LassoProt: server to analyze biopolymers with lassos.

The LassoProt server, http://lassoprot.cent.uw.edu.pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes.

A preliminary assessment of a new dedicated endodontic software for use with CBCT images to evaluate the canal complexity of mandibular molars.

AIM: To investigate in vivo the complexity of canals within mesial roots of mandibular molars using 3D Endo™ software linked to CBCT images. METHODOLOGY: The CBCT images of 100 mandibular first molars were analysed using the 3D Endo™ software. The number of canals in the mesial roots, the presence of apical confluences, the canal lengths and the canal configurations using Vertucci's classification were evaluated in buccolingual (BL) and mesiodistal (MD) views. The software allowed the visualization of canal trajectories in three dimensions using a coloured outline, which was used to develop a new objective scoring system to provide an overall assessment of canal complexity. Data were analysed statistically using anova and t-tests with the significance set at P < 0.05. RESULTS: Vertucci type IV canals were found in 44% of the cases, whilst 54% were type II. The mean distance from the apical foramen to the orifice was 13.15 mm (±1.21) and that between a confluence and the foramen, 2.81 mm (±1.13). The number of curvatures and the canal complexity scores in the MD view were significantly higher than in the BL view (P < 0.05). The scores were not directly correlated to the canal (MB versus ML), to the canal length or to the presence of confluences. CONCLUSIONS: 3D Endo software features the automatic detection and measurement of several anatomical canal parameters, and is a promising tool for the study of canal complexity in vivo. The unpredictable anatomy of the mesial roots of mandibular molars highlights the value of a three-dimensional preoperative evaluation of each case. The proposed scoring system aims to provide the clinician with an overall assessment of canal complexity.

OPEN-SOURCE SOFTWARE IN DENTISTRY: A SYSTEMATIC REVIEW.

OBJECTIVES: Technological development and the need for electronic health records management resulted in the need for a computer with dedicated, commercial software in daily dental practice. The alternative for commercial software may be open-source solutions. Therefore, this study reviewed the current literature on the availability and use of open-source software (OSS) in dentistry. METHODS: A comprehensive database search was performed on February 1, 2017. Only articles published in peer-reviewed journals with a focus on the use or description of OSS were retrieved. The level of evidence, according to Oxford EBM Centre Levels of Evidence Scale was classified for all studies. Experimental studies underwent additional quality reporting assessment. RESULTS: The screening and evaluation process resulted in twenty-one studies from 1,940 articles found, with 10 of them being experimental studies. None of the articles provided level 1 evidence, and only one study was considered high quality following quality assessment. Twenty-six different OSS programs were described in the included studies of which ten were used for image visualization, five were used for healthcare records management, four were used for educations processes, one was used for remote consultation and simulation, and six were used for general purposes. CONCLUSIONS: Our analysis revealed that the dental literature on OSS consists of scarce, incomplete, and methodologically low quality information.

Radiographic technique and brackets affect measurements of proximal enamel thickness on mandibular incisors.

OBJECTIVE: To investigate the influence of radiographic film and tube positioning, the presence and the size of brackets on in vitro measurements of proximal enamel thickness of mandibular incisors on periapical radiographs aimed to aid planning of interproximal enamel reduction procedures in orthodontics. MATERIALS AND METHODS: Eighty human mandibular incisors were assigned to sets of four and located in a customized base. Periapical radiographs were taken with the film positioned at three different angles (0°, 2°, and 5°) in relation to the frontal plane and the tube head positioned at five angles (0°, -2°, -5°, +2°, and +5°) in relation to the sagittal plane. The proximal enamel width was calculated by means of computerized image analysis and compared with measurements obtained at 0°. Statistical analysis was carried out to compare the enamel measurements on radiographs made with all angular combinations with and without the presence of brackets of different dimensions. RESULTS: A significant difference (P < 0.05) was found between the measurements of proximal enamel width obtained at the different angles in relation to the frontal and sagittal planes for all sets with or without brackets. The presence of brackets significantly affected the measured width only for the enamel side further away from the radiation source at the sagittal plane (P < 0.05). CONCLUSION: Angular changes in taking periapical radiographs of mandibular incisors and the presence of brackets significantly affect interproximal enamel measurements made with image analysis software.

