Neurons upregulate PD-L1 via IFN/STAT1/IRF1 to alleviate damage by CD8+ T cells in cerebral malaria.

BACKGROUND: Cerebral malaria (CM) is the most lethal complication of malaria, and survivors usually endure neurological sequelae. Notably, the cytotoxic effect of infiltrating Plasmodium-activated CD8+ T cells on cerebral microvasculature endothelial cells is a prominent feature of the experimental CM (ECM) model with blood-brain barrier disruption. However, the damage effect of CD8+ T cells infiltrating the brain parenchyma on neurons remains unclear. Based on the immunosuppressive effect of the PD-1/PD-L1 pathway on T cells, our previous study demonstrated that the systemic upregulation of PD-L1 to inhibit CD8+ T cell function could effectively alleviate the symptoms of ECM mice. However, it has not been reported whether neurons can suppress the pathogenic effect of CD8+ T cells through the PD-1/PD-L1 negative immunomodulatory pathway. As the important inflammatory factor of CM, interferons can induce the expression of PD-L1 via different molecular mechanisms according to the neuro-immune microenvironment. Therefore, this study aimed to investigate the direct interaction between CD8+ T cells and neurons, as well as the mechanism of neurons to alleviate the pathogenic effect of CD8+ T cells through up-regulating PD-L1 induced by IFNs. METHODS: Using the ECM model of C57BL/6J mice infected with Plasmodium berghei ANKA (PbA), morphological observations were conducted in vivo by electron microscope and IF staining. The interaction between the ECM CD8+ T cells (immune magnetic bead sorting from spleen of ECM mice) and primary cultured cortical neurons in vitro was observed by IF staining and time-lapse photography. RNA-seq was performed to analyze the signaling pathway of PD-L1 upregulation in neurons induced by IFNß or IFNγ, and verified through q-PCR, WB, IF staining, and flow cytometry both in vitro and in vivo using IFNAR or IFNGR gene knockout mice. The protective effect of adenovirus-mediated PD-L1 IgGFc fusion protein expression was verified in ECM mice with brain stereotaxic injection in vivo and in primary cultured neurons via viral infection in vitro. RESULTS: In vivo, ECM mice showed infiltration of activated CD8+ T cells and neuronal injury in the brain parenchyma. In vitro, ECM CD8+ T cells were in direct contact with neurons and induced axonal damage, as an active behavior. The PD-L1 protein level was elevated in neurons of ECM mice and in primary cultured neurons induced by IFNß, IFNγ, or ECM CD8+ T cells in vitro. Furthermore, the IFNß or IFNγ induced neuronal expression of PD-L1 was mediated by increasing STAT1/IRF1 pathway via IFN receptors. The increase of PD-L1 expression in neurons during PbA infection was weakened after deleting the IFNAR or IFNGR. Increased PD-L1 expression by adenovirus partially protected neurons from CD8+ T cell-mediated damage both in vitro and in vivo. CONCLUSION: Our study demonstrates that both type I and type II IFNs can induce neurons to upregulate PD-L1 via the STAT1/IRF1 pathway mediated by IFN receptors to protect against activated CD8+ T cell-mediated damage, providing a targeted pathway to alleviate neuroinflammation during ECM.

NLRX1: a key regulator in mitochondrial respiration and colorectal cancer progression.

Colorectal cancer (CRC) is a prevalent and aggressive malignancy with high mortality rates and significant risks to human well-being. Population-wide screening for tumor suppressor genes and oncogenes shows promise for reducing the incidence and fatality of CRC. Recent studies have suggested that NLRX1, an innate immunity suppressor, may play a role in regulating chronic inflammation and tumorigenesis. However, further investigation is needed to understand the specific role of NLRX1 in CRC. To evaluate the impact of NLRX1 on migration, invasion, and metastasis, two human colon cancer cell lines were studied in vitro. Additionally, a knockout mouse tumor-bearing model was used to validate the inhibitory effect of NLRX1 on tumor emergence and progression. The Seahorse XF96 technology was employed to assess mitochondrial function and glycolysis in colorectal cancer cells overexpressing NLRX1. Moreover, public databases were consulted to analyze gene and protein expression levels of NLRX1. Finally, the results were validated using a series of CRC patient samples. Our findings demonstrate that downregulation of NLRX1 enhances proliferation, colony formation, and tumor-forming capacity in HCT116 and LoVo cells. Conversely, overexpression of NLRX1 negatively impacts basal respiration and mitochondrial ATP-linked respiration in both cell lines, resulting in a notable decrease in maximal respiration during the standard mitochondrial stress test. Furthermore, analysis of data from the TCGA database reveals a significant reduction in NLRX1 expression in colon and rectal cancer tissues compared to normal tissues. This result was validated using clinical samples, where immunohistochemistry staining and western blotting demonstrated a notable reduction in NLRX1 protein levels in CRC compared to adjacent normal tissues. The decreased expression of NLRX1 may serve as a significant prognostic indicator and diagnostic biomarker for CRC patients.

