MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins

Abstract Motivation The earlier version of MobiDB-lite is currently used in large-scale proteome annotation platforms to detect intrinsic disorder. However, new theoretical models allow for the classification of intrinsically disordered regions into subtypes from sequence features associated with specific polymeric properties or compositional bias. Results MobiDB-lite 3.0 maintains its previous speed and performance but also provides a finer classification of disorder by identifying regions with characteristics of polyolyampholytes, positive or negative polyelectrolytes, low-complexity regions or enriched in cysteine, proline or glycine or polar residues. Subregions are abundantly detected in IDRs of the human proteome. The new version of MobiDB-lite represents a new step for the proteome level analysis of protein disorder. Availability and implementation Both the MobiDB-lite 3.0 source code and a docker container are available from the GitHub repository: https://github.com/BioComputingUP/MobiDB-lit

Mapping of stones and their deterioration forms : the Clock Tower, Venice (Italy)

The HYPERION EU project aims to develop a Decision Support System to improve resilience and sustainable reconstruction of historic areas faced with climate change and extreme events. In this context, Venice presents an outstanding example of urban and architectural complexity and richness. The mapping of the ornamental stones of the facade of the Venice Clock Tower (Torre dell'Orologio) and their deterioration patterns acts as a milestone on which to build the knowledge-acquisition process of the system as regards stone artefacts and their decay products. The Clock Tower is an early Renaissance building (1499) in Lombardesque style and stands over the entrance to the Mercerie on the northern side of St. Mark's Square. Detailed surveys and mapping of both building materials (mainly stones) and deterioration patterns were carried out, the latter following the glossary of weathering forms, coupled with an easy-to-use scale of evaluation of their intensity. The data output consists of several monothematic maps which can be handled separately, each one focusing on precise lithological or specific deterioration aspects. This study also proposes a simple approach to summarizing the total state of deterioration of the building in the form of a Total Deterioration Rank (TDR) and its representation. The stones used in the facade are regional (Ammonitico Rosso and Scaglia Rossa) and extra-regional limestones (Istrian Stone), as well as Mediterranean white and coloured marbles and stones already used in antiquity (i.e., Fior di Pesco or marmor chalcidicum, lapis porphyrites, a volcanic rock from the Egyptian Eastern Desert, Proconnesian marble from the Island of Marmara, Pavonazzetto toscano and white Carrara marble from the Italian Apuan Alps). The most frequent forms of deterioration detected are black crusts, patinas, discoloration and patterns linked to erosion processes. The interrelation of different mappings led to a number of useful considerations concerning differences in the effectiveness of maintenance procedures between public and private management of the monument

Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2

Protein intrinsic disorder (ID) is a complex and context-dependent phenomenon that covers a continuum between fully disordered states and folded states with long dynamic regions. The lack of a ground truth that fits all ID flavors and the potential for order-to-disorder transitions depending on specific conditions makes ID prediction challenging. The CAID2 challenge aimed to evaluate the performance of different prediction methods across different benchmarks, leveraging the annotation provided by the DisProt database, which stores the coordinates of ID regions when there is experimental evidence in the literature. The CAID2 challenge demonstrated varying performance of different prediction methods across different benchmarks, highlighting the need for continued development of more versatile and efficient prediction software. Depending on the application, researchers may need to balance performance with execution time when selecting a predictor. Methods based on AlphaFold2 seem to be good ID predictors but they are better at detecting absence of order rather than ID regions as defined in DisProt. The CAID2 predictors can be freely used through the CAID Prediction Portal, and CAID has been integrated into OpenEBench, which will become the official platform for running future CAID challenges

Interventional Radiology Approaches for Liver Metastases from Thyroid Cancer: A Case Series and Overview of the Literature

BACKGROUND: Liver metastases (LMs) from thyroid cancer (TC) are relatively uncommon in clinical practice and their management is challenging. Interventional radiology loco-regional treatments (LRTs), including radiofrequency ablation (RFA) and trans-arterial chemoembolization (TACE), have been successfully employed to treat LMs from various types of cancer. METHODS: We analyzed the role of LRTs in the management of unresectable LMs from differentiated and medullary TCs performed at our institution from 2015 to 2020. A review of the available English literature regarding this topic was also performed. RESULTS: Six hepatic LRTs were performed in 4 TC patients with LMs, in 2 cases after the start of treatment with a tyrosine kinase inhibitor (TKI). A partial response was obtained in 2 patients; the diameter of the largest targeted lesion was 18 mm in both of them. The remaining procedures were performed on larger lesions and a stable disease was achieved in all but one case. Acute LRT-related complications were transient and mild. In literature, the largest studies were focused on TACE in LMs from MTC, showing good tolerance and remarkable disease control, especially in case of limited liver tumour involvement. CONCLUSION: LRTs for LMs represent a valuable option for the treatment of metastatic TC in case of isolated hepatic progression or for symptoms relief, also after the start of TKI treatment as part of a multimodal approach. The best disease control is obtained when hepatic metastatic burden is limited. These procedures are generally well tolerated; however, a cautious multidisciplinary selection of the candidates is mandatory

CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins

Intrinsic disorder (ID) in proteins is well-established in structural biology, with increasing evidence for its involvement in essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published ID predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult to compare performance, confounding biologists wanting to make an informed choice. To address this issue, the Critical Assessment of protein Intrinsic Disorder (CAID) benchmarks predictors for ID and binding regions as a community blind-test in a standardized computing environment. Here we present the CAID Prediction Portal, a web server executing all CAID methods on user-defined sequences. The server generates standardized output and facilitates comparison between methods, producing a consensus prediction highlighting high-confidence ID regions. The website contains extensive documentation explaining the meaning of different CAID statistics and providing a brief description of all methods. Predictor output is visualized in an interactive feature viewer and made available for download in a single table, with the option to recover previous sessions via a private dashboard. The CAID Prediction Portal is a valuable resource for researchers interested in studying ID in proteins. The server is available at the URL: https://caid.idpcentral.org