Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions.

MOTIVATION: Approaches such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) represent the standard for the identification of binding sites of DNA-associated proteins, including transcription factors and histone marks. Public repositories of omics data contain a huge number of experimental ChIP-seq data, but their reuse and integrative analysis across multiple conditions remain a daunting task. RESULTS: We present the Combinatorial and Semantic Analysis of Functional Elements (CombSAFE), an efficient computational method able to integrate and take advantage of the valuable and numerous, but heterogeneous, ChIP-seq data publicly available in big data repositories. Leveraging natural language processing techniques, it integrates omics data samples with semantic annotations from selected biomedical ontologies; then, using hidden Markov models, it identifies combinations of static and dynamic functional elements throughout the genome for the corresponding samples. CombSAFE allows analyzing the whole genome, by clustering patterns of regions with similar functional elements and through enrichment analyses to discover ontological terms significantly associated with them. Moreover, it allows comparing functional states of a specific genomic region to analyze their different behavior throughout the various semantic annotations. Such findings can provide novel insights by identifying unexpected combinations of functional elements in different biological conditions. AVAILABILITY AND IMPLEMENTATION: The Python implementation of the CombSAFE pipeline is freely available for non-commercial use at: https://github.com/DEIB-GECO/CombSAFE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Accurate and highly interpretable prediction of gene expression from histone modifications.

BACKGROUND: Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with several diseases, including cancer. HMs are, however, reversible modifications: understanding their role in disease would allow the design of 'epigenetic drugs' for specific, non-invasive treatments. Standard statistical techniques were not entirely successful in extracting representative features from raw HM signals over gene locations. On the other hand, deep learning approaches allow for effective automatic feature extraction, but at the expense of model interpretation. RESULTS: Here, we propose ShallowChrome, a novel computational pipeline to model transcriptional regulation via HMs in both an accurate and interpretable way. We attain state-of-the-art results on the binary classification of gene transcriptional states over 56 cell-types from the REMC database, largely outperforming recent deep learning approaches. We interpret our models by extracting insightful gene-specific regulative patterns, and we analyse them for the specific case of the PAX5 gene over three differentiated blood cell lines. Finally, we compare the patterns we obtained with the characteristic emission patterns of ChromHMM, and show that ShallowChrome is able to coherently rank groups of chromatin states w.r.t. their transcriptional activity. CONCLUSIONS: In this work we demonstrate that it is possible to model HM-modulated gene expression regulation in a highly accurate, yet interpretable way. Our feature extraction algorithm leverages on data downstream the identification of enriched regions to retrieve gene-wise, statistically significant and dynamically located features for each HM. These features are highly predictive of gene transcriptional state, and allow for accurate modeling by computationally efficient logistic regression models. These models allow a direct inspection and a rigorous interpretation, helping to formulate quantifiable hypotheses.

SMfinder: Small Molecules Finder for Metabolomics and Lipidomics Analysis.

Metabolomics and lipidomics studies are becoming increasingly popular but available tools for automated data analysis are still limited. The major issue in untargeted metabolomics is linked to the lack of efficient ranking methods allowing accurate identification of metabolites. Herein, we provide a user-friendly open-source software, named SMfinder, for the robust identification and quantification of small molecules. The software introduces an MS2 false discovery rate approach, which is based on single spectral permutation and increases identification accuracy. SMfinder can be efficiently applied to shotgun and targeted analysis in metabolomics and lipidomics without requiring extensive in-house acquisition of standards as it provides accurate identification by using available MS2 libraries in instrument independent manner. The software, downloadable at www.ifom.eu/SMfinder, is suitable for untargeted, targeted, and flux analysis.

A comparison of femorocrural bypasses performed with modified heparin-bonded expanded polytetrafluorethylene grafts and those with great saphenous vein grafts to treat critical limb ischemia.

