The text2term tool to map free-text descriptions of biomedical terms to ontologies.

There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types-such as disease names, cell types, or chemicals-that are used in metadata associated with biomedical data. When metadata are not well-structured or precise, the associated data are harder to find and are often burdensome to reuse, analyze, or integrate with other datasets due to the upfront curation effort required to make the data usable-typically through retrospective standardization and cleaning of the (meta)data. With the goal of facilitating the task of standardizing metadata-either in bulk or in a one-by-one fashion, e.

Effect of whitening toothpastes and activated charcoal powder on enamel wear and surface roughness.

This study aimed to evaluate surface roughness (Sa), roughness profile (Rv), and enamel wear after brushing with different whitening toothpastes and charcoal powders. Sixty (n = 10) bovine enamel blocks (6 × 6 × 3 mm) were randomly distributed into six groups according to toothpaste type: regular toothpaste (CONT), toothpaste containing 2% hydrogen peroxide (HP), toothpaste containing titanium dioxide (TiO2), toothpaste containing charcoal (COAL), toothpaste containing charcoal and TiO2 (COAL+TiO2), and activated charcoal powder (COAL_PWD). Each block was subjected to 30,000 reciprocal cycles at a 1:3 proportion slurry.

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.

The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures.

Two-year randomized clinical trial of different restorative techniques in non-carious cervical lesions and MMP activity in gingival crevicular fluid.

Objectives: To evaluate different restorative techniques for non-carious cervical lesions (NCCLs) and the activity of matrix metalloproteinases (MMPs) in gingival crevicular fluid.

Materials And Methods: Two hundred restorations were performed in 50 patients using resin composite restorative system without (I) and with selective enamel conditioning (II) and resin-modified glass-ionomer cement without (III) and with EDTA pretreatment (IV). Gingival crevicular fluid samples were collected in 15 patients.

Obstacles to the reuse of study metadata in ClinicalTrials.gov.

Metadata that are structured using principled schemas and that use terms from ontologies are essential to making biomedical data findable and reusable for downstream analyses. The largest source of metadata that describes the experimental protocol, funding, and scientific leadership of clinical studies is ClinicalTrials.gov.

Performance of MDP-based system in eroded and carious dentin associated with proteolytic inhibitors: 18-Month exploratory study.

The aim of this study was to explore the impact of the interaction between an MDP-based universal adhesive system in etch-and-rinse mode and two proteolytic inhibitors on the longevity of restorations bonded to artificially-affected-dentin substrates. 90 sound human third molars were randomly distributed into three groups according to the substrate: N-no challenges-control (stored in artificial saliva), ACD-artificial caries dentin (6 h DE + 18 h-RE/5 days + 48 h RE) and ERO-artificial erosion dentin (3 × 5 min/5 days with orange juice). They were further redistributed according to dentin pretreatment: W- water (control), CHX-2% digluconate chlorhexidine and E64- 5 μM E64-Trans-Epoxysuccinyl-L-Leucylamido-(4-guanidino) butane, which resulted in the following 9 groups (n = 10): N-W, N-CHX, N-E64, ACD-W, ACD-CHX, ACD-E64, ERO-W, ERO-CHX and ERO-E64.

MDP-based universal adhesive system irradiated with Er,CR:YSGG: Analysis of its performance up to 6 months.

This study aimed to analyze the interaction of a MDP-based universal dentin bonding system (DBS) with Er, Cr: YSGG laser irradiation, measuring the microtensile bond strength to dentin over a six-month period. The experimental design involved three factors: DBS (Adper Scotchbond Universal; Clearfil SE Bond, Adper Scotchbond Multipurpose and Adper Single Bond 2), laser (Control and Er, Cr: YSGG), and time (initial- 7 days and 6 months). Eighty dentin samples from molars were prepared (n=10) with laser irradiation after primer and DBS application.

Profile of a 10-MDP-based universal adhesive system associated with chlorhexidine: Dentin bond strength and in situ zymography performance.

The incorporation of functional monomers and proteolytic inhibitors into adhesive systems have shown to be promising strategies to improve the longevity of adhesive restorations. The aim of this study was to evaluate the long-term bonding performance and anti-gelatinolytic effect of a 10-MDP-based universal adhesive system applied in combination with 2% chlorhexidine digluconate (CHX). For that, this study assessed the resin-dentin bond strength and the in situ gelatinolytic activity profile at the adhesive interface at initial and after 6 month of storage.

ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

Background: The genus Paracoccidioides consists of thermodymorphic fungi responsible for Paracoccidioidomycosis (PCM), a systemic mycosis that has been registered to affect ~10 million people in Latin America. Biogeographical data subdivided the genus Paracoccidioides in five divergent subgroups, which have been recently classified as different species. Genomic sequencing of five Paracoccidioides isolates, representing each of these subgroups/species provided an important framework for the development of post-genomic studies with these fungi.

The variable quality of metadata about biological samples used in biomedical experiments.

We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample-a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples-a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.

Neurosensory analysis of tooth sensitivity during at-home dental bleaching: a randomized clinical trial.

Objective The objective of this study was to evaluate dental sensitivity using visual analogue scale, a Computerized Visual Analogue Scale (CoVAS) and a neurosensory analyzer (TSA II) during at-home bleaching with 10% carbamide peroxide, with and without potassium oxalate. Materials and Methods Power Bleaching 10% containing potassium oxalate was used on one maxillary hemi-arch of the 25 volunteers, and Opalescence 10% was used on the opposite hemi-arch. Bleaching agents were used daily for 3 weeks.

Sodium Trimetaphosphate as a Novel Strategy for Matrix Metalloproteinase Inhibition and Dentin Remineralization.

The effect of sodium trimetaphosphate (STMP) as an antiproteolytic and remineralizing agent on demineralized dentin was evaluated in vitro. The inhibitory potential of STMP at 0.5, 1.

Use of sodium trimetaphosphate in the inhibition of dentin matrix metalloproteinases and as a remineralizing agent.

Objectives: Because of its ability to act as an antiproteolytic agent, the effect of sodium trimetaphosphate (STMP) against specific enzymes extracted from sound dentin and its performance under acidic challenge on demineralized dentin were investigated.

Methods: The antiproteolytic potential of STMP (0.5%, 1.

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments.

The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed-the CEDAR Workbench-is a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies.

An ontology-driven tool for structured data acquisition using Web forms.

Background: Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g.

The OWL Reasoner Evaluation (ORE) 2015 Competition Report.

The OWL Reasoner Evaluation competition is an annual competition (with an associated workshop) that pits OWL 2 compliant reasoners against each other on various standard reasoning tasks over naturally occurring problems. The 2015 competition was the third of its sort and had 14 reasoners competing in six tracks comprising three tasks (consistency, classification, and realisation) over two profiles (OWL 2 DL and EL). In this paper, we discuss the design, execution and results of the 2015 competition with particular attention to lessons learned for benchmarking, comparative experiments, and future competitions.

Transenamel and Transdentinal Penetration of H2O2 in Restored Bovine Teeth.

Purpose: To quantify hydrogen peroxide (H2O2) penetration into restored bovine teeth subjected to whitening treatment.

Materials And Methods: Seventy-five enamel/dentin disks were divided into 5 groups (n = 15): intact disks (G1); cavity preparation only (G2); conventional adhesive system and composite resin (G3); resin-modified glass-ionomer cement (G4); and self-etching adhesive only (G5). After 24 h, the disks were placed into artificial pulp chambers containing an acetate buffer solution, and the first whitening session was performed using a 35% H2O2 (hydrogen peroxide) product.

Effectiveness of plant-derived proanthocyanidins on demineralization on enamel and dentin under artificial cariogenic challenge.

Unlabelled: Dental caries is considered a disease of high prevalence and a constant problem in public health. Proanthocyanidins (PAs) are substances that have been the target of recent studies aiming to control or treat caries.

Objective: The aim of this in vitro study was to evaluate the efficacy of a treatment with grape seed extract, under cariogenic challenge, to minimize or even prevent the onset of caries in the enamel and dentin.

Demineralization and hydrogen peroxide penetration in teeth with incipient lesions.

The aim of this study was to evaluate the demineralization and hydrogen peroxide (HP) penetration in teeth with incipient lesions submitted to bleaching treatment. For analysis of HP penetration, sound and demineralized enamel/dentin discs were placed in artificial pulp chambers containing acetate buffer solution. After bleaching treatment, this solution was subjected for analysis of optical density by spectrophotometry and the disc surfaces were analyzed with scanning electron microscopy (SEM) and polarized light microscopy (PLM).