The new technique was also found to have excellent inter- and intra-rater reliability . The main finding of this study is that the technique presented is a valid and reliable method that provides the advantage of 3D-assessment of graft resorption at long-term follow-up without the need of an early postoperative CT-scan.Bone graft resorption following the Latarjet procedure has received considerable concern. Current methods quantifying bone graft resorption rely on two-dimensional (2D) CT-scans or three-dimensional (3D) techniques, which do not represent the whole graft volume/resorption  or expose patients to additional radiation  as this technique relies on early postoperative CT-scans. The aim of the present study was to develop and validate a patient-specific, CT-morphometric technique combining image registration with 3D CT-reconstruction to quantify bone graft resorption following the Latarjet procedure for recurrent anterior shoulder instability. Pre-operative and final follow-up CT-scans were segmented to digitally reconstruct 3D scapula geometries. A virtual Latarjet procedure was then conducted to model the timepoint-0 graft volume, which was compared with the final follow-up graft volume. Graft resorption at final follow-up was highly correlated to the 2D gold standard-technique by Zhu (Kendall tau coefficient = 0.73;  The Latarjet procedure has become one of the most commonly used bone block procedures for the treatment of recurrent anterior shoulder instability ,2,3. ThoDespite excellent clinical outcomes, the Latarjet procedure has a number of complications including ongoing apprehension, recurrent instability and complications related to the metalware ,7,10. ThZhu et al. (2015) developed a classification system to grade the severity of graft resorption following the open Latarjet procedure . Rather Three-dimensional techniques for quantifying bone graft volume have been used by various authors to measure Latarjet-graft osteolysis at short-term follow-up. Di Giacomo et al. (2011) used a 3-dimensional (3D) CT-based technique to reconstruct patient’s scapulas 3 days after surgery and after a mean of 1.5 years . Haeni eIt was therefore the aim of the current study to develop and validate a patient-specific, CT-morphometric technique combining image registration with 3D CT reconstruction to quantify coracoid bone graft resorption at long-term follow-up in patients that have undergone an open Latarjet procedure for recurrent anterior shoulder instability. It was hypothesized that CT-morphometric measurements of graft resorption at long-term follow-up will positively correlate with the Zhu classification  and that this new technique has good inter- and intra-rater reliability. This retrospective study was approved by the Cantonal Ethics Committee (No. 2018-01929). All patients included gave written consent for the purpose of this study.From January 2008 to December 2013, 105 consecutive patients older than 18 years of age were treated with an open Latarjet procedure for recurrent anterior instability. Patients with (1) previous surgery on the affected side; (2) revision of the Latarjet; (3) multidirectional instability; (4) contralateral instability; (5) medical conditions affecting shoulder function ; (6) advanced dislocation arthropathy; and (7) incomplete imaging were excluded from this study. The reviewed cohort consisted thus of 31 patients  with a mean age of 37 years  at the time of the primary open Latarjet procedure. Patients were interviewed and examined at a mean follow-up of 8.5  years. Decision for a primary open Latarjet procedure was based on preoperative glenoid bone loss >15% , and/or Patients received a CT-scan of the involved shoulder before surgery and after a mean of 8.5 years postoperatively. Scout images were used to confirm the CT was in the plane of the scapula body for all CT scans assessed. All CT scans were obtained using a 64-slice Somatom Sensation 64 CT scanner  with a slice thickness of 0.75mm and a pitch of 0.8. These CT-scans were assessed for bone graft resorption according to the Zhu classification , and forThe open Latarjet procedure was performed according to the Walch refinement of the original technique ,19. A deBone graft resorption was assessed as per the Zhu classification  for eachAs per the classification system, bone resorption was evaluated around both screws, with the highest grade between the two being used to classify the patients’ overall bone resorption .The pre-operative and final follow-up CT scans of each patient were manually segmented to digitally reconstruct the entire three-dimensional geometry of the scapulas . The pre-operative scapula geometry was then registered with the post-operative scapula, and the site of the coracoid process osteotomy performed for the Latarjet procedure was identified and digitally marked on the pre-operative scan A,B. A virtual osteotomy was then performed on the pre-operative scapula geometry at this site in order to reproduce the 3D geometry of the bone graft used during the initial Latarjet procedure . The modeled coracoid graft was then virtually placed on the glenoid of the pre-operative scapula, to produce a third scapula geometry equivalent to an immediate post-operative scapula C. The inTo help distinguish the graft at final follow-up from the glenoid, the registered geometry of the pre-operative scapula and of the post-operative scapula were used. The actual Latarjet graft at final follow-up was then digitally segmented and identified from the scapula D. To redCT-scans segmentation, reconstruction and graft identification were performed by one fellowship-trained upper limb surgeon (LE) and one medical student (FFP).p < 0.05. Statistical analysis was performed using the Statistical Package Social Science (SPSS) .Normal distribution was tested with the Shapiro–Wilk test. Bivariate correlation between Zhu resorption grade and CT-morphometric graft resorption was assessed using the Kendall tau correlation coefficient, which allows correlation between ordinal (Zhu grading) and continuous variables (graft resorption). Significance level was set at Inter- and intra-observer reliability was assessed for the CT-morphometric volume measurements by means of the Intraclass Correlation Coefficient (ICC) for absolute agreement, with 1 indicating perfect reliability.3 compared to 2010 mm3 at final follow-up, which represented an overall graft resorption of 30.9% (921 mm3).According to the Zhu classification, all patients  demonstrated bone graft resorption. The majority of patients displayed Grade II resorption  of the coracoid bone graft, followed by Grade I , with only 5 (16%) of patients showing Grade III resorption . The meap < 0.001). The technique demonstrated excellent inter-rater reliability with an ICC value of 0.930 . Intra-rater reliability, was also excellent with an ICC value of 0.991 .Bone graft resorption was strongly correlated with the Zhu resorption grade, with a Kendall tau correlation coefficient 0.73  to create a bleeding surface area. Second, the study does not include a control group which, with early post-operative scans, would allow for actual intraoperative graft loss to be quantified and accounted for. A further limitation of the study is the low number of patients, particularly in the grade I and grade III resorption groups. However, the correlation coefficients were high with high significance, proving the validity of our technique. Last, high-quality CT-scans are a prerequisite for the technique, which are expensive and not available in every hospital.This study describes a novel CT morphometric technique that uses combined image registration and 3D reconstruction to accurately measure graft volume and long-term bone resorption in patients that have undergone the Latarjet procedure. The main finding of the study is that measured 3D bone graft resorption had excellent correlation to the 2D gold standard classification by Zhu, and that the technique is highly reliable. This technique could be readily utilized in future research for the study of bone resorption at long-term follow-up and in clinical assessments of graft osteolysis following the Latarjet procedure, thus guiding surgeons regarding possible revision surgery when faced with significant resorption of the coracoid bone graft.


It is a delicate task to write the first editorial of the Brazilian Journal of Otorhinolaryngology. Owing to its rich scientific content and feature of interesting articles, RBORL has a fascinating history. It is this history that challenges us. The Sao Paulo Journal of Otorhinolaryngology was founded in January 1933. At the time, its Editors were focusing on putting aside “bitter criticism” that was given to them by publishing the article “regionalism act”. In the first years of the 1950's, the Journal was incorporated into the Brazilian Federation of the Societies of Otorhinolaryngology and Bronchoesophagology. As expected, it became a national journal, owing to its new and definitive denomination. It is curious (and maybe not a mere coincidence) that the journal we originally obtained our name from was founded in Recife in 1935, as the Journal of Anais Otorhinolaryngology - a scientific periodical of national circulation highly acclaimed by otorhinolaryngologists in Recife and in the Northeast of Brazil.Since then, the Journal has made an upward curve and more recently – why not? – a sharp curve. It is not surprising that this publication has been coordinated by people such as: Mário Ottoni de Rezende, Homero Cordeiro, José Rezende Barbosa, Rudolph Lang, Arthur Kós, Fernando Portinho, Ricardo Bento, Paulo Pontes, Carlos Alberto Campos and Henrique Olival Costa .The Brazilian Journal of Otorhinolaryngology has adapted to global changes following various parameters regarding scientific publication. One of these changes is that periodicals have been steadily edited in a highly professional way. In addition, it has been easy to understand the journal scientific articles, which point out the level of scientific knowledge of researchers, graduate studies programs and universities. Furthermore, the considerable progress of RBORL not only reflects the ascension of Otorhinolaryngology as a medical specialty in Brazil, but also demonstrates great intellectual development in the country.We need to highlight that we are undertaking the challenging task of coordinating ABORL-CCF Board of Publications when our Journal finds itself in the final stage of indexation by Medline. It is an outstanding merit to all individuals who have managed it so far, more specifically to Henrique Olival, who hands over the Journal among the top journals in the Brazilian Medical Publishing Houses. In addition, he provides us with an extremely workable and effective editorial management system, which has been recently implemented and might need few improvements to meet the long run needs of contributors.It is necessary to index a journal in a database if we want to pursue visibility and prestige, as well as achieve national and international market penetration. Amongst all main databases for Brazilian publications, in order of importance, are: LILACS, SciELO, Medline and ISI (Institute for Scientific Information) that publish journals of major impact. Indexing in Medline and publishing editions in English are part of the last managements' accomplishments. These were decisive steps towards achieving our last goal, which is to increase our impact of 0.0512 points in the past three years, whereas a similar journal, called Acta Cirúrgica Brasileira, has 0.1401 points. Memórias do Instituto Oswaldo Cruz, indexed in ISI, has an impact of 0.2022.The qualification of a journal and its impact depend on its regularity, periodicity and scientific quality. This last criterion is directly related to original articles and case studies. In the case of RBORL, the above-mentioned criteria are very good, but they can be better. As the number of case studies submitted is great, they generate a major and restrained demand, which we have to find a solution for, without affecting the scientific quality. We find ourselves obliged to examine the relevance of facts and sometimes stop receiving these types of articles. We want to employ stricter methods to review and select articles, which will optimize the publishing time of the approved ones. We are going to provide space for those who wish to publish their case studies in our website. Case studies that have already been submitted will be treated as usual.The improvement of our indicators is essential to achieve the highest categories of periodical classification of CAPES. This will help us to add more value to our articles, offer more places in graduate studies courses, raise funds, have more decisive influence in universities and university hospitals, and gain more respect to our specialty. This is the path. This is the main challenge presented to us. It is not less than what was faced by Sylvio Caldas  who, in Recife, driven by the same spirit that has motivated everyone from the RBORL History 70 years ago, founded, managed and gave financial support to Journal of Anais Otorhinolaryngology, using his own resources for three years. This editorial is dedicated to him and to this type of spirit.