BACKGROUND: The purpose of this study was to evaluate our results involving femorocrural bypasses by comparing heparin-bonded expanded polytetrafluoroethylene (HePTFE) graft (Propaten) modified with handmade distal compliant HePTFE cuffs (mHePTFE graft) to great saphenous vein (GSV) graft. METHODS: A retrospective study involving 74 femorocrural bypasses performed from January 2010 to May 2013 at a single institution was carried out. The indication for revascularization was critical limb ischemia (Rutherford stages 4-6. Forty-one femorocrural bypasses were created in 37 patients with unavailable GSVs using modified ringed HePTFE grafts with a handmade distal radial stretch HePTFE cuff to reduce the mismatch compliance between the graft and the artery wall. Thirty-three femorocrural bypasses were created using a reversed GSV graft. The results were analyzed in terms of primary graft patency, limb salvage, and patient survival using univariate (Kaplan-Meier curves and log-rank test) and multivariate (Cox regression) analyses. RESULTS: The 2 groups were statistically comparable for main risk factors, Rutherford stage, and target artery for distal anastomoses. The run-off anatomy did not significantly differ between the prosthetic and the vein bypass group. The cumulative 30-day operative mortality rate was 2.9%. At 1, 2, and 3 years, the 2 groups were equivalent in primary graft patency (the mHePTFE group: 84%, 80%, and 70%, respectively; the GSV group: 84%,71%, and 71%, respectively; P = 0.93) and were also equivalent in terms of limb salvage (the mHePTFE group: 87%, 87%, and 76%, respectively; the GSV group: 84%, 75%, and 75%, respectively; P = 0.78) and patient survival (the mHePTFE group: 87%, 75%, and 75%, respectively; the GSV group: 87%, 73%, and 65%, respectively; P = 0.86). At Cox regression analysis, only postoperative treatment with warfarin therapy compared with double antiplatelet therapy was independently associated with poorer primary patency (P = 0.003; 95% confidence interval, 1.80-18.00; hazard ratio, 5.7). CONCLUSIONS: In this retrospective study regarding femorocrural bypasses, the mHePTFE grafts had 1-, 2-, and 3-year primary patency and limb salvage results which were not significantly different from those in the GSV grafts. Additional randomized data and larger studies are needed to confirm these results.

GeMI: interactive interface for transformer-based Genomic Metadata Integration.

The Gene Expression Omnibus (GEO) is a public archive containing >4 million digital samples from functional genomics experiments collected over almost two decades. The accompanying metadata describing the experiments suffer from redundancy, inconsistency and incompleteness due to the prevalence of free text and the lack of well-defined data formats and their validation. To remedy this situation, we created Genomic Metadata Integration (GeMI; http://gmql.eu/gemi/), a web application that learns to automatically extract structured metadata (in the form of key-value pairs) from the plain text descriptions of GEO experiments. The extracted information can then be indexed for structured search and used for various downstream data mining activities. GeMI works in continuous interaction with its users. The natural language processing transformer-based model at the core of our system is a fine-tuned version of the Generative Pre-trained Transformer 2 (GPT2) model that is able to learn continuously from the feedback of the users thanks to an active learning framework designed for the purpose. As a part of such a framework, a machine learning interpretation mechanism (that exploits saliency maps) allows the users to understand easily and quickly whether the predictions of the model are correct and improves the overall usability. GeMI's ability to extract attributes not explicitly mentioned (such as sex, tissue type, cell type, ethnicity and disease) allows researchers to perform specific queries and classification of experiments, which was previously possible only after spending time and resources with tedious manual annotation. The usefulness of GeMI is demonstrated on practical research use cases. Database URL http://gmql.eu/gemi/.

Large-Scale Transdisciplinary Collaboration for Adaptation Research: Challenges and Insights.

An increasing number of research programs seek to support adaptation to climate change through the engagement of large-scale transdisciplinary networks that span countries and continents. While transdisciplinary research processes have been a topic of reflection, practice, and refinement for some time, these trends now mean that the global change research community needs to reflect and learn how to pursue collaborative research on a large scale. This paper shares insights from a seven-year climate change adaptation research program that supports collaboration between more than 450 researchers and practitioners across four consortia and 17 countries. The experience confirms the importance of attention to careful design for transdisciplinary collaboration, but also highlights that this alone is not enough. The success of well-designed transdisciplinary research processes is also strongly influenced by relational and systemic features of collaborative relationships. Relational features include interpersonal trust, mutual respect, and leadership styles, while systemic features include legal partnership agreements, power asymmetries between partners, and institutional values and cultures. In the new arena of large-scale collaborative science efforts, enablers of transdisciplinary collaboration include dedicated project coordinators, leaders at multiple levels, and the availability of small amounts of flexible funds to enable nimble responses to opportunities and unexpected collaborations.

