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Abstract Background This study aimed to analyze the effects of maxillary molar distalization using clear aligners with different intramaxillary and intermaxillary traction via the three-dimensional (3D) finite element method. Methods A 3D finite element model consisting of the maxilla, mandible, dentitions, periodontal ligaments (PDLs), attachments, and clear aligners was constructed. Five groups were established based on different traction modalities: group 1 (control group); group 2 (orthodontic mini-implants (OMIs) were implanted between the maxillary first molars and the second premolars on the buccal side); group 3 (OMIs were implanted in the infrazygomatic crest area between the maxillary first and second molars on the buccal side); group 4 (OMIs were implanted between the maxillary first molars and the second premolars on the palatal side); and group 5 (class II elastics were utilized between the maxillary canines and the mandibular first molars). OMIs were implanted 4 mm away from the alveolar crest in each experimental group. A force of 1.5 N was applied to each experimental group. The 3D displacement of the target teeth and stress distribution around the PDLs were analyzed. Results Group 4 exhibited the least amount of torque change in the upper anterior teeth and the highest displacement of the maxillary second molars. Group 3 showed smaller changes in anterior teeth torque and higher molar distalization efficiency compared to group 2. Group 5 showed adverse effects such as anterior teeth extrusion and mandibular anchorage loss. Conclusion OMIs implanted on the palatal side have advantages in preserving anterior teeth anchorage and improving the efficiency of molar distalization compared to those positioned on the buccal side. OMIs implanted in the infrazygomatic crest area between the first and second molars on the buccal side demonstrate benefits in the aforementioned aspects when compared to OMIs implanted between the first molars and the second premolars on the buccal side.

Abstract Background Malnutrition is a complication of chronic kidney disease (CKD). Whether malnutrition, assessed via the geriatric nutritional risk index (GNRI), is associated with the incidence and risk of CKD in older individuals remains unclear. Methods Data from the National Health and Nutrition Examination Survey and the UK Biobank database were used. Older participants over 60 years old with available data for GNRI assessment and CKD diagnosis were enrolled. Logistic regression models and Cox regression models were used to assess associations between the geriatric nutritional risk index and the risk of and mortality associated with CKD. Results This study enrolled 13,162 participants from the NHANES and 66,326 participants from the UK Biobank. We identified 6,135 and 16,662 CKD patients in the NHANES and UK Biobank, respectively, with the majority being male (74% in the NHANES and 52% in the UK Biobank). The average age of CKD patients was 72.3 (SD 7.2) years in the NHANES and 64.9 (SD 2.9) years in the UK Biobank. The median follow-up times of older CKD patients were 81 months and 162 months in the NHANES and UK Biobank, respectively. According to the cross-sectional analysis, individuals with a lower GNRI had an increased likelihood of having CKD, with odds ratios of 1.38 (95% CI: 1.05–1.80, P = 0.020) in the NHANES and 2.35 (95% CI: 1.89–2.92, P

Abstract Background Mesenchymal stem cells (MSCs) are multipotent stem cells that are under investigation for use in clinical trials because they are capable of self-renewal and differentiating into different cell types under defined conditions. Nonetheless, the therapeutic effects of MSCs have been constrained by low engraftment rates, cell fusion, and cell survival. Various strategies have been explored to improve the therapeutic efficacy of MSCs, with platelet-derived growth factor (PDGF)-BB emerging as a promising candidate. To enhance our comprehension of the impact of PDGF-BB on the gene expression profile and chromosomal accessibility of MSCs, RNA-sequencing and analysis of chromatin accessibility profiles were conducted on three human primary MSCs in culture, both with and without stimulation by PDGF-BB. Results Integrative analysis of gene expression and chromatin accessibility demonstrated that PDGF-BB treatment modified the chromatin accessibility landscape, marking regions for activation or repression through the AP-1 family transcription factors TEAD, CEBP, and RUNX2. These changes in AP-1 transcription factor expression, in turn, led to cell proliferation and differentiation potential towards osteoblasts, adipocytes, or chondrocytes. The degree of MSC differentiation varies among cells isolated from different donors. The presence of an enrichment of exosome-related genes is also noted among all the differentially expressed genes. Conclusions In conclusion, the observed changes in AP-1 transcription factor expression not only induced cellular proliferation and differentiation, but also revealed variations in the degree of MSC differentiation based on donor-specific differences. Moreover, the enrichment of exosome-related genes among differentially expressed genes suggests a potential significant role for PDGF-BB in facilitating intercellular communication.

Introduction Gingivitis is a prevalent complication in adolescents undergoing fixed orthodontic treatments. However, changes in the supragingival microbiome associated with gingivitis and the impact of Candida albicans remain elusive. Therefore, we investigated supragingival microbiome discrepancy and C. albicans colonization in adolescent orthodontic patients with gingivitis.Methods Dental plaques were collected from 30 gingivitis patients and 24 healthy adolescents, all undergoing fixed orthodontic treatment. The supragingival microbiome composition was analyzed using 16S rRNA sequencing. C. albicans colonization was determined using fungal culture and real-time quantitative polymerase chain reaction.Results Our analysis revealed significantly heightened microbial diversity in the Gingivitis group. Notably, patients with gingivitis exhibited an enrichment of periodontal pathogens, such as Saccharibacteria (TM7) [G-1], Selenomonas, Actinomyces dentalis, and Selenomonas sputigena. Additionally, 33% of the gingivitis patients tested positive for C. albicans, exhibiting significantly elevated levels of absolute abundance, while all healthy patients tested negative. Significant differences in microbial composition were also noted between C. albicans-positive and -negative samples in the Gingivitis group.Conclusion Significant disparities were observed in the supragingival microbiome of adolescent orthodontic patients with and without gingivitis. The presence of C. albicans in the supragingival plaque may alter the microbiome composition and potentially contribute to gingivitis pathogenesis.

In the field of breast cancer treatment, the immunotherapy involving natural killer (NK) cells is increasingly highlighting its distinct potential and significance. Members of the interleukin (IL) family play pivotal regulatory roles in the growth, differentiation, survival, and apoptosis of NK cells, and are central to their anti-tumor activity. These cytokines enhance the ability of NK cells to recognize and eliminate tumor cells by binding to specific receptors and activating downstream signaling pathways. Furthermore, interleukins do not function in isolation; the synergistic or antagonistic interactions between different interleukins can drive NK cells toward various functional pathways, ultimately leading to diverse outcomes for breast cancer patients. This paper reviews the intricate relationship between NK cells and interleukins, particularly within the breast cancer tumor microenvironment. Additionally, we summarize the latest clinical studies and advancements in NK cell therapy for breast cancer, along with the potential applications of interleukin signaling in these therapies. In conclusion, this article underscores the critical role of NK cells and interleukin signaling in breast cancer treatment, providing valuable insights and a significant reference for future research and clinical practice.

