| 1. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 2. |
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| 3. |
- Abelev, Betty, et al.
(author)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Journal article (peer-reviewed)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 4. |
- Abelev, Betty, et al.
(author)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :11
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Journal article (peer-reviewed)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 5. |
- Calderón-Contreras, Rafael, et al.
(author)
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A regional PECS node built from place-based social-ecological sustainability research in Latin America and the Caribbean
- 2022
-
In: Ecosystems and People. - : Informa UK Limited. - 2639-5908 .- 2639-5916. ; 18:1, s. 1-14
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Journal article (peer-reviewed)abstract
- Sustainability requires a combination of meaningful co-production of locally relevant solutions, synthesis of insights gained across regions, and increased cooperation between science, policy and practice. The Programme for Ecosystem Change and Society (PECS) has been coordinating Place-Based Social-Ecological Sustainability Research (PBSESR) across the globe and emphasizes the need for regional scientific nodes from diverse biocultural regions to inform sustainability science and action. In this paper, we assess the strengths of the PBSESR communities in Latin America and the Caribbean (LAC). We provide an overview of PBSESR literature associated with this region and highlight the achievements of two prominent regional networks: The Social-Ecological Systems and Sustainability Research Network from Mexico (SocioEcoS) and the South American Institute for Resilience and Sustainability Studies from Uruguay (SARAS Institute). Finally, we identify the potential in these nodes to constitute a regional PECS node in Latin America and discuss the capacity needed to ensure such function. The results of the literature review show that while still loosely interconnected across the region, networks play key roles in connecting otherwise cloistered teams and we illustrate how the SocioEcoS network (focusing on transdisciplinary co-production of knowledge towards sustainability) and the SARAS Institute (focusing on innovative approaches for looking at complex social-ecological problems, rooted in slow science and arts) operate as key connectors in the region. We conclude that these organizations combined can embody a Latin American node for PECS, and would thereby not only contribute to regional but also global capacities to advance the sustainability agenda.
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| 6. |
- Lembrechts, Jonas J., et al.
(author)
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SoilTemp : A global database of near-surface temperature
- 2020
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In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 26:11, s. 6616-6629
-
Journal article (peer-reviewed)abstract
- Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
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| 7. |
- Marto, João Pedro, et al.
(author)
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Safety and Outcome of Revascularization Treatment in Patients With Acute Ischemic Stroke and COVID-19: The Global COVID-19 Stroke Registry.
- 2023
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In: Neurology. - 1526-632X. ; 100:7
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Journal article (peer-reviewed)abstract
- COVID-19-related inflammation, endothelial dysfunction, and coagulopathy may increase the bleeding risk and lower the efficacy of revascularization treatments in patients with acute ischemic stroke (AIS). We aimed to evaluate the safety and outcomes of revascularization treatments in patients with AIS and COVID-19.This was a retrospective multicenter cohort study of consecutive patients with AIS receiving intravenous thrombolysis (IVT) and/or endovascular treatment (EVT) between March 2020 and June 2021 tested for severe acute respiratory syndrome coronavirus 2 infection. With a doubly robust model combining propensity score weighting and multivariate regression, we studied the association of COVID-19 with intracranial bleeding complications and clinical outcomes. Subgroup analyses were performed according to treatment groups (IVT-only and EVT).Of a total of 15,128 included patients from 105 centers, 853 (5.6%) were diagnosed with COVID-19; of those, 5,848 (38.7%) patients received IVT-only and 9,280 (61.3%) EVT (with or without IVT). Patients with COVID-19 had a higher rate of symptomatic intracerebral hemorrhage (SICH) (adjusted OR 1.53; 95% CI 1.16-2.01), symptomatic subarachnoid hemorrhage (SSAH) (OR 1.80; 95% CI 1.20-2.69), SICH and/or SSAH combined (OR 1.56; 95% CI 1.23-1.99), 24-hour mortality (OR 2.47; 95% CI 1.58-3.86), and 3-month mortality (OR 1.88; 95% CI 1.52-2.33). Patients with COVID-19 also had an unfavorable shift in the distribution of the modified Rankin score at 3 months (OR 1.42; 95% CI 1.26-1.60).Patients with AIS and COVID-19 showed higher rates of intracranial bleeding complications and worse clinical outcomes after revascularization treatments than contemporaneous non-COVID-19 patients receiving treatment. Current available data do not allow direct conclusions to be drawn on the effectiveness of revascularization treatments in patients with COVID-19 or to establish different treatment recommendations in this subgroup of patients with ischemic stroke. Our findings can be taken into consideration for treatment decisions, patient monitoring, and establishing prognosis.The study was registered under ClinicalTrials.gov identifier NCT04895462.
