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ObjectiveTo explore the relationship between serum calcium levels and the prognosis of severe acute osteomyelitis, and to assess the effectiveness of calcium levels in prognostic evaluation.MethodsRelevant patient records of individuals diagnosed with severe acute osteomyelitis were obtained for this retrospective study from the Medical Information Mart for Intensive Care (MIMIC-IV). The study aimed to assess the impact of different indicators on prognosis by utilizing COX regression analysis. To enhance prognostic prediction for critically ill patients, a nomogram was developed. The discriminatory capacity of the nomogram was evaluated using the Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) curve, in addition to the calibration curve.ResultThe study analyzed a total of 1,133 cases of severe acute osteomyelitis, divided into the survivor group (1,025 cases) and the non-survivor group (108 cases). Significant differences were observed between the two groups in terms of age, hypertension, sepsis, renal injury, and various laboratory indicators, including WBC, PLT, Ca2+, CRP, hemoglobin, albumin, and creatinine (P0.05). To predict the survival time, a nomogram was developed using the aforementioned indicators and achieved an AUC of 0.841. The accuracy of the nomogram was further confirmed by the ROC curve and calibration curve.ConclusionAccording to the findings, this study establishes that a reduction in serum calcium levels serves as a distinct and standalone predictor of mortality among individuals diagnosed with severe acute osteomyelitis during their stay in the Intensive Care Unit (ICU) within a span of two years.

ObjectiveElastic stable intramedullary nail (ESIN) is a commonly used method for treating diaphyseal fractures of the tibia, but its application in Distal Tibial Diaphyseal Metaphyseal Junction (DTDMJ) fractures has been a subject of controversy. This study aims to evaluate the clinical efficacy of the Elastic stable intramedullary nail-Kirschner wire (E-K) technique in treating pediatric DTDMJ fractures, providing better clinical decision-making for clinicians in diagnosing and treating such fractures.MethodsWe conducted a retrospective analysis of patients aged 3–9 years who received treatment at our hospital from January 2019–January 2021 for distal tibial diaphyseal metaphyseal junction (DTDMJ) fractures. Based on their surgical procedures, they were categorized into the Elastic Stable Intramedullary Nail—Kirschner wire group (E-K) and the ESIN group. Demographic data, surgical duration, clinical outcomes, complications, and imaging data were recorded.ResultsThe study included a total of 57 patients, with 24 cases in the E-K group and 33 cases in the ESIN group. There were 30 males and 27 females. The average age was (6.25 ± 1.59) years in the E-K group and (6.27 ± 1.48) years in the ESIN group. There were no significant differences between the two groups in terms of gender, age, weight, time from injury to surgery, follow-up time, side of injury, associated injuries, nail site infection, deep infection, and nail removal time (P > 0.05). Neither group experienced nonunion or refracture. The E-K group exhibited significantly lower coronal and sagittal plane angular values at the final follow-up compared to the ESIN group (P

ObjectiveThis study aims to identify factors influencing university students' participation in time banking volunteer services for older adults and provides evidence to promote the involvement.MethodsConducted in November 2022, we utilized a convenience sampling method to recruit students from the School of Aging Service and Management at Nanjing University of Chinese Medicine, China. Data was collected through an online questionnaire focusing on various aspects related to time banking volunteer services for older adults. Factor analysis was employed to extract variables, and logistic regression was applied to identify key determinants.ResultsA significant majority (82.67%) of participants expressed willingness to engage in volunteer services for older adults. Factor analysis uncovered six influential factors explaining 62.55% of the variance. Logistic regression highlighted four key determinants of students' willingness: value judgment (OR = 4.392, CI = 2.897–6.658), social support (OR = 1.262, CI = 0.938–1.975), social influence (OR = 1.777, CI = 1.598–3.799), and socioeconomic conditions (OR = 1.174, CI = 1.891–3.046).ConclusionTo foster sustainability and continuous time banking among university students majoring in aging service and management, a multifaceted support involving governmental, social, and university is recommended.

