Do the Mechanical and Chemical Properties of Invisalign\u3csup\u3eTM\u3c/sup\u3e Appliances Change After Use? A Retrieval Analysis

Aim: To investigate the mechanical and chemical alterations of Invisalign appliances after intraoral aging. Materials and methods: Samples of Invisalign appliances (Align Technology, San Jose, California, USA) were collected following routine treatment for a mean period of 44±15 days (group INV), whereas unused aligners of the same brand were used as reference (group REF). A small sample from the central incisors region was cut from each appliance and the buccal surface was analysed by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy (n = 5). Then the appliances were cut (n = 25) and embedded in acrylic resin, ground/polished in a grinding polishing machine, and the prepared surfaces were subjected to Instrumented Indentation Testing under 4.9 N load. Force-indentation depth curves were recorded for each group and the following parameters were calculated according to ISO 14577-1; 2002 specification: indentation modulus (E IT), elastic to total work ratio also known as elastic index (ηIT), Martens Hardness (HM), and indentation creep (C IT) The mean values of the mechanical properties were statistically analysed by unpaired t-test (a = 0.05). Results: ATR-FTIR analysis confirmed the urethane based structure of the appliances, without important chemical differences attributed to the aging process. INV group showed significantly lower E IT (REF: 2466±20, INV: 2216±168MPa), HM (REF: 119±1, INV: 110±6 N mm−2) and higher ηIT (REF: 40.0±0.3, INV: 41.5±1.2%), and C IT (REF: 3.7±0.2 INV: 4.0±0.1%). The increase in ηIT indicates that INV is a more brittle than REF, whereas the increase in C IT, a decrease in creep resistance. Conclusion: Despite the lack of detectable chemical changes, intraoral aging adversely affected the mechanical properties of the Invisalign appliance

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Optimization of miRNA-seq data preprocessing.

The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments

A Comparison of Three-Dimensional Printing Technologies on the Precision, Trueness, and Accuracy of Printed Retainers

Purpose: The aim of this study was to evaluate the differences in the precision, trueness, and accuracy of 3D printed orthodontic clear retainers produced using printer systems with various printing technologies. Methods: Retainers (n=15) were printed using four different 3D printers: a stereolithography (SLA) printer, two different digital light processing (DLP and cDLP) printers, and a polyjet photopolymer (PPP) printer. The 3D printed retainers were transformed into a digital file through a cone-beam computed tomography scan that was compared to the original image using a 3D superimposition analysis software. At previously chosen landmarks (R6, L6, R3, L3, R1, L1) retainers were compared to the reference model. The intercanine and the intermolar width measurements were also analyzed for deviations between the samples and the original file. A discrepancy up to 0.25mm was considered clinically acceptable. Precision of printers was evaluated on 5 randomly chosen samples. Trueness was determined by comparing the measurements on printed retainers to those on the original image file. Root mean square (RMS) and percent of points within the tolerance level (inTOL) were also calculated with respect to precision and trueness for each retainer. Samples were analyzed for intra-printer reliability (precision), and inter-printer trueness. Statistical significance was set at P\u3c0.05. Results: Interrater correlation coefficient indicated good agreement and all measurements were within 0.10mm at least 95% of the time. Statistically significant differences were found between printer types among each of the 6 landmarks and the arch widths. When evaluating inTOL and RMS, statistically significant differences in both median precision and trueness among each printer type were found. SLA and PPP printing technologies exhibited both excellent precision and trueness. Conclusion: Retainers fabricated by SLA, DLP, cDLP, and PPP technologies were shown to be clinically acceptable and accurate compared to the standard reference file. SLA and PPP printers showed greater accuracy, and the DLP and cDLP printers exhibited greater precision. The PPP printer had the most accurate intra-arch measurements followed by the SLA printer, and therefore, based on their high trueness and precision values, were deemed to be the most accurate overall

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

The combined use of computer-guided, minimally invasive, flapless corticotomy and clear aligners as a novel approach to moderate crowding: a case report

The aim of this case report was to describe an innovative orthodontic treatment method that combined surgical and orthodontic techniques. The novel method was used to achieve a positive result in a case of moderate crowding by employing a computer-guided piezocision procedure followed by the use of clear aligners. A 23-year-old woman had a malocclusion with moderate crowding. Her periodontal indices, oral health-related quality of life (OHRQoL), and treatment time were evaluated. The treatment included interproximal corticotomy cuts extending through the entire thickness of the cortical layer, without a fullthickness flap reflection. This was achieved with a three-dimensionally printed surgical guide using computer-aided design and computer-aided manufacturing. Orthodontic force was applied to the teeth immediately after surgery by using clear appliances for better control of tooth movement. The total treatment time was 8 months. The periodontal indices improved after crowding correction, but the oral health impact profile showed a slight deterioration of OHRQoL during the 3 days following surgery. At the 2-year retention follow-up, the stability of treatment was excellent. The reduction in surgical time and patient discomfort, increased periodontal safety and patient acceptability, and accurate control of orthodontic movement without the risk of losing anchorage may encourage the use of this combined technique in appropriate cases

