Sclerotome-derived PDGF signaling functions as a niche cue responsible for primitive erythropoiesis.

Primitive erythropoiesis serves a vital role in embryonic development, generating primitive red blood cells responsible for transportation of oxygen throughout the body. Although diverse niche factors are known to function in definitive hematopoiesis, the microenvironment contributing to primitive hematopoiesis remains largely elusive. Here, we report that platelet-derived growth factor (PDGF) signaling is required for erythroid progenitor differentiation in zebrafish. Ablating pdgfαa (also known as pdgfaa) and pdgfαb (also known as pdgfab) or blocking PDGF signaling with an inhibitor impairs erythroid progenitor differentiation, thus resulting in a significant decrease in the number of erythrocytes. We reveal that pdgfαb is expressed in sclerotomal cells, and that its receptor genes, pdgfra and pdgfrb, are expressed in the adjacent erythroid progenitor cells. Sclerotome-specific overexpression of pdgfαb effectively restores primitive erythropoiesis in pdgfαa-/-;pdgfαb-/- mutant embryos. In addition, we have defined ERK1/2 signaling as a downstream pathway of PDGF signaling during embryonic erythropoiesis. Taken together, our findings indicate that PDGF signaling derived from sclerotome functions as a niche cue for primitive erythropoiesis.

DNA methylation regulates biosynthesis of tanshinones and phenolic acids during growth of Salvia miltiorrhiza.

DNA methylation plays a crucial role in the regulation of plant growth and the biosynthesis of secondary metabolites. Danshen (Salvia miltiorrhiza) is a valuable Chinese herbal medicine commonly used to treat cardiovascular diseases; its active ingredients are tanshinones and phenolic acids, which primarily accumulate in roots. Here, we conducted a targeted metabolic analysis of S. miltiorrhiza roots at 3 distinct growth stages: 40 d old (r40), 60 d old (r60), and 90 d old (r90). The contents of tanshinones (cryptotanshinone, tanshinone I, tanshinone IIA, and rosmariquinone) and phenolic acids (rosmarinic acid and salvianolic acid B) gradually increased during plant development. Whole-genome bisulfite sequencing and transcriptome sequencing of roots at the 3 growth stages revealed an increased level of DNA methylation in the CHH context (H represents A, T, or C) context at r90 compared with r40 and r60. Increased DNA methylation levels were associated with elevated expression of various genes linked to epigenetic regulations, including CHROMOMETHYLASE2 (SmCMT2), Decrease in DNA Methylation 1 (SmDDM1), Argonaute 4 (SmAGO4), and DOMAINS REARRANGED METHYLTRANSFERASE 1 (SmDRM1). Moreover, expression levels of many genes involved in tanshinone and salvianolic acid biosynthesis, such as copalyldiphosphate synthase 5 (SmCPS5), cytochrome P450-related enzyme (SmCYP71D464), geranylgeranyl diphosphate synthase (SmGGPPS1), geranyl diphosphate synthase (SmGPPS), hydroxyphenylpyruvate reductase (SmHPPR), and hydroxyphenylpyruvate dioxygenase (SmHPPD), were altered owing to hyper-methylation, indicating that DNA methylation plays an important role in regulating tanshinone and phenolic acid accumulation. Our data shed light on the epigenetic regulation of root growth and the biosynthesis of active ingredients in S. miltiorrhiza, providing crucial clues for further improvement of active compound production via molecular breeding in S. miltiorrhiza.

Constructing maps between distinct cell fates and parametric conditions by systematic perturbations.

