Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.)

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.

Single-cell profiling of murine bladder cancer identifies sex-specific transcriptional signatures with prognostic relevance

Bladder cancer (BLCA) is more common in men but more aggressive in women. Sex-based differences in cancer biology are commonly studied using a murine model with BLCA generated by N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN). While tumors in the BBN model have been profiled, these profiles provide limited information on the tumor microenvironment. Here, we applied single-cell RNA sequencing to characterize cell-type specific transcriptional differences between male and female BBN-induced tumors. We found proportional and gene expression differences in epithelial and non-epithelial subpopulations between male and female tumors. Expression of several genes predicted sex-specific survival in several human BLCA datasets. We identified novel and clinically relevant sex-specific transcriptional signatures including immune cells in the tumor microenvironment and it validated the relevance of the BBN model for studying sex differences in human BLCA. This work highlights the importance of considering sex as a biological variable in the development of new and accurate cancer markers.

A Bayesian multivariate mixture model for high throughput spatial transcriptomics

High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seek to identify sub-populations of cells within a tissue sample that may inform biological phenomena. Existing computational methods either ignore the spatial heterogeneity in gene expression profiles, fail to account for important statistical features such as skewness, or are heuristic-based network clustering methods that lack the inferential benefits of statistical modeling. To address this gap, we develop SPRUCE: a Bayesian spatial multivariate finite mixture model based on multivariate skew-normal distributions, which is capable of identifying distinct cellular sub-populations in HST data. We further implement a novel combination of Pólya-Gamma data augmentation and spatial random effects to infer spatially correlated mixture component membership probabilities without relying on approximate inference techniques. Via a simulation study, we demonstrate the detrimental inferential effects of ignoring skewness or spatial correlation in HST data. Using publicly available human brain HST data, SPRUCE outperforms existing methods in recovering expertly annotated brain layers. Finally, our application of SPRUCE to human breast cancer HST data indicates that SPRUCE can distinguish distinct cell populations within the tumor microenvironment. An R package spruce for fitting the proposed models is available through The Comprehensive R Archive Network.

Transcriptome profiling of intact bowel wall reveals that PDE1A and SEMA3D are possible markers with roles in enteric smooth muscle apoptosis, proliferative disorders, and dysautonomia in Crohn's disease

Background: Inflammatory bowel disease (IBD) is a complex and multifactorial inflammatory condition, comprising Crohn's disease (CD) and ulcerative colitis (UC). While numerous studies have explored the immune response in IBD through transcriptional profiling of the enteric mucosa, the subtle distinctions in the pathogenesis of Crohn's disease and ulcerative colitis remain insufficiently understood. Methods: The intact bowel wall specimens from IBD surgical patients were divided based on their inflammatory status into inflamed Crohn's disease (iCD), inflamed ulcerative colitis (iUC) and non-inflamed (niBD) groups for RNA sequencing. Differential mRNA GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes), and GSEA (Gene Set Enrichment Analysis) bioinformatic analyses were performed with a focus on the enteric autonomic nervous system (ANS) and smooth muscle cell (SMC). The transcriptome results were validated by quantitative polymerase chain reaction (qPCR) and immunohistochemistry (IHC). Results: A total of 2099 differentially expressed genes were identified from the comparison between iCD and iUC. Regulation of SMC apoptosis and proliferation were significantly enriched in iCD, but not in iUC. The involved gene PDE1A in iCD was 4-fold and 1.5-fold upregulated at qPCR and IHC compared to that in iUC. Moreover, only iCD was significantly associated with the gene sets of ANS abnormality. The involved gene SEMA3D in iCD was upregulated 8- and 5-fold at qPCR and IHC levels compared to iUC. Conclusion: These findings suggest that PDE1A and SEMA3D may serve as potential markers implicated in enteric smooth muscle apoptosis, proliferative disorders, and dysautonomia specifically in Crohn's disease.

Rapid Detection of Streptococcus mutans Using an Integrated Microfluidic System with Loop-Mediated Isothermal Amplification

Streptococcus mutans is the primary causative agent of caries, which is one of the most common human diseases. Thus, rapid and early detection of cariogenic bacteria is critical for its prevention. This study investigated the combination of loop-mediated isothermal amplification (LAMP) and microfluid technology to quantitatively detect S. mutans. A low-cost, rapid microfluidic chip using LAMP technology was developed to amplify and detect bacteria at 2.2-2.2 × 106 colony-forming units (CFU)/ml and its detection limits were compared to those of standard polymerase chain reaction. A visualization system was established to quantitatively determine the experimental results, and a functional relationship between the bacterial concentration and quantitative results was established. The detection limit of S. mutans using this microfluidic chip was 2.2 CFU/ml, which was lower than that of the standard approach. After quantification, the experimental results showed a good linear relationship with the concentration of S. mutans, thereby confirming the effectiveness and accuracy of the custom-made integrated LAMP microfluidic system for the detection of S. mutans. The microfluidic system described herein may represent a promising simple detection method for the specific and rapid testing of individuals at risk of caries.

In vitro and in vivo Efficacies of Novel Harmine Derivatives in the Treatment of Cystic Echinococcosis

Introduction

Cystic echinococcosis (CE) is a chronic zoonotic parasitic disease caused by the larvae of the Echinococcus granulosus sensu lato (s.l.) cluster. The current existing drugs have limited therapeutic efficacy against cystic echinococcosis, and thus, there is an urgent need to develop new drugs.

Methods

In this study, 7 harmine (HM) derivatives were screened and the effects of HM derivatives on E. granulosus sensu stricto (s.s.) were evaluated by in vitro and mouse experiments. The safety of the HM derivatives was assessed by cytotoxicity assays, acute toxicity study in animals and subacute toxicity study.

Results

These results show that the HM derivatives H-2-168 and DH-004 exhibited more significant antiparasitic effects at an initial concentration of 40 μM. The results of further studies showed that H-2-168 and DH-004 had dose-dependent effects against protoscoleces and had satisfactory therapeutic outcomes in vivo. Electron microscopy observations demonstrated that H-2-168 and DH-004 caused severe disruption of the parasite ultrastructure. Notably, the results of the acute toxicity and subchronic toxicity studies showed that H-2-168 and DH-004 had significantly improved safety. In addition, we found that H-2-168 and DH-004 induced DNA damage in E. granulosus s.s., which may be the mechanism by which these drugs produce their therapeutic effects.

Discussion

Overall, the data from this work demonstrate that H-2-168 and DH-004 are highly effective candidate compounds with low toxicity for the treatment of CE and will provide a new therapeutic strategy for CE pharmacological treatment.

MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer

Rare cell populations are key in neoplastic progression and therapeutic response, offering potential intervention targets. However, their computational identification and analysis often lag behind major cell types. To fill this gap, we introduced MarsGT: Multi-omics Analysis for Rare population inference using Single-cell Graph Transformer. It identifies rare cell populations using a probability-based heterogeneous graph transformer on single-cell multi-omics data. MarsGT outperformed existing tools in identifying rare cells across 400 simulated and four real human datasets. In mouse retina data, it revealed unique subpopulations of rare bipolar cells and a Müller glia cell subpopulation. In human lymph node data, MarsGT detected an intermediate B cell population potentially acting as lymphoma precursors. In human melanoma data, it identified a rare MAIT-like population impacted by a high IFN-I response and revealed the mechanism of immunotherapy. Hence, MarsGT offers biological insights and suggests potential strategies for early detection and therapeutic intervention of disease.

Etiological Study of Acute Conjunctivitis Caused by Human Adenovirus in Shanxi Province, China, between 2016 and 2019

Human adenovirus (HAdV) is the primary cause of acute conjunctivitis. To improve our understanding of the etiology of adenoviral conjunctivitis, ocular samples were collected from 160 conjunctivitis cases in the Shanxi province of northern China between 2016 and 2019. Through preliminary identification, virus isolation, and type identification, a total of 63 HAdV isolates were obtained from the samples. Three species and seven types (HAdV-3, HAdV-4, HAdV-8, HAdV-37, HAdV-53, HAdV-64, and HAdV-85) were detected, with HAdV-64, HAdV-3, and HAdV-8 being the predominant types in 2016, 2018, and 2019, respectively. Further phylogenetic analysis indicated the relative genomic stability of seven HAdV-type strains, except for 4 HAdV-3 strains in 2018 with a novel amino acid insertion site (Pro) between P19 and S20 in the penton base gene. It is worth noting that the genomes of two Shanxi HAdV-85 strains from 2016 were almost identical to those of previously reported HAdV-85 strains that circulated in Japan in 2014 to 2018. China was the second country to sample and isolate HAdV-85, suggesting that HAdV-85 might be underreported as an ocular pathogen. Data obtained in this study provide valuable information on the prevalence of acute conjunctivitis caused by HAdV. IMPORTANCE HAdV types in cases of conjunctivitis in Shanxi province, China, in 2016 to 2019 showed evident diversity, with seven types (HAdV-3, HAdV-4, HAdV-8, HAdV-37, HAdV-53, HAdV-64, and HAdV-85) being identified, and relative genome stability of these viruses was observed. In addition, China was the second country to sample and isolate HAdV-85, which suggests that HAdV-85 might be underreported as an important pathogen associated with ocular infections. These results enhance the understanding of the etiology of adenoviral conjunctivitis and may aid in the development of prevention and control strategies for HAdV-related ocular infections in China.

Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis

Human Papillomaviruses (HPVs) are associated with around 5-10% of human cancer, notably nearly 99% of cervical cancer. The mechanisms HPV interacts with stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study viral gene and host cell differentiation-associated heterogeneity of HPV-positive cervical cancer tissue. We examined the HPV16 genes - E1, E6, and E7, and found they expressed differently across nine epithelial clusters. We found that three epithelial clusters had the highest proportion of HPV-positive cells (33.6%, 37.5%, and 32.4%, respectively), while two exhibited the lowest proportions (7.21% and 5.63%, respectively). Notably, the cluster with the most HPV-positive cells deviated significantly from normal epithelial layer markers, exhibiting functional heterogeneity and altered epithelial structuring, indicating that significant molecular heterogeneity existed in cancer tissues and that these cells exhibited unique/different gene signatures compared with normal epithelial cells. These HPV-positive cells, compared to HPV-negative, showed different gene expressions related to the extracellular matrix, cell adhesion, proliferation, and apoptosis. Further, the viral oncogenes E6 and E7 appeared to modify epithelial function via distinct pathways, thus contributing to cervical cancer progression. We investigated the HPV and host transcripts from a novel viewpoint focusing on layer heterogeneity. Our results indicated varied HPV expression across epithelial clusters and epithelial heterogeneity associated with viral oncogenes, contributing biological insights to this critical field of study.

Van der Waals isotope heterostructures for engineering phonon polariton dispersions

Element isotopes are characterized by distinct atomic masses and nuclear spins, which can significantly influence material properties. Notably, however, isotopes in natural materials are homogenously distributed in space. Here, we propose a method to configure material properties by repositioning isotopes in engineered van der Waals (vdW) isotopic heterostructures. We showcase the properties of hexagonal boron nitride (hBN) isotopic heterostructures in engineering confined photon-lattice waves-hyperbolic phonon polaritons. By varying the composition, stacking order, and thicknesses of h10BN and h11BN building blocks, hyperbolic phonon polaritons can be engineered into a variety of energy-momentum dispersions. These confined and tailored polaritons are promising for various nanophotonic and thermal functionalities. Due to the universality and importance of isotopes, our vdW isotope heterostructuring method can be applied to engineer the properties of a broad range of materials.

Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis

Human Papillomaviruses (HPVs) are associated with around 5%-10% of human cancer, notably nearly 99% of cervical cancer. The mechanisms HPV interacts with stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study viral gene and host cell differentiation-associated heterogeneity of HPV-positive cervical cancer tissue. We examined the HPV16 genes-E1, E6, and E7, and found they expressed differently across nine epithelial clusters. We found that three epithelial clusters had the highest proportion of HPV-positive cells (33.6%, 37.5%, and 32.4%, respectively), while two exhibited the lowest proportions (7.21% and 5.63%, respectively). Notably, the cluster with the most HPV-positive cells deviated significantly from normal epithelial layer markers, exhibiting functional heterogeneity and altered epithelial structuring, indicating that significant molecular heterogeneity existed in cancer tissues and that these cells exhibited unique/different gene signatures compared with normal epithelial cells. These HPV-positive cells, compared to HPV-negative, showed different gene expressions related to the extracellular matrix, cell adhesion, proliferation, and apoptosis. Further, the viral oncogenes E6 and E7 appeared to modify epithelial function via distinct pathways, thus contributing to cervical cancer progression. We investigated the HPV and host transcripts from a novel viewpoint focusing on layer heterogeneity. Our results indicated varied HPV expression across epithelial clusters and epithelial heterogeneity associated with viral oncogenes, contributing biological insights to this critical field of study.

Research Progress of Immunomodulation on Anti-COVID-19 and the Effective Components from Traditional Chinese Medicine

SARS-CoV-2 has posed a threat to the health of people around the world because of its strong transmission and high virulence. Currently, there is no specific medicine for the treatment of COVID-19. However, for a wide variety of medicines used to treat COVID-19, traditional Chinese medicine (TCM) plays a major role. In this paper, the effective treatment of COVID-19 using TCM was consulted first, and several Chinese medicines that were frequently used apart from their huge role in treating it were found. Then, when exploring the active ingredients of these herbs, it was discovered that most of them contained flavonoids. Therefore, the structure and function of the potential active substances of flavonoids, including flavonols, flavonoids, and flavanes, respectively, are discussed in this paper. According to the screening data, these flavonoids can bind to the key proteins of SARS-CoV-2, 3CLpro, PLpro, and RdRp, respectively, or block the interface between the viral spike protein and ACE2 receptor, which could inhibit the proliferation of coronavirus and prevent the virus from entering human cells. Besides, the effects of flavonoids on the human body systems are expounded on in this paper, including the respiratory system, digestive system, and immune system, respectively. Normally, flavonoids boost the body's immune system. However, they can suppress the immune system when over immunized. Ultimately, this study hopes to provide a reference for the clinical drug treatment of COVID-19 patients, and more TCM can be put into the market accordingly, which is expected to promote the development of TCM on the international stage.

