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Random forest results plotted according to mean decrease in accuracy, show the strongest discriminators, namely, IL-4, IL-13, IL-2-RA, and eotaxin/CCL11.

Random forest results plotted according to mean decrease in accuracy, show the strongest discriminators, namely, IL-4, IL-13, IL-2-RA, and eotaxin/CCL11.

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This study investigated the potential of salivary bacterial and protein markers for evaluating the disease status in healthy individuals or patients with gingivitis or caries. Saliva samples from caries- and gingivitis-free individuals (n = 18), patients with gingivitis (n = 17), or patients with deep caries lesions (n = 38) were collected and anal...

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... the PCA, another multidimensional approach (a random forest supervised learning model) was applied to the training dataset in order to extract the strongest discriminators that were potentially capable of correctly assigning patients into the three clinical study groups. Figure 4 illustrates the strongest discriminators plotted according to the Figure 3. Results obtained from a principal component analysis (PCA) with the first dimension on the x-axis (36%) and the second dimension on the y-axis (8.4%). The groups are separated by color and shape (caries = red square; gingivitis = green triangle; caries = red circle). ...
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... the PCA, another multidimensional approach (a random forest supervised learning model) was applied to the training dataset in order to extract the strongest discriminators that were potentially capable of correctly assigning patients into the three clinical study groups. Figure 4 illustrates the strongest discriminators plotted according to the mean decrease in accuracy: IL-4, IL-13, and IL-2-RA, followed by eotaxin/CCL11. These were the four classifiers that enabled the best distinction of caries, healthy, and gingivitis patients considering all the measured markers. ...
Context 3
... were the four classifiers that enabled the best distinction of caries, healthy, and gingivitis patients considering all the measured markers. Interestingly, only four markers were needed to generate the best discrimination between the different oral health groups, i.e., IL-4, IL-13, and IL-2-RA as well as the chemokine eotaxin/CCL11 (Figure 4). Oral bacteria did not play an important role. ...
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... biomarker IL-13 was below the detection limit in the healthy and gingivitis groups. Interestingly, only four markers were needed to generate the best discrimination between the different oral health groups, i.e., IL-4, IL-13, and IL-2-RA as well as the chemokine eotaxin/CCL11 (Figure 4). Oral bacteria did not play an important role. ...