MOTIVATION: Cell fate transitions are common in many developmental processes. Therefore, identifying the mechanisms behind them is crucial. Traditionally, due to complexity of networks and existence of plenty of kinetic parameters, dynamical analysis of biomolecular networks can only be performed by simultaneously perturbing a small number of parameters. Although many efforts have focused on how cell states change under specific perturbations, conversely, how to infer parametric conditions underlying distinct cell fates by systematic perturbations is less clear and needs to be further investigated. RESULTS: In this article, we present a general computational method by integrating systematic perturbations, unsupervised clustering, principal component analysis, and fitting analysis. The method can be used to to construct maps between distinct cell fates and parametric conditions by systematic perturbations. In particular, there are no needs of accurate parameter measurements and occurrence of bifurcations to establish the maps. To validate feasibility and inference performance of the method, we use toggle switch, inner cell mass, and epithelial mesenchymal transition as model systems to show how the maps are constructed and how system parameters encode essential information on cell fates. The maps tell us how systematic perturbations drive cell fate decisions and transitions, and allow us to purposefully predict, manipulate, and even control cell states. The approach is especially helpful in understanding crucial roles of certain parameter combinations during fate transitions. We hope that the approach can provide us valuable information on parametric or perturbation conditions so some specific targets, e.g. directional differentiation, can be realized. AVAILABILITY AND IMPLEMENTATION: No public data are used. The data we used are generated by randomly chosen values of model parameters in certain ranges, and the corresponding parameters are already attached in supplementary materials.

Infection with 'Candidatus Liberibacter asiaticus' improves the fecundity of Diaphorina citri aiding its proliferation: A win-win strategy.

The evolution of insect vector-pathogen relationships has long been of interest in the field of molecular ecology. One system of special relevance, due to its economic impacts, is that between Diaphorina citri and 'Candidatus Liberibacter asiaticus' (CLas), the cause of the severe Asian form of huanglongbing. CLas-positive D. citri are more fecund than their CLas-negative counterparts, boosting opportunities for pathogens to acquire new vector hosts. The molecular mechanism behind this life-history shift remains unclear. Here, we found that CLas promoted ovarian development and increased the expression of the vitellogenin receptor (DcVgR) in ovaries. DcVgR RNAi significantly decreased fecundity and CLas titer in ovaries, extended the preoviposition period, shortened the oviposition period and blocked ovarian development. Given their importance in gene regulation, we explored the role of miRNAs in shaping these phenotypes and their molecular triggers. Our results showed that one miRNA, miR-275, suppressed DcVgR expression by binding to its 3' UTR. Overexpression of miR-275 knocked down DcVgR expression and CLas titer in ovaries, causing reproductive defects that mimicked DcVgR knockdown phenotypes. We focused, further, on roles of the Juvenile Hormone (JH) pathway in shaping the observed fecundity phenotype, given its known impacts on ovarian development. After CLas infection, this pathway was upregulated, thereby increasing DcVgR expression. From these combined results, we conclude that CLas hijacks the JH signalling pathway and miR-275, thereby targeting DcVgR to increase D. citri fecundity. These changes simultaneously increase CLas replication, suggesting a pathogen-vector host mutualism, or a seemingly helpful, but cryptically costly life-history manipulation.

Nutritional support during the first week for infants with bronchopulmonary dysplasia and respiratory distress: a multicenter cohort study in China.

BACKGROUND: Bronchopulmonary dysplasia (BPD) is a major complication affecting the survival rate and long-term outcomes of preterm infants. A large, prospective, multicenter cohort study was conducted to evaluate early nutritional support during the first week of life for preterm infants with a gestational age < 32 weeks and to verify nutritional risk factors related to BPD development. METHODS: A prospective multicenter cohort study of very preterm infants was conducted in 40 tertiary neonatal intensive care units across mainland China between January 1, 2020, and December 31, 2021. Preterm infants who were born at a gestational age < 32 weeks, < 72 h after birth and had a respiratory score > 4 were enrolled. Antenatal and postnatal information focusing on nutritional parameters was collected through medical systems. Statistical analyses were also performed to identify BPD risk factors. RESULTS: The primary outcomes were BPD and severity at 36 weeks postmenstrual age. A total of 1410 preterm infants were enrolled in this study. After applying the exclusion criteria, the remaining 1286 infants were included in this analysis; 614 (47.7%) infants were in the BPD group, and 672 (52.3%) were in the non-BPD group. In multivariate logistic regression model, the following six factors were identified of BPD: birth weight (OR 0.99, 95% CI 0.99-0.99; p = 0.039), day of full enteral nutrition (OR 1.03, 95% CI 1.02-1.04; p < 0.001), parenteral protein > 3.5 g/kg/d during the first week (OR 1.65, 95% CI 1.25-2.17; p < 0.001), feeding type (formula: OR 3.48, 95% CI 2.21-5.49; p < 0.001, mixed feed: OR 1.92, 95% CI 1.36-2.70; p < 0.001; breast milk as reference), hsPDA (OR 1.98, 95% CI 1.44-2.73; p < 0.001), and EUGR ats 36 weeks (OR 1.40, 95% CI 1.02-1.91; p = 0.035). CONCLUSIONS: A longer duration to achieve full enteral nutrition in very preterm infants was associated with increased BPD development. Breastfeeding was demonstrated to have a protective effect against BPD. Early and rapidly progressive enteral nutrition and breastfeeding should be promoted in very preterm infants. TRIAL REGISTRATION: The trial was registered in the Chinese Clinical Trial Registry (No. ChiCTR2000030125 on 24/02/2020) and in www.ncrcch.org (No. ISRCTN84167642 on 25/02/2020).

