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Aim: Previous research has shown patients and the public in Australia generally support medical researchers in making de-identified research data available to other scientists. However, this research has focussed on certain types of data and recipients. We surveyed Australians affected by cancer to characterize their attitudes toward the sharing of research data with multiple third parties, including the public., Methods: A short, anonymous online survey of Australians with a previous diagnosis of cancer was advertised between October 27, 2022, and February 27, 2023. Quantitative responses were analyzed with descriptive statistics. Free-text responses were coded deductively and summarised using content analysis., Results: In total, 551 respondents contributed data to the survey. There was strong support for cancer researchers sharing non-human and de-identified human research data with clinicians (90% and 95%, respectively) and non-profit researchers (both 94%). However, fewer participants supported sharing data with for-profit researchers (both 64%) or publicly (both 61%). When asked if they would hypothetically consent to researchers at their treatment location using and sharing their de-identified data publicly, only half agreed. In contrast, after being shown a visual representation of the de-identified survey data, 80% of respondents supported sharing it publicly., Conclusion: Australians affected by cancer support the sharing of research data, particularly with clinicians and non-profit researchers. Our results also imply that visualization of the data to be shared may enhance support for making it publicly available. These results should help alleviate any concerns about research participants' attitudes toward data sharing, as well as boost researchers' motivation for sharing., (© 2024 The Authors. Asia‐Pacific Journal of Clinical Oncology published by John Wiley & Sons Australia, Ltd.)

Top carnivores can influence the structure of ecological communities, primarily through competition and predation; however, communities are also influenced by bottom-up forces such as anthropogenic habitat disturbance. Top carnivore declines will likely alter competitive dynamics within and amongst sympatric carnivore species. Increasing intraspecific competition is generally predicted to drive niche expansion and/or individual specialisation, while interspecific competition tends to constrain niches. Using stable isotope analysis of whiskers, we studied the effects of Tasmanian devil Sarcophilus harrisii declines upon the population- and individual-level isotopic niches of Tasmanian devils and sympatric spotted-tailed quolls Dasyurus maculatus subsp. maculatus. We investigated whether time since the onset of devil decline (a proxy for severity of decline) and landscape characteristics affected the isotopic niche breadth and overlap of devil and quoll populations. We quantified individual isotopic niche breadth for a subset of Tasmanian devils and spotted-tailed quolls and assessed whether between-site population niche variation was driven by individual-level specialisation. Tasmanian devils and spotted-tailed quolls demonstrated smaller population-level isotopic niche breadths with increasing human-modified habitat, while time since the onset of devil decline had no effect on population-level niche breadth or interspecific niche overlap. Individual isotopic niche breadths of Tasmanian devils and spotted-tailed quolls were narrower in human-modified landscapes, likely driving population isotopic niche contraction, however, the degree of individuals' specialisation relative to one another remained constant. Our results suggest that across varied landscapes, mammalian carnivore niches can be more sensitive to the bottom-up forces of anthropogenic habitat disturbance than to the top-down effects of top carnivore decline., (© 2024. The Author(s).)

Coevolution is common and frequently governs host-pathogen interaction outcomes. Phenotypes underlying these interactions often manifest as the combined products of the genomes of interacting species, yet traditional quantitative trait mapping approaches ignore these intergenomic interactions. Devil facial tumor disease (DFTD), an infectious cancer afflicting Tasmanian devils ( Sarcophilus harrisii ), has decimated devil populations due to universal host susceptibility and a fatality rate approaching 100%. Here, we used a recently developed joint genome-wide association study (i.e., co-GWAS) approach, 15 y of mark-recapture data, and 960 genomes to identify intergenomic signatures of coevolution between devils and DFTD. Using a traditional GWA approach, we found that both devil and DFTD genomes explained a substantial proportion of variance in how quickly susceptible devils became infected, although genomic architectures differed across devils and DFTD; the devil genome had fewer loci of large effect whereas the DFTD genome had a more polygenic architecture. Using a co-GWA approach, devil-DFTD intergenomic interactions explained ~3× more variation in how quickly susceptible devils became infected than either genome alone, and the top genotype-by-genotype interactions were significantly enriched for cancer genes and signatures of selection. A devil regulatory mutation was associated with differential expression of a candidate cancer gene and showed putative allele matching effects with two DFTD coding sequence variants. Our results highlight the need to account for intergenomic interactions when investigating host-pathogen (co)evolution and emphasize the importance of such interactions when considering devil management strategies., Competing Interests: Competing interests statement:The authors declare no competing interest.