Clustering by soft-constraint affinity propagation: applications to gene-expression data.

MOTIVATION: Similarity-measure-based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck (2007a). In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, e.g. in analyzing gene expression data. RESULTS: This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new a priori free parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.

Immediate functional loading of implants placed with flapless surgery versus conventional implants in partially edentulous patients: a 3-year randomized controlled clinical trial.

PURPOSE: To compare the efficacy of immediate functionally loaded implants placed with a flapless procedure (test group) versus implants placed after flap elevation and conventional load-free healing (control group) in partially edentulous patients. MATERIALS AND METHODS: Forty patients were randomized: 20 to the flapless immediately loaded group and 20 to the conventional group. To be immediately loaded, implants had to be inserted with a minimum torque > 45 Ncm. Implants in the immediately loaded group were provided with full acrylic resin temporary restorations the same day. Implants in the conventional group were submerged (anterior region) or left unsubmerged (posterior region) and were left load-free for 3 months (mandibles) or 4 months (maxillae). Provisional restorations were replaced with definitive single metal-ceramic crowns 1 month postloading. Outcome measures were prosthesis and implant failures, biological and prosthetic complications, postoperative edema, pain, and use of analgesics. Independent sample chi2 tests, Mann-Whitney tests, t tests, and paired t tests were used with a significance level of .05. RESULTS: Fifty-two implants were placed in the flapless group and 56 in the conventionally loaded group. In the flapless group, 1 flap had to be raised to control the direction of the bur and 1 implant did not reach the planned primary stability and was treated as belonging to the conventional group. After 3 years no dropouts or failures occurred. There was no statistically significant difference for complications; however, patients in the conventional group had significantly more postoperative edema and pain and consumed more analgesics than those in the flapless group. Osstell values were significantly higher at baseline in the flapless group (P = .033). When comparing baseline data with years 1, 2, and 3 within each group, mean Osstell values of the flapless group did not increase, whereas there were statistically significant increases in the Periotest values. CONCLUSIONS: Implants can be successfully placed flapless and loaded immediately without compromising success rates; the procedure decreases treatment time and patient discomfort.

Immediate functional loading of implants placed with flapless surgery in the edentulous maxilla: 1-year follow-up of a single cohort study.

PURPOSE: To evaluate success rates and complications of implants placed with a flapless technique and immediately loaded in fully edentulous maxillae. MATERIALS AND METHODS: Implants were placed in fully edentulous maxillae with a minimum insertion torque of 45 Ncm in underprepared sites to allow maximum stability at insertion using a flapless technique. Implants were immediately loaded. Outcome measures were prosthesis and implant success, biologic and prosthetic complications, pain, and edema evaluation. Stability of individual implants was assessed both manually and with Osstell at baseline and after 12 months of loading. A single sample t test was used with a significance level of .05. RESULTS: Thirty-three consecutively treated edentulous patients received 202 implants in the maxilla. In 10 patients, 53 implants were immediately inserted in fresh extraction sockets. At implant insertion, a flap had to be elevated to control the direction of the drill in 5 patients. Three implants in 2 patients did not reach sufficient stability and were left to heal for 45 to 90 days. All restorations (21 fixed prostheses and 12 overdentures) were delivered the same day of the surgery. Twenty-six patients experienced no or slight postoperative pain; 7 experienced moderate to severe pain. No or slight edema was recorded for 19 patients and moderate to severe edema for 14 patients. Two implants failed in 2 patients but were successfully replaced the same day they were removed. No major complications occurred. Five patients experienced biologic complications, eg, peri-implantitis; 10 experienced prosthetic complications. No prosthesis failed; however, 1 patient was unsatisfied with his overdenture and requested a fixed alternative. There was a highly significant difference (P < .001) between the stability at implant insertion and after 12 months. CONCLUSION: Implants placed in the edentulous maxilla with a flapless procedure can be successfully loaded the same day of surgery.