Aeromonas hydrophila is a kind of zoonotic pathogen, which can cause bacterial septicemia in fish and bring huge economic losses to global aquaculture. Outer membrane proteins (Omps) are conserved antigens of Aeromonas hydrophila, which can be developed as subunit vaccines. To evaluate the protective efficacy of inactivated vaccine and recombinant outer membrane protein A (OmpA) subunit vaccine against A. hydrophila in juvenile Megalobrama amblycephala, the present study investigated the immunogenicity and protective effects of both vaccines, as well as the non-specific and specific immune response of M. amblycephala. Compared with the non-vaccinated group, both inactivated and OmpA subunit vaccines improved the survival rate of M. amblycephala upon infection. The protective effects of OmpA vaccine groups were better than that of the inactivated vaccine groups, which should be attributed to the reduced bacterial load and enhanced host immunity in the vaccinated fish. ELISA assay showed that the titer of serum immunoglobulin M (IgM) specific to A. hydrophila up-regulated significantly in the OmpA subunit vaccine groups at 14 d post infection (dpi), which should contribute to better immune protective effects. In addition, vaccination enhanced host bactericidal abilities might also attribute to the regulation of the activities of hepatic and serum antimicrobial enzymes. Moreover, the expression of immune-related genes (SAA, iNOS, IL-1 β, IL-6, IL-10, TNF α, C3, MHC I, MHC II, CD4, CD8, TCR α, IgM, IgD and IgZ) increased in all groups post infection, which was more significant in the vaccinated groups. Furthermore, the number of immunopositive cells exhibiting different epitopes (CD8, IgM, IgD and IgZ) that were detected by immunohistochemical assay had increased in the vaccinated groups post infection. These results show that vaccination effectively stimulated host immune response (especially OmpA vaccine groups). In conclusion, these results indicated that both the inactivated vaccine and OmpA subunit vaccine could protect juvenile M. amblycephala against A. hydrophila infection, of which OmpA subunit vaccine provided more effective immune protection and can be used as an ideal candidate for the A. hydrophila vaccine.

Fucoidan and laminarin are polymolecular compounds that extracted from seaweed. As functional polysaccharides, they possess various biological functions such as immunomodulatory, anti-inflammatory, antiviral and antioxidant bioactivities. Fucoidan and laminarin modulate host immune responses by activating immune cells (macrophages, neutrophils, T lymphocytes) and inducing the expression of cytokines (TNFα, IL-1β, IL-6, IL-8, NF-κB). Intelectin is a novel lectin that plays important roles in bacterial agglutination and bactericidal effects by recognizing the polysaccharide components on the cell surface of pathogens, which can also enhance the phagocytosis of macrophages. The present study intends to explore the immunomodulatory effects of fucoidan, laminarin and intelectin on the macrophages of Megalobrama amblycephala. The results showed that the incubation of both fucoidan and laminarin at the concentration of 100 μg/mL for 4 h could enhance the phagocytic capacity of M. amblycephala macrophages, which also showed remodeled cytoskeleton with extended pseudopodia. In addition, fucoidan and laminarin could induce the expression of M. amblycephala intelectin (MaINTL) in the primary hepatocytes and macrophages, and the recombinant MaINTL (rMaINTL) could bind with fucoidan and laminarin. Furthermore, fucoidan and laminarin induced the expression of cytoskeletal remodeling related genes in the primary M. amblycephala macrophages, such as Rac1 and WASP, which should contribute to the enhancement of seaweed polysaccharides (fucoidan and laminarin) and MaINTL on the phagocytosis of M. amblycephala macrophages. However, even though fucoidan and laminarin could induced the expression of CXCL8, while the chemotaxis of M. amblycephala macrophages on neutrophils was not affected by them. These findings suggested that fucoidan and laminarin enhanced the phagocytic capacity of M. amblycephala macrophages via activation of MaINTL and up-regulation of the expression of downstream cytoskeletal remodeling related genes Rac1 and WASP. Therefore, fucoidan and laminarin could be used as immune enhancers to improve host immunity and disease resistance in M. amblycephala, which provided novel insights into the prevention and protection of fish bacterial diseases.

