Construction of a Full-Length Transcriptome of Western Honeybee Midgut Tissue and Improved Genome Annotation.

Honeybees are an indispensable pollinator in nature with pivotal ecological, economic, and scientific value. However, a full-length transcriptome for Apis mellifera, assembled with the advanced third-generation nanopore sequencing technology, has yet to be reported. Here, nanopore sequencing of the midgut tissues of uninoculated and Nosema ceranae-inoculated A. mellifera workers was conducted, and the full-length transcriptome was then constructed and annotated based on high-quality long reads. Next followed improvement of sequences and annotations of the current reference genome of A. mellifera. A total of 5,942,745 and 6,664,923 raw reads were produced from midguts of workers at 7 days post-inoculation (dpi) with N. ceranae and 10 dpi, while 7,100,161 and 6,506,665 raw reads were generated from the midguts of corresponding uninoculated workers. After strict quality control, 6,928,170, 6,353,066, 5,745,048, and 6,416,987 clean reads were obtained, with a length distribution ranging from 1 kb to 10 kb. Additionally, 16,824, 17,708, 15,744, and 18,246 full-length transcripts were respectively detected, including 28,019 nonredundant ones. Among these, 43,666, 30,945, 41,771, 26,442, and 24,532 full-length transcripts could be annotated to the Nr, KOG, eggNOG, GO, and KEGG databases, respectively. Additionally, 501 novel genes (20,326 novel transcripts) were identified for the first time, among which 401 (20,255), 193 (13,365), 414 (19,186), 228 (12,093), and 202 (11,703) were respectively annotated to each of the aforementioned five databases. The expression and sequences of three randomly selected novel transcripts were confirmed by RT-PCR and Sanger sequencing. The 5' UTR of 2082 genes, the 3' UTR of 2029 genes, and both the 5' and 3' UTRs of 730 genes were extended. Moreover, 17,345 SSRs, 14,789 complete ORFs, 1224 long non-coding RNAs (lncRNAs), and 650 transcription factors (TFs) from 37 families were detected. Findings from this work not only refine the annotation of the A. mellifera reference genome, but also provide a valuable resource and basis for relevant molecular and -omics studies.

Delivery of CRISPR/Cas9 system by AAV as vectors for gene therapy.

The adeno-associated virus (AAV) is a defective single-stranded DNA virus with the simplest structure reported to date. It constitutes a capsid protein and single-stranded DNA. With its high transduction efficiency, low immunogenicity, and tissue specificity, it is the most widely used and promising gene therapy vector. The clustered regularly interspaced short palindromic sequence (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system is an emerging technology that utilizes cas9 nuclease to specifically recognize and cleave target genes under the guidance of small guide RNA and realizes gene editing through homologous directional repair and non-homologous recombination repair. In recent years, an increasing number of animal experiments and clinical studies have revealed the great potential of AAV as a vector to deliver the CRISPR/cas9 system for treating genetic diseases and viral infections. However, the immunogenicity, toxicity, low transmission efficiency in brain and ear tissues, packaging size limitations of AAV, and immunogenicity and off-target effects of Cas9 protein pose several clinical challenges. This research reviews the role, challenges, and countermeasures of the AAV-CRISPR/cas9 system in gene therapy.

Amphiphilic Superspreading Polymer Membranes Prepared by Capillary Force-Driven Self-Assembly.

To overcome the two main obstacles of large-scale application of superspreading material, self assembly is used to prepare superspreading polymer membrane (SPPM) in this work. An amphiphilic SPPM is prepared by capillary force-driven self assembly using PP melt-blown nonwovens and polyvinyl alcohol (PVA). The prepared SPPM has low preparation cost and stable performance since self assembly needs low energy consumption, and the production is thermodynamically stable. By using cryo-electron microscopy, transmission electron microscopy, X-ray photoelectron spectrum and scanning electron microscope with energy dispersive X-ray spectroscopy. It is proved that PVA is successfully assembled on the fiber surface of PP melt-blown nonwovens. The prepared SPPM has excellent spreading performance, the "spreading times" of both water and oil are less than 0.5 s. They showed much superior performance compared to traditional materials when applied in oil-water separation, seawater desalination, and ion separation. This work will definitely promote the development of self assembly, superspreading materials, and related sciences.

