Optimal settings for different tooth types in the virtual bracket removal technique.

OBJECTIVES: To determine the optimal settings for reconstructing the buccal surfaces of different tooth types using the virtual bracket removal (VBR) technique. MATERIALS AND METHODS: Ten postbonded digital dentitions (with their original prebonded dentitions) were enrolled. The VBR protocol was carried out under five settings from three commonly used computer-aided design (CAD) systems: OrthoAnalyzer (O); Meshmixer (M); and curvature (G2), tangent (G1), and flat (G0) from Geomagic Studio. The root mean squares (RMSs) between the reconstructed and prebonded dentitions were calculated for each tooth and compared with the clinically acceptable limit (CAL) of 0.10 mm. RESULTS: The overall prevalences of RMSs below the CAL were 66.80%, 70.08%, 62.30%, 94.83%, and 56.15% under O, M, G2, G1, and G0, respectively. For the upper dentition, the mean RMSs were significantly lower than the CAL for all tooth types under G1 and upper incisors and canines under M and G2. For the lower dentition, the mean RMSs were significantly lower than the CAL for all tooth types under G1 and lower incisors and canines under M, G2, and G0 (all P < .05). Additionally, the mean RMSs of all teeth under G1 were significantly lower than those under the other settings (all P < .001). CONCLUSIONS: The optimal settings varied among different tooth types. G1 performed best for most tooth types compared to the other four settings.

TissueSpace: a web tool for rank-based transcriptome representation and its applications in molecular medicine.

BACKGROUND: Cross-platform or cross-experiment transcriptome data is hard to compare as the original gene expression values from different platforms cannot be compared directly. The inherent gene expression ranking information is rarely utilized. OBJECTIVE: Use of reduced vector to represent transcriptome data independent of platforms. METHODS: Thus, we turned the expression profile into a rank vector, where a higher expression has a higher rank value, then applied Latent semantic analysis (LSA) to get compact and continuous 100-dimensional vector representations for samples. RESULTS: Results showed that the reconstructed vector has a precision of 96.7% in recovering tissue labels from an independent dataset. A user-friendly tool TissueSpace was developed, which provides users the following functionalities: (1) convert different gene ID types to Ensembl gene IDs; (2) project any human transcriptome profile to get vector representation for downstream analysis; (3) functional enrichment for each of the 100-dimensional vector features. Case studies for its applications in human common diseases indicate its usefulness. CONCLUSIONS: TissueSpace could be used to generate testable hypotheses for translational medicine. The TissueSpace tool is available at http://bioinformatics.fafu.edu.cn/tissuespace/ .

Fabrication of oxidized sodium alginate-collagen heterogeneous bilayer barrier membrane with osteogenesis-promoting ability.

Guided bone regeneration technique is an effective approach to repair bone defects, in which a barrier membrane is essential. However, the collagen barrier membranes commonly used lose stability quickly, leading to connective tissue invasion and failure of osteogenesis. Herein, we presented an oxidized sodium alginate (OSA)-collagen heterogeneous bilayer barrier membrane with well-controlled pore size and osteogenesis-promoting ability. The OSA crosslinking significantly improved the structural stability, compressive strength, swelling behavior, and slowed down the biodegradation rate of collagen membranes. Meanwhile, the collagen-based membranes exhibited superior cytocompatibility, osteogenesis-promotion, and barrier function against fibroblasts. Especially, the osteogenic differentiation was most promoted on the membrane with a large pore size (240-310 µm), while the barrier function was most improved on the membrane with a small pore size (30-60 µm). Then the above two membranes were combined together to obtain a heterogeneous bilayer membrane. This bilayer barrier membrane showed excellent osteogenesis-promoting ability in rats.

Nonsurgical treatment of a hyperdivergent skeletal Class III patient with mini-screw-assisted mandibular dentition distalization and flattening of the occlusal plane.