Assessing the accuracy of computer color matching with a new dental porcelain shade system.

STATEMENT OF PROBLEM: In a previous study, a novel computer color matching system for dental ceramic restoration was developed, and 21 new shades were established. Theoretically, a natural tooth color can be accurately reproduced by combining 2 or 3 ceramic mixtures from the database of 21 new shades. PURPOSE: The purpose of this study was to test the use of these shades in conjunction with the computer color matching system to determine their ability to accurately reproduce the body color of 29 shade tabs from a shade guide (VITAPAN 3D-Master). MATERIAL AND METHODS: Disks of 21 reference shades were prepared with porcelain (Cerabien CZR) and polished to 1.0 mm thickness. A spectrophotometer was used to measure the reflectance values from 380 to 780 nm for each disk; the scattering coefficient and absorption coefficient were determined. By using the reflectance values and the scattering and absorption coefficients, the computer color matching program generated porcelain prescriptions incorporating proportions from the 21 reference shades to reproduce the shade tabs. Disks were fabricated from the prescriptions, polished to 1.0 mm thickness, then placed over a zirconia core plate and measured with the spectrophotometer. The color differences (ΔE*) between the shade tabs and the corresponding ceramic disks were calculated. Statistical analysis was performed with the 1-sample t test. RESULTS: The ΔE* values between computer color matching specimens and the target shade tabs varied from 0.5 to 1.9, with an average ΔE* of 1.3, which was significantly less than the clinically detectable ΔE* threshold of 1.6 (P<.001). CONCLUSIONS: The computer color matching system with the established 21 new shades is accurate and effective for reproducing tooth shades.

A new method to measure mesiodistal angulation and faciolingual inclination of each whole tooth with volumetric cone-beam computed tomography images.

INTRODUCTION: The purpose of this study was to develop a methodology to measure the mesiodistal angulation and the faciolingual inclination of each whole tooth (including the root) by using 3-dimensional volumetric images generated from cone-beam computed tomography scans. METHODS: A plastic typodont with 28 teeth in ideal occlusion was fixed in position in a dry human skull. Stainless steel balls were fixed to the occlusal centers of the crowns and to the apices or bifurcation or trifurcation centers of the roots. Cone-beam computed tomography images were taken and rendered in Dolphin 3D (Dolphin, Chatsworth, Calif). The University of Southern California root vector analysis program was developed and customized to digitize the crown and root centers that define the long axis of each whole tooth. Special algorithms were used to automatically calculate the mesiodistal angulation and the faciolingual inclination of each whole tooth. Angulation measurements repeated 5 times by using this new method were compared with the true values from the coordinate measuring machine measurements. Next, the root points of 8 selected typodont teeth were modified to generate known angulation and inclination values, and 5-time repeated measurements of these teeth were compared with the known values. RESULTS: Intraclass correlation coefficients for the repeated mesiodistal angulation and faciolingual inclination measurements were close to 1. Comparisons between our 5-time repeated angulation measurements and the coordinate measuring machine's true angulation values showed 5 teeth with statistically significant differences. However, only the maxillary right lateral incisor showed a mean difference that might exceed 2.5° for clinical significance. Comparisons between the 5-repeated measurements of 8 teeth with known mesiodistal angulation and faciolingual inclination values showed no statistically significant differences between the measured and the known values, and no measurement had a 95% confidence interval beyond 1°. CONCLUSIONS: We have developed the novel University of Southern California root vector analysis program to accurately measure each whole tooth mesiodistal angulation and faciolingual inclination, in a clinically significant level, directly from the cone-beam computed tomography volumetric images.

Optimization of protocell of silica nanoparticles using 3² factorial designs.