Noninvasive diagnosis of interstitial fibrosis in chronic kidney disease: a systematic review and meta-analysis.

RATIONALE AND OBJECTIVES: Researchers have delved into noninvasive diagnostic methods of renal fibrosis (RF) in chronic kidney disease, including ultrasound (US), magnetic resonance imaging (MRI), and radiomics. However, the value of these diagnostic methods in the noninvasive diagnosis of RF remains contentious. Consequently, the present study aimed to systematically delineate the accuracy of the noninvasive diagnosis of RF. MATERIALS AND METHODS: A systematic search covering PubMed, Embase, Cochrane Library, and Web of Science databases for all data available up to 28 July 2023 was conducted for eligible studies. RESULTS: We included 21 studies covering 4885 participants. Among them, nine studies utilized US as a noninvasive diagnostic method, eight studies used MRI, and four articles employed radiomics. The sensitivity and specificity of US for detecting RF were 0.81 (95% CI: 0.76-0.86) and 0.79 (95% CI: 0.72-0.84). The sensitivity and specificity of MRI were 0.77 (95% CI: 0.70-0.83) and 0.92 (95% CI: 0.85-0.96). The sensitivity and specificity of radiomics were 0.69 (95% CI: 0.59-0.77) and 0.78 (95% CI: 0.68-0.85). CONCLUSIONS: The current early noninvasive diagnostic methods for RF include US, MRI, and radiomics. However, this study demonstrates that US has a higher sensitivity for the detection of RF compared to MRI. Compared to US, radiomics studies based on US did not show superior advantages. Therefore, challenges still exist in the current radiomics approaches for diagnosing RF, and further exploration of optimized artificial intelligence (AI) algorithms and technologies is needed.

Genome-Wide Identification and Expression Analysis of GATA Family Genes in Dimocarpus longan Lour.

GATA transcription factors, which are DNA-binding proteins with type IV zinc finger binding domains, have a role in transcriptional regulation in biological organisms. They have an indispensable role in the growth and development of plants, as well as in improvements in their ability to face various environmental stresses. To date, GATAs have been identified in many gene families, but the GATA gene in longan (Dimocarpus longan Lour) has not been studied in previous explorations. Various aspects of genes in the longan GATA family, including their identification and classification, the distribution of their positions on chromosomes, their exon/intron structures, a synteny analysis, their expression at different temperatures, concentration of PEG, early developmental stages of somatic embryos and their expression levels in different tissues, and concentrations of exogenous hormones, were investigated in this study. This study showed that the 22 DlGATAs could be divided into four subfamilies. There were 10 pairs of homologous GATA genes in the synteny analysis of DlGATA and AtGATA. Four segmental replication motifs and one pair of tandem duplication events were present among the DlGATA family members. The cis-acting elements located in promoter regions were also found to be enriched with light-responsive elements, which contained related hormone-responsive elements. In somatic embryos, DlGATA4 is upregulated for expression at the globular embryo (GE) stage. We also found that DlGATA expression was strongly up-regulated in roots and stems. The study demonstrated the expression of DlGATA under hormone (ABA and IAA) treatments in embryogenic callus of longan. Under ABA treatment, DlGATA4 was up-regulated and the other DlGATA genes did not respond significantly. Moreover, as demonstrated with qRT-PCR, the expression of DlGATA genes showed strong up-regulated expression levels under 100 µmol·L-1 concentration IAA treatment. This experiment further studied these and simulated their possible connections with a drought response mechanism, while correlating them with their expression under PEG treatment. Overall, this experiment explored the GATA genes and dug into their evolution, structure, function, and expression profile, thus providing more information for a more in-depth study of the characteristics of the GATA family of genes.