The world's largest extant carnivorous marsupial, the Tasmanian devil, is challenged by Devil Facial Tumor Disease (DFTD), a fatal, clonally transmitted cancer. In two decades, DFTD has spread across 95% of the species distributional range. A previous study has shown that factors such as season, geographic location, and infection with DFTD can impact the expression of immune genes in Tasmanian devils. To date, no study has investigated within-individual immune gene expression changes prior to and throughout the course of DFTD infection. To explore possible changes in immune response, we investigated four locations across Tasmania that differed in DFTD exposure history, ranging between 2 and >30 years. Our study demonstrated considerable complexity in the immune responses to DFTD. The same factors (sex, age, season, location and DFTD infection) affected immune gene expression both across and within devils, although seasonal and location specific variations were diminished in DFTD affected devils. We also found that expression of both adaptive and innate immune genes starts to alter early in DFTD infection and continues to change as DFTD progresses. A novel finding was that the lower expression of immune genes MHC-II, NKG2D and CD8 may predict susceptibility to earlier DFTD infection. A case study of a single devil with regressed tumor showed opposite/contrasting immune gene expression patterns compared to the general trends observed across devils with DFTD infection. Our study highlights the complexity of DFTD's interactions with the host immune system and the need for long-term studies to fully understand how DFTD alters the evolutionary trajectory of devil immunity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Raven, Klaassen, Madsen, Jones, Hamilton, Ruiz-Aravena, Thomas, Hamede and Ujvari.)

Background: Despite wide recognition of the benefits of sharing research data, public availability rates have not increased substantially in oncology or medicine more broadly over the last decade., Methods: We surveyed 285 cancer researchers to determine their prior experience with sharing data and views on known drivers and inhibitors., Results: We found that 45% of respondents had shared some data from their most recent empirical publication, with respondents who typically studied non-human research participants, or routinely worked with human genomic data, more likely to share than those who did not. A third of respondents added that they had previously shared data privately, with 74% indicating that doing so had also led to authorship opportunities or future collaborations for them. Journal and funder policies were reported to be the biggest general drivers toward sharing, whereas commercial interests, agreements with industrial sponsors and institutional policies were the biggest prohibitors. We show that researchers' decisions about whether to share data are also likely to be influenced by participants' desires., Conclusions: Our survey suggests that increased promotion and support by research institutions, alongside greater championing of data sharing by journals and funders, may motivate more researchers in oncology to share their data.

Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Objectives: To synthesise research investigating data and code sharing in medicine and health to establish an accurate representation of the prevalence of sharing, how this frequency has changed over time, and what factors influence availability., Design: Systematic review with meta-analysis of individual participant data., Data Sources: Ovid Medline, Ovid Embase, and the preprint servers medRxiv, bioRxiv, and MetaArXiv were searched from inception to 1 July 2021. Forward citation searches were also performed on 30 August 2022., Review Methods: Meta-research studies that investigated data or code sharing across a sample of scientific articles presenting original medical and health research were identified. Two authors screened records, assessed the risk of bias, and extracted summary data from study reports when individual participant data could not be retrieved. Key outcomes of interest were the prevalence of statements that declared that data or code were publicly or privately available (declared availability) and the success rates of retrieving these products (actual availability). The associations between data and code availability and several factors (eg, journal policy, type of data, trial design, and human participants) were also examined. A two stage approach to meta-analysis of individual participant data was performed, with proportions and risk ratios pooled with the Hartung-Knapp-Sidik-Jonkman method for random effects meta-analysis., Results: The review included 105 meta-research studies examining 2 121 580 articles across 31 specialties. Eligible studies examined a median of 195 primary articles (interquartile range 113-475), with a median publication year of 2015 (interquartile range 2012-2018). Only eight studies (8%) were classified as having a low risk of bias. Meta-analyses showed a prevalence of declared and actual public data availability of 8% (95% confidence interval 5% to 11%) and 2% (1% to 3%), respectively, between 2016 and 2021. For public code sharing, both the prevalence of declared and actual availability were estimated to be <0.5% since 2016. Meta-regressions indicated that only declared public data sharing prevalence estimates have increased over time. Compliance with mandatory data sharing policies ranged from 0% to 100% across journals and varied by type of data. In contrast, success in privately obtaining data and code from authors historically ranged between 0% and 37% and 0% and 23%, respectively., Conclusions: The review found that public code sharing was persistently low across medical research. Declarations of data sharing were also low, increasing over time, but did not always correspond to actual sharing of data. The effectiveness of mandatory data sharing policies varied substantially by journal and type of data, a finding that might be informative for policy makers when designing policies and allocating resources to audit compliance., Systematic Review Registration: Open Science Framework doi:10.17605/OSF.IO/7SX8U., Competing Interests: Competing interests: All authors have completed the ICMJE uniform disclosure form at https://www.icmje.org/disclosure-of-interest/ and declare: support from the Australian Research Council during the conduct of this research for the submitted work; some authors had support from research institutions listed in the funding statement; some authors received financial support to attend an international congress to present preliminary results of this project; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work., (© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

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.)