Preliminary Study on the Pathogenic Mechanism of Jujube Flower Disease in Honeybees (Apis mellifera ligustica) Based on Midgut Transcriptomics.

Honeybees are prone to poisoning, also known as jujube flower disease, after collecting nectar from jujube flowers, resulting in the tumultuous demise of foragers. The prevalence of jujube flower disease has become one of the main factors affecting the development of the jujube and beekeeping industries in Northern China. However, the pathogenic mechanisms underlying jujube flower disease in honeybees are poorly understood. Herein, we first conducted morphological observations of the midgut using HE-staining and found that jujube flower disease-affected honeybees displayed midgut damage with peritrophic membrane detachment. Jujube flower disease was found to increase the activity of chitinase and carboxylesterase (CarE) and decrease the activity of superoxide dismutase (SOD), catalase (CAT), glutathione S-transferase (GST), and the content of CYP450 in the honeybee midgut. Transcriptomic data identified 119 differentially expressed genes in the midgut of diseased and healthy honeybees, including CYP6a13, CYP6a17, CYP304a1, CYP6a14, AADC, and AGXT2, which are associated with oxidoreductase activity and vitamin binding. In summary, collecting jujube flower nectar could reduce antioxidant and detoxification capacities of the honeybee midgut and, in more severe cases, damage the intestinal structure, suggesting that intestinal damage might be the main cause of honeybee death due to jujube nectar. This study provides new insights into the pathogenesis of jujube flower disease in honeybees.

Transcriptional dynamics and regulatory function of milRNAs in Ascosphaera apis invading Apis mellifera larvae.

In the present study, small RNA (sRNA) data from Ascosphaera apis were filtered from sRNA-seq datasets from the gut tissues of A. apis-infected Apis mellifera ligustica worker larvae, which were combined with the previously gained sRNA-seq data from A. apis spores to screen differentially expressed milRNAs (DEmilRNAs), followed by trend analysis and investigation of the DEmilRNAs in relation to significant trends. Additionally, the interactions between the DEmilRNAs and their target mRNAs were verified using a dual-luciferase reporter assay. In total, 974 A. apis milRNAs were identified. The first base of these milRNAs was biased toward U. The expression of six milRNAs was confirmed by stem-loop RT-PCR, and the sequences of milR-3245-y and milR-10285-y were validated using Sanger sequencing. These miRNAs grouped into four significant trends, with the target mRNAs of DEmilRNAs involving 42 GO terms and 120 KEGG pathways, such as the fungal-type cell wall and biosynthesis of secondary metabolites. Further investigation demonstrated that 299 DEmilRNAs (novel-m0011-3p, milR-10048-y, bantam-y, etc.) potentially targeted nine genes encoding secondary metabolite-associated enzymes, while 258 (milR-25-y, milR-14-y, milR-932-x, etc.) and 419 (milR-4561-y, milR-10125-y, let-7-x, etc.) DEmilRNAs putatively targeted virulence factor-encoded genes and nine genes involved in the MAPK signaling pathway, respectively. Additionally, the interaction between ADM-B and milR-6882-x, as well as between PKIA and milR-7009-x were verified. Together, these results not only offer a basis for clarifying the mechanisms underlying DEmilRNA-regulated pathogenesis of A. apis and a novel insight into the interaction between A. apis and honey bee larvae, but also provide candidate DEmilRNA-gene axis for further investigation.

Rhodium-Catalyzed Tandem Asymmetric Allylic Decarboxylative Addition and Cyclization of Vinylethylene Carbonates with N-Nosylimines.