Phosphoethanolamine cytidylyltransferase ameliorates mitochondrial function and apoptosis in hepatocytes in T2DM in vitro.

Liver function indicators are often impaired in patients with type 2 diabetes mellitus (T2DM), who present higher concentrations of aspartate aminotransferase, alanine aminotransferase, and gamma-glutamyl transferase than individuals without diabetes. However, the mechanism of liver injury in patients with T2DM has not been clearly elucidated. In this study, we performed a lipidomics analysis on the liver of T2DM mice, and we found that phosphatidylethanolamine (PE) levels were low in T2DM, along with an increase in diglyceride, which may be due to a decrease in the levels of phosphoethanolamine cytidylyltransferase (Pcyt2), thus likely affecting the de novo synthesis of PE. The phosphatidylserine decarboxylase pathway did not change significantly in the T2DM model, although both pathways are critical sources of PE. Supplementation with CDP-ethanolamine (CDP-etn) to increase the production of PE from the CDP-etn pathway reversed high glucose and FFA (HG&FFA)-induced mitochondrial damage including increased apoptosis, decreased ATP synthesis, decreased mitochondrial membrane potential, and increased reactive oxygen species, whereas supplementation with lysophosphatidylethanolamine, which can increase PE production in the phosphatidylserine decarboxylase pathway, did not. Additionally, we found that overexpression of PCYT2 significantly ameliorated ATP synthesis and abnormal mitochondrial morphology induced by HG&FFA. Finally, the BAX/Bcl-2/caspase3 apoptosis pathway was activated in hepatocytes of the T2DM model, which could also be reversed by CDP-etn supplements and PCYT2 overexpression. In summary, in the liver of T2DM mice, Pcyt2 reduction may lead to a decrease in the levels of PE, whereas CDP-etn supplementation and PCYT2 overexpression ameliorate partial mitochondrial function and apoptosis in HG&FFA-stimulated L02 cells.

FNDC5/irisin facilitates muscle-adipose-bone connectivity through ubiquitination-dependent activation of runt-related transcriptional factors RUNX1/2.

In the past decade, the cleavage protein irisin derived from fibronectin type III domain-containing protein 5 (FNDC5) in exercise-stimulated skeletal muscle has increasingly become a biomarker associated with metabolic syndrome and osteoporosis in humans. However, it is unclear how this protein facilitates muscle-adipose-bone connectivity in metabolic and skeletal homeostasis. In this study, we unexpectedly observed that the FNDC5 gene can be markedly activated during the differentiation of brown adipocytes but not white adipocytes, and that FNDC5 is specifically expressed in mouse brown adipose tissues (BATs). But unlike it in the skeletal muscles, the expression of FNDC5/irisin in BAT is promoted by cold exposure rather than exercise in mice. Analysis of promoter activity and chromatin immunoprecipitation further showed that peroxisome proliferator-activated receptor γ coactivator-1α and thyroid hormone receptors cooperate on the FNDC5 gene promoter to induce its transcription. We found that FNDC5/irisin stimulates the runt-related transcriptional factors RUNX1/2 via a focal adhesion kinase-dependent pathway in both bone and subcutaneous white adipose tissues. Mechanistically, focal adhesion kinase is stimulated by FNDC5/irisin and then facilitates E3 ubiquitin-protein ligase WW domain-containing protein 2 to ubiquitinate and subsequently activate RUNX1/2, culminating in the activation of osteoblast-related or thermogenesis-related genes. Interestingly, the PR domain containing protein 16 that is crucial for subcutaneous white adipose "browning" and skeletal development was found to form a complex with RUNX1/2 in a WW domain-containing protein 2-dependent manner. These findings elucidate a signaling mechanism by which FNDC5/irisin supports the muscle-adipose-bone connectivity, especially BAT-bone connectivity.