As replications of individual studies are resource intensive, techniques for predicting the replicability are required. We introduce the repliCATS (Collaborative Assessments for Trustworthy Science) process, a new method for eliciting expert predictions about the replicability of research. This process is a structured expert elicitation approach based on a modified Delphi technique applied to the evaluation of research claims in social and behavioural sciences. The utility of processes to predict replicability is their capacity to test scientific claims without the costs of full replication. Experimental data supports the validity of this process, with a validation study producing a classification accuracy of 84% and an Area Under the Curve of 0.94, meeting or exceeding the accuracy of other techniques used to predict replicability. The repliCATS process provides other benefits. It is highly scalable, able to be deployed for both rapid assessment of small numbers of claims, and assessment of high volumes of claims over an extended period through an online elicitation platform, having been used to assess 3000 research claims over an 18 month period. It is available to be implemented in a range of ways and we describe one such implementation. An important advantage of the repliCATS process is that it collects qualitative data that has the potential to provide insight in understanding the limits of generalizability of scientific claims. The primary limitation of the repliCATS process is its reliance on human-derived predictions with consequent costs in terms of participant fatigue although careful design can minimise these costs. The repliCATS process has potential applications in alternative peer review and in the allocation of effort for replication studies., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Fraser 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.)

Objective: The ongoing COVID-19 pandemic has caused an indefinite delay to cancer screening programs worldwide. This study aims to explore the impact on breast cancer screening outcomes such as mammography and diagnosis rates., Methods: We searched Ovid MEDLINE, Ovid Embase, medRxiv and bioRxiv between January 2020 to October 2021 to identify studies that reported on the rates of screening mammography and breast cancer diagnosis before and during the pandemic. The effects of 'lockdown' measures, age and ethnicity on outcomes were also examined. All studies were assessed for risk of bias using the Newcastle-Ottawa Scale (NOS). Rate ratios were calculated for all outcomes and pooled using standard inverse-variance random effects meta-analysis., Results: We identified 994 articles, of which 7 registry-based and 24 non-registry-based retrospective cohort studies, including data on 4,860,786 and 629,823 patients respectively across 18 different countries, were identified. Overall, breast cancer screening and diagnosis rates dropped by an estimated 41-53% and 18-29% respectively between 2019 and 2020. No differences in mammogram screening rates depending on patient age or ethnicity were observed. However, countries that implemented lockdown measures were associated with a significantly greater reduction in mammogram and diagnosis rates between 2019 and 2020 in comparison to those that did not., Conclusion: The pandemic has caused a substantial reduction in the screening and diagnosis of breast cancer, with reductions more pronounced in countries under lockdown restrictions. It is early yet to know if delayed screening during the pandemic translates into higher breast cancer mortality.

Objectives: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time; and factors associated with these changes., Design: Cross sectional meta-research study., Population: Random sample of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020., Main Outcome Measures: The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals., Results: Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113; 38%), a full search strategy for at least one database (n=214; 71%), methods used to assess risk of bias (n=185; 62%), methods used to prepare data for meta-analysis (n=101; 34%), and source of funding for the review (n=215; 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%))., Conclusion: Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials., Competing Interests: Competing interests: All authors have completed the ICMJE uniform disclosure form at https://www.icmje.org/disclosure-of-interest/ and declare: support from the Australian Research Council for the submitted work; some authors had support from research institutions listed in the funding statement; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work., (© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Various stakeholders are calling for increased availability of data and code from cancer research. However, it is unclear how commonly these products are shared, and what factors are associated with sharing. Our objective was to evaluate how frequently oncology researchers make data and code available and explore factors associated with sharing., Methods: A cross-sectional analysis of a random sample of 306 cancer-related articles indexed in PubMed in 2019 which studied research subjects with a cancer diagnosis was performed. All articles were independently screened for eligibility by two authors. Outcomes of interest included the prevalence of affirmative sharing declarations and the rate with which declarations connected to data complying with key FAIR principles (e.g. posted to a recognised repository, assigned an identifier, data license outlined, non-proprietary formatting). We also investigated associations between sharing rates and several journal characteristics (e.g. sharing policies, publication models), study characteristics (e.g. cancer rarity, study design), open science practices (e.g. pre-registration, pre-printing) and subsequent citation rates between 2020 and 2021., Results: One in five studies declared data were publicly available (59/306, 19%, 95% CI: 15-24%). However, when data availability was investigated this percentage dropped to 16% (49/306, 95% CI: 12-20%), and then to less than 1% (1/306, 95% CI: 0-2%) when data were checked for compliance with key FAIR principles. While only 4% of articles that used inferential statistics reported code to be available (10/274, 95% CI: 2-6%), the odds of reporting code to be available were 5.6 times higher for researchers who shared data. Compliance with mandatory data and code sharing policies was observed in 48% (14/29) and 0% (0/6) of articles, respectively. However, 88% of articles (45/51) included data availability statements when required. Policies that encouraged data sharing did not appear to be any more effective than not having a policy at all. The only factors associated with higher rates of data sharing were studying rare cancers and using publicly available data to complement original research., Conclusions: Data and code sharing in oncology occurs infrequently, and at a lower rate than would be expected given the prevalence of mandatory sharing policies. There is also a large gap between those declaring data to be available, and those archiving data in a way that facilitates its reuse. We encourage journals to actively check compliance with sharing policies, and researchers consult community-accepted guidelines when archiving the products of their research., (© 2022. The Author(s).)

