Construction and Application of YOLOv3-Based Diatom Identification Model of Scanning Electron Microscope Images.

OBJECTIVES: To construct a YOLOv3-based model for diatom identification in scanning electron microscope images, explore the application performance in practical cases and discuss the advantages of this model. METHODS: A total of 25 000 scanning electron microscopy images were collected at 1 500× as an initial image set, and input into the YOLOv3 network to train the identification model after experts' annotation and image processing. Diatom scanning electron microscopy images of lung, liver and kidney tissues taken from 8 drowning cases were identified by this model under the threshold of 0.4, 0.6 and 0.8 respectively, and were also identified by experts manually. The application performance of this model was evaluated through the recognition speed, recall rate and precision rate. RESULTS: The mean average precision of the model in the validation set and test set was 94.8% and 94.3%, respectively, and the average recall rate was 81.2% and 81.5%, respectively. The recognition speed of the model is more than 9 times faster than that of manual recognition. Under the threshold of 0.4, the mean recall rate and precision rate of diatoms in lung tissues were 89.6% and 87.8%, respectively. The overall recall rate in liver and kidney tissues was 100% and the precision rate was less than 5%. As the threshold increased, the recall rate in all tissues decreased and the precision rate increased. The F1 score of the model in lung tissues decreased with the increase of threshold, while the F1 score in liver and kidney tissues with the increase of threshold. CONCLUSIONS: The YOLOv3-based diatom electron microscope images automatic identification model works at a rapid speed and shows high recall rates in all tissues and high precision rates in lung tissues under an appropriate threshold. The identification model greatly reduces the workload of manual recognition, and has a good application prospect.

Petrocodonliboensis (Gesneriaceae), a new species from Guizhou, China.

Petrocodonliboensis Sheng H.Tang & Jia W.Yang is a new species of Gesneriaceae from Guizhou, southwestern China. The new taxon has a pale-yellow corolla and is most similar to P.luteoflorus. However, it differs from the latter by having a urceolate (vs. cannulate) corolla tube, an abaxial corolla lip 0.8-1.1 mm (vs. 2-2.2 mm) long, and filaments 1.5-1.7 mm (vs. ca. 7 mm) long that are straight (vs. S-shaped or geniculate near the middle). The new taxon is assessed as "Data Deficient" (DD) according to the IUCN standards.

Impatiensbeipanjiangensis (Balsaminaceae), a new species from Guizhou, China.

Impatiensbeipanjiangensis Jian Xu & H. F. Hu (Balsaminaceae), a new species of Impatienssubg.Clavicarpa discovered in Guizhou, China, is described and illustrated in this study along with its molecular phylogenetic analysis. I.beipanjiangensis is similar to I.liboensis, I.chishuiensis and I.clavigera in morphology, but I.tubulosa has the closest relationship to it. However, there are various ways in which the new species can be easily distinguished from these four species: Inferior nodes swollen rhizoid, pale green and with hooked outer sepals, longer lateral united petals, subovate auricle, deeper lower sepal and shorter spur that is reflexed towards the lower sepal. Furthermore, I.beipanjiangensis is distinguished from other Impatiens species, based on morphological, micromorphological and palynological evidence and molecular data (PP 0.967).

Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements.

Regulatory sequences and transposable elements (TEs) account for a large proportion of the genomic sequences of species; however, their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations. Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily (LTR4C_SS), containing binding motifs for SIX1 and SIX4, showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat (LTR), MLT1F1, acting as a testis-specific alternative promoter in SRPK2 (a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.

Single-cell profiling of the pig cecum at various developmental stages.

The gastrointestinal tract is essential for food digestion, nutrient absorption, waste elimination, and microbial defense. Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity, functional heterogeneity, and their importance in intestinal tract development and disease. Although such profiling has been extensively conducted in humans and mice, the single-cell gene expression landscape of the pig cecum remains unexplored. Here, single-cell RNA sequencing was performed on 45 572 cells obtained from seven cecal samples in pigs at four different developmental stages (days (D) 30, 42, 150, and 730). Analysis revealed 12 major cell types and 38 subtypes, as well as their distinctive genes, transcription factors, and regulons, many of which were conserved in humans. An increase in the relative proportions of CD8 + T and Granzyme A (low expression) natural killer T cells (GZMA low NKT) cells and a decrease in the relative proportions of epithelial stem cells, Tregs, RHEX + T cells, and plasmacytoid dendritic cells (pDCs) were noted across the developmental stages. Moreover, the post-weaning period exhibited an up-regulation in mitochondrial genes, COX2 and ND2, as well as genes involved in immune activation in multiple cell types. Cell-cell crosstalk analysis indicated that IBP6 + fibroblasts were the main signal senders at D30, whereas IBP6 - fibroblasts assumed this role at the other stages. NKT cells established interactions with epithelial cells and IBP6 + fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs. This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

