Impact of smoking habit on the subgingival proteome in patients with periodontitis.

Background: Few investigations evaluated smoking's impact on the periodontal proteome. Therefore, this study aimed to analyse the influence of tobacco on the overall periodontal proteome and the differential expression of gingival crevicular fluid (GCF) proteins using sequential window acquisition of all theoretical mass spectra (SWATH-MS).

Methods: GCF samples were collected from 40 periodontitis subjects (stages III-IV).

The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects.

Introduction: Microbiome-based clinical applications that improve diagnosis related to oral health are of great interest to precision dentistry. Predictive studies on the salivary microbiome are scarce and of low methodological quality (low sample sizes, lack of biological heterogeneity, and absence of a validation process). None of them evaluates the impact of confounding factors as batch effects (BEs).

PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome.

Background: The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions.

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis.

The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results.

Biomarkers for diagnosis of stage III, grade C with molar incisor pattern periodontitis in children and young adults: a systematic review and meta-analysis.

Aim: To explore the existing salivary, gingival crevicular fluid (GCF), blood, and serum biomarkers associated with grade C molar-incisor pattern (C/MIP) periodontitis in systemically healthy children and young adults.

Materials And Methods: Cross-sectional, case-control, and cohort studies on stage III grade C periodontitis or former equivalent diagnosis with analysis of molecular biomarkers in saliva, GCF, blood, or serum were retrieved from six databases and screened based on the eligibility criteria. The risk of bias in included studies was evaluated.

A systematic overview of dental methods for age assessment in living individuals: from traditional to artificial intelligence-based approaches.

Dental radiographies have been used for many decades for estimating the chronological age, with a view to forensic identification, migration flow control, or assessment of dental development, among others. This study aims to analyse the current application of chronological age estimation methods from dental X-ray images in the last 6 years, involving a search for works in the Scopus and PubMed databases. Exclusion criteria were applied to discard off-topic studies and experiments which are not compliant with a minimum quality standard.

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.

Background: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.

Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing.

This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated.

Adapting Demirjian Standards for Portuguese and Spanish Children and Adolescents.

Unlabelled: Estimation of children's chronological age is highly important in human and forensic sciences. The Demirjian method has been reported as accurate for this purpose. The literature review shows some evidence that the accuracy of estimating chronological age via the Demirjian standards is not a straightforward process.

XAS: Automatic yet eXplainable Age and Sex determination by combining imprecise per-tooth predictions.

Chronological age and biological sex estimation are two key tasks in a variety of procedures, including human identification and migration control. Issues such as these have led to the development of both semiautomatic and automatic prediction models, but the former are expensive in terms of time and human resources, while the latter lack the interpretability required to be applicable in real-life scenarios. This paper therefore proposes a new, fully automatic methodology for the estimation of age and sex.

Update on the Role of Cytokines as Oral Biomarkers in the Diagnosis of Periodontitis.

Periodontitis is one of the world's most common chronic human diseases and has a significant impact on oral health. Recent evidence has revealed a link between periodontitis and certain severe systemic conditions. Moreover, periodontal patients remain so for life, even following successful therapy, requiring ongoing supportive care to prevent the disease's recurrence.

Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs.

Although clustering by operational taxonomic units (OTUs) is widely used in the oral microbial literature, no research has specifically evaluated the extent of the limitations of this sequence clustering-based method in the oral microbiome. Consequently, our objectives were to: 1) evaluate the coverage of a set of previously selected primer pairs to detect oral species having 16S rRNA sequence segments with ≥97% similarity; 2) describe oral species with highly similar sequence segments and determine whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain the amplicons from the complete genomes of 186 bacterial and 135 archaeal species.

Polymicrobial Aggregates in Human Saliva Build the Oral Biofilm.

Biofilm community development has been established as a sequential process starting from the attachment of single cells on a surface. However, microorganisms are often found as aggregates in the environment and in biological fluids. Here, we conduct a comprehensive analysis of the native structure and composition of aggregated microbial assemblages in human saliva and investigate their spatiotemporal attachment and biofilm community development.

Automated description of the mandible shape by deep learning.

Purpose: The shape of the mandible has been analyzed in a variety of fields, whether to diagnose conditions like osteoporosis or osteomyelitis, in forensics, to estimate biological information such as age, gender, and race or in orthognathic surgery. Although the methods employed produce encouraging results, most rely on the dry bone analyses or complex imaging techniques that, ultimately, hamper sample collection and, as a consequence, the development of large-scale studies. Thus, we proposed an objective, repeatable, and fully automatic approach to provide a quantitative description of the mandible in orthopantomographies (OPGs).

Students' Perceptions of Educational Climate in a Spanish School of Dentistry Using the Dundee Ready Education Environment Measure: A Longitudinal Study.

