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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/

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.

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.

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 extend replica bounds and free energy subadditivity arguments to diluted spin-glass models on graphs with arbitrary, non-Poissonian degree distribution. The new difficulties specific of this case are overcome introducing an interpolation procedure that stresses the relation between interpolation methods and the cavity method. As a byproduct we obtain self-averaging identities that generalize the Ghirlanda-Guerra ones to the multi-overlap case., Latex file, 15 pages, 2 eps figures; Weak point revised and corrected; Misprints corrected

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.

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 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.

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.