Code-sharing policies are associated with increased reproducibility potential of ecological findings

Peer Community Journal, Год журнала: 2025, Номер 5

Опубликована: Апрель 2, 2025

Язык: Английский

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Fishing during extreme heatwaves alters ecological interactions and increases indirect fishing mortality in a ubiquitous nearshore system

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Май 12, 2025

Abstract Heatwaves may have multifaceted ecological impacts; however, field studies assessing the ramifications of nearshore fishing during heatwaves are rare. We leverage a experiment simulating clam to document such effects on ubiquitous system at land-sea interface. During monthly trials from May-September 2024, we experimentally fished clams low tide and tracked reburrowing mortality rates marked, sub-legal sized returned sediment. Half were protected crab predation estimates predator scavenger activity recorded. Clams typically reburrowed quickly was low. heatwave, appeared unhealthy, failed reburrow, suffered near-complete mortality. Predator in experimental plots >4× higher heatwave compared other months. Clam likely combined result physiological death increased predation. When put into context air temperature fishing, there clear shift 30 °C, whereby plummeted, predator/scavenger dramatically increased. These results provide situ documentation human-climate interactions influencing indirect altering dynamics, ultimately generating pertinent information for ecosystem-based fisheries management.

Язык: Английский

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Evidence for energy reallocation, not oxygen limitation, driving the deceleration in growth of adult fish

Journal of Experimental Biology, Год журнала: 2023, Номер 226(13)

Опубликована: Июнь 19, 2023

The lifetime growth of almost all fishes follows a biphasic relationship - juvenile is rapid and adult subsequently decelerates. For trend that so ubiquitous, there no general agreement as to the underlying mechanisms causing decelerate. Ongoing theories argue slows because either gills fail supply body with surplus oxygen needed for continued somatic gain (i.e. limited), or sexual maturation induces switch in energy allocation towards reproduction away from limited). Here, we empirically tested these notions by tracking individual trajectories ∼100 female Galaxias maculatus, ranging size, during their first 3 months adulthood. At summer temperature 20°C, provided subsets fish additional (fed once versus twice day), supplementary (normoxia hyperoxia), combination two, assess whether could change trajectory growth. We found improved marginally energy, yet remained unaffected oxygen, thereby providing evidence role reallocation deceleration Interestingly, dietary had disproportionately larger effect on matured at greater revealing size-dependent variance acquisition and/or budgets temperatures. Overall, findings contribute understanding driving widespread declines size climate warming.

Язык: Английский

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Welcoming More Participation in Open Data Science for the Oceans

Annual Review of Marine Science, Год журнала: 2023, Номер 16(1), С. 537 - 549

Опубликована: Июль 7, 2023

Open science is a global movement happening across all research fields. Enabled by technology and the open web, it builds on years of efforts individuals, grassroots organizations, institutions, agencies. The goal to share knowledge broaden participation in science, from early ideation making outputs openly accessible (open access). With an emphasis transparency collaboration, dovetails with increase diversity, equity, inclusion, belonging society. US Biden-Harris Administration many other government agencies have declared 2023 Year Science, providing great opportunity boost for oceans. For researchers day-to-day, critical piece modern analytical workflows increasing amounts data. Therefore, we focus this article data science-the tooling people enabling reproducible, transparent, inclusive practices data-intensive research-and its intersection marine sciences. We discuss state various dimensions argue that technical advancements outpaced our field's culture change incorporate them. Increasing inclusivity skill building are interlinked must be prioritized within community find collaborative solutions responding climate threats biodiversity

Язык: Английский

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Biomedical supervisors’ role modeling of open science practices

eLife, Год журнала: 2023, Номер 12

Опубликована: Май 22, 2023

Supervision is one important way to socialize Ph.D. candidates into open and responsible research. We hypothesized that should be more likely identify science practices (here publishing access sharing data) in empirical publications were part of a thesis when the candidates' supervisors engaged these compared those whose did not or less often did. Departing from repositories at four Dutch University Medical centers, we included 211 pairs candidates, resulting sample 2062 publications. determined status using UnpaywallR Open Data Oddpub, where also manually screened with potential data statements. Eighty-three percent our was published openly, 9% had Having supervisor who than national average associated an odds 1.99 publish access. However, this effect became nonsignificant correcting for institutions. shared 2.22 (CI:1.19-4.12) times share having not. This ratio increased 4.6 (CI:1.86-11.35) after removing false positives. The prevalence comparable international studies; rates higher. Whilst spearhead initiatives promote science, study adds value by investigating role promoting science.

Язык: Английский

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Can Siphon Hole Morphometrics Be Used for Population Assessments of Intertidal Soft-Shell Clams, Mya arenaria?

Estuaries and Coasts, Год журнала: 2024, Номер 47(8), С. 2423 - 2438

Опубликована: Июль 11, 2024

Abstract Measuring infaunal population dynamics relies on destructive sampling that disturbs sediments and removes animals from their habitat. Establishing effective, non-invasive methods for monitoring populations can reduce the impact of scientific facilitate efficient assessments. Using intertidal soft-shell clams ( Mya arenaria L.) in eastern Canada, we explored whether density size structure could be estimated visible siphon holes. Across four sites with varying sediment characteristics species assemblages, predicted presence M. 78–100% accuracy by visually assessing Smaller holes (< 7.5 mm) were more likely to misidentified. Siphon hole count was a strong predictor actual clam biomass at most sites, except site wet muddy high densities other species. length positively related shell weight all sites; however, relationships typically had low R 2 values 0.35). Ultimately, visual assessments effective estimating some habitats. Testing application this method habitats is warranted.