Background: Paraquat (PQ) is a widely used herbicide that poisons human by accident or intentional ingestion. PQ poisoning causes systemic inflammatory response syndrome (SIRS) resulting in acute lung injury (ALI) with an extremely high mortality rate. Blood trematode Schistosoma japonicum-produced cystatin (Sj-Cys) is a strong immunomodulatory protein that has been experimentally used to treat inflammation related diseases. In this study, Sj-Cys recombinant protein (rSj-Cys) was used to treat PQ-induced lung injury and the immunological mechanism underlying the therapeutic effect was investigated. Methods: PQ-induced acute lung injury mouse model was established by intraperitoneally injection of 20 mg/kg of paraquat. The poisoned mice were treated with rSj-Cys and the survival rate was observed up to 7 days compared with the group without treatment. The pathological changes of PQ-induced lung injury were observed by examining the histochemical sections of affected lung tissue and the wet to dry ratio of lung as a parameter for inflammation and edema. The levels of the inflammation related cytokines IL-6 and TNF-α and regulatory cytokines IL-10 and TGF-β were measured in sera and in affected lung tissue using ELISA and their mRNA levels in lung tissue using RT-PCR. The macrophages expressing iNOS were determined as M1 and those expressing Arg-1 as M2 macrophages. The effect of rSj-Cys on the transformation of inflammatory M1 to regulatory M2 macrophages was measured in affected lung tissue in vivo (EKISA and RT-PCR) and in MH-S cell line in vitro (flow cytometry). The expression levels of TLR2 and MyD88 in affected lung tissue were also measured to determine their role in the therapy of rSj-Cys on PQ-induced lung injury. Result: We identified that treatment with rSj-Cys significantly improved the survival rate of mice with PQ-induced lung injury from 30 % (untreated) to 80 %, reduced the pathological damage of poisoning lung tissue, associated with significantly reduced levels of proinflammatory cytokines (IL-6 from 1490 to 590 pg/ml, TNF-α from 260 to 150 pg/ml) and increased regulatory cytokines (IL-10 from360 to 550 pg/ml, and TGF-β from 220 to 410 pg/ml) in both sera (proteins) and affected lung tissue (proteins and mRNAs). The polarization of macrophages from M1to M2 type was found to be involved in the therapeutic effect of rSj-Cys on the PQ-induced acute lung injury, possibly through inhibiting TLR2/MyD88 signaling pathway. Conclusions: Our study demonstrated the therapeutic effect of rSj-Cys on PQ poisoning caused acute lung injury by inducing M2 macrophage polarization through inhibiting TLR2/MyD88 signaling pathway. The finding in this study provides an alternative approach for the treatment of PQ poisoning and other inflammatory diseases.

Abstract Background In the context of breast cancer (BC), the correlation between lymphocytes and clinical outcomes, along with treatment response, has garnered attention. Despite this, few investigations have delved into the interplay among distinct peripheral blood lymphocyte (PBL) types, immune attributes, and their clinical implications within the BC landscape. Methods The primary objective of this study was to scrutinize the baseline status of PBL subsets in patients with primary BC, track their dynamic changes throughout treatment, and ascertain their interrelation with prognosis. Flow cytometry was employed to analyse PBLs from a cohort of 74 BC patients. Results Our analysis revealed that baseline levels of Treg and PD-L1 + T cells were lower in BC patients compared to the reference values. Notably, a disparity in baseline PD-L1 + T cell levels surfaced between patients who underwent adjuvant therapy and those subjected to neoadjuvant therapy (NAT). Furthermore, a meticulous evaluation of PBL subsets before and after treatment underscored discernible alterations in 324 + T cells and CD19 + CD32 + B cells over the course of therapy. Strikingly, heightened CD4 + T cell levels at baseline were linked to enhanced event-free survival (EFS) (p = 0.02) and a robust response to chemotherapy. Conclusions These results indicate that PBLs may serve as a significant marker to assess the immune status of BC patients, and therapy has the potential to modify patient immune profiles. In addition, peripheral blood CD4 + T cell levels may serve as promising biomarkers for diagnosis and prognosis in future studies of BC.

Summary: Most cells in solid tumors are exposed to oxygen levels between 0.5% and 5%. We developed an approach that allows collection, processing, and evaluation of cancer and non-cancer cells under physioxia, while preventing exposure to ambient air. This aided comparison of baseline and drug-induced changes in signaling pathways under physioxia and ambient oxygen. Using tumor cells from transgenic models of breast cancer and cells from breast tissues of clinically breast cancer-free women, we demonstrate oxygen-dependent differences in cell preference for epidermal growth factor receptor (EGFR) or platelet-derived growth factor receptor beta (PDGFRβ) signaling. Physioxia caused PDGFRβ-mediated activation of AKT and extracellular regulated kinase (ERK) that reduced sensitivity to EGFR and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) inhibition and maintained PDGFRβ+ epithelial-mesenchymal hybrid cells with potential cancer stem cell (CSC) properties. Cells in ambient air displayed differential EGFR activation and were more sensitive to targeted therapies. Our data emphasize the importance of oxygen considerations in preclinical cancer research to identify effective drug targets and develop combination therapy regimens.

Breast cancer (BC) stands out as the cancer with the highest incidence of morbidity and mortality among women worldwide, and its incidence rate is currently trending upwards. Improving the efficiency of breast cancer diagnosis and treatment is crucial, as it can effectively reduce the disease burden. Circulating tumor DNA (ctDNA) originates from the release of tumor cells and plays a pivotal role in the occurrence, development, and metastasis of breast cancer. In recent years, the widespread application of high-throughput analytical technology has made ctDNA a promising biomarker for early cancer detection, monitoring minimal residual disease, early recurrence monitoring, and predicting treatment outcomes. ctDNA-based approaches can effectively compensate for the shortcomings of traditional screening and monitoring methods, which fail to provide real-time information and prospective guidance for breast cancer diagnosis and treatment. This review summarizes the applications of ctDNA in various aspects of breast cancer, including screening, diagnosis, prognosis, treatment, and follow-up. It highlights the current research status in this field and emphasizes the potential for future large-scale clinical applications of ctDNA-based approaches.

Given the importance of peroxisome proliferator-activated receptor (PPAR)-gamma in epidermal inflammation and carcinogenesis, we analyzed the transcriptomic changes observed in epidermal PPARγ-deficient mice (Pparg-/-epi). A gene set enrichment analysis revealed a close association with epithelial malignancy, inflammatory cell chemotaxis, and cell survival. Single-cell sequencing of Pparg-/-epi mice verified changes to the stromal compartment, including increased inflammatory cell infiltrates, particularly neutrophils, and an increase in fibroblasts expressing myofibroblast marker genes. A comparison of transcriptomic data from Pparg-/-epi and publicly available human and/or mouse actinic keratoses (AKs) and cutaneous squamous cell carcinomas (SCCs) revealed a strong correlation between the datasets. Importantly, PPAR signaling was the top common inhibited canonical pathway in AKs and SCCs. Both AKs and SCCs also had significantly reduced PPARG expression and PPARγ activity z-scores. Smaller reductions in PPARA expression and PPARα activity and increased PPARD expression but reduced PPARδ activation were also observed. Reduced PPAR activity was also associated with reduced PPARα/RXRα activity, while LPS/IL1-mediated inhibition of RXR activity was significantly activated in the tumor datasets. Notably, these changes were not observed in normal sun-exposed skin relative to non-exposed skin. Finally, Ppara and Pparg were heavily expressed in sebocytes, while Ppard was highly expressed in myofibroblasts, suggesting that PPARδ has a role in myofibroblast differentiation. In conclusion, these data provide strong evidence that PPARγ and possibly PPARα represent key tumor suppressors by acting as master inhibitors of the inflammatory changes found in AKs and SCCs.

Metasurfaces can flexibly manipulate electromagnetic waves by engineering subwavelength structures, which have attracted enormous attention in holography, cloaking, and functional multiplexing. For structures with n-fold (n > 2) rotational symmetry, they have been utilized to realize broadband and high-efficiency wavefront manipulation with generalized Pancharatnam–Berry phase, whereas spin-selective wavefront manipulation is still a challenge limited by their symmetrical spin–orbit interactions. Here, we demonstrate the spin-selective wavefront manipulations with generalized Pancharatnam–Berry phase in the range of 560–660 nm with a metal–insulator–metal metasurface consisting of the chiral C3 logarithmic spiral nanostructures. As a proof of concept, two deflectors and a bifocal metalens are designed. This configuration may provide a platform for various applications in polarimetry, polarization-selective images, and nonlinear optical responses.

