Search

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. In each of the articles which had shared both (n = 26), we selected a target result and attempted to reproduce it. Using the shared data and code files, we successfully reproduced the targeted results in 27-73% of the 26 articles, depending on the stringency of the criteria applied for a successful reproduction. The results from this sample of meta-analyses in the 2015-17 literature can provide a benchmark for future meta-research studies gauging the computational reproducibility of published research in ecology and evolutionary biology., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Kambouris et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

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. Participants assessed the probability that each of the 25 research claims would replicate (i.e. that a replication study would find a statistically significant result in the same direction as the original study) and described the reasoning behind those judgements. We quantitatively analysed possible correlates of predictive accuracy, including self-rated expertise and updating of judgements after feedback and discussion. We qualitatively analysed the reasoning data to explore the cues, heuristics and patterns of reasoning used by participants. Participants achieved 84% classification accuracy in predicting replicability. Those who engaged in a greater breadth of reasoning provided more accurate replicability judgements. Some reasons were more commonly invoked by more accurate participants, such as 'effect size' and 'reputation' (e.g. of the field of research). There was also some evidence of a relationship between statistical literacy and accuracy., Competing Interests: We declare we have no competing interests., (© 2023 The Authors.)

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. This has provided insight into the exposure of the animals to 1,2-epoxy-3-butene (BDO), 1,2,3,4-diepoxybutane (BDO2), and 1,2-dihydroxy-3,4-epoxybutane (BDO-diol), the three oxidative metabolites of BD thought to be responsible for BD-mediated carcinogenesis. The liver DNA of mice contained more of the two N7-guanine adducts of BDO--N7-2-hydroxy-3-butenyl-1-guanine (2HB1G) and N7-1-hydroxy-3-butenyl-2-guanine (1HB2G)--than the amounts in rats during the 10-day BD exposure and the 6 days after exposure that were monitored. An excess of 1HB2G over 2HB1G by a factor of approximately 10 in the rat liver and a factor of approximately 5 in the mouse liver was also observed. This regioselective difference was apparent during both the 10-day exposure and the 6 days after exposure. The half-lives of 2HB1G and 1HB2G were estimated as 4.3 days and 3.5 days, respectively, in the DNA of BD-exposed mice and rats. Higher amounts of 2HB1G and 1HB2G appeared in rat urine compared with mouse urine after the 10-day exposure to 1,250 ppm BD. Analysis of liver DNA for N7-guanine adducts derived from BDO2 revealed the presence of two diastereomeric forms of N7-(2,3,4-trihydroxybutyl)-1-guanine (THBG). One of the diastereomers [(+/-)-THBG] was formed by reaction of DNA with (+/-)-BDO2 or BDO-diol, and the other diastereomer (meso-THBG) was formed by reaction of DNA with meso-BDO2 or BDO-diol. There was more (+/-)-THBG and meso-THBG in liver DNA of mice compared with amounts in rats during the 10 days of BD exposure and the 6 days after exposure. A twofold excess of (+/-)-THBG over meso-THBG in rat liver was found at all of the time points monitored. After 10 days of exposure to BD, (+/-)-THBG in mouse liver was also present in an almost twofold excess over meso-THBG. At 6 days after exposure to BD, however, (+/-)-THBG and meso-THBG were present in almost equal amounts in mouse liver. Furthermore, amounts of the two THBG diastereomers in mouse liver 6 days after exposure to BD were almost fivefold greater than amounts in rat liver. The half-lives of (+/-)-THBG and meso-THBG appeared to be longer in mouse liver (4.1 days and 5.5 days, respectively) than in rat liver (3.6 days and 4.0 days, respectively). Higher amounts of (+/-)-THBG were excreted in rat urine compared with mouse urine. It is noteworthy that each of the N7-guanine adducts derived from BD was present in higher concentrations in the liver DNA of mice exposed to 1,250 ppm BD than in the liver DNA of rats exposed to the same dose. Conversely, each of the adducts was present in higher concentrations in the urine of rats compared with the urine of mice after exposure to 1,250 ppm BD.

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. Reaction of BDO with A resulted in the formation of seven A-BDO adducts with MH+ ions at m/z 206. Two of these adducts were observed in the ethanol supernatant. In addition, two formaidopyrimidine (FAPY)-adducts were detected with MH+ ions at m/z 224 in DNA hydrolysate. These data are consistent with formation of regioisomeric N-7 or N-9 adducts which can be released by spontaneous depurination or ring opening. Four other A-BDO adducts were detected in DNA hydrolysate. Similar adducts were observed for Gua. This new methodology permits simultaneous determination of initially formed adducts as well as those arising as a consequence of depurination. The latter adducts provide the opportunity for monitoring exposure to BDO through analysis of N-7 or N-3 adducts excreted in the urine.