A enantioselective tandem transformation, concerning asymmetric allylic decarboxylative addition and cyclization of N-nosylimines with vinylethylene carbonates (VECs), in the presence of [Rh(C2H4)2Cl]2, chiral sulfoxide-N-olefin tridentate ligand has been developed. The reaction of VECs with various substituted N-nosylimines proceeded smoothly under mild conditions, providing highly functionalized oxazolidine frameworks in good to high yields with good to excellent enantioselectivity.

Temporal attention networks for biomedical hypothesis generation.

OBJECTIVES: Hypothesis Generation (HG) is a task that aims to uncover hidden associations between disjoint scientific terms, which influences innovations in prevention, treatment, and overall public health. Several recent studies strive to use Recurrent Neural Network (RNN) to learn evolutional embeddings for HG. However, the complex spatiotemporal dependencies of term-pair relations will be difficult to depict due to the inherent recurrent structure. This paper aims to accurately model the temporal evolution of term-pair relations using only attention mechanisms, for capturing crucial information on inferring the future connectivities. METHODS: This paper proposes a Temporal Attention Networks (TAN) to produce powerful spatiotemporal embeddings for Biomedical Hypothesis Generation. Specifically, we formulate HG problem as a future connectivity prediction task in a temporal attributed graph. Our TAN develops a Temporal Spatial Attention Module (TSAM) to establish temporal dependencies of node-pair (term-pair) embeddings between any two time-steps for smoothing spatiotemporal node-pair embeddings. Meanwhile, a Temporal Difference Attention Module (TDAM) is proposed to sharpen temporal differences of spatiotemporal embeddings for highlighting the historical changes of node-pair relations. As such, TAN can adaptively calibrate spatiotemporal embeddings by considering both continuity and difference of node-pair embeddings. RESULTS: Three real-world biomedical term relationship datasets are constructed from PubMed papers. TAN significantly outperforms the best baseline with 12.03%, 4.59 and 2.34% Micro-F1 Score improvement in Immunotherapy, Virology and Neurology, respectively. Extensive experiments demonstrate that TAN can model complex spatiotemporal dependencies of term-pairs for explicitly capturing the temporal evolution of relation, significantly outperforming existing state-of-the-art methods. CONCLUSION: We proposed a novel TAN to learn spatiotemporal embeddings based on pure attention mechanisms for HG. TAN learns the evolution of relationships by modeling both the continuity and difference of temporal term-pair embeddings. The important spatiotemporal dependencies of term-pair relations are extracted based solely on attention mechanism for generating hypotheses.

Ferrostatin-1 attenuates hypoxic-ischemic brain damage in neonatal rats by inhibiting ferroptosis.

Background: Hypoxic-ischemic brain damage (HIBD) is a type of brain damage that is caused by perinatal asphyxia and serious damages the central nervous system. At present, there is no effective drug for the treatment of this disease. Besides, the pathogenesis of HIBD remains elusive. While studies have shown that ferroptosis plays an important role in HIBD, its role and mechanism in HIBD are yet to be fully understood. Methods: The HIBD model of neonatal rats was established using the Rice-Vannucci method. A complete medium of PC12 cells was adjusted to a low-sugar medium, and the oxygen-glucose deprivation model was established after continuous hypoxia for 12 h. Laser Doppler blood flow imaging was used to detect the blood flow intensity after modeling. 2,3,5-triphenyl tetrazolium chloride staining was employed to detect ischemic cerebral infarction in rat brain tissue, and hematoxylin and eosin staining and transmission electron microscopy were used to observe brain injury and mitochondrial damage. Immunofluorescence was applied to monitor the expression of GFAP. Real-time quantitative polymerase chain reaction, western blot, and immunofluorescence were utilized to detect the expression of messenger RNA and protein. The level of reactive oxygen species (ROS) in cells was detected using the ROS detection kit. Results: The results showed that ferrostatin-1 (Fer-1) significantly alleviated the brain injury caused by hypoxia and ischemia. Fer-1 significantly increased the expression of SLC3A2, SLC7A11, ACSL3, GSS, and GPX4 (P<0.05) and dramatically decreased the expressions of GFAP, ACSL4, TFRC, FHC, FLC, 4-HNE, HIF-1α, and ROS (P<0.05). Conclusions: Fer-1 inhibits ferroptosis and alleviates HIBD by potentially targeting the GPX4/ACSL3/ACSL4 axis; however, its specific mechanism warrants further exploration.

Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts.

Circular RNAs (circRNAs) are a class of novel non-coding RNAs (ncRNAs) that play essential roles in the development and growth of vertebrates through multiple manners. However, the mechanism by which circRNAs modulate the honey bee gut development is currently poorly understood. Utilizing the transcriptome data we obtained earlier, the highly expressed circRNAs in the Apis mellifera worker 4-, 5-, and 6-day-old larval guts were analyzed, which was followed by an in-depth investigation of the expression pattern of circRNAs during the process of larval guts development and the potential regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 1728 expressed circRNAs were detected in the A. mellifera larval guts. Among the most highly expressed 10 circRNAs, seven (novel_circ_000069, novel_circ_000027, novel_circ_000438, etc.) were shared by the 4-, 5-, and 6-day-old larval guts. In addition, 21 (46) up-regulated and 22 (27) down-regulated circRNAs were, respectively, screened in the Am4 vs. Am5 (Am5 vs. Am6) comparison groups. Additionally, nine DEcircRNAs, such as novel_circ_000340, novel_circ_000758 and novel_circ_001116, were shared by these two comparison groups. These DEcircRNAs were predicted to be transcribed from 14 and 29 parental genes; these were respectively annotated to 15 and 22 GO terms such as biological regulation and catalytic activity as well as 16 and 21 KEGG pathways such as dorsoventral axis formation and apoptosis. Moreover, a complicated competing endogenous RNA (ceRNA) network was observed; novel_circ_000838 in the Am4 vs. Am5 comparison group potentially targeted ame-miR-6000a-3p, further targeting 518 mRNAs engaged in several developmental signaling pathways (e.g., TGF-beta, hedgehog, and wnt signaling pathway) and immune pathways (e.g., phagosome, lysosome, and MAPK signaling pathway). The results demonstrated that the novel_circ_000838-ame-miR-6000a-3p axis may plays a critical regulatory part in the larval gut development and immunity. Furthermore, back-splicing sites of six randomly selected DEcircRNAs were amplified and verified by PCR; an RT-qPCR assay of these six DEcircRNAs confirmed the reliability of the used high-throughput sequencing data. Our findings provide a novel insight into the honey bee gut development and pave a way for illustration of the circRNA-modulated developmental mechanisms underlying the A. mellifera worker larval guts.

First Characterization and Regulatory Function of piRNAs in the Apis mellifera Larval Response to Ascosphaera apis Invasion.

piRNAs are a class of small non-coding RNAs that play essential roles in modulating gene expression and abundant biological processes. To decode the piRNA-regulated larval response of western honeybees (Apis mellifera) to Ascosphaera apis infection, the expression pattern of piRNAs in Apis mellifera ligustica larval guts after A. apis inoculation was analyzed based on previously obtained high-quality small RNA-seq datasets, followed by structural characterization, target prediction, regulatory network investigation, and functional dissection. Here, 504, 657, and 587 piRNAs were respectively identified in the 4-, 5-, and 6-day-old larval guts after inoculation with A. apis, with 411 ones shared. These piRNAs shared a similar length distribution and first base bias with mammal piRNAs. Additionally, 96, 103, and 143 DEpiRNAs were detected in the 4-, 5-, and 6-day-old comparison groups. Targets of the DEpiRNAs were engaged in diverse pathways such as the phosphatidylinositol signaling system, inositol phosphate metabolism, and Wnt signaling pathway. These targets were involved in three energy metabolism-related pathways, eight development-associated signaling pathways, and seven immune-relevant pathways such as the Jak-STAT signaling pathway. The expression trends of five randomly selected DEpiRNAs were verified using a combination of RT-PCR and RT-qPCR. The effective overexpression and knockdown of piR-ame-945760 in A. apis-infected larval guts were achieved by feeding a specific mimic and inhibitor. Furthermore, piR-ame-945760 negatively regulated the expression of two target immune mRNAs, SOCS5 and ARF1, in the larval gut during the A. apis infection. These findings indicated that the overall expression level of piRNAs was increased and the expression pattern of piRNAs in larval guts was altered due to the A. apis infection, DEpiRNAs were putative regulators in the A. apis-response of A. m. ligustica worker larvae. Our data provide not only a platform for the functional investigation of piRNAs in honeybees, especially in bee larvae, but also a foundation for illuminating the piRNA-involved mechanisms underlying the host response to the A. apis infection.