Energetic Electron Precipitation Driven by Electromagnetic Ion Cyclotron Waves from ELFIN's Low Altitude Perspective

We review comprehensive observations of electromagnetic ion cyclotron (EMIC) wave-driven energetic electron precipitation using data collected by the energetic electron detector on the Electron Losses and Fields InvestigatioN (ELFIN) mission, two polar-orbiting low-altitude spinning CubeSats, measuring 50-5000 keV electrons with good pitch-angle and energy resolution. EMIC wave-driven precipitation exhibits a distinct signature in energy-spectrograms of the precipitating-to-trapped flux ratio: peaks at >0.5 MeV which are abrupt (bursty) (lasting ∼17 s, or Δ L ∼ 0.56 ) with significant substructure (occasionally down to sub-second timescale). We attribute the bursty nature of the precipitation to the spatial extent and structuredness of the wave field at the equator. Multiple ELFIN passes over the same MLT sector allow us to study the spatial and temporal evolution of the EMIC wave - electron interaction region. Case studies employing conjugate ground-based or equatorial observations of the EMIC waves reveal that the energy of moderate and strong precipitation at ELFIN approximately agrees with theoretical expectations for cyclotron resonant interactions in a cold plasma. Using multiple years of ELFIN data uniformly distributed in local time, we assemble a statistical database of ∼50 events of strong EMIC wave-driven precipitation. Most reside at L ∼ 5 - 7 at dusk, while a smaller subset exists at L ∼ 8 - 12 at post-midnight. The energies of the peak-precipitation ratio and of the half-peak precipitation ratio (our proxy for the minimum resonance energy) exhibit an L -shell dependence in good agreement with theoretical estimates based on prior statistical observations of EMIC wave power spectra. The precipitation ratio's spectral shape for the most intense events has an exponential falloff away from the peak (i.e., on either side of ∼ 1.45 MeV). It too agrees well with quasi-linear diffusion theory based on prior statistics of wave spectra. It should be noted though that this diffusive treatment likely includes effects from nonlinear resonant interactions (especially at high energies) and nonresonant effects from sharp wave packet edges (at low energies). Sub-MeV electron precipitation observed concurrently with strong EMIC wave-driven >1 MeV precipitation has a spectral shape that is consistent with efficient pitch-angle scattering down to ∼ 200-300 keV by much less intense higher frequency EMIC waves at dusk (where such waves are most frequent). At ∼100 keV, whistler-mode chorus may be implicated in concurrent precipitation. These results confirm the critical role of EMIC waves in driving relativistic electron losses. Nonlinear effects may abound and require further investigation.

LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity

Single-cell RNA sequencing (scRNA-seq) data has been widely used for cell trajectory inference, with the assumption that cells with similar expression profiles share the same differentiation state. However, the inferred trajectory may not reveal clonal differentiation heterogeneity among T cell clones. Single-cell T cell receptor sequencing (scTCR-seq) data provides invaluable insights into the clonal relationship among cells, yet it lacks functional characteristics. Therefore, scRNA-seq and scTCR-seq data complement each other in improving trajectory inference, where a reliable computational tool is still missing. We developed LRT, a computational framework for the integrative analysis of scTCR-seq and scRNA-seq data to explore clonal differentiation trajectory heterogeneity. Specifically, LRT uses the transcriptomics information from scRNA-seq data to construct overall cell trajectories and then utilizes both the TCR sequence information and phenotype information to identify clonotype clusters with distinct differentiation biasedness. LRT provides a comprehensive analysis workflow, including preprocessing, cell trajectory inference, clonotype clustering, trajectory biasedness evaluation, and clonotype cluster characterization. We illustrated its utility using scRNA-seq and scTCR-seq data of CD8+ T cells and CD4+ T cells with acute lymphocytic choriomeningitis virus infection. These analyses identified several clonotype clusters with distinct skewed distribution along the differentiation path, which cannot be revealed solely based on scRNA-seq data. Clones from different clonotype clusters exhibited diverse expansion capability, V-J gene usage pattern and CDR3 motifs. The LRT framework was implemented as an R package 'LRT', and it is now publicly accessible at https://github.com/JuanXie19/LRT. In addition, it provides two Shiny apps 'shinyClone' and 'shinyClust' that allow users to interactively explore distributions of clonotypes, conduct repertoire analysis, implement clustering of clonotypes, trajectory biasedness evaluation, and clonotype cluster characterization.

Repression of ferroptotic cell death by mitochondrial calcium signaling

The uptake of Ca2+ into and extrusion of calcium from the mitochondrial matrix, regulated by the mitochondrial Ca2+ uniporter (MCU), is a fundamental biological process that has crucial impacts on cellular metabolism, signaling, growth and survival. Herein, we report that the embryonic lethality of Mcu-deficient mice is fully rescued by orally supplementing ferroptosis inhibitor lipophilic antioxidant vitamin E and ubiquinol. Mechanistically, we found MCU promotes acetyl-CoA-mediated GPX4 acetylation at K90 residue, and K90R mutation impaired the GPX4 enzymatic activity, a step that is crucial for ferroptosis. Structural analysis supports the possibility that GPX4 K90R mutation alters the conformational state of the molecule, resulting in disruption of a salt bridge formation with D23, which was confirmed by mutagenesis studies. Finally, we report that deletion of MCU in cancer cells caused a marked reduction in tumor growth in multiple cancer models. In summary, our study provides a first direct link between mitochondrial calcium level and sustained GPX4 enzymatic activity to regulate ferroptosis, which consequently protects cancer cells from ferroptosis.

Case Report: Systemic treatment for breast and vulvar metastases from resected rectal signet ring cell carcinoma

Background

Breast and vulvar metastases from rectal signet ring cell carcinoma (SRCC) represent a rare and obscure clinical entity associated with poor survival. Managing patients with metastatic rectal SRCC is extremely challenging due to the absence of high-quality evidence.

Case presentation

A 26-year-old woman presented with progressively worsening anal pain, constipation, and hematochezia for approximately two years. Following the diagnosis of locally advanced rectal cancer (_cT₃N_0-1M₀), she received neoadjuvant chemotherapy with modified FOLFOX6 regimen and underwent laparoscopic abdominoperineal resection. Metastases to the breast and vulva developed during postoperative chemotherapy. Genetic testing revealed RAS/BRAF wild-type and microsatellite instability (MSI)-low status. Though sequential administration of irinotecan plus tegafur and tegafur plus raltitrexed-based chemotherapy in combination with bevacizumab, the disease progressed rapidly. Sadly, the patient passed away 15 months after initial diagnosis due to rapidly progressive disease.

