CoInsight: Visual Storytelling for Hierarchical Tables With Connected Insights.

Extracting data insights and generating visual data stories from tabular data are critical parts of data analysis. However, most existing studies primarily focus on tabular data stored as flat tables, typically without leveraging the relations between cells in the headers of hierarchical tables. When properly used, rich table headers can enable the extraction of many additional data stories. To assist analysts in visual data storytelling, an approach is needed to organize these data insights efficiently. In this work, we propose CoInsight, a system to facilitate visual storytelling for hierarchical tables by connecting insights. CoInsight extracts data insights from hierarchical tables and builds insight relations according to the structure of table headers. It further visualizes related data insights using a nested graph with edge bundling. We evaluate the CoInsight system through a usage scenario and a user experiment. The results demonstrate the utility and usability of CoInsight for converting data insights in hierarchical tables into visual data stories.

Towards Natural Language Interfaces for Data Visualization: A Survey.

Utilizing Visualization-oriented Natural Language Interfaces (V-NLI) as a complementary input modality to direct manipulation for visual analytics can provide an engaging user experience. It enables users to focus on their tasks rather than having to worry about how to operate visualization tools on the interface. In the past two decades, leveraging advanced natural language processing technologies, numerous V-NLI systems have been developed in academic research and commercial software, especially in recent years. In this article, we conduct a comprehensive review of the existing V-NLIs. In order to classify each article, we develop categorical dimensions based on a classic information visualization pipeline with the extension of a V-NLI layer. The following seven stages are used: query interpretation, data transformation, visual mapping, view transformation, human interaction, dialogue management, and presentation. Finally, we also shed light on several promising directions for future work in the V-NLI community.

Efficient assembly of long DNA fragments and multiple genes with improved nickase-based cloning and Cre/loxP recombination.

Functional genomics, synthetic biology and metabolic engineering require efficient tools to deliver long DNA fragments or multiple gene constructs. Although numerous DNA assembly methods exist, most are complicated, time-consuming and expensive. Here, we developed a simple and flexible strategy, unique nucleotide sequence-guided nicking endonuclease (UNiE)-mediated DNA assembly (UNiEDA), for efficient cloning of long DNAs and multigene stacking. In this system, a set of unique 15-nt 3' single-strand overhangs were designed and produced by nicking endonucleases (nickases) in vectors and insert sequences. We introduced UNiEDA into our modified Cre/loxP recombination-mediated TransGene Stacking II (TGSII) system to generate an improved multigene stacking system we call TGSII-UNiE. Using TGSII-UNiE, we achieved efficient cloning of long DNA fragments of different sizes and assembly of multiple gene cassettes. Finally, we engineered and validated the biosynthesis of betanin in wild tobacco (Nicotiana benthamiana) leaves and transgenic rice (Oryza sativa) using multigene stacking constructs based on TGSII-UNiE. In conclusion, UNiEDA is an efficient, convenient and low-cost method for DNA cloning and multigene stacking, and the TGSII-UNiE system has important application prospects for plant functional genomics, genetic engineering and synthetic biology research.

An Efficient Marker Gene Excision Strategy Based on CRISPR/Cas9-Mediated Homology-Directed Repair in Rice.

In order to separate transformed cells from non-transformed cells, antibiotic selectable marker genes are usually utilized in genetic transformation. After obtaining transgenic plants, it is often necessary to remove the marker gene from the plant genome in order to avoid regulatory issues. However, many marker-free systems are time-consuming and labor-intensive. Homology-directed repair (HDR) is a process of homologous recombination using homologous arms for efficient and precise repair of DNA double-strand breaks (DSBs). The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) system is a powerful genome editing tool that can efficiently cause DSBs. Here, we isolated a rice promoter (Pssi) of a gene that highly expressed in stem, shoot tip and inflorescence, and established a high-efficiency sequence-excision strategy by using this Pssi to drive CRISPR/Cas9-mediated HDR for marker free (PssiCHMF). In our study, PssiCHMF-induced marker gene deletion was detected in 73.3% of T0 plants and 83.2% of T1 plants. A high proportion (55.6%) of homozygous marker-excised plants were obtained in T1 progeny. The recombinant GUS reporter-aided analysis and its sequencing of the recombinant products showed precise deletion and repair mediated by the PssiCHMF method. In conclusion, our CRISPR/Cas9-mediated HDR auto-excision method provides a time-saving and efficient strategy for removing the marker genes from transgenic plants.

PhieABEs: a PAM-less/free high-efficiency adenine base editor toolbox with wide target scope in plants.