Abstract Ferroptosis is a recently recognized form of regulated cell death, characterized by iron-dependent accumulation of lipid peroxidation. Ample evidence has depicted that ferroptosis plays an essential role in the cause or consequence of human diseases, including cancer, neurodegenerative disease and acute kidney injury. However, the exact role and underlying mechanism of ferroptosis in fibrotic kidney remain unknown. Acyl-CoA synthetase long-chain family member 4 (ACSL4) has been demonstrated as an essential component in ferroptosis execution by shaping lipid composition. In this study, we aim to discuss the potential role and underlying mechanism of ACSL4-mediated ferroptosis of tubular epithelial cells (TECs) during renal fibrosis. The unbiased gene expression studies showed that ACSL4 expression was tightly associated with decreased renal function and the progression of renal fibrosis. To explore the role of ACSL4 in fibrotic kidney, ACSL4 specific inhibitor rosiglitazone (ROSI) was used to disturb the high expression of ACSL4 in TECs induced by TGF-β, unilateral ureteral obstruction (UUO) and fatty acid (FA)-modeled mice in vivo, and ACSL4 siRNA was used to knockdown ACSL4 in TGF-β-induced HK2 cells in vitro. The results demonstrated that inhibition and knockdown of ACSL4 effectively attenuated the occurrence of ferroptosis in TECs and alleviated the interstitial fibrotic response. In addition, the expression of various profibrotic cytokines all decreased after ROSI-treated in vivo and in vitro. Further investigation showed that inhibition of ACSL4 obviously attenuates the progression of renal fibrosis by reducing the proferroptotic precursors arachidonic acid- and adrenic acid- containing phosphatidylethanolamine (AA-PE and AdA-PE). In conclusion, these results suggest ACSL4 is essential for tubular ferroptotic death during kidney fibrosis development and ACSL4 inhibition is a viable therapeutic approach to preventing fibrotic kidney diseases.

Abstract Accurate segmentation of brain gliomas (BG) is a crucial and challenging task for effective treatment planning in BG therapy. This study presents the weight loss function and dropout U‐Net with ConvNeXt block (WD‐UNeXt), which precisely segments BG from few shot MRI. The ConvNeXt block, which comprises the main body of the network, is a structure that can extract more detailed features from images. The weight loss function addresses the issue of category imbalance, thereby enhancing the network's ability to achieve more precise segmentation. The training set of BraTS2019 was used to train the network and apply it to test data. Dice similarity coefficient (DSC), sensitivity (Sen), specificity (Spec) and Hausdorff distance (HD) were used to assess the performance of the method. The experimental results demonstrate that the DSC of whole tumour, tumour core and enhancing tumour reached 0.934, 0.911 and 0.851, respectively. Sen of the sub‐regions achieved 0.922, 0.911 and 0.867. Spec and HD reached 1.000, 1.000, 1.000 and 3.224, 2.990, 2.844, respectively. Compared with the performance of state‐of‐the‐art methods, the DSC and HD of WD‐UNeXt were improved to varying degrees. Therefore, this method has considerable potential for the segmentation of BG.

Abstract Background Microbial dysbiosis has emerged as an important element in the development and progression of various cancers, including breast cancer. However, the microbial composition of the breast from healthy individuals, even relative to risk of developing breast cancer, remains unclear. Here, we performed a comprehensive analysis of the microbiota of the normal breast tissue, which was analyzed in relation to the microbial composition of the tumor and adjacent normal tissue. Methods The study cohorts included 403 cancer-free women (who donated normal breast tissue cores) and 76 breast cancer patients (who donated tumor and/or adjacent normal tissue samples). Microbiome profiling was obtained by sequencing the nine hypervariable regions of the 16S rRNA gene (V1V2, V2V3, V3V4, V4V5, V5V7, and V7V9). Transcriptome analysis was also performed on 190 normal breast tissue samples. Breast cancer risk score was assessed using the Tyrer-Cuzick risk model. Results The V1V2 amplicon sequencing resulted more suitable for the analysis of the normal breast microbiome and identified Lactobacillaceae (Firmicutes phylum), Acetobacterraceae, and Xanthomonadaceae (both Proteobacteria phylum) as the most abundant families in the normal breast. However, Ralstonia (Proteobacteria phylum) was more abundant in both breast tumors and histologically normal tissues adjacent to malignant tumors. We also conducted a correlation analysis between the microbiome and known breast cancer risk factors. Abundances of the bacterial taxa Acetotobacter aceti, Lactobacillus vini, Lactobacillus paracasei, and Xanthonomas sp. were associated with age (p

Abstract The establishment of left–right patterning in mice occurs at a transient structure called the embryonic node or left–right organizer (LRO). Previous analysis of the LRO has proven challenging due to the small cell number and transient nature of this structure. Here, we seek to overcome these difficulties to define the transcriptome of the LRO. Specifically, we used single cell RNA sequencing of 0–1 somite embryos to identify LRO enriched genes which were compared to bulk RNA sequencing of LRO cells isolated by fluorescent activated cell sorting. Gene ontology analysis indicated an enrichment of genes associated with cilia and laterality terms. Furthermore, comparison to previously identified LRO genes identified 127 novel LRO genes, including Ttll3, Syne1 and Sparcl1, for which the expression patterns were validated using whole mount in situ hybridization. This list of novel LRO genes will be a useful resource for further studies on LRO morphogenesis, the establishment of laterality and the genetic causes of heterotaxy.

In this article, a novel ensemble framework of improved siamese network (SN) is proposed to address the small sample issue that deep learning approaches encounter, as well as to enhance the precision of pipeline leakage detection (PLD) under small sample conditions. Firstly, training samples are input in pairs to the feature extraction network, and a combination of one-dimensional convolution neural network (1DCNN) and long short-term memory (LSTM) network is introduced to extract features of the time-series data, thus enhancing the effectiveness and robustness of feature extraction. Then, an improved relational metric network is designed to measure the similarity of features, to further strengthen the discriminative nature of the whole framework. In addition, the framework has been augmented with a classification network that can be used directly for PLD. The proposed SN-1DCNN-LSTM framework not only increases the number of training samples from the side, but also fully exploits the similarity information and data features between samples, overcoming the problem of instability and overfitting of deep learning models under small sample conditions. Finally, the experimental results verify the validity and superiority of the method under small sample conditions.

ObjectiveBempedoic acid, an innovative oral medication, has garnered significant interest in recent times due to its potential as a therapeutic intervention for hypercholesterolemia. Nonetheless, the outcomes of the initial investigations might have been more definitive and coherent. Our objective was to perform a quantitative meta-analysis in order to evaluate bempedoic acid's safety and effectiveness.MethodsA search was conducted on ClinicalTrials.gov, and PubMed from the time of inception until September 28, 2023. Randomized controlled trials comparing the safety and efficacy of bempedoic acid among patients with statin intolerance and those without were included in our analysis. The trial outcomes were summarized using a random effects model and were provided as mean differences or odds ratios (ORs) with a confidence interval of 95%. Additionally, trial heterogeneity and the possibility of bias were evaluated and investigated.ResultsBempedoic acid treatment reduced low-density lipoprotein cholesterol levels more than placebo (mean difference -2.97%, 95% CI -5.89% to -0.05%), according to a pooled analysis of 16 eligible trials. The risk of death (OR 1.18, 95% CI 0.70 to 1.98) and muscle-associated occurrences (OR 1.00, 95% CI 0.77 to 1.31) was not impacted by bempedoic acid. In contrast, discontinuation of treatment was more frequently caused by adverse events in the bempedoic acid group (OR 1.13, 95% CI 1.01 to 1.27).ConclusionsIn patients with statin intolerance as well as those without, bempedoic acid is a safe and efficacious lipid-lowering agent, according to findings from randomized controlled trials.

The cavity form of complex microcavity lasers predominantly relies on disordered structures, whether found in nature or artificially prepared. These structures, characterized by disorder, facilitate random lasing through the feedback effect of the cavity boundary and the internal scattering medium via various mechanisms. In this paper, we report on a random fiber laser employing a disordered scattering cladding medium affixed to the inner cladding of a hollow-core fiber. The internal flowing liquid gain establishes a stable liquid-core waveguide environment, enabling long-term directional coupling output for random laser emission. Through theoretical analysis and experimental validation, we demonstrate that controlling the disorder at the cavity boundary allows liquid-core fiber random microcavities to exhibit random lasing output with different mechanisms. This provides a broad platform for in-depth research into the generation and control of complex microcavity lasers, as well as the detection of scattered matter within micro- and nanostructures.