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.

ObjectiveTo systematically review the current articles to compare the efficacy and safety of 3D navigation-assisted osteotomy of DDH with conventional osteotomy of DDH in children. Study design Databases such as PubMed, Embase, Cochrane Library were searched, from inception to April, 2022, for studies applying 3D navigation-assisted osteotomy in DDH children.MethodsThere were 626 articles identified. According to the search strategy and inclusion criteria, 7 studies were finally included, with a total of 288 cases. Study screening, data extraction, and quality assessment were conducted by two reviewers independently. Data analyses were performed using RevMan 5.4 software.ResultsThere were 7 retrospective cohort studies included. Meta-analysis showed that 3D navigation-assisted DDH osteotomy resulted in shorter duration of surgery [I2 = 88%, REM, MD = 22.86, 95%CI (−27.29, −18.43), p 0.05).Conclusion3D navigation-assisted pelvis and thighbone osteotomy for DDH children could shorten duration of surgery and reduce intraoperative bleeding and x-ray exposure, presenting definite therapeutic effect.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/#myprospero, identifier: CRD42022333767.

Vaginal and cervical canal bacteria are associated with women’s health and pregnancy outcomes. Here, we compared their composition and characteristics in 37 reproductive-aged Chinese women including 24 pregnant women with cervical incompetence (vaginal and cervical canal bacteria formed Groups A and B, respectively) and 13 healthy pregnant women (vaginal and cervical canal bacteria formed Groups C and D, respectively) using high-throughput sequencing of the V4 region of 16S rRNA gene. The results of alpha and beta diversity analysis, respectively, indicated no statistical differences between Groups A and B (p = 0.32, 0.06), nor Groups B and D (p = 0.69, 0.74); however, differences were found between Groups C and D (p = 0.02, 0.01) and between Groups A and C (p = 0.04, 0.02). PLS-DA analysis showed that the individuals from each group were irregularly distributed according to their clade. Lactobacillus, Bifidobacterium and Ureaplasma were the dominant genera in all groups. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSts) analysis identified 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs associated with the bacterial communities from the four groups, including membrane transport, folding, sorting and degradation, xenobiotics biodegradation and metabolism, and nucleotide metabolism. We further determined relationships between pregnancy outcomes (Apgar scores) and certain bacterial species. A significant positive correlation was found between Apgar scores and Actinomyces neuii and Anoxybacillus flavithermus in the vagina and cervical canal of pregnant women with cervical incompetence while Bacteroides plebeius, Bifidobacterium pseudopodium and Staphylococcus petrasii in the cervical canal displayed negative correlations with Apgar scores. Moreover, Clostridium fimetarium, Methanobacterium congolense, Pseudomonas chlororaphis, and Psychrobacter nivimaris in the vagina were negatively correlated with Apgar scores. These bacteria may serve as potential biomarkers, however, additional research is warranted to verify their role in clinical outcomes.

Mannan oligosaccharides (MOS) have been studied and applied as a feed additive, whereas their regulation on the growth performance and immunity of aquatic animals lacks consensus. Furthermore, their immunoprotective effects on the freshwater fish Megalobrama amblycephala have not been sufficiently studied. Thus, we investigated the effects of dietary MOS of 0, 200, and 400 mg/kg on the growth performance, non-specific immunity, intestinal health, and resistance to Aeromonas hydrophila infection in juvenile M. amblycephala. The results showed that the weight gain rate of juvenile M. amblycephala was not significantly different after 8 weeks of feeding, whereas the feed conversion ratio decreased in the MOS group of 400 mg/kg. Moreover, dietary MOS increased the survival rate of juvenile M. amblycephala upon infection, which may be attributed to enhanced host immunity. For instance, dietary MOS increase host bactericidal and antioxidative abilities by regulating the activities of hepatic antimicrobial and antioxidant enzymes. In addition, MOS supplementation increased the number of intestinal goblet cells, and the intestine was protected from necrosis of the intestinal folds and disruption of the microvilli and junctional complexes, thus maintaining the stability of the intestinal epithelial barrier. The expression levels of M. amblycephala immune and tight junction-related genes increased after feeding dietary MOS for 8 weeks. However, the upregulated expression of immune and tight junction-related genes in the MOS supplemental groups was not as notable as that in the control group postinfection. Therefore, MOS supplementation might suppress the damage caused by excessive intestinal inflammation. Furthermore, dietary MOS affected the richness and composition of the gut microbiota, which improved the gut health of juvenile M. amblycephala by increasing the relative abundance of beneficial gut microbiota. Briefly, dietary MOS exhibited significant immune protective effects to juvenile M. amblycephala, which is a functional feed additive and immunostimulant.

