PST-Diff: Achieving High-consistency Stain Transfer by Diffusion Models with Pathological and Structural Constraints.

Histopathological examinations heavily rely on hematoxylin and eosin (HE) and immunohistochemistry (IHC) staining. IHC staining can offer more accurate diagnostic details but it brings significant financial and time costs. Furthermore, either re-staining HE-stained slides or using adjacent slides for IHC may compromise the accuracy of pathological diagnosis due to information loss. To address these challenges, we develop PST-Diff, a method for generating virtual IHC images from HE images based on diffusion models, which allows pathologists to simultaneously view multiple staining results from the same tissue slide. To maintain the pathological consistency of the stain transfer, we propose the asymmetric attention mechanism (AAM) and latent transfer (LT) module in PST-Diff. Specifically, the AAM can retain more local pathological information of the source domain images through the design of asymmetric attention mechanisms, while ensuring the model's flexibility in generating virtual stained images that highly confirm to the target domain. Subsequently, the LT module transfers the implicit representations across different domains, effectively alleviating the bias introduced by direct connection and further enhancing the pathological consistency of PST-Diff. Furthermore, to maintain the structural consistency of the stain transfer, the conditional frequency guidance (CFG) module is proposed to precisely control image generation and preserve structural details according to the frequency recovery process. To conclude, the pathological and structural consistency constraints provide PST-Diff with effectiveness and superior generalization in generating stable and functionally pathological IHC images with the best evaluation score. In general, PST-Diff offers prospective application in clinical virtual staining and pathological image analysis.

Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing.

Adenosine-to-inosine (A-to-I) RNA editing recodes the genetic information. Apart from diversifying the proteome, another tempting advantage of RNA recoding is to correct deleterious DNA mutation and restore ancestral allele. Solid evidences for beneficial restorative editing are very rare in animals. By searching for "convergent recoding" under a phylogenetic context, we proposed this term for judging the potential restorative functions of particular editing site. For the well-known mammalian Gln>Arg (Q>R) recoding site, its ancestral state in vertebrate genomes was the pre-editing Gln, and all 470 available mammalian genomes strictly avoid other three equivalent ways to achieve Arg in protein. The absence of convergent recoding from His>Arg, or synonymous mutations on Gln codons, could be attributed to the strong maintenance on editing motif and structure, but the absence of direct A-to-G mutation is extremely unexpected. With similar ideas, we found cases of convergent recoding in Drosophila genus, reducing the possibility of their restorative function. In summary, we defined an interesting scenario of convergent recoding, the occurrence of which could be used as preliminary judgements for whether a recoding site has a sole restorative role. Our work provides novel insights to the natural selection and evolution of RNA editing.

Danshen-Shanzha formula for the treatment of atherosclerosis: ethnopharmacological relevance, preparation methods, chemical constituents, pharmacokinetic properties, and pharmacological effects.

Danshen-Shanzha Formula (DSF) is a well-known herbal combination comprising Radix Salvia Miltiorrhiza (known as Danshen in Chinese) and Fructus Crataegi (known as Shanzha in Chinese), It has been documented to exhibit considerable benefits for promoting blood circulation and removing blood stasis, and was used extensively in the treatment of atherosclerotic cardiac and cerebral vascular diseases over decades. Despite several breakthroughs achieved in the basic research and clinical applications of DSF over the past decades, there is a lack of comprehensive reviews summarizing its features and research, which hinders further exploration and exploitation of this promising formula. This review aims to provide a comprehensive interpretation of DSF in terms of its ethnopharmacological relevance, preparation methods, chemical constituents, pharmacokinetic properties and pharmacological effects. The related information on Danshen, Shanzha, and DSF was obtained from internationally recognized online scientific databases, including Web of Science, PubMed, Google Scholar, China National Knowledge Infrastructure, Baidu Scholar, ScienceDirect, ACS Publications, Online Library, Wan Fang Database as well as Flora of China. Data were also gathered from documentations, printed works and classics, such as the Chinese Pharmacopoeia, Chinese herbal classics, etc. Three essential avenues for future studies were put forward as follows: a) Develop and unify the standard preparation method of DSF as to achieve optimized pharmacological properties. b) Elucidate the functional mechanisms as well as the rationality and rule for the compatibility art of DSF by focusing on the clinic syndromes together with the subsequent development of preclinic study system in vitro and in vivo with consistent pathological features, pharmacokinetical behaviour and biomarkers. c) Perform more extensive clinical studies towards the advancement of mechanism-based on evidence-based medicine on the safety application of DSF. This review will provide substantial data support and broader perspective for further research on the renowned formula.

Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites.

Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed 'conserved editing with non-conserved recoding' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.

Melanasterasinica He & Burckhardt, sp. nov., a new psylloid species (Hemiptera, Psylloidea, Liviidae) from China developing on Grewia sp. (Malvaceae).

Melanasterasinica He & Burckhardt, sp. nov., a new psylloid species developing on Grewia sp., is described from Hainan, China. It is the first Melanastera species reported from Asia and China, and the second species from the Old World. While New World species of Melanastera are mostly associated with the plant families Melastomataceae and Annonaceae, the two Old World species develop on the malvaceous Grewia, a host otherwise used in psylloids by two Haplaphalara species. The new species is described, diagnosed and illustrated, and its host plant and biogeographic ranges are discussed.

Lactylome analyses suggest systematic lysine-lactylated substrates in oral squamous cell carcinoma under normoxia and hypoxia.

Cancer cells tend to live in hypoxic environment characterized by enhanced glycolysis and accumulation of lactate. Intracellular lactate is shown to drive a novel type of post-translational modification (PTM), lysine lactylation (Kla). Kla has been confirmed to affect the malignant progression of tumors such as hepatocellular carcinoma (HCC) and colon cancer, whereas the global lactylomic profiling of oral squamous cell carcinoma (OSCC) is unclear. Here, the integrative lactylome and proteome analyses by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1011 Kla sites within 532 proteins and 1197 Kla sites within 608 proteins in SCC25 cells under normoxic and hypoxic environments, respectively. Among these lactylated proteins, histones accounted for only a small fraction, suggesting the presence of Kla modification of OSCC in a large number of non-histone proteins. Notably, Kla preferred to enrich in spliceosome, ribosome and glycolysis/gluconeogenesis pathway in both normoxic and hypoxic cultures. Compared with normoxia, 589 differential proteins with 898 differentially lactylated sites were detected under hypoxia, which were mainly associated with the glycolysis/gluconeogenesis pathway by KEGG analysis. Importantly, we verified the presence of lactylation modification in the spliceosomal proteins hnRNPA1, SF3A1, hnRNPU and SLU7, as well as in glycolytic enzyme PFKP. In addition, the differential alternative splicing analysis described the divergence of pre-mRNA splicing patterns in the presence or absence of sodium lactate and at different oxygen concentrations. Finally, a negative correlation between tissue Kla levels and the prognosis of OSCC patients was revealed by immunohistochemistry. Our study is the first report to elucidate the lactylome and its biological function in OSCC, which deepens our understanding of the mechanisms underlying OSCC progression and provides a novel strategy for targeted therapy for OSCC.

Comparative genomic analyses reveal evidence for adaptive A-to-I RNA editing in insect Adar gene.

Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking. We performed a comparative genomic analysis on 113 Diptera species, focusing on the Adar Ser>Gly auto-recoding site in Drosophila. We only found one species having a derived Gly at the corresponding site, and this occurrence was significantly lower than genome-wide random expectation. This suggests that the Adar Ser>Gly site is unlikely to be genomically replaced with G during evolution, and thus indicating the advantage of editable status over hardwired genomic alleles. Similar trends were observed for the conserved Ile>Met recoding in gene Syt1. In the light of evolution, we established a comparative genomic approach for quantitatively justifying the adaptiveness of individual editing sites. Priority should be given to such adaptive editing sites in future functional studies.

Osmotic Pressure and Its Biological Implications.

Gaining insight into osmotic pressure and its biological implications is pivotal for revealing mechanisms underlying numerous fundamental biological processes across scales and will contribute to the biomedical and pharmaceutical fields. This review aims to provide an overview of the current understanding, focusing on two central issues: (i) how to determine theoretically osmotic pressure and (ii) how osmotic pressure affects important biological activities. More specifically, we discuss the representative theoretical equations and models for different solutions, emphasizing their applicability and limitations, and summarize the effect of osmotic pressure on lipid phase separation, cell division, and differentiation, focusing on the mechanisms underlying the osmotic pressure dependence of these biological processes. We highlight that new theory of osmotic pressure applicable for all experimentally feasible temperatures and solute concentrations needs to be developed, and further studies regarding the role of osmotic pressure in other biological processes should also be carried out to improve our comprehensive and in-depth understanding. Moreover, we point out the importance and challenges of developing techniques for the in vivo measurement of osmotic pressure.