Upper limb impairments are common in women following surgery for breast cancer. Range of movement (ROM) exercises are commonly prescribed, but the optimal timing to begin these exercises is not clear. The aim of this systematic review and meta-analysis was to evaluate the effectiveness of early ROM exercises (Early ROM) compared to delayed ROM exercises (Delayed ROM) or usual care (UC) in reducing common complications in women following breast cancer surgery. Cochrane Central Register of Controlled Trials, Pubmed, EMBASE, CINAHL, and PEDro were searched from date of inception until the 15th of February 2021, to identify randomized controlled trials which compared Early ROM to either Delayed ROM or UC in women following surgery for breast cancer. Outcomes included shoulder range, wound outcomes and lymphedema incidence. Risk of bias was evaluated with the PEDro scale. Data analysis was conducted in R (version 3.6.0), with a priori sensitivity analyses conducted for studies with low risk of bias and published after the year 2000. Of the 703 articles retrieved, 20 trials (2442 participants) were eligible for inclusion. There were few differences between groups in ROM, except for flexion ROM when more recent evidence was considered. Total drainage time and hematoma incidence were significantly higher in the Early ROM group compared to Delayed ROM (WMD 1·2 days [95%CI 0·7,1·7], and RR 1·6 [95%CI 1·1,2·3], respectively). When considering more recent evidence, there were no differences between groups for these outcomes. There were no differences between groups in other wound outcomes. Lymphedema incidence was higher in the Early ROM group compared to Delayed ROM in the short-term only (RR 3·7 [95% CI 1·3;10·9]), and there was no difference when compared to UC. The quality of evidence using the GRADE approach was generally low to very low. This review found that when considering more contemporary evidence, the timing of exercise may influence ROM, but not wound outcomes. Further research is recommended to understand the effect on lymphedema incidence. No funding was sought for this review. A protocol for this systematic review was posted on the Open Science Framework prior to commencement (DOI: 10.17605/OSF.IO/Q5FHS)., (Crown Copyright © 2022. Published by Elsevier Inc. All rights reserved.)

Slow oxidative muscle, most notably the soleus, is inherently well equipped with the molecular machinery for regulating blood-borne substrates. However, the entire human musculature accounts for only ∼15% of the body's oxidative metabolism of glucose at the resting energy expenditure, despite being the body's largest lean tissue mass. We found the human soleus muscle could raise local oxidative metabolism to high levels for hours without fatigue, during a type of soleus-dominant activity while sitting, even in unfit volunteers. Muscle biopsies revealed there was minimal glycogen use. Magnifying the otherwise negligible local energy expenditure with isolated contractions improved systemic VLDL-triglyceride and glucose homeostasis by a large magnitude, e.g., 52% less postprandial glucose excursion (∼50 mg/dL less between ∼1 and 2 h) with 60% less hyperinsulinemia. Targeting a small oxidative muscle mass (∼1% body mass) with local contractile activity is a potent method for improving systemic metabolic regulation while prolonging the benefits of oxidative metabolism., Competing Interests: We, the authors and our immediate family members, have no related patents to declare. The authors have been developing technologies to help instruct people how to do the SPU movement optimally. The University of Houston has the intent to patent potential intellectual property., (© 2022 The Author(s).)

