in biomedical terminologies.

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  10. Abstract Background

    This paper introduces DynamoVis version 1.0, an open-source software developed to design, record and export custom animations and multivariate visualizations from movement data, enabling visual exploration and communication of patterns capturing the associations between animals’ movement and its affecting internal and external factors. Proper representation of these dependencies grounded on cartographic principles and intuitive visual forms can facilitate scientific discovery, decision-making, collaborations, and foster understanding of movement.

    Results

    DynamoVis offers a visualization platform that is accessible and easily usable for scientists and general public without a need for prior experience with data visualization or programming. The intuitive design focuses onmore »a simple interface to apply cartographic techniques, giving ecologists of all backgrounds the power to visualize and communicate complex movement patterns.

    Conclusions

    DynamoVis 1.0 offers a flexible platform to quickly and easily visualize and animate animal tracks to uncover hidden patterns captured in the data, and explore the effects of internal and external factors on their movement path choices and motion capacities. Hence, DynamoVis can be used as a powerful communicative and hypothesis generation tool for scientific discovery and decision-making through visual reasoning. The visual products can be used as a research and pedagogical tool in movement ecology.

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