ProteinBERT: A universal deep-learning model of protein sequence and function

Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis. We introduce ProteinBERT, a deep language model specifically designed for proteins. Our pretraining scheme consists of masked language modeling combined with a novel task of Gene Ontology (GO) annotation prediction. We introduce novel architectural elements that make the model highly efficient and flexible to very large sequence lengths. The architecture of ProteinBERT consists of both local and global representations, allowing end-to-end processing of these types of inputs and outputs. ProteinBERT obtains state-of-the-art performance on multiple benchmarks covering diverse protein properties (including protein structure, post translational modifications and biophysical attributes), despite using a far smaller model than competing deep-learning methods. Overall, ProteinBERT provides an efficient framework for rapidly training protein predictors, even with limited labeled data. Code and pretrained model weights are available at https://github.com/nadavbra/protein_bert.

The influence of landscape context on the production of cultural ecosystem services

Context: Recent efforts to apply sustainability concepts to entire landscapes have seen increasing interest in approaches that connect socioeconomic and biophysical aspects of landscape change. Evaluating these connections through a cultural ecosystem services lens clarifies how different spatiotemporal scales and levels of organisation influence the production of cultural benefits. Currently, however, the effects of multi-level and multi-scale ecological variation on the production of cultural benefits have not yet been disentangled.Objectives: To quantify the amount of variation in cultural ecosystem service provision by birds to birders that is due to landscape-level attributes.Methods: We used data from 293 birding routes and 101 different birders in South African National Parks to explore the general relationships between birder responses to bird species and environmental conditions, bird-related observations, the biophysical attributes of the landscape and their effect on bird-related cultural benefits.Results: Biophysical attributes (particularly biome, vegetation type, and variance in elevation) significantly increased the percentage of variance explained in birder benefits from 57–65%, demonstrating that birder benefits are derived from multi-level (birds to ecosystems) and multi-scale (site to landscape) social and ecological interactions.Conclusions: Landscape attributes influence people’s perceptions of cultural ecosystem service provision by individual species. Recognition of the complex, localised and inextricable linkage of cultural ecosystem services to biophysical attributes can improve our understanding of the landscape characteristics that affect the supply and demand of cultural ecosystem services.

Whispering tales: using augmented reality to enhance cultural landscapes and indigenous values

© The Author(s) 2019. Increasingly, our built and natural environments are becoming hybrids of real and digital entities where objects, buildings and landscapes are linked online in websites, blogs and texts. In the case of Aotearoa New Zealand, modern lifestyles have put Māori Indigenous oral narratives at risk of being lost in a world dominated by text and digital elements. Intangible values, transmitted orally from generation to generation, provide a sense of identity and community to Indigenous Māori as they relate and experience the land based on cultural, spiritual, emotion, physical and social values. Retaining the storytelling environment through the use of augmented reality, this article extends the biophysical attributes of landscape through embedded imagery and auditory information. By engaging with Ngāti Kahungunu ki Wairarapa, a design approach has been developed to illustrate narratives through different media, in a way that encourages a deeper and broader bicultural engagement with landscape.

Whispering tales: using augmented reality to enhance cultural landscapes and indigenous values

© The Author(s) 2019. Increasingly, our built and natural environments are becoming hybrids of real and digital entities where objects, buildings and landscapes are linked online in websites, blogs and texts. In the case of Aotearoa New Zealand, modern lifestyles have put Māori Indigenous oral narratives at risk of being lost in a world dominated by text and digital elements. Intangible values, transmitted orally from generation to generation, provide a sense of identity and community to Indigenous Māori as they relate and experience the land based on cultural, spiritual, emotion, physical and social values. Retaining the storytelling environment through the use of augmented reality, this article extends the biophysical attributes of landscape through embedded imagery and auditory information. By engaging with Ngāti Kahungunu ki Wairarapa, a design approach has been developed to illustrate narratives through different media, in a way that encourages a deeper and broader bicultural engagement with landscape.

The basement membrane as a structured surface – role in vascular health and disease

ABSTRACTThe basement membrane (BM) is a thin specialized extracellular matrix that functions as a cellular anchorage site, a physical barrier and a signaling hub. While the literature on the biochemical composition and biological activity of the BM is extensive, the central importance of the physical properties of the BM, most notably its mechanical stiffness and topographical features, in regulating cellular function has only recently been recognized. In this Review, we focus on the biophysical attributes of the BM and their influence on cellular behavior. After a brief overview of the biochemical composition, assembly and function of the BM, we describe the mechanical properties and topographical structure of various BMs. We then focus specifically on the vascular BM as a nano- and micro-scale structured surface and review how its architecture can modulate endothelial cell structure and function. Finally, we discuss the pathological ramifications of the biophysical properties of the vascular BM and highlight the potential of mimicking BM topography to improve the design of implantable endovascular devices and advance the burgeoning field of vascular tissue engineering.