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The three-dimensional (3D) organization of the human genome plays a crucial role in gene regulation. EXPloration of Regulatory Epigenome with Spatial and Sequence Observations (EXPRESSO) is a novel multi-omics database for exploration and visualization of multi-layered 3D genomic features across 46 different human tissues. Integrating 1360 3D genomic datasets (Hi-C, HiChIP, ChIA-PET) and 842 1D genomic and transcriptomic datasets (ChIP-seq, ATAC-seq, RNA-seq) from the same biosample, EXPRESSO provides a comprehensive resource for studying the interplay between 3D genome architecture and transcription regulation. This database offers diverse 3D genomic feature types (compartments, contact matrix, contact domains, stripes as diagonal lines extending from a genomic locus in contact matrix, chromatin loops, etc.) and user-friendly interface for both data exploration and download. Other key features include REpresentational State Transfer application programming interfaces for programmatic access, advanced visualization tools for 3D genomic features and web-based applications that correlate 3D genomic features with gene expression and epigenomic modifications. By providing extensive datasets and tools, EXPRESSO aims to deepen our understanding of 3D genomic architecture and its implications for human health and disease, serving as a vital resource for the research community. EXPRESSO is freely available at https://expresso.sustech.edu.cn., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

RNA silencing negatively regulates gene expression at the transcriptional and post-transcriptional levels through DNA methylation, histone modification, mRNA cleavage, and translational inhibition. Small interfering RNAs (siRNAs) of 21 to 24 nucleotides are processed from double-stranded RNAs by Dicer-like enzymes and play essential roles in RNA silencing in plants. Here, we demonstrated that ALTERED MERISTEM PROGRAM1 (AMP1) and its putative paralog LIKE AMP1 (LAMP1) impair RNA silencing by repressing the biogenesis of a subset of inverted repeat (IR)-derived siRNAs in Arabidopsis (Arabidopsis thaliana). AMP1 and LAMP1 inhibit Pol II-dependent IR gene transcription by suppressing ARGONAUTE 1 (AGO1) protein levels. Genetic analysis indicates that AMP1 acts upstream of RNA polymerase IV subunit 1 (NRPD1), RNA-dependent RNA polymerase 2 (RDR2), and Dicer-Like 4 (DCL4), which are required for IR-induced RNA silencing. We also show that AMP1 and LAMP1 inhibit siRNA-mediated silencing in a different mechanism from AGO4 and DCL3. Together, these results reveal two previously unknown players in siRNA biogenesis from IRs - AGO1, which promotes IR transcription, and AMP1, which inhibits IR transcription indirectly through the repression of AGO1 expression., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. Firstly, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn (cDBTL) procedure including function specification, chassis selection, interaction design, system build, performance test, modelling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Fibrosis characterized by intestinal strictures is a common complication of Crohn's disease (CD), without specific antifibrotic drugs, which usually relies on surgical intervention. The transcription factor XBP1, a key component of endoplasmic reticulum (ER) stress, is required for degranulation of mast cells and linked to PAR2 activation and fibrosis. Many studies have confirmed that naringin (NAR) can inhibit ER stress and reduce organ fibrosis. We hypothesized that ER stress activated the PAR2-induced epithelial-mesenchymal transition process by stimulating mast cell degranulation to release tryptase and led to intestinal fibrosis in CD patients; NAR might play an antifibrotic role by inhibiting ER stress-induced PAR2 activation. We report that the expression levels of XBP1, mast cell tryptase, and PAR2 are upregulated in fibrotic strictures of CD patients. Molecular docking simulates the interaction of NAR and spliced XBP1. ER stress stimulates degranulation of mast cells to secrete tryptase, activates PAR2-induced epithelial-mesenchymal transition process, and promotes intestinal fibrosis in vitro and vivo experiments, which is inhibited by NAR. Moreover, F2rl1 (the coding gene of PAR2) deletion in intestinal epithelial cells decreases the antifibrotic effect of NAR. Hence, the ER stress-mast cell tryptase-PAR2 axis can promote intestinal fibrosis, and NAR administration can alleviate intestinal fibrosis by inhibiting ER stress-induced PAR2 activation., (© The Author(s) 2024. Published by Oxford University Press on behalf of Crohn’s & Colitis Foundation. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The implication of 5-hydroxytryptamine 2C receptor (5-HT2CR) activity in depression is a topic of debate, and the underlying mechanisms remain largely unclear. Here, we elucidate how hippocampal excitation-inhibition (E/I) balance underlies the regulatory effects of 5-HT2CR in depression. Molecular biological analyses showed that chronic mild stress (CMS) reduced the expression of 5-HT2CR in hippocampus. We revealed that inhibition of 5-HT2CR induced depressive-like behaviours, reduced GABA release and shifted the E/I balance towards excitation in CA3 pyramidal neurons using behavioural analyses, microdialysis coupled with mass spectrometry and electrophysiological recordings. Moreover, 5-HT2CR modulated the neuronal nitric oxide synthase (nNOS)-carboxy-terminal PDZ ligand of nNOS (CAPON) interaction by influencing intracellular Ca2+ release, as determined by fibre photometry and coimmunoprecipitation. Notably, disruption of nNOS-CAPON with the specific small molecule compound ZLc-002 or AAV-CMV-CAPON-125C-GFP abolished 5-HT2CR inhibition-induced depressive-like behaviours, as well as the impairment in soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex assembly-mediated GABA vesicle release and consequent E/I imbalance. Importantly, optogenetic inhibition of CA3 GABAergic neurons prevented the effects of AAV-CMV-CAPON-125C-GFP on depressive behaviours in the presence of a 5-HT2CR antagonist. Conclusively, our findings disclose the regulatory role of 5-HT2CR in depressive-like behaviours and highlight hippocampal nNOS-CAPON coupling-triggered E/I imbalance as a pivotal cellular event underpinning the behavioural consequences of 5-HT2CR inhibition., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Objectives: Intracapillary monoclonal IgM deposits disease (ICMDD) has long been considered a hallmark of Waldenström macroglobulinemia (WM) nephropathy. Intracapillary immunoglobulin thrombi are the characteristic features of cryoglobulinemic glomerulonephritis. Here, we reported 4 cases of ICMDD with massive pseudothrombi but without WM or cryoglobulinemia., Methods: We retrospectively analyzed the clinical and pathologic features of patients diagnosed with ICMDD with massive pseudothrombi., Results: A total of 4 patients (2 men and 2 women) aged 62 to 73 years were enrolled in this study. Microscopic hematuria, edema, and renal insufficiency were present in all patients, along with low serum C3 and C4 in 2 patients. Hematologic examination showed abnormal serum free light chain ratios in all patients and high levels of serum IgM in 3 patients. IgM-κ monoclonal band was identified by serum immunofixation electrophoresis in 3 patients. One patient was diagnosed with small B-cell lymphoma by bone marrow aspiration. Renal biopsy specimen showed massive periodic acid-Schiff-positive hyaline thrombi in the glomerular capillary lumens and also less mesangial, subendothelial, and subepithelial deposits on light microscopy. Immunofluorescence indicated positive staining for IgM (++) and κ light chain staining in the glomerular capillary lumens, capillary walls, and mesangium in all patients. By electron microscopy, the glomerular capillary lumens were filled with homogeneous high-electron-dense deposits without substructure. Two patients were treated with prednisone combined with cyclophosphamide, and 2 received plasma cell-targeted chemotherapy. One patient achieved partial renal remission., Conclusions: Intracapillary monoclonal IgM deposits disease is a rare disease and not always related to WM. Most patients have IgM monoclonal immunoglobulinemia; renal biopsy specimens mainly show a large number of pseudothrombi in the glomerular capillary lumens. Cyclophosphamide is effective in some patients., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society for Clinical Pathology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease and is characterized by primary left ventricular hypertrophy usually caused by mutations in sarcomere genes. The mechanism underlying cardiac remodeling in HCM remains incompletely understood. An investigation of HCM through integrative analysis at multi-omics levels will be helpful for treating HCM. DNA methylation and chromatin accessibility, as well as gene expression, were assessed by nucleosome occupancy and methylome sequencing (NOMe-seq) and RNA-seq, respectively, using the cardiac tissues of HCM patients. Compared with those of the controls, the transcriptome, DNA methylome, and chromatin accessibility of the HCM myocardium showed multifaceted differences. At the transcriptome level, HCM hearts returned to the fetal gene program through decreased sarcomeric and metabolic gene expression and increased extracellular matrix gene expression. In the DNA methylome, hypermethylated and hypomethylated differentially methylated regions were identified in HCM. At the chromatin accessibility level, HCM hearts showed changes in different genome elements. Several transcription factors, including SP1 and EGR1, exhibited a fetal-like pattern of binding motifs in nucleosome-depleted regions in HCM. In particular, the inhibition of SP1 or EGR1 in an HCM mouse model harboring sarcomere mutations markedly alleviated the HCM phenotype of the mutant mice and reversed fetal gene reprogramming. Overall, this study not only provides a high-precision multi-omics map of HCM heart tissue but also sheds light on the therapeutic strategy by intervening in the fetal gene reprogramming in HCM., (© The Author(s) 2024. Published by Oxford University Press on behalf of Higher Education Press.)

