A manifesto for reproducible science Munafò, Marcus R; Nosek, Brian A; Bishop, Dorothy V M ...
Nature human behaviour,
01/2017, Letnik:
1, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Improving the reliability and efficiency of scientific research will increase the credibility of the published scientific literature and accelerate discovery. Here we argue for the adoption of ...measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives. There is some evidence from both simulations and empirical studies supporting the likely effectiveness of these measures, but their broad adoption by researchers, institutions, funders and journals will require iterative evaluation and improvement. We discuss the goals of these measures, and how they can be implemented, in the hope that this will facilitate action toward improving the transparency, reproducibility and efficiency of scientific research.
Objective To synthesise the association of shift work with major vascular events as reported in the literature.Data sources Systematic searches of major bibliographic databases, contact with experts ...in the field, and review of reference lists of primary articles, review papers, and guidelines.Study selection Observational studies that reported risk ratios for vascular morbidity, vascular mortality, or all cause mortality in relation to shift work were included; control groups could be non-shift (“day”) workers or the general population.Data extraction Study quality was assessed with the Downs and Black scale for observational studies. The three primary outcomes were myocardial infarction, ischaemic stroke, and any coronary event. Heterogeneity was measured with the I2 statistic and computed random effects models.Results 34 studies in 2 011 935 people were identified. Shift work was associated with myocardial infarction (risk ratio 1.23, 95% confidence interval 1.15 to 1.31; I2=0) and ischaemic stroke (1.05, 1.01 to 1.09; I2=0). Coronary events were also increased (risk ratio 1.24, 1.10 to 1.39), albeit with significant heterogeneity across studies (I2=85%). Pooled risk ratios were significant for both unadjusted analyses and analyses adjusted for risk factors. All shift work schedules with the exception of evening shifts were associated with a statistically higher risk of coronary events. Shift work was not associated with increased rates of mortality (whether vascular cause specific or overall). Presence or absence of adjustment for smoking and socioeconomic status was not a source of heterogeneity in the primary studies. 6598 myocardial infarctions, 17 359 coronary events, and 1854 ischaemic strokes occurred. On the basis of the Canadian prevalence of shift work of 32.8%, the population attributable risks related to shift work were 7.0% for myocardial infarction, 7.3% for all coronary events, and 1.6% for ischaemic stroke.Conclusions Shift work is associated with vascular events, which may have implications for public policy and occupational medicine.
Re-operation for positive resection margins following breast-conserving surgery occurs frequently (average = 20-25%), is cost-inefficient, and leads to physical and psychological morbidity. Current ...margin assessment techniques are slow and labour intensive. Rapid evaporative ionisation mass spectrometry (REIMS) rapidly identifies dissected tissues by determination of tissue structural lipid profiles through on-line chemical analysis of electrosurgical aerosol toward real-time margin assessment.
Electrosurgical aerosol produced from ex-vivo and in-vivo breast samples was aspirated into a mass spectrometer (MS) using a monopolar hand-piece. Tissue identification results obtained by multivariate statistical analysis of MS data were validated by histopathology. Ex-vivo classification models were constructed from a mass spectral database of normal and tumour breast samples. Univariate and tandem MS analysis of significant peaks was conducted to identify biochemical differences between normal and cancerous tissues. An ex-vivo classification model was used in combination with bespoke recognition software, as an intelligent knife (iKnife), to predict the diagnosis for an ex-vivo validation set. Intraoperative REIMS data were acquired during breast surgery and time-synchronized to operative videos.
A classification model using histologically validated spectral data acquired from 932 sampling points in normal tissue and 226 in tumour tissue provided 93.4% sensitivity and 94.9% specificity. Tandem MS identified 63 phospholipids and 6 triglyceride species responsible for 24 spectral differences between tissue types. iKnife recognition accuracy with 260 newly acquired fresh and frozen breast tissue specimens (normal n = 161, tumour n = 99) provided sensitivity of 90.9% and specificity of 98.8%. The ex-vivo and intra-operative method produced visually comparable high intensity spectra. iKnife interpretation of intra-operative electrosurgical vapours, including data acquisition and analysis was possible within a mean of 1.80 seconds (SD ±0.40).