Citations

... One of the diseases caused by S. mutans is dental caries. There are several factors that cause dental caries to get worse including sugar, saliva, and also putrefactive bacteria [25][26][27]. In addition, the growth of bacteria in the mouth and forming biofilms is caused by several factors, namely saliva which plays a role in modulating the plaque layer on the teeth, the temperature in the environment around the mouth in the range of 35-36°C, and pH 6.75-7.25 [28,29]. ...
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Based on data from The Global Burden of Disease Study in 2016, dental and oral health problems, especially dental caries, are a disease experienced by almost half of the world’s population (3.58 billion people). One of the main causes of dental caries is the pathogenesis of Streptococcus mutans. Prevention can be achieved by controlling S. mutans using an antibacterial agent. The most commonly used antibacterial for the treatment of dental caries is chlorhexidine. However, long-term use of chlorhexidine has been reported to cause resistance and some side effects. Therefore, the discovery of a natural antibacterial agent is an urgent need. A natural antibacterial agent that can be used are herbal medicines derived from medicinal plants. Piper crocatum Ruiz and Pav has the potential to be used as a natural antibacterial agent for treating dental and oral health problems. Several studies reported that the leaves of P. crocatum Ruiz and Pav contain secondary metabolites such as essential oils, flavonoids, alkaloids, terpenoids, tannins, and phenolic compounds that are active against S. mutans. This review summarizes some information about P. crocatum Ruiz and Pav, various isolation methods, bioactivity, S. mutans bacteria that cause dental caries, biofilm formation mechanism, antibacterial properties, and the antibacterial mechanism of secondary metabolites in P. crocatum Ruiz and Pav.
... It is the dynamic changes over time of bacteria among the oral microbiota, rather than their mere presence/absence, that drives the dysbiotic changes that lead to oral disease [72]. The fact that the OralDisk has demonstrated its capacity to analyze oral bacteria provides a basis upon which the platform can be implemented in time-course studies associated with patient monitoring, similar to the rationale reported by Paqué et al. [73]. In such future studies, we will have the opportunity to proceed to the quantification of bacteria, using OralDisk-derived calibration curves to convert Cq values into numeric bacterial loads. ...
... This will increase the interoperability between immunological and microbiological diagnostic outputs using this platform [76]. Subsequently, by using combined computational technologies and the OralDisk device, new diagnostic predictive models of disease development and progression may be generated [73]. Such developments will enable evidence-based pre-and post-treatment monitoring of a range of oral (OralDisk) and non-oral (application-specific LabDisk) diseases. ...
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Periodontitis and dental caries are two major bacterially induced, non-communicable diseases that cause the deterioration of oral health, with implications in patients' general health. Early, precise diagnosis and personalized monitoring are essential for the efficient prevention and management of these diseases. Here, we present a disk-shaped microfluidic platform (OralDisk) compatible with chair-side use that enables analysis of non-invasively collected whole saliva samples and molecular-based detection of ten bacteria: seven periodontitis-associated (Aggregatibacter actinomycetemcomitans, Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola) and three caries-associated (oral Lactobacilli, Streptococcus mutans, Streptococcus sobrinus). Each OralDisk test required 400 µL of homogenized whole saliva. The automated workflow included bacterial DNA extraction, purification and hydrolysis probe real-time PCR detection of the target pathogens. All reagents were pre-stored within the disk and sample-to-answer processing took < 3 h using a compact, customized processing device. A technical feasibility study (25 OralDisks) was conducted using samples from healthy, periodontitis and caries patients. The comparison of the OralDisk with a lab-based reference method revealed a ~90% agreement amongst targets detected as positive and negative. This shows the OralDisk's potential and suitability for inclusion in larger prospective implementation studies in dental care settings.
... Paqué et al. [15] investigated the potential of salivary bacterial and protein markers for evaluating the disease status in healthy individuals with caries. Saliva samples from caries and gingivitis-free individuals (n = 18), patients with deep caries lesions (n = 38) was collected and analysed for 44 candidate biomarkers namely: selected oral bacteria, growth factors, chemokines and proteolytic enzymes among others. ...
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Dental Caries are one of the most prevalent chronic diseases around the globe. Detecting carious lesions is a challenging task. Conventional computer aided diagnosis and detection methods in the past have heavily relied on the visual inspection of teeth. These methods are only effective on large and clearly visible caries on affected teeth. Conventional methods have been limited in performance due to the complex visual characteristics of dental caries images, which consist of hidden or inaccessible lesions. The early detection of dental caries is an important determinant for treatment and benefits much from the introduction of new tools, such as dental radiography. In this paper, we propose a deep learning-based technique for dental caries detection namely: blob detection. The proposed technique automatically detects hidden and inaccessible dental caries lesions in bitewing radio-graphs. The approach employs data augmentation to increase the number of images in the data set to have a total of 11,114 dental images. Image pre-processing on the data set was through the use of Gaussian blur filters. Image segmentation was handled through thresholding, erosion and dilation morphology, while image boundary detection was achieved through active contours method. Furthermore, the deep learning based network through the sequential model in Keras extracts features from the images through blob detection. Finally, a convexity threshold value of 0.9 is introduced to aid in the classification of caries as either present or not present. The process of detection and classifying dental caries achieved the results of 97% and 96% for the precision and recall values, respectively.
... This article is protected by copyright. All rights reserved Paqué et al. 2021), or qualitative detection of antibiotic resistance genes (Belibasakis et al. 2020). Saliva sampling may also conveniently replace the uncomfortable nasal or oropharyngeal sampling for select applications, such as SARS-CoV-2 RNA detection, with high specificity and sensitivity (Atieh et al. 2021). ...