Qizhi Xiangfu Pills (QZXFPs) is one of the most commonly used traditional Chinese medicine preparations for the treatment of dysmenorrhea, but the existing quality evaluation standards have certain shortcomings and deficiencies. An effective and scientific quality evaluation method plays a vital role in medication safety. In this study, fingerprint combined with chemometric analysis and quantitative analysis of multi-components by a single marker (QAMS) method was used to comprehensively evaluate the quality of QZXFPs. The fingerprints of 28 batches samples were established and 23 common peaks were distinguished, of which 7 peaks were identified as albiflorin, paeoniflorin, baicalin, ligustilide, cyperotundone, nootkatone and α-cyperone. The content of these seven active ingredients was determined simultaneously by the QAMS method and there was no significantly different between QAMS and the external standard method. Additionally, similarity analysis, hierarchical cluster analysis, principal component analysis and orthogonal partial least squares discrimination analysis were applied for classifying the 28 batches of samples, and to find the main components causing the quality differences between different batches. In conclusion, the established method can comprehensively evaluate the consistency of quality between different batches and provide a reference for formulation quality evaluation to ensure safe and effective application of QZXFPs., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Piercing/sucking insects such as green peach aphid (GPA) (Myzus persicae) cause direct damage by obtaining phloem nutrients and indirect damage by spreading plant viruses. To investigate the response of peach trees (Prunus persica) to aphids, the leaf transcriptome and metabolome of two genotypes with different sensitivities to GPA were studied. The gene expression of aphid-susceptible plants infested with aphids was similar to that of control plants, whereas the gene expression of aphid-resistant plants infested with aphids showed strong induced changes in gene expression compared with control plants. Furthermore, gene transcripts in defense-related pathways, including plant-pathogen interaction, MAPK signaling, and several metabolic pathways, were strongly enriched upon aphid infestation. Untargeted secondary metabolite profiling confirmed that aphid infestation induced larger changes in aphid-resistant than in aphid-susceptible peaches. Consistent with transcriptomic alterations, nine triterpenoids showed highly significant GPA-induced accumulation in aphid-resistant peaches, whereas triterpenoid abundance remained predominantly unchanged or undetected in aphid-susceptible peaches. Furthermore, some types of transcription factors (including WRKYs, ERFs, and NACs) were strongly induced upon GPA infestation in aphid-resistant, but not in aphid-susceptible peaches. These results suggested that the accumulation of specialized triterpenoids and the corresponding pathway transcripts may play a key role in peach GPA resistance., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background: An estimated 80% of individuals with chronic kidney disease (CKD) experience concomitant skin disorders, yet experimental research that elucidates the pathological changes in CKD-affected skin is limited. Cold atmospheric plasma (CAP) has shown promise in regulating keratinocyte proliferation, skin barrier function and anti-inflammatory activity. We hypothesize that CAP will emerge as a promising therapeutic avenue for CKD-related skin diseases., Methods: Male and female C57BL/6 mice were administered a 0.2% adenine diet to generate a CKD mouse model. Skin samples from dialysis patients were also collected. These models were used to investigate the pathological alterations in the renal glomeruli, tubules and epidermis. Subsequently, the potential impact of CAP on the stratum corneum, keratinocytes, skin hydration and inflammation in mice with CKD was examined., Results: Renal biopsies revealed glomerular and tubular atrophy, epithelial degeneration and necrosis in uriniferous tubules and significant renal interstitial fibrosis. Skin biopsies from patients with CKD and mice showed stratum corneum thickening, epidermis atrophy, skin hydration dysfunction and excessive inflammation. CAP attenuated skin atrophy, hydration dysfunction and inflammation in mice with CKD, as evidenced by the activated level of YAP1/β-catenin and Nrf-2/OH-1; enhanced expression of K5 and Ki67; increased levels of AQP3, collagen I and GLUT1; reduced infiltration of CD3+ T cells and diminished levels of IL-6 and TNF-α., Conclusions: This study provides valuable insights into the pathological changes in skin associated with CKD in both patients and animal models. It also establishes that CAP has the potential to effectively mitigate skin atrophy, hydration dysfunction and inflammation, suggesting a novel therapeutic avenue for the treatment of CKD-related skin disorders., (© The Author(s) 2024. Published by Oxford University Press on behalf of the ERA.)

Efficient DNA replication requires highly coordinated programs for the timely recruitment of protein complexes to DNA replication forks. Defects in this process result in replication stress, which in turn activates cell cycle checkpoints, suppresses cell proliferation and induces apoptosis. In response to persistent cell growth signals that speed up DNA replication processes, cells accelerate the recruitment of DNA replication proteins to avoid DNA replication stress. The mechanisms by which cell growth signals induce processes to facilitate the recruitment of DNA replication proteins onto the replication sites remain unclear. Here, we report that the epidermal growth factor receptor (EGFR) phosphorylates heat shock protein 70 (HSP70) for DNA replication. Such a modification promotes nuclear localization and chromatin association of HSP70, which interacts with the DNA replication coordinator, proliferating cell nuclear antigen (PCNA). HSP70 subsequently facilitates the loading of PCNA onto chromatin. Knockdown or chemical inhibition of HSP70 suppresses PCNA association with chromatin and impairs DNA synthesis and Okazaki fragment maturation, leading to replicative DNA double-strand breaks and apoptosis. Furthermore, chemical inhibition of HSP70 potentiates EGFR-tyrosine kinase inhibitor-induced tumor reduction in vivo. This work expands our understanding of oncogenesis-induced DNA replication processes and provides a foundation for improved treatments for EGFR-mutated lung cancer by simultaneously targeting HSP70., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Germline DICER1 mutations cause familial multinodular goiter (MNG). However, the prevalence of somatic DICER1 mutations in non-MNG benign thyroid nodules and their characteristics remain unknown., Methods: Adult-onset thyroid nodules with a pathological diagnosis were genotyped via targeted sequencing. DICER1-mutant nodules were assessed clinically and pathologically. Organoids were established to investigate follicular formation and growth. Transcriptomic analysis was conducted to evaluate transcriptional features, which were validated by immunofluorescence., Results: Among 931 adult-onset thyroid nodules, we identified 13 benign thyroid nodules with DICER1 hotspot mutations. The majority harbored a somatic DICER1 hotspot mutation with a somatic DICER1 truncating variant. Clinically, 38.5% of the DICER1-mutant nodules exhibited substantial growth. DICER1-mutant nodules with durations longer than 2 years were substantially enlarged (P=.0448). Pathologically, all DICER1-mutant nodules were defined as thyroid follicular nodular disease (TFND). The TFND nodules with DICER1 mutations grew faster than those with wild-type DICER1. Organoid culture of a DICER1-mutant nodule revealed increased active follicular formation. Compared with the normal thyroid tissues, the DICER1-mutant nodules had comparable thyroid differentiation scores, significantly higher ERK scores (P=.0141) and lower epithelial‒mesenchymal transition scores (P=.0001). Moreover, the expression of genes related to follicular polarity, such as CDH16, SLC5A5, TSHR and TPO, was downregulated in the DICER1-mutant nodules., Conclusions: Somatic DICER1 two-hit mutations represent a notable percentage in adult TFND patients, and DICER1-mutant benign thyroid nodules were characterized by continuous growth., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com. See the journal About page for additional terms.)