Augmentation of the posterior atrophic edentulous maxilla with implants placed in the ulna: a prospective single-blind controlled clinical trial.

PURPOSE: To evaluate a new method to treat the posterior atrophic edentulous maxilla: dental implants placed in the ulna and transplanted with their surrounding bone blocks as inlays into the sinus. Conventional sinus augmentation with particulated autogenous bone grafts served as a control procedure. MATERIALS AND METHODS: Fifty-two implants were placed in the ulnas of 20 patients. After 6 weeks, bone blocks containing 1 to 3 implants were harvested and transplanted into the sinuses protruding 3 to 4 mm. Implants were left to heal for 6 weeks. Twenty patients with similar treatment indications treated with particulated bone grafts from the mental symphysis, tibia, or iliac crest acted as controls. Grafts were allowed to heal for 6 months in the control group. Fifty-two control-group implants were allowed to heal for 4 months. The main outcome measures were prosthetic and implant success. Stability of individual implants was assessed with Osstell and Periotest at baseline and after 6 and 12 months of loading. Independent sample chi-square tests, t tests, and paired t tests were used with a significance level of .05. RESULTS: No patient dropped out or withdrew; no prosthesis or implant failed. No major surgical complications were occurred. There were no differences between the 2 groups at any time point in implant stability. Both modalities resulted in a significant increase of implant stability at 6 and 12 months. The mean change (SD) from baseline to 1 year in Periotest measurements was 1.44 (0.48) in the test and 1.29 (0.58) in the control (paired t tests; P < .001). For the Osstell, these values were -5.88 (4.18) and -5.48 (3.93) for the test and control groups, respectively (paired t tests: P < .001). CONCLUSIONS: Ulna implant block grafting represents an alternative to conventional sinus augmentation, particularly when vertical augmentation is desirable or large iliac crest grafts are needed.

Immediate loading of two (fixed-on-2) vs four (fixed-on-4) implants placed with a flapless technique supporting mandibular cross-arch fixed prostheses: 3-year results from a pilot randomised controlled trial.

PURPOSE: To evaluate the outcome of two vs four implants placed flapless in fully edentulous mandibles and immediately restored with metal-resin screw-retained cross-arch prostheses. MATERIALS AND METHODS: A total of 60 patients from two different centres were randomised: 30 to the fixed-on-2 group and 30 to the fixed-on-4 group according to a parallel group design. To be immediately loaded implants had to be inserted with a minimum torque of 40 Newton/cm (Ncm). Outcome measures were prosthesis and implant failures, complications, and marginal bone level changes. RESULTS: Flaps were raised in 18 patients. Two implants in two patients did not reach the planned insertion torque and were replaced immediately by larger diameter ones. Three years after loading, two patients dropped out from the fixed-on-2 group and one from the fixed-on-4 group. No implant failure or prosthetic failure occurred. A total of 12 fixed-on-2 patients were affected by one complication each vs 13 fixed-on-4 patients. There were no statistically significant differences for complications between groups (difference in proportion = -0.03; 95% CI -29 to 0.22; P [Fisher's exact test] =1.000). There were no statistically significant differences for marginal peri-implant bone loss between the two groups (mean difference = 0.14; CI 95% -0.17 to 0.45; P [ANCOVA] = 0.356), with both groups losing marginal bone in a statistically significant way (1.70 mm for fixed-on-2 implants and 1.56 mm for fixed-on-4 implants). There were statistically significant differences between the two centres, with more bone being lost for the Bologna centre (2.18 vs 1.13 mm; P (ANCOVA) < 0.001). CONCLUSIONS: Up to 3 years after loading, these preliminary results suggest that immediately loaded mandibular cross-arch fixed prostheses can be supported by only two dental implants. Longer follow-ups (about 10 years) are needed to properly evaluate this therapeutic option. Conflict of interest statement: This study was completely self-financed and no funding from the implant manufacturers has been sought or obtained, not even in the form of free materials.