Conclusion

Rectal SRCC is associated with younger on-set, aggressive behaviors, and worse survival outcomes. Due to poor cohesiveness, SRCC tends to develop metastases. A patient's medical history and immunohistochemical staining (such as CK20, CK7, and CDX-2) can aid in identifying the tumor origin of breast and vulvar metastases. Mutations and signaling pathways predominant in the tumorigenesis of SRCC remains unveiled. There is poor effect of conventional chemotherapies, targeted and immunotherapies for colorectal adenocarcinoma on SRCC, so novel therapies are needed to treat this patient population.

Modulation effect of black rice dietary fiber on the metabolism and fermentation of cyanidin-3-glucoside in an in vitro human colonic model

Black rice (Oryza sativa L.) is a great source of anthocyanins and dietary fiber and possesses various health-promoting properties. The modulating effect of insoluble dietary fiber (IDF) from black rice on the fermentation of cyanidin-3-O-glucoside (Cy3G) in an in vitro human colonic model, together with the possible microbiota-mediated mechanisms, was investigated. The combined Cy3G and IDF fermentation can promote the biotransformation of Cy3G into phenolic compounds such as cyanidin and protocatechuic acid with stronger antioxidant activities and increase the total production of SCFAs during the fermentation of Cy3G. 16S rRNA sequencing analysis revealed that the addition of IDF modulated the microbiota structure and bloomed Bacteroidota and Prevotellaceae-related genera, which were positively correlated with metabolites of Cy3G, thus potentially regulating the microbial metabolism of Cy3G. The work is of great significance for elucidating the material basis of the health benefits of black rice.

Computational methods and challenges in analyzing intratumoral microbiome data

The human microbiome is intimately related to cancer biology and plays a vital role in the efficacy of cancer treatments, including immunotherapy. Extraordinary evidence has revealed that several microbes influence tumor development through interaction with the host immune system, that is, immuno-oncology-microbiome (IOM). This review focuses on the intratumoral microbiome in IOM and describes the available data and computational methods for discovering biological insights of microbial profiling from host bulk, single-cell, and spatial sequencing data. Critical challenges in data analysis and integration are discussed. Specifically, the microorganisms associated with cancer and cancer treatment in the context of IOM are collected and integrated from the literature. Lastly, we provide our perspectives for future directions in IOM research.

Ferritin-dependent cellular autophagy pathway promotes ferroptosis in beef during cold storage

Ferroptosis plays a pivotal role in regulating various physiological processes and quality of post-mortem muscle. However, the molecular mechanisms underlying ferroptosis remain unclear. The study investigated how ferroptosis was induced in beef during cold storage. Results showed that the expression of autophagy-related genes, LC3, ATG5, ATG7, and NCOA4 in beef during cold storage promoted the degradation of ferritin heavy chains. Ferritin evoked ferroptosis by releasing free iron, inducing reactive oxygen species (ROS) accumulation and inhibiting the glutathione (GSH)-glutathione peroxidase 4 (GPX4) pathway. Furthermore, treatment of myoblasts with GSK 2656157 (autophagy inhibitor) showed that ferritin degradation was lower in the GSK 2656157-treated myoblasts than in the control, while GSH content and GPX4 activity were higher than the control (P < 0.05), and the contents of free iron, ROS and malondialdehyde, and apoptosis were lower than the control (P < 0.05). These results suggest that ferroptosis is induced by degradation of ferritin via the autophagic pathway.

[Effect of acupuncture on protein kinase R-like endoplasmic reticulum kinase/eukaryotic translation initiation factor 2α signaling pathway in hippocampus of rats with post-traumatic stress disorder]

OBJECTIVE

To observe the effect of acupuncture on the protein kinase R-like endoplasmic reticulum kinase (PERK)/eukaryotic translation initiation factor 2α (eIF2α) signaling pathway in the hippocampus of rats with post-traumatic stress disorder (PTSD), so as to explore the underlying mechanism of acupuncture in treating PTSD.

METHODS

Twenty-eight SD rats were randomly divided into normal, model, acupuncture and sertraline groups, with 7 rats in each group. The PTSD model was established by single prolonged stress method. The next day after modeling, acupuncture was applied to "Baihui" (GV20) and "Dazhui" (GV14) of rats in the acupuncture group for 10 min, once a day for 7 days. Sertraline (10 mg/kg) was given by gavage to rats of the sertraline group daily for 7 days. The behavioral changes of rats were detected by elevated cross maze experiment and new object recognition experiment. The expression levels of PERK,phosphorylated(p)-PERK, eIF2α, p-eIF2α and activating transcription factor 4 (ATF4) proteins in hippocampus were detected by Western blot. The ultrastructure of hippocampal neurons was observed by transmission electron microscopy.

RESULTS

Compared with the normal group, the percentage of times and retention time of entering the open arm of the elevated cross maze experiment, and new object recognition index were significantly decreased (P<0.01); the expression levels of p-PERK, p-eIF2α and ATF4 proteins in hippocampus were significantly increased (P<0.05) of rats in the model group. Compared with the model group, the percentage of times and retention time of entering the open arm, and new object recognition index were significantly increased (P<0.05，P<0.01), the expression levels of p-PERK, p-eIF2α and ATF4 proteins in hippocampus were significantly decreased (P<0.05, P<0.01) of rats in the acupuncture and sertraline groups; the expression level of eIF2α protein was significantly decreased (P<0.05) in the sertraline group. Hippocampal neurons in the model group were damaged, the rough endoplasmic reticulum showed severe dilation, the mitochondrial cristae showed reduction or mild cavitation; compared with the model group, hippocampal neurons structural damage and the rough endoplasmic reticulum dilation were alleviated， and only some of the mitochondrial cristae decreased in the acupuncture and sertraline groups.

CONCLUSION

Acupuncture can alleviate the anxiety behavior as well as the recognition and memory ability of PTSD rats, and its mechanism may be related to the inhibition of hippocampus PERK/eIF2α signaling pathway and the reduction of hippocampal neuron damage caused by endoplasmic reticulum stress.

[Association of body fat distribution with depression and social anxiety in children and adolescents: A cross-sectional study based on dual-energy X-ray detection]

OBJECTIVE

To investigate the status of depression and social anxiety in children and adolescents, and to analyze the association between body fat distribution and depression, social anxiety in children and adolescents.

METHODS

A total of 1 412 children aged 7 to 18 years in Beijing were included by stratified cluster random sampling method. Body fat distribution, including total body fat percentage (total BF%), Android BF%, Gynoid BF% and Android-to-Gynoid fat ratio (AOI), were obtained by dual-energy X-ray absorption method. Depression and social anxiety were evaluated by Children Depression Inventory and Social Anxiety Scale for Children. Multivariate linear regression and restricted cubic spline analysis were used to estimate the linear and non-linear correlation between body fat distribution and depression and social anxiety.