The first A-to-I RNA editome of hemipteran species Coridius chinensis reveals overrepresented recoding and prevalent intron editing in early-diverging insects.

BACKGROUND: Metazoan adenosine-to-inosine (A-to-I) RNA editing resembles A-to-G mutation and increases proteomic diversity in a temporal-spatial manner, allowing organisms adapting to changeable environment. The RNA editomes in many major animal clades remain unexplored, hampering the understanding on the evolution and adaptation of this essential post-transcriptional modification. METHODS: We assembled the chromosome-level genome of Coridius chinensis belonging to Hemiptera, the fifth largest insect order where RNA editing has not been studied yet. We generated ten head RNA-Seq libraries with DNA-Seq from the matched individuals. RESULTS: We identified thousands of high-confidence RNA editing sites in C. chinensis. Overrepresentation of nonsynonymous editing was observed, but conserved recoding across different orders was very rare. Under cold stress, the global editing efficiency was down-regulated and the general transcriptional processes were shut down. Nevertheless, we found an interesting site with "conserved editing but non-conserved recoding" in potassium channel Shab which was significantly up-regulated in cold, serving as a candidate functional site in response to temperature stress. CONCLUSIONS: RNA editing in C. chinensis largely recodes the proteome. The first RNA editome in Hemiptera indicates independent origin of beneficial recoding during insect evolution, which advances our understanding on the evolution, conservation, and adaptation of RNA editing.

Perfect cooperative pest control via nano-pesticide and natural predator: High predation selectivity and negligible toxicity toward predatory stinkbug.

The improper use of synthetic pesticides has caused adverse effects on global ecosystems and human health. As a part of sustainable pest management strategy, natural predators, along with nano-pesticides, have made significant contributions to ecological agriculture. The cooperative application of both approaches may overcome their limitations, substantially reducing pesticide application while controlling insect pests efficiently. Herein, the current study introduced a cationic star polymer (SPc) to prepare two types of nano-pesticides, which were co-applied with predatory stinkbugs Picromerus lewisi to achieve perfect cooperative pest control. The SPc exhibited nearly no toxicity against predatory stinkbugs at the working concentration, but it led to the death of predatory stinkbugs at extremely high concentration with the lethal concentration 50 (LC50) value of 13.57 mg/mL through oral feeding method. RNA-seq analysis revealed that the oral feeding of SPc could induce obvious stress responses, leading to stronger phagocytosis, exocytosis, and energy synthesis to ultimately result in the death of predatory stinkbugs. Then, the broflanilide and chlorobenzuron were employed to prepare the self-assembled nano-pesticides via hydrogen bond and Van der Waals force, and the complexation with SPc broke the self-aggregated structures of pesticides and reduced their particle sizes down to nanoscale. The bioactivities of prepared nano-pesticides were significantly improved toward common cutworm Spodoptera litura with the corrected mortality increase by approximately 30%. Importantly, predatory stinkbugs exhibited a strong predation selectivity for alive common cutworms to reduce the exposure risk of nano-pesticides, and the nano-pesticides showed negligible toxicity against predators. Thus, the nano-pesticides and predatory stinkbugs could be applied simultaneously for efficient and sustainable pest management. The current study provides an excellent precedent for perfect cooperative pest control via nano-pesticide and natural predator.

Early Predicting Osteogenic Differentiation of Mesenchymal Stem Cells Based on Deep Learning Within One Day.

Osteogenic differentiation of mesenchymal stem cells (MSCs) is proposed to be critical for bone tissue engineering and regenerative medicine. However, the current approach for evaluating osteogenic differentiation mainly involves immunohistochemical staining of specific markers which often can be detected at day 5-7 of osteogenic inducing. Deep learning (DL) is a significant technology for realizing artificial intelligence (AI). Computer vision, a branch of AI, has been proved to achieve high-precision image recognition using convolutional neural networks (CNNs). Our goal was to train CNNs to quantitatively measure the osteogenic differentiation of MSCs. To this end, bright-field images of MSCs during early osteogenic differentiation (day 0, 1, 3, 5, and 7) were captured using a simple optical phase contrast microscope to train CNNs. The results showed that the CNNs could be trained to recognize undifferentiated cells and differentiating cells with an accuracy of 0.961 on the independent test set. In addition, we found that CNNs successfully distinguished differentiated cells at a very early stage (only 1 day). Further analysis showed that overall morphological features of MSCs were the main basis for the CNN classification. In conclusion, MSCs differentiation detection can be achieved early and accurately through simple bright-field images and DL networks, which may also provide a potential and novel method for the field of cell detection in the near future.