Pile foundations are widely used in all types of soils including expansive and collapsible soils that are typically found in nature in a state of unsaturated condition. Opposite trends in volume change behavior are typically observed when water infiltrates into expansive and collapsible soils. The design of pile foundations in these soils is conventionally based on saturated soil mechanics assuming drained conditions ignoring the influence of unsaturated conditions. In this study, infiltration tests were performed on two model piles; one of these piles was tested in an expansive soil and the other in a collapsible soil. The focus of this study was to determine the pile mechanical behavior including the pile head load, displacement response, pile axial force, shaft friction, and pile base pressure taking account of suction changes associated with water infiltration. The pile mechanical behavior is significantly influenced due to changes in the pile shaft friction in both expansive and collapsible soils. The responses of the pile mechanical behavior variations were explained extending the concepts of unsaturated soil mechanics. The results of this study provide valuable information for the practicing engineers to gain a more comprehensive understanding of mechanical behaviors of pile foundations in expansive soils and collapsible soils upon water infiltration.

Calcium oxalate nephrolithiasis is a common and highly recurrent disease in urology; however, its precise pathogenesis is still unknown. Recent research has shown that renal inflammatory injury as a result of the cell-crystal reaction plays a crucial role in the development of calcium oxalate kidney stones. An increasing amount of research have confirmed that inflammation mediated by the cell-crystal reaction can lead to inflammatory injury of renal cells, promote the intracellular expression of NADPH oxidase, induce extensive production of reactive oxygen species, activate NLRP3 inflammasome, discharge a great number of inflammatory factors, trigger inflammatory cascading reactions, promote the aggregation, nucleation and growth process of calcium salt crystals, and ultimately lead to the development of intrarenal crystals and even stones. The renal tubular epithelial cells (RTECs)-crystal reaction, macrophage-crystal reaction, calcifying nanoparticles, endoplasmic reticulum stress, autophagy activation, and other regulatory factors and mechanisms are involved in this process.

Single-cell sequencing (scRNA-seq) has enabled researchers to study cellular heterogeneity. Accurate cell type identification is crucial for scRNA-seq analysis to be valid and robust. Marker genes, genes specific for one or a few cell types, can improve cell type classification; however, their specificity varies across species, samples, and cell subtypes. Current marker gene databases lack standardization, cell hierarchy consideration, sample diversity, and/or the flexibility for updates as new data become available. Most of these databases are derived from a single statistical analysis despite many such analyses scattered in the literature to identify marker genes from scRNA-seq data and pure cell populations. An R Shiny web tool called GeneMarkeR was developed for researchers to retrieve marker genes demonstrating cell type specificity across species, methodology and sample types based on a novel algorithm. The web tool facilitates online submission and interfaces with MySQL to ensure updatability. Furthermore, the tool incorporates reactive programming to enable researchers to retrieve standardized public data supporting the marker genes. GeneMarkeR currently hosts over 261,000 rows of standardized marker gene results from 25 studies across 21,012 unique genomic entities and 99 unique cell types mapped to hierarchical ontologies.

