Computationally reproducing results from meta-analyses in ecology and evolutionary biology using shared code and data.

Many journals in ecology and evolutionary biology encourage or require authors to make their data and code available alongside articles. In this study we investigated how often this data and code could be used together, when both were available, to computationally reproduce results published in articles. We surveyed the data and code sharing practices of 177 meta-analyses published in ecology and evolutionary biology journals published between 2015-17: 60% of articles shared data only, 1% shared code only, and 15% shared both data and code.

Predicting and reasoning about replicability using structured groups.

This paper explores judgements about the replicability of social and behavioural sciences research and what drives those judgements. Using a mixed methods approach, it draws on qualitative and quantitative data elicited from groups using a structured approach called the IDEA protocol ('investigate', 'discuss', 'estimate' and 'aggregate'). Five groups of five people with relevant domain expertise evaluated 25 research claims that were subject to at least one replication study.

1,3-butadiene: cancer, mutations, and adducts. Part IV: Molecular dosimetry of 1,3-butadiene.

Analysis of N7-guanine adducts derived from 1,3-butadiene (BD) was conducted with use of liquid chromatography-mass spectrometry (LC-MS) in combination with stable isotope methods. The N7-guanine adducts were shown to undergo spontaneous depurination from DNA in vitro in both calf-thymus DNA and TK6-cell DNA. A comparison was made between BD-derived N7-guanine adduct concentrations both in liver DNA and urine of rats and mice exposed to BD.

Persistence of N7-(2,3,4-trihydroxybutyl)guanine adducts in the livers of mice and rats exposed to 1,3-butadiene.

Liquid chromatography (LC) in combination with tandem mass spectrometry (MS/MS) and stable isotope methodology was employed for the analysis of the N7-guanine (Gua) adducts derived from 1,2:3, 4-diepoxybutane (BDO2) a reactive metabolite of 1,3-butadiene (BD). Two diastereomeric forms of N7-(2,3,4-trihydroxybutyl)guanine (THBG) were identified in the livers of both mice and rats. One of the diastereomers [(+/-)-THBG] was formed by reaction of DNA with (+/-)-BDO2, and the other diastereomer (meso-THBG) was formed by reaction of DNA with meso-BDO2.

Liquid chromatography/electrospray ionization tandem mass spectroscopy (LC/ESI MS/MS) analysis of 1,2-epoxybutene adducts of purine deoxynucleosides.

Calf thymus DNA was reacted with 1,2-epoxybutene (BDO) in phosphate buffered saline at 37 degrees C for 12 h. DNA was ethanol precipitated and hydrolyzed with 1 M HCl to release DNA bases. Adenine (A)-BDO and guanine (Gua)-BDO adducts were analyzed in the ethanol supernatant and DNA hydrolysate using LC/ESI MS/MS.