Treatment of hyperdivergent skeletal Class III malocclusion is challenging for orthodontists, and orthognathic-orthodontic treatment is usually required. This report presents the successful nonsurgical treatment of a 20-year-old man who had a skeletal Class III malocclusion with anterior open bite, anterior and posterior crossbite, hyperdivergent growth pattern, steep occlusal plane, early loss of three first molars, and an uncommon convex profile with a retruded chin. An orthodontic camouflage treatment plan was chosen based on the etiology and the patient's complaints. Tooth #37 was extracted. Miniscrews were used for uprighting and intruding of the lower molars, distalization of the lower dentition, and flattening of the occlusal plane. After 34 months of active treatment, Class I relationships, proper anterior overjet and overbite, flat occlusal plane, and an esthetic facial profile were achieved. The results demonstrated that the biomechanics involved in the nonsurgical treatment assisted with miniscrews to distalize the mandibular dentition and flatten the occlusal plane while keeping the mandibular plane stable was effective for treating this hyperdivergent skeletal Class III patient with a convex profile and anterior open bite.

lncRNA NEAT1 ameliorates LPS­induced inflammation in MG63 cells by activating autophagy and suppressing the NLRP3 inflammasome.

The mechanisms of inflammation in bone and joint tissue are complex and involve long non­coding RNAs (lncRNAs), which play an important role in this process. The aim of the present study was to screen out differentially expressed genes in human osteoblasts stimulated by inflammation, and to further explore the mechanisms underlying inflammatory responses and the functional activity of human osteoblasts through bioinformatics methods and in vitro experiments. For this purpose, MG63 cells were stimulated with various concentrations of lipopolysaccharide (LPS) for different periods of time to construct an optimal inflammatory model and RNA sequencing was then performed on these cells. The levels of nuclear enriched abundant transcript 1 (NEAT1), various inflammatory factors, Nod­like receptor protein 3 (NLRP3) protein and osteogenesis­related proteins, as well as the levels of cell apoptosis­ and cell cycle­related markers were measured in MG63 cells stimulated with LPS, transfected with NEAT1 overexpression plasmid and treated with bexarotene by western blot analysis, RT­qPCR, immunofluorescence, FISH, TEM and flow cytometry. There were 427 differentially expressed genes in the LPS­stimulated MG63 cells, in which NEAT1 was significantly downregulated. LPS upregulated the expression of inflammatory cytokines and NLRP3, inhibited the expression of autophagy­related and osteogenesis­related proteins, promoted apoptosis and altered the cell cycle, which was partially inhibited by NEAT1 overexpression and promoted by bexarotene. LPS stimulated inflammation in the MG63 cells and inhibited the retinoid X receptor (RXR)­α to downregulate the expression of NEAT1 and decrease levels of autophagy, which promoted the activation of NLRP3 and the release of inflammatory factors, and impaired the functional activity of osteoblasts, thus promoting the development of inflammation.

Rice Stress-Resistant SNP Database.

BACKGROUND: Rice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Thus, it is of great importance to perform in-depth explorations on the genes that are closely associated with the stress-resistant traits in rice. The existing rice SNP databases have made considerable contributions to rice genomic variation information but none of them have a particular focus on integrating stress-resistant variation and related phenotype data into one web resource. RESULTS: Rice Stress-Resistant SNP database (http://bioinformatics.fafu.edu.cn/RSRS) mainly focuses on SNPs specific to biotic and abiotic stress-resistant ability in rice, and presents them in a unified web resource platform. The Rice Stress-Resistant SNP (RSRS) database contains over 9.5 million stress-resistant SNPs and 797 stress-resistant candidate genes in rice, which were detected from more than 400 stress-resistant rice varieties. We incorporated the SNPs function, genome annotation and phenotype information into this database. Besides, the database has a user-friendly web interface for users to query, browse and visualize a specific SNP efficiently. RSRS database allows users to query the SNP information and their relevant annotations for individual variety or more varieties. The search results can be visualized graphically in a genome browser or displayed in formatted tables. Users can also align SNPs between two or more rice accessions. CONCLUSION: RSRS database shows great utility for scientists to further characterize the function of variants related to environmental stress-resistant ability in rice.

Periodontal ligament fibroblasts regulate osteoblasts by exosome secretion induced by inflammatory stimuli.