Язык: Английский

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Rates and predictors of data and code sharing in the medical and health sciences: A systematic review with meta-analysis of individual participant data

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 24, 2023

Objectives Many meta-research studies have investigated rates and predictors of data code sharing in medicine. However, most these been narrow scope modest size. We aimed to synthesise the findings this body research provide an accurate picture how common is, frequency has changed over time, what factors are associated with sharing. Design Systematic review meta-analysis individual participant (IPD) from studies. Data sources: Ovid MEDLINE, Embase, MetaArXiv, medRxiv, bioRxiv were searched inception July 1 st , 2021. Eligibility criteria Studies that or across a sample scientific articles presenting original medical health research. extraction synthesis Two authors independently screened records, assessed risk bias, extracted summary study reports. IPD requested when not publicly available. Key outcomes interest prevalence statements declared available, ‘available on request’ (declared availability), success retrieving products (actual availability). The associations between availability several (e.g., journal policy, type, design, subjects) also examined. A two-stage approach was performed, proportions ratios pooled using Hartung-Knapp-Sidik-Jonkman method for random-effects meta-analysis. Three-level meta-regressions performed evaluate influence publication year rate. Results 105 examining 2,121,580 31 specialties included review. Eligible examined median 195 primary (IQR: 113-475), 2015 2012-2018). Only eight (8%) classified as low bias. Useable assembled 100 (2,121,197 articles), which 94 datasets passed independent reproducibility checks. Meta-analyses revealed actual public 8% (95% CI: 5-11%, 95% PI: 0-30%, k=27, o=700,054) 2% 1-3%, 0-11%, k=25, o=11,873) respectively since 2016. Meta-regression indicated only increased significantly time. For sharing, both estimated be less than 0.5% 2016, neither demonstrated any meaningful increases 33% 5-69%, k=3, o=429) comply mandatory policies journals. Conclusion Code remains persistently medicine In contrast, declarations low, but they increasing. do always correspond data. Mandatory journals may effective expected, vary effectiveness according type - finding informative policymakers designing allocating resources audit compliance.

Язык: Английский

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Extreme original data yield extreme decline effects

PLoS Biology, Год журнала: 2023, Номер 21(2), С. e3001996 - e3001996

Опубликована: Фев. 6, 2023

Our meta-analysis showing a dramatic decline effect in ocean acidification (OA) studies on fish behavior [1] was criticized and reanalyzed by Dr. Munday [2].After applying changes to the dataset seemingly biased direction (see Supp.Data 1 at https://osf.io/7spzx/),Munday found slightly less "extreme" than original.Nonetheless, Munday's remains one of strongest examples this phenomenon ecology [3], despite claim that his "reanalysis shows there is not an extreme studies."Why still present reanalysis, why did early have such inflated sizes?The reason many papers colleagues included data are themselves, likely nonbiological origin [4].Alongside specific comments revisions our based subjective criteria (some we accept, do not; 1, Supp.Table critiques how assigned values means zero when computing sizes.Since biological rarely variances precisely zero, treating metaanalyses has been extensively explored.We agree with discussion about handle mean calculations size warranted, which elaborate upon Box 1. critique use small fractional for percentage proportional where original "artificially inflates" estimates.But context matters-the inflated" sizes derived from initial highly unlikely begin with.For example, paper Dixson [5], choice-flume experiments measuring time spent predator chemical cues yielded control OA-exposed 0% 100%, respectively, each exactly 0%.Further extremely variances, other led (e.g., [6,7]).Using bootstrapping simulations Supp.Appendix https://osf.io/7spzx/for details), behavioral extracted videos available online lab [8], demonstrate low improbable (Fig 1A -1C).These data, methods used obtain them, consistent results three publications were contain fabricated [4,9].Among these Science retracted fabrication [10].Thus, while argues estimates artificially "extreme," fact those implausible data.Indeed, as concluded analysis, factor highest explanatory power influence "authors," specifically and/or 1D and1E).

Язык: Английский

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Kinematics and behaviour in fish escape responses: guidelines for conducting, analysing and reporting experiments

Journal of Experimental Biology, Год журнала: 2023, Номер 226(14)

Опубликована: Июль 15, 2023

Work carried out since the late 1970s has provided key insights into comparative biomechanics, kinematics, behaviour and neurobiology of fish escape responses. An response is an ecologically important used by fishes to evade predation aggression via rapid swimming movements. With environmental change expected affect physiology biomechanics aquatic ectotherms, there a growing interest in understanding how stressors performance during responses, particularly context predator-prey interactions. As study continues expand, have been repeated calls standardise experiments reporting practices facilitate integrative studies. Here, we provide set practical guidelines for conducting, analysing on responses fish, including checklist assist authors undertaking these experiments. These resources will executing rigorous transparent fashion, helping advance era change.

Язык: Английский

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Reply to: Recognizing and marshalling the pre-publication error correction potential of open data for more reproducible science

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(10), С. 1595 - 1596

Опубликована: Июль 31, 2023

Язык: Английский

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