Intense Left-handed Circularly Polarized Luminescence in Chiral Nematic Hydroxypropyl Cellulose Composite Films.

Integrating optically active components into chiral photonic cellulose to fabricate circularly polarized luminescent materials has transformative potential in disease detection, asymmetric reactions, and anticounterfeiting techniques. However, the lack of cellulose-based left-handed circularly polarized light (L-CPL) emissions hampers the progress of these chiral functionalizations. Here, this work proposes an unprecedented strategy: incorporating a chiral nematic organization of hydroxypropyl cellulose with robust aggregation-induced emission luminogens to generate intense L-CPL emission. By utilizing N,N-dimethylformamide as a good solvent for fluorescent components and cellulose matrices, this work produces a right-handed chiral nematic structure film with a uniform appearance in reflective and fluorescent states. Remarkably, this system integrates a high asymmetric factor (0.51) and an impressive emission quantum yield (55.8%) into one fascinating composite. More meaningfully, this approach is versatile, allowing for the incorporation of luminogen derivatives emitting multicolored L-CPL. These chiral fluorescent films possess exceptional mechanical flexibility (toughness up to 0.9 MJ m-3) and structural stability even under harsh environmental exposures, making them promising for the fabrication of various products. Additionally, these films can be cast on the fabrics to reveal multilevel and durable anticounterfeiting capabilities or used as a chiral light source to induce enantioselective photopolymerization, thereby offering significant potential for diverse practical applications.

Dynamic changes of Th1/Th2/Th17 cytokines and hBD-2/3 in erosive oral lichen planus patients saliva before and after prednisone acetate treatment.

Objective: This study aimed to investigate the expression of T helper 1 (Th1)/Th2/Th17- related cytokines and human beta defensins 2 and 3 (hBD-2 and -3) in the saliva of patients with erosive oral lichen planus (EOLP) and to explore their role in the pathogenesis of EOLP and the effects of glucocorticoids on EOLP. Methods: A total of 30 patients with EOLP and 20 age- and sex-matched healthy individuals were included in this study. The patients were treated with prednisone at a dose of 0.4 mg/(kg·d) for 1 week and examined before and after treatment. Unstimulated whole saliva samples were collected to determine the levels of cytokines (interleukin 1 beta [IL-1ß], tumour necrosis factor alpha [TNF]-α, interferon gamma [IFN-γ], IL-4, IL-6, IL-10 and IL-17) by cytometric bead array and those of hBD-2 and -3 b y enzyme-linked immunosorbent assay. In addition, oral rinse samples were collected to detect Candida load. Results: The levels of salivary IL-1ß, IL-6, hBD-2 and hBD-3 were higher and the IFN-γ/IL-4 and IL-1ß/IL-6 ratios were lower in patients with EOLP than in healthy individuals. In patients with EOLP, hBD-2 levels were positively correlated with IFN-γ levels and negatively correlated with IL-17 levels, whereas hBD-3 levels were negatively correlated with IL-17 and IL-10 levels. In addition, the prevalence of EOLP was positively correlated with IL-6 levels and negatively correlated with the IFN-γ/IL-4 ratio. The levels of IL-1ß, TNF-α, IFN-γ, IL-6, hBD-2 and hBD-3 and the IFN-γ/IL-4 ratio decreased after treatment with prednisone for 1 week. The levels of IL-6, hBD-2 and hBD-3 were significantly higher in EOLP patients than in healthy individuals; while TNF-α levels and the IFN-γ/IL-4 ratio were significantly lower in EOLP patients than in healthy individuals. Furthermore, the oral counts of Candida spp. (colony forming unit [CFU]) were negatively correlated with TNF-α levels. Numerical Rating Scale(NRS) and Sign scores decreased in EOLP patients after treatment. Approximately 80 % of patients were effectively treated. Salivary TNF-α levels were significantly higher in the treatment-ineffective group than in the treatment-effective group before treatment with prednisone, and differences in salivary IL-6 levels before and after treatment were significantly higher in the treatment-effective group than in the treatment-ineffective group. Conclusions: High expression of IL-1ß, IL-6, hBD-2 and Th1/Th2 imbalance in saliva may be associated with the pathogenesis of EOLP. IFN-γ/IL-4 balance may serve as a protective factor for EOLP. Glucocorticoids significantly alleviate the symptoms of EOLP and inhibit the expression of Th1/Th2 cytokines.