The purpose of the research is to carry out systemic optimization of protocells (liposomes entrapped with silica particles). Optimization was carried out using 3(2) factorial designs for the selection of the optimized protocell composition with reference to particle size distribution and zetapotential. This design was carried out to study the effect of independent variables such as molar ratio of phosphatidylcholine to cholesterol and concentration of silica nanoparticles. A total of nine formulations of protocells were prepared and analyzed using Design expert® software from Stat-Ease, Inc. (Version 8.0.4.1 trial 2010) for the selection of the optimized combination. Contour plots were constructed with independent variables like size and potential. Protocell with 7:3 ratio of phosphatidyl choline to cholesterol and 0.5 mg/ml of silica nanoparticles demonstrated better colloidal behaviors. The findings obtained from the software corresponding to independent variables demonstrated accurate means for the optimization of the pharmaceutical formulations.

System dynamics modeling for tooth decay treatment in Brazilian children.

Prevention and health promotion are considered important strategies to control oral diseases. Dental caries is preventable disease and remains the most common chronic disease that affects mainly low income children and still considered the main cause of tooth loss in adulthood in Brazil. The aim of this study is to present a System Dynamics model (SDM) specifically developed with the Stella Architect software to estimate the cost and clinical hours required to control the evolution of dental caries in preschool children in Maringá, Brazil. Two main strategies to control caries were considered in the model: the application of fluoride varnish on teeth presenting white spots, and the use of Atraumatic Restorative Treatment (ART) in cavitated carious lesions without pulp involvement. The parameters used in the model were: number of people covered by a local oral health team = 4,000; number of children up to 5 years = 7% of the population; children's decayed, missing, filled teeth (dmft) index = 2.4; time/cost of 4 applications of fluoride varnish = 5 minutes/US$ 0.716; and time/cost of each ART restoration = 15 minutes/US$ 1.475. The SDM generated an estimated total cost of US$698.00, and a total of 112 clinical hours to treat the population in question. The use of the SDM presented here has the potential to assist decision making by measuring the material and human resources required to prevent and control dental caries at an early age.

Reliability of a Virtual Prosthodontic Project Realized through a 2D and 3D Photographic Acquisition: An Experimental Study on the Accuracy of Different Digital Systems.

AIMS: The study aims to assess the accuracy of digital planning in dentistry, evaluating the characteristics of different intraoral 3D scanners and comparing it with traditional imaging 2D recording methods. Specifically, using computer aided design (CAD) software and measuring inside CAD software, authors want to verify the reliability of different models obtained with different techniques and machines. METHODS: 12 patients that needed aesthetic restorative treatment were enrolled in the study. All the patients underwent recording data of the height and width dental elements 1.1, 1.2, and 1.3 size using different technologies and comparing 2D with 3D methods. A T test was then applied in order to verify whether there was a statistically significant difference between the measurements obtained, comparing the different tools data (Emerald, TRIOS, Photogrammetry and DSS (Digital Smile System)) with the reference values. RESULTS: No significant differences emerged in the measurements made with the different scanners (Trios 3Shape ®, Planmeca Emerald ®) and photogrammetry. Therefore, what should be underlined regarding the 2D measurements is the speed and simplicity compared to all 3D techniques, so this work can help to better define the field of application and the limits connected to 2D techniques, giving a good window of the technique. CONCLUSIONS: The low number of patients is not sufficient to provide statistically significant results, but the digital planning future prospects seem to be promising. This study results highlighted how a photogrammetric scanner for dental arches would only have a much smaller shooting field size and greater accuracy. Despite these considerations, the photogrammetric facial scanner provided excellent results for the measurement of individual teeth, showing a great versatility of use.

Effect of software version and parameter settings on the marginal and internal adaptation of crowns fabricated with the CAD/CAM system.