The REIMS method has been optimised for real-time iKnife analysis of heterogeneous breast tissues based on subtle changes in lipid metabolism, and the results suggest spectral analysis is both accurate and rapid. Proof-of-concept data demonstrate the iKnife method is capable of online intraoperative data collection and analysis. Further validation studies are required to determine the accuracy of intra-operative REIMS for oncological margin assessment.
Silver nanoparticles (Ag NPs) have been used in numerous consumer products and may enter the soil through the land application of biosolids. However, little is known about the relationship between Ag ...NP exposure and their bioavailability for soil organisms. This study aims at comparing the uptake and elimination kinetics of Ag upon exposures to different Ag forms (NPs and ionic Ag (as AgNO₃)) in the isopod Porcellionides pruinosus. Isopods were exposed to contaminated Lufa 2.2 soil or alder leaves as food. Uptake and elimination rate constants for soil exposure did not significantly differ between Ag NPs and ionic Ag at 30 and 60 mg Ag/kg. For dietary exposure, the uptake rate constant was up to 5 times higher for Ag NPs than for AgNO₃, but this was related to feeding activity and exposure concentrations, while no difference in the elimination rate constants was found. When comparing both routes, dietary exposure resulted in lower Ag uptake rate constants but elimination rate constants did not differ. A fast Ag uptake was observed from both routes and most of the Ag taken up seemed not to be eliminated. Synchrotron X-ray fluorescence showed Ag in the S-cells of the hepatopancreas, thus supporting the observations from the kinetic experiment (i.e. low elimination). In addition, our results show that isopods have an extremely high Ag accumulation capacity, suggesting the presence of an efficient Ag storage compartment.
Extreme precipitation and flood episodes in the Himalayas are oftentimes traced to synoptic situations involving connections between equatorward advancing upper level extratropical circulations and ...moisture-laden tropical monsoon circulation. While previous studies have documented precipitation characteristics in the Himalayan region during severe storm cases, a comprehensive understanding of circulation dynamics of extreme precipitation mechanisms is still warranted. In this study, a detailed analysis is performed using rainfall observations and reanalysis circulation products to understand the evolution of monsoon-extratropical circulation features and their interactions based on 34 extreme precipitation events which occurred in the Western Himalayas (WEH) during the period 1979–2013. Our results provide evidence for a common large-scale circulation pattern connecting the extratropics and the South Asian monsoon region, which is favorable for extreme precipitation occurrences in the WEH region. This background upper level large-scale circulation pattern consists of a deep southward penetrating midlatitude westerly trough, a blocking high over western Eurasia and an intensifying Tibetan anticyclone. It is further seen from our analysis that the key elements of monsoon-midlatitude interactions, responsible for extreme precipitation events over the WEH region, are: (1) midlatitude Rossby wave breaking, (2) west-northwest propagation of monsoon low-pressure system from the Bay of Bengal across the Indian subcontinent, (3) eddy shedding of the Tibetan anticyclone, (4) ageostrophic motions and transverse circulation across the Himalayas, and (5) strong moist convection over the Himalayan foothills. Furthermore, high-resolution numerical simulations indicate that diabatic heating and mesoscale ageostrophic effects can additionally amplify the convective motions and precipitation in the WEH region.
Malaria remains a global health burden. Elimination of the hypnozoite is required in patients infected with
P. vivax
to prevent relapse. In this report, the safety of a single dose of tafenoquine was ...similar to that of a 14-day course of primaquine in patients with normal G6PD activity.