The first canton in Switzerland to implement an organized colorectal cancer screening program (OSP) was Uri. Starting in 2013, it offered 50–69-year-olds free testing with colonoscopy every 10 years or fecal occult blood test (FOBT) every 2 years. We tested the association between the OSP and testing rates over time.We analyzed claims data of 50–69-year-olds from Uri and neighboring cantons (NB) provided by a large health insurance and complemented it with data from the OSP. We fitted multivariate adjusted logistic regression models to compare overall testing rates and by method (colonoscopy or FOBT/both) We computed the 2018 rate of the population up-to-date with testing (colonoscopy within 9 years/FOBT within 2 years).Yearly overall testing rates in Uri increased from 8.7% in 2010 to 10.8% in 2018 and from 6.5% to 7.9% in NB. In Uri, the proportion tested with FOBT/both increased from 4.7% to 6.0% but decreased from 2.8% to 1.1% in NB. Testing by FOBT/both increased more between 2015 and 2018 than 2010–2012 in Uri than in NB (OR:2.1[95%CI:1.8–2.4]), it increased less for colonoscopy (OR:0.60[95%CI:0.51–0.70]), with no change in overall CRC testing (OR:0.91[95%CI:0.81–1.02]). In 2018 in Uri, 42.5% were up-to-date with testing ; in NBs, 40.7% .Yearly FOBT rates in Uri were always higher than in NB. Though the OSP in Uri was not associated with a greater increase in overall testing rates, the OSP was associated with increased FOBT. Eligible residents are encouraged to talk to their family physician about CRC screening and are offered an informed choice between an iFOBT, also called FIT, or a colonoscopy. The program organizers track participation rates to determine the effectiveness and reach of their invitations. But they cannot measure the overall effect of the program on cantonal screening rates because they do not know if participants who are screened within the program would have otherwise elected to be screened outside the program. Since opportunistic CRC screening and diagnostic testing is high in Switzerland compared to other countries  and contOne type of data that can help determine overall testing rates in the whole population and specific subgroups is insurance claims data . This daWe aimed to assess the effect of the OSP in the canton of Uri on CRC testing rates over time and compared to neighboring cantons (NB) without an OSP, in a country with high prevalent opportunistic CRC testing. We used claims data from a large health insurance to describe yearly changes in CRC testing before and after Uri implemented its OSP, and to compare testing rates with NBs that lack a CRC OSP. We also contrasted the proportion of the population in Uri and NB that was up-to-date with CRC testing (colonoscopy within 9 years or FOBT within 2 years) in 2018.22.1This is a set of yearly cross-sectional analyses and a cross-sectional analysis in 2018 of a prospective cohort of insurees of one large health insurance, all of whom reside in Uri or one of five NBs.2.2We used data from a large Swiss health insurance (CSS) that contains about 1.6 million insurees per year  and represents the general population of all 26 cantons . The resSince in 2013 and 2014, FOBTs were free to participants in the Uri program and were not billed to health insurances, the cantonal health department provided the number of tests billed to Uri. We used this billing data to estimate testing rates in 2013–2014 and validate our findings overall.. The OSP only shared the total number of tests billed and Swiss law on human research prevented us from linking the individual FOBTs billed in the cantonal dataset to the CSS health insurance.We also compared the testing rates we computed from claims data and OSP data to data from the Swiss Health Survey dataset (SHS), a population-based survey conducted every five years . , we restricted the dataset to insurees continuously insured between 2010 and 2018. Since we were tracking participants aged 50–69 in 2010 over a 9-year period, we limited our analyses to participants aged 59–69 in 2018.2.4We compared insurees across Uri and NBs and used the same inclusion criteria for the populations of Lucerne, Nidwalden, Obwalden, Schwyz, and Glarus. We included these cantons because of a similar socio-demographic structure as well as areal and economic linkage. The residents of Glarus also participated in the 2000 cohort study .2.5We extracted billing codes associated with CRC testing methods. We used the Swiss analysis list for laboratory measures (AL) to identify billed FOBTs. The AL uses the same billing code for guiaiac-based FOBT (gFOBT) and iFOBT. We used the billing code for FOBT t without the possibility of distinguishing the type of test billed. We used Swiss ambulatory procedures codes (TARMED) to identify colonoscopies, sigmoidoscopies, and recto-sigmoidoscopies . Since sIn 2013 and 2014, Uri gave participants free iFOBT which were not billed to health insurances. But OSP conductors gave us data on overall program participation. We then used CSS data to compute the market share of CSS insurance among eligible people in Uri. Overall program participation and CSS market share allowed us to estimate FOBT testing rates inside the program and overall testing rates in Uri in 2013 and 2014 .2.6We collected demographic data  from CSS standard insuree data. Based on the list provided by the Federal Statistics Office (FSO), we converted zip codes to FSO community numbers to determine canton and residence . For each year, we extracted the participant’s deductible (in CHF), and health plan . Health insurance data in Switzerland does not include clinical diagnoses. Since pharmacy-based cost groups (PCGs) identify medications used to treat chronic diseases, we used these as a proxy for chronic disease, and extracted the number of PCGs for each enrollee .2.7To analyze yearly CRC testing rates, we defined: a) “any testing for CRC” as insurees with a bill for at least one test (FOBT or colonoscopy) in that calendar year; b) “FOBT/both” as insurees billed for one or more FOBTs with or without a colonoscopy; and c) “colonoscopy” as insurees who had had a colonoscopy and no FOBT that calendar year. People who had taken both tests were placed in the FOBT group because a positive FOBT likely led to a colonoscopy. .We used descriptive statistics to characterize enrollees and calculated percentages of these characteristics for each study year, determining the proportions of people who had had a) any test for CRC, b) FOBT/both, and c) colonoscopy only. We did this for each year (2010 to 2018) and each geographical area (Uri vs NB). We then stratified results into two age groups (50–59 and 60–69) and differentiated between three different types of residence . Patients with family physician, telemedicine or HMO insurance model plans were classed as managed care.To compute the percentage of insurees in 2018 tested for CRC at recommended intervals in each geographical region, we restricted the dataset to those continuously insured from 2010 to 2018. We tracked insurees backward to identify bills for FOBT in 2018 or 2017 or any colonoscopy between 2010 and 2018. Insurees were a) up-to-date with any CRC testing if they had had at least one colonoscopy between 2010 and 2018 and/or any FOBT in 2017–2018.They were b) up-to-date with FOBT if they were billed for one or more FOBTs in 2017 or 2018, with or without a colonoscopy. And they were c) up-to-date with colonoscopy if they had had any colonoscopy between 2010 and 2018 and no FOBT in 2017–2018.We fitted a multivariate adjusted logistic regression model to compute OR of any CRC testing (tested vs. not tested) and a multinomial regression model to compute OR of colonoscopy only, FOBT/both, and no test. Covariates of adjustment were age, gender, residence, comorbidities (PCGs), health insurance plan, and location (Uri vs NBs).To test for an effect of the OSP on testing rates, we defined two time periods: 2010–2012 (before the program was implemented in 2013) and 2015–2018 (after the program was implemented). Data on FOBT were incomplete in the claims dataset in 2013 and 2014 because the canton did not bill the health insurance for FOBTs inside the program, so we excluded 2013–2014 from these analyses. We included year of testing as a categorical predictor and tested for an interaction between time period (2010–2012 vs 2015–2018) and canton. We further