Objectives: To estimate the frequency of data and code availability statements in a random sample of systematic reviews with meta-analysis of aggregate data, summarize the content of the statements and investigate how often data and code files were shared., Methods: We searched for systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioral, or educational intervention that were indexed in PubMed, Education Collection via ProQuest, Scopus via Elsevier, or Social Sciences Citation Index and Science Citation Index Expanded via Web of Science during a 4-week period (between November 2, and December 2, 2020). Records were randomly sorted and screened independently by two authors until our target sample of 300 systematic reviews was reached. Two authors independently recorded whether a data or code availability statement (or both) appeared in each review and coded the content of the statements using an inductive approach., Results: Of the 300 included systematic reviews with meta-analysis, 86 (29%) had a data availability statement, and seven (2%) had both a data and code availability statement. In 12/93 (13%) data availability statements, authors stated that data files were available for download from the journal website or a data repository, which we verified as being true. While 39/93 (42%) authors stated data were available upon request, 37/93 (40%) implied that sharing of data files was not necessary or applicable to them, most often because "all data appear in the article" or "no datasets were generated or analyzed"., Discussion: Data and code availability statements appear infrequently in systematic review manuscripts. Authors who do provide a data availability statement often incorrectly imply that data sharing is not applicable to systematic reviews. Our results suggest the need for various interventions to increase data and code sharing by systematic reviewers., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background: Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown., Results: We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation., Conclusions: Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival., (© 2021. The Author(s).)

Numerous studies have demonstrated low but increasing rates of data and code sharing within medical and health research disciplines. However it remains unclear how commonly data and code are shared across all fields of medical and health research, as well as whether sharing rates are positively associated with implementation of progressive policies by publishers and funders, or growing expectations from the medical and health research community at large. Therefore this systematic review aims to synthesise the findings of medical and health science studies that have empirically investigated the prevalence of data or code sharing, or both. Objectives include the investigation of: (i) the prevalence of public sharing of research data and code alongside published articles (including preprints), (ii) the prevalence of private sharing of research data and code in response to reasonable requests, and (iii) factors associated with the sharing of either research output (e.g., the year published, the publisher's policy on sharing, the presence of a data or code availability statement). It is hoped that the results will provide some insight into how often research data and code are shared publicly and privately, how this has changed over time, and how effective some measures such as the institution of data sharing policies and data availability statements have been in motivating researchers to share their underlying data and code., Competing Interests: Competing interests: DGH is a PhD candidate supported by an Australian Commonwealth Government Research Training Program Scholarship. The Laura and John Arnold Foundation funds the RIAT Support Centre (no grant number), which supports the salaries of ARF and KH. KH's project was supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services (HHS) as part of a financial assistance award U01FD005946 totalling US$5,000 with 100 per cent funded by FDA/HHS. The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement, by FDA/HHS, or the U.S. Government. The authors declare that no grants were involved in supporting this work., (Copyright: © 2021 Hamilton DG et al.)

Devil facial tumor disease (DFTD) is a transmissible cancer affecting Tasmanian devils Sarcophilus harrisii . The disease has caused severe population declines and is associated with demographic and behavioral changes, including earlier breeding, younger age structures, and reduced dispersal and social interactions. Devils are generally solitary, but social encounters are commonplace when feeding upon large carcasses. DFTD tumors can disfigure the jaw and mouth and so diseased individuals might alter their diets to enable ingestion of alternative foods, to avoid conspecific interactions, or to reduce competition. Using stable isotope analysis (δ 13 C and δ 15 N) of whiskers, we tested whether DFTD progression, measured as tumor volume, affected the isotope ratios and isotopic niches of 94 infected Tasmanian devils from six sites in Tasmania, comprising four eucalypt plantations, an area of smallholdings and a national park. Then, using tissue from 10 devils sampled before and after detection of tumors and 8 devils where no tumors were detected, we examined whether mean and standard deviation of δ 13 C and δ 15 N of the same individuals changed between healthy and diseased states. δ 13 C and δ 15 N values were generally not related to tumor volume in infected devils, though at one site, Freycinet National Park, δ 15 N values increased significantly as tumor volume increased. Infection with DFTD was not associated with significant changes in the mean or standard deviation of δ 13 C and δ 15 N values in individual devils sampled before and after detection of tumors. Our analysis suggests that devils tend to maintain their isotopic niche in the face of DFTD infection and progression, except where ecological conditions facilitate a shift in diets and feeding behaviors, demonstrating that ecological context, alongside disease severity, can modulate the behavioral responses of Tasmanian devils to DFTD., Competing Interests: The authors declare no conflict of interest., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Background: Investigations of transparency, reproducibility and replicability in science have been directed largely at individual studies. It is just as critical to explore these issues in syntheses of studies, such as systematic reviews, given their influence on decision-making and future research. We aim to explore various aspects relating to the transparency, reproducibility and replicability of several components of systematic reviews with meta-analysis of the effects of health, social, behavioural and educational interventions., Methods: The REPRISE (REProducibility and Replicability In Syntheses of Evidence) project consists of four studies. We will evaluate the completeness of reporting and sharing of review data, analytic code and other materials in a random sample of 300 systematic reviews of interventions published in 2020 (Study 1). We will survey authors of systematic reviews to explore their views on sharing review data, analytic code and other materials and their understanding of and opinions about replication of systematic reviews (Study 2). We will then evaluate the extent of variation in results when we (a) independently reproduce meta-analyses using the same computational steps and analytic code (if available) as used in the original review (Study 3), and (b) crowdsource teams of systematic reviewers to independently replicate a subset of methods (searches for studies, selection of studies for inclusion, collection of outcome data, and synthesis of results) in a sample of the original reviews; 30 reviews will be replicated by 1 team each and 2 reviews will be replicated by 15 teams (Study 4)., Discussion: The REPRISE project takes a systematic approach to determine how reliable systematic reviews of interventions are. We anticipate that results of the REPRISE project will inform strategies to improve the conduct and reporting of future systematic reviews.

