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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/

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.

The aim of this study is to compare early and follow-up outcomes of late open conversions (LOC, with complete or partial endograft explantation) and semi-conversions (SC, with endograft preservation) after endovascular aneurysm repair in a multicenter experience.All LOC and SC performed from 1997 to 2020 in 11 vascular centers were compared. Endograft infections or thrombosis were excluded. Primary endpoints were early mortality and long-term survival estimates. Secondary endpoints were differences in postoperative complication rates and conversion-related complications during follow-up.In the considered period, 347 patients underwent surgery for endovascular aneurysm repair complications. Among these, 270 were operated on for endoleaks (222 LOC, 48 SC). The two groups were homogeneous in terms of American Society of Anesthesiologists score (LOC, 3.2 ± 0.7; SC, 3 ± 0.5; P = .128) and main endograft characteristics (suprarenal fixation, bifurcated/aorto-uni-iliac configuration). The mean age was 75 ± 8 years for LOC and 79 ± 7 years for SC (P = .009). Reasons for LOC were: 62.2% (138/222) type I endoleak, 21.6% (48/222) type II endoleak, 7.7% (17/222) type III endoleak, and 8.5% (19/222) endotension. Indications for SC were: 64.6% (31/48) type II endoleak, 33.3% (16/48) type I endoleak, and 2.1% (1/48) type III endoleak. Thirty-day mortality was 12.2% (27/222) in the LOC group, and 10.4% (5/48) in the SC group (P = .73). Postoperative complication rate was higher in the LOC group (45.5% vs 29.2%; P = .04). The estimated survival rate after LOC was 80% at 1 year and 64% at 5 years; after SC, it was 72% at 1 year and 37% at 5 years (log-rank P = .01). During the median follow-up of 21.5 months (interquartile range, 2.4-61 months), an endoleak after SC was found in the 38.3% of the cases; sac growth was recorded in the 27.7% of SC patients.SC has an early benefit over LOC in terms of reduced postoperative complications but has a significantly inferior mid-term survival. The high rates of persistent and/or recurrent endoleaks reduce SC durability.

While exponential growth in public genomic data can afford great insights into biological processes underlying diseases, a lack of structured metadata often impedes its timely discovery for analysis. In the Gene Expression Omnibus, for example, descriptions of genomic samples lack structure, with different terminology (such as “breast cancer”, “breast tumor”, and “malignant neoplasm of breast”) used to express the same concept. To remedy this, we learn models to extract salient information from this textual metadata. Rather than treating the problem as classification or named entity recognition, we model it as machine translation, leveraging state-of-the-art sequence-to-sequence (seq2seq) models to directly map unstructured input into a structured text format. The application of such models greatly simplifies training and allows for imputation of output fields that are implied but never explicitly mentioned in the input text.

The way in which climate change research funds are managed is shifting dramatically toward investments in large collaborative research networks. This poses significant challenges for researchers, and requires changes from the institutions and funders that support them.

We present the output of a research combining field based, expert knowledge and remote sensing identification of the rates of change, pathways and drivers of these changes, during the past 35 years and more where possible, in four Western Indian Ocean River Deltas: Tana River and Delta (Kenya), Rufiji River and Delta (Tanzania), Limpopo River and Delta (Mozambique) as well as Betsiboka River and Delta (Madagascar). These findings are a set of preliminary results of the collaborative and multidisciplinary effort produced during the WIODER project () that brings together the National Museum of Kenya, Kenweb Kenya, University of Dar Es Salaam in Tanzania, University Eduardo Mondlane in Mozambique, Centre National de Recherches sur l'Environnement in Madagascar, University of Southampton in UK, IHE Delft in the Netherlands, Institut de Recherches pour le Développement in France, and International Development Research Center in Canada and Kenya.We highlight the similarities in the physical environment and, to some degree, also in the socio-economic-political environments that are leading the actual changes, affecting resilience of the local population and their sustainable development.We focused on the substantial changes in the following aspects: precipitation seasonality and intensity, flooding patterns and frequency, land cover, dry forest cover, mangrove cover, crop production, soil erosion, fish population, human population, human migration flow, frequency of human conflicts within the delta population.The IPCC foreseen changes in climate towards an aridification of the Southern Africa river basins and a wetter condition in the Eastern Africa region. Some signals of these climatic forecast are already recorded in both regions.Assuming that these trends will continue for the next 10 years or so, we created and here we present two main scenarios of what will happen in these deltas: one with mainly climate change drivers, and another one with climate change and dam drivers.