Immediate loading of two (fixed-on-2) versus three (fixed-on-3) implants placed flapless supporting cross-arch fixed prostheses: One-year results from a randomised controlled trial.

PURPOSE: To evaluate the outcome of two (fixed-on-2 = FO2) versus three (fixed-on-3 = FO3) implants placed flapless in fully edentulous jaws and immediately restored with metal-resin screw-retained crossarch prostheses. MATERIALS AND METHODS: Forty edentulous or to be rendered edentulous patients (20 in the maxilla and 20 in the mandible) were randomised to the FO2 group (20 patients: 10 in the maxilla and 10 in the mandible) and to the FO3 group (20 patients: 10 in the maxilla and 10 in the mandible) according to a parallel group design. To be immediately loaded, implants had to be inserted with a minimum torque of 60 Ncm. Outcome measures were prosthesis and implant failures, complications and periimplant marginal bone level changes evaluated up to 1-year post-loading. RESULTS: Flaps were raised in four patients and two prostheses were loaded early at 8 weeks in the FO2 group. One year after loading no dropout or implant failure occurred, however one FO2 maxillary prosthesis had to be remade because of repeated screw-loosening (risk difference = 0.05; 95% CI: -0.05 to 0.15; Fisher's exact test P = 1.000). Three FO2 patients were affected by complications versus five FO3 patients (risk difference = -0.1; 95% CI: -0.35 to 0.15; Fisher's exact test; P = 0.695). There were no statistically significant differences for prosthetic failures and complications between groups. There were no statistically significant differences for marginal peri-implant bone levels between the two groups (estimate of the difference = 0.031 mm; 95% Cl: -0.22 to 0.28; P (ancova) = 0.803), with both groups losing marginal bone in a statistically significant way (0.27 mm for FO2 patients and 0.24 mm for FO3 patients). CONCLUSIONS: These preliminary results suggest that immediately loaded cross-arch prostheses can be supported by only two or three dental implants at least up to 1-year post-loading. Longer follow-ups are needed to properly evaluate both these therapeutic options.

Immediate loading of two flapless placed mandibular implants supporting cross-arch fixed prostheses: A 5-year follow-up prospective single cohort study.

PURPOSE: To evaluate the clinical outcome of two implants placed flapless in fully edentulous mandibles and immediately restored with metal-resin screw-retained cross-arch prostheses 5 years after loading. MATERIALS AND METHODS: Eighty consecutive patients were recruited. To be immediately loaded, implants had to be inserted with a minimum torque of 80 Ncm. Forty-six laser-welded titanium and 34 cast silver-palladium frameworks with resin teeth were initially delivered within 8 and 48 h, respectively. Outcome measures, evaluated by two independent assessors included prosthesis and implant failures, complications, marginal bone level changes, implant stability quotient (ISQ) values and patient satisfaction. RESULTS: Five years after loading one patient did not return to the control and 10 prostheses were remade. Two implants failed early in two patients, but they were successfully replaced. Thirty-six complications occurred in 28 patients but were all successfully treated. After 5 years, mean marginal bone loss was 0.69 mm, mean ISQ values decreased from 75.4 to 73.8, and all patients were fully satisfied with the therapy. A post-hoc comparison between the outcome of laser-welded and cast frameworks showed that laser-welded frameworks were affected by significantly more complications (19 patients out of 46 and 6 patients out of 34, respectively; difference in proportion = 0.23, 95% CI: 0.03 to 0.43; Pearson's chi-square test, P = 0.032), therefore such a framework construction should be considered as a long-term temporary prosthesis and not a definitive prosthesis. CONCLUSIONS: Immediately loaded mandibular cross-arch prostheses can be supported by only two implants up to 5 years, if made with a robust cast framework. Longer follow-ups (around 10 years) are still needed to know the prognosis of this treatment modality.

Immediate loading of bimaxillary total fixed prostheses supported by five flapless-placed implants with machined surfaces: A 6-month follow-up prospective single cohort study.