performed stratified analyses by gender to test gender differences in the effect of the OSP on testing rate.The threshold for statistical significance for all analyses was p < 0.05. We used Stata Software for all statistical analyses.33.1For this analysis we included between 40,323 to 48,655 insurees aged 50–69 per year.The proportion of older insurees and people living in rural regions was higher in Uri than in NBs and insurees in Uri were less likely to subscribe to a form of managed care, but this difference narrowed over the years .Table 1DIn Uri, overall testing rates increased from 8.7% in 2010 to 10.8% in 2018. In NBs it increased from 6.5% to 7.9. Testing with FOBT/both in Uri increased from 4.7% to 6.0% while it decreased from 2.8% to 1.1% in NBs. Colonoscopy rates in Uri increased from 4.1% to 4.8%, while it increased from 3.7% to 6.8% in NBs. In 2013, 2.8% of the included population participated in the program and took an FOBT. In 2018, this proportion rose to 4.2%. The rest who received FOBT were tested outside of the program (1.7% in 2018).2015 was the first year we could distinguish between colonoscopies performed within and outside the OSP. In 2015, 0.9% of eligible insurees had a colonoscopy within the program, increasing to 1.3% by 2018). The same year, 3.5% had a colonoscopy outside the program , Table 2In a multivariate adjusted logistic and multinomial regression model, we found that insurees in Uri were always more likely to have been tested for CRC than insurees in NBs  and more likely to have been tested with FOBT/both  and colonoscopy  .Table 3OWe compared testing in Uri before and after the OSP was initiated (2010–2012 vs 2015–2018) to testing in NBs (interaction term between time periods and canton) and found Uri insurees were more likely to have been tested with FOBT/both (OR 2.08 [95%CI:1.78–2.44]) and less likely to have had colonoscopies (OR 0.60 [95%CI:0.51–0.70]) after the OSP start. Overall testing rates did not change . The res3.2We included 12′838 continuously insured insurees in our analysis of the proportion up-to-date with CRC testing: 600 for Uri and 12′238 for NB .In 2018, 42.5% of eligible Uri insurees were up-to-date with CRC testing; 9.2% were billed a FOBT/both in 2018 or 2017 and 35.7% were billed for a colonoscopy only within the last 9 years. In NBs, 40.7% were up-to-date with CRC testing; 2.7% had had an FOBT/both, and 39.0% had had a colonoscopy .In multivariate adjusted analyses, insurees in Uri were more likely to be up-to-date with FOBT/both (OR 3.78 [95%CI:2.84–5.02]) than insurees in NB, but less likely to be up-to-date with colonoscopy (OR 0.81 [95%CI:0.68–0.95]). There was no significant difference in being up-to-date overall. Other covariates significantly associated with being up-to-date with testing were being a man, being 65–69 years old, living in urban areas, and having more than one PCG .44.1Our analysis of claims data from a large health insurance revealed that yearly CRC testing rates between 2010 and 2018 were always higher in Uri than in NBs, even before the OSP implementation. Testing rates increased over time in all regions. The trend in FOBT testing was upward in Uri and downward in NBs. The OSP implementation was significantly associated with higher FOBT testing rates in Uri. The downward trend was evident in FOBT tests outside the Uri program same as in NBs, which indicates that improved screening rates within the OSP likely account for the overall increase in FOBT . Over ti4.2In the context of Uri, were colonoscopy and overall testing rates were already relatively high and a new OSP offered participants a choice of CRC screening tests, we found that the FOBT rate increased more steeply than the colonoscopy rate. The OSP in Uri automatically sends information that helps eligible participants make an informed choice between FOBT and colonoscopy, which may explain the increase in FOBT rates . The OSPStudies comparing regions before and after an OSP start or across regions are scarce. A study in France compared the likelihood of having had an FOBT between one area with and one without an OSP and found an OR of 3.9 . A New YWe know from previous studies, that OSPs have the potential to enhance testing rates and therefore lower CRC mortality. OSPs have devised various strategies to increase program participation. Giving people an informed choice of testing strategies is one option. Testing rates may also rise if an OSP reminds eligible participants or their health care providers to schedule and attend screening appointments and then follows up if individuals do not respond. OSPs can also remind participants to repeat a test or send FOBT-kits directly to their home . The Net4.3Our study has several potential limitations that we made efforts to mitigate. Three gaps in claims data might have caused our estimates to deviate from true yearly testing rates. Regarding FOBT numbers, we have no insurance bills for FOBTs performed within the OSP in 2013 and 2014 and instead substituted data from the OSP and estimated testing rates. We knew that the OSP data might less accurately report the number of FOBTs than claims data, so we excluded 2013 and 2014 from our logistic regression model. In addition, we cannot distinguish between different kinds of FOBT testing in our dataset. Evidence from the UK suggest that changing from gFOBT to iFOBT was associated with increased participation . We wereSecond, our claims data omitted inpatient tests. We had earlier estimated in another claims dataset that between 3.5 and 5% of colonoscopies in Switzerland are performed on inpatients . When coThird, when the Uri OSP began, it excluded those who participated in the 2000–2001 cohort study because they had already been offered free colonoscopies and FOBTs. This exclusion criterion was later rescinded, but we estimate that, in 2013, between 100 and 150 eligible people were insured by CSS and excluded from the Uri OSP. This exclusion may have artificially lowered the colonoscopy rate in the early years of the Uri program. Participants who underwent colonoscopy in 2000/2001 might also be less willing to undergo a second colonoscopy. We assume some of them would be in our dataset and this factor could also lower the colonoscopy rate in Uri during our study period.Finally, claims data often underestimates testing rates because it misses tests for which participants did not enter claims. We thus balanced it with SHS data to compare our retrieved rates. Survey data tends to overestimate testing by recall and reporting bias. As expected, we found a slightly higher proportion of the eligible population up-to-date with testing in the SHS data than in the CSS dataset. The slight difference had little effect on our study because, overall, testing rates were similar and FOBT rates were still higher in Uri than NB . The muc5Because evaluating the effects of OSPs on testing rates is a precursor to effectively raising them and maintaining them, we encourage insurance companies to provide national datasets and suggest independent researchers use these datasets to track the effect of OSPs on testing rates. Since a decline in mortality can only be detected many years after implementing a CRC screening program, we need to collect informative data earlier. As a proxy for mortality, we can measure polyp numbers and monitor cancer stages in the larger cantons  and use national numbers to compare the effect of OSPs across countries. In all cantons, we can test interventions, e.g., send FOBT kits directly to people’s homes or use reminder systems, to determine if they increase testing rates. Our finding that FOBT rates increased in Uri after it implemented an OSP supports the claim that offering people an informed choice will raise the FOBT rate and may increase overall screening rates.Our work was funded by the Swiss Cancer Research Foundation, Health Services Research (HSR-4366-11-2017) and the Swiss National Science Foundation, National Research Program 74 (NFP74 407440-167519) “Smarter Health Care”. Funders played no role in designing or conducting the study. They did not participate in collecting, managing, analyzing, or interpreting the data, or in preparing, reviewing, or approving the manuscript.CS is employed by the Research Center of the Swiss health insurance company CSS. The remaining authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.