OBJECTIVE: This study investigated the marginal and internal adaptation of individual dental crowns fabricated using a CAD/CAM system (Sirona's BlueCam), also evaluating the effect of the software version used, and the specific parameter settings in the adaptation of crowns. MATERIAL AND METHODS: Forty digital impressions of a master model previously prepared were acquired using an intraoral scanner and divided into four groups based on the software version and on the spacer settings used. The versions 3.8 and 4.2 of the software were used, and the spacer parameter was set at either 40 µm or 80 µm. The marginal and internal fit of the crowns were measured using the replica technique, which uses a low viscosity silicone material that simulates the thickness of the cement layer. The data were analyzed using a Friedman two-way analysis of variance (ANOVA) and paired t-tests with significance level set at p<0.05. RESULTS: The two-way ANOVA analysis showed the software version (p<0.05) and the spacer parameter (p<0.05) significantly affected the crown adaptation. The crowns designed with the version 4.2 of the software showed a better fit than those designed with the version 3.8, particularly in the axial wall and in the inner margin. The spacer parameter was more accurately represented in the version 4.2 of the software than in the version 3.8. In addition, the use of the version 4.2 of the software combined with the spacer parameter set at 80 µm showed the least variation. On the other hand, the outer margin was not affected by the variables. CONCLUSION: Compared to the version 3.8 of the software, the version 4.2 can be recommended for the fabrication of well-fitting crown restorations, and for the appropriate regulation of the spacer parameter.

Influence of mandibular positioning on the accuracy and reliability of linear measurements on cone beam CT using different voxels and two software programs / Influência do posicionamento mandibular na acurácia e confiabilidade de medidas lineares em tomografia computadorizada de feixe cônico utilizando diferentes voxels e dois softwares

Objetivo: este estudo avaliou a acurácia e confiabilidadedas medidas lineares em exames detomografia computadorizada de feixe cônico(TCFC), em dois softwares, utilizando diferentesvoxels e variando o posicionamento da mandíbula.Material e Métodos: 10 imagens de TCFC demandíbulas humanas com 25 pontos foram obtidas,usando diferentes protocolos de aquisição(0.250, 0.300, 0.400-mm voxels) e orientações damandíbula (centralizada, rotacionada 10° lateralmentepara direita e esquerda, inclinada 10° para cima e para baixo); 14 medidas foram realizadasnas reconstruções multiplanares nos softwares XoranCate OsiriX. Os achados foram comparadoscom as medidas físicas através de um paquímetrodigital. O teste ANOVA e o coeficiente de correlaçãoforam utilizados com p < 0,05. Resultados:não houve diferença estatisticamente significantequando as medidas foram comparadas em aquisiçõescom diferentes tamanhos de voxels emambos os softwares. A posição da mandíbula nãoinfluenciou nas medidas. Nenhuma diferença foiencontrada quando os valores foram comparadosentre os softwares e o paquímetro digital. Conclusão:as medidas lineares em ambos os softwaresforam confiáveis e acurados comparados a mensuraçãofísica em todos os protocolos. A acuráciae a confiabilidade das mensurações não influenciaramde acordo com as variações de posicionamentoda mandíbula.(AU)

Objective: this study evaluated the accuracy and reliability of linear measurements on cone beam CT (CBCT) scans in two software programs, using different voxels and varying mandible positioning. Material and methods: CBCT images of 10 human mandibles with 25 markers were obtained using different acquisition protocols (0.250, 0.300, 0.400-mm voxels) and mandible orientations (centered, rotated 10° laterally to right and left, tilted 10 up and down); fourteen measurements were carried out on the multiplanar reconstructions in XoranCat and OsiriX Lite software programs. The findings were compared to physical measurements using a digital caliper. ANOVA and correlation coefficient tests were used, at α = 0.05. Results: there was no statistically significant difference when the measurements were compared in acquisitions with different voxel sizes analysed in both software programs. Mandibular positioning changes did not influence the measurements. No differences were found when the values were compared between the software programs and the digital caliper. Conclusion: linear measurements in both programs were reliable and accurate compared with physical measurements when using all acquisition protocols. The accuracy and reliability of the measurements were not influenced by variations in the mandible positioning.(AU)

