Objectives
This study aimed to establish a difference in mandibular bone density between bruxer and non-bruxer patients, based on panoramic radiographs.
Methods
Panoramic radiographs of bruxer and ...non-bruxer patients were analyzed with ImageJ
®
. Several radiological determinants were studied on the patients' panoramic radiographs: gray values of cancellous bone and cortical bone, and bony exostoses at the mandibular angle.
Results
Thirty-seven bruxers and forty-seven non-bruxers were included in the study.
A statistically significant difference (
p
< 0.05) was noted in the cancellous to cortical bone ratios of bruxers and non-bruxers: the density of cancellous bone was greater in bruxers than in non-bruxers.
The number of bony exostoses at the mandibular angle was significantly higher in bruxers (
p
< 0.05).
Conclusions
This study obtained radiological determinants of bruxism from panoramic radiographs. Further studies are needed to supplement this preliminary approach, especially via the analysis of three-dimensional imaging to overcome the limitations of panoramic radiography.
Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are ...challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms.
Abstract
DNA replication initiates from multiple genomic locations called replication origins. In metazoa, DNA sequence elements involved in origin specification remain elusive. Here, we examine ...pluripotent, primary, differentiating, and immortalized human cells, and demonstrate that a class of origins, termed core origins, is shared by different cell types and host ~80% of all DNA replication initiation events in any cell population. We detect a shared G-rich DNA sequence signature that coincides with most core origins in both human and mouse genomes. Transcription and G-rich elements can independently associate with replication origin activity. Computational algorithms show that core origins can be predicted, based solely on DNA sequence patterns but not on consensus motifs. Our results demonstrate that, despite an attributed stochasticity, core origins are chosen from a limited pool of genomic regions. Immortalization through oncogenic gene expression, but not normal cellular differentiation, results in increased stochastic firing from heterochromatin and decreased origin density at TAD borders.
Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases ...and used in a plethora of biological applications. This calls for comprehensive benchmarking of public PWM models with large experimental reference sets.
Here we report results from all-against-all benchmarking of PWM models for DNA binding sites of human TFs on a large compilation of in vitro (HT-SELEX, PBM) and in vivo (ChIP-seq) binding data. We observe that the best performing PWM for a given TF often belongs to another TF, usually from the same family. Occasionally, binding specificity is correlated with the structural class of the DNA binding domain, indicated by good cross-family performance measures. Benchmarking-based selection of family-representative motifs is more effective than motif clustering-based approaches. Overall, there is good agreement between in vitro and in vivo performance measures. However, for some in vivo experiments, the best performing PWM is assigned to an unrelated TF, indicating a binding mode involving protein-protein cooperativity.
In an all-against-all setting, we compute more than 18 million performance measure values for different PWM-experiment combinations and offer these results as a public resource to the research community. The benchmarking protocols are provided via a web interface and as docker images. The methods and results from this study may help others make better use of public TF specificity models, as well as public TF binding data sets.
Over the past 50 years, dental informatics has developed significantly in the field of health information systems. Accordingly, several studies have been conducted on standardized clinical coding ...systems, data capture, and clinical data reuse in dentistry.
Based on the definition of health information systems, the literature search was divided into three specific sub-searches: "standardized clinical coding systems," "data capture," and "reuse of routine patient care data." PubMed and Web of Science were searched for peer-reviewed articles. The review was conducted following the PRISMA-ScR protocol.
A total of 44 articles were identified for inclusion in the review. Of these, 15 were related to "standardized clinical coding systems," 15 to "data capture," and 14 to "reuse of routine patient care data." Articles related to standardized clinical coding systems focused on the design and/or development of proposed systems, on their evaluation and validation, on their adoption in academic settings, and on user perception. Articles related to data capture addressed the issue of data completeness, evaluated user interfaces and workflow integration, and proposed technical solutions. Finally, articles related to reuse of routine patient care data focused on clinical decision support systems centered on patient care, institutional or population-based health monitoring support systems, and clinical research.