Emerging infectious diseases pose one of the greatest threats to human health and biodiversity. Phylodynamics is often used to infer epidemiological parameters essential for guiding intervention strategies for human viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Here, we applied phylodynamics to elucidate the epidemiological dynamics of Tasmanian devil facial tumor disease (DFTD), a fatal, transmissible cancer with a genome thousands of times larger than that of any virus. Despite prior predictions of devil extinction, transmission rates have declined precipitously from ~3.5 secondary infections per infected individual to ~1 at present. Thus, DFTD appears to be transitioning from emergence to endemism, lending hope for the continued survival of the endangered Tasmanian devil. More generally, our study demonstrates a new phylodynamic analytical framework that can be applied to virtually any pathogen., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Infectious diseases, including transmissible cancers, can have a broad range of impacts on host behaviour, particularly in the latter stages of disease progression. However, the difficulty of early diagnoses makes the study of behavioural influences of disease in wild animals a challenging task. Tasmanian devils ( Sarcophilus harrisii ) are affected by a transmissible cancer, devil facial tumour disease (DFTD), in which tumours are externally visible as they progress. Using telemetry and mark-recapture datasets, we quantify the impacts of cancer progression on the behaviour of wild devils by assessing how interaction patterns within the social network of a population change with increasing tumour load. The progression of DFTD negatively influences devils' likelihood of interaction within their network. Infected devils were more active within their network late in the mating season, a pattern with repercussions for DFTD transmission. Our study provides a rare opportunity to quantify and understand the behavioural feedbacks of disease in wildlife and how they may affect transmission and population dynamics in general.

Peer review practices differ substantially between journals and disciplines. This study presents the results of a survey of 322 editors of journals in ecology, economics, medicine, physics and psychology. We found that 49% of the journals surveyed checked all manuscripts for plagiarism, that 61% allowed authors to recommend both for and against specific reviewers, and that less than 6% used a form of open peer review. Most journals did not have an official policy on altering reports from reviewers, but 91% of editors identified at least one situation in which it was appropriate for an editor to alter a report. Editors were also asked for their views on five issues related to publication ethics. A majority expressed support for co-reviewing, reviewers requesting access to data, reviewers recommending citations to their work, editors publishing in their own journals, and replication studies. Our results provide a window into what is largely an opaque aspect of the scientific process. We hope the findings will inform the debate about the role and transparency of peer review in scholarly publishing., Competing Interests: DH, HF, RH, FF No competing interests declared, (© 2020, Hamilton et al.)

The impact of emerging infectious diseases is increasingly recognised as a major threat to wildlife. Wild populations of the endangered Tasmanian devil, Sarcophilus harrisii , are experiencing devastating losses from a novel transmissible cancer, devil facial tumour disease (DFTD); however, despite the rapid decline of this species, there is currently no information on the presence of haemoprotozoan parasites. In the present study, 95 Tasmanian devil blood samples were collected from four populations in Tasmania, Australia, which underwent molecular screening to detect four major groups of haemoprotozoa: (i) trypanosomes, (ii) piroplasms, (iii) Hepatozoon , and (iv) haemosporidia. Sequence results revealed Trypanosoma infections in 32/95 individuals. Trypanosoma copemani was identified in 10 Tasmanian devils from three sites and a second Trypanosoma sp. was identified in 22 individuals that were grouped within the poorly described T. cyclops clade. A single blood sample was positive for Babesia sp., which most closely matched Babesia lohae . No other blood protozoan parasite DNA was detected. This study provides the first insight into haemoprotozoa from the Tasmanian devil and the first identification of Trypanosoma and Babesia in this carnivorous marsupial., Competing Interests: The authors declare no conflicts of interest.