Adenine base editors (ABEs), which are generally engineered adenosine deaminases and Cas variants, introduce site-specific A-to-G mutations for agronomic trait improvement. However, notably varying editing efficiencies, restrictive requirements for protospacer-adjacent motifs (PAMs) and a narrow editing window greatly limit their application. Here, we developed a robust high-efficiency ABE (PhieABE) toolbox for plants by fusing an evolved, highly active form of the adenosine deaminase TadA8e and a single-stranded DNA-binding domain (DBD), based on PAM-less/free Streptococcus pyogenes Cas9 (SpCas9) nickase variants that recognize the PAM NGN (for SpCas9n-NG and SpGn) or NNN (for SpRYn). By targeting 29 representative targets in rice and assessing the results, we demonstrate that PhieABEs have significantly improved base-editing activity, expanded target range and broader editing windows compared to the ABE7.10 and general ABE8e systems. Among these PhieABEs, hyper ABE8e-DBD-SpRYn (hyABE8e-SpRY) showed nearly 100% editing efficiency at some tested sites, with a high proportion of homozygous base substitutions in the editing windows and no single guide RNA (sgRNA)-dependent off-target changes. The original sgRNA was more compatible with PhieABEs than the evolved sgRNA. In conclusion, the DBD fusion effectively promotes base-editing efficiency, and this novel PhieABE toolbox should have wide applications in plant functional genomics and crop improvement.

Natural Language to Visualization by Neural Machine Translation.

Supporting the translation from natural language (NL) query to visualization (NL2VIS) can simplify the creation of data visualizations because if successful, anyone can generate visualizations by their natural language from the tabular data. The state-of-the-art NL2VIS approaches (e.g., NL4DV and FlowSense) are based on semantic parsers and heuristic algorithms, which are not end-to-end and are not designed for supporting (possibly) complex data transformations. Deep neural network powered neural machine translation models have made great strides in many machine translation tasks, which suggests that they might be viable for NL2VIS as well. In this paper, we present ncNet, a Transformer-based sequence-to-sequence model for supporting NL2VIS, with several novel visualization-aware optimizations, including using attention-forcing to optimize the learning process, and visualization-aware rendering to produce better visualization results. To enhance the capability of machine to comprehend natural language queries, ncNet is also designed to take an optional chart template (e.g., a pie chart or a scatter plot) as an additional input, where the chart template will be served as a constraint to limit what could be visualized. We conducted both quantitative evaluation and user study, showing that ncNet achieves good accuracy in the nvBench benchmark and is easy-to-use.

Doping bioactive elements into a collagen scaffold based on synchronous self-assembly/mineralization for bone tissue engineering.

Pure collagen is biocompatible but lacks inherent osteoinductive, osteoimmunomodulatory and antibacterial activities. To obtain collagen with these characteristics, we developed a novel methodology of doping bioactive elements into collagen through the synchronous self-assembly/mineralization (SSM) of collagen. In the SSM model, amorphous mineral nanoparticles (AMN) (amorphous SrCO3, amorphous Ag3PO4, etc.) stabilized by the polyampholyte, carboxymethyl chitosan (CMC), and collagen molecules were the primary components under acidic conditions. As the pH gradually increased, intrafibrillar mineralization occurred via the self-adaptive interaction between the AMNs and the collagen microfibrils, which were self-assembling; the AMNs wrapped around the microfibrils became situated in the gap zones of collagen and finally transformed into crystals. Sr-doped collagen scaffolds (Sr-CS) promoted in vitro cell proliferation and osteogenic differentiation of rat bone marrow mesenchymal stromal cells (rBMSCs) and synergistically improved osteogenesis of rBMSCs by altering the macrophage response. Ag-doped collagen scaffolds (Ag-CS) exhibited in vitro antibacterial effects on S. aureus, as well as cell/tissue compatibility. Moreover, Sr-CS implanted into the calvarial defect of a rat resulted in improved bone regeneration. Therefore, the SSM model is a de novo synthetic strategy for doping bioactive elements into collagen, and can be used to fabricate multifunctional collagen scaffolds to meet the clinical challenges of encouraging osteogenesis, boosting the immune response and fighting severe infection in bone defects.

MicroRNA-206 regulates vascular smooth muscle cell phenotypic switch and vascular neointimal formation.

MiR-206 has been found to play a critical role in skeletal muscle proliferation, differentiation, and regeneration. However, little is known about the function of miR-206 in vascular smooth muscle cells (VSMCs) biology. In this study, we will investigate its roles in phenotypic switching of VSMCs and neointimal lesion formation. First, we identified the expression of miR-206 in VSMCs treated with various concentrations of TGFß1 and in rat carotid arteries after angioplasty by using qPCR. TGFß1 inhibited the expression of miR-206 and TGFß1 inhibitor induced miR-206 expression. In VSMCs of injured vascular walls, miR-206 expression was upregulated. Then, we overexpressed miR-206 using lentivirus Lv-rno-mir-206 and knocked down miR-206 using LV-rno-mir-206-inhibitor in rat carotid arteries after angioplasty. Overexpression of miR-206 resulted in decreasing SM22α expression in VSMCs in vitro and knockdown of miR-206 suppressed neointimal lesion formation in vivo. Finally, ZFP580 (zinc finger protein 580) was identified as the direct target of miR-206 in VSMCs by using luciferase report assay. The results indicate that miR-206 is involved in phenotypic switching of VSMCs and neointimal lesion formation after angioplasty through targeting ZFP580. These findings may provide a novel therapeutic target in post-angioplasty restenosis.

