BioModels-15 years of sharing computational models in life science.

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world's largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.

Sonographic features of Rosai-Dorfman disease in the breast: A case report.

Rosai-Dorfman disease (sinus histiocytosis with massive lymphadenopathy) is an uncommon histiocytic disease of the lymph nodes. Extranodal presentation, especially in breast parenchymal tissue, is rare. A 54-year-old woman presented with a painful and palpable lump in the right breast. Ultrasonography revealed an irregular, indistinct, hypoechoic mass with a hyperechoic halo. Pathological analysis revealed proliferation of large histiocytes and stromal fibrosis with emperipolesis and positive immunoreactivity for S-100 and CD68. The clinical and radiologic manifestations of Rosai-Dorfman disease may vary, and differentiation from other inflammatory diseases and malignancies is challenging; thus, accurate pathological diagnosis plays an important role in appropriate management.

The EBI search engine: EBI search as a service-making biological data accessible for all.

We present an update of the EBI Search engine, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types that include nucleotide and protein sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, as well as the life science literature. EBI Search provides a powerful RESTful API that enables its integration into third-party portals, thus providing 'Search as a Service' capabilities, which are the main topic of this article.

Single-Port Versus Multiport da Vinci System for Transoral Robotic Surgery of Hypopharyngeal and Laryngeal Carcinoma.

OBJECTIVE: Da Vinci single port (SP) has been recently approved for transoral robotic surgery (TORS). Its characteristics make it particularly feasible for laryngeal and hypopharyngeal surgery. We report our experience comparing intra- and postoperative outcomes, technical advantages, and shortcomings of transoral laryngeal and hypopharyngeal resections performed with the da Vinci SP and the da Vinci Si/Xi systems. STUDY DESIGN: Retrospective database review. SETTING: Single academic tertiary care hospital. METHODS: Subjects included adult patients with laryngeal and hypopharyngeal carcinoma who underwent TORS between 2008 and 2022. The SP and multiport (MP) systems were compared in terms of intraoperative times, short-term postoperative outcomes, and TORS-related complications after a propensity score matching. RESULTS: A total of 185 patients were enrolled (56 SP vs 129 MP patients), and a cohort of 112 patients was analyzed after matching. The docking time was reduced in the SP group (8.84 ± 4.67 vs 6.45 ± 3.11 minutes; p = .003), as well as console time (53.91 ± 29.38 vs 42.70 ± 13.72 minutes; p = .035). Positive margins were more frequent in the MP group (52% vs 43%; p = .34). The mean decannulation time was 1.86 days longer in the SP group (p = .046). No significant differences emerged from the analysis of the duration of hospitalization, enteral feeding, and TORS-related complications. CONCLUSION: SP safety profile is comparable to that of previous models, while it showed advantages in terms of reduced docking times. Console times were also shortened due to improved maneuverability and field visualization.

Insulin promotes macrophage foam cell formation: potential implications in diabetes-related atherosclerosis.

The prevalence of atherosclerotic cardiovascular disease is higher in patients with type 2 diabetes, a disorder characterized by hyperinsulinemia and insulin resistance. The role of hyperinsulinemia as an independent participant in the atherogenic process has been controversial. In the current study, we tested the effect of insulin and the insulin sensitizer, adiponectin, on human macrophage foam cell formation. We found that both insulin and adiponectin increased the expression of the type 2 scavenger receptor CD36 by approximately twofold and decreased the expression of the ATP-binding cassette transporter ABCA1 by >80%. In both cases regulation was post-transcriptional. As a consequence of these changes, we found that oxidized LDL (oxLDL) uptake was increased by 80% and cholesterol efflux to apolipoprotein A1 (apoA1) was decreased by ∼25%. This led to two- to threefold more cholesterol accumulation over a 16-h period. As reported previously in studies of murine systems, scavenger receptor-A (SR-A) expression on human macrophages was downregulated by insulin and adiponectin. Insulin and adiponectin did not affect oxLDL-induced secretion of monocyte attractant protein-1 (MCP-1) and interleukin-6 (IL-6). These studies suggest that hyperinsulinemia could promote macrophage foam cell formation and thus may contribute to atherosclerosis in patients with type 2 diabetes.

Intralesional phosphatidylcholine and sodium deoxycholate: a possible treatment option for nevus lipomatosus superficialis.

Treatment options are limited for classic nevus lipomatosus superficialis, in which clustered lesions present over a large area. We present a case of nevus lipomatosus superficialis that showed clinical and histological improvement after treatment with intralesional phosphatidylcholine and sodium deoxy-cholate.

Long-term outcomes of early stage oral tongue cancer: Main cause of treatment failure and second primary malignancy.

Objective: We attempted to investigate the long-term outcomes, prognostic factors, treatment failures, second primary malignancies, and salvage therapies in early (pT1-2N0) oral tongue squamous cell carcinoma (OTSCC). Methods: We retrospectively analyzed the medical records of 295 early stage OTSCC patients. Results: Two hundred ninety-five patients were enrolled. The average follow-up period was 64.5 months (range, 1-190 months). Five-year recurrence-free survival rate was 84.8% and disease-specific survival rate was 91.2%. On multivariate analysis, only the depth of invasion (DOI) exhibited significant correlations with the disease recurrence. Patient's age and DOI demonstrated a significant association with survival. A total of 53 recurrence and 35 death events occurred, with the main cause of treatment failure being regional or local recurrence. In recurrent cases, the success rate of salvage treatment was 42% at 5 years. During the follow-up period, second primary malignancy occurred in 13 patients, and 8 (61.5%) of those patients were successfully treated. Conclusions: In pT1-2N0 OTSCC, regional or local recurrence is the main recurrence pattern, whereas age and DOI >5 mm are significant prognostic factors related to recurrence and survival. Since several patients experienced second primary malignancies in the head and neck, careful and thorough surveillance may be required to detect second primary lesions. Level of Evidence: 4.

Creating a human brain proteome atlas--13th HUPO BPP Workshop March 30-31, 2010, Ochang, Korea.

The HUPO Brain Proteome Project (HUPO BPP) held its 13th workshop in Ochang from March 30th to 31st, 2010 prior to the Korean HUPO 10th Annual International Proteomics Conference. The principal aim of this project is to obtain a better understanding of neurodiseases and aging with the ultimate objective of discovering prognostic and diagnostic biomarkers, in addition to the development of novel diagnostic techniques and new medications. The attendees came together to discuss progress in the clinical neuroproteomics of human and to define the needs and guidelines required for more advanced proteomics approaches.

Creating a human brain proteome atlas--14th HUPO BPP workshop September 20-21, 2010, Sydney, Australia.

The HUPO Brain Proteome Project (HUPO BPP) held its 14th workshop during the HUPO 9th Annual World Congress in Sydney, Australia. The principal aim of this project is to discover prognostic and diagnostic biomarkers associated with neurodegenerative diseases and brain aging, with the ultimate objective of obtaining a better understanding of these conditions and creating roads for the development of novel diagnostic techniques and effective treatments. The attendees came together to discuss progress in the human clinical neuroproteomics and to define the needs and guidelines required for more advanced proteomics approaches.

Clinical aspects of neurodegenerative diseases - 15th HUPO BPP Workshop April 8-9, 2011, Bochum, Germany.

The HUPO Brain Proteome Project (HUPO BPP) held its 15th workshop in Bochum, Germany, from April 8th to 9th, 2011 directly after the Proteomic Forum 2011 in Berlin. Like on every spring workshop, the focus was more on clinical aspects, so that especially clinicians participated in this workshop.