The CAP superfamily protein PsCAP1 secreted by Phytophthora triggers immune responses in Nicotiana benthamiana through a leucine-rich repeat receptor-like protein.

The role of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 (CAP) superfamily proteins in the innate immune responses of mammals is well characterized. However, the biological function of CAP superfamily proteins in plant-microbe interactions is poorly understood. We used proteomics and transcriptome analyses to dissect the apoplastic effectors secreted by the oomycete Phytophthora sojae during early infection of soybean leaves. By transiently expressing these effectors in Nicotiana benthamiana, we identified PsCAP1, a novel type of secreted CAP protein that triggers immune responses in multiple solanaceous plants including N. benthamiana. This secreted CAP protein is conserved among oomycetes, and multiple PsCAP1 homologs can be recognized by N. benthamiana. PsCAP1-triggered immune responses depend on the N-terminal immunogenic fragment (aa 27-151). Pretreatment of N. benthamiana with PsCAP1 or the immunogenic fragment increases plant resistance against Phytophthora. The recognition of PsCAP1 and different homologs requires the leucine-rich repeat receptor-like protein RCAP1, which associates with two central receptor-like kinases BRI1-associated receptor kinase 1 (BAK1) and suppressor of BIR1-1 (SOBIR1) in planta. These findings suggest that the CAP-type apoplastic effectors act as an important player in plant-microbe interactions that can be perceived by plant membrane-localized receptor to activate plant resistance.

Application of image super-resolution recognition and artificial intelligence system in repairing students' psychological education problems.

With the continuous development of society, people's life pressure is constantly increasing, and the mental health problems of college students are becoming increasingly prominent, bringing many challenges to their education and management. Universities should not only cultivate students' theoretical and professional knowledge and practical skills, but also attach importance to their mental health and effectively implement psychological education. Therefore, it is very necessary to develop and design a simple and effective student psychological evaluation system. As a new form of ideological and political transformation in universities in the era of big data, online ideological and political work has potential development space. It is necessary to carry out mental health education in universities, fully utilize online education forms, and improve ability of universities to repair mental health problems. Based on this, this system designs and implements software for typical image resolution based recognition and artificial intelligence. The use of B/S architecture in the development and use of. net technology and web server technology will enable more students to connect and use different terminals. In addition, an algorithm for image super-resolution recognition was proposed, which uses clustering convolution to improve residual blocks, improves modeling ability by extracting features on a larger scale, reduces the number of parameters to improve model calculation efficiency, and enables mental health educators and managers to work better. This article combines image super-resolution recognition technology with artificial intelligence technology to apply it to the process of psychological education in universities, thereby promoting the development of problem repair applications.

Expression Profile, Regulatory Network, and Putative Role of microRNAs in the Developmental Process of Asian Honey Bee Larval Guts.