The reality of global climate change demands novel approaches to science that are reflective of the scales at which changes are likely to occur, and of the new forms of knowledge required to positively influence policy to support vulnerable populations. We examine some of the opportunities and challenges presented by a collaborative, transdisciplinary research project on climate change adaptation in Africa and Asia that utilised a hotspot approach. A large scale effort to develop appropriate baselines was a key challenge at the outset of the program, as was the need to develop innovative methodologies to enable researchers to work at appropriate spatial scales. Efforts to match research to the biophysical scales at which change occurs need to be aware of the mismatch that can develop between these regional scales and the governance scales at which decisions are made.

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.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.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).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.

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.

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 \cite{Frey07}. 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, {\it 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 {\it 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., 11 pages, supplementary material: http://isiosf.isi.it/~weigt/scap_supplement.pdf

In this paper we generalize to the case of diluted spin models and random combinatorial optimization problems a technique recently introduced by Guerra (cond-mat/0205123) to prove that the replica method generates variational bounds for disordered systems. We analyze a family of models that includes the Viana–Bray model, the diluted p-spin model or random XOR-SAT problem, and the random K-SAT problem, showing that the replica/cavity method, at the various levels of approximation, provides systematic schemes to obtain lower bounds of the free-energy at all temperatures and of the ground state energy. In the case of K-SAT and XOR-SAT it thus gives upper bounds of the satisfiability threshold. Our analysis underlines deep connections with the cavity method which are not evident in the long range case.

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.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.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).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.

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.

To compare the outcome of immediately loaded single implants inserted with medium (from 25 to 35 Ncm) or high insertion torques (80 Ncm).Fifty patients received two single non-adjacent implants, each randomly inserted flapless with a torque between 25 to 35 Ncm or80 Ncm according to a split-mouth design. Non-occluding temporary crowns were immediately placed on provisional abutments and definitive crowns were delivered after 6 weeks. Patients were followed for 6 months after initial loading. Outcome measures were crown/implant failures, complications, peri-implant marginal bone level changes, postoperative pain and presence of peri-implant apical radiolucency.No drop-out occurred. Seven implants inserted with a torque between 25 to 35 Ncm failed versus none of the implants inserted with a torque35 Ncm. With the exception of crown/implant failures (exact McNemar significance P = 0.0156, difference in proportions: -0.12; 95% CI -0.21 to -0.02) there were no statistically significant differences between groups for the other outcome measures.It is preferable to insert single implants with a high insertion torque (80 Ncm), to minimise early implant failures, when loading them immediately.

To evaluate the clinical outcome of 2 implants placed flapless in fully edentulous mandibles and immediately restored with a metal-resin screw-retained cross-arch prosthesis 1 year after loading.Eighty consecutive patients were recruited. To be immediately loaded, implants 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.Flaps were raised in 7 patients. Twelve implants in 7 patients did not reach the planned insertion torque. Four implants in 3 patients were immediately replaced by larger diameter implants and achieved the desired torque, whereas the remaining implants were immediately loaded anyway. Two implants failed early in 2 patients, but were successfully replaced and their prostheses remade. One month after loading, 72 (90%) patients declared to be completely satisfied with the therapy, 7 (9%) partially satisfied and 1 (1%) unsatisfied. One year after loading, all prostheses were in function, though one patient did not attend the 1-year control. Eight (10%) complications occurred, all successfully treated. After 1 year, the mean marginal bone loss was 0.3 mm and mean ISQ values decreased from 75.4 to 72.4.These short-term results at 1 year after loading suggest that immediately loaded mandibular cross-arch fixed prostheses can be supported by only 2 dental implants. Longer follow-ups (around 10 years) are needed to know the prognosis of this treatment modality.