The benefits and risks of menopause hormone therapy for the cardiovascular system in postmenopausal women: a systematic review and meta-analysis.

BACKGROUND: Menopause hormone therapy (MHT), as an effective method to alleviate the menopause-related symptoms of women, its benefits, risks, and potential influencing factors for the cardiovascular system of postmenopausal women are not very clear. OBJECTIVES: To evaluate cardiovascular benefits and risks of MHT in postmenopausal women, and analyze the underlying factors that affect both. SEARCH STRATEGY: The EMBASE, MEDLINE, and CENTRAL databases were searched from 1975 to July 2022. SELECTION CRITERIA: Randomized Clinical Trials (RCTs) that met pre-specified inclusion criteria were included. DATA COLLECTION AND ANALYSIS: Two reviewers extracted data independently. A meta-analysis of random effects was used to analyze data. MAIN RESULTS: This systematic review identified 33 RCTs using MHT involving 44,639 postmenopausal women with a mean age of 60.3 (range 48 to 72 years). There was no significant difference between MHT and placebo (or no treatment) in all-cause death (RR = 0.96, 95%CI 0.85 to 1.09, I2 = 14%) and cardiovascular events (RR = 0.97, 95%CI 0.82 to 1.14, I2 = 38%) in the overall population of postmenopausal women. However, MHT would increase the risk of stroke (RR = 1.23, 95%CI 1.08 to 1.41,I2 = 0%) and venous thromboembolism (RR = 1.86, 95%CI 1.39 to 2.50, I2 = 24%). Compared with placebo, MHT could improve flow-mediated arterial dilation (FMD) (SMD = 1.46, 95%CI 0.86 to 2.07, I2 = 90%), but it did not improve nitroglycerin-mediated arterial dilation (NMD) (SMD = 0.27, 95%CI - 0.08 to 0.62, I2 = 76%). Compared with women started MHT more than 10 years after menopause, women started MHT within 10 years after menopause had lower frequency of all-cause death (P = 0.02) and cardiovascular events (P = 0.002), and more significant improvement in FMD (P = 0.0003). Compared to mono-estrogen therapy, the combination therapy of estrogen and progesterone would not alter the outcomes of endpoint event. (all-cause death P = 0.52, cardiovascular events P = 0.90, stroke P = 0.85, venous thromboembolism P = 0.33, FMD P = 0.46, NMD P = 0.27). CONCLUSIONS: MHT improves flow-mediated arterial dilation (FMD) but fails to lower the risk of all-cause death and cardiovascular events, and increases the risk of stroke and venous thrombosis in postmenopausal women. Early acceptance of MHT not only reduces the risk of all-cause death and cardiovascular events but also further improves FMD, although the risk of stroke and venous thrombosis is not reduced. There is no difference in the outcome of cardiovascular system endpoints between mono-estrogen therapy and combination therapy of estrogen and progesterone.

CD8+ T cell infiltration and proliferation in the brainstem during experimental cerebral malaria.

INTRODUCTION: Cerebral malaria (CM) is a lethal neuroinflammatory disease caused by Plasmodium infection. Immune cells and brain parenchyma cells contribute to the pathogenesis of CM. However, a systematic examination of the changes that occur in the brain parenchyma region during CM at the single-cell resolution is still poorly studied. AIMS: To explore cell composition and CD8+ T cell infiltration, single-cell RNA sequencing (scRNA-seq) was performed on the brainstems of healthy and experimental cerebral malaria (ECM) mice. Then CD8+ T cell infiltration was confirmed by flow cytometry and immunofluorescence assays. Subsequently, the characteristics of the brain-infiltrated CD8+ T cells were analyzed. Finally, the interactions between parenchyma cells and brain-infiltrated CD8+ T cells were studied with an astrocytes-CD8+ T cell cocultured model. RESULTS: The brainstem is the most severely damaged site during ECM. ScRNA-seq revealed a large number of CD8+ T cells infiltrating into the brainstem in ECM mice. Brain-infiltrated CD8+ T cells were highly activated according to scRNA-seq, immunofluorescence, and flow cytometry assays. Further analysis found a subset of ki-67+ CD8+ T cells that have a higher transcriptional level of genes related to T cell function, activation, and proliferation, suggesting that they were exposed to specific antigens presented by brain parenchyma cells. Brain-infiltrated CD8+ T cells were the only prominent source of IFN-γ in this single-cell analysis. Astrocytes, which have a high interferon response, act as cross-presenting cells to recruit and re-activate brain-infiltrated CD8+ T cells. We also found that brain-infiltrated CD8+ T cells were highly expressed immune checkpoint molecule PD-1, while parenchyma cells showed up-regulation of PD-L1 after infection. CONCLUSIONS: These findings reveal a novel interaction between brain-infiltrated CD8+ T cells and parenchyma cells in the ECM brainstem, suggesting that the PD-1/PD-L1 signal pathway is a promising adjunctive therapeutic strategy for ECM targeting over-activated CD8+ T cells.