Efficient in-situ conversion of low-concentration carbon dioxide in exhaust gas using silver nanoparticles in N-heterocyclic carbene polymer.

Efficient utilizing CO2 is crucial approaches in achieving carbon neutralization. One of the challenges lies in the in-situ conversion of low concentration CO2 found in waste gases. This study introduces a novel heterogeneous catalyst known as silver nanoparticles in porous N-heterocyclic carbene polymer (Ag@POP-NL-3). The catalyst is synthesized via a streamlined pre-coordination method. Ag@POP-NL-3 exhibits uniform distribution of silver nanoparticles, a porous structure and nitrogen activation groups. It demonstrates high efficiency and selectivity in absorbing and activating CO2 and enabling the conversion of low concentration CO2 (30 vol%) from lime kiln waste gas into cyclic carbonate under mild conditions. This catalytic system achieves both CO2 capture and resource utilization of CO2 simultaneously, effectively fixing low-concentration CO2 from waste gases into C2+ valuable chemicals. This approach elegantly addresses two goals in one solution.

Copper-Catalyzed, N-Directed Distal C(sp3)-H Functionalization toward Azepanes.

We herein report a copper-catalyzed formal [5 + 2] aza-annulation of N-fluorosulfonamides and 1,3-dienes/1,3-enynes for synthesis of structurally diverse alkene/alkyne-containing azepanes. The reaction features selective functionalization of distal unactivated C(sp3)-H bonds and a broad substrate scope, thus allowing the late-stage modification of pharmaceuticals and natural products. A radical mechanism involving 1,5-hydrogen atom transfer of N-radicals, facile coupling of alkyl radicals with 1,3-dienes/1,3-enynes, and the construction of azepane motifs via C-N bond formation is proposed.

Oreocharisqianyuensis, a new species of Gesneriaceae from Southwest, China based on morphological and molecular evidence.

Oreocharisqianyuensis, a new species of Gesneriaceae from Southwest, China, is described and illustrated based on morphological comparisons and molecular phylogenetic analyses. Phylotranscriptomic analyses of the new species in the context of a comprehensive phylogeny with dense sampling of 88% (111/126) of all species of the genus indicated that the new species was most closely-related to O.fargesii. The new species is morphologically similar to O.fargesii and O.nanchuanica in the shape, color and structure of flowers and the number of stamens, but differs in the leaf blade shape, margin and the indumentum characters of the inflorescence. Its morphological relationship with similar species is discussed, the detailed descriptions, colour photographs, distribution, as well as the IUCN threatened status based on the IUCN Red List Categories and Criteria are also provided.

Smilax weniae, a New Species of Smilacaceae from Limestone Areas Bordering Guizhou and Guangxi, China.

A new species, Smilax weniae (Smilacaceae), from Southwest China, is described and illustrated. The new species bears peltate leaves, which was previously a unique feature of S. luei. However, it differs from the latter by having a broad ovate leaf blade, longer peduncle, and sexual dimorphic flowers. Further phylogenetic analyses revealed that the new species were placed in a unique position in a subclade of Old World Smilax based on ptDNA and nrITS sequences. Combining detailed morphological comparisons and molecular evidence, we validated that S. weniae is an undescribed new species. Moreover, the plastome characteristics of S. weniae are reported.

Petrocosmeaduyunensis (Gesneriaceae), a new species from Guizhou, China.

Plants belonging to the genus Petrocosmea are rare and small herbs difficult to find in the wild. In the present study, a new species, Petrocosmeaduyunensis, from Guizhou, China, is described. The species is most similar to P.leiandra and differs from it by a distinctly recurved abaxial corolla lip, free anthers and included pistil. Detailed morphological comparisons are given. One population with about 100 mature individuals was found at the type locality. This new taxon was assessed as "Data Deficient" (DD) according to the IUCN standards.