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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 »Free, publicly-accessible full text available May 1, 2023
Evolutionary genomics of APSE: a tailed phage that lysogenically converts the bacterium Hamiltonella defensa into a heritable protective symbiont of aphids
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.
Each APSE genome was organized into four modules and two predicted functional units. Gene content and order were near-fully conserved in modules 1more »
APSEs are most closely related to phage elements in the genus
Arsenophonusand other bacteria in the Morganellaceae.
Reducing Kidney Discard With Artificial Intelligence Decision Support: the Need for a Transdisciplinary Systems Approach
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.
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 »
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.
Mosquito-borne dengue virus (DENV) causes major disease worldwide, impacting 50–100 million people every year, and is spread by the major mosquito vector
Aedes 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 in
Ae. aegypti, we examined the activation of this pathway in Aag-2 cells, an Ae. aegypti-derived cell line, infectedmore » 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.
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.
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.
In a longitudinal study of doctoral students in STEM disciplines, we demonstrate that students’ beliefs that their STEM colleagues believe intelligence is amore »
These findings identify one potential pathway by which women leave their STEM fields, perpetuating gender disparities in STEM.
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.
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.
The PGV software can be installed via conda or downloaded from
https://github.com/ucrbioinfo/PGV. The companion PGV browser at http://pgv.cs.ucr.educan be tested using example bed tracksmore »
Identification of missing concepts in biomedical terminologies using sequence-based formal concept analysis
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.
We consider the concept name sequences as FCA attributes to construct the formal context.more »
We applied our sequenced-based FCA approach to all the sub-hierarchies under
Disease or Disorderin the NCI Thesaurus (19.08d version) and five sub-hierarchies under Clinical Findingand Procedurein 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.
DynamoVis 1.0: an exploratory data visualization software for mapping movement in relation to internal and external factors
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.
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 »
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.