Transcription factor PbMYB80 regulates lignification of stone cells and undergoes RING finger protein PbRHY1-mediated degradation in pear fruit.

The Chinese white pear (Pyrus bretschneideri) fruit carries a high proportion of stone cells, adversely affecting fruit quality. Lignin is a main component of stone cells in pear fruit. In this study, we discovered that a pear MYB transcription factor, PbMYB80, binds to the promoters of key lignin biosynthesis genes and inhibits their expression. Stable overexpression of PbMYB80 in Arabidopsis showed that lignin deposition and secondary wall thickening were inhibited, and the expression of the lignin biosynthesis genes in transgenic Arabidopsis was decreased. Transient overexpression of PbMYB80 in pear fruit inhibited lignin metabolism and stone cell development, and the expression of some genes in the lignin metabolism pathway was reduced. In contrast, silencing PbMYB80 with VIGS increased the lignin and stone cell content in pear fruit, and increased expression of genes in the lignin metabolism pathway. By screening a pear fruit cDNA library in yeast, we found that PbMYB80 binds to a RING finger (PbRHY1) protein. We also showed that PbRHY1 exhibits E3 ubiquitin ligase activity and degrades ubiquitinated PbMYB80 in vivo and in vitro. This investigation contributes to a better understanding of the regulation of lignin biosynthesis in pear fruit, and provides a theoretical foundation for increasing pear fruit quality at the molecular level.

Visualizing and Comparing Machine Learning Predictions to Improve Human-AI Teaming on the Example of Cell Lineage.

We visualize the predictions of multiple machine learning models to help biologists as they interactively make decisions about cell lineage-the development of a (plant) embryo from a single ovum cell. Based on a confocal microscopy dataset, traditionally biologists manually constructed the cell lineage, starting from this observation and reasoning backward in time to establish their inheritance. To speed up this tedious process, we make use of machine learning (ML) models trained on a database of manually established cell lineages to assist the biologist in cell assignment. Most biologists, however, are not familiar with ML, nor is it clear to them which model best predicts the embryo's development. We thus have developed a visualization system that is designed to support biologists in exploring and comparing ML models, checking the model predictions, detecting possible ML model mistakes, and deciding on the most likely embryo development. To evaluate our proposed system, we deployed our interface with six biologists in an observational study. Our results show that the visual representations of machine learning are easily understandable, and our tool, LineageD+, could potentially increase biologists' working efficiency and enhance the understanding of embryos.

A Survey of Designs for Combined 2D+3D Visual Representations.

We examine visual representations of data that make use of combinations of both 2D and 3D data mappings. Combining 2D and 3D representations is a common technique that allows viewers to understand multiple facets of the data with which they are interacting. While 3D representations focus on the spatial character of the data or the dedicated 3D data mapping, 2D representations often show abstract data properties and take advantage of the unique benefits of mapping to a plane. Many systems have used unique combinations of both types of data mappings effectively. Yet there are no systematic reviews of the methods in linking 2D and 3D representations. We systematically survey the relationships between 2D and 3D visual representations in major visualization publications-IEEE VIS, IEEE TVCG, and EuroVis-from 2012 to 2022. We closely examined 105 articles where 2D and 3D representations are connected visually, interactively, or through animation. These approaches are designed based on their visual environment, the relationships between their visual representations, and their possible layouts. Through our analysis, we introduce a design space as well as provide design guidelines for effectively linking 2D and 3D visual representations.

The blood routine test holds screening values for influenza A in 2023: a retrospective study.

Background: Influenza A is the most common viral pathogen isolated from pediatric clinics during influenza seasons. Some young patients with influenza manifest rapid progression with high fever and severe sequelae, such as pneumonia and meningitis. Therefore, early diagnosis and prompt treatment are highly important. Specific diagnostic tests currently include antigen detection, antibody detection, nucleic acid test and virus isolation. Rapid antigen testing is the most commonly adopted method in the outpatient setting, but false negative results are frequently observed, which causes delayed treatment and severe outcome. Routine blood test is the most commonly used detection for the outpatients. Incorporating specific blood cell counts into rapid antigen test may overcome some technical issues and enable accurate early diagnosis. Methods: We enrolled 537 children with influenza-like symptoms like fever or respiratory symptoms from pediatric outpatients and 110 children without infectious diseases for control. Routine blood tests detected by a routine analyzer and influenza A virus antigen detection were performed in the patients. Significant blood routine parameters between groups were examined by statistical tests. Parameters in routine blood test were assessed by the receiver operating characteristic curve to find the screening indicators of influenza A. Multivariate logistic regression were used to establish the optimal combinations of blood routine parameters in our screening model. Results: Two subgroups were set according to age: ≤6 years old group and >6 years old group. In each group, patients were further divided into three subgroups: the influenza A-positive-result group (A+ group) (n=259), influenza A-negative-result group (A- group) (n=277) and healthy control group (H group) (n=110). Most routine blood parameters showed significant differences among the three subgroups in each age group. Notably, lymphocyte (LYM) number, platelet (PLT) number, lymphocyte-to-monocyte ratio (LMR) and LYM multiplied by PLT (LYM*PLT) exhibited extremely significant differences. Using A- group as a reference based on the area under the curve (AUC), both age groups had a similar trend. For A- group, the optimal cutoff value of LYM*PLT was 221.6, the AUC, the sensitivity and specificity were 0.6830, 55.71% and 76.92% in the ≤6 years old group. Meanwhile, the cutoff value of LYM*PLT was 196.7, and the AUC, the sensitivity and specificity were 0.6448, 53.97% and 70.81%, respectively in the >6 years old group. Screening model based on multivariate logistic regression model revealed that LYM*PLT was the optimal parameter combinations in ≤6 years old group (AUC =0.7202), while LYM and PLT were the optimal parameter combinations in >6 years old group (AUC =0.6760). Conclusions: Several blood routine parameters in children with influenza A demonstrate differential levels in both age subgroups. The LYM*PLT exhibits the potential screening value of influenza infection.