Background and Aims: Salicornia europaea L., a succulent euhalophyte plant, has been found to exhibit optimal reproductive capabilities under appropriate salinity concentrations. However, the underlying metabolic changes are not yet fully understood., Methods: This study conducted a comprehensive analysis combining transcriptomic and lipidomic techniques to investigate the molecular mechanisms of lipid metabolism in response to different NaCl concentrations (0 and 200 mM)., Results: Transcriptomic data demonstrated that salt treatment mainly affected processes including lipid biosynthesis, phosphatidylinositol signaling, and glycerophospholipid metabolism. The expression levels of several key genes involved in salt tolerance, namely SeSOS1, SeNHX1, SeVHA-A, SeVP1, and SePSS, were found to be upregulated upon NaCl treatment. A total of 485 lipid compounds were identified, of which 27 changed in abundance under salt treatment, including the enrichment of phospholipids and sphingolipids. Moreover, the increase in the double-bond index (DBI) was mainly due to phospholipids and sphingolipids. Comparing the acyl chain length (ACL) showed that the ACL coefficient of S1P significantly decreased under 200 mM NaCl., Conclusions: This study suggests that S. europaea adapt to saline environments through altering phospholipids and sphingolipids to improve salt tolerance. The salinity response of S. europaea can provide important insights into the action of lipids and their salt adaptation mechanisms., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Investigating mutations, including single nucleotide variations (SNVs), gene fusions, alternative splicing and copy number variations (CNVs), is fundamental to cancer study. Recent computational methods and biological research have demonstrated the reliability and biological significance of detecting mutations from single-cell transcriptomic data. However, there is a lack of a single-cell-level database containing comprehensive mutation information in all types of cancer. Establishing a single-cell mutation landscape from the huge emerging single-cell transcriptomic data can provide a critical resource for elucidating the mechanisms of tumorigenesis and evolution. Here, we developed scTML (http://sctml.xglab.tech/), the first database offering a pan-cancer single-cell landscape of multiple mutation types. It includes SNVs, insertions/deletions, gene fusions, alternative splicing and CNVs, along with gene expression, cell states and other phenotype information. The data are from 74 datasets with 2 582 633 cells, including 35 full-length (Smart-seq2) transcriptomic single-cell datasets (all publicly available data with raw sequencing files), 23 datasets from 10X technology and 16 spatial transcriptomic datasets. scTML enables users to interactively explore multiple mutation landscapes across tumors or cell types, analyze single-cell-level mutation-phenotype associations and detect cell subclusters of interest. scTML is an important resource that will significantly advance deciphering intra-tumor and inter-tumor heterogeneity, and how mutations shape cell phenotypes., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers, and the current knowledge of enhancers in plants, including how they impact plant development, response to environment, and evolutionary adaptation., (© The Author(s) 2024. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.)

Escherichia coli K1 is the leading cause of neonatal gram-negative bacterial meningitis, but the pathogenesis of E coli K1 meningitis remains unclear. Blood-brain barrier (BBB) penetration is a crucial step in E coli meningitis development. Here, we uncovered the crucial role of CsiR, a GntR family regulator, in E coli K1 virulence. During infection, csiR expression was induced due to the derepression by Fur in the blood and human brain microvascular endothelial cells (HBMECs). CsiR positively regulated ilvB expression, which is associated with branched chain amino acid synthesis. Furthermore, we revealed that IlvB activated the FAK/PI3K pathway of HBMECs to induce actin cytoskeleton rearrangements, thereby promoting the bacterial invasion and penetration of the BBB. Overall, this study reveals a CsiR-mediated virulence regulation pathway in E coli K1, which may provide a useful target for the prevention or therapy of E coli meningitis., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Motivation: Recent brain mapping efforts are producing large-scale whole-brain images using different imaging modalities. Accurate alignment and delineation of anatomical structures in these images are essential for numerous studies. These requirements are typically modeled as two distinct tasks: Registration and segmentation. However, prevailing methods, fail to fully explore and utilize the inherent correlation and complementarity between the two tasks. Furthermore, variations in brain anatomy, brightness and texture pose another formidable challenge in designing multi-modal similarity metrics. A high-throughput approach capable of overcomingthe bottleneck of multi-modal similarity metric design, while effective leveraging the highly correlated and complementary nature of two tasks is highly desirable., Results: We introduce a deep learning framework for joint registration and segmentation of multi-modal brain images. Under this framework, registration and segmentation tasks are deeply coupled and collaborated at two hierarchical layers. In the inner layer, we establish a strong feature-level coupling between the two tasks by learning a unified common latent feature representation. In the outer layer, we introduce a mutually supervised dual-branch network to decouple latent features and facilitate task-level collaboration between registration and segmentation. Since the latent features we designed are also modality-independent, the bottleneck of designing multi-modal similarity metric is essentially addressed. Another merit offered by this framework is the interpretability of latent features, which allows intuitive manipulation of feature learning, thereby further enhancing network training efficiency and the performance of both tasks. Extensive experiments conducted on both multi-modal and mono-modal datasets of mouse and human brains demonstrate the superiority of our method., Availability: The code is available at https://github.com/tingtingup/DCRS., Supplementary Information: Supplementary data are available at Bioinformaticsonline., (© The Author(s) 2024. Published by Oxford University Press.)

Dichromatic color vision is mediated by two cone visual pigments in many eutherian mammals. After reentry into the sea, early cetaceans lost their violet-sensitive visual pigment (short wavelength-sensitive 1) independently in the baleen and toothed whale ancestors and thus obtained only monochromatic cone vision. Subsequently, losses of the middle/long wavelength-sensitive (M/LWS) pigment have also been reported in multiple whale lineages, leading to rhodopsin (RH1)-mediated rod monochromatic vision. To further elucidate the phenotypic evolution of whale visual pigments, we assessed the spectral tuning of both M/LWS and RH1 from representative cetacean taxa. Interestingly, although the coding sequences for M/LWS are intact in both the pygmy right whale and the Baird's beaked whale, no spectral sensitivity was detected in vitro. Pseudogenization of other cone vision-related genes is observed in the pygmy right whale, suggesting a loss of cone-mediated vision. After ancestral sequence reconstructions, ancient M/LWS pigments from cetacean ancestors were resurrected and functionally measured. Spectral tuning of M/LWS from the baleen whale ancestor shows that it is green sensitive, with a 40-nm shift in sensitivity to a shorter wavelength. For the ancestor of sperm whales, although no spectral sensitivity could be recorded for its M/LWS pigment, a substantial sensitivity shift (20 to 30 nm) to a shorter wavelength may have also occurred before its functional inactivation. The parallel phenotypic evolution of M/LWS to shorter wavelength sensitivity might be visual adaptations in whales allowing more frequent deep-sea activities, although additional ecological differentiations may have led to their subsequent losses., Competing Interests: Conflict of Interest There is no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Aims: To explore the therapeutic potential of Forsythoside B in treating Streptococcus pneumoniae (S. pneumoniae) infections, focusing on its ability to inhibit pneumolysin activity and protect cells from damage., Methods and Results: Hemolysis tests were used to evaluate Forsythoside B's inhibitory effect on pneumolysin activity, while growth curve analysis assessed its impact on S. pneumoniae growth. Western blotting and oligomerization analysis were conducted to examine its influence on pneumolysin oligomerization. Cytotoxicity assays, including LDH release and live/dead cell staining, evaluated the protective effects of Forsythoside B against pneumolysin-induced damage in A549 cells. Additionally, a mouse model was employed to test the effects on survival rates, lung bacterial load, and inflammation. The results showed that Forsythoside B significantly inhibited pneumolysin activity, reduced its oligomerization, and protected A549 cells from damage without affecting bacterial growth. In the mouse model, it improved survival rates and reduced lung inflammation, indicating its potential as a therapeutic agent against S. pneumoniae infections., Conclusions: Forsythoside B shows potential as a therapeutic agent for treating pneumonia, particularly in infections caused by S. pneumoniae., (© The Author(s) 2024. Published by Oxford University Press on behalf of Applied Microbiology International.)