We created patient-based 3D finite-element (FE) models that simulate the congruent-arc Latarjet (CAL) and traditional Latarjet (TL) procedures and then compared their stress distribution patterns with different arm positions and glenoid defects.The computed tomography data of 10 adult patients  were used to develop the 3D FE glenohumeral joint models. Twenty-five and 35% bony defects were created on the anterior glenoid rim, and the coracoid process was transferred flush with the glenoid by the traditional and congruent-arc techniques using two half-threaded screws. A load was applied to the greater tuberosity toward the center of the glenoid, and a tensile force (20 N) was applied to the coracoid tip along the direction of the conjoint tendon. The distribution patterns of the von Mises stress in the traditional and congruent-arc Latarjet techniques were compared.The mean von Mises on the graft was significantly greater for the TL technique than for the CAL. While the von Mises stress was greater in the distal medial part of the graft in the TL models, a higher stress concentration was observed in the distal lateral edge of the coracoid graft in the CAL models. The proximal medial part of the graft exhibited significantly lower von Mises stress than the distal medial part when compared according to technique, defect size, and arm position. Increasing the glenoid defect from 25 to 35% resulted in a significant increase in stress on the lateral side of the graft in both models.The stress distribution patterns and stress magnitude of the coracoid grafts differed according to the procedure. Due to placing less stress on the proximal–medial part of the graft, the CAL technique may lead to insufficient stimulation for bone formation at the graft–glenoid interface, resulting in a higher incidence of graft osteolysis.Clinical relevance The CAL technique may lead to a higher incidence of graft osteolysis.Basic Science Study; Computer Modeling. The Latarjet procedure, also known as the coracoid process transfer, is one of the most performed and reliable procedures for treating recurrent anterior shoulder instability in patients with a significant bone defect of the glenoid surface Multiple technique modifications to the Latarjet procedure have been reported. For example, Burkhart et al. proposed the “congruent-arc Latarjet’’ (CAL) technique, in which the coracoid is rotated 90° along its longitudinal axis, allowing the medial surface of the coracoid to be fixed to the anteroinferior of the glenoid and making the inferior surface compatible with the articular surface of the glenoid Graft osteolysis is a complication of the Latarjet procedure A computed tomography (CT)-based 3D finite-element (FE) method has been widely used to assess the stress distribution within the bone to describe the risk of osteolysis –23. By pIn this study, we created patient-based 3D FE models that simulate the CAL and TL procedures, and then compared their stress distribution patterns in different arm positions and glenoid defects. We hypothesized that there would be significant differences in the stress distribution patterns of the two techniques.For the creation of the study’s humerus and scapula bone model, the CT data of 10 adult patients  without shoulder trauma were used. The CT data were reconstructed with a slice thickness of 0.1 mm and were transferred to the 3D Slicer software in the DICOM (.dcm) format. The CT data in DICOM format were separated according to appropriate Hounsfield values using 3D Slicer software and converted into a 3D model by segmentation. The model was exported in an.stl format.Arrangement of the 3D mesh structure and its transformation into a mathematically appropriate solid mesh structure creation of 3D FE analysis models and FE stress analysis were performed on HP workstations equipped with an INTEL Xeon E-2286 processor (2.40 GHz and 64 GB ECC memory). The 3D.stl model of the bone structure created from the CT data was obtained using 3D Slicer software. Reverse engineering and 3D CAD activities were carried out with Altair Evolve software; the Nastran-based Altair Optistruct  implicit solver was used to solve the FE models. The mathematical mesh models and the force transfer between the models were created in Altair HyperMesh. The prepared models were placed in the correct 3D space coordinates via the Altair Evolve software, and the modeling process was completed.The maximum glenoid defect size that could be restored by a TL graft ranged between 19.2% and 38.8% The defect was set parallel to the longitudinal axis of the glenoid according to previous studies The inferior part of the coracoid was transferred to the anterior glenoid defect to simulate the TL method. To simulate the congruent-arc method, the graft was rotated 90° around the y-axis. Two half-threaded titanium screws  were created similar to commercial models  and were used to fix the coracoid process. Care was taken to ensure that the coracoid process was placed flush with the glenoid cartilage. Soft tissues were not modeled in this study.The initial FE models were created at the hanging arm position in a neutral position. To clarify the stress distribution pattern, a 90° shoulder abduction position was simulated according to previous studies In all models, the screw–bone  interface was modeled with friction contact using a coefficient of μ = 0.3; therefore, all models were run nonlinearly, with the exception of the freeze-type contact that was defined in all contact areas  The linear material properties of the materials were used in the analysis A force of 50 N was applied from the humeral bone head to the glenoid region of the scapula All models were subjected to elastic analysis by visualizing the distribution pattern of von Mises stress (VMS). Each coracoid graft was divided into four parts  to specifically identify the mean VMS of these areas. The stress distribution over the TL and CAL grafts was analyzed for different defect sizes to compare the extent of the stress shielding associated with each procedure.The data analysis was performed with SPSS 26.0, and the data were studied with a 95% confidence level. Because of the small sample size, nonparametric methods were used in the study, as well as Mann–Whitney and Kruskal–Wallis tests.The mean VMS values for all scenarios are summarized in Fig. p > 0.05). The stress distribution patterns of the coracoids differed according to the procedure: while the VM stress was greater in the distal medial part of the graft in the TL models, a higher stress concentration was observed in the distal lateral edge of the coracoid graft in the CAL models (p > 0.05) .The mean VMS on the graft was significantly greater in the TL technique than in the CAL technique in the 25 and 35% defect models (05) Fig. . In all p > 0.05). However, there was no significant increase or decrease in the VMS in the remaining parts of the graft for either technique. In the 90° abduction models, significantly greater VMS was observed in both the CAL and TL grafts than in the neutral position models (p > 0.05).Increasing the glenoid defect from 25 to 35% resulted in a significant increase in stress on the lateral side of the graft in both models (To our knowledge, this is the first study comparing stress distribution patterns between the TL and the CAL procedures. Since the Latarjet procedure is a non-anatomical augmentation of the glenoid surface, it can alter the intra-articular stress distribution dramatically. Previous biomechanical and FE model studies have shown that graft osteolysis is expected in the proximal part of the graft in the LT technique 29]That the medial stress is less in the CAL technique than in the TL may cause insufficient stimulation for bone formation at the graft–glenoid interface, which could eventually lead to a greater incidence of graft osteolysis or nonunion. Mengers et al. analyzed 26 studies comparing TL and CAL techniques, identifying that the fibrous or nonunion incidence was greater for the CAL technique Less stress was observed at the proximal half of the coracoid bone graft in both the TL and CAL techniques for both glenoid defects and arm positions. A high stress concentration was identified at the distal part of the coracoid graft caused by the tensile force created by the conjoint tendon. Similar to the findings of Sano et al., the proximal–medial part represented the lowest equivalent stress of the four parts of the coracoid graft in both models Latarjet is one of the most widely used surgical procedures for treating significant bone defects of the glenoid surface and failed Bankart repairs [30]The small contact area between the graft and glenoid makes the CAL technique significantly less resistant to load to failure compared with the TL tchnique This study has the following limitations. First, we did not perform the analysis on a 3D dynamic motion model of the shoulder joint. Future studies, including dynamic analyses, are necessary to describe the true biomechanical environment created following the TL and CAL techniques. Second, there were numerous assumptions with respect to the material properties, as well as the boundary and contact conditions, each of which may have affected the results. Third, our results were not subjected to further biomechanical validation because of the technical difficulties associated with measuring the actual stress distribution during cadaveric testing. However, because our results are consistent with those of previous studies, we believe our simulation is an effective and accurate recreation of real-world conditions.The TL and CAL techniques exhibited different stress distribution patterns and stress magnitudes on coracoid grafts. Although the CAL modification provides a more significant bone-blocking effect and decreases the contact pressure across the glenohumeral joint, less stress on the medial part of the graft may lead to insufficient stimulation for bone formation at the graft–glenoid interface, which could eventually lead to a higher incidence of graft osteolysis. Surgeons should be aware of this risk when considering the CAL technique, especially for small glenoid defects not exceeding 35% of glenoid width.


