| 1. |
- Abbafati, Cristiana, et al.
(author)
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- 2020
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Journal article (peer-reviewed)
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Cachim, Afonso, et al.
(author)
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Measuring adherence to inhaled control medication in patients with asthma : Comparison among an asthma app, patient self-report and physician assessment
- 2023
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In: Clinical and Translational Allergy. - : John Wiley & Sons. - 2045-7022 .- 2045-7022. ; 13:2
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Journal article (peer-reviewed)abstract
- BackgroundPrevious studies have demonstrated the feasibility of using an asthma app to support medication management and adherence but failed to compare with other measures currently used in clinical practice. However, in a clinical setting, any additional adherence measurement must be evaluated in the context of both the patient and physician perspectives so that it can also help improve the process of shared decision making. Thus, we aimed to compare different measures of adherence to asthma control inhalers in clinical practice, namely through an app, patient self-report and physician assessment.MethodsThis study is a secondary analysis of three prospective multicentre observational studies with patients (≥13 years old) with persistent asthma recruited from 61 primary and secondary care centres in Portugal. Patients were invited to use the InspirerMundi app and register their inhaled medication. Adherence was measured by the app as the number of doses taken divided by the number of doses scheduled each day and two time points were considered for analysis: 1-week and 1-month. At baseline, patients and physicians independently assessed adherence to asthma control inhalers during the previous week using a Visual Analogue Scale (VAS 0–100).ResultsA total of 193 patients (72% female; median [P25–P75] age 28 [19–41] years old) were included in the analysis. Adherence measured by the app was lower (1 week: 31 [0–71]%; 1 month: 18 [0–48]%) than patient self-report (80 [60–95]) and physician assessment (82 [51–94]) (p < 0.001). A negligible non-significant correlation was found between the app and subjective measurements (ρ 0.118–0.156, p > 0.05). There was a moderate correlation between patient self-report and physician assessment (ρ = 0.596, p < 0.001).ConclusionsAdherence measured by the app was lower than that reported by the patient or the physician. This was expected as objective measurements are commonly lower than subjective evaluations, which tend to overestimate adherence. Nevertheless, the low adherence measured by the app may also be influenced by the use of the app itself and this needs to be considered in future studies.
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| 4. |
- de Almeida, Daniela S., et al.
(author)
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Genotoxic effects of daily personal exposure to particle mass and number concentrations on buccal cells
- 2018
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In: Atmospheric Environment. - : Elsevier BV. - 1352-2310. ; 176, s. 148-157
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Journal article (peer-reviewed)abstract
- The aim of this study is to assess personal exposure to Particle Number Concentrations (PNC) in four size ranges between 0.3 and 10 μm, and particulate matter (PM1; PM2.5; PM4; PM10) in order to evaluate possible genotoxic effects through a comet assay in buccal cells. A convenience cohort of 30 individuals from a Brazilian medium-sized city was selected. These individuals aged between 20 and 61 and worked in typical job categories (i.e., administrative, commerce, education, general services and transport). They were recruited to perform personal exposure measurements during their typical daily routine activities, totaling 240 h of sampling. The 8-h average mass concentrations in air for volunteers ranged from 2.4 to 31.8 μg m−3 for PM1, 4.2–45.1 μg m−3 for PM2.5, 7.9–66.1 μg m−3 for PM4 and from 23.1 to 131.7 μg m−3 for PM10. The highest PNC variation was found for 0.3–0.5 range, between 14 and 181 particles cm−3, 1 to 14 particles cm−3 for the 0.5–1.0 range, 0.2 to 2 particles cm−3 for the 1.0–2.5 range, and 0.06 to 0.7 particles cm−3 for the 2.5–10 range. Volunteers in the ‘education’ category experienced the lowest inhaled dose of PM2.5 as opposed to those involved in ‘commercial‘ activities with the highest doses for PM10 (1.63 μg kg−1 h−1) and PM2.5 (0.61 μg kg−1 h−1). The predominant cause for these high doses was associated with the proximity of the workplace to the street and vehicle traffic. The comet assay performed in buccal cells indicated that the volunteers in ‘commerce’ category experienced the highest damage to their DeoxyriboNucleic Acid (DNA) compared with the control category (i.e. ‘education’). These results indicate the variability in personal exposure of the volunteers in different groups, and the potential damage to DNA was much higher for those spending time in close proximity to the vehicle sources (e.g. commercial services) leading to exposure to a higher fraction of fine particles. This study builds understanding on the exposure of people in different job categories, and provide policy makers with useful information to tackle this neglected issue.
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| 5. |
- Hudson, Lawrence N, et al.
(author)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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In: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Journal article (peer-reviewed)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 6. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 7. |
- Marinho, Daniela Hespanha, et al.
(author)
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The challenge of long-term follow-up of survivors of childhood acute leukemia after hematopoietic stem cell transplantation in resource-limited countries: A single-center report from Brazil.
