The main goal of dental education is to develop health professionals who will maintain and improve the oral health of patients. This requires the quantitative and qualitative assessment of dental ...student activity. The aim of this work is to describe the ECHO information system that was developed at Timone Hospital (France) for the monitoring and evaluation of dental student activity and to present the results of a qualitative evaluation of student perceptions of this system. According to the analysis of the UML model of care-related procedures and data, the pre-existing process of student evaluation was characterized by redundancy between administrative and educational data. ECHO was developed in PHP/MySQL and designed to centralize the two types of data in a unified computerized process. The qualitative evaluation of dental student perceptions of ECHO was performed using an anonymous online Google Form questionnaire. Among the respondents (102/254 students), 96% stated that ECHO is easy to use, 86% that it saves time, and 81% that it gives them a better overview of their activity. After several years of use, ECHO has solved many of the difficulties related to the use of internship paper booklets, while also providing a documentary database of the activities of our dental department. The student activity data stored in ECHO are directly accessible by faculty members and can be reused to facilitate departmental management and research and to improve patient follow-up.
The oncogenic pathways in mitochondrial-rich thyroid carcinomas are not clearly understood. To investigate the possible implication of mitochondrial abundance in the genesis of thyroid tumors, we ...have explored the gene expression profile of six oncocytic carcinomas and six mitochondrial-rich papillary carcinomas using cDNA-microarray technology. A supervised approach allowed us to identify 83 genes differentially expressed in the two types of carcinoma. These genes were classified according to their ontologic profiles. Three genes, NOS3, alpha-actinin-2 and alpha-catenin, suspected of playing a role in tumor genesis, were explored by quantitative RT-PCR analysis and immunohistochemistry. Of the 59 genes overexpressed in papillary carcinomas, 51% were involved in cell communication. Of the 24 genes overexpressed in oncocytic carcinomas, 84% were involved in mitochondrial and cellular metabolism. Our results suggest that mitochondrial respiratory chain complexes III and IV play a significant role in the regulation of reactive oxygen species production by oncocytic tumors.
The large diversity of functional genomic assays allows for the characterization of non-coding and coding events at the tissue level or at a single-cell resolution. However, this diversity also leads ...to protocol differences, widely varying sequencing depths, substantial disparities in sample sizes, and number of features. In this work, we have built a Python package, MUFFIN, which offers a wide variety of tools suitable for a broad range of genomic assays and brings many tools that were missing from the Python ecosystem. First, MUFFIN has specialized tools for the exploration of the non-coding regions of genomes, such as a function to identify consensus peaks in peak-called assays, as well as linking genomic regions to genes and performing Gene Set Enrichment Analyses. MUFFIN also possesses a robust and flexible count table processing pipeline, comprising normalization, count transformation, dimensionality reduction, Differential Expression, and clustering. Our tools were tested on three widely different scRNA-seq, ChIP-seq and ATAC-seq datasets. MUFFIN integrates with the popular Scanpy ecosystem and is available on Conda and at https://github.com/pdelangen/Muffin.
Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively ...translating the results from the microarray into a biological interpretation requires an accurate mapping between the probesets on the array and the genes that they are targeting. Although major array manufacturers provide annotations of their gene expression arrays, the methods used by various manufacturers are different and the annotations are difficult to keep up to date in the rapidly changing world of biological sequence databases.
We have created a consistent microarray annotation protocol applicable to all of the major array manufacturers. We constantly keep our annotations updated with the latest Ensembl Gene predictions, and thus cross-referenced with a large number of external biomedical sequence database identifiers. We show that these annotations are accurate and address in detail reasons for the minority of probesets that cannot be annotated. Annotations are publicly accessible through the Ensembl Genome Browser and programmatically through the Ensembl Application Programming Interface. They are also seamlessly integrated into the BioMart data-mining tool and the biomaRt package of BioConductor.
Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles.