The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408-PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408-PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

During the floral transition, many plant species including chrysanthemum (Chrysanthemum morifolium) require continuous photoperiodic stimulation for successful anthesis. Insufficient photoperiodic stimulation results in flower bud arrest or even failure. The molecular mechanisms underlying how continuous photoperiodic stimulation promotes anthesis are not well understood. Here, we reveal that in wild chrysanthemum (Chrysanthemum indicum), an obligate short-day (SD) plant, floral evocation is not limited to SD conditions. However, SD signals generated locally in the inflorescence meristem (IM) play a vital role in ensuring anthesis after floral commitment. Genetic analyses indicate that the florigen FLOWERING LOCUS T-LIKE3 (CiFTL3) plays an important role in floral evocation, but a lesser role in anthesis. Importantly, our data demonstrate that AGAMOUS-LIKE 24 (CiAGL24) is a critical component of SD signal perception in the IM to promote successful anthesis, and that floral evocation and anthesis are two separate developmental events in chrysanthemum. We further reveal that the central circadian clock component PSEUDO-RESPONSE REGULATOR 7 (CiPRR7) in the IM activates CiAGL24 expression in response to SD conditions. Moreover, our findings elucidate a negative feedback loop in which CiAGL24 and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (CiSOC1) modulate LEAFY (CiLFY) expression. Together, our results demonstrate that the CiPRR7-CiAGL24 module is vital for sustained SD signal perception in the IM to ensure successful anthesis in chrysanthemum., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background: Super-enhancers (SEs) typically govern the expression of critical oncogenes and play a fundamental role in the initiation and progression of cancer. Focusing on genes that are abnormally regulated by SE in cancer may be a new strategy for understanding pathogenesis. In the context of this investigation, we have identified a previously unreported SE-driven gene IRF2BP2 in neuroblastoma (NB)., Methods: The expression and prognostic value of IRF2BP2 were detected in public databases and clinical samples. The effect of IRF2BP2 on NB cell growth and apoptosis was evaluated through in vivo and in vitro functional loss experiments. The molecular mechanism of IRF2BP2 was investigated by the study of chromatin regulatory regions and transcriptome sequencing., Results: The sustained high expression of IRF2BP2 results from the activation of a novel SE established by NB master transcription factors MYCN, MEIS2, and HAND2, and they form a new complex that regulates the gene network associated with the proliferation of NB cell populations. We also observed a significant enrichment of the AP-1 family at the binding sites of IRF2BP2. Remarkably, within NB cells, AP-1 plays a pivotal role in shaping the chromatin accessibility landscape, thereby exposing the binding site for IRF2BP2. This orchestrated action enables AP-1 and IRF2BP2 to collaboratively stimulate the expression of the NB susceptibility gene ALK, thereby upholding the highly proliferative phenotype characteristic of NB., Conclusions: Our findings indicate that SE-driven IRF2BP2 can bind to AP-1 to maintain the survival of tumor cells via regulating chromatin accessibility of the NB susceptibility gene ALK., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Grey matter ageing-related tau astrogliopathy (ARTAG) pathology is common in aged brains and detected in multiple brain regions. However, the associations of grey matter ARTAG with Alzheimer's disease and other common age-related proteinopathies, in addition to clinical phenotypes, including Alzheimer's dementia and cognitive decline, remain unclear. We examined 442 decedents (mean age at death = 90 years, males = 32%) from three longitudinal community-based clinical-pathological studies. Using AT8 immunohistochemistry, grey matter ARTAG pathology was counted in the superior frontal region, anterior temporal tip and amygdala and summarized as a severity score ranging from zero (none) to six (severe). Alzheimer's disease and other common age-related neuropathologies were also evaluated. The diagnosis of Alzheimer's dementia was based on clinical evaluations; annual tests of cognitive performance were summarized as global cognition and five cognitive domains. Multivariable logistic regression tested the associations of grey matter ARTAG pathology with an array of age-related neuropathologies. To evaluate associations of grey matter ARTAG pathology with Alzheimer's dementia and cognitive decline, we used logistic regression and linear mixed-effect models. Grey matter ARTAG pathology was seen in 324 (73%) participants, of which 303 (68%) participants had ARTAG in the amygdala, 246 (56%) in the anterior temporal tip and 137 (31%) in the superior frontal region. Grey matter ARTAG pathology from each of the three regions was associated with a pathological diagnosis of Alzheimer's disease and limbic-predominant age-related TAR DNA-binding protein 43 encephalopathy-neuropathological change but not with vascular pathology. In fully adjusted models that controlled for demographics, Alzheimer's disease and common age-related pathologies, an increase in severity of grey matter ARTAG pathology in the superior frontal cortex, but not in the amygdala or the anterior temporal tip, was associated with higher odds of Alzheimer's dementia and faster decline in global cognition, episodic memory and semantic memory. These results provide compelling evidence that grey matter ARTAG, specifically in the superior frontal cortex, contributes to Alzheimer's dementia and cognitive decline in old age., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Although the strigolactone (SL) signaling pathway and SL-mediated anthocyanin biosynthesis have been reported, the molecular association between SL signaling and anthocyanin biosynthesis remains unclear. In this study, we identified the SL signal transduction pathway associated with anthocyanin biosynthesis and the crosstalk between gibberellin (GA) and SL signaling in apple (Malus × domestica). ELONGATED HYPOCOTYL5 (HY5) acts as a key node integrating SL signaling and anthocyanin biosynthesis, and the SL-response factor AGAMOUS-LIKE MADS-BOX9 (AGL9) promotes anthocyanin biosynthesis by activating HY5 transcription. The SL signaling repressor SUPPRESSOR OF MAX2 1-LIKE8 (SMXL8) interacts with AGL9 to form a complex that inhibits anthocyanin biosynthesis by downregulating HY5 expression. Moreover, the E3 ubiquitin ligase PROTEOLYSIS1 (PRT1) mediates the ubiquitination-mediated degradation of SMXL8, which is a key part of the SL signal transduction pathway associated with anthocyanin biosynthesis. In addition, the GA signaling repressor REPRESSOR-of-ga1-3-LIKE2a (RGL2a) mediates the crosstalk between GA and SL by disrupting the SMXL8-AGL9 interaction that represses HY5 transcription. Taken together, our study reveals the regulatory mechanism of SL-mediated anthocyanin biosynthesis and uncovers the role of SL-GA crosstalk in regulating anthocyanin biosynthesis in apple., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Developing an intracellular delivery system is of key importance in the expansion of protein-based therapeutics acting on cytosolic or nuclear targets. Recently, extracellular vesicles (EVs) have been exploited as next-generation delivery modalities due to their natural role in intercellular communication and biocompatibility. However, fusion of protein of interest to a scaffold represents a widely used strategy for cargo enrichment in EVs, which could compromise the stability and functionality of cargo. Herein, we report intracellular delivery via EV-based approach (IDEA) that efficiently packages and delivers native proteins both in vitro and in vivo without the use of a scaffold. As a proof-of-concept, we applied the IDEA to deliver cyclic GMP-AMP synthase (cGAS), an innate immune sensor. The results showed that cGAS-carrying EVs activated interferon signaling and elicited enhanced antitumor immunity in multiple syngeneic tumor models. Combining cGAS EVs with immune checkpoint inhibition further synergistically boosted antitumor efficacy in vivo. Mechanistically, scRNA-seq demonstrated that cGAS EVs mediated significant remodeling of intratumoral microenvironment, revealing a pivotal role of infiltrating neutrophils in the antitumor immune milieu. Collectively, IDEA, as a universal and facile strategy, can be applied to expand and advance the development of protein-based therapeutics., (© The Author(s) 2024. Published by Oxford University Press on behalf of Higher Education Press.)