Cellular cheating leading to cancers exists in all branches of multicellular life, favoring the evolution of adaptations to avoid or suppress malignant progression, and/or to alleviate its fitness consequences. Ecologists have until recently largely neglected the importance of cancer cells for animal ecology, presumably because they did not consider either the potential ecological or evolutionary consequences of anticancer adaptations. Here, we review the diverse ways in which the evolution of anticancer adaptations has significantly constrained several aspects of the evolutionary ecology of multicellular organisms at the cell, individual, population, species, and ecosystem levels and suggest some avenues for future research., (© 2020.)

Genetic structure in host species is often used to predict disease spread. However, host and pathogen genetic variation may be incongruent. Understanding landscape factors that have either concordant or divergent influence on host and pathogen genetic structure is crucial for wildlife disease management. Devil facial tumour disease (DFTD) was first observed in 1996 and has spread throughout almost the entire Tasmanian devil geographic range, causing dramatic population declines. Whereas DFTD is predominantly spread via biting among adults, devils typically disperse as juveniles, which experience low DFTD prevalence. Thus, we predicted little association between devil and tumour population structure and that environmental factors influencing gene flow differ between devils and tumours. We employed a comparative landscape genetics framework to test the influence of environmental factors on patterns of isolation by resistance (IBR) and isolation by environment (IBE) in devils and DFTD. Although we found evidence for broad-scale costructuring between devils and tumours, we found no relationship between host and tumour individual genetic distances. Further, the factors driving the spatial distribution of genetic variation differed for each. Devils exhibited a strong IBR pattern driven by major roads, with no evidence of IBE. By contrast, tumours showed little evidence for IBR and a weak IBE pattern with respect to elevation in one of two tumour clusters we identify herein. Our results warrant caution when inferring pathogen spread using host population genetic structure and suggest that reliance on environmental barriers to host connectivity may be ineffective for managing the spread of wildlife diseases. Our findings demonstrate the utility of comparative landscape genetics for identifying differential factors driving host dispersal and pathogen transmission., (© 2020 John Wiley & Sons Ltd.)

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil ( Sarcophilus harrisii ), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil's geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.

Purpose: The purpose of this study was to quantify the number and explore the nature of citations of retracted articles in the radiation oncology literature occurring after publication of the retraction note., Methods and Materials: A list of previously identified retracted articles within the field of radiation oncology was updated in June 2017. The number of publications citing retracted articles was quantified using Google Scholar, Web of Science, and Scopus. Studies citing retracted publications after publication of the retraction note were individually assessed to determine the nature of the reference., Results: Forty-seven retracted articles were identified for this study. Thirty-seven studies (79%) received 1017 citations before retraction, and 34 articles (72%) received 407 English and 169 foreign-language citations afterward. The average number of citations dropped from 22 to 11 after publication of the retraction note (95% confidence interval, 0.3-21.0, P = .043). Most postretraction citations occurred during the second year after the article's retraction, originated from North America and Asia (N = 124 each, 31%) and Europe (N = 122, 30%), and featured in original articles (N = 254, 62%) and reviews (N = 73, 18%). Of the 358 individually evaluable citing studies, 92% referenced the retracted article as legitimate work. Three guidelines and 15 systematic reviews and meta-analyses were also identified that cited retracted articles as valid work., Conclusions: Postretraction citations are an avoidable phenomenon. The results of the study emphasize the need for investigators to adhere to good research practices to mitigate the influence and propagation of flawed and unethical research. Journal editors, peer reviewers, and the broader radiation oncology readership should remain diligent in ensuring that citations of retracted work are identified and removed before, during, and possibly even after publication., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Purpose: The purpose of this study was to characterize retracted studies within the field of radiation oncology., Methods and Materials: Computerized searches were performed in Ovid MEDLINE, PubMed, Ovid EMBASE, and the Cochrane Library up to May 2017 looking for retracted studies using the terms "retraction note," "retracted note," "withdrawn" and "radiotherapy," and "radiation oncology." Additional studies were identified by hand-searching 10 discipline-specific journals. Two authors independently screened papers and then extracted author demographics, journal characteristics, and retraction-specific variables., Results: Of the 58 studies identified, the most common reasons for retraction were misconduct (43%), methodological error (21%), authorship issues (5%), unknown causes (5%), and journal (administrative) errors (3%). A total of 13 systematic reviews or protocols (22%) were withdrawn from the Cochrane Library for being out-of-date or redundant. All but one retracted study and retraction notice were available in portable document format. Of the 57 retrieved papers, 79% were identified as retracted via in-text notations or watermarks. Overall median time to retraction was 44 months (interquartile range, 11-98 months). However, 42 studies (72%) were still cited after retraction notices were published., Conclusions: A retracted study within the field of radiation oncology remains a relatively uncommon event. Although promising, our data suggest that the majority of these retracted articles continue to be cited as valid research. As such, there is still a need for clinicians to remain vigilant with their academic rigor and good clinical research practices. There is an urgent need for publication houses to foster universal publishing standards along with discipline-specific retraction guidelines., (Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.)