MiRNAs, as a kind of key regulators in gene expression, play vital roles in numerous life activities from cellular proliferation and differentiation to development and immunity. However, little is known about the regulatory manner of miRNAs in the development of Asian honey bee (Apis cerana) guts. Here, on basis of our previously gained high-quality transcriptome data, transcriptome-wide identification of miRNAs in the larval guts of Apis cerana cerana was conducted, followed by investigation of the miRNAs' differential expression profile during the gut development. In addition to the regulatory network, the potential function of differentially expressed miRNAs (DEmiRNAs) was further analyzed. In total, 330, 351, and 321 miRNAs were identified in the 4-, 5-, and 6-day-old larval guts, respectively; among these, 257 miRNAs were shared, while 38, 51, and 36 ones were specifically expressed. Sequences of six miRNAs were confirmed by stem-loop RT-PCR and Sanger sequencing. Additionally, in the "Ac4 vs. Ac5" comparison group, there were seven up-regulated and eight down-regulated miRNAs; these DEmiRNAs could target 5041 mRNAs, involving a series of GO terms and KEGG pathways associated with growth and development, such as cellular process, cell part, Wnt, and Hippo. Comparatively, four up-regulated and six down-regulated miRNAs detected in the "Ac5 vs. Ac6" comparison group and the targets were associated with diverse development-related terms and pathways, including cell, organelle, Notch and Wnt. Intriguingly, it was noticed that miR-6001-y presented a continuous up-regulation trend across the developmental process of larval guts, implying that miR-6001-y may be a potential essential modulator in the development process of larval guts. Further investigation indicated that 43 targets in the "Ac4 vs. Ac5" comparison group and 31 targets in the "Ac5 vs. Ac6" comparison group were engaged in several crucial development-associated signaling pathways such as Wnt, Hippo, and Notch. Ultimately, the expression trends of five randomly selected DEmiRNAs were verified using RT-qPCR. These results demonstrated that dynamic expression and structural alteration of miRNAs were accompanied by the development of A. c. cerana larval guts, and DEmiRNAs were likely to participate in the modulation of growth as well as development of larval guts by affecting several critical pathways via regulation of the expression of target genes. Our data offer a basis for elucidating the developmental mechanism underlying Asian honey bee larval guts.

Effect of arctigenin on neurological diseases: A review.

ETHNOPHARMACOLOGICAL RELEVANCE: Arctium lappa L. is a common specie of Asteraceae. Its main active ingredient, Arctigenin (AG), in mature seeds exerts pharmacological effects on the Central Nervous System (CNS). AIM OF THE STUDY: To review studies on the specific effects of the AG mechanism on various CNS diseases and elucidate signal transduction mechanisms and their pharmacological actions. MATERIALS AND METHODS: This investigation reviewed the essential role of AG in treating neurological disorders. Basic information on Arctium lappa L. was retrieved from the Pharmacopoeia of the People's Republic of China. The related articles from 1981 to 2022 on the network database (including CNKI, PubMed, and Wan Fang and so on) were reviewed using AG and CNS diseases-related terms such as Arctigenin and Epilepsy. RESULTS: It was confirmed that AG has a therapeutic effect on Alzheimer's disease, Glioma, infectious CNS diseases (such as Toxoplasma and Japanese Encephalitis Virus), Parkinson's disease, Epilepsy, etc. In these diseases, related experiments such as a Western blot analysis revealed that AG could alter the content of some key factors (such as the reduction of Aß in Alzheimer's disease). However, in-vivo AG's metabolic process and possible metabolites are still undetermined. CONCLUSION: Based on this review, the existing pharmacological research has indeed made objective progress to elucidate how AG prevents and treats CNS diseases, especially senile degenerative disease such as Alzheimer's diseases. It was revealed that AG could be used as a potential nervous system drug as it has a wide range of effects in theory with markedly high application value, especially in the elder group. However, the existing studies are limited to in-vitro experiments; therefore, little is known about how AG metabolizes and functions in-vivo, limiting its clinical application and requiring further research.

In vivo study of a reserved atrial septal puncture area patent foramen ovale occluder.