Single-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the bulk starting material. To obtain an accurate assessment of patient samples, single-cell suspensions need to be generated as soon as possible once the tissue or sample has been collected. However, this requirement poses logistical challenges for experimental designs involving multiple samples from the same subject since these samples would ideally be processed at the same time to minimize technical variation in data analysis. Although cryopreservation has been shown to largely preserve the transcriptome, it is unclear whether the freeze-thaw process might alter gene expression profiles in a cell-type specific manner or whether changes in cell-type proportions might also occur. To address these questions in the context of multiple myeloma clinical studies, we performed single-cell RNA sequencing (scRNA-seq) to compare fresh and frozen cells isolated from bone marrow aspirates of six multiple myeloma patients, analyzing both myeloma cells (CD138+) and cells constituting the microenvironment (CD138−). We found that cryopreservation using 90% fetal calf serum and 10% dimethyl sulfoxide resulted in highly consistent gene expression profiles when comparing fresh and frozen samples from the same patient for both CD138+ myeloma cells (R ≥ 0.96) and for CD138– cells (R ≥ 0.9). We also demonstrate that CD138– cell-type proportions showed minimal alterations, which were mainly related to small differences in immune cell subtype sensitivity to the freeze-thaw procedures. Therefore, when processing fresh multiple myeloma samples is not feasible, cryopreservation is a useful option in single-cell profiling studies.

Background: Accumulating evidence suggests that coronavirus disease 2019 (COVID-19) is associated with hypercoagulative status, particularly for critically ill patients in the intensive care unit. However, the prevalence of venous thromboembolism (VTE) in these patients under routine prophylactic anticoagulation remains unknown. A meta-analysis was performed to evaluate the prevalence of VTE in these patients by pooling the results of these observational studies.Methods: Observational studies that reported the prevalence of VTE in critically ill patients with COVID-19 were identified by searching the PubMed and Embase databases. A random-effect model was used to pool the results by incorporating the potential heterogeneity.Results: A total of 19 studies with 1,599 patients were included. The pooled results revealed that the prevalence of VTE, deep venous thrombosis (DVT), and pulmonary embolism (PE) in critically ill patients with COVID-19 was 28.4% [95% confidence interval (CI): 20.0–36.8%], 25.6% (95% CI: 17.8–33.4%), and 16.4% (95% CI: 10.1–22.7%), respectively. Limited to studies, in which all patients received routine prophylactic anticoagulation, and the prevalence for VTE, DVT, and PE was 30.1% (95% CI: 19.4–40.8%), 27.2% (95% CI: 16.5–37.9%), and 18.3% (95% CI: 9.8%−26.7%), respectively. The prevalence of DVT was higher in studies with routine screening for all patients, when compared to studies with screening only in clinically suspected patients (47.5% vs. 15.1%, P < 0.001).Conclusion: Critically ill patients with COVID-19 have a high prevalence of VTE, despite the use of present routine prophylactic anticoagulation.

Expression quantitative trait loci (eQTL) analysis is useful for identifying genetic variants correlated with gene expression, however, it cannot distinguish between causal and nearby non-functional variants. Because the majority of disease-associated SNPs are located in regulatory regions, they can impact allele-specific binding (ASB) of transcription factors and result in differential expression of the target gene alleles. In this study, our aim was to identify functional single-nucleotide polymorphisms (SNPs) that alter transcriptional regulation and thus, potentially impact cellular function. Here, we present regSNPs-ASB, a generalized linear model-based approach to identify regulatory SNPs that are located in transcription factor binding sites. The input for this model includes ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) raw read counts from heterozygous loci, where differential transposase-cleavage patterns between two alleles indicate preferential transcription factor binding to one of the alleles. Using regSNPs-ASB, we identified 53 regulatory SNPs in human MCF-7 breast cancer cells and 125 regulatory SNPs in human mesenchymal stem cells (MSC). By integrating the regSNPs-ASB output with RNA-seq experimental data and publicly available chromatin interaction data from MCF-7 cells, we found that these 53 regulatory SNPs were associated with 74 potential target genes and that 32 (43%) of these genes showed significant allele-specific expression. By comparing all of the MCF-7 and MSC regulatory SNPs to the eQTLs in the Genome-Tissue Expression (GTEx) Project database, we found that 30% (16/53) of the regulatory SNPs in MCF-7 and 43% (52/122) of the regulatory SNPs in MSC were also in eQTL regions. The enrichment of regulatory SNPs in eQTLs indicated that many of them are likely responsible for allelic differences in gene expression (chi-square test, p-value < 0.01). In summary, we conclude that regSNPs-ASB is a useful tool for identifying causal variants from ATAC-seq data. This new computational tool will enable efficient prioritization of genetic variants identified as eQTL for further studies to validate their causal regulatory function. Ultimately, identifying causal genetic variants will further our understanding of the underlying molecular mechanisms of disease and the eventual development of potential therapeutic targets.