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads.

Contigs assembled from the third-generation sequencing long reads are usually more complete than the second-generation short reads. However, the current algorithms still have difficulty in assembling the long reads into the ideal complete and accurate genome, or the theoretical best result [1]. To improve the long read contigs and with more and more fully sequenced genomes available, it could still be possible to use the similar genome-assisted reassembly method [2], which was initially proposed for the short reads making use of a closely related genome (similar genome) to the sequencing genome (target genome). The method aligns the contigs and reads to the similar genome, and then extends and refines the aligned contigs with the aligned reads. Here, we introduce AlignGraph2, a similar genome-assisted reassembly pipeline for the PacBio long reads. The AlignGraph2 pipeline is the second version of AlignGraph algorithm proposed by us but completely redesigned, can be inputted with either error-prone or HiFi long reads, and contains four novel algorithms: similarity-aware alignment algorithm and alignment filtration algorithm for alignment of the long reads and preassembled contigs to the similar genome, and reassembly algorithm and weight-adjusted consensus algorithm for extension and refinement of the preassembled contigs. In our performance tests on both error-prone and HiFi long reads, AlignGraph2 can align 5.7-27.2% more long reads and 7.3-56.0% more bases than some current alignment algorithm and is more efficient or comparable to the others. For contigs assembled with various de novo algorithms and aligned to similar genomes (aligned contigs), AlignGraph2 can extend 8.7-94.7% of them (extendable contigs), and obtain contigs of 7.0-249.6% larger N50 value and 5.2-87.7% smaller number of indels per 100 kbp (extended contigs). With genomes of decreased similarities, AlignGraph2 also has relatively stable performance. The AlignGraph2 software can be downloaded for free from this site: https://github.com/huangs001/AlignGraph2.

Genomic and phenotypic analysis of a novel clinical isolate of Corynebacterium pyruviciproducens.

BACKGROUND: Corynebacterium pyruviciproducens is a recently described species of Corynebacterium. There are few reports on the microbiological characteristics of the new species, and there is a lack of reports on the genomic analysis of the species. RESULTS: This study involved a clinical isolate from the pus of a hospital patient with sebaceous gland abscesses. The clinically isolated strain was identified as C. pyruviciproducens strain WYJY-01. In this study, referring to Koch's postulates, we observed the pathological changes of animal models infected by intraperitoneal injection and subcutaneous injection of pure culture of the strain WYJY-01. Furthermore, the strain WYJY-01 was isolated and cultured again from animal models' subcutaneous abscess drainage fluid. Subsequently, the genomics of the strain WYJY-01 was analyzed. By comparing various gene databases, this study predicted the core secondary metabolite gene cluster of the strain WYJY-01, virulence factor genes carried by prophage, pathogenicity islands, and resistance islands. In addition, the genomes of C. pyruviciproducens strain WYJY-01, ATCC BAA-1742 T, and UMB0763 were analyzed by comparative genomics, and the differential genes of strain WYJY-01 were compared, and their functions were analyzed. CONCLUSION: The findings showed that the strain WYJY-01 had pathogenicity, supplementing the phenotype characteristics of C. pyruviciproducens. Meanwhile, this research revealed the possible molecular mechanism of the pathogenicity of the strain WYJY-01 at the gene level through whole genome sequence analysis, providing a molecular basis for further research.

Epidemiological characteristics of norovirus infection in pediatric patients during the COVID-19 pandemic.