Integrated Transcriptomics and Metabolomics Analyses Provide Insights into Qingke in Response to Cold Stress.

The survival and productivity of qingke in high altitude (>4300 m, average yearly temperature <0 °C) of the Tibetan Plateau are significantly impacted by low-temperature stress. Uncovering the mechanisms underlying low-temperature stress response in cold-tolerant qingke varieties is crucial for qingke breeding. Herein, we conducted a comprehensive transcriptomic and metabolomic analysis on cold-sensitive (ZQ) and cold-tolerant (XL) qingke varieties under chilling and freezing treatments and identified lipid metabolism pathways as enriched in response to freezing treatment. Additionally, a significant positive correlation was observed between the expression of C-repeat (CRT) binding factor 10A (HvCBF10A) and Gly-Asp-Ser-Leu-motif lipase (HvGDSL) and the accumulation of multiple lipids. Functional analysis confirmed that HvCBF10A directly binds to HvGDSL, and silencing HvCBF10A resulted in a significant decrease in both HvGDSL and lipid levels, consequently impairing the cold tolerance. Overall, HvCBF10A and HvGDSL are functional units in actively regulating lipid metabolism to enhance freezing stress tolerance in qingke.

Investigation of a subunit protein vaccine for HFRS based on a consensus sequence between envelope glycoproteins of HTNV and SEOV.

Due to the global resurgence of hemorrhagic fever with renal syndrome (HFRS), more attention is being focused on this dangerous illness. In China and Korea, the only vaccines available are the virus-inactivated vaccine against Hantaan virus (HTNV) or Seoul virus (SEOV), but their efficacy and safety are inadequate. Therefore, it is important to develop new vaccines that are safer and more efficient to neutralize and regulate areas with a high prevalence of HFRS. We employed bioinformatics methods to design a recombinant protein vaccine based on conserved regions of protein consensus sequences in HTNV and SEOV membranes. The S2 Drosophila expression system was utilized to enhance protein expression, solubility and immunogenicity. After the Gn and Gc proteins of HTNV and SEOV were successfully expressed, mice were immunized, and the humoral immunity, cellular immunity, and in vivo protection of the HFRS universal subunit vaccine were systematically evaluated in mouse models. These results indicated that the HFRS subunit vaccine generated elevated levels of binding and neutralizing antibodies, particularly IgG1, compared to that of the traditional inactivated HFRS vaccine. Additionally, the spleen cells of immunized mice secreted IFN-r and IL-4 cytokines effectively. Moreover, the HTNV-Gc protein vaccine successfully protected suckling mice from HTNV infection and stimulated GC responses. In this research, a new scientific approach is investigated to develop a universal HFRS subunit protein vaccine that is capable of producing effective humoral and cellular immunity in mice. The results suggest that this vaccine could be a promising candidate for preventing HFRS in humans.

Sustainable, Insoluble, and Photonic Cellulose Nanocrystal Patches for Calcium Ion Sensing in Sweat.