Context: To investigate how short sleep duration (SSD) during pregnancy is related to neurodevelopmental delays in offspring, we aimed to inform pregnancy sleep guidelines and promote maternal health and child development., Objective: To identify the associations between SSD during pregnancy and offspring neurodevelopmental delay and to determine whether fetal glucose metabolism plays a role in SSD and neurodevelopmental delays., Methods: This cohort study followed 7059 mother-child pairs from the Maternal & Infants Health in Hefei cohort, and collected sleep data during pregnancy via the Pittsburgh Sleep Quality Index at weeks 24 to 28 and 32 to 36. Neurodevelopmental outcomes from 6 to 36 months postpartum were assessed via the Denver Developmental Screening Test-II and the Gesell Development Diagnosis Scale. Cox proportional hazard regression was used to analyze the link between maternal SSD and neurodevelopmental delay risk. Mediation analysis was used to evaluate the role of cord blood serum C-peptide levels. Three hospitals and children's health centers in Hefei were involved., Results: The stratified analysis revealed a significant association between mothers with SSD during midpregnancy and neurodevelopmental delay in boys (adjusted HR 2.05, 95% CI 1.29, 3.25). Cord blood marker analysis revealed a positive relationship between cord blood serum C-peptide levels and neurodevelopmental delay in offspring (RR 0.04, 95% CI 0.00, 0.08). The proportion of the association between SSD and neurodevelopmental delay mediated by cord blood C-peptide was 11.05%., Conclusion: Maternal SSD during pregnancy was continuously associated with an increased incidence of neurodevelopmental delay with sex differences among offspring. This association may be mediated in part by increased higher levels of cord C-peptide., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com. See the journal About page for additional terms.)

Background: Nirmatrelvir-ritonavir is recommended for persons at risk for severe coronavirus disease 2019 (COVID-19) but remains underutilized. Information on which eligible groups are likely to benefit from treatment is needed., Methods: We conducted a target trial emulation study in the Veterans Health Administration comparing nirmatrelvir-ritonavir treated versus matched untreated veterans at risk for severe COVID-19 who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from April 2022 through March 2023. We measured incidence of any hospitalization or all-cause mortality at 30 days. Outcomes were measured for the entire cohort, as well as among subgroups defined by 30-day risk of death or hospitalization, estimated using an ensemble risk prediction model., Results: Participants were 87% male with median age 66 years and 16% unvaccinated. Compared with matched untreated participants, those treated with nirmatrelvir-ritonavir (n = 24 205) had a lower 30-day risk for hospitalization (1.80% vs 2.30%; risk difference [RD], -0.50% points [95% confidence interval {CI}: -.69 to -.35]) and death (0.11% vs 0.30%; RD, -0.20 [95% CI: -.24 to -.13]). The greatest reductions in combined hospitalization or death were observed in the highest risk quartile (RD -2.85 [95% CI: -3.94 to -1.76]), immunocompromised persons (RD -1.91 [95% CI: -3.09 to -.74]), and persons aged ≥75 years (RD -1.16 [95% CI: -1.73 to -.59]). No reductions were observed in the 2 lowest risk quartiles or persons younger than 65 years., Conclusions: Nirmatrelvir-ritonavir was effective in reducing 30-day hospitalization and death in older veterans, those at highest predicted risk for severe outcomes, and immunocompromised groups. Benefit was not observed in younger veterans or groups at lower predicted risk for hospitalization and death., Competing Interests: Potential conflicts of interest. D. H. reports consulting fees from Quality Insights, research consulting co-ownership in Van-Breemen & Hynes, LLC, and a subcontract at Oregon State University for a PCORI grant through the University of North Carolina, grants from VA Health Services Research and Development (HSRD), Quality Insight. G. I. reports grants from Department of Veterans Affairs. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (Published by Oxford University Press on behalf of Infectious Diseases Society of America 2024.)

Introduction: Bladder cancer ranks 17th in prevalence of cancer types among women, and the trend is rising. The increased risk of female sexual dysfunction (FSD) after radical cystectomy (RC) underscores the need for greater focus on preserving and mitigating FSD., Objectives: To place greater emphasis on the importance of female sexual function (FSF) in the treatment of bladder cancer and stimulate additional research to discover more effective solutions for enhancing the overall quality of life., Methods: This review used a narrative approach. Previous reviews on FSF after RC have provided limited and 1-sided solutions due to the lack of research. What makes this review unique is its innovative approach: it includes all available measures curing FSD as well as comparative analyses based on experimental data, thus making the findings more comprehensive. A detailed perspective of treatments for female bladder cancer is provided, including nerve- and organ-sparing RC, robot-assisted RC, and radiotherapy. We also analyze the impact of treatments for female bladder cancer on postoperative FSD. Additionally, solutions for addressing or alleviating postoperative FSD are summarized, such as urinary diversion, vaginal reconstruction, and drug and nondrug treatment., Results: Research has suggested that robot-assisted nerve- and organ-sparing RC is promising. Moreover, orthotopic neobladder among urinary diversions without a stoma helps to maintain a positive female body image. If part of the anterior vaginal wall must be removed during RC, vaginal reconstruction can restore the dimensions with synthetic grafts and biologic scaffolds. Additionally, postoperative measures, such as vaginal laser and hormone therapy, and use of vaginal dilators and lubricants have a significant role in reducing distress caused by FSD to provide maximum relief., Conclusions: To support FSF after RC, various interventions are needed, and urologists must focus on patient recovery while minimizing treatment impact on FSF as much as possible., (© The Author(s) 2024. Published by Oxford University Press on behalf of The International Society of Sexual Medicine. All rights reserve d. For permissions, please e-mail: journals.permissions@oup.com.)

Introduction: The penis serves as a vital receptor in men, playing a significant role in sexual intercourse. While there are discernible disparities between the glans penis and the penile shaft, a comprehensive and detailed analysis of these distinctions is currently lacking., Objectives: This study aimed to review the existing literature on the variances between the glans penis and the penile shaft, providing a systematic examination of their anatomical and histological dissimilarities., Methods: Our investigation encompassed a thorough search of the published literature, including original articles, reviews, letters to the editor, and case reports focused on the penis. We conducted a comprehensive review of the anatomical and histological dissimilarities between the glans penis and the penile shaft., Results: The following key differences were identified. First, regarding innervation, the glans penis and the penile shaft possess distinct neural pathways. The glans penis exhibits a 3-dimensional structure, while the penile shaft exhibits a 2-dimensional distribution. Notably, the nerves of the penile shaft extend penetrating branches into the corpus cavernosum. Furthermore, there are variations in nerve-specific antibodies between the 2 regions. Second, regarding composition, the glans penis and the penile shaft consist of dissimilar cavernous bodies. The glans penis contains unique epithelial structures and receptors, setting it apart from the penile shaft. Third, regarding the veins, there are disparities in the venous systems of the glans penis and the penile shaft. Fourth, regarding biothesiometry, variances in biothesiometry research have been observed between the 2 regions., Conclusion: There are differences between the glans and the shaft. To further advance our understanding, future research should delve deeper into the discrepancies between the glans penis and the penile shaft. Additionally, a more specialized subdivision of the glans penis and the penile shaft would facilitate more precise and tailored treatments., (© The Author(s) 2024. Published by Oxford University Press on behalf of The International Society of Sexual Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Bioinformatics has undergone a paradigm shift in artificial intelligence (AI), particularly through foundation models (FMs), which address longstanding challenges in bioinformatics such as limited annotated data and data noise. These AI techniques have demonstrated remarkable efficacy across various downstream validation tasks, effectively representing diverse biological entities and heralding a new era in computational biology. The primary goal of this survey is to conduct a general investigation and summary of FMs in bioinformatics, tracing their evolutionary trajectory, current research landscape, and methodological frameworks. Our primary focus is on elucidating the application of FMs to specific biological problems, offering insights to guide the research community in choosing appropriate FMs for tasks like sequence analysis, structure prediction, and function annotation. Each section delves into the intricacies of the targeted challenges, contrasting the architectures and advancements of FMs with conventional methods and showcasing their utility across different biological domains. Further, this review scrutinizes the hurdles and constraints encountered by FMs in biology, including issues of data noise, model interpretability, and potential biases. This analysis provides a theoretical groundwork for understanding the circumstances under which certain FMs may exhibit suboptimal performance. Lastly, we outline prospective pathways and methodologies for the future development of FMs in biological research, facilitating ongoing innovation in the field. This comprehensive examination not only serves as an academic reference but also as a roadmap for forthcoming explorations and applications of FMs in biology., (© The Author(s) 2024. Published by Oxford University Press.)