While the development of health information systems, and especially standardized clinical coding systems, has led to significant progress in research and quality measures, most reviewed articles were published in the US. Clinical decision support systems that reuse EDR data have been little studied. Likewise, few studies have examined the working environment of dental practitioners or the pedagogical value of using health information systems in dentistry.
Objectives
To assess related studies and discuss the clinical implications of endodontic access cavity (AC) designs.
Materials and methods
A systematic review of studies comparing the fracture ...resistance and/or endodontic outcomes between different AC designs was conducted in two electronic search databases (PubMed and Web of Science) following the PRISMA guidelines. Study selection, data extraction, and quality assessment were performed. Meta-analyses were undertaken for fracture resistance and root canal detection, with the level of significance set at 0.05 (
P
= 0.05).
Results
A total of 33 articles were included in this systematic review. The global evaluation of the risk of bias in the included studies was assessed as moderate, and the level of evidence was rated as low. Four types of AC designs were categorized: traditional (TradAC), conservative (ConsAC), ultraconservative (UltraAC), and truss (TrussAC). Their impact on fracture resistance, cleaning/disinfection, procedural errors, root canal detection, treatment time, apical debris extrusion, and root canal filling was discussed. Meta-analysis showed that compared to TradAC, (i) there is a significant higher fracture resistance of teeth with ConsAC, TrussAC, or ConsAC/TrussAC when all marginal ridges are preserved (
P
< 0.05), (ii) there is no significant effect of the type of AC on the fracture resistance of teeth when one or two marginal ridges are lost (
P
> 0.05), and (iii) there is a significantly higher risk of undetected canals with ConsAC if not assisted by dental operating microscope and ultrasonic troughing (
P
< 0.05).
Conclusions
Decreasing the AC extent does not necessarily present mechanical and biological advantages especially when one or more surfaces of the tooth structure are lost. To date, the evidence available does not support the application of TrussAC. UltraAC might be applied in limited occasions.
Clinical relevance
Maintaining the extent of AC design as small as practical without jeopardizing the root canal treatment quality remains a pragmatic recommendation. Different criteria can guide the practitioner for the optimal extent of AC outline form which varies from case to case.
This scoping review aimed to assess the current state of knowledge regarding the relationship between bruxism and changes in density or volume of mandibular bone, based on medical imaging.
Literature ...review was conducted following the PRISMA-ScR protocol. PubMed, Web of Science and Cochrane library databases were searched for peer-reviewed articles by two blinded reviewers. Studies based on the evaluation of mandibular bone density and/or bone volume with imaging examination in adult patients were examined. The selected articles were summarized in PICOS tables and assessed for methodological quality.
Nine articles were included, according to the inclusion criteria. They showed that bruxer patients had more bony exostoses of the mandibular angle, smaller condyles, and morphological changes for cancellous and cortical mandibular bone compared to non-bruxer patients.
Bruxism seems to induce morphological and anatomical changes in the different regions of the mandibular bone (condyles, mandibular angle, mandible body). Given the heterogeneity of the included studies, these results should be interpreted with caution. Further studies are needed to support these results, in particular via the analysis of three-dimensional imaging to overcome the limitations of panoramic radiograph.
As exome sequencing gives way to genome sequencing, the need to interpret the function of regulatory DNA becomes increasingly important. To test whether evolutionary conservation of cis-regulatory ...modules (CRMs) gives insight into human gene regulation, we determined transcription factor (TF) binding locations of four liver-essential TFs in liver tissue from human, macaque, mouse, rat, and dog. Approximately, two thirds of the TF-bound regions fell into CRMs. Less than half of the human CRMs were found as a CRM in the orthologous region of a second species. Shared CRMs were associated with liver pathways and disease loci identified by genome-wide association studies. Recurrent rare human disease causing mutations at the promoters of several blood coagulation and lipid metabolism genes were also identified within CRMs shared in multiple species. This suggests that multi-species analyses of experimentally determined combinatorial TF binding will help identify genomic regions critical for tissue-specific gene control.
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