Chromosome-level genome of the poultry shaft louse Menopon gallinae provides insight into the host-switching and adaptive evolution of parasitic lice.

BACKGROUND: Lice (Psocodea: Phthiraptera) are one important group of parasites that infects birds and mammals. It is believed that the ancestor of parasitic lice originated on the ancient avian host, and ancient mammals acquired these parasites via host-switching from birds. Here we present the first chromosome-level genome of Menopon gallinae in Amblycera (earliest diverging lineage of parasitic lice). We explore the transition of louse host-switching from birds to mammals at the genomic level by identifying numerous idiosyncratic genomic variations. RESULTS: The assembled genome is 155 Mb in length, with a contig N50 of 27.42 Mb. Hi-C scaffolding assigned 97% of the bases to 5 chromosomes. The genome of M. gallinae retains a basal insect repertoire of 11,950 protein-coding genes. By comparing the genomes of lice to those of multiple representative insects in other orders, we discovered that gene families of digestion, detoxification, and immunity-related are generally conserved between bird lice and mammal lice, while mammal lice have undergone a significant reduction in genes related to chemosensory systems and temperature. This suggests that mammal lice have lost some of these genes through the adaption to environment and temperatures after host-switching. Furthermore, 7 genes related to hematophagy were positively selected in mammal lice, suggesting their involvement in the hematophagous behavior. CONCLUSIONS: Our high-quality genome of M. gallinae provides a valuable resource for comparative genomic research in Phthiraptera and facilitates further studies on adaptive evolution of host-switching within parasitic lice.

Translating color fundus photography to indocyanine green angiography using deep-learning for age-related macular degeneration screening.

Age-related macular degeneration (AMD) is the leading cause of central vision impairment among the elderly. Effective and accurate AMD screening tools are urgently needed. Indocyanine green angiography (ICGA) is a well-established technique for detecting chorioretinal diseases, but its invasive nature and potential risks impede its routine clinical application. Here, we innovatively developed a deep-learning model capable of generating realistic ICGA images from color fundus photography (CF) using generative adversarial networks (GANs) and evaluated its performance in AMD classification. The model was developed with 99,002 CF-ICGA pairs from a tertiary center. The quality of the generated ICGA images underwent objective evaluation using mean absolute error (MAE), peak signal-to-noise ratio (PSNR), structural similarity measures (SSIM), etc., and subjective evaluation by two experienced ophthalmologists. The model generated realistic early, mid and late-phase ICGA images, with SSIM spanned from 0.57 to 0.65. The subjective quality scores ranged from 1.46 to 2.74 on the five-point scale (1 refers to the real ICGA image quality, Kappa 0.79-0.84). Moreover, we assessed the application of translated ICGA images in AMD screening on an external dataset (n = 13887) by calculating area under the ROC curve (AUC) in classifying AMD. Combining generated ICGA with real CF images improved the accuracy of AMD classification with AUC increased from 0.93 to 0.97 (P < 0.001). These results suggested that CF-to-ICGA translation can serve as a cross-modal data augmentation method to address the data hunger often encountered in deep-learning research, and as a promising add-on for population-based AMD screening. Real-world validation is warranted before clinical usage.

A new ant species of the genus Carebara Westwood, 1840 (Hymenoptera, Formicidae, Myrmicinae) with a key to Chinese species.

A new Chinese ant species Carebaralaevicepssp. nov. is described based on the major and minor workers. This species is most similar to C.lusciosa (Wheeler, 1928) due to a spineless propodeum, the absence of horns, and a smooth head capsule. It is distinguished by the following features: (1) antenna 10-segmented; (2) katepisternum rugose-reticulate; (3) in major workers, lateral sides of head in full-face view parallel; (4) metanotal groove distinct, anterodorsal corner forming an acute tooth behind metanotal groove. Moreover, an updated key to Chinese Carebara species is presented based on major workers, with a checklist comprising a total of 36 Chinese Carebara species and subspecies. Morphological structures and scanning electron micrographs of the newly discovered species' minor and major workers are provided.

The complete mitochondrial genome of Aphidius colemani (Hymenoptera: Braconidae: Aphidiinae).