Prostate cancer (PCa) is the most prevalent cancer affecting American men. Castration-resistant prostate cancer (CRPC) can emerge during hormone therapy for PCa, manifesting with elevated serum prostate-specific antigen levels, continued disease progression, and/or metastasis to the new sites, resulting in a poor prognosis. A subset of CRPC patients shows a neuroendocrine (NE) phenotype, signifying reduced or no reliance on androgen receptor signaling and a particularly unfavorable prognosis. In this study, we incorporated computational approaches based on both gene expression profiles and protein-protein interaction networks. We identified 500 potential marker genes, which are significantly enriched in cell cycle and neuronal processes. The top 40 candidates, collectively named CDHu40, demonstrated superior performance in distinguishing NE PCa (NEPC) and non-NEPC samples based on gene expression profiles. CDHu40 outperformed most of the other published marker sets, excelling particularly at the prognostic level. Notably, some marker genes in CDHu40, absent in the other marker sets, have been reported to be associated with NEPC in the literature, such as DDC, FOLH1, BEX1, MAST1, and CACNA1A. Importantly, elevated CDHu40 scores derived from our predictive model showed a robust correlation with unfavorable survival outcomes in patients, indicating the potential of the CDHu40 score as a promising indicator for predicting the survival prognosis of those patients with the NE phenotype. Motif enrichment analysis on the top candidates suggests that REST and E2F6 may serve as key regulators in the NEPC progression., (© The Author(s) 2024. Published by Oxford University Press.)

Background: Photodynamic therapy (PDT) has been strongly recommended as an excellent alternative treatment for Bowen disease (BD). However, reported data on 5-aminolaevulinic acid-mediated PDT (ALA-PDT) with red-light irradiation are limited and the long-term effectiveness remains to be determined, especially in dark-skinned populations., Objectives: We aimed to review routine clinical practice in the field of BD treatment with ALA-PDT over an extended study period (2011-2021), calculate the overall clearance rate, and explore and evaluate factors that might affect the effectiveness of therapy in a real-world setting., Methods: The medical records of patients with BD who received ALA-PDT with red-light irradiation between February 2011 and June 2021 were reviewed and summarized. Univariate and multivariate analyses of clinically relevant variables that may affect treatment outcomes were conducted to identify risk predictors., Results: The overall clearance rate of 122 BD lesions was 89.3% with a median follow-up time of 36 months. The correlation between the effectiveness and fluorescence intensity of pre-PDT or PDT sessions was statistically significant after eliminating the interference of confounding factors. All recurrences occurred in the first 2 years following ALA-PDT., Conclusions: ALA-PDT is an effective treatment for BD in patients with darker-coloured skin. Well-executed operations and effective pretreatment are the determinants of effectiveness. Fluorescence intensity of pre-PDT appeared to be a significant predictor of final effectiveness. In addition, 2 years of follow-up is necessary following ALA-PDT., Competing Interests: Conflicts of interest The authors declare they have no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Association of Dermatologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Study Question: How many couples with at least one child under 3 years would like to have another one or more child(ren) in Eastern China and will an in-cash subsidy be conducive to couple's fertility intentions?, Summary Answer: In sum, only 15.1% of respondents had further fertility intentions (FFI) before learning about the subsidy, and the planned in-cash subsidy policy increased respondents' overall FFI by 8.5%., What Is Known Already: Fertility has been declining globally and has reached a new low in China. The reasons why the Chinese three-child policy was under-realized, and how couples will react to a planned monthly ¥1000 (€141.2) subsidy policy, are not fully understood., Study Design Size Duration: During January and February 2022, a cross-sectional online survey aiming to understand families' expenses of raising a child under 3 years old, and couples' FFI, was conducted. During the survey period, 272 510 respondents scanned the QR code. This study reports the findings pertaining to questions on respondents' sociodemographic characteristics, household factors, FFI, and changes in intention from negative to positive after learning about the planned in-cash subsidy. After exclusion, 144 893 eligible responses were included., Participants/materials Setting Methods: Respondents' FFI, the effect of a planned ¥1000/month*36 months' in-cash subsidy (€5083.2 in total) on people with a negative FFI before the subsidy, and potential reasons for persistent negative FFI after learning about the subsidy were collected through an anonymous online survey. Stepwise binary logistic regression models were used to select associated factors. The potential fertility rate change and government costs were estimated. A stratified analysis by current child number and sensitivity analysis were also conducted., Main Results and the Role of Chance: In sum, 15.7% (22 804/144 893) of respondents were male, 15.1% of respondents reported a positive FFI, and 10.0% (12 288/123 051) without an FFI at first changed their intention after learning about the planned in-cash subsidy policy. For those who still said 'no FFI', 46.5%, 20.6%, and 14.7% chose pressure on housing status, expenses on children's education, and lack of time or energy for caring for another child as their first reasons. FFI was strongest in participants receiving the most financial support from their parents, i.e. grandparents (OR = 1.73, 95% CI = 1.63-1.84 for the >¥100 000/year group), and weakest in those already having two children (OR = 0.23, 95% CI = 0.22-0.24). For those with no FFI before learning about the subsidy policy, respondents with the highest house loan/rent (>¥120 000/year, OR = 1.27, 95% CI = 1.18-1.36) were more likely to change their FFI from 'No' to 'Yes', and those with the highest household income (>¥300 000/year, OR = 0.65, 95% CI = 0.60-0.71) were least susceptible to the policy. In our study population, about 1843 more births every year and an additional 0.3 children per woman were projected under a conservative estimation. Annual estimated cost at the provincial scale would be ¥817.7 (€115.5) million, about 1.02‰ of the total General Public Budget Revenue in 2022. The findings were generally robust in the stratified analysis and sensitivity analysis., Limitations Reasons for Caution: Selection bias and information errors may exist in the online survey responses. The large sample size and detailed further analysis were used to minimize such biases., Wider Implications of the Findings: Fertility intentions in Eastern China are rather low. Policymakers should focus more on financial and childcare burdens for a better realization of the three-child policy, including housing, education and childcare services. An in-cash subsidy, which has never been used in China previously, shows promising potential for increasing FFI. However, the application of such policy should be in line with local conditions for better cost-effectiveness regarding fertility-boosting and fiscal sustainability for the government in the long run., Study Funding/competing Interests: This work was supported by the National Key Research and Development Plan of China (2019YFC0840702). The authors declare no conflict of interests., Trial Registration Number: N/A., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology.)