Novel zinc finger transcription factor ZFP580 promotes differentiation of bone marrow-derived endothelial progenitor cells into endothelial cells via eNOS/NO pathway.

BACKGROUND: The differentiation of endothelial progenitor cells (EPCs) plays a pivotal role in endothelial repair and re-endothelialization after vascular injury. However, the underlying mechanisms still remain largely elusive. Here, we investigated the role of the novel C2H2 zinc finger transcription factor ZFP580 in EPC differentiation and the molecular mechanisms behind EPC-mediated endothelial repair. METHODS: Bone marrow-derived EPCs were isolated, cultured, and identified. EPCs were infected with an adenovirus encoding ZFP580 or Ad-siRNA to silence ZFP580. Fluorescence-activated cell sorting (FACS) analysis was performed to analyze EPC surface makers. The expression of ZFP580, eNOS, VEGFR-2, CD31, CD34, CD45 and vWF was performed by Q-PCR, Western blot and immunostaining. NO donor SNAP or NOS inhibitor L-NAME was used to elucidate the possible molecular mechanism. Tube formation in vitro and angiogenesis assay in vivo were also used in this study. RESULTS: Both ZFP580 and eNOS were displayed dynamic expression during EPC differentiation. Overexpression of ZFP580 enhanced EPC differentiation, while knockdown suppressed it. ZFP580 also enhanced eNOS expression, and eNOS inhibition suppressed differentiation. Upregulation/knockdown of ZFP580 also enhanced/reduced endothelial tube formation from EPC in vitro, and angiogenesis in vivo in response to Matrigel plugs containing EPC. CONCLUSIONS: ZFP580 promotes not only the differentiation of EPCs into ECs by increasing the expression of eNOS and the availability of nitric oxide, but also the vessel formation in vitro and in vivo. This might represent a novel mechanism of ZFP580 in EPC differentiation and its therapeutic value in the treatment of vascular disease.

ZNF580 mediates eNOS expression and endothelial cell migration/proliferation via the TGF-ß1/ALK5/Smad2 pathway.

ZNF580 is a novel C2H2 zinc-finger nuclear transcription factor with potential involvement in the transforming growth factor-ß1 (TGF-ß1) signal transduction pathway. Emerging evidence suggests that TGF-ß1 can regulate endothelial nitric oxide synthase (eNOS) expression in endothelial cells. This study aimed to determine if ZNF580 mediated eNOS expression and participated in endothelial cell migration and proliferation via the TGF-ß1/Smad2/ZNF580/eNOS signaling pathway. Overexpression/downexpression of ZNF580 in EAhy926 cells leads to the enhancement/decrease of eNOS expression. TGF-ß1 downregulated both ZNF580 and eNOS at the mRNA and protein levels in concentration- and time-dependent manners. ZNF580 and eNOS downregulation induced by TGF-ß1 was blocked by the specific TGF-ß1 type I receptor ALK5 inhibitor, SB431542. Overexpression of ZNF580 attenuated TGF-ß1-induced inhibition of EAhy926 cell growth and mobility, and vice versa. These results suggest that ZNF580 mediates eNOS expression and endothelial cell migration/proliferation via the TGF-ß1/ALK5/Smad2 pathway, and thus plays a crucial role in vascular endothelial cells.

ZNF580, a novel C2H2 zinc-finger transcription factor, interacts with the TGF-ß signal molecule Smad2.

ZNF580 (gene ID 51157), a novel gene encoding a C2H2 (Cys2-His2) zinc-finger transcription factor, may be involved in the maintenance of vascular endothelium homoeostasis. To investigate the physiological role of the transcription factor ZNF580, we screened human foetal brain cDNA library with a yeast two-hybrid system and identified 14 proteins that interact with ZNF580. The interaction between ZNF580 and Smad2 was confirmed by co-immunoprecipitation. Co-localization between endogenous ZNF580 and Smad2 was mainly found in the nuclei of EA.hy926 endothelial cells with immunofluorescence and confocal microscopy. Our results suggest that ZNF580 is a binding partner of Smad2 and is involved in the signal transduction of the TGF-ß (transforming growth factor-ß) signalling pathway, which provides a basis for additional research to investigate the role of ZNF580 in the maintenance of vascular endothelium homoeostasis and the onset of atherosclerotic diseases.

Application of x-ray phase contrast imaging to microscopic identification of Chinese medicines.

In the last decade, x-ray phase contrast imaging (XPCI) has received considerable attention as a novel imaging technique, which has proved to be suitable for weakly absorbing materials such as biomedical samples and polymers. In this paper, the microstructures of traditional Chinese medicines (TCMs), which are used as judging criteria in the identification of TCMs, were investigated by XPCI based on a nano-focus x-ray tube. The results demonstrated that XPCI is a promising new method for the identification of TCMs, with advantages such as nondestructivity, no special sample preparation and suitability for thick samples.