OBJECTIVES: This study evaluated the role of human periodontal ligament fibroblasts (hPDLFs)-derived exosomes in periodontitis progression and discovered whether hPDLFs influence bone remodeling activity via exosome secretion. MATERIALS AND METHODS: Exosomes were isolated and quantified from Porphyromonas gingivalis lipopolysaccharide (LPS)-treated primary hPDLFs and evaluated by western blotting, dynamic light scattering, and transmission electron microscopy. GW4869 was used to block exosome secretion in conditioned medium (CM). hPDLFs-derived CM, CM containing GW4869 (CM + GW4869) and exosomes were used to stimulate MG-63 cell lines. The expression levels of proinflammatory mediators, osteogenic genes, and osteoclastogenesis-related genes were measured by quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, western blotting, and alkaline phosphatase staining. RESULTS: Exosome-enriched protein and total exosomal protein levels were higher in the LPS-treated group than in the vehicle controls. hPDLFs-derived exosomes were incorporated into MG-63 osteoblasts and slightly upregulated the expression of Interleukin-6 and tumor necrosis factor-alpha. CM and exosomes inhibited alkaline phosphatase, Collagen-I, Runt-related transcription factor 2, and Osteoprotegerin expression as well as ALP activity, and blocking exosome secretion by GW4869 eliminated the inhibitory effects. CONCLUSION: These results indicate that LPS-pretreated hPDLFs induce inflammation and inhibit osteogenic activity of osteoblasts through secreting exosomes. This study provides a potential mechanism by which localized periodontal inflammation may influence bone remodeling by release exosomes.

YAP regulates periodontal ligament cell differentiation into myofibroblast interacted with RhoA/ROCK pathway.

During orthodontic tooth movement (OTM), periodontal ligament cells (PDLCs) receive the mechanical stimuli and transform it into myofibroblasts (Mfbs). Indeed, previous studies have demonstrated that mechanical stimuli can promote the expression of Mfb marker α-smooth muscle actin (α-SMA) in PDLCs. Transforming growth factor ß1 (TGF-ß1), as the target gene of yes-associated protein (YAP), has been proven to be involved in this process. Here, we sought to assess the role of YAP in Mfbs differentiation from PDLCs. The time-course expression of YAP and α-SMA was manifested in OTM model in vivo as well as under tensional stimuli in vitro. Inhibition of RhoA/Rho-associated kinase (ROCK) pathway using Y27632 significantly reduced tension-induced Mfb differentiation and YAP expression. Moreover, overexpression of YAP with lentiviral transfection in PDLCs rescued the repression effect of Mfb differentiation induced by Y27632. These data together suggest a crucial role of YAP in regulating tension-induced Mfb differentiation from PDLC interacted with RhoA/ROCK pathway.

Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks.

Caenorhabditis elegans (C. elegans) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through systematic analysis of gene co-expression relationships. We collected 2101 microarray data from National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), and identified 48 modules of co-expressed genes that correspond to tissues, development stages, and other experimental conditions. These modules provide an overview of the transcriptional organizations that may work under different conditions. By analyzing higher-order module networks, we found that nucleus and plasma membrane modules are more connected than other intracellular modules. Module-based gene function annotation may help to extend the candidate cuticle gene list. A comparison with other published data validates the credibility of our result. Our findings provide a new source for future gene discovery in C. elegans.

Transversal changes, space closure, and efficiency of conventional and self-ligating appliances : A quantitative systematic review.

OBJECTIVE: Self-ligating brackets (SLBs) were compared to conventional brackets (CBs) regarding their effectiveness on transversal changes and space closure, as well as the efficiency of alignment and treatment time. METHODS: All previously published randomized controlled clinical trials (RCTs) dealing with SLBs and CBs were searched via electronic databases, e.g., MEDLINE, Cochrane Central Register of Controlled Trials, EMBASE, World Health Organization International Clinical Trials Registry Platform, Chinese Biomedical Literature Database, and China National Knowledge Infrastructure. In addition, relevant journals were searched manually. Data extraction was performed independently by two reviewers and assessment of the risk of bias was executed using Cochrane Collaboration's tool. Discrepancies were resolved by discussion with a third reviewer. Meta-analyses were conducted using Review Manager (version 5.3). RESULTS: A total of 976 patients in 17 RCTs were included in the study, of which 11 could be produced quantitatively and 2 showed a low risk of bias. Meta-analyses were found to favor CB for mandibular intercanine width expansion, while passive SLBs were more effective in posterior expansion. Moreover, CBs had an apparent advantage during short treatment periods. However, SLBs and CBs did not differ in closing spaces. CONCLUSIONS: Based on current clinical evidence obtained from RCTs, SLBs do not show clinical superiority compared to CBs in expanding transversal dimensions, space closure, or orthodontic efficiency. Further high-level studies involving randomized, controlled, clinical trials are warranted to confirm these results.