RESULTS

13.1% and 31.1% of the children and adolescents had depressive symptoms and social anxiety symptoms respectively, and the detection rate of depression and social anxiety in the boys and young groups was significantly lower than those in the girls and old groups. There was no significant linear correlation between total BF%, Android BF%, Gynoid BF%, AOI and depression and social anxiety in the children and adolescents. However, total BF% and Gynoid BF% had significant nonlinear correlation with depression, showing an inverted U-shaped curve relationship with the tangent points of 26.8% and 30.9%, respectively. In terms of the nonlinear association of total BF%, Android BF%, Gynoid BF% and AOI with depression and social anxiety, the change trends of the boys and girls, low age group and high age group were consistent. The overall anxiety risk HR of body fat distribution in the boys was significantly higher than that in the girls, and the risk HR of depression and social anxiety were significantly higher in the high age group than those in the low age group.

CONCLUSION

There was no significant linear correlation between body fat distribution and depression and social anxiety in children and adolescents. Total BF% and depression showed an inverted U-shaped curve, mainly manifested in Gynoid BF%, and this trend was consistent in different genders and different age groups. Maintaining children and adolescents' body fat distribution at an appropriate level is the future direction of the prevention and control of depression and social anxiety in children and adolescents.

CD200R signaling contributes to unfavorable tumor microenvironment through regulating production of chemokines by tumor-associated myeloid cells

CD200 is overexpressed in many solid tumors and considered as an immune checkpoint molecule dampening cancer immunity. In this study, we found that CD200R^-/- mice were significantly more potent in rejecting these CD200⁺ tumors. scRNA sequencing demonstrated that tumors from CD200R^-/- mice had more infiltration of CD4⁺ and CD8⁺ T cells, and NK cells but less infiltration of neutrophils. Antibody depletion experiments revealed that immune effector cells are crucial in inhibiting tumor growth in CD200R^-/- mice. Mechanistically, we found that CD200R signaling regulates the expression of chemokines in tumor-associated myeloid cells (TAMCs). In the absence of CD200R, TAMCs increased expression of CCL24 and resulted in increased infiltration of eosinophils, which contributes to anti-tumor activity. Overall, we conclude that CD200R signaling contributes to unfavorable TME through chemokine-dependent recruitment of immune suppressive neutrophils and exclusion of anti-cancer immune effectors. Our study has implications in developing CD200-CD200R targeted immunotherapy of solid tumors.

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors

Emerging evidence supports the important role of the tumor microbiome in oncogenesis, cancer immune phenotype, cancer progression, and treatment outcomes in many malignancies. In this study, we investigated the metastatic melanoma tumor microbiome and potential roles in association with clinical outcomes, such as survival, in patients with metastatic disease treated with immune checkpoint inhibitors (ICIs). Baseline tumor samples were collected from 71 patients with metastatic melanoma before treatment with ICIs. Bulk RNA-seq was conducted on the formalin-fixed paraffin-embedded (FFPE) tumor samples. Durable clinical benefit (primary clinical endpoint) following ICIs was defined as overall survival ≥24 months and no change to the primary drug regimen (responders). We processed RNA-seq reads to carefully identify exogenous sequences using the {exotic} tool. The 71 patients with metastatic melanoma ranged in age from 24 to 83 years, 59% were male, and 55% survived >24 months following the initiation of ICI treatment. Exogenous taxa were identified in the tumor RNA-seq, including bacteria, fungi, and viruses. We found differences in gene expression and microbe abundances in immunotherapy responsive versus non-responsive tumors. Responders showed significant enrichment of several microbes including Fusobacterium nucleatum, and non-responders showed enrichment of fungi, as well as several bacteria. These microbes correlated with immune-related gene expression signatures. Finally, we found that models for predicting prolonged survival with immunotherapy using both microbe abundances and gene expression outperformed models using either dataset alone. Our findings warrant further investigation and potentially support therapeutic strategies to modify the tumor microbiome in order to improve treatment outcomes with ICIs.

A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, MEGA, to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of 9 cancer centers in the Oncology Research Information Exchange Network (ORIEN). This package has 3 unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2704 tumor RNA-seq samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

Laparoscopic versus ultrasound-guided transversus abdominis plane block for postoperative pain management in minimally invasive colorectal surgery: a meta-analysis protocol

Introduction

Transversus abdominis plane block (TAPB) is now commonly administered for postoperative pain control and reduced opioid consumption in patients undergoing major colorectal surgeries, such as colorectal cancer, diverticular disease, and inflammatory bowel disease resection. However, there remain several controversies about the effectiveness and safety of laparoscopic TAPB compared to ultrasound-guided TAPB. Therefore, the aim of this study is to integrate both direct and indirect comparisons to identify a more effective and safer TAPB approach.

Materials and methods

Systematic electronic literature surveillance will be performed in the PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and ClinicalTrials.gov databases for eligible studies through July 31, 2023. The Cochrane Risk of Bias version 2 (RoB 2) and Risk of Bias in Non-randomized Studies of Interventions (ROBINS-I) tools will be applied to scrutinize the methodological quality of the selected studies. The primary outcomes will include (1) opioid consumption at 24 hours postoperatively and (2) pain scores at 24 hours postoperatively both at rest and at coughing and movement according to the numerical rating scale (NRS). Additionally, the probability of TAPB-related adverse events, overall postoperative 30-day complications, postoperative 30-day ileus, postoperative 30-day surgical site infection, postoperative 7-day nausea and vomiting, and length of stay will be analyzed as secondary outcome measures. The findings will be assessed for robustness through subgroup analyses and sensitivity analyses. Data analyses will be performed using RevMan 5.4.1 and Stata 17.0. P value of less than 0.05 will be defined as statistically significant. The certainty of evidence will be examined via the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) working group approach.

Ethics and dissemination

Owing to the nature of the secondary analysis of existing data, no ethical approval will be required. Our meta-analysis will summarize all the available evidence for the effectiveness and safety of TAPB approaches for minimally invasive colorectal surgery. High-quality peer-reviewed publications and presentations at international conferences will facilitate disseminating the results of this study, which are expected to inform future clinical trials and help anesthesiologists and surgeons determine the optimal tailored clinical practice for perioperative pain management.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=281720, identifier (CRD42021281720).

Properties of Pickering emulsions stabilized by cellulose nanocrystals extracted from litchi peels

The development of Pickering emulsions which are applicable to the food industry still remains challenges due to the limited availability for biocompatible, edible and natural emulsifiers. The purpose of this study was to extract cellulose nanocrystals from litchi peels (LP-CNCs), and evaluate their emulsifying properties. The results showed that the LP-CNCs were needle-like and they possessed high crystallinity (72.34 %) and aspect ratio. When the concentrations of LP-CNCs were >0.7 wt% or the contents of oil were no >0.5, stable Pickering emulsions were obtained. The microstructures of emulsions confirmed that LP-CNCs formed dense interfacial layers on the surface of oil droplets, which functioned as barriers to prevent aggregation and flocculation among droplets. Rheological results showed that the emulsions exhibited typical shear thinning behavior. The elastic of emulsions was dominant, and their gel strength could be enhanced by regulating the contents of emulsifiers or oil. Additionally, the Pickering emulsions stabilized by LP-CNCs showed extremely high pH, ionic strength, and temperature tolerance. This strategy provides an innovative alternative to tackle the dilemma of preparing highly stable Pickering emulsions using natural particles in food products.