Noni fruits have gained considerable popularity as dietary supplements. However, the major constituents, the laxative activity, and the toxicity of Noni fruit remains still unknown. The purpose of the present study was, therefore, to analyze the constituents of methanol extract of Noni fruit by UPLC-MS, and further evaluate laxative activity and safety aspects of this Noni fruit-derived products in mice. UPLC-MS analysis identified eleven major constituents from this Noni fruit extract. Administration of this extract obviously shortened the time of first fecal excrement, significantly increased the total number and the weight of stools, and remarkably restored the intestinal transit to normal level in the constipated mice, with low toxicity to liver and kidney, and meanwhile, the abundance, composition, and function of gut microbiota remained homeostasis. These results revealed the laxative activity of the methanol extract of Noni fruit with low toxicity and no influence on gut microbiota.

BackgroundGuillain-Barré syndrome (GBS) is a medical condition characterized by the immune system of the body attacking the peripheral nerves, including those in the spinal nerve roots, peripheral nerves, and cranial nerves. It can cause limb weakness, abnormal sensations, and facial nerve paralysis. Some studies have reported clinical cases associated with the severe coronavirus disease 2019 (COVID-19) and GBS, but how COVID-19 affects GBS is unclear.MethodsWe utilized bioinformatics techniques to explore the potential genetic connection between COVID-19 and GBS. Differential expression of genes (DEGs) related to COVID-19 and GBS was collected from the Gene Expression Omnibus (GEO) database. By taking the intersection, we obtained shared DEGs for COVID-19 and GBS. Subsequently, we utilized bioinformatics analysis tools to analyze common DEGs, conducting functional enrichment analysis and constructing Protein–protein interaction networks (PPI), Transcription factors (TF) -gene networks, and TF-miRNA networks. Finally, we validated our findings by constructing the Receiver Operating Characteristic (ROC) curves.ResultsThis study utilizes bioinformatics tools for the first time to investigate the close genetic relationship between COVID-19 and GBS. CAMP, LTF, DEFA1B, SAMD9, GBP1, DDX60, DEFA4, and OAS3 are identified as the most significant interacting genes between COVID-19 and GBS. In addition, the signaling pathway of NOD-like receptors is believed to be essential in the link between COVID-19 and GBS.

In this paper, a recursive filtering problem is analyzed for nonlinear systems with sensor saturation under duty cycle scheduling (DCS). The sensor saturation is taken into account to describe practical engineering better. The DCS is introduced to conserve energy by alternating sensor nodes between active and dormant states. The considered problem aims to design a collaboration-prediction-based recursive filtering algorithm for nonlinear systems with sensor saturation such that, under the sparse measurements due to DCS, satisfactory filtering performance is guaranteed. By solving a set of matrix difference equations, the upper bound on the filtering error covariance is first obtained, and then the gain matrix of the filter that minimizes the upper limit is calculated. In addition, the boundedness of the upper bound of the filtering error covariance is analyzed. Finally, the effectiveness of the proposed collaboration-prediction-based recursive filtering algorithm is verified by the simulation example.

Oral administration of antigen induces regulatory T cells (Treg) that can not only control local immune responses in the small intestine, but also traffic to the central immune system to deliver systemic suppression. Employing murine models of the inherited bleeding disorder hemophilia, we find that oral antigen administration induces three CD4+ Treg subsets, namely FoxP3+LAP-, FoxP3+LAP+, and FoxP3-LAP+. These T cells act in concert to suppress systemic antibody production induced by therapeutic protein administration. Whilst both FoxP3+LAP+ and FoxP3-LAP+ CD4+ T cells express membrane-bound TGF-β (latency associated peptide, LAP), phenotypic, functional, and single cell transcriptomic analyses reveal distinct characteristics in the two subsets. As judged by an increase in IL-2Rα and TCR signaling, elevated expression of co-inhibitory receptor molecules and upregulation of the TGFβ and IL-10 signaling pathways, FoxP3+LAP+ cells are an activated form of FoxP3+LAP- Treg. Whereas FoxP3-LAP+ cells express low levels of genes involved in TCR signaling or co-stimulation, engagement of the AP-1 complex members Jun/Fos and Atf3 is most prominent, consistent with potent IL-10 production. Single cell transcriptomic analysis further reveals that engagement of the Jun/Fos transcription factors is requisite for mediating TGFβ expression. This can occur via an Il2ra dependent or independent process in FoxP3+LAP+ or FoxP3-LAP+ cells respectively. Surprisingly, both FoxP3+LAP+ and FoxP3-LAP+ cells potently suppress and induce FoxP3 expression in CD4+ conventional T cells. In this process, FoxP3-LAP+ cells may themselves convert to FoxP3+ Treg. We conclude that orally induced suppression is dependent on multiple regulatory cell types with complementary and interconnected roles.

BackgroundOrigin recognition complex 6 (ORC6) is one of the six highly conserved subunit proteins required for DNA replication and is essential for maintaining genome stability during cell division. Recent research shows that ORC6 regulates the advancement of multiple cancers; however, it remains unclear what regulatory impact it has on the tumor immune microenvironment.MethodsUnpaired Wilcoxon rank sum and signed rank tests were used to analyze the differences in the expression of ORC6 in normal tissues and corresponding tumor tissues. Multiple online databases have evaluated the genetic alterations, protein expression and localization, and clinical relevance of ORC6. To evaluate the potential prognostic impact and diagnostic significance of ORC6 expression, we carried out log-rank, univariate Cox regression, and receiver operating characteristic curve analysis. The ICGC-LIRI-JP cohort, CGGA-301 cohort, CGGA-325 cohort, CGGA-693 cohort, and GSE13041 cohort were used for external validation of the study findings. The associations between ORC6 expression and immune cell infiltration, immune checkpoint expression, and immunotherapy cohorts was further analyzed. To explore the functional and signaling pathways related to ORC6 expression, gene set enrichment analysis was performed. To clarify the expression and function of ORC6 in hepatocellular carcinoma (LIHC) and glioma, we conducted in vitro experiments.ResultsExpression of ORC6 is upregulated in the majority of cancer types and is associated with poor patient prognosis, notably in cases of LIHC and gliomas. In addition, ORC6 may be involved in multiple signaling pathways related to cancer progression and immune regulation. High expression of ORC6 correlates with an immunosuppressive state in the tumor microenvironment. The results of further immunotherapy cohort analysis suggested that patients in the ORC6 high-expression group benefited from immunotherapy. Inhibiting ORC6 expression suppressed the proliferative and migratory abilities of LIHC and glioma cells.ConclusionHigh expression of ORC6 may be used as a biomarker to predict the poor prognosis of most tumor patients. The high expression of ORC6 may be involved in the regulation of the tumor immunosuppressive environment, and it is expected to become a molecular target for inhibiting tumor progression.

Summary: Lysine succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the tricarboxylic acid cycle. Deficiency of succinyl-CoA synthetase (SCS), the tricarboxylic acid cycle enzyme catalyzing the interconversion of succinyl-CoA to succinate, results in mitochondrial encephalomyopathy in humans. This report presents a conditional forebrain-specific knockout (KO) mouse model of Sucla2, the gene encoding the ATP-specific beta isoform of SCS, resulting in postnatal deficiency of the entire SCS complex. Results demonstrate that accumulation of succinyl-CoA in the absence of SCS leads to hypersuccinylation within the murine cerebral cortex. Specifically, increased succinylation is associated with functionally significant reduced activity of respiratory chain complex I and widescale alterations in chromatin landscape and gene expression. Integrative analysis of the transcriptomic data also reveals perturbations in regulatory networks of neuronal transcription in the KO forebrain. Together, these findings provide evidence that protein succinylation plays a significant role in the pathogenesis of SCS deficiency.