Differences between active and passive self-ligating brackets for orthodontic treatment : Systematic review and meta-analysis based on randomized clinical trials.

PURPOSE: In orthodontic treatment, the effects of differences in the design between active and passive self-ligating bracket (ASLB and PSLB, respectively) are usually neglected. This study investigated differences in effectiveness and efficiency between ASLBs and PSLBs. METHODS: To identify randomized, controlled clinical trials (RCTs) comparing ASLB with PSLB, the electronic databases Medline, Embase, Cochrane Central Register of Controlled Trials, Chinese Biomedical Literature Database, China National Knowledge Infrastructure, and Chinese Medical Journal Database were searched without language or time limits. Relevant available dental journals and reference lists from included studies were manually searched for applicable reports. Meta-analyses were conducted with the Review Manager program. Two independent reviewers performed all search processes; disagreements were discussed with a third reviewer. RESULTS: Eight studies were included in the systematic review, of which six were included in the meta-analysis due to the data consistency. Three had a low risk of bias, four had an unclear risk of bias, and one had a high risk of bias. With regard to alignment efficiency, meta-analysis favors ASLB [mean difference (MD) -10.24 days, 95% confidence interval (CI) -17.68 to -2.80]. However, the same analysis does not favor either design in terms of width change due to treatment for intercanine (MD -0.49 mm, 95% CI -1.10 to 0.13 mm) interfirst premolar (MD -0.07 mm, 95% CI -0.69, 0.56 mm) intersecond premolar (MD -0.58 mm, 95% CI -1.25 to 0.08 mm) and intermolar (MD 0.10 mm, 95% CI -0.82 to 1.02 mm) width. CONCLUSIONS: Based on current clinical evidence from RCTs, ASLB appears to be more efficient for alignment, while neither design shows an advantage for width change. Further research is needed to confirm present results.

Sclerostin Promotes Bone Remodeling in the Process of Tooth Movement.

Tooth movement is a biological process of bone remodeling induced by mechanical force. Sclerostin secreted by osteocytes is mechanosensory and important in bone remodeling. However, little is known regarding the role of sclerostin in tooth movement. In this study, models of experimental tooth movement were established in rats and mice. Sclerostin expression was investigated with immunohistochemistry staining, and osteoclastic activity was analyzed with tartrate-resistant acid phosphatase (TRAP) staining. MLO-Y4 osteocyte-like cells underwent uniaxial compression and tension stress or were cultured in hypoxia conditions. Expression of sclerostin was assessed by RT-qPCR and ELISA. MLO-Y4 cells were cultured with recombinant human sclerostin (rhSCL) interference and then co-cultured with RAW264.7 osteoclast precursor cells. Expressions of RANKL and OPG were analyzed by RT-qPCR, and osteoclastic activity was assessed by TRAP staining. During tooth movement, sclerostin was expressed differently in compression and tension sites. In SOST knock-out mice, there were significantly fewer TRAP-positive cells than in WT mice during tooth movement in compression sites. In-vitro studies showed that the expression of sclerostin in MLO-Y4 osteocyte-like cells was not different under a uniaxial compression and tension force, whereas hypoxia conditions significantly increased sclerostin expression in MLO-Y4 cells. rhSCL interference increased the expression of RANKL and the RANKL/OPG ratio in MLO-Y4 cells and the osteoclastic induction ability of MLO-Y4 cells in experimental osteocyte-osteoclast co-culture. These data suggest that sclerostin plays an important role in the bone remodeling of tooth movement.