Ischemic stroke is a major cause of global death and permanent disability. Major consequences of ischemic stroke include neuronal mitochondrial dysfunction. We investigated the effects of senescence marker protein 30 (SMP30) on mitochondria-mediated apoptosis and histone deacetylase 4 (HDAC4)/postsynaptic density-95 (PSD-95) signaling in stroke models in vivo and in vitro. Rats with middle cerebral artery occlusion/reperfusion (MCAO/R) were used to simulate cerebral ischemia/reperfusion (I/R) injury. SMP30 was downregulated in the brain tissues of rats after I/R induction. SMP30 overexpression decreased MCAO/R-induced infarct volumes and improved neurologic function and histopathological changes. Increasing SMP30 expression suppressed neuronal apoptosis and reduced mitochondrial dysfunction. SMP30 overexpression in SH-SY5Y and PC12 cells treated with oxygen-glucose deprivation/reoxygenation (OGD/R) decreased HDAC4 and PSD-95 expression; PSD-95 could bind to HDAC4. Furthermore, HDAC4 upregulation abolished the effects of SMP30 overexpression on OGD/R-induced apoptosis and mitochondrial dysfunction in SH-SY5Y cells. Together, these findings indicate that SMP30 alleviates cerebral I/R-induced neuronal injury by inhibiting HDAC4/PSD-95 to preserve mitochondrial function. These interactions might provide new treatment methods for patients with ischemic stroke., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Association of Neuropathologists, Inc. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The Blaps rhynchopetera Fairmaire is a significant medicinal resource in southwestern China. We utilized Nanopore and Hi-C technologies in combination to generate a high-quality, chromosome-level assembly of the B. rhynchopetera genome and described its genetic features. Genome surveys revealed that B. rhynchopetera is a highly heterozygous species. The assembled genome was 379.24 Mb in size, of which 96.03% was assigned to 20 pseudochromosomes. A total of 212.93 Mb of repeat sequences were annotated and 26,824 protein-coding genes and 837 non-coding RNAs were identified. Phylogenetic analysis indicated that the divergence of the ancestors of B. rhynchopetera and its closely related species Tenebrio molitor at about 85.6 mya. The co-linearity analysis showed that some chromosomes of B. rhynchopetera may have happen fission events and it has a good synteny relationship with Tribolium castaneum. Furthermore, in the enrichment analyses, the gene families related to detoxification and immunity of B. rhynchopetera facilitated the understanding its environmental adaptations, which will serve as a valuable research resource for pest control strategies and conservation efforts of beneficial insects. This high-quality reference genome will also contribute to the conservation of insect species diversity and genetic resources., (© The Author(s) 2024. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

Cryptococcal meningitis (CM) is a well-recognized fungal infection, with substantial mortality in individuals infected with the human immunodeficiency virus (HIV). However, the incidence, risk factors, and outcomes in non-HIV adults remain poorly understood. This study aims to investigate the characteristics and prognostic indicators of CM in non-HIV adult patients, integrating a novel predictive model to guide clinical decision-making. A retrospective cohort of 64 non-HIV adult CM patients, including 51 patients from previous studies and 13 from the First Hospital of Shanxi Medical University, was analyzed. We assessed demographic features, underlying diseases, intracranial pressure, cerebrospinal fluid characteristics, and brain imaging. Using the least absolute shrinkage and selection operator (LASSO) method, and multivariate logistic regression, we identified significant variables and constructed a Nomogram prediction model. The model's calibration, discrimination, and clinical value were evaluated using the Bootstrap method, calibration curve, C index, goodness-of-fit test, receiver operating characteristic (ROC) analysis, and decision curve analysis. Age, brain imaging showing parenchymal involvement, meningeal and ventricular involvement, and previous use of immunosuppressive agents were identified as significant variables. The Nomogram prediction model displayed satisfactory performance with an akaike information criterion (AIC) value of 72.326, C index of 0.723 (0.592-0.854), and area under the curve (AUC) of 0.723, goodness-of-fit test P = 0.995. This study summarizes the clinical and imaging features of adult non-HIV CM and introduces a tailored Nomogram prediction model to aid in patient management. The identification of predictive factors and the development of the nomogram enhance our understanding and capacity to treat this patient population. The insights derived have potential clinical implications, contributing to personalized care and improved patient outcomes., (© The Author(s) 2024. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

Background: The prognostic significance of lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC) remains controversial. Notably, there is evidence suggesting an association between tissue stiffness and the aggressiveness of the disease. We therefore aimed to explore the effect of tissue stiffness on LNM-related invasiveness in PTC patients., Method: A total of 2492 PTC patients from 3 hospitals were divided into an LNM group and a non-LNM group based on their pathological results. The effects of interior lesion stiffness (E) and peri-cancerous tissue stiffness (Eshell) on the LNM-related recurrence rate and mortality in each patient with PTC subgroup were analyzed. The activation of cancer-associated fibroblasts (CAFs) and extracellular matrix component type 1 collagen (COL-I) in the lesion were compared and analyzed across different subgroups. The underlying biological basis of differences in each subgroup was identified using RNA sequencing (RNA-seq) data., Results: The Eshell value and Eshell/E in the LNM group were significantly higher than those in the non-LNM group of patients with PTC (Eshell: 72.72 ± 5.63 vs 66.05 ± 4.46; Eshell/E: 1.20 ± 1.72 vs 1.09 ± 1.10, P < .001). When Eshell/E > 1.412 and LNM were both present, the recurrence rate and mortality were significantly increased compared to those of group of patients with LNM (91.67% and 7.29%, respectively). The CAF activation and COL-I content in the Eshell/E+ group were significantly higher than those in the Eshell/E- group (all P < .001), and the RNA-seq results revealed significant extracellular matrix (ECM) remodeling in the LNM-Eshell/E+ group., Conclusions: Stiff peri-cancerous tissue induced CAF activation, COL-I deposition, and ECM remodeling, resulting in a poor prognosis for PTC patients with LNM., (© The Author(s) 2024. Published by Oxford University Press.)

While some studies have used a transdiagnostic approach to relate depression to metabolic or functional brain alterations, the structural substrate of depression across clinical diagnostic categories is underexplored. In a cross-sectional study of 52 patients with major depressive disorder and 51 with post-traumatic stress disorder, drug-naïve, and spanning mild to severe depression severity, we examined transdiagnostic depressive correlates with regional gray matter volume and the topological properties of gray matter-based networks. Locally, transdiagnostic depression severity correlated positively with gray matter volume in the right middle frontal gyrus and negatively with nodal topological properties of gray matter-based networks in the right amygdala. Globally, transdiagnostic depression severity correlated positively with normalized characteristic path length, a measure implying brain integration ability. Compared with 62 healthy control participants, both major depressive disorder and post-traumatic stress disorder patients showed altered nodal properties in regions of the fronto-limbic-striatal circuit, and global topological organization in major depressive disorder in particular was characterized by decreased integration and segregation. These findings provide evidence for a gray matter-based structural substrate underpinning depression, with the prefrontal-amygdala circuit a potential predictive marker for depressive symptoms across clinical diagnostic categories., (© The Author(s) 2024. Published by Oxford University Press.)

Background: Studies have demonstrated that Sertoli cells are the direct target of Dibutyl phthalate (DBP). However, the role of neurotransmitter receptors is not elucidated., Methods: Based on our previous studies, maternal Sprague-Dawley (SD) rats in Gestation Day (GD) 14-18 and TM4 cells exposure to 750 mg/kg/day and 100 μM DBP were regarded as treated groups. Firstly, qRT-PCR array was used to determine the different expression of neurotransmitter receptors. We examined the OX1R expression on Rats in Control and DBP groups by immunohistochemistry. Real-time PCR and Western Blot were used to detect the protein and mRNA expression levels of OX1R in vivo and in vitro. The potential downstream signaling pathways were explored by analyzing the GSE99690 cohort. In addition, we extracted Primary Sertoli Cells (PSCs) from the testis of control group. The apoptosis-related proteins, AKT signaling pathway-related proteins and mRNA expressions were detected by Western Blot and Real-time PCR in PSCs. The validity of PSCs was measured by CCK-8 assay and flow cytometric analysis was used to demonstrate the apoptotic rates of PSCs after DBP exposure., Results: The Orexin receptor 1 (OX1R) was screened out by qRT-PCR array. Our results showed that DBP could significantly suppress the OX1R expression of Sertoli cells in vivo and in vitro. Functional analysis showed the AKT signaling pathway was mediated by OX1R. The highly expressed apoptosis level and impaired cell activity were observed in PSCs, which can be reversed by Orexin A. Meanwhile, the p-AKT signaling pathway were hindered after DBP exposure while rescued in DBP + Orexin-A group., Conclusions: DBP can induce Sertoli cell apoptosis through its toxicological effect by suppressing OX1R and p-AKT expression, which provide a novel insight on the role of neurotransmitter receptors., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Alzheimer's disease (AD) is a progressive neurodegenerative disorder primarily affecting the elderly, characterized by severe cognitive impairment and memory loss. Emerging evidence suggests that neuroinflammation plays a significant role in AD pathogenesis, with cytokines like interleukin-6 (IL-6) and C-X-C motif chemokine ligand 8 (CXCL8) contributing to the disease progression., Methods: We utilized GEO datasets to identify IL-6 and CXCL8 as pivotal inflammatory markers in AD. In vitro experiments were conducted using SK-N-BE(2)-M17 and THP-1 cell lines treated with IL-6 and CXCL8 to model AD. Additionally, in vivo tests on Amyloid Precursor Protein/Presenilin 1 (APP/PS1) AD mouse models were performed to assess the impact of these cytokines on cognitive functions and brain pathology., Results: The results indicated a significant decrease in cell viability, increased apoptosis, and elevated inflammatory factor secretion following IL-6 and CXCL8 treatment in vitro. In vivo, AD mouse models treated with these cytokines exhibited exacerbated emotional distress, decreased social interaction, impaired cognitive functions, and increased amyloid protein deposition in neural tissues., Conclusions: The study highlights the detrimental effects of IL-6 and CXCL8 on neuronal health and cognitive functions in AD. These findings suggest that targeting these cytokines could offer potential therapeutic interventions for improving patient outcomes in Alzheimer's disease., (© The Author(s) 2024. Published by Oxford University Press on behalf of CINP.)