Abstract Osteocytes act within a hypoxic environment to control key steps in bone formation. FGF23, a critical phosphate-regulating hormone, is stimulated by low oxygen/iron in acute and chronic diseases, however the molecular mechanisms directing this process remain unclear. Our goal was to identify the osteocyte factors responsible for FGF23 production driven by changes in oxygen/iron utilization. Hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHI) which stabilize HIF transcription factors, increased Fgf23 in normal mice, as well as in osteocyte-like cells; in mice with conditional osteocyte Fgf23 deletion, circulating iFGF23 was suppressed. An inducible MSC cell line (‘MPC2’) underwent FG-4592 treatment and ATACseq/RNAseq, and demonstrated that differentiated osteocytes significantly increased HIF genomic accessibility versus progenitor cells. Integrative genomics also revealed increased prolyl hydroxylase Egln1 (Phd2) chromatin accessibility and expression, which was positively associated with osteocyte differentiation. In mice with chronic kidney disease (CKD), Phd1-3 enzymes were suppressed, consistent with FGF23 upregulation in this model. Conditional loss of Phd2 from osteocytes in vivo resulted in upregulated Fgf23, in line with our findings that the MPC2 cell line lacking Phd2 (CRISPR Phd2-KO cells) constitutively activated Fgf23 that was abolished by HIF1α blockade. In vitro, Phd2-KO cells lost iron-mediated suppression of Fgf23 and this activity was not compensated for by Phd1 or −3. In sum, osteocytes become adapted to oxygen/iron sensing during differentiation and are directly sensitive to bioavailable iron. Further, Phd2 is a critical mediator of osteocyte FGF23 production, thus our collective studies may provide new therapeutic targets for skeletal diseases involving disturbed oxygen/iron sensing.

Satellite galaxies can be used to indicate the dynamic mass of galaxy groups and clusters. In this study, we apply the axisymmetric Jeans Anisotropic Multi-Gaussian Expansion ( JAM ) modeling to satellite galaxies in 28 galaxy clusters selected from the TNG300-1 simulation with halo masses of ${\mathrm{log}}_{10}{M}_{200}/{M}_{\odot }\gt 14.3$ . If using true bound satellites as tracers, the best constrained total mass within the half-mass radius of satellites, M (< r _half ), and the virial mass, M _200 , have average biases of −0.01 and 0.03 dex, with average scatters of 0.11 dex and 0.15 dex. If selecting companions in the redshift space with a line-of-sight depth of 2000 km s ^−1 , the biases are −0.06 and 0.01 dex, while the scatters are 0.12 and 0.18 dex for M (< r _half ) and M _200 . By comparing the best-fitting and actual density profiles, we find that ∼29% of the best-fitting density profiles show very good agreement with the truth, ∼32% display over/underestimates at most of the radial range with biased M (< r _half ), and 39% show under/overestimates in central regions and over/underestimates in the outskirts, with good constraints on M (< r _half ); yet most of the best constraints are still consistent with the true profiles within 1 σ statistical uncertainties for the three circumstances. Using a mock DESI Bright Galaxy Survey catalog with the effect of fiber incompleteness, we find DESI fiber assignments and the choice of flux limits barely modify the velocity dispersion profiles and are thus unlikely to affect the dynamical modeling outcomes. Our results show that with current and future deep spectroscopic surveys, JAM can be a powerful tool to constrain the underlying density profiles of individual massive galaxy clusters.

Magnification serves as an independent and complementary gravitational lensing measurement to shear. We develop a novel method to achieve an accurate and robust magnification measurement around BOSS CMASS galaxies across physical scales of 0.016 h ^−1 Mpc < r _p < 10 h ^−1 Mpc. We first measure the excess total flux density δ M of the source galaxies in the deep DECaLS photometric catalog that are lensed by CMASS galaxies. We convert δ M to magnification μ by establishing the δ μ – δ M relation using a deeper photometric sample. By comparing magnification measurements in three optical bands ( grz ), we constrain the dust attenuation curve and its radial distribution, discovering a steep attenuation curve in the circumgalactic medium of CMASS galaxies. We further compare dust-corrected magnification measurements to model predictions from high-resolution dark matter-only (DMO) simulations in Wilkinson Microwave Anisotropy Probe (WMAP) and Planck cosmologies, as well as the hydrodynamic simulation TNG300-1 , using precise galaxy–halo connections from the Photometric objects Around Cosmic webs method and the accurate ray-tracing algorithm P3MLens . For r _p > 70 h ^−1 kpc, our magnification measurements are in good agreement with both WMAP and Planck cosmologies, resulting in an estimation of the matter fluctuation amplitude of S _8 = 0.816 ± 0.024. However, at r _p < 70 h ^−1 kpc, we observe an excess magnification signal, which is higher than the DMO model in Planck cosmology at 2.8 σ and would be exacerbated if significant baryon feedback is included. Implications of the potential small scale discrepancy for the nature of dark matter and for the processes governing galaxy formation are discussed.

The roles that mass and environment play in galaxy quenching are still under debate. Leveraging the Photometric objects Around Cosmic webs method, we analyze the excess surface distribution ${\bar{n}}_{2}{w}_{{\rm{p}}}({r}_{{\rm{p}}})$ of photometric galaxies in different colors (rest-frame u − r ) within the stellar mass range of 10 ^9.0 ∼ 10 ^11.0 M _⊙ around spectroscopic massive central galaxies (10 ^10.9 ∼ 10 ^11.7 M _⊙ ) at the redshift interval of 0 < z _s < 0.7, utilizing data from the Hyper Suprime-Cam Subaru Strategic Program and the spectroscopic samples of Slogan Digital Sky Survey (i.e., Main, LOWZ, and CMASS samples). We find that both mass and environmental quenching contribute to the evolution of companion galaxies. To isolate the environmental effect, we quantify the quenched fraction excess (QFE) of companion galaxies encircling massive central galaxies within 0.01 h ^−1 Mpc < r _p < 20 h ^−1 Mpc, representing the surplus quenched fraction relative to the average. We find that the high-density halo environment affects star formation quenching up to about three times the virial radius, and this effect becomes stronger at lower redshift. We also find that even after being scaled by the virial radius, the environmental quenching efficiency is higher for more massive halos or for companion galaxies of higher stellar mass, though the trends are quite weak. We present a fitting formula that comprehensively captures the QFE across central and companion stellar mass bins, halo-centric distance bins, and redshift bins, offering a valuable tool for constraining galaxy formation models. Furthermore, we have made a quantitative comparison with IllustrisTNG that underscores some important differences, particularly in the excessive quenching of low-mass companion galaxies (

The Photometric objects Around Cosmic webs (PAC) approach developed in Xu et al. has the advantage of making full use of spectroscopic and deeper photometric surveys. With the merits of PAC, the excess surface density ${\bar{n}}_{2}{w}_{{\rm{p}}}$ of neighboring galaxies can be measured down to stellar mass 10 ^10.80 M _⊙ around quasars at redshift 0.8 < z _s < 1.0, with the data from the Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey and the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys. We find that ${\bar{n}}_{2}{w}_{{\rm{p}}}$ generally increases quite steeply with the decrease of the separation. Using the subhalo abundance-matching method, we can accurately model the ${\bar{n}}_{2}{w}_{{\rm{p}}}$ both on small and large scales. We show that the steep increase of ${\bar{n}}_{2}{w}_{{\rm{p}}}$ toward the quasars requires that a large fraction ${f}_{\mathrm{sate}}={0.29}_{-0.06}^{+0.05}$ of quasars should be satellites in massive halos, and we find that this fraction measurement is insensitive to the assumptions of our modeling. This high satellite fraction indicates that the subhalos have nearly the same probability of hosting quasars as the halos for the same (infall) halo mass and that the large-scale environment has negligible effect on the quasar activity. We show that even with this high satellite fraction, each massive halo on average does not host more than one satellite quasar, due to the sparsity of quasars.

Galactic conformity is the phenomenon whereby a galaxy of a certain physical property is correlated with its neighbors of the same property, implying a possible causal relationship. The observed auto correlations of emission-line galaxies (ELGs) from the highly complete DESI One-Percent Survey exhibit a strong clustering signal on small scales, providing clear evidence for the conformity effect of ELGs. Building upon the original subhalo abundance-matching (SHAM) method developed by Gao et al., we propose a concise conformity model to improve the ELG–halo connection. In this model, the number of satellite ELGs is boosted by a factor of ∼5 in the halos whose central galaxies are ELGs. We show that the mean ELG satellite number in such central halos is still smaller than 1 and that the model does not significantly increase the overall satellite fraction. With this model, we can well recover the ELG auto correlations to the smallest scales explored with the current data (i.e., r _p > 0.03 Mpc h ^−1 in real space and at s > 0.3 Mpc h ^−1 in redshift space), while the cross correlations between luminous red galaxies and ELGs are nearly unchanged. Although our SHAM model has only eight parameters, we further verify that it can accurately describe the ELG clustering in the entire redshift range from z = 0.8 to 1.6. We therefore expect that this method can be used to generate high-quality ELG lightcone mocks for DESI.