The chemical modification of starch helped to further alter the functional properties of the obtained aerogels, making them more effective oil binders, emulsifiers, and stabilizers (increasing the stability from 55 to 90%), which was especially evident for E 1450 preparation. Amylose content improved the aerogel properties, as waxy preparations were characterized by worse functional properties with the only exception of improved thickening ability. The most beneficial properties for the preparation of emulsions were observed for the aerogel obtained based on E 1450 normal potato starch.Aerogels are of increasing interest because of their exceptionally large surface area, porous structure, and low weight. Despite the significant increase in interest in the subject of starch-based aerogels, the number of detailed studies is rather scarce, which is especially evident in the case of chemically modified derivatives. Therefore, the study aims to evaluate the physicochemical properties of aerogels from chemically modified potato starch preparations (E 1422 and E 1450) obtained both from normal and waxy starches. Aerogels were prepared through the retrogradation of starch pastes followed by the gradual replacement of water with ethyl alcohol. The obtained preparations were characterized in terms of their bulk density, oil-binding capacity, as well as the texture and rheological properties of the formed pastes. Moreover, their usefulness was evaluated in an emulsion system employing rheological and low-field NMR methods. The obtained aerogels were characterized by a lower bulk density of 0.18–0.59 g/cm Among naturally occurring polymers, starch is characterized by the greatest diversity of physicochemical properties, and is significantly influenced by the biodiversity of the raw materials from which it is obtained ,2,3,4,5.Aerogels are of increasing interest because of their exceptionally large surface area, porous structure, and low weight. They have been studied in several applications such as heat insulators, support materials, fillers, and filters. Depending on the parameters used for their production, numerous materials can be created with a wide range of possibilities and properties . The mosThe interest in starch as a raw material for the production of aerogels was initiated by Glenn and Irving in 1995 . DespiteAt the current stage, the applicability of starch aerogels is mostly experimental and potential fields of application are still to be discovered . Aerogel3, and for bio aerogels, even lower-g/cm3. The properties of aerogels based on starch depend on the botanical origin, especially the amylose content [3) in 3, whereas the normal one was 0.24 g/cm3 [Bulk density is one of the basic parameters characterizing aerogels. Its typical value is usually reported around 0.2 g/cm content . The met content . The val24 g/cm3 . The che24 g/cm3 ,17,21,25Native potato starch, regardless of its variety, is characterized by the similar shape of granules, which are round or oval spheres with a smooth surface. Moreover, they are relatively large in size with a median of approximately 35 μm and a broad granule size distribution with extreme deciles reaching as low as 17 μm and as high as 59 μm . As a rep = 0.0423) role in oil-binding effectiveness, whereas the effect of starch variety is insignificant (p = 0.1257).Aerogels have a highly developed surface so it can be assumed that they are able to adsorb much more oil than native starches, as confirmed in our study . As a re2 exceeding 0.95. As can be seen in n and flow behavior index of 0.468, whereas the waxy one had 10.9 Pa·sn and 0.495, respectively [The rheological properties of starch are crucial for its functionality in food products ,30. As sectively .The chemical modification of starch used for aerogel production resulted in an increase in consistency indexes and thixotropy, especially in the case of OSA preparation. Extremely high values of the consistency index accompanied by low values of the flow index for the OSA starch are most likely due to the strong gelling phenomenon of this sample. The observed characteristics are especially atypical, as starch crosslinking is the standard method for increasing the viscosity of starch pastes, while modification with octenylsuccinic anhydride is carried out primarily to impart emulsifying properties to the starch ,28,31,34Texture is a multiparameter sensory property of a food product which is perceived by various human senses. The perception is mostly related to a product’s macro-, micro- and molecular structure . Food prThe highest values of hardness, adhesiveness, and gumminess were found for aerogels based on OSA starch (E 1450). These results are consistent with rheological data, as E 1450 preparations formed highly viscous and thixotropic pastes . Next inThe stability of model emulsions which, apart from oil and water, contain only starch as the emulsifying and stabilizing agent, enables the clear assessment of the functionality of studied preparations in food production. As can be seen in 2 exceeding 0.95. One of the factors influencing that phenomenon was the extremely high shear forces applied during emulsion formation. Nevertheless, the rheological studies confirmed the observations on the stability of model emulsions. Viscosity, expressed by the consistency index value, obtained with the use of an aerogel based on normal potato starch, was higher than that observed for waxy counterparts. This may suggest a higher stability of those emulsions, as high viscosity in one of the factors slows the emulsion aging processes [The rheological characteristics of emulsions  did not rocesses . Howeverrocesses  may sugg1 and by the energy exchange described by the spin–spin relaxation time T2. In biopolymer solutions, T1 is always higher than T2 [12 and T22) reflect the relaxation processes of the proton fraction associated mainly with the starch paste, while the short components (T11 and T21) relate to the oil fraction of the emulsion. In pure oil, the values of the spin–lattice and spin–spin relaxation times are, respectively, T1 = 102.8 ± 0.8 ms and T2 = 88.4 ± 1.1 ms. In emulsions, the values of the short components are significantly lower than the values of T1 and T2 in pure oil [12 and T22 components of the relaxation times that have been reported in the literature [1 and T2 in oil. The degree of shortening of the relaxation times depended on the type of starch. The effect of the raw material used for obtaining the aerogel on T11 time values was multidirectional. However, in the case of the T21 time, the chemical modification of the raw material applied to obtain aerogels made the product more efficient in the immobilization of protons of the oil phase. This can be explained by the presence of hydrophobic sequences in the structure of ester substituents, which increases the affinity of starch for the oil phase. This is also the reason for the surface activity exhibited by E 1422 and especially E 1450 starch preparations [Low-field magnetic resonance studies provide important information on the quality of emulsions due to the strong correlation between their stability and rheological properties ,39,40. W than T2 . In emulpure oil ,43. As cterature ,45,46. Iterature . It was arations .In order to systematize the obtained data on the properties of starch aerogels and emulsions formed by them, principal component analysis was performed. The presented PCA plots  explain 11) was positively correlated with the consistency index. Both of these parameters were also negatively correlated with the flow behavior index, whereas the consistency index of the aerogel paste was correlated with cohesiveness. Breakdown and TPA parameters including hardness and gumminess were positively correlated with each other as well as negatively with adhesiveness. The observations regarding correlations between rheological and texture parameters are in accordance with PCA data obtained for chemically modified starch pastes [The PCA loadings plot pointed to a few noticeable corrections between the investigated parameters. The stability of the obtained emulsion was positively correlated with the oil-binding capacity of the aerogel used for its production. The spin–lattice relaxation rate associated with oil fraction of the emulsion  and waxy potato starch  as well as acetylated distarch adipate (E 1422) prepared according to the procedure described by Luo et al.  and sodiAerogels were prepared using a method consisting of the successive displacement of water from the gel network structure by ethanol  in accorStarch aerogel was suspended in deionized water (5 g/100 mL) and placed in a boiling-water bath for 15 min under continuous stirring  at 150 rpm. The prepared aerogel starch pastes were allowed to set at 22 ± 2 °C for 1 h prior to further analysis. All further investigations were made on freshly prepared pastes unless otherwise stated.The emulsions were prepared by mixing rapeseed oil and deionized water in a ratio of 1:3. The starch concentration was 5%. To prepare the emulsion, aerogel powders were dispersed in rapeseed oil; afterwards, the water was added and the sample was immediately homogenized using a Silent Crusher homogenizer  with a rotation speed of 21,000 rpm for 3 min.3 and then the bottom of the measuring cylinder was gently tapped ten times on the laboratory table. Bulk density was calculated as the weight of the aerogel divided by the volume of the sample.The bulk density of the aerogels was determined using the method described by Kaur, Kaushala, and Sandhu . In brieThe scanning electron microphotographs were taken with the assistance of an Evo 40 series microscope  operating at 17 kV accelerating voltage. Samples were coated with gold using an SCD 050 sputter coater .The oil-binding capacity (OBC) was determined using the method described by Jeżowski et al.  with a s−1 range for a time of 60 s for both upwards and downwards curves. The obtained data were fitted to the Ostwald de Waele model using RheoWin v. 3.61  software:K—consistency index (Pa·sn), and The rheological properties of starch pastes and emulsions were determined using a RotoVisco1 rheometer  equipped with Z20 DIN coaxial measurement geometry. The samples were allowed to rest in a measuring cylinder for 5 min at 20 °C. The flow curves were determined at a controlled shear rate in the 1-600-1 sThe universal texture profile (TPA) of the aerogel pastes was determined with a TA.XT2 texturometer, Stable Micro Systems . The “double bite test” was performed with a 35 mm-diameter aluminum cylindrical probe and at a distance of 20 mm and test speed of 0.5 mm/s. The following TPA parameters were determined: Hardness (N), adhesiveness (N·s), cohesiveness, springiness, and gumminess (N).g during 10 min. Emulsion stability (ES) in % was calculated from the following formulaeV—initial volume of emulsion (cm3) and oV—volume of separated oil (cm3).Emulsion stability was determined according to the procedure of Acton and Saffle . The emu1, an inversion recovery pulse sequence (π-τ-π/2) was used [1 relaxation times were calculated using CracSpin software [zM) is described by the formula:zM(t) is the actual magnetization value, M0 is the equilibrium magnetization value, and ip is the fractions of protons relaxing with Ti1 relaxation times.Low-field NMR measurements were taken with the assistance of a PS20 pulse spectrometer operating at 20 MHz . To measure the spin–lattice relaxation time Twas used ,40. The software , in whicA bi-exponential regrowth of magnetization was noted.2), the CPMG pulse train (π/2-t/2(π-t)n) was used [t) were 2 ms. The repetition time between the sequences was 15 s. Each sequence consisted of 100 spin echoes. The decay of the spin–echo amplitudes  is described by the formula:xMy,(t) is the actual echo amplitude; M0 is the equilibrium amplitude; and ip is the fraction of protons relaxing with the Ti2 spin–spin time.In order to measure spin–spin relaxation times  program was used and the least squares method was used to fit the decay of the spin echoes’ amplitudes to the above formula.For the calculations of the TThe aerogels were synthetized three times and each synthetized material was analyzed three times, unless otherwise stated. Statistical analysis of the data was performed using the Statistica v. 13.3 software . The data were studied using one-way analysis of variance. Tukey’s honest significant difference post hoc test was used to determine statistically homogeneous subsets at α = 0.05. Principal component analysis (PCA) was performed based on a correlation matrix using selected data obtained in the analyses.


Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing mutations can increase the virus's pathogenicity and virulence; reduce the efficacy of vaccines, antibodies neutralization, and even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) in different variants with appropriate antigenicity to target the variants by an appropriate vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, mutations in the immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, and also predicted epitopes were calculated. In the following, epitopes conservity score against the total number of events (mutations) and the number of mutated sites in each epitope was weighted by Shannon entropy and then calculated by the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). Based on the TOPSIS conservity score and antigenicity score, the epitopes were plotted. The result demonstrates that almost all epitopes and IDRs with various lengths have gained different numbers of mutations in dissimilar sites. Herein, our two-step calculation for conservity recommends only 8 IDRs, 14 IEDB epitopes, and 10 predicted epitopes among all epitopes. The selected ones have higher conservity and higher immunogenicity. This method is an open-source multi-criteria decision-making platform, which provides a scientific approach to selecting epitopes with appropriate conservity and immunogenicity; against ever-changing viruses. On 11 March 2020, the World Health Organization (WHO) announced this worldwide health problem as a new pandemic. Although the pandemic is quite young, now our knowledge about the etiology, pathogenesis, and treatment of COVID-19 has improved6. SARS-CoV-2, the new member of the Coronaviridae family (Betacoronavirus), has improved its ability to survive and preserve its generation5. Compared to other Coronaviridae members, higher virulence besides significant pathogenicity may justify this unprecedented pandemic7.About 2 years have passed since the first case of new coronavirus disease-19 (COVID-19) has been identified in Wuhan, China. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the notorious claimant behind COVID-19, has spread all around the world, soon after confirmation of the first cases in Wuhan, which resulted in a global health problem till now1. COVID-19 clinical presentations range from non-symptomatic infection to severe acute respiratory distress syndrome (ARDS) and even death, but it is best known for its flu-like symptoms , as well as pneumonia9. By passing time, observations in clinical practice declared other organ involvement like the gastrointestinal and central nervous system in COVID-19 that just complicated the issue11. The impact of COVID-19 on individuals and also public health although is drastic, it is far to be understood. So far, several vaccines with different platforms have been approved by Food and Drug Administration (FDA) or local authorities12. Vaccination and adhering to safety protocols  are promising possible options14.According to the latest report of WHO on 2/13/2022, so far 404,910,528 people in the world have been infected with the SARS-CoV-2, and 5,783,776 have died from COVID-1915. So, the importance of developing vaccines to target SARS-CoV-2 during this particular circumstance is undeniable16. Many noteworthy considerable efforts have been made in this field around the world. Till now, different approaches have been administrated for COVID-19 vaccine design, such as mRNA-based vaccines  and Moderna), adenovirus vaccine (AstraZeneca), recombinant adenovirus vaccine (Sputnik V), non-replicating viral vector (Janssen (JNJ)), inactivated vaccine (CoronaVac), peptide vaccine (EpiVacCorona), nanoparticle vaccine (NVX-CoV2373), and DNA vaccine (plasmid) (ZyCoV-D). Meanwhile, some have international approval for global use, some have limited licenses in some countries, and a large number of vaccines are under the clinical trials and development phase (more information on vaccine tracker-NY)17. According to WHO, as of 2/13/2021, 10,095,615,243 vaccine doses have been administrated in the world1.Therefore, the vaccine-mediated immunity (vaccination) of the population seems to be even more important in the current situation of the COVID-19 pandemic, where SARS-CoV-2 spreads rapidly and there are therapeutic challenges in the management of patients suffering from COVID-19. In another hand, the naturally acquired immunity (NAI) could not prevent the spread of the SARS-CoV-220. According to the United States centers for disease control and prevention (CDC), variant of interest (VOI) stands for a variant with specific genetic markers, which potentiate changes to receptor binding, decreased neutralization by antibodies generated against vaccination, and some other clinical issues in diagnosis and treatment. In another hand, variant of high consequence (VOHC) indicates a variant with significantly reduced effectiveness of prevention measures or medical countermeasures relative to previously circulating variants, in literature with acceptable evidence21.As vaccines are being developed in the laboratories and vaccination is under process, the novel coronavirus is cleverly changing and mutating in nature. So far, lots of mutations have been identified in the SARS-CoV-2 genome, which resulted in new specific variants. Potentially developing mutations can result in structural changes in key proteins involved in the pathogenesis and spread of the virus. The frequent and rapid genetic mutations and the consequent changes in SARS-CoV-2 implicate the necessity of a method for naming new variants. As expected, new mutations in the target sequences of vaccines could decrease vaccines efficacy against new variants, besides increasing pathogenicity, transmission, and virulence, a point that has also been shown in studies24.The CDC illustrated that B.1.617.2 and AY lineages (Delta), B.1.1.529 (Omicron), are categorized as current variant of concern (VOC), which means they are associated with reduced neutralizing antibodies titer in the convalescent and post-vaccination sera besides increased transmissibility and more severe disease25.It shows regardless of various approaches to vaccine design; the vaccine target needs to be selected precisely. As SARS-CoV-2 evolves spontaneously, two major points should be considered in selected parts’ properties; first, the selected part must have an acceptable antigenicity to induce the significant immune response, second, it must be conserved during mutations in order to obtain proper coverage against different present variants. Also, it helps to maintain its efficacy against new variants. But on the other side of the coin, it might be more tremendous. Deployment of data and tools to understand the manner of SARS-CoV-2 mutations and simulation of the immune response against new variants seem to be a reliable way to deal with this issue28, designing vaccines30, and finding the concept behind COVID-19 pathogenesis32. Many complex biochemical processes that have to be spent in the laboratory with a lot of time and money can be modeled and predicted34. For example, finding herbal drugs’ interaction with SARS-CoV-2 proteins36, predicting immunogen and antigen epitopes from SARS-CoV-2 proteins38, and finding new potential pathways in COVID-19 progression and pathogenicity39 and etcetera are all available through different bioinformatics techniques.On the other hand, different bioinformatics approaches have been utilized for finding potential drugs42. Because of the necessity of finding the appropriate target for vaccines, we wondered how an algorithm could propose an epitope with significant antigenicity besides being adequately conserved.In this study, first, we demonstrated how investigated immune-dominant parts of SARS-CoV-2 proteins have mutated significantly. Furthermore, we presented evidence of alterations the spike (S), membrane (M), nucleocapsid (N), and envelope (E) proteins of SARS-CoV-2, which are discussed in peer reviews from the immune epitope database (IEDB)Here, we predicted B cell, helper T lymphocyte (HTL), and cytotoxic T lymphocyte (CTL) epitopes and then aligned them to their reference sequence to find mutations in each epitope. Then we scored their events (mutations) with the Shannon entropy and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) method to quantify their conserved manner. In the setting of this algorithm, the final output still included dozens of different types of epitopes from different proteins making the decision hard to select the best epitope. To select ones with superiority, epitopes were illustrated in a plot of antigenicity score–conserved manner, and then epitopes were undergone illustrated two-dimensional comparison, which allows facile and confident selection of epitopes among a large volume of data. In this logical analysis, we tried to clarify the importance of the conserved property of epitopes along with the immunogenicity of the selected parts of SARS-CoV-2 proteins for the vaccine design , with the hope that this protocol will aid in the development of methods to design vaccines against ever-changing viruses such as SARS-CoV-2, human immunodeficiency virus (HIV) and so on.43. Perhaps, the most important issue in dealing with the coronavirus vaccine design is its genetic variation46. Not only does it affects the vaccine design, but also it challenged the immune system response and treatment47. This issue, typicality is not a new concern, as we have seen this challenge in other viruses 50. The most prominent example of these is HIV, where all these problems  are perspicuous52. As previously predicted, this problem grew rapidly with the introduction of VOC , which prompted the WHO to quickly propose a system for naming new variants of the virus. We could be optimistic that by developing a strategy to deal with RNA virus mutations, the main burden against these viruses will be removed.Genetic mutations elsewhere in the SARS-CoV-2 genome resulted in sophisticated conditions both in the virus virulence and pathogenicity and also in the host's immune system response by repeated infections with other variants that rechallenge adaptive immunity responseNextalign. According to literature and the National Center for Biotechnology Information (NCBI), NC_045512.2 was considered as the reference sequence55. After that, sequences that were incomplete or much shorter than the reference sequence [having more than 3000 (non-template nucleotide) Ns and gaps (‘–’)] were excluded (Sup. Algorithm IQ-TREE & TreeTime (phylogenic tree—S1)56. Afterward, using the augur ancestral module, sites of mutations in genomes and phylogenetic tree’s internal nodes were detected, as well as in the following translated into amino acids by the augur translate module. In the following, the number of mutations in each site was calculated with Python programming  database  of the spike (S), membrane (M), nucleocapsid (N), and envelope (E) proteins have been magnified and illustrated Fig. . As demoSuppose the population A Fig. , where aThis strain has an immunodominant region (IDR) in the red area of the S protein. In another hand, consider population D, where a majority of its community has been infected with the strain D of SARS-CoV-2, previously. Strain D also has one IDR in the green area of the S protein. In the dissemination and infection of all 4 populations with a new strain of SARS-CoV-2, which shares lots of mutations in all areas mainly in red areas; the difference will be more noticeable. In this example, it is somewhat obvious that populations A and D are more affected by the new strain of the virus. These populations would have higher infected patients in hospitals and higher mortality rate. With this view of the epidemic and considering the ever-changing virus, it is possible to better analyze that population is more affected by the new strains. With this in mind, it is also possible to reduce the burden of the disease