Self-assembly of cellulose nanocrystals (CNCs) is invaluable for the development of sustainable optics and photonics. However, the functional failure of CNC-derived materials in humid or liquid environments inevitably impairs their development in biomedicine, membrane separation, environmental monitoring, and wearable devices. Here, a facile and robust method to fabricate insoluble hydrogels in a self-assembled CNC-polyvinyl alcohol (PVA) system is reported. Due to the reconstruction of inter- or intra-molecular hydrogen bond interactions, thermal dehydration makes an optimized CNC/PVA photonic film form a stable hydrogel network in an aqueous solution rather than dissolve. Notably, the resulting hydrogel exhibits superb mechanical performance (stress up to 3.3 Mpa and tough up to 0.73 MJ m-3 ) and reversible conversion between dry and wet states, enabling it convenient for specific functionalization. Sodium alginate (SA) can be adsorbed into the CNC photonic structure by swelling dry CNC/PVA film in a SA solution. The prepared hydrogel showcases the comprehensive properties of freezing resistance (-20°C), strong adhesion, satisfactory biocompatibility, and highly sensitive and selective Ca2+ sensing. The material could act as a portable wearable patch on the skin for the continuous analysis of calcium trends during different physical exercises, facilitating their development in precision nutrition and health monitoring.

The over-expression of miRNA-206 in peripheral blood of patients with burning mouth syndrome and its relationship with anxiety and depression.

BACKGROUND: Burning mouth syndrome (BMS) is characterised by persisting burning pain of the oral mucosa, and its etiopathogenesis remains poorly understood. OBJECTIVES: Our study aimed to detect the expression of miRNA-206 in the blood and clarify the relationship among miRNA-206, pain, anxiety and depression of BMS patients. METHODS: Thirty patients with BMS and 30 healthy individuals were enrolled in the experimental and control groups, respectively. Data on medical history and clinical oral examination for all participants were collected. Simultaneously, scores of Visual Analogous Scale (VAS), Self-rating Anxiety Scale (SAS) and Self-rating Depression Scale (SDS) were administered. The expression level of miRNA-206 in plasma were determined by RT-(q)PCR. Finally, the relationship of miRNA-206 expression with the VAS score, SAS score, and SDS score was analysed. Chi-square test and t-test were used for statistical analysis of the data, and p < .05 was considered statistically significant. RESULTS: The majority of the patients with BMS identified the tongue as the main pain area, and showed dry mouth and poor sleep quality. The SAS and SDS scores of patients with BMS were higher than those of healthy controls (p < .05) and were positively correlated with VAS pain score. In addition, miRNA-206 expression was higher in patients with BMS than in healthy individuals (p < .05), and was positively correlated with the VAS and SDS scores (p < .05). CONCLUSIONS: Patients with BMS suffer from pain and tend to be more anxious and depressed than healthy controls. miRNA-206 expression in the peripheral blood of patients with BMS is positively correlated with pain and depression, which may be involved in the pathogenesis of BMS.

Amer: A New Attribute-Missing Network Embedding Approach.

Network embedding which aims to learn a low dimensional representation of nodes is a powerful technique for network analysis. While network embedding for networks with complete attributes has been widely investigated, in many real-world applications the attributes of partial nodes are unobserved (i.e., missing) due to privacy concern or resource limit. Very recently, several network embedding methods have been proposed for attribute-missing networks. They first complete the missing attributes and then use the complemented network to learn network embedding. The parameters of these two processes cannot be adjusted by each other, resulting in compromised results. To address this problem, we propose a unified model in which the process of completing missing attributes and the process of learning embedding are not separated but closely intertwined. Being specific, completing missing attributes is under the guidance of learning network representation via mutual information maximization, and the complemented attributes directly enter network representation module which will generate further feedback for completing missing attributes. We further impose attribute-structure relationship constraint for completing missing attributes by designing a new generative adversarial networks (GANs) model. To the best of our knowledge, this is the first unified model for attribute-missing network embedding. Empirical results on real-world datasets show the superiority of our new method over other state-of-the-art methods on four network analysis tasks, including node classification, node clustering, link prediction, and network visualization.

Research trends and hotspots of recurrent pregnancy loss with thrombophilia: a bibliometric analysis.

BACKGROUND: Thrombophilia is a group of disorders that result in a blood hypercoagulable state and induce thrombosis, which was found widely existed in recurrent pregnancy loss (RPL). More and more research about thrombophilia has been conducted but the association between thrombophilia and RPL remains uncertain. Thus, it's necessary to combine relevant literature to find the research hotspots and analyze the internal link between different study points, and then predict the development trend in RPL with thrombophilia. METHODS: Relevant articles between 1970 and 2022 were obtained from the Web of Science (WoS) database. Software VOSviewer and CiteSpace were used to perform the analysis and conduct visualization of scientific productivity and emerging trends. RESULTS: Seven hundred twenty-five articles published in recent 30 years by 3205 authors from 1139 organizations and 68 countries were analyzed. 37authors, 38 countries, and 53 organizations published papers ≥5. The United States was the most productive country and Univ Amsterdam was the most productive institution. Journal thrombosis and haemostasis had the most total citations. In keyword and clusters, factor-v-Leiden, inherited thrombophilia, activated protein-c, low-dose aspirin, molecular-weigh heparin, polymorphism had high-frequency focus on its etiology, diagnostics, and therapeutics. The strongest keyword bursts showed the research hotspots changed over time. CONCLUSIONS: There could be differences in the clinical relevance of different type of thrombophilia, as well as single and multiple thrombophilic factors. Anticoagulation and immunotherapy are currently the main treatment options. More clinical trials and basic research are expected and we should attach more attention to the whole management of in-vitro fertilization in the future.