An observational study on the safety of COVID-19 vaccination in patients with myasthenia gravis

OBJECTIVE

There is concern that the coronavirus disease (COVID-19) vaccine may trigger or worsen autoimmune diseases. The objective of this study was to determine the impacts of COVID-19 vaccination on symptom severity in patients with myasthenia gravis (MG).

METHODS

A total of 106 enrolled patients with MG who were vaccinated against COVID-19 were followed up, and a questionnaire was used to document in detail the exacerbation of muscle weakness after vaccination and all other uncomfortable reactions after vaccination. Demographic, clinical characteristics, medication, and vaccination data were collected by follow-up interview. The main observation outcome was whether the MG symptoms of patients were exacerbated. The definition of exacerbation is according to the subjective feeling of the patient or a 2-point increase in daily life myasthenia gravis activity score relative to before vaccination, within 30 days after vaccination.

RESULTS

Of 106 enrolled patients [median age (SD) 41.0 years, 38 (35.8%) men, 53 (50.0%) with generalized MG, 74 (69.8%) positive for acetylcholine receptor antibody, and 21 (19.8%) with accompanying thymoma], muscle weakness symptoms were stable in 102 (96.2%) patients before vaccine inoculation. Muscle weakness worsened in 10 (9.4%) people after vaccination, of which 8 patients reported slight symptom worsening that resolved quickly (within a few days). Two (1.9%) of patients showed serious symptom aggravation that required hospitalization.

CONCLUSION

Our results suggest that inactivated virus vaccines against COVID-19 may be safe for patients with MG whose condition is stable. Patients with generalized MG may be more likely to develop increased muscle weakness after vaccination.

Two colors, one-step, self-drive fluorescent strategy for chloramphenicol detection base on DNAzyme cleavage triggered hybridization chain reaction

A two colors, one-step, self-drive fluorescent strategy was developed for chloramphenicol (CAP) detection based on cyclic cleavage of molecular beacon (MB) by pincer DNA sequences. CAP can bind with its aptamer and active the enzyme-strand (E-DNA). Then the E-DNA can circularly cleave the MB on the both side of pincer DNA sequences. The cleaved fragments can self-assembly to form a long duplex and cause the great recovery of the two colors fluorescent signal. The limit of detection was as low as 0.7 pM. Importantly, the whole detection process is very simple with only one-step operation. Moreover, the two colors fluorescent signals can greatly enhance the accuracy of the result. It was also successfully used to detect CAP in actual samples.

Reduced water-holding capacity of beef during refrigeration is associated within creased heme oxygenase 1 expression, oxidative stress and ferroptosis

Low molecular weight iron (LMW-Fe)-mediated oxidative stress from heme degradation may reduce beef water-holding capacity (WHC). However, the underlying mechanism of heme degradation is still unknown. In the present study, we assessed the WHC, tissue morphology, reactive oxygen species (ROS), apoptosis, heme oxygenase(HMOX) 1 expression, and ferroptosis characteristics of beef chilled at 4 °C for 6 days. Results showed that water loss increased and WHC decreased during beef storage (P < 0.05). Increased protein and mRNA expression of HMOX1 promoted the decomposition of heme and facilitated the liberation of iron ions (P < 0.05), and excess LMW-Fe was associated with ROS formation, depletion of glutathione, and inhibition of glutathione peroxidase 4 activity (P < 0.05). Muscle tissue showed typical features of ferroptosis, including expression of ferroptosis-related genes, malondialdehyde accumulation, and structural damage to mitochondria (P < 0.05). It was also found that HMOX1 and the heme pathway-mediated ferroptosis were associated with structural changes in myofibrils and reduced WHC in chilled beef.

AuNPs-DNAzyme motor triggered two colors DNA tweezer for fluorescent amplified detection of bisphenol A

An AuNPs-DNAzyme motor triggered ultrasensitive, two colors DNA tweezer was developed for fluorescent detection of bisphenol A (BPA). BPA can bind with its aptamer on the gold nanoparticles (AuNPs) and reactivate the Pb²⁺ enzyme strands. Thus, Pb²⁺ enzyme strands can cleave the substrate strand on AuNPs and release a DNA fragment from AuNPs. The released DNA fragment can bind with the loop of the Y shaped DNA tweezer to form Mg²⁺-specific DNAzyme, the following cleavage causing the leaving of another two DNA fragments. Then, these two DNA fragments can open the two ends of the Y shaped DNA tweezer, causing the recovery of fluorescent signals. This strategy shows a good linear relationship for BPA detection from 0.44 to 2.2 × 10³ pM. The sensitivity has been significantly improved by the two levels of amplification strategy DNAzyme motor and cyclic cleavage of the loop. Importantly, it also can significantly reduce the false positive result by two colors signals. Moreover, it also exhibits satisfactory performance in practical sample detection.

Priorities to Promote Participant Engagement in the Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network

BACKGROUND

Engaging diverse populations in cancer genomics research is of critical importance and is a fundamental goal of the NCI Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Established as part of the Cancer Moonshot, PE-CGS is a consortium of stakeholders including clinicians, scientists, genetic counselors, and representatives of potential study participants and their communities. Participant engagement is an ongoing, bidirectional, and mutually beneficial interaction between study participants and researchers. PE-CGS sought to set priorities in participant engagement for conducting the network's research.

METHODS

PE-CGS deliberatively engaged its stakeholders in the following four-phase process to set the network's research priorities in participant engagement: (i) a brainstorming exercise to elicit potential priorities; (ii) a 2-day virtual meeting to discuss priorities; (iii) recommendations from the PE-CGS External Advisory Panel to refine priorities; and (iv) a virtual meeting to set priorities.

RESULTS

Nearly 150 PE-CGS stakeholders engaged in the process. Five priorities were set: (i) tailor education and communication materials for participants throughout the research process; (ii) identify measures of participant engagement; (iii) identify optimal participant engagement strategies; (iv) understand cancer disparities in the context of cancer genomics research; and (v) personalize the return of genomics findings to participants.

CONCLUSIONS

PE-CGS is pursuing these priorities to meaningfully engage diverse and underrepresented patients with cancer and posttreatment cancer survivors as participants in cancer genomics research and, subsequently, generate new discoveries.

IMPACT

Data from PE-CGS will be shared with the broader scientific community in a manner consistent with participant informed consent and community agreement.

Explainable Deep Hypergraph Learning Modeling the Peptide Secondary Structure Prediction

Accurately predicting peptide secondary structures remains a challenging task due to the lack of discriminative information in short peptides. In this study, PHAT is proposed, a deep hypergraph learning framework for the prediction of peptide secondary structures and the exploration of downstream tasks. The framework includes a novel interpretable deep hypergraph multi-head attention network that uses residue-based reasoning for structure prediction. The algorithm can incorporate sequential semantic information from large-scale biological corpus and structural semantic information from multi-scale structural segmentation, leading to better accuracy and interpretability even with extremely short peptides. The interpretable models are able to highlight the reasoning of structural feature representations and the classification of secondary substructures. The importance of secondary structures in peptide tertiary structure reconstruction and downstream functional analysis is further demonstrated, highlighting the versatility of our models. To facilitate the use of the model, an online server is established which is accessible via http://inner.wei-group.net/PHAT/. The work is expected to assist in the design of functional peptides and contribute to the advancement of structural biology research.

