A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.

Low coverage 'genome-skims' are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections.

Mayfly taxonomy (Arthropoda: Hexapoda: Ephemeroptera) during the first two decades of the twenty-first century and the concentration of taxonomic publishing.

The twentieth anniversary of the first issue of Zootaxa (De Moraes Freire, 2001) provides an appropriate opportunity to reflect on some trends in global Ephemeroptera taxonomy publishing over the last two decades, with a focus on the description of new species and the outsized role of the journals Zootaxa and ZooKeys, in particular. Detailed reviews of world Ephemeroptera knowledge up to about 2000 were collected in a series of nine papers from a symposium on the subject, published together in the proceedings of the ninth International Conference on Ephemeroptera (Domínguez 2001). Domínguez Dos Santos (2014) provided updates and analysis for South America up to the year 2012.

BioAcoustica: a free and open repository and analysis platform for bioacoustics.

We describe an online open repository and analysis platform, BioAcoustica (http://bio.acousti.ca), for recordings of wildlife sounds.

Singing from the grave: DNA from a 180 year old type specimen confirms the identity of Chrysoperla carnea (Stephens).

Historically serving as repositories for morphologically-based taxonomic research, natural history collections are now increasingly being targeted in studies utilizing DNA data. The development of advanced molecular techniques has facilitated extraction of useable DNA from old specimens, including type material. Sequencing diagnostic molecular markers from type material enables accurate species designation, especially where modern taxonomic hypotheses confirm morphologically cryptic species complexes.

An electrically-activated dynamic tissue-equivalent phantom for assessment of diffuse optical imaging systems.

A novel design of solid dynamic phantom with tissue-like optical properties is presented, which contains variable regions of contrast which are activated electrically. Reversible changes in absorption are produced by localized heating of targets impregnated with thermochromic pigment. A portable, battery-operated prototype has been constructed, and its optical and temporal characteristics have been investigated.

A soft deformable tissue-equivalent phantom for diffuse optical tomography.

A recipe is presented for the manufacture of highly compressible phantoms for diffuse optical tomography. The recipe is based on polyvinyl alcohol (PVA) slime, a viscoelastic fluid which readily deforms under moderate pressure. Scattering particles and absorbing compounds can be added to provide a uniform material with stable and reproducible optical properties.

Photolysis of methylethyl, diethyl and methylvinyl ketones and their role in the atmospheric HOx budget.

Quantum yields for acyl (RCO) radical production from ketone photolysis as a function of temperature, pressure and the atmospherically relevant wavelengths (308 and 320 nm) have been determined for methylethyl ketone (MEK), methylvinyl ketone (MVK) and diethyl ketone (DEK) via direct observation of the OH product from the RCO + O2 reaction. The methodology has been applied previously to acetone photolysis. The kinetics and OH yields of the RCO + O2 reactions have been investigated to demonstrate that this technique can be used to monitor the dissociation of higher ketones.