Analysis of subgingival micro-organisms based on multi-omics and Treg/Th17 balance in type 2 diabetes with/without periodontitis.

Type 2 diabetes mellitus (T2DM) and periodontitis are common and interrelated diseases, resulting in altered host response microbiota. The subgingival micro-organisms play a key role in periodontitis pathogenesis. To assess the shift of subgingival microbiome and metabolome in T2DM, we performed an analysis of the subgingival microbiome in patients with T2DM (n = 20) compared with non-diabetes (ND) subjects (n = 21). Furthermore, patients were subdivided into 10 T2DM with periodontitis (DP), 10 T2DM without periodontitis (DNP), 10 periodontitis (P), and 11 healthy control (H) groups. 16SrRNA gene sequencing combined with ultra high-performance liquid chromatography-mass spectrometry (UHPLC-MS) based metabolomics was performed in all participants. T lymphocyte immunity was analyzed by flow cytometry. Furthermore, the network relationship among subgingival micro-organisms, metabolites, blood glucose level, and T lymphocyte immunity were analyzed. The results showed that the difference of the subgingival microbiome from healthy to periodontitis status was less prominent in T2DM compared with ND, though the clinical signs of disease were similar. The bacteria Eubacterium nodatum group, Filifactor, Fretibacterium, Peptostreptococcus, and Desulfovibrio, amongst others, may be important in the pathopoiesia of periodontitis in the T2DM state. In addition, some dominant bacteria showed network relationships. The Treg/Th17 ratio was lower in the DP and DNP groups than in the P and H groups-though that of P was lower than for H. The percentage of CD4+/CD8+ PD1 and CD8+ PDL1 was higher in the DP and DNP groups than in the H group; the percentage of CD8+ PDL1 was higher in the DP than P groups. Subgingival micro-organisms in periodontitis had a significant metabolic shift in terms of their signature metabolites. Butyrate metabolism and phenylalanine metabolism may play a role in the pathogenesis of periodontitis with/without T2DM. Specifically, biphenyl degradation, tryptophan metabolism, and the two-component system may play important roles in periodontitis with T2DM. Lastly, the network relationship among subgingival micro-organisms, metabolites, blood glucose level, and T lymphocyte immunity were unbalanced. This study identified the changes in the subgingival microbiome associated with periodontitis in T2DM, as well as the associated network between bacterial flora, metabolism dysbiosis, and immune regulation.

Integrative metabolomic and transcriptomic analyses reveal the mechanisms of Tibetan hulless barley grain coloration.

Cereal grains accumulate anthocyanin during developmental process. The anthocyanin content increases at grain filling stages to develop grain coloration in cereals. However, anthocyanin biosynthesis responsible for grain coloring and its regulatory mechanisms controlled by structural and functional genes remain unclear. Therefore, this study aimed to explore the global map of metabolic changes linked to grain coloration of Tibetan hulless barley (qingke) using an integrative metabolome and transcriptome approach. Grains from three colored qingke cultivars at different developmental stages were considered for molecular and metabolic investigations. A total of 120 differentially accumulated metabolites (DAMs) and 8,327 differentially expressed genes (DEGs) were filtered. DEGs were mainly enriched in the phenylpropanoid and flavonoid pathways. The transcript levels of anthocyanin biosynthesis genes (PAL, C4H, 4CL, CHS, FLS, F3H, F3'H, DFR, ANS, GT, OMT, and MAT) significantly upregulate in colored qingke compared to the non-colored variety. During grain development and maturation, the strong correlation of HvMYC2 expression with anthocyanin contents and anthocyanin biosynthesis genes suggested it as a critical gene in anthocyanin accumulation. Further results confirmed that HvMYC2 could be activated by HvMYB and be a positive regulator of UV-B and cold tolerance in qingke. In addition, verification based on enzymatic assays indicated that six key modifier enzymes could catalyze glycosylation, malonylation, and methylation of anthocyanins, thereby dissecting the major anthocyanin modification pathway in colored qingke. Overall, our study provides global insight into anthocyanin accumulation and the mechanism underlying grain coloration in qingke.

