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Biology subjects

Reynolds, G.

Publications and source records attributed to Reynolds, G..

3 recordsLinked to original sources

The mechanical stability of the worlds tallest broadleaf trees

The factors that limit the maximum height of trees, whether ecophysiological or mechanical, are the subject of longstanding debate. Here we examine the role of mechanical stability in limiting tree height and focus on trees from the tallest tropical forests on Earth, in Sabah, Malaysian Borneo, including the recently discovered tallest tropical tree, a 100.8 m Shorea faguetiana. We use terrestrial laser scans, in situ strain gauge data and finite-element simulations to map the architecture of tall broadleaf trees and monitor their response to wind loading. We demonstrate that a trees risk of breaking due to gravity or self-weight decreases with tree height and is much more strongly affected by tree architecture than by material properties. In contrast, wind damage risk increases with tree height despite the larger diameters of tall trees, resulting in a U-shaped curve of mechanical risk with tree height. The relative rarity of extreme wind speeds in north Borneo may be the reason it is home to the tallest trees in the tropics.

ecology

Decoding the development of the blood and immune systems during human fetal liver haematopoiesis

Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells/multipotent progenitors (HSC/MPPs), yet remains poorly defined in humans. Using single cell transcriptome profiling of ~133,000 fetal liver and ~65,000 fetal skin and kidney cells, we identify the repertoire of blood and immune cells in first and early second trimesters of development. From this data, we infer differentiation trajectories from HSC/MPPs, and evaluate the impact of tissue microenvironment on blood and immune cell development. We predict coupling of mast cell differentiation with erythro-megakaryopoiesis and identify physiological erythropoiesis in fetal skin. We demonstrate a shift in fetal liver haematopoietic composition during gestation away from being erythroid-predominant, accompanied by a parallel change in HSC/MPP differentiation potential, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a valuable reference for understanding and harnessing the therapeutic potential of HSC/MPPs.

developmental biology

PPPred: Classifying Protein-phenotype Co-mentions Extracted from Biomedical Literature

The MEDLINE database provides an extensive source of scientific articles and heterogeneous biomedical information in the form of unstructured text. One of the most important knowledge present within articles are the relations between human proteins and their phenotypes, which can stay hidden due to the exponential growth of publications. This has presented a range of opportunities for the development of computational methods to extract these biomedical relations from the articles. However, currently, no such method exists for the automated extraction of relations involving human proteins and human phenotype ontology (HPO) terms. In our previous work, we developed a comprehensive database composed of all co-mentions of proteins and phenotypes. In this study, we present a supervised machine learning approach called PPPred (Protein-Phenotype Predictor) for classifying the validity of a given sentence-level co-mention. Using an in-house developed gold standard dataset, we demonstrate that PPPred significantly outperforms several baseline methods. This two-step approach of co-mention extraction and classification constitutes a complete biomedical relation extraction pipeline for extracting protein-phenotype relations.\n\nCCS CONCEPTS*Computing methodologies [->] Information extraction; Supervised learning by classification; *Applied computing [->]Bioinformatics;

bioinformatics