PURPOSE: After patent foramen ovale interventional closure, puncture of the interatrial septum through the occluder is difficult but sometimes needed for further interventional treatment. This paper presents findings from an in vivo experimental study of a reserved atrial septal puncture area patent foramen ovale occluder. MATERIALS AND METHODS: A patent foramen ovale model was established in canines using trans-septal puncture of the fossa ovale and high-pressure balloon dilation. Then, patent foramen ovale closure was performed with a reserved atrial septal puncture area and all canines were raised for 3 months. Then, the occluder was crossed and left atrial angiography was performed on the septal area with the occluder. Finally, DSA angiography, echocardiography, and histology were used to evaluate the performance and feasibility of the reserved atrial septal puncture area. RESULTS: A patent foramen ovale model was successfully established in 10 canines using the atrial septal puncture method. The average diameter of the patent foramen ovale was 3.77 ±0.19 mm, and the patent foramen ovale was successfully closed in all canines using a reserved atrial septal puncture area. As assessed using transoesophageal echocardiography, the new occluder exhibited an ideal position and was occluded entirely without a residual shunt intraoperatively and postoperatively. A 100% success rate of atrial septum puncture was achieved across the new occluder. The occluders were completely endothelialised 3 months post-implantation. CONCLUSIONS: The reserved atrial septal puncture area was effective in patent foramen ovale closure and exhibited positive sealing performance and biological compatibility. Trans-septal puncture was feasible and effective after reserved atrial septal puncture area patent foramen ovale closure.

Experimental study of the bilateral asymmetric single-rivet occluder device for transcatheter patent foramen ovale closure with reserved interatrial septal puncture area.

Purpose: To evaluate a noval bilateral asymmetric single-rivet occluder with reserved interatrial septal puncture area for treating patent foramen ovale (PFO). Materials and methods: The study established a pig model of patent foramen ovale (PFO) by puncturing the oval fossa and then performing high-pressure balloon dilation. A specially designed bilateral asymmetric occluder for the reserved interatrial septal puncture area was then. used to close the PFO through catheter-based intervention. The pigs were kept for 3 months before undergoing a second catheter-based intervention, involving interatrial septal puncture using a newly developed occluder in the reserved interatrial septal puncture area. During 6 months, the experimental pigs underwent assessment using digital subtraction angiography (DSA), echocardiography, and histological evaluation. Results: A patent foramen ovale (PFO) model was successfully established in 6 pigs using the puncture atrial septum high-pressure balloon dilation method. The diameter of the unclosed PFO was measured (3.56 ± 0.25 mm). Using the newly developed occluder device, all 6 pigs with unclosed PFO underwent successful catheter-based closure surgeries, with intraoperative and postoperative transesophageal echocardiography showing excellent device positioning and complete closure without residual shunting. After 3 months of implantation, the catheter-based interatrial septal puncture was performed through the reserved interatrial septal puncture area, and all procedures were successful. Immediately following euthanasia, a histological examination revealed intact and undamaged occluder devices with visible puncture holes in the reserved interatrial septal puncture area. No fracture of the nitinol wire was observed, and the surface of the occluder device showed coverage of endothelial and connective tissues. Utilizing a bilateral asymmetric single-rivet occluder device implanted through the reserved interatrial septal puncture area has proven effective in closing PFO. After implantation, the occluder device allows subsequent interatrial septal puncture procedures through the reserved area. Conclusion: The novel occluder device demonstrated excellent closure performance, biocompatibility, and puncturability in the experiment. This indicates the feasibility of conducting further catheter-based interventions on the interatrial septum.

Learning temporal difference embeddings for biomedical hypothesis generation.