The traditional view of the planktonic food web describes consumption of inorganic nutrients by photoautotrophic phytoplankton, which in turn supports zooplankton and ultimately higher trophic ...levels. Pathways centred on bacteria provide mechanisms for nutrient recycling. This structure lies at the foundation of most models used to explore biogeochemical cycling, functioning of the biological pump, and the impact of climate change on these processes. We suggest an alternative new paradigm, which sees the bulk of the base of this food web supported by protist plankton communities that are mixotrophic - combining phototrophy and phagotrophy within a single cell. The photoautotrophic eukaryotic plankton and their heterotrophic microzooplankton grazers dominate only during the developmental phases of ecosystems (e.g. spring bloom in temperate systems). With their flexible nutrition, mixotrophic protists dominate in more-mature systems (e.g. temperate summer, established eutrophic systems and oligotrophic systems); the more-stable water columns suggested under climate change may also be expected to favour these mixotrophs. We explore how such a predominantly mixotrophic structure affects microbial trophic dynamics and the biological pump. The mixotroph-dominated structure differs fundamentally in its flow of energy and nutrients, with a shortened and potentially more efficient chain from nutrient regeneration to primary production. Furthermore, mixotrophy enables a direct conduit for the support of primary production from bacterial production. We show how the exclusion of an explicit mixotrophic component in studies of the pelagic microbial communities leads to a failure to capture the true dynamics of the carbon flow. In order to prevent a misinterpretation of the full implications of climate change upon biogeochemical cycling and the functioning of the biological pump, we recommend inclusion of multi-nutrient mixotroph models within ecosystem studies.
Heatwaves are likely to increase in frequency and intensity with climate change, which may impair tree function and forest C uptake. However, we have little information regarding the impact of ...extreme heatwaves on the physiological performance of large trees in the field. Here, we grew Eucalyptus parramattensis trees for 1 year with experimental warming (+3°C) in a field setting, until they were greater than 6 m tall. We withheld irrigation for 1 month to dry the surface soils and then implemented an extreme heatwave treatment of 4 consecutive days with air temperatures exceeding 43°C, while monitoring whole‐canopy exchange of CO2 and H2O, leaf temperatures, leaf thermal tolerance, and leaf and branch hydraulic status. The heatwave reduced midday canopy photosynthesis to near zero but transpiration persisted, maintaining canopy cooling. A standard photosynthetic model was unable to capture the observed decoupling between photosynthesis and transpiration at high temperatures, suggesting that climate models may underestimate a moderating feedback of vegetation on heatwave intensity. The heatwave also triggered a rapid increase in leaf thermal tolerance, such that leaf temperatures observed during the heatwave were maintained within the thermal limits of leaf function. All responses were equivalent for trees with a prior history of ambient and warmed (+3°C) temperatures, indicating that climate warming conferred no added tolerance of heatwaves expected in the future. This coordinated physiological response utilizing latent cooling and adjustment of thermal thresholds has implications for tree tolerance of future climate extremes as well as model predictions of future heatwave intensity at landscape and global scales.
Heatwaves are likely to increase in frequency and intensity, but we know relatively little about how trees will respond. Here, we documented that large trees growing in the field responded to an extreme heatwave with a coordinated physiological response involving continued leaf cooling from transpiration and a rapid increase in leaf thermal tolerance. The Eucalyptus trees that we studied were remarkably capable of tolerating an extreme heatwave via mechanisms that have implications for future heatwave intensity and forest resilience in a warmer world.
Green synthesis of silver nanoparticles (Ag NPs) using an extract of dried Zingiber officinale (ginger) root as a reducing and capping agent in the presence of microwave irradiation was herein ...reported for the first time. The formation of symmetrical spheres is confirmed from the UV–Visible spectrum of Ag NPs. Fourier transform infra-red spectroscopy confirms the formation of the Ag NPs. X-ray diffraction analysis was utilized to calculate the crystallite size of Ag NPs and the value was found to be 10nm. High-resolution transmission electron microscopy and high-resolution scanning electron microscopy were used to investigate the morphology and size of the synthesized samples. The sphere like morphology is confirmed from the images. The purity and crystallinity of Ag NPs is confirmed by energy-dispersive X-Ray analysis and selected area electron diffraction respectively. The electrochemical behavior of the synthesized Ag NPs was assessed by cyclic voltammetry (CV) and shows the redox peaks in the potential range of −1.1 to +1.1V. Agar diffusion method is used to examine the antibacterial activity of Ag NPs. For this purpose, two gram positive and two gram negative bacteria were studied. This single step approach was found to be simple, short time, cost-effective, reproducible, and eco-friendly.
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•Green synthesis of silver nanoparticles (Ag NPs) is reported.•Zingiber officinale (ginger) root extract is first time used for the first time to synthesize Ag NPs.•Biosynthetic approach was found to be simple, cost-effective, reproducible, and eco-friendly.•Study of antibacterial activities is discussed.
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