System dynamics modeling for tooth decay treatment in Brazilian children

Abstract Prevention and health promotion are considered important strategies to control oral diseases. Dental caries is preventable disease and remains the most common chronic disease that affects mainly low income children and still considered the main cause of tooth loss in adulthood in Brazil. The aim of this study is to present a System Dynamics model (SDM) specifically developed with the Stella Architect software to estimate the cost and clinical hours required to control the evolution of dental caries in preschool children in Maringá, Brazil. Two main strategies to control caries were considered in the model: the application of fluoride varnish on teeth presenting white spots, and the use of Atraumatic Restorative Treatment (ART) in cavitated carious lesions without pulp involvement. The parameters used in the model were: number of people covered by a local oral health team = 4,000; number of children up to 5 years = 7% of the population; children's decayed, missing, filled teeth (dmft) index = 2.4; time/cost of 4 applications of fluoride varnish = 5 minutes/US$ 0.716; and time/cost of each ART restoration = 15 minutes/US$ 1.475. The SDM generated an estimated total cost of US$698.00, and a total of 112 clinical hours to treat the population in question. The use of the SDM presented here has the potential to assist decision making by measuring the material and human resources required to prevent and control dental caries at an early age.

Vertical bone measurements from cone beam computed tomography images using different software packages.

This article aimed at comparing the accuracy of linear measurement tools of different commercial software packages. Eight fully edentulous dry mandibles were selected for this study. Incisor, canine, premolar, first molar and second molar regions were selected. Cone beam computed tomography (CBCT) images were obtained with i-CAT Next Generation. Linear bone measurements were performed by one observer on the cross-sectional images using three different software packages: XoranCat®, OnDemand3D® and KDIS3D®, all able to assess DICOM images. In addition, 25% of the sample was reevaluated for the purpose of reproducibility. The mandibles were sectioned to obtain the gold standard for each region. Intraclass coefficients (ICC) were calculated to examine the agreement between the two periods of evaluation; the one-way analysis of variance performed with the post-hoc Dunnett test was used to compare each of the software-derived measurements with the gold standard. The ICC values were excellent for all software packages. The least difference between the software-derived measurements and the gold standard was obtained with the OnDemand3D and KDIS3D (-0.11 and -0.14 mm, respectively), and the greatest, with the XoranCAT (+0.25 mm). However, there was no statistical significant difference between the measurements obtained with the different software packages and the gold standard (p> 0.05). In conclusion, linear bone measurements were not influenced by the software package used to reconstruct the image from CBCT DICOM data.

CARL: a LabVIEW 3 computer program for conducting exposure therapy for the treatment of dental injection fear.

This paper describes CARL (Computer Assisted Relaxation Learning), a computerized, exposure-based therapy program for the treatment of dental injection fear. The CARL program operates primarily in two different modes; in vitro, which presents a video-taped exposure hierarchy, and in vivo, which presents scripts for a dentist or hygienist to use while working with a subject. Two additional modes are used to train subjects to use the program and to administer behavioral assessment tests. The program contains five different modules, which function to register a subject, train subjects to use physical and cognitive relaxation techniques, deliver an exposure hierarchy, question subjects about the helpfulness of each of the therapy components, and test for memory effects of anxiolytic medication. Nine subjects have completed the CARL therapy program and 1-yr follow-up as participants in a placebo-controlled clinical trial examining the effects of alprazolam on exposure therapy for dental injection phobia. All nine subjects were able to receive two dental injections, and all reduced their general fear of dental injections. Initial results therefore indicate that the CARL program successfully reduces dental injection fear.

Development and evaluation of digital subtraction radiography computer program.

OBJECTIVE: We developed a new program for digital subtraction radiography (DSR) having useful functions to get the DSR image more accurately and efficiently. The purpose of this study was to evaluate the accuracy of the DSR image acquired using the new program as compared with the ready-made program. STUDY DESIGN: Four observers performed the DSR process using our program and the ready-made program for digital intraoral radiographs taken from incisor, premolar, and molar regions. The statistical difference was evaluated between the programs, between the observers, and between the regions. RESULTS: The DSR image using our program was superior to that with the ready-made program in all the observers and all the radiographed regions. Also, there was the statistical difference among the observers, especially in our program. CONCLUSION: The DSR image using the new program was very accurate compared with ready-made program, so the program was useful to get an accurate DSR image.