The role of IL-9 in the tumor microenvironment and its effects on macrophages remains unclear. Here, the authors show that IL-9 promotes the expansion of pulmonary macrophages and that targeting the IL-9R/arginase 1 axis restricts tumor growth, thus identifying this cytokine pathway as a potential therapeutic target.

Summary: Skeletal muscle dysfunction or reprogramming due to the effects of the cancer secretome is observed in multiple malignancies. Although mouse models are routinely used to study skeletal muscle defects in cancer, because of species specificity of certain cytokines/chemokines in the secretome, a human model system is required. Here, we establish simplified multiple skeletal muscle stem cell lines (hMuSCs), which can be differentiated into myotubes. Using single nuclei ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq), we document chromatin accessibility and transcriptomic changes associated with the transition of hMuSCs to myotubes. Cancer secretome accelerated stem to myotube differentiation, altered the alternative splicing machinery and increased inflammatory, glucocorticoid receptor, and wound healing pathways in hMuSCs. Additionally, cancer secretome reduced metabolic and survival pathway associated miR-486, AKT, and p53 signaling in hMuSCs. hMuSCs underwent myotube differentiation when engrafted into NSG mice and thus providing a humanized in vivo skeletal muscle model system to study cancer cachexia.

Abstract Improved understanding of local breast biology that favors the development of estrogen receptor negative (ER−) breast cancer (BC) would foster better prevention strategies. We have previously shown that overexpression of specific lipid metabolism genes is associated with the development of ER− BC. We now report results of exposure of MCF-10A and MCF-12A cells, and mammary organoids to representative medium- and long-chain polyunsaturated fatty acids. This exposure caused a dynamic and profound change in gene expression, accompanied by changes in chromatin packing density, chromatin accessibility, and histone posttranslational modifications (PTMs). We identified 38 metabolic reactions that showed significantly increased activity, including reactions related to one-carbon metabolism. Among these reactions are those that produce S-adenosyl-L-methionine for histone PTMs. Utilizing both an in-vitro model and samples from women at high risk for ER− BC, we show that lipid exposure engenders gene expression, signaling pathway activation, and histone marks associated with the development of ER− BC.

Most circulating endothelial cells are apoptotic, but rare circulating endothelial colony-forming cells (C-ECFCs), also known as blood outgrowth endothelial cells, with proliferative and vasculogenic activity can be cultured; however, the origin and naive function of these C-ECFCs remains obscure. Herein, detailed lineage tracing revealed murine C-ECFCs emerged in the early postnatal period, displayed high vasculogenic potential with enriched frequency of clonal proliferative cells compared with tissue-resident ECFCs, and were not committed to or derived from the BM hematopoietic system but from tissue-resident ECFCs. In humans, C-ECFCs were present in the CD34bright cord blood mononuclear subset, possessed proliferative potential and in vivo vasculogenic function in a naive or cultured state, and displayed a single cell transcriptome sharing some umbilical venous endothelial cell features, such as a higher protein C receptor and extracellular matrix gene expression. This study provides an advance for the field by identifying the origin, naive function, and antigens to prospectively isolate C-ECFCs for translational studies.

Summary: Background: Tongue images (the colour, size and shape of the tongue and the colour, thickness and moisture content of the tongue coating), reflecting the health state of the whole body according to the theory of traditional Chinese medicine (TCM), have been widely used in China for thousands of years. Herein, we investigated the value of tongue images and the tongue coating microbiome in the diagnosis of gastric cancer (GC). Methods: From May 2020 to January 2021, we simultaneously collected tongue images and tongue coating samples from 328 patients with GC (all newly diagnosed with GC) and 304 non-gastric cancer (NGC) participants in China, and 16 S rDNA was used to characterize the microbiome of the tongue coating samples. Then, artificial intelligence (AI) deep learning models were established to evaluate the value of tongue images and the tongue coating microbiome in the diagnosis of GC. Considering that tongue imaging is more convenient and economical as a diagnostic tool, we further conducted a prospective multicentre clinical study from May 2020 to March 2022 in China and recruited 937 patients with GC and 1911 participants with NGC from 10 centres across China to further evaluate the role of tongue images in the diagnosis of GC. Moreover, we verified this approach in another independent external validation cohort that included 294 patients with GC and 521 participants with NGC from 7 centres. This study is registered at ClinicalTrials.gov, NCT01090362. Findings: For the first time, we found that both tongue images and the tongue coating microbiome can be used as tools for the diagnosis of GC, and the area under the curve (AUC) value of the tongue image-based diagnostic model was 0.89. The AUC values of the tongue coating microbiome-based model reached 0.94 using genus data and 0.95 using species data. The results of the prospective multicentre clinical study showed that the AUC values of the three tongue image-based models for GCs reached 0.88–0.92 in the internal verification and 0.83–0.88 in the independent external verification, which were significantly superior to the combination of eight blood biomarkers. Interpretation: Our results suggest that tongue images can be used as a stable method for GC diagnosis and are significantly superior to conventional blood biomarkers. The three kinds of tongue image-based AI deep learning diagnostic models that we developed can be used to adequately distinguish patients with GC from participants with NGC, even early GC and precancerous lesions, such as atrophic gastritis (AG). Funding: The National Key R&D Program of China (2021YFA0910100), Program of Zhejiang Provincial TCM Sci-tech Plan (2018ZY006), Medical Science and Technology Project of Zhejiang Province (2022KY114, WKJ-ZJ-2104), Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer (JBZX-202006), Natural Science Foundation of Zhejiang Province (HDMY22H160008), Science and Technology Projects of Zhejiang Province (2019C03049), National Natural Science Foundation of China (82074245, 81973634, 82204828), and Chinese Postdoctoral Science Foundation (2022M713203).

IntroductionIt is critical to identify the stroke onset time of patients with acute ischemic stroke (AIS) for the treatment of endovascular thrombectomy (EVT). However, it is challenging to accurately ascertain this time for patients with wake-up stroke (WUS). The current study aimed to construct a deep learning approach based on computed tomography perfusion (CTP) or perfusion weighted imaging (PWI) to identify a 6-h window for patients with AIS for the treatment of EVT.MethodsWe collected data from 377 patients with AIS, who were examined by CTP or PWI before making a treatment decision. Cerebral blood flow (CBF), time to maximum peak (Tmax), and a region of interest (ROI) mask were preprocessed from the CTP and PWI. We constructed the classifier based on a convolutional neural network (CNN), which was trained by CBF, Tmax, and ROI masks to identify patients with AIS within a 6-h window for the treatment of EVT. We compared the classification performance among a CNN, support vector machine (SVM), and random forest (RF) when trained by five different types of ROI masks. To assess the adaptability of the classifier of CNN for CTP and PWI, which were processed respectively from CTP and PWI groups.ResultsOur results showed that the CNN classifier had a higher performance with an area under the curve (AUC) of 0.935, which was significantly higher than that of support vector machine (SVM) and random forest (RF) (p = 0.001 and p = 0.001, respectively). For the CNN classifier trained by different ROI masks, the best performance was trained by CBF, Tmax, and ROI masks of Tmax > 6 s. No significant difference was detected in the classification performance of the CNN between CTP and PWI (0.902 vs. 0.928; p = 0.557).DiscussionThe CNN classifier trained by CBF, Tmax, and ROI masks of Tmax > 6 s had good performance in identifying patients with AIS within a 6-h window for the treatment of EVT. The current study indicates that the CNN model has potential to be used to accurately estimate the stroke onset time of patients with WUS.