To evaluate the efficacy of immediate loading versus early loading at 6 weeks of bar-retained mandibular overdentures supported by two implants placed with a flapless technique.Sixty patients were randomised: 30 to the immediately loaded group and 30 to the early loaded group. To be immediately loaded, implants had to be inserted with a minimum torque48 Ncm. Outcome measures were prosthesis and implant failures, biological and biomechanical complications, patient satisfaction, and Implant Stability Quotient (ISQ) assessed with a resonance frequency analysis instrument.Sixty implants were placed in each group. Flaps had to be raised in nine patients to check drill direction or to better visualise the area after multiple teeth extraction. Two implants in two patients did not reach the planned insertion torque and were immediately replaced by larger diameters ones. After 1 year no drop out occurred and two early loaded implants failed in two patients. There were no statistically significant differences between groups for prosthesis failures, implant losses, complications, and mean ISQ values; however, patients in the immediately loaded group were significantly more satisfied than those loaded early. When comparing mean ISQ values taken 6 weeks after placement with 1-year data within each group, values decreased significantly.Mandibular overdentures can be successfully loaded the same day of implant placement with a minimally invasive surgery, increasing patient satisfaction while decreasing treatment time and patient discomfort. No apparent advantages were seen when loading the overdentures at 6 weeks.

To evaluate the efficacy of 7-mm-long flapless placed single implants immediately or early loaded at 6 weeks.Thirty patients received two single Nanotite External Hex Biomet 3i implants that were then randomised for immediate or early loading. All implants had to be inserted with a minimum torque40Ncm. Provisional crowns were put in slight occlusal contact and replaced by definitive crowns 3 months after loading. Outcome measures were implant failures, biological and biomechanical complications, peri-implant marginal bone level changes and patient preference.Twenty-nine implants were immediately loaded and 31 early loaded. Thirteen flaps had to be elevated in 12 patients. Eleven implants in ten patients did not reach the planned insertion torque. Eight implants in seven patients were immediately replaced by implants with a larger diameter, two were loaded anyway, and one implant that was randomised to immediate loading was early loaded instead. Nine months after loading, no drop-out occurred. One implant failed in each group. There were no statistically significant differences between groups for implant losses, complications, mean marginal bone level changes, and patient preferences.Flapless placed 7-mm-long single implants can be successfully loaded the day of insertion. Longer follow-ups are needed to monitor the long-term prognosis of short implants.

To evaluate the efficacy of flapless placed implants immediately or early loaded at 2 months with full-arch prostheses.Thirty patients were randomised: 15 to the immediately loaded group and 15 to the early loaded group. All implants had to be inserted with a minimum torque48 Ncm. Outcome measures were prosthesis and implant failures, biological and biomechanical complications, peri-implant marginal bone level changes, patient satisfaction and implant stability quotient (ISQ) assessed with a resonance frequency analysis instrument.Ninety implants were placed in the immediately loaded and 87 in the early loaded group. Four localised flaps had to be elevated. Six implants in five patients did not reach the planned insertion torque. Four were immediately replaced by larger diameters ones, one was early loaded and another removed just after placement. After 1 year no drop-out occurred. One implant failed in the immediately loaded group versus three early loaded implants in two patients. There were no statistically significant differences between groups for implant losses, complications, and mean marginal bone level changes. There were borderline significant differences for mean ISQ values, and patients in the immediately loaded group were significantly more satisfied than those early loaded. When comparing mean ISQ values taken 2 months after placement with year 1 data within each group, values increased significantly.Maxillary cross-arch prostheses can be successfully loaded the same day of flapless implant placement, increasing patient satisfaction while decreasing treatment time and patient discomfort. No apparent advantages were seen when loading implants at 2 months.