To assess the epidemiological characteristics of norovirus infection. We included 5564 patients under the age of 18 years who visited the hospital in which the study took place from December 2020 to November 2022 with a primary diagnosis of acute diarrhea. Clinical information was extracted from the electronic health record system. We calculated the prevalence of norovirus infection by age, gender, season, year, and type of patients. A nonlinear association between age and prevalence rates was assessed using a restricted cubic spline regression model. A total of 5564 patients completed the test for human norovirus, among whom 1442 (25.9%) tested positive. The prevalence of norovirus infection was significantly lower in 2022 than in 2021 (35.9% vs. 53.7%, p < 0.001), and the highest prevalence was observed in winter (35.1%) and then followed by autumn (27.5%). Regarding the age pattern, the highest rate was seen in children aged 1-3 years (37.5%). Children at age 1.5 years may have the highest risk of having norovirus infection (Pnonlinear < 0.001). The prevalence of norovirus infection of norovirus during the COVID-19 pandemic was similar to that before the pandemic shown in literatures. A relatively high rate was observed in cool seasons and in younger children (i.e., 1-3 years).

Ginsenoside Rh2 augmented anti-PD-L1 immunotherapy by reinvigorating CD8+ T cells via increasing intratumoral CXCL10.

Profiting from the sustained clinical improvement and prolonged patient survival, immune checkpoint blockade of programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) axis has emerged as a revolutionary cancer therapy approach. However, the anti-PD-1/PD-L1 antibodies only achieve a clinical response rate of approximately 20%. Herein, we identified a novel combination strategy that Chinese medicine ginseng-derived ginsenoside Rh2 (Rh2) markedly improved the anti-cancer efficacy of anti-PD-L1 antibody in mice bearing MC38 tumor. Rh2 combined with anti-PD-L1 antibody (combo treatment) further triggered the infiltration, proliferation and activation of CD8+ T cells in the tumor microenvironment (TME). Depletion of CD8+ T cells by mouse CD8 blocking antibody abolished the anti-cancer effect of combo treatment totally. Mechanistically, combo treatment further increased the expression of CXCL10 through activating TBK1-IRF3 signaling pathway, explaining the increased infiltration of T cells. Employing anti- CXC chemokine receptor 3 (CXCR3) blocking antibody prevented the T cells infiltration and abolished the anti-cancer effect of combo treatment. Meanwhile, combo treatment increased the percentage of M1-like macrophages and raised the ratio of M1/M2 macrophages in TME. By comparing the anti-cancer effect of combo treatment among MC38, CT26 and 4T1 tumors, resident T cells were considered as a prerequisite for the effectiveness of combo treatment. These findings demonstrated that Rh2 potentiated the anti-cancer effect of PD-L1 blockade via promoting the T cells infiltration and activation, which shed a new light on the combination strategy to enhance anti-PD-L1 immunotherapy by using natural product Rh2.

Production, characterization, and application of phage-derived PK34 recombinant anti-microbial peptide.

PK34 is a D29 mycobacteriophage-derived anti-microbial peptide (AMP) with anti-Mycobacterium tuberculosis activity. It is expected to become an auxiliary drug for the treatment of M. tuberculosis infection, or as a template for the development of anti-M. tuberculosis drugs. The focus of this paper is to obtain recombinant PK34 by a novel method of prokaryotic expression and purification by affinity chromatography. The minimum inhibitory concentration (MIC) of recombinant PK34 was better than that of synthetic PK34 as measured by the microplate-based Alamar Blue assay (MABA). In order to further compare the different anti-bacterial effects of PK34 obtained by the two methods on M. tuberculosis, the bacterial changes after drug incubation were observed at the microscopic level by transmission electron microscopy (TEM). In order to apply PK34 to clinical treatment earlier in the future, this paper tested the maximum non-toxic concentration of recombinant PK34 to the two most studied immune cells, RAW264.7 and THP-1, through cytotoxicity experiments. The maximum non-toxic concentration was the same as the MIC of recombinant PK34 to M. tuberculosis H37Rv, and both were 12.5 µg/mL. The monoclonal antibodies against PK34 and their hybridoma cell lines were prepared using recombinant PK34 as the antigen. Next, we obtained the gene sequence of the monoclonal antibody, which was prepared for the basic research of PK34 in M. tuberculosis treatment. In addition, the possible molecular docking mode between PK34 and trehalose-6,6-dimycolate (TDM) was predicted by AI simulation. To sum up, this paper provides a new idea for the birth of more new AMPs of the same type as PK34 in the future. KEY POINTS: • Design and prepare a novel recombinant PK34 anti-microbial peptide. • Recombinant PK34 has higher purity and anti-bacterial activity than synthetic PK34. • The monoclonal antibody against recombinant PK34 was prepared and sequenced.