Alternative splicing alterations can contribute to human disease. The ability of an RNA-binding protein to regulate alternative splicing outcomes can be modulated by a variety of genetic and epigenetic mechanisms. In this study, we use a computational framework to investigate the roles of certain genes, termed modulators, on changing RBPs’ effect on splicing regulation. A total of 1,040,254 modulator-mediated RBP-splicing interactions were identified, including 137 RBPs, 4,309 splicing events and 2,905 modulator candidates from TCGA-KIRC RNA sequencing data. Modulators function categories were defined according to the correlation changes between RBPs expression and their targets splicing outcomes. QKI, as one of the RBPs influencing the most splicing events, attracted our attention in this study: 2,014 changing triplets were identified, including 1,101 modulators and 187 splicing events. Pathway enrichment analysis showed that QKI splicing targets were enriched in tight junction pathway, endocytosis and MAPK signaling pathways, all of which are highly associated with cancer development and progression. This is the first instance of a comprehensive study on how alternative splicing outcomes changes are associated with different expression level of certain proteins, even though they were regulated by the same RBP. Our work may provide a novel view on understanding alternative splicing mechanisms in kidney cancer.

Genetic variants can influence the expression of mRNA and protein. Genetic regulatory loci such as expression quantitative trait loci (eQTLs) and protein quantitative trait loci (pQTLs) exist in several species. However, it remains unclear how human genetic variants regulate mRNA and protein expression. Here, we characterized six mechanistic models for the genetic regulatory patterns of single-nucleotide polymorphisms (SNPs) and their actions on post-transcriptional expression. Data from Yoruba HapMap lymphoblastoid cell lines were analyzed to identify human cis-eQTLs and pQTLs, as well as protein-specific QTLs (psQTLs). Our results indicated that genetic regulatory loci primarily affected mRNA and protein abundance in patterns where the two were well-correlated. While this finding was observed in both humans and mice (57.5% and 70.3%, respectively), the genetic regulatory patterns differed between species, implying evolutionary differences. Mouse SNPs generally targeted changes in transcript expression (51%), whereas in humans, they largely regulated protein abundance, independent of transcription levels (55.9%). The latter independent function can be explained by psQTLs. Our analysis suggests that local functional genetic variants in the human genome mainly modulate protein abundance independent of mRNA levels through post-transcriptional mechanisms. These findings clarify the impact of genetic variation on phenotype, which is of particular relevance to disease risk and treatment response.

Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA–mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05); 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3′ UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line.

Voltage instability, power imbalance, and unreliability are caused mainly by equipment failure in the distribution system, so it is important to accurately and quickly assess the status of distribution network equipment. However, it is challenging to detect equipment failures, the traditional XGBoost algorithm is unsuitable because some evaluation indices are incompetent to quantify. To address these issues, we propose a fast evaluation method for the state of electrical distribution equipment based on fuzzy decision-making. Firstly, key indices are selected from the multi-source equipment information. Secondly, this paper constructs the mapping between key indices and equipment status scores by combining the fuzzy iterative method and the XGBoost algorithm. Finally, the proposed assessment model is confirmed by using the distribution transformers as an example. The result shows that the proposed multi-source information assessment method can quickly and accurately determine the operation status of electrical distribution equipment, and the proposed method has better accuracy than the traditional method. [ABSTRACT FROM AUTHOR]