PURPOSE: To evaluate the clinical outcome of fully edentulous patients rehabilitated with immediately loaded bimaxillary screw-retained metal-resin prostheses supported by five implants placed flapless: two in the mandible and three in the maxillae. MATERIALS AND METHODS: Twenty-five consecutively treated patients were recruited. To be immediately loaded, implants had to be inserted with a minimum torque of 80 Ncm. Outcome measures were prosthesis and implant failures, and complications. RESULTS: Six months after loading no patients dropped out and no prosthesis or implant failed. Two maxillary prostheses were loaded early at 8 weeks because implants were inserted with a torque inferior to 45 Ncm. Three complications occurred in two patients but they were all successfully treated. CONCLUSIONS: Six months after loading, immediately loaded bimaxillary cross-arch prostheses can be supported by only two mandibular and three maxillary flapless-placed dental implants. Longer follow-ups of approximately 10 years are needed to understand the prognosis of this treatment modality.

Machined versus roughened immediately loaded and finally restored single implants inserted flapless: Preliminary 6-month data from a split- mouth randomised controlled trial.

PURPOSE: To compare the outcome of immediately loaded single implants with a machined or a roughened surface. MATERIALS AND METHODS: Fifty patients had two implant sites randomly allocated to receive flaplessplaced single Syra implants (Sweden & Martina), one with a machined and one with a roughened surface (sand-blasted with zirconia powder and acid etched), according to a split-mouth design. To be loaded immediately, implants had to be inserted with a torque superior to 50 Ncm. Implants were restored with definitive crowns in direct occlusal contact within 48 h. Patients were followed for 6 months after loading. Outcome measures were prosthetic and implant failures and complications. RESULTS: Two machined implants and four roughened implants were not loaded immediately. Six months after loading no dropout occurred. One implant loaded late, which had a rough implant surface, failed 20 days after loading (P (McNemar test) = 0.625; difference in proportions = -0.04; 95% CI: -0.15 to 0.07). Three crowns had to be remade on machined implants and four on roughened implants (P (McNemar test) = 1.000; difference in proportions = -0.02; 95% CI: -0.12 to 0.08). Three machined and five roughened implants experienced complications (P (McNemar test) = 0.625; difference in proportions = -0.04; 95% CI: -0.15 to 0.07). There were no statistically significant differences between groups for crown and implant losses as well as complications. CONCLUSIONS: Up to 6 months after loading both machined and roughened flapless-placed and immediately loaded single implants provided good and similar results, however, longer follow-ups are needed to evaluate the long-term prognosis of implants with different surfaces.

Immediate loading of fixed cross-arch prostheses supported by flapless-placed supershort or long implants: 1-year results from a randomised controlled trial.

PURPOSE: To compare the outcome of cross-arch prostheses supported either by supershort (5 mm) or long (11.5 mm) implants, placed flapless and immediately restored with metal-resin screw-retained cross-arch prostheses. MATERIALS AND METHODS: Thirty patients with edentulous (or to be rendered edentulous) mandibles and 30 with edentulous maxillas, who had sufficient bone to allow the placement of four and six implants respectively, which were at least 11.5 mm-long, were randomised according to a parallel group design into 2 equal groups, where they received either 5 mm or 11.5 mm-long implants at one centre. Implants with a diameter of 5 mm, were to be placed flapless with an insertion torque of at least 50 Ncm. Mandibles received four implants between the mental foramina. Implants were to be immediately loaded with metal-resin-definitive prostheses on the same day of implant placement. Patients were followed up to 1 year after loading and the outcome measures were: prosthesis and implant failures, complications, and peri-implant marginal bone level changes. RESULTS: No patients dropped-out. Two prostheses were remade, one on short maxillary implants and one on long mandibular implants. Two 5 mm maxillary implants which did not achieve 50 Ncm torque in soft bone of one patient, but were immediately loaded anyway, failed after 3 weeks compared to one mandibular 11.5 mm-long implant that failed after 60 days. Two complications occurred in each group. There were no statistically significant differences for prosthesis failures, implant failures and complications. Patients with mandibular short implants lost on average 0.08 mm of peri-implant bone at 1 year and patients with long mandibular implants lost 0.51 mm. Patients with short maxillary implants lost on average 0.15 mm of peri-implant bone at 1 year and patients with long maxillary implants lost 0.62 mm. Short implants showed less bone loss when compared to long implants and the differences up to 1 year were statistically significant both in maxillae (mean difference = 0.48 mm, 95% CI 0.22 to 0.73, P = 0.0011) and in mandibles (mean difference = 0.44 mm, 95% CI 0.21 to 0.66, P = 0.0009). CONCLUSIONS: Flapless-placed 5 mm-long implants achieved similar results as 11.5 mm-long implants when supporting immediately loaded cross-arch prostheses both in maxillae and mandibles up to 1 year after loading. These preliminary results must be confirmed by other trials, and 5- to 10-year post-loading data is necessary before making reliable recommendations.