Continuing dental education on the World Wide Web.

Continuing dental education (CDE) courses delivered on the World Wide Web (Web CDE) offer numerous advantages over traditional CDE; however, two major issues--location of suitable courses and course quality--need resolution. Locating high-quality courses is difficult due to the lack of the standardized metadata that allows search engines to match courses to practitioners' needs. Web directories created by professional organizations are beginning to show promise, but require further development. Search engines and Web directories are discussed and improvements currently underway summarized. Course quality remains a highly significant concern. A national effort to create Web CDE course quality standards is underway that includes proposed standards. These proposed standards are summarized and used to comment on the current state of Web CDE courses. Examples are given when possible. Three emerging Web CDE technologies and a look to the future of Web CDE are discussed.

Instructional characteristics of online continuing education courses.

OBJECTIVE: The purpose of this study was to determine the instructional characteristics of online continuing dental education courses on the World Wide Web. METHOD AND MATERIALS: One hundred fifty-seven online courses offered by 32 providers were reviewed for 34 criteria. RESULTS: Courses of various types spanned a variety of topics. Approximately half of all courses offered continuing dental education credit. The relationship between credit hours and course length was quite variable. Most courses consisted of text and images. Very few courses used advanced media such as video clips. Measured against an index of instructional quality developed for this study, the instructional quality of the courses, in general, was poor. Most for-credit courses contained self-assessment questions, but only 28% of courses scored the questions online. Basic information that was missing on many courses included the authors' names (29%); the intended audience (81%); goals and objectives (77%); and references (85%). In 47% of the courses, there was no opportunity to provide feedback to either the author or the provider. CONCLUSION: The theoretical advantages of Web-based continuing dental education are numerous, but the currently available online resources are mostly of unacceptable quality.

Developing high-quality educational software.

The development of effective educational software requires a systematic process executed by a skilled development team. This article describes the core skills required of the development team members for the six phases of successful educational software development. During analysis, the foundation of product development is laid including defining the audience and program goals, determining hardware and software constraints, identifying content resources, and developing management tools. The design phase creates the specifications that describe the user interface, the sequence of events, and the details of the content to be displayed. During development, the pieces of the educational program are assembled. Graphics and other media are created, video and audio scripts written and recorded, the program code created, and support documentation produced. Extensive testing by the development team (alpha testing) and with students (beta testing) is conducted. Carefully planned implementation is most likely to result in a flawless delivery of the educational software and maintenance ensures up-to-date content and software. Due to the importance of the sixth phase, evaluation, we have written a companion article on it that follows this one. The development of a CD-ROM product is described including the development team, a detailed description of the development phases, and the lessons learned from the project.

Evaluation of educational software.

Evaluation is an important component of developing educational software. Ideally, such evaluation quantifies and qualifies the effects of a new educational intervention on the learning process and outcomes. Conducting meaningful and rigorous educational evaluation is difficult, however. Challenges include defining and measuring educational outcomes, accounting for media effects, coping with practical problems in designing studies, and asking the right research questions. Practical considerations that make the design of evaluation studies difficult include confounding, potentially small effect sizes, contamination effects, and ethics. Two distinct approaches to evaluation are objectivist and subjectivist. These two complement each other in describing the whole range of effects a new educational program can have. Objectivist demonstration studies should be preceded by measurement studies that assess the reliability and validity of the evaluation instrument(s) used. Many evaluation studies compare the performance of learners who are exposed to either the new program or a more traditional approach. However, this method is problematic because test or exam performance is often a weak indicator of competence and may fail to capture important nuances in outcomes. Subjectivist studies are more qualitative in nature and may provide insights complementary to those gained with objectivist studies. Several published examples are used in this article to illustrate different evaluation methods. Readers are encouraged to contemplate a wide range of evaluation study designs and explore increasingly complex questions when evaluating educational software.