on the community at risk by properly planning vaccination with the appropriate vaccine against the new species spreading. As a large number of mutations are found in different regions of the virus surface proteins, selecting areas that are less mutated is difficult to target with vaccination. But if such an area can be detected to target with the vaccination, it can be hoped that the designed vaccine will work well against the variants so far. In addition, this vaccine will also be less likely to be targeted by new mutations in the virus.In the following, we tried to target regions in the virus genome that have appropriate immunogenicity besides acceptable conservity.The immune response to SARS-CoV-2 has been investigated in past years. As of May 2021, 3330 SARS-CoV2 linear epitopes were available on IEDB as they have been reported in the peer-reviewed literature. About 2/3th of them (2203 epitopes) were from S, M, N, and E proteins. These epitopes are derived from the SARS-CoV-2 genome and they have been investigated in the laboratory if they could stimulate the immune response. In this study, we have focused on S, M, N, and E protein derived B cell, HTL, and CTL epitopes (Sup. file 53 using the IEDB’s immunobrowser tool57. This tool helps to identify the IDRs by considering their response frequency (RF) score or lower bound in the diagram (where the RF score was RF ≥ 0.3 considered as IDR)  class I and class II molecules. Then, extracted epitopes were mapped back to a SARS-CoV-2 reference sequenceDR) Fig. . As all Our result demonstrated several IDRs in each protein. S protein has about 12 IDRs in terms of B cell epitopes and 5 IDRs in terms of HTL epitopes  in the neutralization and treatment of patients suffering from COVID-19Here IDRs are plotted, to make a quantitative comparison among all IDRs in terms of several mutated sites and events. As a number of events and mutated sites are not comparable due to the different lengths of IDRs, we normalized these parameters by dividing them using the length of each IDR Fig. .Figure 5As illustrated in Fig. As mentioned, each IDR includes several epitopes. According to significant mutations in IDRs, we wondered if past reported epitopes were affected by mutations in new variants of SARS-CoV-2. In the next section, we try to understand how different mutations in the SARS-CoV-2 genome affected IEDB suggested epitopes in past laboratory research and also predicted ones.As mentioned before, we mapped all mutations from known variants to SARS-CoV-2 M, N, E, and S protein sequences Fig. . Also, wA list of IEDB epitopes and their identity code is available in the supplement  and maximum stability (higher conservity). While considering epitopes conservity, maintaining immunogenicity properties also should be noted. Given that, choosing the best epitope should be considered several factors that make the choice more difficult. This makes the issue more complicated than previous approaches (where just immunologic properties were important). Hence, we kept our research on new variants with a focus on how to choose the best epitope for further investigations and application in vaccine design and development.We choose RF representative IEDB epitopes immunologic property as X-axis value. Besides, all mutations (without considering the site of mutation) in each epitope have been selected as events of the Y-axis. In this way Epitope Event—RF Plot (EVRP) depicts past events to each epitope beside their immunologic property  we compared epitopes of equal length, but in reality, we face epitopes with different lengths from different proteins. These issues make analogy difficult. So, we utilized another method for epitope evaluation to differentiate these cases.65. In addition, TOPSIS is a concept that the chosen alternative (parameters) should have the shortest geometric distance from the positive ideal solution (PIS) and the longest geometric distance from the negative ideal solution (NIS).TOPSIS is a multi-criteria decision-making approach, suitable in situations where several factors influence the decision. This technique was developed in the late twentieth century by Ching-Lai Hwang and YoonHere, we used TOPSIS to quantify and Shannon entropy to weight events of epitopes logically considering two parameters: the sites of mutations and, the number of mutations in each site.So, we kept RF on X-axis but we changed the Y-axis value to the TOPSIS score of mutations for epitopes. Epitope RF–TOPSIS Plot (ERTP) is designed to solve previous problems and facilitate comparison among epitopes while considering several factors Fig. . By rearIt should be noted that the lower the TOPSIS score, the more conservative the epitope is. Epitopes are worth more research in the laboratory or clinic, which are in a more appropriate area in the chart than others. We are currently facing a pandemic of a constantly evolving virus; we must use the best of the available vaccines based on the strain spreading in each region. Vaccines made from the inactivated pathogen should be screened for IDRs in the same system as introduced, and other vaccines targeting a specific epitope should be evaluated by the same system. As mentioned, mutations are inevitable in IDRs and epitopes in the case of SARS-CoV-2. But to counter the new variants and especially VOC, we can administrate immunogenic regions that have been less mutated so far for vaccine design.So far, we have discussed the epitopes that have been discovered and tested in the laboratory. Herein, we wonder if this system could be effective to evaluate the new predicted epitopes by immunoinformatic databases. Predicting and evaluating epitopes with ERTP can facilitate designing new vaccines against the spreading variants. This not only helps to produce more effective vaccines but can also greatly reduce the cost of vaccine production and save time.At this point we decided to run the ERTP method on SARS-CoV-2 predicted epitopes as well. To find epitopes those, despite high immunogenicity, are less mutated between different variants (conserve among variants so far).67 in the case of antigenicity and their scores were recorded for plotting as the X-axis value  and non-allergenic (by AllerTOP 2.0 server) ones were predicted and selected for further evaluation. In the end, 114 immunogenic, non-toxic, and non-allergenic epitopes were analyzed by the Vaxijen server69. In the case of HTL predicted epitopes, 64 epitopes were non-allergenic and nontoxic by AllerTOP 2.070 and ToxinPred72 server, respectively. As induction of interferon (IFN)-γ, interleukin (IL)-4, and IL-10 secretion by these epitopes play a pivotal role in regulating immune response, HTL predicted epitopes were analyzed for these properties. Using the IFN epitope73, IL4pred74, and IL10pred75 servers, 5 epitopes were left for the next step. Thereby, epitopes were analyzed by the VaxiJen server for antigenicity, and their scores were recorded for further analysis 76, 53 LBL epitopes were predicted for S, M, N, and E proteins. 42 of them had the appropriate length of more than 6 amino acids. Out of the 42, 20 of these epitopes had been predicted to be non-toxic (by ToxinPred server) and non-allergenic (by AllerTOP 2.0 server). Like other predicted epitopes, VaxiJen scores of antigenicity were calculated for 15 predicted LBL epitopes  in terms of conservity unequally with Shannon entropy. In this case, TOPSIS was preferred as the best choice for further scoring.92. After prediction of epitopes, we ran Shannon entropy and TOPSIS scoring and plotting through antigenicity and conservity, successfully for identification of best epitopes with two factors. In addition, having a quantitative view in terms of conservity and antigenicity with efficient illustration and plotting can help to simplify rational decision-making in a variety of epitopes.Also, we have tested this approach (TOPSIS scoring and plotting) in predicted epitopes. To predict the epitopes there are different databases and approaches. In this article, we have predicted epitopes with a platform designed in Ahammad et al. studyThe next and final section was to select the best epitopes. Illustration of epitopes scores (by plotting) helps to understand their different properties on a large scale. Besides, having a quantitative measurement in terms of conservity can help to make rational decisions. This plot provides a roadmap understanding antigens and epitopes alteration in variants. Also, this could help to select epitopes by considering different criteria. This method is an open-source multi-criteria platform for deciding on the best epitopes.Our findings indicated the rapid and significant changes in IDRs and epitopes. This highlights the importance of a system for the efficient development of vaccines against new strains and variants. As this platform retrospectively finds previous changes and mutations in epitopes and IDRs, it could help to understand the development of recent emerging variants.95. As we aimed to understand changes in the sequence of proteins, we focused on linear epitopes of IEDB and predicted ones. Of course, mutations can make conformational changes in epitopes and antigens tertiary structure and affects B cells' recognition of epitopes. This issue  is important to be addressed by further research.There are two main categories of epitopes: linear epitopes and conformational or 3 d epitopes. T cells recognize linear epitopes and B cells can recognize conformational epitopes and linear onesIn this study, we faced with the limitation of computing power, so instead of using all the genomes found in the world, we tried to use those that have the most differences and located in different components of the phylogeny tree. Although this problem has been solved with a scientific and algorithmic approach . Then, the collected sequences were aligned with the reference genome (hCoV-19/Wuhan/Hu-1/2019) by Multiple Alignment using Fast Fourier Transform . In the following, sequences with more than 3000 not read bases (Ns) and gaps (‘–’), wrong dates before 2019, and sequences shorter than 1000 base pairs (bp) were excluded from the analysis.In order to detect mutations made over the past year in the SARS-CoV-2 genome, the following procedure was done Fig. . First, 56 [Cibiv/IQ-TREE: Efficient phylogenomic software by maximum likelihood (github.com)] phylogenetic tree was constructed for all remaining sequences. In the next step phylogenetic tree needed to reroot and resolve polytomies. Therefore, TreeTime [neherlab/treetime: Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction (github.com)] infers the tree’s internal nodes dates and prone sequences.Herein, using IQ-TREEAfterward, using the augur Ancestral module [augur/ancestral.py at master next strain/augur (github.com)], mutations in genomes, and the phylogenetic tree’s internal nodes were inferred in their sequence.In order to translate sequences and their mutations into Amino Acids, we used the augur translate module [augur/translate.py at master nextstrain/augur (github.com)]. Employing predefined Amino acids mutations (mutations in protein sequence) as input, we calculated the diversity of each SARS-CoV-2 genome region by Python programming (version 3.8).53 using the IEDB’s immunobrowser tool57. As all available records aligned along the reference sequence, the RF score was calculated by the positivity rate (positive response noted) divided by the total number of records (number of independent assays) (see the following equation) 58.B cell, HTL, and CTL epitopes from S, M, N, and E proteins were extracted from IEDB. Then search result was restricted to epitopes with recognition by human leukocyte antigen (HLA) that is the human version of MHC molecules, In the following, extracted epitopes were mapped back to a SARS-CoV-2 reference sequenceIn this way, IDRs were identified by considering their RF score or lower bound in the diagram (where the RF score was