fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences

Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.

Supplemental Material: Progressive accretion recorded in sedimentary rocks of the 3.28–3.23 Ga Fig Tree Group, Barberton Greenstone Belt

Supplemental File S1: Additional figures; Supplemental File S2: List of dated tuffs of the Fig Tree Group; Supplemental File S3: U-Pb geochronological data; Supplemental File S4: Mudstone geochemical data.

Introduction to statistical simulations in health research

In health research, statistical methods are frequently used to address a wide variety of research questions. For almost every analytical challenge, different methods are available. But how do we choose between different methods and how do we judge whether the chosen method is appropriate for our specific study? Like in any science, in statistics, experiments can be run to find out which methods should be used under which circumstances. The main objective of this paper is to demonstrate that simulation studies, that is, experiments investigating synthetic data with known properties, are an invaluable tool for addressing these questions. We aim to provide a first introduction to simulation studies for data analysts or, more generally, for researchers involved at different levels in the analyses of health data, who (1) may rely on simulation studies published in statistical literature to choose their statistical methods and who, thus, need to understand the criteria of assessing the validity and relevance of simulation results and their interpretation; and/or (2) need to understand the basic principles of designing statistical simulations in order to efficiently collaborate with more experienced colleagues or start learning to conduct their own simulations. We illustrate the implementation of a simulation study and the interpretation of its results through a simple example inspired by recent literature, which is completely reproducible using the R-script available from online supplemental file 1.

Supplemental Material: Evidence for a late glacial advance near the beginning of the Younger Dryas in western New York State: An event postdating the record for local Laurentide ice sheet recession

An extended discussion relating to the identification of glacial tills at the critical sites in this investigation is provided as a Supplemental File to eliminate any concerns that the exposures might be landslide debris as opposed to primary glacial till. The supplement also speculates as to why the advance in western New York State may not have been obvious in the extensive research published for the St. Lawrence Valley.

Supplemental Material: Evidence for a late glacial advance near the beginning of the Younger Dryas in western New York State: An event postdating the record for local Laurentide ice sheet recession

An extended discussion relating to the identification of glacial tills at the critical sites in this investigation is provided as a Supplemental File to eliminate any concerns that the exposures might be landslide debris as opposed to primary glacial till. The supplement also speculates as to why the advance in western New York State may not have been obvious in the extensive research published for the St. Lawrence Valley.

Supplemental material: Detrital zircon U-Pb geochronology and Hf isotope geochemistry of Paleozoic and Triassic passive margin strata of western North America

Geosphere, February 2014, v. 10, p. 49-65, doi:10.1130/GES00889.1, Supplemental File 1 - Analytical methods file (32 pages, 20 figures). File size is ~6.7 MB.

Humanity and the 21st century’s resource gauntlet: a commentary on Ripple et al.’s article “World Scientists’ Warning to Humanity: a Second Notice”

The 21st century will undeniably represent a major turn in the development of human societies, as Earth’s limiting resources can no longer support the current pace of material consumption (supplemental file S1). In this context, Ripple et al. (2017) identified thirteen critical shifts in our ways of life to reduce humanity’s ecological footprint and achieve sustainable development. While we endorse the pertinence and urgency of this call, we direct attention to critical shortcomings in the proposed solutions, which limit their potential to promote sustainability. Indeed, several prescriptions in Ripple et al. address symptoms rather than root causes, or seem to result from a simplistic consideration of inherently complex processes. We emphasize the importance of accounting for historical patterns and underlying drivers of the global socio-economic system, especially in relation to wealth inequality, human demography, and food production, which need deeper consideration than presently given in the warning and subsequent follow-up articles. Without such considerations, this second warning to humanity can be interpreted as prescriptive suggestions from a narrow, western-biased vision of the global socio-ecosystem, rendering it all but ineffective.

Humanity and the 21st century’s resource gauntlet: a commentary on Ripple et al.’s article “World Scientists’ Warning to Humanity: a Second Notice”

The 21st century will undeniably represent a major turn in the development of human societies, as Earth’s limiting resources can no longer support the current pace of material consumption (supplemental file S1). In this context, Ripple et al. (2017) identified thirteen critical shifts in our ways of life to reduce humanity’s ecological footprint and achieve sustainable development. While we endorse the pertinence and urgency of this call, we direct attention to critical shortcomings in the proposed solutions, which limit their potential to promote sustainability. Indeed, several prescriptions in Ripple et al. address symptoms rather than root causes, or seem to result from a simplistic consideration of inherently complex processes. We emphasize the importance of accounting for historical patterns and underlying drivers of the global socio-economic system, especially in relation to wealth inequality, human demography, and food production, which need deeper consideration than presently given in the warning and subsequent follow-up articles. Without such considerations, this second warning to humanity can be interpreted as prescriptive suggestions from a narrow, western-biased vision of the global socio-ecosystem, rendering it all but ineffective.