Background: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help focus limited experimental resources on the most likely hypotheses. Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated. Results: In this study, a standardized collection of mouse functional genomic data was assembled; nine bioinformatics teams used this data set to independently train classifiers and generate predictions of function, as defined by Gene Ontology (GO) terms, for 21,603 mouse genes; and the best performing submissions were combined in a single set of predictions. We identified strengths and weaknesses of current functional genomic data sets and compared the performance of function prediction algorithms. This analysis inferred functions for 76% of mouse genes, including 5,000 currently uncharacterized genes. At a recall rate of 20%, a unified set of predictions averaged 41% precision, with 26% of GO terms achieving a precision better than 90%. Conclusion: We performed a systematic evaluation of diverse, independently developed computational approaches for predicting gene function from heterogeneous data sources in mammals. The results show that currently available data for mammals allows predictions with both breadth and accuracy. Importantly, many highly novel predictions emerge for the 38% of mouse genes that remain uncharacterized.

We study the problem of recovering a known cluster structure in a sparse network, also known as the planted partitioning problem, by means of statistical mechanics. We find a sharp transition from un-recoverable to recoverable structure as a function of the separation of the clusters. For multivariate data, such transitions have been observed frequently, but always as a function of the number of data points provided, i.e. given a large enough data set, two point clouds can always be recognized as different clusters, as long as their separation is non-zero. In contrast, for the sparse networks studied here, a cluster structure remains undetectable even in an infinitely large network if a critical separation is not exceeded. We give analytic formulas for this critical separation as a function of the degree distribution of the network and calculate the shape of the recoverability-transition. Our findings have implications for unsupervised learning and data-mining in relational data bases and provide bounds on the achievable performance of graph clustering algorithms., 4 Pages, 2 Figures

To evaluate success rates and complications of implants placed with a flapless technique and immediately loaded in fully edentulous maxillae.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.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.Implants placed in the edentulous maxilla with a flapless procedure can be successfully loaded the same day of surgery.

Combinatorial auctions are formulated as frustrated lattice gases on sparse random graphs, allowing the determination of the optimal revenue by methods of statistical physics. Transitions between computationally easy and hard regimes are found and interpreted in terms of the geometric structure of the space of solutions. We introduce an iterative algorithm to solve intermediate and large instances, and discuss competing states of optimal revenue and maximal number of satisfied bidders. The algorithm can be generalized to the hard phase and to more sophisticated auction protocols., 4 pages, 4 figures, minor changes, references added. To appear on PRL

Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most relevant issues has recently become that of correctly and reliably predicting the functions of observed but still functionally undetermined proteins starting from information coming from the network of co-observed proteins of known functions. Method: The method proposed in this article is based on a message passing algorithm known as Belief Propagation, which takes as input the network of proteins physical interactions and a catalog of known proteins functions, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast on-line analysis, and can be easily generalized to more complex graph topologies taking into account hyper-graphs, {\em i.e.} complexes of more than two interacting proteins., Comment: 12 pages, 9 eps figures, 1 additional html table

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.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.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.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.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.

The state-of-the-art error correcting codes are based on large random constructions (random graphs, random permutations, ...) 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 from the dynamic points of view. We analyze the behavior of decoding algorithms using the mapping onto statistical-physics models. This allows to understand the intrinsic (i.e. algorithm independent) features of this behavior., Comment: 40 pages, 29 eps figures

We present a detailed study of the phase diagram of the Ising model in random graphs with arbitrary degree distribution. By using the replica method we compute exactly the value of the critical temperature and the associated critical exponents as a function of the minimum and maximum degree, and the degree distribution characterizing the graph. As expected, there is a ferromagnetic transition provided < \infty. However, if the fourth moment of the degree distribution is not finite then non-trivial scaling exponents are obtained. These results are analyzed for the particular case of power-law distributed random graphs., Comment: 9 pages, 1 figure

We study the computational complexity of a very basic problem, namely that of finding solutions to a very large set of random linear equations in a finite Galois Field modulo q. Using tools from statistical mechanics we are able to identify phase transitions in the structure of the solution space and to connect them to changes in performance of a global algorithm, namely Gaussian elimination. Crossing phase boundaries produces a dramatic increase in memory and CPU requirements necessary to the algorithms. In turn, this causes the saturation of the upper bounds for the running time. We illustrate the results on the specific problem of integer factorization, which is of central interest for deciphering messages encrypted with the RSA cryptosystem., Comment: 23 pages, 8 figures