Homology-based inference sets the bar high for protein function prediction

Background: Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference. Methods: Here, we describe a few methods that predict protein function exclusively through homology. Together, they set the bar or lower limit for future improvements. Results and conclusions: During the development of these methods, we faced two surprises. Firstly, our most successful implementation for the baseline ranked very high at CAFA1. In fact, our best combination of homology-based methods fared only slightly worse than the top-of-the-line prediction method from the Jones group. Secondly, although the concept of homology-based inference is simple, this work revealed that the precise details of the implementation are crucial: not only did the methods span from top to bottom performers at CAFA, but also the reasons for these differences were unexpected. In this work, we also propose a new rigorous measure to compare predicted and experimental annotations. It puts more emphasis on the details of protein function than the other measures employed by CAFA and may best reflect the expectations of users. Clearly, the definition of proper goals remains one major objective for CAFA

Principles of cartilage tissue engineering in TMJ reconstruction

Diseases and defects of the temporomandibular joint (TMJ), compromising the cartilaginous layer of the condyle, impose a significant treatment challenge. Different regeneration approaches, especially surgical interventions at the TMJ's cartilage surface, are established treatment methods in maxillofacial surgery but fail to induce a regeneration ad integrum. Cartilage tissue engineering, in contrast, is a newly introduced treatment option in cartilage reconstruction strategies aimed to heal cartilaginous defects. Because cartilage has a limited capacity for intrinsic repair, and even minor lesions or injuries may lead to progressive damage, biological oriented approaches have gained special interest in cartilage therapy. Cell based cartilage regeneration is suggested to improve cartilage repair or reconstruction therapies. Autologous cell implantation, for example, is the first step as a clinically used cell based regeneration option. More advanced or complex therapeutical options (extracorporeal cartilage engineering, genetic engineering, both under evaluation in pre-clinical investigations) have not reached the level of clinical trials but may be approached in the near future. In order to understand cartilage tissue engineering as a new treatment option, an overview of the biological, engineering, and clinical challenges as well as the inherent constraints of the different treatment modalities are given in this paper

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Resplendence of al-Andalus: exchange and transfer processes in Mudéjar and neo-Moorish Architecture

This contribution presents preliminary results of the research project Mudejarismo and Moorish Revival in Europe (2014–2018), funded by the Swiss National Science Foundation and based at the University of Zurich. By focusing on the appropriation of Hispano-Islamic architecture and ornaments in Christian and Jewish contexts, the seven sub-chapters examine the underlying exchange and transfer processes in the Middle Ages and the Modern period, in relation to the complex and multi-faceted phenomena of cross-cultural appropriation and hybridization, as well as the current debates on otherness and national identity

Resplendence of al-Andalus: Exchange and Transfer Processes in Mudéjar and Neo-Moorish Architecture

This contribution presents preliminary results of the research project Mudejarismo and Moorish Revival in Europe (2014-2018), funded by the Swiss National Science Foundation and based at the University of Zurich. By focusing on the appropriation of Hispano-Islamic architecture and ornaments in Christian and Jewish contexts, the seven sub-chapters examine the underlying exchange and transfer processes in the Middle Ages and the Modern period, in relation to the complex and multi-faceted phenomena of cross-cultural appropriation and hybridization, as well as the current debates on otherness and national identity