Impact of interactions between peanut protein isolate and cellulose nanocrystals on the properties of Pickering emulsions: Rheological properties and physical stabilities

The interactions between cellulose nanocrystals and proteins can regulate the interfacial properties of Pickering emulsions, which plays a leading role in the stabilities of Pickering emulsions. In this work, oil-in-water (O/W) Pickering emulsions with different oil-water ratios were prepared using peanut protein isolate modified by cellulose nanocrystals (PPI/CL-CNCs). The distributions of PPI/CL-CNCs at the oil-water interfaces and the microstructures of Pickering emulsions were observed by CLSM and cryo-SEM. The results showed that stable complexes PPI/CL-CNCs formed thick and dense interface layers on the surface of oil droplets. The results of rheological tests clarified that the Pickering emulsions showed an elastic and gel texture, and their gel strength could be enhanced by regulating the oil-water ratios from 3:7 to 7:3. In addition, after one month of storage, the EI of all emulsions remained above 92 % with no obvious phase separation or demulsification. These results suggested that the PPI/CL-CNCs-stabilized Pickering emulsions showed good physical stabilities. The study on the rheological properties and physical stabilities of PPI/CL-CNCs-based Pickering emulsions provided novel insights on developing highly stable Pickering emulsions.

Integration of epigenetic and genetic profiles identifies multiple sclerosis disease-critical cell types and genes

Genome-wide association studies (GWAS) successfully identified multiple sclerosis (MS) susceptibility variants. Despite this notable progress, understanding the biological context of these associations remains challenging, due in part to the complexity of linking GWAS results to causative genes and cell types. Here, we aimed to address this gap by integrating GWAS data with single-cell and bulk chromatin accessibility data and histone modification profiles from immune and nervous systems. MS-GWAS associations are significantly enriched in regulatory regions of microglia and peripheral immune cell subtypes, especially B cells and monocytes. Cell-specific polygenic risk scores were developed to examine the cumulative impact of the susceptibility genes on MS risk and clinical phenotypes, showing significant associations with risk and brain white matter volume. The findings reveal enrichment of GWAS signals in B cell and monocyte/microglial cell-types, consistent with the known pathology and presumed targets of effective MS therapeutics.

Meta-analysis of the relationship between bullying and depressive symptoms in children and adolescents

Childhood and adolescence are critical periods for physical and mental development; thus, they are high-risk periods for the occurrence of mental disorders. The purpose of this study was to systematically evaluate the association between bullying and depressive symptoms in children and adolescents. We searched the PubMed, MEDLINE and other databases to identify studies related to bullying behavior and depressive symptoms in children and adolescents. A total of 31 studies were included, with a total sample size of 133,688 people. The results of the meta-analysis showed that the risk of depression in children and adolescents who were bullied was 2.77 times higher than that of those who were not bullied; the risk of depression in bullying individuals was 1.73 times higher than that in nonbullying individuals; and the risk of depression in individuals who bullied and experienced bullying was 3.19 times higher than that in nonbullying-bullied individuals. This study confirmed that depression in children and adolescents was significantly associated with being bullied, bullying, and bullying-bullied behavior. However, these findings are limited by the quantity and quality of the included studies and need to be confirmed by future studies.

Dimension-agnostic and granularity-based spatially variable gene identification

Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a spatial granularity-guided and non-parametric model to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This new method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.

Dimension-agnostic and granularity-based spatially variable gene identification

Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a spatial granularity-guided and non-parametric model to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This new method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.

Top Canopy Height and Stem Size Variation Enhance Aboveground Biomass across Spatial Scales in Seasonal Tropical Forests

Tropical forests are biologically diverse and structurally complex ecosystems that can store a large quantity of carbon and support a great variety of plant and animal species. However, tropical forest structure can vary dramatically within seemingly homogeneous landscapes due to subtle changes in topography, soil fertility, species composition and past disturbances. Although numerous studies have reported the effects of field-based stand structure attributes on aboveground biomass (AGB) in tropical forests, the relative effects and contributions of UAV LiDAR-based canopy structure and ground-based stand structural attributes in shaping AGB remain unclear. Here, we hypothesize that mean top-of-canopy height (TCH) enhances AGB directly and indirectly via species richness and horizontal stand structural attributes, but these positive relationships are stronger at a larger spatial scale. We used a combined approach of field inventory and LiDAR-based remote sensing to explore how stand structural attributes (stem abundance, size variation and TCH) and tree species richness affect AGB along an elevational gradient in tropical forests at two spatial scales, i.e., 20 m × 20 m (small scale), and 50 m × 50 m (large scale) in southwest China. Specifically, we used structural equation models to test the proposed hypothesis. We found that TCH, stem size variation and abundance were strongly positively associated with AGB at both spatial scales, in addition to which increasing TCH led to greater AGB indirectly through increased stem size variation. Species richness had negative to negligible influences on AGB, but species richness increased with increasing stem abundance at both spatial scales. Our results suggest that light capture and use, modulated by stand structure, are key to promoting high AGB stocks in tropical forests. Thus, we argue that both horizontal and vertical stand structures are important for shaping AGB, but the relative contributions vary across spatial scales in tropical forests. Importantly, our results highlight the importance of including vertical forest stand attributes for predicting AGB and carbon sequestration that underpins human wellbeing.

A High Performance Wheat Disease Detection Based on Position Information

Protecting wheat yield is a top priority in agricultural production, and one of the important measures to preserve yield is the control of wheat diseases. With the maturity of computer vision technology, more possibilities have been provided to achieve plant disease detection. In this study, we propose the position attention block, which can effectively extract the position information from the feature map and construct the attention map to improve the feature extraction ability of the model for the region of interest. For training, we use transfer learning to improve the training speed of the model. In the experiment, ResNet built on positional attention blocks achieves 96.4% accuracy, which is much higher compared to other comparable models. Afterward, we optimized the undesirable detection class and validated its generalization performance on an open-source dataset.