Drought is a significant global issue affecting agricultural production, and the utilization of beneficial rhizosphere microorganisms is one of the effective ways to increase the productivity of crops and forest under drought. In this study, we characterized a novel growth-promoting dark septate endophytes (DSE) fungus R16 (Dothideomycetes sp.) derived from blueberry roots. Hyphae or microsclerotia were visible within the epidermal or cortical cells of R16-colonized blueberry roots, which was consistent with the typical characteristics of DSE fungi. Inoculation with R16 promoted the growth of blueberry seedlings, and the advantage over the control group was more significant under PEG-induced drought. Comparison of physiological indicators related to drought resistance between the inoculated and control groups was performed on the potted blueberry plants, including the chlorophyll content, net photosynthetic rate, root activities, malondialdehyde and H2O2 content, which indicated that R16 colonization mitigated drought injury in blueberry plants. We further analyzed the effects of R16 on phytohormones and non-structural carbohydrates (NSCs) to explore the mechanism of increased drought tolerance by R16 in blueberry seedlings. The results showed that except for the gibberellin content, indole-3-acetic acid, zeatin and abscisic acid varied significantly between the inoculated and control groups. Sucrose phosphate synthase and sorbitol-6-phosphate dehydrogenase activities in mature leaves, the key enzymes responsible for sucrose and sorbitol synthesis, respectively, as well as sorbitol dehydrogenase, sucrose synthase, cell wall invertase, hexokinase and fructokinase in roots, the key enzymes involved in the NSCs metabolism, showed significant differences between the inoculated and control groups before and after drought treatment. These results suggested that the positive effects of R16 colonization on the drought tolerance of blueberry seedlings are partially attributable to the regulation of phytohormone and sugar metabolism. This study provided valuable information for the research on the interaction between DSE fungi and host plants as well as the application of DSE preparations in agriculture., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Crossover number and distribution are highly regulated by different mechanisms that are not yet fully understood, including crossover interference. The chromosome axis is crucial for crossover formation. Here, we explore the function of the axis protein ASYNAPSIS3. To this end, we use the allotetraploid species Brassica napus; due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all 4 ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with 2 functional ASY3 alleles is comparable to that in wild type, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing ASY3 dosage increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with 1 functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the distinct dosage-dependent effects of ASY3 on crossover formation and provide insights into the role of the chromosome axis in patterning recombination., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Motivation: Single-cell RNA sequencing (scRNA-seq) data are important for studying the laws of life at single-cell level. However, it is still challenging to obtain enough high-quality scRNA-seq data. To mitigate the limited availability of data, generative models have been proposed to computationally generate synthetic scRNA-seq data. Nevertheless, the data generated with current models are not very realistic yet, especially when we need to generate data with controlled conditions. In the meantime, diffusion models have shown their power in generating data with high fidelity, providing a new opportunity for scRNA-seq generation., Results: In this study, we developed scDiffusion, a generative model combining the diffusion model and foundation model to generate high-quality scRNA-seq data with controlled conditions. We designed multiple classifiers to guide the diffusion process simultaneously, enabling scDiffusion to generate data under multiple condition combinations. We also proposed a new control strategy called Gradient Interpolation. This strategy allows the model to generate continuous trajectories of cell development from a given cell state. Experiments showed that scDiffusion could generate single-cell gene expression data closely resembling real scRNA-seq data. Also, scDiffusion can conditionally produce data on specific cell types including rare cell types. Furthermore, we could use the multiple-condition generation of scDiffusion to generate cell type that was out of the training data. Leveraging the Gradient Interpolation strategy, we generated a continuous developmental trajectory of mouse embryonic cells. These experiments demonstrate that scDiffusion is a powerful tool for augmenting the real scRNA-seq data and can provide insights into cell fate research., Availability and Implementation: scDiffusion is openly available at the GitHub repository https://github.com/EperLuo/scDiffusion or Zenodo https://zenodo.org/doi/10.5281/zenodo.13268742., (© The Author(s) 2024. Published by Oxford University Press.)

Precise synapse elimination is essential for the establishment of a fully developed neural circuit during brain development and higher function in adult brain. Beyond immune and nutrition support, recent groundbreaking studies have revealed that phagocytic microglia and astrocytes can actively and selectively eliminate synapses in normal and diseased brains, thereby mediating synapse loss and maintaining circuit homeostasis. Multiple lines of evidence indicate that the mechanisms of synapse elimination by phagocytic glia are not universal but rather depend on specific contexts and detailed neuron-glia interactions. The mechanism of synapse elimination by phagocytic glia is dependent on neuron-intrinsic factors and many innate immune and local apoptosis-related molecules. During development, microglial synapse engulfment in the visual thalamus is primarily influenced by the classic complement pathway, whereas in the barrel cortex, the fractalkine pathway is dominant. In Alzheimer's disease, microglia employ complement-dependent mechanisms for synapse engulfment in tauopathy and early β-amyloid pathology, but microglia are not involved in synapse loss at late β-amyloid stages. Phagocytic microglia also engulf synapses in a complement-dependent way in schizophrenia, anxiety, and stress. In addition, phagocytic astrocytes engulf synapses in a MEGF10-dependent way during visual development, memory, and stroke. Furthermore, the mechanism of a phenomenon that phagocytes selectively eliminate excitatory and inhibitory synapses is also emphasized in this review. We hypothesize that elucidating context-dependent synapse elimination by phagocytic microglia and astrocytes may reveal the molecular basis of synapse loss in neural disorders and provide a rationale for developing novel candidate therapies that target synapse loss and circuit homeostasis., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Leukocyte Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Motivation: Effective molecular representation is critical in drug development. The complex nature of molecules demands comprehensive multi-view representations, considering 1D, 2D, and 3D aspects, to capture diverse perspectives. Obtaining representations that encompass these varied structures is crucial for a holistic understanding of molecules in drug-related contexts., Results: In this study, we introduce an innovative multi-view contrastive learning framework for molecular representation, denoted as MolMVC. Initially, we use a Transformer encoder to capture 1D sequence information and a Graph Transformer to encode the intricate 2D and 3D structural details of molecules. Our approach incorporates a novel attention-guided augmentation scheme, leveraging prior knowledge to create positive samples tailored to different molecular data views. To align multi-view molecular positive samples effectively in latent space, we introduce an adaptive multi-view contrastive loss (AMCLoss). In particular, we calculate AMCLoss at various levels within the model to effectively capture the hierarchical nature of the molecular information. Eventually, we pre-train the encoders via minimizing AMCLoss to obtain the molecular representation, which can be used for various down-stream tasks. In our experiments, we evaluate the performance of our MolMVC on multiple tasks, including molecular property prediction (MPP), drug-target binding affinity (DTA) prediction and cancer drug response (CDR) prediction. The results demonstrate that the molecular representation learned by our MolMVC can enhance the predictive accuracy on these tasks and also reduce the computational costs. Furthermore, we showcase MolMVC's efficacy in drug repositioning across a spectrum of drug-related applications., Availability and Implementation: The code and pre-trained model are publicly available at https://github.com/Hhhzj-7/MolMVC., (© The Author(s) 2024. Published by Oxford University Press.)