Introduction: Due 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. Methods: To 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. Results: Clustering 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. Conclusion: In 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 FROM AUTHOR]

Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA-mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05); 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3' UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line. [ABSTRACT FROM AUTHOR]

Membrane drug transporters contribute to the disposition of many drugs. In human liver, drug transport is controlled by two main superfamilies of transporters, the solute carrier transporters (SLC) and the ATP Binding Cassette transporters (ABC). Altered expression of these transporters due to drug-drug interactions can contribute to differences in drug exposure and possibly effect. In this study, we determined the effect of rifampin on gene expression of hundreds of membrane transporters along with all clinically relevant drug transporters. Methods: In this study, primary human hepatocytes (n = 7 donors) were cultured and treated for 24 h with rifampin and vehicle control. RNA was isolated from the hepatocytes, mRNA expression was measured by RNA-seq, and miRNA expression was analyzed by Taqman OpenArray. The effect of rifampin on the expression of selected transporters was also tested in kidney cell lines. The impact of rifampin on the expression of 410 transporter genes from 19 different transporter gene families was compared with vehicle control. Results: Expression patterns of 12 clinically relevant drug transporter genes were changed by rifampin (FDR < 0.05). For example, the expressions of ABCC2, ABCB1, and ABCC3 were increased 1.9-, 1.7-, and 1.2-fold, respectively. The effects of rifampin on four uptake drug transporters (SLCO1B3, SLC47A1, SLC29A1, SLC22A9) were negatively correlated with the rifampin effects on specific microRNA expression (SLCO1 B3/miR-92a, SLC47A1/miR-95, SLC29A1/miR-30d#, and SLC22A9/miR-20; r < -0.79; p < 0.05). Seven hepatic drug transporter genes (SLC22A1, SLC22A5, SLC15A1, SLC29A1, SLCO4C1, ABCC2, and ABCC4), whose expression was altered by rifampin in hepatocytes, were also present in a renal proximal tubular cell line, but in renal cells rifampin did not alter their gene expression. PXR expression was very low in the kidney cells; this may explain why rifampin induces gene expression in a tissue-specific manner. Conclusion: Rifampin alters the expression of many of the clinically relevant hepatic drug transporters, which may provide a rational basis for understanding rifampin-induced drug-drug interactions reported in vivo. The relevance of its effect on many other transporters remains to be studied. [ABSTRACT FROM AUTHOR]

Maternal alcohol consumption inflicts a multitude of phenotypic consequences that range from undetectable changes to severe dysmorphology. Using tightly controlled murine studies that deliver precise amounts of alcohol at discrete developmental stages, our group and other labs demonstrated in prior studies that the C57BL/6 and DBA/2 inbred mouse strains display differential susceptibility to the teratogenic effects of alcohol. Since the phenotypic diversity extends beyond the amount, dosage and timing of alcohol exposure, it is likely that an individual's genetic background contributes to the phenotypic spectrum. To identify the genomic signatures associated with these observed differences in alcohol-induced dysmorphology, we conducted a microarray-based transcriptome study that also interrogated the genomic signatures between these two lines based on genetic background and alcohol exposure. This approach is called a gene x environment (GxE) analysis; one example of a GxE interaction would be a gene whose expression level increases in C57BL/6, but decreases in DBA/2 embryos, following alcohol exposure. We identified 35 candidate genes exhibiting GxE interactions. To identify cis-acting factors that mediated these interactions, we interrogated the proximal promoters of these 35 candidates and found 241 single nucleotide variants (SNVs) in 16 promoters. Further investigation indicated that 186 SNVs (15 promoters) are predicted to alter transcription factor binding. In addition, 62 SNVs created, removed or altered the placement of a CpG dinucleotide in 13 of the proximal promoters, 53 of which overlapped putative transcription factor binding sites. These 53 SNVs are also our top candidates for future studies aimed at examining the effects of alcohol on epigenetic gene regulation. [ABSTRACT FROM AUTHOR]