LncRNA CARMN facilitates odontogenic differentiation of dental pulp cells by impairing EZH2.

OBJECTIVE: This study aimed to reveal the potential role of CARMN in odontogenic differentiation of dental pulp cells (DPCs). METHODS: Laser capture microdissection was used to detect Carmn in DPCs and odontoblasts in P0 mice. After manipulating CARMN expression in odontogenic differentiation induced hDPCs, the state of odontogenic differentiation was evaluated by ALP staining, ARS, and related marker expression in qRT-PCR and western blotting. The subcutaneous transplantation of HA/ß-TCP loaded with hDPCs was performed to verify CARMN's role in promoting odontogenic differentiation in vivo. RNAplex and RIP were employed to reveal potential mechanism of CARMN in hDPCs. RESULTS: CARMN expressed more abundantly in odontoblasts than DPCs in P0 mice. CARMN expression boosted during in vitro odontogenic differentiation of hDPCs. CARMN overexpression enhanced odontogenic differentiation of hDPCs in vitro, while inhibition impaired the process. CARMN overexpression in HA/ß-TCP composites promoted more mineralized nodule formation in vivo. CARMN knockdown led to soared EZH2, while CARMN overexpression brought about EZH2 inhibition. CARMN functioned via direct interaction with EZH2. CONCLUSIONS: The results uncovered CARMN as a modulator during the odontogenic differentiation of DPCs. CARMN promoted odontogenic differentiation of DPCs by impairing EZH2.

The association between parental risks and childhood development: findings from a community-based survey in East China.

BACKGROUND: Nurturing care is necessary for optimal early childhood development. This study aimed to investigate the prevalence of parental risks in rural East China and assess their impacts on early development in children younger than three years old. METHODS: This community-based cross-sectional survey was conducted among 3852 caregiver-child pairs in Zhejiang Province from December 2019 to January 2020. Children aged 0 to 3 years were recruited from China's Early Childhood Development Program (ECD). Local child health care providers conducted face-to-face interviews with the primary caregivers. Demographic information of the participants was collected by questionnaire. Each child was screened for parental risk through the Parental Risk Checklist designed by the ECD program. The Ages and Stages Questionnaire (ASQ) was used to identify children with potential developmental delays. Multinomial logistic regression model and linear trend test were applied to assess the association between parental risks and suspected developmental delays. RESULTS: Among the 3852 children included in the analyses, 46.70% had at least one parental risk and 9.01% presented suspected developmental delays in any domain of ASQ. Parental risk was statistically associated with the overall suspected developmental delay in young children (Relative Risk Ratio (RRR): 1.36; 95% confidence interval (CI): 1.08, 1.72; P = 0.010) after adjusting potential confounders. Compared with children with no parental risk, children exposed to 3 or more parental risks had 2.59, 5.76, 3.95, and 2.84 times higher risk of the suspected developmental delay in overall ASQ, communication, problem-solving, and personal-social domain, respectively (P values < 0.05). The linear trend tests found that the more parental risks, the higher possibility of developmental delay (P values < 0.05). CONCLUSIONS: Parental risks are prevalent among children under three years in rural East China, which may increase the risk of developmental delays in children. Meanwhile, parental risk screening can be used to recognize poor nurturing care in primary health care settings. Targeted interventions are warranted to improve nurturing care for optimal early childhood development.

Transient apical peak pressure measurement of Er:YAG laser-activated irrigation in different in vitro tooth models using a high-frequency sensor system.

