Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data

We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems’ responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension

SPIRITS: Uncovering Unusual Infrared Transients with Spitzer

We present an ongoing, five-year systematic search for extragalactic infrared transients, dubbed SPIRITS—SPitzer InfraRed Intensive Transients Survey. In the first year, using Spitzer/IRAC, we searched 190 nearby galaxies with cadence baselines of one month and six months. We discovered over 1958 variables and 43 transients. Here, we describe the survey design and highlight 14 unusual infrared transients with no optical counterparts to deep limits, which we refer to as SPRITEs (eSPecially Red Intermediate-luminosity Transient Events). SPRITEs are in the infrared luminosity gap between novae and supernovae, with [4.5] absolute magnitudes between −11 and −14 (Vega-mag) and [3.6]–[4.5] colors between 0.3 mag and 1.6 mag. The photometric evolution of SPRITEs is diverse, ranging from 7 mag yr−1. SPRITEs occur in star-forming galaxies. We present an in-depth study of one of them, SPIRITS 14ajc in Messier 83, which shows shock-excited molecular hydrogen emission. This shock may have been triggered by the dynamic decay of a non-hierarchical system of massive stars that led to either the formation of a binary or a protostellar merger

Derivation of Ecologically Based Soil Standards for Trace Elements

A comprehensive and practical overview of the state of the science, Soil Quality Standards for Trace Elements: Derivation, Implementation, and Interpretation addresses the derivation of soil quality standards for trace elements and the implementation of these standards within regulatory and risk assessment frameworks. Forty experts from 11 countries across Europe, Asia, and North America—a multidisciplinary group of government policy makers and regulators, academics, industry representatives, and consultants—provide a focused discussion on the science and methods underpinning the derivation of soil quality standards for trace elements. Outlines the supporting science for setting environmental and human health standards Covers the application and practical use of soil quality standards for trace elements Contains recommendations on the development and use of soil quality standards for trace elements Identifies best practices in accounting for (bio)availability and exposure modelling in standard setting for soils The book provides a clear description of how to derive and implement soil quality standards for trace elements in order to assess human and environmental risks. It covers scientific developments useful for resolving discrepancies in the setting and implementation of soil quality standards. It provides useful tips, including do's, and don'ts on how to deal with issues such as variation of the natural background and soil type dependent toxicity

Taxonomy and species boundaries in the coral genus Favia Milne Edwards and Haime, 1857 (Cnidaria: Scleractinia) from Thailand revealed by morphological and genetic data

While Faviidae is a widely and uniformly distributed coral family throughout the Indo-Pacific, the extensive phenotypic plasticity of colony surface and corallite features often confounds the use of macromorphological characters in species identification, and contributes to conflict between traditional classification and molecular analyses of the group. Recent advances in morphological and molecular techniques now provide a suite of methods to re-address coral taxonomy in complex groups, such as that represented by the Faviidae. This study combines morphologic measurements including "3D coordinates landmarks" data with phylogenetic assessments of nuclear (ITS) and mitochondrial (COI-trnM) DNA to assess species boundaries in nine species of Faviidae with para-septothecal walls from Thailand. Strong concordance was found between morphological features and a priori groupings based on both morphospecies and genetically defined groups (ITS and COI-trnM). Favia truncatus was the most well-defined species based on morphological analyses, and it was also shown to be monophyletic using phylogenetic analyses. Besides F. truncatus, the only other species that was found to be monophyletic in analyses of both genes was F. cf. helianthoides, but its skeletal morphology overlapped with the F. favus species complex (comprised of F. favus, F. speciosa, F. matthaii and F. rotumana). Although not genetically monophyletic, the F. favus species complex and F. pallida were fairly well delineated morphologically. Morphospecies within the F. favus species complex are therefore possibly a result of genetic drift and/or stable polymorphisms driven by divergent selection. These results represent a first step toward a taxonomic revision of the Indo-Pacific Favia, which will integrate morphological methods with the study of type material, genetic information, reproductive data, and tests of phenotypic plasticity-given that multiple lines of evidence are needed to resolve ambiguous species and assign species names