Abstract Populations that are born and raised at high altitude develop under conditions of chronic developmental hypoxia (CDH), which results in pulmonary adaptations of increased lung volume and diffusion capacity to increase gas exchange. It is not clear how CDH may alter allergic inflammation in the lung. In this study, we sought to characterize the impact of CDH on immune cell populations in the rat lung during a murine model of asthma. Rats were bred and raised in either hypoxic (15% oxygen, CDH) or normobaric room air (20% oxygen). At 3‐weeks of age, animals were sensitized to ovalbumin (OVA) or physiologic saline (phosphate‐buffered saline [PBS]) as a control, followed by three consecutive days of intra‐nasal OVA or PBS at 6‐weeks of age. We then assessed airway reactivity and allergic‐associated cytokine levels. This was followed by single‐cell transcriptomic profiling of lung cell populations. In scRNA‐seq analysis, we assessed differentially expressed genes, differentially enriched functional pathways, immune cell exhaustion/activation markers, and immune cell secretory products. Our results show that while OVA heightened airway reactivity, CDH suppressed airway reactivity in OVA‐challenged and control animals. Through scRNA‐seq analysis, we further demonstrate that CDH alters the transcriptional landscape in the lung and alters transcriptional programs in immune cells. These data define CDH‐dependent changes in the lung that impact airway reactivity.

IntroductionDue to a lack of spatial-temporal resolution at the single cell level, the etiologies of the bone dysfunction caused by diseases such as normal aging, osteoporosis, and the metabolic bone disease associated with chronic kidney disease (CKD) remain largely unknown.MethodsTo this end, flow cytometry and scRNAseq were performed on long bone cells from Sost-cre/Ai9+ mice, and pure osteolineage transcriptomes were identified, including novel osteocyte-specific gene sets.ResultsClustering analysis isolated osteoblast precursors that expressed Tnc, Mmp13, and Spp1, and a mature osteoblast population defined by Smpd3, Col1a1, and Col11a1. Osteocytes were demarcated by Cd109, Ptprz1, Ramp1, Bambi, Adamts14, Spns2, Bmp2, WasI, and Phex. We validated our in vivo scRNAseq using integrative in vitro promoter occupancy via ATACseq coupled with transcriptomic analyses of a conditional, temporally differentiated MSC cell line. Further, trajectory analyses predicted osteoblast-to-osteocyte transitions via defined pathways associated with a distinct metabolic shift as determined by single-cell flux estimation analysis (scFEA). Using the adenine mouse model of CKD, at a time point prior to major skeletal alterations, we found that gene expression within all stages of the osteolineage was disturbed.ConclusionIn sum, distinct populations of osteoblasts/osteocytes were defined at the single cell level. Using this roadmap of gene assembly, we demonstrated unrealized molecular defects across multiple bone cell populations in a mouse model of CKD, and our collective results suggest a potentially earlier and more broad bone pathology in this disease than previously recognized.

Abstract Myasthenia gravis (MG) is a complex neurological autoimmune disease with a pathogenetic mechanism that has yet to be elucidated. Emerging evidence has revealed that genes, non-coding RNAs and genetic variants play significant roles in the pathogenesis of MG. However, the molecular mechanisms of single nucleotide polymorphisms (SNPs) located on lncRNAs could disturb lncRNA-mediated ceRNA regulatory functions still unclear in MG. In this study, we collated 276 experimentally confirmed MG risk genes and 192 MG risk miRNAs. We then constructed a lncRNA-mediated ceRNA network for MG based on multi-step computational strategies. Next, we systematically integrated risk pathways and identified candidate SNPs in lncRNAs for MG based on data acquired from public databases. In addition, we constructed a pathway-based lncRNA-SNP mediated network (LSPN) that contained 128 lncRNAs targeting 8 MG risk pathways. By analyzing network, we propose a latent mechanism for how the “lncRNA-SNP-mRNA-pathway” axis affects the pathogenesis of MG. Moreover, 25 lncRNAs and 51 SNPs on lncRNAs were extracted from the “lncRNA-SNP-mRNA-pathway” axis. Finally, functional analyses demonstrated lncRNA-SNPs mediated ceRNA regulation pairs associated with MG participated in the MAPK signaling pathway. In summary, we constructed MG-specific lncRNA-SNPs mediated ceRNA regulatory networks based on pathway in the present study, which was helpful to elucidate the roles of lncRNA-SNPs in the pathogenesis of MG and provide novel insights into mechanism of lncRNA-SNPs as potential genetic risk biomarkers of MG.

Abstract Methadone is a synthetic opioid used as an analgesic and for the treatment of opioid abuse disorder. The analgesic dose in the pediatric population is not well‐defined. The pharmacokinetics (PKs) of methadone is highly variable due to the variability in alpha‐1 acid glycoprotein (AAG) and genotypic differences in drug‐metabolizing enzymes. Additionally, the R and S enantiomers of methadone have unique PK and pharmacodynamic properties. This study aims to describe the PKs of R and S methadone and its metabolite 2‐ethylidene‐1,5‐dimethyl‐3,3‐diphenylpyrrolidine (EDDP) in pediatric surgical patients and to identify sources of inter‐ and intra‐individual variability. Children aged 8–17.9 years undergoing orthopedic surgeries received intravenous methadone 0.1 mg/kg intra‐operatively followed by oral methadone 0.1 mg/kg postoperatively every 12 h. Pharmacokinetics of R and S methadone and EDDP were determined using liquid chromatography tandem mass spectrometry assays and the data were modeled using nonlinear mixed‐effects modeling in NONMEM. R and S methadone PKs were well‐described by two‐compartment disposition models with first‐order absorption and elimination. EDDP metabolites were described by one compartment disposition models with first order elimination. Clearance of both R and S methadone were allometrically scaled by bodyweight. CYP2B6 phenotype was a determinant of the clearance of both the enantiomers in an additive gene model. The intronic CYP3A4 single‐nucleotide polymorphism (SNP) rs2246709 was associated with decreased clearance of R and S methadone. Concentrations of AAG and the SNP of AAG rs17650 independently increased the volume of distribution of both the enantiomers. The knowledge of these important covariates will aid in the optimal dosing of methadone in children.

ABSTRACT Few studies have investigated host-bacterial interactions at sites of infection in humans using transcriptomics and metabolomics. Haemophilus ducreyi causes cutaneous ulcers in children and the genital ulcer disease chancroid in adults. We developed a human challenge model in which healthy adult volunteers are infected with H. ducreyi on the upper arm until they develop pustules. Here, we characterized host-pathogen interactions in pustules using transcriptomics and metabolomics and examined interactions between the host transcriptome and metabolome using integrated omics. In a previous pilot study, we determined the human and H. ducreyi transcriptomes and the metabolome of pustule and wounded sites of 4 volunteers (B. Griesenauer, T. M. Tran, K. R. Fortney, D. M. Janowicz, et al., mBio 10:e01193-19, 2019, https://doi.org/10.1128/mBio.01193-19). While we could form provisional transcriptional networks between the host and H. ducreyi, the study was underpowered to integrate the metabolome with the host transcriptome. To better define and integrate the transcriptomes and metabolome, we used samples from both the pilot study (n = 4) and new volunteers (n = 8) to identify 5,495 human differentially expressed genes (DEGs), 123 H. ducreyi DEGs, 205 differentially abundant positive ions, and 198 differentially abundant negative ions. We identified 42 positively correlated and 29 negatively correlated human-H. ducreyi transcriptome clusters. In addition, we defined human transcriptome-metabolome networks consisting of 9 total clusters, which highlighted changes in fatty acid metabolism and mitigation of oxidative damage. Taken together, the data suggest a mixed pro- and anti-inflammatory environment and rewired central metabolism in the host that provides a hostile, nutrient-limited environment for H. ducreyi. IMPORTANCE Interactions between the host and bacteria at sites of infection in humans are poorly understood. We inoculated human volunteers on the upper arm with the skin pathogen H. ducreyi or a buffer control and biopsied the resulting infected and sham-inoculated sites. We performed dual transcriptome sequencing (RNA-seq) and metabolic analysis on the biopsy samples. Network analyses between the host and bacterial transcriptomes and the host transcriptome-metabolome network were used to identify molecules that may be important for the virulence of H. ducreyi in the human host. Our results suggest that the pustule is highly oxidative, contains both pro- and anti-inflammatory components, and causes metabolic shifts in the host, to which H. ducreyi adapts to survive. To our knowledge, this is the first study to integrate transcriptomic and metabolomic responses to a single bacterial pathogen in the human host.