MOTIVATION: Hypothesis generation (HG) refers to the discovery of meaningful implicit connections between disjoint scientific terms, which is of great significance for drug discovery, prediction of drug side effects and precision treatment. More recently, a few initial studies attempt to model the dynamic meaning of the terms or term pairs for HG. However, most existing methods still fail to accurately capture and utilize the dynamic evolution of scientific term relations. RESULTS: This article proposes a novel temporal difference embedding (TDE) learning framework to model the temporal difference information evolution of term-pair relations for predicting future interactions. Specifically, the HG problem is formulated as a future connectivity prediction task on a temporal sequence of a dynamic attributed graph. Our approach models both the local neighbor changes of the term-pairs and the changes of the global graph structure over time, learning local and global TDE of node-pairs, respectively. Future term-pair relations can be inferred in a recurrent network based on the local and global TDE. Experiments on three real-world biomedical term relationship datasets show the effectiveness and superiority of the proposed approach. AVAILABILITY AND IMPLEMENTATION: The data and source codes related to TDE are publicly available at https://github.com/Huiweizhou/TDE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ID proteins promote the survival and primed-to-naive transition of human embryonic stem cells through TCF3-mediated transcription.

Inhibition of DNA binding proteins 1 and 3 (ID1 and ID3) are important downstream targets of BMP signalling that are necessary for embryonic development. However, their specific roles in regulating the pluripotency of human embryonic stem cells (hESCs) remain unclear. Here, we examined the roles of ID1 and ID3 in primed and naive-like hESCs and showed that ID1 and ID3 knockout lines (IDs KO) exhibited decreased survival in both primed and naive-like state. IDs KO lines in the primed state also tended to undergo pluripotent dissolution and ectodermal differentiation. IDs KO impeded the primed-to-naive transition (PNT) of hESCs, and overexpression of ID1 in primed hESCs promoted PNT. Furthermore, single-cell RNA sequencing demonstrated that ID1 and ID3 regulated the survival and pluripotency of hESCs through the AKT signalling pathway. Finally, we showed that TCF3 mediated transcriptional inhibition of MCL1 promotes AKT phosphorylation, which was confirmed by TCF3 knockdown in KO lines. Our study suggests that IDs/TCF3 acts through AKT signalling to promote survival and maintain pluripotency of both primed and naive-like hESCs.

Single-cell RNA sequencing reveals that BMPR2 mutation regulates right ventricular function via ID genes.

BACKGROUND: Mutations in bone morphogenetic protein type II receptor (BMPR2) have been found in patients with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH). Our study aimed to clarify whether deficient BMPR2 signalling acts through downstream effectors, inhibitors of DNA-binding proteins (IDs) during heart development to contribute to the progress of PAH in CHD patients. METHODS: To confirm that IDs are downstream effectors of BMPR2 signalling in cardiac mesoderm progenitors (CMPs) and contribute to PAH, we generated cardiomyocyte-specific Id 1/3 knockout mice (Ids cDKO), and 12 out of 25 developed mild PAH with altered haemodynamic indices and pulmonary vascular remodelling. Moreover, we generated ID1 and ID3 double-knockout (IDs KO) human embryonic stem cells that recapitulated the BMPR2 signalling deficiency of CHD-PAH induced pluripotent stem cells (iPSCs). RESULTS: Cardiomyocytes differentiated from iPSCs derived from CHD-PAH patients with BMP receptor mutations exhibited dysfunctional cardiac differentiation and reduced calcium (Ca2+) transients, as evidenced by confocal microscopy experiments. Smad1/5 phosphorylation and ID1 and ID3 expression were reduced in CHD-PAH iPSCs and in Bmpr2 +/- rat right ventricles. Moreover, ultrasound revealed that 33% of Ids cDKO mice had detectable defects in their ventricular septum and pulmonary regurgitation. Cardiomyocytes isolated from mouse right ventricles also showed reduced Ca2+ transients and shortened sarcomeres. Single-cell RNA sequencing analysis revealed impaired differentiation of CMPs and downregulated USP9X expression in IDs KO cells compared with wild-type cells. CONCLUSION: We found that BMPR2 signals through IDs and USP9X to regulate cardiac differentiation, and the loss of ID1 and ID3 expression contributes to cardiomyocyte dysfunction in CHD-PAH patients with BMPR2 mutations.