RF ≥ 0.3 considered as IDR)  in each epitope have been selected as events of epitopes for the Y-axis. In this way EVRP clearly depicts past events to each epitope besides their immunologic property.71. This server integrates the prediction score of MHC class I binding peptides and; proteasomal C terminal cleavage with transporter associated with antigen processing (TAP) transport efficiency score; to deliver an integrated score for CTL epitope prediction from a sequence. In this study, 9-mer CTL epitopes were predicted by using the NetCTL v1.2 server for 12 MHC class I supertypes 72. Epitopes that reached above 0.75 scores as threshold was selected for the next step92. There is no reference and definite value for thresholds. Thereupon, we followed other articles used similar methods to find the value of threshold (> 0.75)97.NetCTL v1.2 server is a powerful free source for predicting CTL epitopes40. Epitopes with a positive value for immunogenicity were selected for the next steps (A percentile rank score ≤ 2).To predict the immunogenicity of the CTL epitopes, the Class I immunogenicity tool of the IEDB Analysis Resource was administrated98.Here is to note that there is no reference value for the percentile rank. According to similar studies and our study design, percentile rank ≤ 0.25 was considered for this study100. Epitopes with percentile rank ≤ 0.25 were considered for the next steps. It is important to note that there is no reference value for the percentile rank. According to similar studies and our study design, percentile rank ≤ 0.25 was considered for this study98.To predict 15-mer HTL epitopes and their MHC class II alleles, a consensus algorithm of the IEDB MHC class II binding tool was administrated101. Epitopes with positive values were selected for further analysis.For the prediction of Linear B cell epitopes iBCE-EL server was used70. The non-allergic epitopes were subjected to the next steps for further analysis.Allergenicity of epitopes was assessed using AllerTOP 2.0 server103. The non-toxic epitopes were subjected to the next steps for further analysis.The toxicity of selected epitopes was evaluated using the ToxinPred serverTOPSIS is one of the best multiple decision-making methods. In this method, ’i’ is the number of alternatives that can be evaluated by the number of attributes ‘j’. In the decision matrix, (epitopes) were considered as alternatives , and (the number of sites of mutations) in each epitope was considered as attributes. Attributes were weighted by Shannon entropy. Then, the decision matrix was normalized. The normalized decision matrix (N) was multiplied by a diagonal matrix of attributes weights (Wj × j). The positive ideal solution (Vj+) and negative ideal solution (Vj−) were determined by a weighted normalized decision matrix (V). The difference between each attribute of epitopes from positive and negative ideal solutions  was calculated. The relative closeness of each epitope to the ideal solution was determined. By sorting epitopes into rating order, the epitopes with fewer scores were detected as more conserve ones. It should be mentioned that the epitope, which gets a score of zero in the TOPSIS method, may not be absolutely conserved. The score of zero stands for more conserved epitopes than the other evaluated epitopes. TOPSIS matrix equation and Shannon entropy equation are noted in the supplementary file equation part.We mapped the location of predicted epitopes on their reference protein sequence, in order to find mutations of predicted epitopes. As we have sites of mutations in proteins in past sections, mutations in each predicted epitope could be identified by merging these data.The Vaxijen antigenicity score of each epitope was considered as the value of the Y-axis of the plot. Then, we calculated the TOPSIS scores of predicted epitopes in terms of sites and number of mutations. In the following, the Y-axis value stands for their TOPSIS score for plotting. The same has been done for IEDB epitopes.No human or animal models were utilized in this investigation. All experiments were performed according to the guidelines of the Medical Ethics Committee of the Jahrom University of Medical Sciences (IR.JUMS.REC.1399.090).Supplementary Information 1.Supplementary Information 2.Supplementary Information 3.Supplementary Information 4.Supplementary Information 5.Supplementary Information 6.Supplementary Information 7.


This clinical report describes a mandibular full-arch rehabilitation by means of an implant-supported overdenture on four zirconia implants. A female patient with an edentulous mandibular arch attended our dental clinic seeking a metal-free mandibular restoration. After oral and radiographic evaluation, four one-piece zirconia implants with conical abutments were placed in the intermentonian region. After a 3-month osseointegration period, an acrylic overdenture with plastic matrices was manufactured, supported by a zirconia bar cemented to the conical abutments of the zirconia implants. Radiographic and clinical follow-up after 12 years observed adequate implant evolution, without any signs of peri-implant disease. Maintenance events were principally the periodic replacement of the plastic matrices and prophylaxis. Key words:Zirconia implants, overdenture, full-arch rehabilitation, dental implants, case report. Although titanium implants demonstrate excellent biocompatibility and numerous possibilities for restoring partially and completely edentulous patients, several questions have arisen recently regarding some problems that occur with this type of implant, pointing to a need for an alternative . The firAnother drawback of titanium implants is its grey color, especially when placed in anterior areas with a thin gingival biotype ,6. NowadCurrently, tetragonal zirconia polycrystal, particularly yttrium oxide (yttria) stabilized zirconia, is the ceramic of choice for ceramic dental implants ,7. The wThe present case report describes the use of four zirconia implants to support an overdenture and its evolution over a 12-year follow-up. As far as the authors are aware, this is the first ever case report to describe the use of four zirconia implants supporting this prosthodontic design with a long follow-up period.A 71-year-old female patient, without relevant medical antecedents, visited our dental clinic in June 2008 seeking treatment to improve her oral health status. The only remaining teeth were the upper incisors and lower canines . She refused any treatment options involving titanium implants and metal retainers. Clinical and radiographic examination observed advanced bone loss around teeth #7, #10, #22 and #27, as well as advanced resorption of the residual alveolar ridge in the maxillary arch and in the posterior regions of the mandibular arch, which did not allow implant placement. In the maxillary arch, it was decided to extract #7 and #10 and to fabricate a removable partial denture. In the mandible, since the patient declined metal materials and mucosal support was insufficient, it was decided to place an implant-supported prothesis on four zirconia implants immediately inserted in the intermentonian region following the extraction of #22 and #27. Due to antecedents of poor oral hygiene and the presence of an atrophied mandible an overdenture was preferred to a fixed restoration. Furthermore, the patient refused to undergo more exhaustive regenerative surgical procedures. The patient accepted that this prosthetic design was new and its use in cases such as hers had not been described much in the literature. She also understood and accepted the importance of attending periodic follow-ups.1. Treatment planningAn orthopantomography Fig.  and ConePrior to the surgical phase, all the information needed to fix patient dental casts in a semi-adjusTable articulator was recorded: impressions with irreversible hydrocolloid , facebow and centric relation wax bite registration. Record bases with occlusion rims were manufactured, which allowed the registration of the patient’s occlusal vertical dimension and centric relation. Once the casts were fixed in the articulator, a wax try-in of the future acrylic teeth was realized. This step served to check that prosthetic space was sufficient for the overdenture and the conical abutments of the zirconia implants, and that these abutments would not interfere in the positions of the teeth. The wax try-in was duplicated to fabricate a surgical guide and the complete denture itself.2.Surgical proceduresFour one-piece zirconia implants with conical abutments (Bredent White Sky), two of 3.5x10 mm at positions #23 and #26, and two of 3.5x12 mm at positions #21 and #28, were placed in the intermentonian region in a single surgical session by an experienced oral and maxillofacial surgeon, immediately after the extraction of #22 and #27  and relined with a tissue conditioner . After three months’ osseointegration , lower arch impressions were made with polyether , and with irreversible hydrocolloid  for the upper arch. At the next appointment, all the records needed to mount the working casts in the articulator were taken with the help of a previously manufactured lower record base with occlusal rim: occlusal vertical dimension, centric relation, and facebow. Before the fabrication of the zirconia bar, a wax try-in with acrylic teeth was made in the laboratory to check occlusion and functional and esthetic parameters. Once this wax try-in was approved, a zirconia bar, splinted to all the conical abutments of the zirconia implants, was fabricated. This zirconia bar was designed with Hader cross-section geometry  to avoid4.Recalls and follow-upRigorous follow-up of the patient continued throughout the healing period, and subsequent follow-up visits were scheduled. The patient was recalled for check-ups at 15 days, 1 month, and thereafter every 6 months. After 12-years follow-up, no peri-implant bone loss has been observed in radiographic examination Fig. A. MainteLittle clinical research has reported the clinical behavior of novel prosthodontic designs for overdentures supported by zirconia implants. Nevertheless, they constitute a potentially viable treatment option for edentulous patients sensitive to titanium implants and metallic attachment systems, or those who refuse metallic restorations .et al. (Conventional implant-supported overdenture designs consist of two splinted or non-splinted interforaminal mandibular implants and four maxillary implants. Placement of additional posterior implants, as in the present case, alters this common type of implant-and-mucosa supported overdenture, making it a fully implant-supported overdenture with correspondingly different biomechanical behavior . In a clet al.  with 24 et al. (Brandt et al.  conductein vitro study by Osman et al. (From the biomechanical point of view, an n et al.  used finRegarding the limitations of this technique, it should be noted that one-piece zirconia implants require sufficient prosthetic space to accommodate the abutments. In addition, implant placement may not meet the prosthodontic requirements  and secoThe present case report describes mandibular full-arch rehabilitation by means of an implant-supported overdenture on four one-piece zirconia implants with conical abutments, with a zirconia bar cemented to them. Within the limitations of this clinical case report, the technique was found to be a successful alternative to traditional overdentures on titanium implants. Radiographic and clinical follow-up over 12 years observed adequate implant evolution, without signs of peri-implant disease; maintenance events were principally the periodic replacement of the plastic matrices. The literature lacks information and evidence regarding this technique. Nevertheless, the present case has shown that satisfactory results can be achieved over a 12-year follow-up, providing case selection protocols and treatment planning are adequate.