A Tutorial on Generative Adversarial Networks with Application to Classification of Imbalanced Data.

A challenge unique to classification model development is imbalanced data. In a binary classification problem, class imbalance occurs when one class, the minority group, contains significantly fewer samples than the other class, the majority group. In imbalanced data, the minority class is often the class of interest (e.g., patients with disease). However, when training a classifier on imbalanced data, the model will exhibit bias towards the majority class and, in extreme cases, may ignore the minority class completely. A common strategy for addressing class imbalance is data augmentation. However, traditional data augmentation methods are associated with overfitting, where the model is fit to the noise in the data. In this tutorial we introduce an advanced method for data augmentation: Generative Adversarial Networks (GANs). The advantages of GANs over traditional data augmentation methods are illustrated using the Breast Cancer Wisconsin study. To promote the adoption of GANs for data augmentation, we present an end-to-end pipeline that encompasses the complete life cycle of a machine learning project along with alternatives and good practices both in the paper and in a separate video. Our code, data, full results and video tutorial are publicly available in the paper's github repository.

Functional brain abnormalities in major depressive disorder using a multiscale community detection approach.

Major depressive disorder (MDD) is a serious disease associated with abnormal brain regions, however, the interconnection between specific brain regions related to depression has not been fully explored. To solve this problem, the paper proposes a novel multiscale community detection method to compare the differences in brain regions between normal controls (NC) and MDD patients. This study adopted the Brainnetome Atlas to divide the brain into 246 regions and extract the time series of each region. The Pearson correlation was used to measure the similarity among different brain regions to conduct the brain functional network and to perform multiscale community detection. The optimal brain community structure of each group was further explored based on the modularized Qcut algorithm, normalized mutual information (NMI), and variation of information (VI). The Jaccard index was then applied to compare the abnormalities of each brain region from different community environments between the brain function networks of NC and MDD patients. The experiments revealed several abnormal brain regions between NC and MDD, including the superior frontal gyrus, middle frontal gyrus, inferior frontal gyrus, orbital gyrus, superior temporal gyrus, middle temporal gyrus, inferior temporal gyrus, posterior superior temporal sulcus, inferior parietal gyrus, precuneus, postcentral gyrus, insular gyrus, cingulate gyrus, hippocampus and basal ganglia. Finally, a new subnetwork related to cognitive function was discovered, which was composed of the island gyrus and inferior frontal gyrus. All experiments indicated that the proposed method is useful in detecting functional brain abnormalities in MDD, and it can provide valuable insights into the diagnosis and treatment of MDD.

Ferroptosis participates in neuron damage in experimental cerebral malaria and is partially induced by activated CD8+ T cells.

Cerebral malaria is the most serious complication of malaria infection, with 26% of surviving children having neurological sequelae, which may be caused by neuron damage, but the mechanism is not clear. Ferroptosis has been reported to play an important role in neuron damage in several nervous system diseases. However, the occurrence of ferroptosis in experimental cerebral malaria (ECM) pathogenesis is still unknown. In this study, we firstly detected increased levels of malondialdehyde (MDA) and iron, which are indicators of ferroptosis, in the cerebrum of ECM mice. Some important regulators of ferroptosis, including upregulated expression of transferrin receptor 1 (TfR1) and acyl-CoA synthetase long-chain family member 4 (ACSL4), and downregulation of glutathione peroxidase 4 (GPX4) levels, were also confirmed in ECM mice. Consistently, neuron damage, which was detected in the cerebrum of ECM mice, was positively correlated with reduced GPX4 expression and furtherly rescued by administration of the ferroptosis inhibitor ferrostatin-1 (Fer-1). In addition, primary neurons were damaged by activated CD8+ T cells, an effect that was also partially rescued by Fer-1 on amyloid precursor protein expression and mitochondrial membrane potential levels in vitro. Activated CD8+ T cells were also shown to infiltrate the cerebrum of ECM mice and upregulate TfR1 expression in primary neurons, which may be an important event for inducing ferroptosis in ECM. Altogether, we show that ferroptosis contributes to neuron damage in ECM pathogenesis, and activated CD8+ T cells may be important inducers of neuronal ferroptosis. Hence, targeting ferroptosis may be a promising adjuvant therapeutic strategy for neurological sequelae in patients with cerebral malaria.