Dynamic phase transition for decoding algorithms.

The state-of-the-art error correcting codes are based on large random constructions (random graphs, random permutations, etc.) and are decoded by linear-time iterative algorithms. Because of these features, they are remarkable examples of diluted mean-field spin glasses, both from the static and dynamic points of view. We analyze the behavior of decoding algorithms by mapping them onto statistical-physics models. This allows us to understand the intrinsic (i.e., algorithm independent) features of this behavior.

Restoration of partially edentulous patients using dental implants with a microtextured surface: a prospective comparison of delayed and immediate full occlusal loading.

PURPOSE: The aim of this study was to determine the clinical effectiveness of placing dental implants with microtextured surfaces into full occlusal loading at the time of placement in partially edentulous patients. MATERIALS AND METHODS: Two demographically similar groups of 14 patients each were treated with a total of 92 Spline Twist Implants (Centerpulse Dental, Carlsbad, CA). Test implants were placed into immediate full occlusal loading, and control implants were restored using a conventional delayed loading procedure. Otherwise, both groups of patients received similar therapy from the same treatment team. Radiographs, periodontal indices, and Periotest values were recorded every 6 months during routine clinical follow-up appointments. The mean loading time for all prostheses was 24 months at the time of this report. RESULTS: No implants failed in the test group, and 1 implant failed before loading in the control group. Cumulative implant success was 98.9% for all implants placed (test group = 100%; control group = 92.9%). Periodontal measurements indicated no significant clinical differences between implants placed into immediate full occlusal loading and those loaded via a conventional delayed protocol. DISCUSSION: Immediate full occlusal loading of partial prostheses supported by microtextured implants in partially edentulous patients demonstrated excellent clinical results, with no adverse periodontal effects after 24 months of function. Additional follow-up will provide invaluable information on the long-term effects of this technique. CONCLUSION: Immediate full occlusal loading of partial prostheses supported by microtextured implants can be successfully achieved for 24 months in highly motivated patients with excellent oral hygiene.

Immediate loading of two flapless placed mandibular implants supporting cross-arch fixed prostheses: a 3-year follow-up prospective single cohort study.

PURPOSE: To evaluate the clinical outcome of two implants placed flapless in fully edentulous mandibles and immediately restored with a metal-resin screw-retained cross-arch prostheses 3 years after loading. MATERIALS AND METHODS: Eighty consecutively patients were recruited. Implants for immediate loading had to be inserted with a minimum torque of 80 Ncm. Outcome measures, evaluated by two independent assessors, were: prosthesis and implant failures, complications, marginal bone level changes, implant stability quotient (ISQ) values and patient satisfaction. RESULTS: Three years after loading, all prostheses were in function although one patient did not come back for the 1- and 3-year follow-ups. Two implants failed early in two patients, but were successfully replaced and their prostheses remade. Twelve complications occurred in 10 patients but were all successfully treated. After 3 years, mean marginal bone loss was 0.43 mm, mean ISQ values decreased from 75.4 to 75.3, and all but four patients were fully satisfied with the therapy. Four patients were partially satisfied because, lacking molars, they could not chew as they wished. CONCLUSION: Immediately loaded mandibular cross-arch partial dentures can be supported by only two dental implants up to 3 years. Longer follow-ups (around 10 years) are needed to know the prognosis of this treatment modality.