The genome-level features are crucial genetic resources for species identification and phylogenetic analysis. Here, the complete mitochondrial genome of Aphidius colemani Viereck 1912 (Hymenoptera: Braconidae: Aphidiinae) was sequenced, determined and analyzed. The circular genome is 16,372 bp in length with an overall base composition of 38.9% for A, 46.2% for T, 6.7% for C, and 8.2% for G. The mitochondrial genome of A. colemani contained 13 protein-coding genes that initiated by the ATN codon, 22 transfer RNA genes, two ribosomal RNA genes (rRNAs), and a control region (CR). It shared the same gene arrangement patterns that occurred in two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY with Aphidius gifuensis. Phylogenetic analyses using Bayesian inference and Maximum-likelihood methods supported that the two species of Aphidiinae formed a clade and sister to other subfamilies of Braconidae.

Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application.

Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.

Stem chewing lice on Cretaceous feathers preserved in amber.

Phthirapteran lice (true lice or parasitic lice) are a major group of ectoparasitic insects living on their bird or mammal hosts during their entire life cycle.1 Due to their highly specialized lifestyles, they are extremely poorly represented in fossil records.2 Molecular clock estimations have speculated extensively about the origin time of parasitic lice,3,4 yet none have been confirmed unequivocally. Herein, we report a new family of stem chewing lice, based on two adult insects associated with several semiplume feathers preserved within a piece of Kachin amber from the mid-Cretaceous. They display some defining characteristics of the Amblycera, an early-diverging lineage of the crown lice group. These features include a wingless body, chewing mouthparts, narrow and small thorax, and short tarsus with elongated euplantulae. Our phylogenetic analysis places the new taxa in the Amblycera, and the discovery thus pushes back the lice fossil records by at least 55 million years. Furthermore, the new specimens show primitive characters such as compressed and club-shaped terminal segments of antennae, maxillary and labial palps, and unmodified femora of hind legs, providing key information for the evolutionary relationship between free-living booklice and parasitic lice. This suggests that some ectoparasitic characters defining the crown lice group might have evolved among amblyceran and non-amblyceran lice in parallel. These newly described fossil specimens imply at least a Cretaceous age of Phthiraptera.

Matrix metalloproteinases as attractive therapeutic targets for chronic pain: A narrative review.

Chronic pain constitutes an abnormal pain state that detrimentally affects the quality of life, daily activities, occupational performance, and stability of mood. Despite the prevalence of chronic pain, effective drugs with potent abirritation and minimal side effects remain elusive. Substantial studies have revealed aberrant activation of the matrix metalloproteinases (MMPs) in multiple chronic pain models. Additionally, emerging evidence has demonstrated that the downregulation of MMPs can alleviate chronic pain in diverse animal models, underscoring the unique and crucial role of MMPs in different stages and types of chronic pain. This review delves into the mechanistic insights and roles of MMPs in modulating chronic pain. The aberrant activation of MMPs has been linked to neuropathic pain through mechanisms involving myelin abnormalities in peripheral nerve and spinal dorsal horn (SDH), hyperexcitability of dorsal root ganglion (DRG) neurons, activation of N-methyl-d-aspartate receptors (NMDAR) and Ca2+-dependent signals, glial cell activation, and proinflammatory cytokines release. Different MMPs also contribute significantly to inflammatory pain and cancer pain. Furthermore, we summarized the substantial therapeutic potential of MMP pharmacological inhibitors across different types of chronic pain. Overall, our findings underscore the promising therapeutic prospects of MMPs targeting for managing chronic pain.

Interleukin-17: A Putative Novel Pharmacological Target for Pathological Pain.

Pathological pain imposes a huge burden on the economy and the lives of patients. At present, drugs used for the treatment of pathological pain have only modest efficacy and are also plagued by adverse effects and risk for misuse and abuse. Therefore, understanding the mechanisms of pathological pain is essential for the development of novel analgesics. Several lines of evidence indicate that interleukin-17 (IL-17) is upregulated in rodent models of pathological pain in the periphery and central nervous system. Besides, the administration of IL-17 antibody alleviated pathological pain. Moreover, IL-17 administration led to mechanical allodynia which was alleviated by the IL-17 antibody. In this review, we summarized and discussed the therapeutic potential of targeting IL-17 for pathological pain. The upregulation of IL-17 promoted the development of pathological pain by promoting neuroinflammation, enhancing the excitability of dorsal root ganglion neurons, and promoting the communication of glial cells and neurons in the spinal cord. In general, the existing research shows that IL-17 is an attractive therapeutic target for pathologic pain, but the underlying mechanisms still need to be investigated.