Feature discretization-based deep clustering for thyroid ultrasound image feature extraction.

Ultrasound imaging technology has the advantage of being convenient, less harmful and widely applied, making ultrasonography one of the most popular methods for disease diagnosis. With the rapid development of Computer- Aided Diagnosis (CAD) technology, the use of neural networks to analyze ultrasound images has become a popular method to improve the diagnostic efficiency of ultrasonography. Since the high cost of labeling medical images makes it difficult to train neural networks based on supervised learning, unsupervised CAD techniques without labeling have become a research trend. Most of the current unsupervised approaches focus on the reconstruction task and to some extent ignore the representational capability of models in the feature space. In this paper, we propose a Feature Discretized-based Deep Clustering (FDDC) for improving the deep clustering algorithm by introducing the theory of representation learning, which focuses on improving the representational capability of the model. There are two important strategies proposed in FDDC: 1) the global-local regular discretization method, which improves the expressiveness of the representation network by constraining the feature values; and 2) the greedy-based label reassignment method which is to reduce the loss fluctuations caused by re-clustering. Finally the experiments show that the new FDDC can achieve satisfactory results on six classification tasks, with tumor classification accuracy of 79.06% and machine classification accuracy of 96.17%, which outperforms existing unsupervised baseline methods. Furthermore, we also verify the representational capability of FDDC in feature space using visualization.

Utilization of machine learning methods for predicting surgical outcomes after total knee arthroplasty.

BACKGROUND: Predictive models could help clinicians identify risk factors that cause adverse events after total knee arthroplasty (TKA), allowing for appropriate preoperative preventive interventions and allocation of resources. METHODS: The National Inpatient Sample datasets from 2010-2014 were used to build Logistic Regression (LR), Gradient Boosting Method (GBM), Random Forest (RF), and Artificial Neural Network (ANN) predictive models for three clinically relevant outcomes after TKA-disposition at discharge, any post-surgical complications, and blood transfusion. Model performance was evaluated using the Brier scores as calibration measures, and area under the ROC curve (AUC) and F1 scores as discrimination measures. RESULTS: GBM-based predictive models were observed to have better calibration and discrimination than the other models; thus, indicating comparatively better overall performance. The Brier scores for GBM models predicting the outcomes under investigation ranged from 0.09-0.14, AUCs ranged from 79-87%, and F1-scores ranged from 41-73%. Variable importance analysis for GBM models revealed that admission month, patient location, and patient's income level were significant predictors for all the outcomes. Additionally, any post-surgical complications and blood transfusions were significantly predicted by deficiency anemias, and discharge disposition by length of stay and age groups. Notably, any post-surgical complications were also significantly predicted by the patient undergoing blood transfusion. CONCLUSIONS: The predictive abilities of the ML models were successfully demonstrated using data from the National Inpatient Sample (NIS), indicating a wide range of clinical applications for obtaining accurate prognoses of complications following orthopedic surgical procedures.

The immunomodulatory effect of microglia on ECM neuroinflammation via the PD-1/PD-L1 pathway.

INTRODUCTION: The experimental cerebral malaria (ECM) model in C57BL/6 mice infected with Plasmodium berghei ANKA (PbA) has revealed microglia are involved in the ECM immune microenvironment. However, the regulation of microglia in the ECM immune response is not clear, and there is no safe and efficient treatment clinically for the protection of the nerve cells. AIMS: To elucidate the negative regulation mechanism in the ECM brain mediated by microglia. Furthermore, to investigate protective effect of the appropriate enhancement of the PD-1/PD-L1 pathway in the brain against ECM through the intrathecal injection of the adenovirus expressing PDL1-IgG1Fc fusion protein. RESULTS: The PD-1/PD-L1 pathway was induced in the ECM brain and showed an upregulation in the microglia. Deep single-cell analysis of immune niches in the ECM brainstem indicated that the microglia showed obvious heterogeneity and activation characteristics. Intrathecal injection of recombinant adenovirus expressing PD-L1 repressed the neuroinflammation and alleviated ECM symptoms. In addition, the synergistic effect of artemisinin and intracranial immunosuppression mediated by PD-L1 was more efficacious than either treatment alone. CONCLUSION: The appropriate enhancement of the PD-1/PD-L1 pathway in the early stage of ECM has an obvious protective effect on the maintenance of immune microenvironment homeostasis in the brain. Regulating microglia and the PD-1/PD-L1 pathway could be considered as a promising approach for protection against human cerebral malaria in the future.