- 2020
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In: Pediatric transplantation. - : Wiley. - 1399-3046 .- 1397-3142. ; 24:4
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Journal article (peer-reviewed)abstract
- With the number of long-term HSCT survivors steadily increasing, attention needs to be focused on the late complications and quality of life. We therefore analyzed the outcome of 101 pediatric patients (<18 years old at the time of HSCT) transplanted for acute leukemia between 1981 and 2015 at Complexo Hospital de Clínicas, Federal University of Paraná, Brazil, and who survived at least two years after HSCT. The median follow-up was 5.9 years (2.0-29.0); median age at follow-up was 17.5 years (2.98-39.0). The 5-year cumulative incidence of relapse was 27.5% (95% CI 18.6%-36.4%). Two-year cumulative incidence of chronic GVHD was 21.8% (95% CI 13.7%-29.8%). Of the 101 patients, 72 patients (71.3%) presented with late effects. Those surviving longer after HSCT experienced more complications. Patients who received TBI-based regimen developed more late effects (P = .013) and more endocrinological complications (P = .024). Endocrinological complications were the most common late sequelae found in this study. For childhood survivors, quality of life was not influenced by age (at HSCT or at last visit), time from HSCT, gender, donor, or GVHD. For survivors that no longer were children, only age at last visit impacted financial domain measures, irrespective of gender, donor, or GVHD. The current study confirms the high burden late complications after pediatric HSCT have on the survivors and underlines the importance of extended follow-up.
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| 8. |
- Moreira, Camila A.B., et al.
(author)
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Natural variability in exposure to fine particles and their trace elements during typical workdays in an urban area
- 2018
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In: Transportation Research Part D: Transport and Environment. - : Elsevier BV. - 1361-9209. ; 63, s. 333-346
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Journal article (peer-reviewed)abstract
- Studies on the natural human exposures to fine particulate matter (PM2.5) and their elements composition are practically non-existent in South America. In order to understand the natural exposure of the typical Brazilian population to PM2.5 and their trace element composition, we measured PM2.5 concentrations and collected mass on filters for nine continuous hours during a typical workday of volunteers. In addition, bus routes were performed at peak and non-peak periods, mimicking the routine activity of the population. Mean concentrations of PM2.5 in the bus and car groups were similar while the fraction of BCe was higher for the bus group. For all routes, mean PM2.5 concentrations were higher during peak than non-peak hours, with an average of 43.5 ± 33.1 μg m−3 and 14.3 ± 10.2 μg m−3, respectively. The trace elements S, K and Na originated mainly from vehicle emissions; Na was associated with the presence of biofuel in diesel. Toxic elements (Pb, Cr, Cu, Ni, Zn, Mn) were found at low levels as evident by the total hazard index that ranged from 2.15 × 10−03 to 1.38 for volunteers. For all routes, the hazard index ranged from 2.25 × 10−03 to 5.03. Average PM2.5 respiratory deposition dose was estimated to be 0.60 μg/kg-hour for peak hours. Potential health damages to people during their movements and at workplaces close to the traffic were identified. Improvements in the design of the building to reduce the entrance of air pollutants as well as the use of filters in the buses could help to limit population exposure.
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| 9. |
- Ostaszewski, Marek, et al.
(author)
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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
- 2021
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In: Molecular Systems Biology. - : John Wiley & Sons. - 1744-4292 .- 1744-4292. ; 17:10
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Journal article (peer-reviewed)abstract
- We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
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| 10. |
- Polic, Daniela, et al.
(author)
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Large-scale spatial variation and phenotypic integration in three Argynnini species inform about functions and evolutionary drivers of butterfly wings
- 2023
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In: Frontiers in Ecology and Evolution. - : Frontiers Media S.A.. - 2296-701X. ; 11
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Journal article (peer-reviewed)abstract
- Understanding how large-scale environmental variability may shape the distribution of phenotypic variation remains central to evolutionary biology. Across-species comparisons of trait variation alongside environmental gradients may offer valuable insights into how different species may respond to similar selective pressures. We conducted a comparative morphological study (>32° latitude and >47° longitude) on three closely related Argynnini butterfly species, Speyeria aglaja, Fabriciana adippe, and F. niobe. We measured wing size and coloration to assess (1) whether they respond similarly or differently to environmental factors (longitude, latitude, altitude, temperature, precipitation, solar radiation, wind speed); (2) if these factors correspond with those associated with the species’ genetic structure based on a previous study; and (3) whether correlations between phenotypic traits within individuals are species-specific. We found common and species-specific associations of climatic (precipitation, wind speed) and geographic (longitude, altitude) factors with the composite phenotypic variation. Wing size was associated with different variables in the studied species, while melanisation mainly increased in cooler regions in all species, suggesting that the need for temperature regulation is a strong selective pressure on melanisation. Wing size was associated with the genetic structure in all species, highlighting the functional importance of this trait. The environmental drivers associated with the phenotypic variation in S. aglaja and F. adippe were largely the same as those associated with their genetic structure, hinting at a genetic underpinning of the observed morphological variation due to local adaption. We report some distinct intraspecific trait correlations in S. aglaja and F. adippe, indicative of independent phenotypic integration. These phenotypes seem to be associated with protection against predators and thermal regulation in the respective habitats of both species, suggesting that similar selective pressures have resulted in the evolution of different trait combinations. Some of the inter-specific differences could be related to diverging niche breadths and dispersal capacities, exemplifying that the evolution of trait integration and spatial phenotypic differentiation may differ between closely related species with overlapping distribution ranges. Our findings highlight the importance of comparative assessments of variation, and demonstrate that the relative effects of drivers of variability may vary between sister species.
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