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The authors of this narrative review aimed to address various experimental methods and make recommendations for how research should move forward in the context of studying biomarkers in clinical Endodontic research. The approach adopted is exemplified using two prominent clinical problems, namely a) the "reversible" versus "irreversible" pulpitis conundrum and b) persistent idiopathic dentoalveolar pain (PIDAP). Pulpitis under deep caries or dentinal cracks is understood from a histological perspective, but clinical assessment tools to indicate irreversibly inflamed aspects of the dental pulp are elusive. PIDAP, on the other hand, is a diagnosis of exclusion; its pathophysiology is complex and not understood sufficiently to avoid unnecessary dental treatments. This review addresses how diagnostic biomarkers could further our understanding of those and other clinical problems, and how issues can be tackled from a methodological point of view. Hence, different methodological approaches to identify suitable diagnostic biomarker(s) or use known biomarkers are presented. The importance of asking a relevant research question, collecting the most suitable fluid, and using the ideal collection vehicle for the research question under investigation is discussed based on the defined clinical problems.
... The prevalence and damage generated by these bacteria are influenced by host protective factors, such as immune competence, the production and buffering capacity of saliva, and hygiene and dietary habits [5]. Mechanisms have been sought to diagnose the risk of caries based on these factors using software such as Cariogram [6] or through the identification of biomarkers [7,8,9]. However, a significant amount of new studies are required to evaluate the validity of caries biomarkers, among other things because tooth decay is a multi-factorial disease with genetic, environmental and microbial effects playing a role, and because of a large inter-individual variability that renders the task of finding universal caries markers [10]. ...
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Background: Electrolytes, proteins, and other salivary molecules play an important role in tooth integrity and can serve as biomarkers associated with caries. Objective: To determine the concentration of potential biomarkers in children without caries (CF) and children with caries (CA). Methods: Unstimulated saliva was collected, and the biomarkers quantified in duplicate, using commercial Enzyme Linked Immunosorbent Assay (ELISA) kits to determine IgA, fibronectin, cathelicidin LL-37, and statherin levels, as well as colorimetric tests to detect formate and phosphate. Results: Significantly higher concentrations of statherin was detected in the CF group (Median: 94,734.6; IQR: 92,934.6–95,113.7) compared to the CA2 group (90,875.0; IQR: 83,580.2–94,633.4) (p = 0.03). Slightly higher median IgA (48,250.0; IQR: 31,461.9–67,418.8) and LL-37 levels (56.1; IQR 43.6–116.2) and a lower concentration of formate were detected in the CF group (0.02; IQR 0.0034–0.15) compared to the group with caries (IgA: 37,776.42; IQR: 33,383.9–44,128.5; LL-37: 46.3; IQR: 40.1011–67.7; formate: 0.10; IQR: 0.01–0.18), but these differences were not statistically significant. Conclusion: The fact that these compounds have been identified as good markers for caries among European adults highlights the difficulty of identifying universal biomarkers that are applicable to all ages or to different populations.
Article
Personalized Oral Healthcare has recently become the new trend word in medicine and dentistry. In this context, saliva diagnostics using various biomarkers seem to be the gateway to personalized dental diagnostics and therapy. But the terminology is not (yet) uniformly defined, furthermore it is unclear to what extent which salivary markers play a relevant role in the therapeutic decision making. In this Scoping Review, an electronic search was conducted in PubMed and Web of Science databases using medical subject headings (MESH terms) “saliva”, “biomarker”, “personality/persons”, and “dentistry”. Only human studies were included, in which repeated salivary measurements were performed to analyze monitoring effects with at least ten patients per group. PRISMA-ScR and Tricco guidelines were followed: (i) to examine what salivary biomarkers have been explored in terms of personalized oral healthcare and precision dentistry, (ii) to investigate the clinical relevance for oral health and its correlation to systemic health, and (iii) to summarize an outlook for future developments based on these results. Out of 899 studies, a total of 57 were included for data extraction in this Scoping Review, mainly focusing on periodontal therapy and patient monitoring. Salivary biomarkers have shown the potential to change the field of dentistry in all dental disciplines as a key for personalized workflows. The increasing interest in dental research is obvious, demonstrated by the growing number of publications in recent years. At this time, however, the predominant discipline is periodontology, which allows biomarker-based monitoring of the disease prevention and progression. The studies included showed heterogeneous methods using manifolds biomarkers. Therefore, no uniformly accepted concept can be presented today. Further clinical research with well-defined outcomes including standardized procedures is necessary.
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Diagnosis and treatment in dentistry are based on clinical examination of the patients. Given that the major oral diseases are of microbial biofilm etiology, it can be expected that performing microbiological analysis on samples collected from the patient could deliver supportive evidence to facilitate the decision-making process by the clinician. Applicable microbiological methods range from microscopy, to culture, to molecular techniques, which can be performed easily within dedicated laboratories proximal to the clinics, such as ones in academic dental institutions. Periodontal and endodontic infections, along with odontogenic abscesses, have been identified as conditions in which applied clinical microbiology may be beneficial for the patient. Administration of antimicrobial agents, backed by microbiological analysis, can yield more predictable treatment outcomes in refractory or early-occurring forms of periodontitis. Confirming a sterile root canal using a culture-negative sample during endodontic treatment may ensure the longevity of its outcome and prevent secondary infections. Susceptibility testing of samples obtained from odontogenic abscesses may facilitate the selection of the appropriate antimicrobial treatment to prevent further spread of the infection.