Plaque biofilms play critical roles in the development of dental caries. Mechanical plaque control methods are considered to be most effective for plaque removal, such as brushing teeth or using flosser. Recently, water flosser has been paid much attention. Here, we tested the ability of a water flosser to remove the adhered sucrose and the dental plaque biofilms formed by Streptococcus mutans, Streptococcus sanguinis, and Actinobacillus viscosus. We found that the residual sucrose concentration was 3.54 mg/mL in the control group, 1.75 mg/mL in the syringe group (simulating the ordinary mouthwash), and 0 mg/mL in water flosser group. In addition, the residual bacterial concentration was 3.6 × 108 CFU/mL in the control group, 1.6 × 107 CFU/mL in the syringe group, and only 5.5 × 105 CFU/mL in the water flosser group. In summary, water flosser is effective for cleaning the teeth, which may have significant potential in preventing dental caries and maintaining oral health.

The ability to study the bone microenvironment of failed fracture healing may lead to biomarkers for fracture nonunion. Herein the authors describe a technique for isolating individual cells suitable for single-cell RNA sequencing analyses from intramedullary canal tissue collected by reaming during surgery. The purpose was to detail challenges and solutions inherent to the collection and processing of intramedullary canal tissue samples. The authors then examined single-cell RNA sequencing data from fresh and reanimated samples to demonstrate the feasibility of this approach for prospective studies.

The sliding motion of gold slabs adsorbed on a graphite substrate is simulated using molecular dynamics. The central quantity of interest is the mean lateral force, that is, the kinetic friction rather than the maximum lateral forces, which correlates with the static friction. For most setups, we find Stokesian damping to resist sliding. However, velocity-insensitive (Coulomb) friction is observed for finite-width slabs sliding parallel to the armchair direction if the bottom-most layer of the three graphite layers is kept at zero stress rather than at zero displacement. Although the resulting kinetic friction remains much below the noise produced by the erratic fluctuations of (conservative) forces typical for structurally lubric contacts, the nature of the instabilities leading to Coulomb friction could be characterized as quasi-discontinuous dynamics of the Moiré patterns formed by the normal displacements near a propagating contact line. It appears that the interaction of graphite with the second gold layer is responsible for the symmetry break occurring at the interface when a contact line moves parallel to the armchair rather than to the zigzag direction.

Abstract Kidney fibrosis is a hallmark of chronic kidney disease (CKD) progression that is caused by tubular injury and dysregulated lipid metabolism. Genetic abolition fatty acid-binding protein 4 (FABP4), a key lipid transporter, has been reported to suppress kidney interstitial fibrosis. However, the role and underlying mechanism of chemical inhibition of FABP4 in fibrotic kidney have not been well-documented. Here, we examined preemptive the effect of a FABP4 inhibitor, BMS309403, on lipid metabolism of tubular epithelial cells (TECs) and progression of kidney fibrosis. The expression of FABP4 was significantly elevated, concomitated with the accumulation of lipid droplets in TECs during kidney fibrosis. Treatment with BMS309403 alleviated lipid deposition of TECs, as well as interstitial fibrotic responses both in unilateral ureteral obstruction (UUO)-engaged mice and TGF-β-induced TECs. Moreover, BMS309403 administration enhanced fatty acid oxidation (FAO) in TECs by regulating peroxisome proliferator-activated receptor γ (PPARγ) and restoring FAO-related enzyme activities; In addition, BMS309403 markedly reduced cell lipotoxicity, such as endoplasmic reticulum (ER) stress and apoptosis in fibrotic kidney. Taken together, our results suggest that preemptive pharmacological inhibition of FABP4 by BMS309403 rebalances abnormal lipid metabolism in TECs and attenuates the progression of kidney fibrosis, thus may hold therapeutic potential for the treatment of fibrotic kidney diseases.

Kidney intercalated cells are involved in acid-base homeostasis in the kidneys. Here, the authors use single cell transcriptomics and find that interalated cells exhibit a transcriptional response conducive to defense and can engulf and acidify internalized bacteria, similarly to professional phagocytes.

Abstract We report our discovery of an important player in the development of skin fibrosis, a hallmark of scleroderma. Scleroderma is a fibrotic disease, affecting 70,000 to 150,000 Americans. Fibrosis is a pathological wound healing process that produces an excessive extracellular matrix to interfere with normal organ function. Fibrosis contributes to nearly half of human mortality. Scleroderma has heterogeneous phenotypes, unpredictable outcomes, no validated biomarkers, and no effective treatment. Thus, strategies to slow down scleroderma progression represent an urgent medical need. While a pathological wound healing process like fibrosis leaves scars and weakens organ function, oral mucosa wound healing is a scarless process. After re-analyses of gene expression datasets from oral mucosa wound healing and skin fibrosis, we discovered that several pathways constitutively activated in skin fibrosis are transiently induced during oral mucosa wound healing process, particularly the amphiregulin (Areg) gene. Areg expression is upregulated ~ 10 folds 24hrs after oral mucosa wound but reduced to the basal level 3 days later. During bleomycin-induced skin fibrosis, a commonly used mouse model for skin fibrosis, Areg is up-regulated throughout the fibrogenesis and is associated with elevated cell proliferation in the dermis. To demonstrate the role of Areg for skin fibrosis, we used mice with Areg knockout, and found that Areg deficiency essentially prevents bleomycin-induced skin fibrosis. We further determined that bleomycin-induced cell proliferation in the dermis was not observed in the Areg null mice. Furthermore, we found that inhibiting MEK, a downstream signaling effector of Areg, by selumetinib also effectively blocked bleomycin-based skin fibrosis model. Based on these results, we concluded that the Areg-EGFR-MEK signaling axis is critical for skin fibrosis development. Blocking this signaling axis may be effective in treating scleroderma.

RNA binding protein Quaking (QKI) is known for its broad function in pre-mRNA splicing and modification and its association with several neurodevelopmental disorders. Here the authors reveal that QKI-mediated regulation of RNA splicing is indispensable to cardiac development and contractile physiology.

Background and PurposeMyasthenia gravis (MG) is a T cell-dependent antibody-mediated autoimmune disorder that can seriously affect patients' quality of life. However, few studies have focused on the severity of MG. Moreover, existing therapeutic efforts, including those targeting biomarkers for MG, remain unsatisfactory. Therefore, it is vital that we investigate the pathogenesis of MG and identify new biomarkers that can not only evaluate the severity of the disease but also serve as potential therapeutic targets. Long noncoding RNA LINC00680 has been found to be associated with the progression of a variety of diseases as a competing endogenous RNA (ceRNA). However, the specific role of LINC00680 in MG has yet to be clarified. Here, we aimed to investigate the association between LINC00680 and the severity of MG.MethodsBioinformatics tools, quantitative real-time PCR, Western blotting, and luciferase assays were selected to investigate key signaling pathways and RNA expression in patients with MG. The Quantitative MG Score scale and the MG Composite scale were used to evaluate the severity of MG in the included patients. Cell viability assays and flow cytometry analysis were selected to analyze cell proliferation and apoptosis.ResultsCompared with control subjects, the expression levels of LINC00680 and mitogen-activated protein kinase 1 (MAPK1) in peripheral blood mononuclear cells of patients with MG were both upregulated; the levels of miR-320a were downregulated. A positive correlation was detected between LINC00680 expression and the severity of MG. Luciferase reporter assays identified that LINC00680 acts as a target for miR-320a. The in vitro analysis confirmed that LINC00680 regulates the expression of MAPK1 by sponging miR-320a. Finally, the functional analysis indicated that LINC00680 promoted Jurkat cell proliferation and inhibited cellular apoptosis by sponging miR-320a.ConclusionLINC00680 may be associated with the severity of MG as a ceRNA by sponging miR-320a to upregulate MAPK1. These findings suggest that LINC00680 may represent a potential biomarker which evaluates the severity of MG and may serve as a therapeutic target.