SANA NetGO: A combinatorial approach to using Gene Ontology (GO) terms to score network alignments

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment are not isolated: each pairing is implicitly dependent upon every other pairing via the alignment itself. Current methods fail to take into account the frequency of GO terms across the networks, and attempt to account for common GO terms in an ad hoc fashion by imposing arbitrary rules on when to "allow" GO terms based on their location in the GO hierarchy, rather than using readily available frequency information in the PPI networks themselves. Here we develop a new measure, NetGO, that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without requiring arbitrary cutoffs. In particular, NetGO down-weights the score of frequent GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO by creating alignments of predetermined quality based on homologous pairs of nodes and show that NetGO correlates with alignment quality much better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measures--a feature not shared with existing GO-based network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job than existing measures at separating good alignments from bad ones

The Effect of Orthodontic Appliances on the Evaluation of the Professionalism and Esthetics of an Adult Employee

This study explored the influence of fixed and removable orthodontic appliances on participants’ ratings of the job performance, intelligence, and attractiveness of an adult female. Ninety-four adult subjects were recruited from the Graduate School of Management at Marquette University. Each subject received an identical employee performance review with an attached photograph of a female employee. The smile of the photo was manipulated to represent one of four conditions: no orthodontic appliance, a metal orthodontic appliance, a ceramic orthodontic appliance, or a clear aligner. Subjects then rated the employee on three continuous Likert scales. Ratings of job performance, intelligence, and attractiveness were not correlated. There were no significant differences between the types of orthodontic appliance for overall ratings of job performance, intelligence, and attractiveness. However, when analyzed by the subject’s gender, there was a significant interaction between gender and type of orthodontic appliance pictured for intelligence ratings. Female respondents rated the photos with the metal appliance with lower intelligence than the photo with the clear aligner while male respondents answered in the opposite manner. Background facial attractiveness may be a better predictor than smile esthetics of the psychosocial ratings of individuals. However, both gender and the presence or absence of an orthodontic appliance can influence assessments of perceived intelligence or similar qualities in the workplace

The combined use of corticotomy and clear aligners: a case report

OBJECTIVE:   To describe an orthodontic treatment that combines an esthetic approach (clear aligners) with surgery (alveolar corticotomy). MATERIALS AND METHODS:   A patient with moderate dental crowding and Class I skeletal and molar relationships was selected. Orthodontic records of the patient were taken. Periodontal indexes, oral health-related quality of life (OHRQoL), and treatment time were evaluated. After we reflected a full-thickness flap beyond the teeth apices, the cortical bone was exposed on the buccal aspect and a modified corticotomy procedure was performed. Interproximal corticotomy cuts were extended through the entire thickness of the cortical layer, just barely penetrating into medullary bone. Orthodontic force was applied on the teeth immediately after surgery. RESULTS:   Total treatment time was 2 months. Periodontal indexes were improved after correction of crowding. A deterioration of OHRQoL was limited to 3 days following surgery. CONCLUSION:   This case report may encourage the use, limited to selected cases, of corticotomy associated with clear aligners to treat moderate crowding

A comparison of patient testimonials on YouTube of the most common orthodontic treatment modalities: braces, in-office aligners, and direct-to-consumer aligners

Introduction: The objectives of this research was to investigate and compare the educational value of the most popular YouTube orthodontic patient testimonials between braces (B), in- office aligners (IOA), and direct-to-consumer aligners (DTCA), and to classify the emotional response of the viewers through a sentiment analysis of the video comments. Methods: Three different phrases relevant to B, IOA, and DTCA were searched on YouTube. The 20 most popular patient testimonial videos that met the criteria for each group were selected, for a total of 60 videos. Using the YouTube API for each video, 13 video metrics were extracted, an information completeness score (ICS) was assigned, and an analysis of the video comments was performed using sentiment analysis software. Results: The 60 videos included in this study were viewed 34,384,786 times by internet users. Braces videos have significantly more likes, comments, and a higher viewer interaction score than the IOA and DTCA videos. IOA videos had a higher median ICS than B and DTCA videos. Of the 5149 video comments with polarity, 53.6% were positive and 46.4% were negative (P Conclusions: There is high user engagement on YouTube with orthodontic patient testimonials. YouTube users interact with braces patient testimonials the most. YouTube viewers’ comments on orthodontic patient testimonials express more positive sentiment than negative sentiment. There is no significant difference in positive and negative sentiment between the video comments for the three different treatment modalities