There is more need for "a movement-movement" than ever before. The percentage of seniors in our population is rising exponentially. Sedentary lifestyles throughout the lifespan have become the norm, including inactive youth and a sedentary workforce. Preventable chronic diseases caused by sedentary living have both lowered the quality of life for those directly affected or their families, and have created an unsustainable economic dilemma. In this article, we explain that whether it is a sedentary student, worker, or retiree, the most neglected but essential facts are as follows. By far, the most potent and rapid way to raise the rate of healthy metabolic and cardiovascular processes is through the immediate benefits of muscle contractions. Working muscle demands more energy and fuel than any other tissue in the body, but during inactivity the metabolic rate of muscle is relatively low. Depending on the type of contraction, muscle type, and other factors, the local fuel requirements within the working muscle can help to manage metabolic risks through a variety of processes, such as blood glucose utilization, uptake of unhealthy blood triglycerides, and increased blood flow. Given the large amount of time that people spend inactive each day, there is an enormous opportunity to raise the bar in optimizing health throughout the entire lifespan. Developed correctly, safe and low effort muscular activity can be performed for relatively long periods of time each day by the elderly and all segments of the population to optimize health and well being during aging., (Copyright © 2018. Published by Elsevier Inc.)

The aim of this study was to evaluate the differences in target localization between Calypso ® , kV orthogonal imaging and cone-beam computed tomography (CBCT) for combined translations and rotations of an anthropomorphic pelvic phantom. The phantom was localized using all three systems in 50 different positions, with applied translational and rotational offsets randomly sampled from representative normal distributions of prostate motion. Lin's concordance correlation coefficient (ρc) and 95% confidence intervals were calculated to assess the agreement between the localization systems. Mean differences and difference vectors between the three systems were also calculated. Agreement between systems for lateral, vertical, and longitudinal translations was excellent, with ρc values of greater than 0.98 between all three systems in all axes. There was excellent agreement between the systems for rotations around the lateral axis (pitch) (ρc > 0.99), and around the vertical axis (yaw) (ρc > 0.97). However, somewhat poorer agreement for rotations around the longitudinal axis (roll) was observed, with the lowest correlation observed between Calypso and kV orthogonal imaging (ρc = 0.895). Mean differences between the phantom position reported by Calypso and the radiographic systems were less than 1 mm and 1° for all translations and rotations. The results for translations are consistent with the publications of previous authors. There is no comparable published data for rotations. While there is lower correlation between the three systems for roll than for the other angles, the mean differences in reported rotations are not clinically significant., (© 2017 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.)

This study aimed to assess the design and performance of the preimplant suitability worksheet in determining Calypso eligibility for prostate cancer patients prescribed postprostatectomy radiotherapy with electromagnetic transponder guidance. The medical records and radiotherapy planning datasets of 75 patients prospectively recruited between June 2015 and September 2016 to a Phase 2 trial evaluating electromagnetic transponder-guided postprostatectomy radiotherapy were retrospectively examined. Correlation and differences between computed tomography (CT)-defined greater trochanter and prostatic fossa landmarks were evaluated. Receiver operating characteristic curves were also generated to assess the expected and observed accuracy of the worksheet in determining Calypso eligibility. Strong correlation was demonstrated between anterior surface to planning CT-defined greater trochanter and prostate bed center distances (r = 0.95, p <0.001), with a mean difference between measurements of 1.1 cm (95% confidence interval [CI]: 0.9 to 1.3). A similar correlation coefficient was found for surface to greater trochanter location and posterior beacon location (r = 0.92, p <0.001) but with a reduced mean difference of 0.4 cm (95% CI: 0.1 to 0.6). Performance of the worksheet as assessed by planning CT data demonstrated excellent accuracy as a test to determine eligibility (area under the curve: 0.97; 95% CI: 0.92 to 1.00); however, this was not replicated using the same data captured clinically (area under the curve 0.83; 95% CI: 0.68 to 0.98). Although the greater trochanter is a good surrogate for the prostate bed center, it is better associated with the posterior beacon location. As a result, the worksheet will underestimate the truly eligible population if performed accurately and according to manufacturer guidelines. Theoretically, the worksheet could be improved if a cut off of 20 cm is used and the greater trochanter is accurately identified; however, the latter appears to be difficult to achieve in practice., (Copyright © 2017 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.)