Teaching caries lesion management with operative care requires tooth models with highly realistic anatomical detail and caries lesions that can be assessed using ICDAS. This study aimed to develop ...and evaluate a new 3D-printed teeth model for ICDAS assessment and caries removal for pre-clinical hands-on education.
Printable tooth with different layers for enamel, dentin and carious lesions was designed and tested by 31 dental students. They were asked to visually and radiologically assess the ICDAS severity of the simulated carious lesions, establish the therapeutic strategy according to CariesCare 4D, and perform a qualitative assessment of the models based on five-point Likert scale items.
Concerning carious lesions, the texture was realistic, and the shade was adequate for 94% and 97% of the participants. Ninety per cent of the participants found the model adequate to perform an ICDAS visual assessment. Seventy-four per cent of the students found the hardness adequate. Concerning the difference in shade and the noticeable hardness difference between enamel and dentin, participants have mixed agreement with a proportion of 61% and 55%, respectively. All the participants agreed these 3D-printed models provide a good caries simulation, are suitable for hands-on operative dentistry courses, and that learning outcomes better than the standard model.
The present work shows that rapid prototyping paves the way for customized educational models capable of supporting operative but also preoperative skills. 3D printing opens up new opportunities by reducing the gap between pre-clinical training and clinical reality in caries management, which can positively impact the quality of patient care.
Mantle cell lymphoma (MCL), small lymphocytic lymphoma (SLL), and marginal zone lymphoma (MZL) are small B-cell non-Hodgkin lymphomas (NHLs) that may be difficult to distinguish. In order to identify ...specific proteomic biomarkers, differential proteomic analysis of these three NHLs was performed using surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). Whole cell lysates obtained from 18 MCL, 20 SLL, and 20 MZL biopsies were applied on two different ProteinChips (cationic and anionic). Hierarchical clustering and discriminating scores combined with an innovative bio-informatics microdissection strategy allowed us to distinguish specific lymphoma proteomic signatures based on the expression of 37 protein peaks. SELDI-assisted protein purification combined with nano-liquid chromatography (LC) quadrupole-time of flight tandem mass spectrometry (Q-TOF MS/MS) was used to identify proteins overexpressed in both MCL and SLL tumors. Among them two histones, H2B and H4, were identified in MCL tumor biopsies and the signal recognition particle 9 kDa protein, SRP9, in SLL tumor biopsies.
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected ...model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).
CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. To gain insight into how these DNA elements are conserved and spread through the ...genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages.
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► CTCF-binding locations are highly conserved across mammals ► New locations for CTCF binding are carried by SINE repeats in many mammals ► Ancient and newly born CTCF-binding events similarly demarcate chromatin barriers ► Retroelements can reposition organizing elements throughout the genome
Evolutionary analysis of six divergent mammals uncovers both highly conserved and species-specific binding locations of the chromatin organizer, CTCF. This study reveals that activation of retroelements drives genome evolution by repositioning genome-organizing elements.
Dental caries management requires individualized follow-up and prophylaxis based on patients' caries risk (PCR). In large pre-doctoral clinics, the use of institutional quality measures (QMs) is ...essential to control the quality of patient follow-up and to evaluate the need for improvement measures. The aim of this retrospective study was to evaluate the suitability of reusing student activity data for the development of QMs of caries risk. Two approaches for predicting PCR using student activity data were evaluated and compared. The first approach used the procedure codes recommended by the Dental Quality Alliance and the second used these same codes along with three educational codes. The sensitivity, specificity, overall accuracy of the two approaches were evaluated. A Receiver Operating Characteristic (ROC) curve analysis was carried out, and the areas under the ROC curve of the two approaches were compared using Delong's test. A two-tailed P value ≤0.05 was considered statistically significant. While the two approaches were able to correctly predict PCR, the approach using both procedure and educational codes showed better predictive performance. The reuse of student activity data is an easy and robust method for the development of QMs of caries risk that can help improve monitoring and quality of patient care.
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