Age-dependent mechanical properties of tail tendons in wild-type and mimecan gene-knockout mice - A preliminary study

Mimecan, or osteoglycin, belongs to the family of small leucine-rich proteoglycans. In connective tissues mimecan is implicated in the development and maintenance of normal collagen fibrillar organization. Since collagen fibrils are responsible for tissue reinforcement, the absence of mimecan could lead to abnormal tissue mechanical properties. Here, we carried out a preliminary investigation of possible changes in the mechanical properties of tendons in mice lacking a functional mimecan gene, as a function of age. Tail tendons were dissected from mimecan gene knockout (KO) and wild type (WT) mice at ages 1, 4 and 8 months and mechanical properties evaluated using a microtensile testing equipment. Mimecan gene knockout resulted in changes in tendon elasticity- and fracture-related properties. While tendons of WT mice exhibited enhanced mechanical properties with increasing age, this trend was notably attenuated in mimecan KO tendons, with the exception of fracture strain. When genotype and age were considered as cross factors, the diminution in the mechanical properties of mimecan KO tendons was significant for yield strength, modulus and fracture strength. This effect appeared to affect the mice at 4 month old. These preliminary results suggest that mimecan may have a role in regulating age-dependent mechanical function in mouse tail tendon.

Single-cell biological network inference using a heterogeneous graph transformer

Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities simultaneously to capture the intricacy of complex molecular mechanisms and cellular heterogeneity. Existing tools cannot effectively infer the active biological networks in diverse cell types and the response of these networks to external stimuli. Here we present DeepMAPS for biological network inference from scMulti-omics. It models scMulti-omics in a heterogeneous graph and learns relations among cells and genes within both local and global contexts in a robust manner using a multi-head graph transformer. Benchmarking results indicate DeepMAPS performs better than existing tools in cell clustering and biological network construction. It also showcases competitive capability in deriving cell-type-specific biological networks in lung tumor leukocyte CITE-seq data and matched diffuse small lymphocytic lymphoma scRNA-seq and scATAC-seq data. In addition, we deploy a DeepMAPS webserver equipped with multiple functionalities and visualizations to improve the usability and reproducibility of scMulti-omics data analysis.

Polygenic risk score association with multiple sclerosis susceptibility and phenotype in Europeans

Polygenic inheritance plays a pivotal role in driving multiple sclerosis susceptibility, an inflammatory demyelinating disease of the CNS. We developed polygenic risk scores (PRS) of multiple sclerosis and assessed associations with both disease status and severity in cohorts of European descent. The largest genome-wide association dataset for multiple sclerosis to date (n = 41 505) was leveraged to generate PRS scores, serving as an informative susceptibility marker, tested in two independent datasets, UK Biobank [area under the curve (AUC) = 0.73, 95% confidence interval (CI): 0.72-0.74, P = 6.41 × 10-146] and Kaiser Permanente in Northern California (KPNC, AUC = 0.8, 95% CI: 0.76-0.82, P = 1.5 × 10-53). Individuals within the top 10% of PRS were at higher than 5-fold increased risk in UK Biobank (95% CI: 4.7-6, P = 2.8 × 10-45) and 15-fold higher risk in KPNC (95% CI: 10.4-24, P = 3.7 × 10-11), relative to the median decile. The cumulative absolute risk of developing multiple sclerosis from age 20 onwards was significantly higher in genetically predisposed individuals according to PRS. Furthermore, inclusion of PRS in clinical risk models increased the risk discrimination by 13% to 26% over models based only on conventional risk factors in UK Biobank and KPNC, respectively. Stratifying disease risk by gene sets representative of curated cellular signalling cascades, nominated promising genetic candidate programmes for functional characterization. These pathways include inflammatory signalling mediation, response to viral infection, oxidative damage, RNA polymerase transcription, and epigenetic regulation of gene expression to be among significant contributors to multiple sclerosis susceptibility. This study also indicates that PRS is a useful measure for estimating susceptibility within related individuals in multicase families. We show a significant association of genetic predisposition with thalamic atrophy within 10 years of disease progression in the UCSF-EPIC cohort (P < 0.001), consistent with a partial overlap between the genetics of susceptibility and end-organ tissue injury. Mendelian randomization analysis suggested an effect of multiple sclerosis susceptibility on thalamic volume, which was further indicated to be through horizontal pleiotropy rather than a causal effect. In summary, this study indicates important, replicable associations of PRS with enhanced risk assessment and radiographic outcomes of tissue injury, potentially informing targeted screening and prevention strategies.

Utilizing endosomal capture for tumor therapy via membrane-lytic mechanism-based Pickering emulsion

Nanocarriers are easily captured by endosomes, where the abundant hydrolases inevitably destroy the nanocarriers and the drugs they carry, ultimately resulting in a compromised or lost therapeutic efficacy. Herein, we report a membrane-lytic mechanism-based Pickering emulsion that can in turn utilize this seemingly unfavorable endosomal capture behavior for tumor therapy. This Pickering emulsion is constructed as an oil-in-water (O/W) emulsion stabilized by the hybrid nanoparticles (HNPs) composed of two molecules with opposite charges, cetyl trimethylamine bromide (CTAB) and linoleic acid (LA), through electrostatic interaction (defined as HNPs@PE). After HNPs@PE enters the lysosomes through macropinocytosis-mediated endocytosis, LA can be protonated in response to the acidic stimulus, and causing the swelling or disintegration of HNPs due to the disrupted electrostatic interaction. The released CTAB holds strong membrane-lytic activity and can directly damage the lysosomal membranes. Under the acidic condition and the participation of excessive iron ions (II) in lysosomes, LA induces lipid peroxidation and the resulting lipid peroxides (LPO) will oxidize the lysosomal membranes, collectively causing the leakage of lysosome membranes and the release of contents into cytoplasm. Subsequently, the diffused CTAB and LPO will continue to attack the mitochondrial membranes and cell membranes, resulting in the death of different types of tumor cells both in vitro and in vivo due to membrane damage. This Pickering emulsion with membrane-lytic ability represents a potential self-anticancer nanocarrier.

Ataxin-1 controls the expression of specific noncoding RNAs in B cells upon autoimmune demyelination

B cells play a key mechanistic role in the pathogenesis of multiple sclerosis (MS), a chronic neurological disease of the central nervous system with an autoimmune etiology. B cells contribute to disease initiation and progression by acting as professional antigen-presenting cells as well as via secreting autoantibodies and proinflammatory cytokines. We have recently shown that the polyglutamine protein ataxin-1, which was first linked to the movement disorder spinocerebellar ataxia type 1, also acts as a master regulator of B-cell functions in the context of central nervous system autoimmunity. In fact, ataxin-1-deficient mice display an aggravated manifestation of the MS disease model experimental autoimmune encephalomyelitis along with aberrant B-cell functions. Consistent with this scenario, transcriptomic analysis of Atxn1-null B cells highlighted distinct genetic signatures involved in cell activation, proliferation and antigen presentation. To further characterize the role of ataxin-1, we profiled the noncoding transcriptome controlled by ataxin-1 in the B-cell compartment upon an encephalitogenic challenge. We show that two specific classes of noncoding RNAs, namely, processed pseudogenes and intergenic long noncoding RNAs, are differentially regulated along disease. Furthermore, pathway and protein network analyses on their putative protein-coding gene targets found a significant enrichment in ontologies related to cell mitosis, together with molecular processes relevant to MS such as chitin metabolism. Altogether, these findings shed light on the possible contribution of noncoding RNAs to B-cell biology and MS pathogenesis, and further establish the immunomodulatory role of ataxin-1 in autoimmune demyelination.