Background: Educational Climate (EC) may determine teacher and student behaviour. Our aim was to evaluate EC longitudinally in a period of 'curricular transition' from traditional (teacher-centred learning) to Bologna curricula (interactive student-centred learning).

Methods: The 'Dundee Ready Education Environment Measure' (DREEM) questionnaire was completed by 397 students from a Spanish School of Dentistry.

DenTiUS Plaque, a Web-Based Application for the Quantification of Bacterial Plaque: Development and Usability Study.

Background: In the dentistry field, the analysis of dental plaque is vital because it is the main etiological factor in the 2 most prevalent oral diseases: caries and periodontitis. In most of the papers published in the dental literature, the quantification of dental plaque is carried out using traditional, non-automated, and time-consuming indices. Therefore, the development of an automated plaque quantification tool would be of great value to clinicians and researchers.

Deep Neural Networks for Chronological Age Estimation From OPG Images.

Chronological age estimation is crucial labour in many clinical procedures, where the teeth have proven to be one of the best estimators. Although some methods to estimate the age from tooth measurements in orthopantomogram (OPG) images have been developed, they rely on time-consuming manual processes whose results are affected by the observer subjectivity. Furthermore, all those approaches have been tested only on OPG image sets of good radiological quality without any conditioning dental characteristic.

Accuracy of single molecular biomarkers in saliva for the diagnosis of periodontitis: A systematic review and meta-analysis.

Aim: To analyse, using a meta-analytical approach, the diagnostic accuracy of single molecular biomarkers in saliva for the detection of periodontitis in systemically healthy subjects.

Materials And Methods: Articles on molecular biomarkers in saliva providing a binary contingency table (or sensitivity and specificity values and group sample sizes) in individuals with clinically diagnosed periodontitis were considered eligible. Searches for candidate articles were conducted in six electronic databases.

Accuracy of single molecular biomarkers in gingival crevicular fluid for the diagnosis of periodontitis: A systematic review and meta-analysis.

Aim: To analyse, by means of a meta-analytical approach, the diagnostic accuracy of molecular biomarkers in gingival crevicular fluid (GCF) for the detection of periodontitis in systemically healthy subjects.

Material And Methods: Studies on GCF molecular biomarkers providing a binary classification table (or sensitivity and specificity values and group sample sizes) in individuals with clinically diagnosed periodontitis were considered eligible. The search was performed using six electronic databases.

substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms.

This study aimed to compare the bacterial viability and diversity of a substrate-formed biofilm (SF-biofilm) to a supragingival tooth-formed biofilm (TF-biofilm) in the same group of individuals. The impact of the device/disc position and toothbrushing during the formation of SF-biofilm was also assessed. Two tests were run.

Antibacterial Activity of Essential Oils with and without Alcohol on Oral Biofilm: A Randomized Clinical Trial.

Currently, there is little evidence on the antibacterial activity of essential oils (EO) without alcohol. This study aimed to evaluate the substantivity and antiplaque effect on the plaque-like biofilm (PL-biofilm) of two solutions, a traditional formulation that contains EO with alcohol (T-EO) and an alcohol-free formulation of EO (Af-EO). Eighteen healthy adults performed a single mouthwash of: T-EO, Af-EO, and sterile water (WATER) after wearing an individualized disk-holding splint for 2 days.

Quantification by qPCR of Pathobionts in Chronic Periodontitis: Development of Predictive Models of Disease Severity at Site-Specific Level.

Currently, there is little evidence available on the development of predictive models for the diagnosis or prognosis of chronic periodontitis based on the qPCR quantification of subgingival pathobionts. Our objectives were to: (1) analyze and internally validate pathobiont-based models that could be used to distinguish different periodontal conditions at site-specific level within the same patient with chronic periodontitis; (2) develop nomograms derived from predictive models. Subgingival plaque samples were obtained from control and periodontal sites (probing pocket depth and clinical attachment loss <4 mm and >4 mm, respectively) from 40 patients with moderate-severe generalized chronic periodontitis.

Clinical value of diascopy and other non-invasive techniques on differential diagnosis algorithms of oral pigmentations: A systematic review.

Objectives: To determine the diagnostic value of diascopy and other non-invasive clinical aids on recent differential diagnosis algorithms of oral mucosal pigmentations affecting subjects of any age.

Material And Methods: Data Sources: this systematic review was conducted by searching PubMed, Scopus, Dentistry & Oral Sciences Source and the Cochrane Library (2000-2015); Study Selection: two reviewers independently selected all types of English articles describing differential diagnosis algorithms of oral pigmentations and checked the references of finally included papers; Data Extraction: one reviewer performed the data extraction and quality assessment based on previously defined fields while the other reviewer checked their validity.

Results: Data Synthesis: eight narrative reviews and one single case report met the inclusion criteria.