The transient apical pressure side effect is an important safety consideration for Er:YAG laser-activated irrigation (LAI). Therefore, this study aimed to measure the transient apical peak pressure (TAPP) of LAI under different laser settings in various tooth models using a high-frequency sensor system. Tooth models with different pulp chamber structures, apical diameters, and curvatures were prepared using transparent resin and filled with deionised water. The Er:YAG laser fibre was placed 3 mm from the root canal orifice. Irrigation was performed at 10-40 mJ and 20-50 Hz using the super short pulse mode. The TAPP was measured using a 50,000-sample/second pressure sensor connected to the models' apices. The TAPP of LAI was significantly higher than that of other chemical preparation methods. Among all investigated factors, pulp chamber anatomy and apical diameters had the greatest effects and were highly related to the apical peak pressure. Root canal curvature showed no direct correlation with TAPP. The larger the final prepared working width, the greater the TAPP. Furthermore, both pulse energy and frequency had positive correlations with TAPP. In conclusion, tooth anatomy factors and laser parameter settings influenced TAPP during Er:YAG LAI. Therefore, proper settings of laser parameters are important to improve the safety of Er:YAG LAI.

Identifying key factors in cell fate decisions by machine learning interpretable strategies.

Cell fate decisions and transitions are common in almost all developmental processes. Therefore, it is important to identify the decision-making mechanisms and important individual molecules behind the fate decision processes. In this paper, we propose an interpretable strategy based on systematic perturbation, unsupervised hierarchical cluster analysis (HCA), machine learning (ML), and Shapley additive explanation (SHAP) analysis for inferring the contribution and importance of individual molecules in cell fate decision and transition processes. In order to verify feasibility of the approach, we apply it to the core epithelial to mesenchymal transition (EMT)-metastasis network. The key factors identified in EMT-metastasis are consistent with relevant experimental observations. The approach presented here can be applied to other biological networks to identify important factors related to cell fate decisions and transitions.

A biomedical event extraction method based on fine-grained and attention mechanism.

BACKGROUND: Biomedical event extraction is a fundamental task in biomedical text mining, which provides inspiration for medicine research and disease prevention. Biomedical events include simple events and complex events. Existing biomedical event extraction methods usually deal with simple events and complex events uniformly, and the performance of complex event extraction is relatively low. RESULTS: In this paper, we propose a fine-grained Bidirectional Long Short Term Memory method for biomedical event extraction, which designs different argument detection models for simple and complex events respectively. In addition, multi-level attention is designed to improve the performance of complex event extraction, and sentence embeddings are integrated to obtain sentence level information which can resolve the ambiguities for some types of events. Our method achieves state-of-the-art performance on the commonly used dataset Multi-Level Event Extraction. CONCLUSIONS: The sentence embeddings enrich the global sentence-level information. The fine-grained argument detection model improves the performance of complex biomedical event extraction. Furthermore, the multi-level attention mechanism enhances the interactions among relevant arguments. The experimental results demonstrate the effectiveness of the proposed method for biomedical event extraction.

Hyperuricemia induces liver injury by upregulating HIF-1α and inhibiting arginine biosynthesis pathway in mouse liver and human L02 hepatocytes.

The molecular mechanisms of uric acid (UA)-induced liver injury has not been clearly elucidated. In this study, we aimed to investigate the effect and action mechanisms of UA in liver injury. We analyzed the damaging effect of UA on mouse liver and L02 cells and subsequently performed metabolomics studies on L02 cells to identify abnormal metabolic pathways. Finally, we verified transcription factors that regulate related metabolic enzymes. UA directly activated the hepatic NLRP3 inflammasome and Bax apoptosis pathway invivo and invitro. Related metabolites in the arginine biosynthesis pathway (or urea cycle), l-arginine and l-argininosuccinate were decreased, and ammonia was increased in UA-stimulated L02 cells, which was mediated by carbamoyl phosphate synthase 1 (CPS1), argininosuccinate synthase (ASS) and argininosuccinate lyase (ASL) downregulation. UA upregulated hypoxia inducible factor-1alpha (HIF-1α) invivo and invitro, and HIF-1α inhibition alleviated the UA-induced ASS downregulation and hepatocyte injury. In conclusion, UA upregulates HIF-1α and inhibits urea cycle enzymes (UCEs). This leads to liver injury, with evidence of hepatocyte inflammation, apoptosis and oxidative stress.