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| 8. |
- Nguyen, Thanh N, et al.
(author)
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Global Impact of the COVID-19 Pandemic on Stroke Volumes and Cerebrovascular Events: A 1-Year Follow-up.
- 2023
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In: Neurology. - 1526-632X. ; 100:4
-
Journal article (peer-reviewed)abstract
- Declines in stroke admission, IV thrombolysis (IVT), and mechanical thrombectomy volumes were reported during the first wave of the COVID-19 pandemic. There is a paucity of data on the longer-term effect of the pandemic on stroke volumes over the course of a year and through the second wave of the pandemic. We sought to measure the effect of the COVID-19 pandemic on the volumes of stroke admissions, intracranial hemorrhage (ICH), IVT, and mechanical thrombectomy over a 1-year period at the onset of the pandemic (March 1, 2020, to February 28, 2021) compared with the immediately preceding year (March 1, 2019, to February 29, 2020).We conducted a longitudinal retrospective study across 6 continents, 56 countries, and 275 stroke centers. We collected volume data for COVID-19 admissions and 4 stroke metrics: ischemic stroke admissions, ICH admissions, IVT treatments, and mechanical thrombectomy procedures. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases.There were 148,895 stroke admissions in the 1 year immediately before compared with 138,453 admissions during the 1-year pandemic, representing a 7% decline (95% CI [95% CI 7.1-6.9]; p < 0.0001). ICH volumes declined from 29,585 to 28,156 (4.8% [5.1-4.6]; p < 0.0001) and IVT volume from 24,584 to 23,077 (6.1% [6.4-5.8]; p < 0.0001). Larger declines were observed at high-volume compared with low-volume centers (all p < 0.0001). There was no significant change in mechanical thrombectomy volumes (0.7% [0.6-0.9]; p = 0.49). Stroke was diagnosed in 1.3% [1.31-1.38] of 406,792 COVID-19 hospitalizations. SARS-CoV-2 infection was present in 2.9% ([2.82-2.97], 5,656/195,539) of all stroke hospitalizations.There was a global decline and shift to lower-volume centers of stroke admission volumes, ICH volumes, and IVT volumes during the 1st year of the COVID-19 pandemic compared with the prior year. Mechanical thrombectomy volumes were preserved. These results suggest preservation in the stroke care of higher severity of disease through the first pandemic year.This study is registered under NCT04934020.
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| 9. |
- Pacheco, Gonçalo P., et al.
(author)
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Experimental and Kinetic Investigation of Stoichiometric to Rich NH3/H2/Air Flames in a Swirl and Bluff-Body Stabilized Burner
- 2021
-
In: Energy and Fuels. - : American Chemical Society (ACS). - 0887-0624 .- 1520-5029. ; 35:9, s. 7201-7216
-
Journal article (peer-reviewed)abstract
- Ammonia (NH3) is an inorganic substance considered as a promising fuel for power sector decarbonization. As a result of the absence of carbon in its structure, ammonia is capable of producing energy with zero CO2 emissions when burned. However, the combustion of NH3 presents several challenges as a result of its low reactivity and low flame speed as well as the formation of large quantities of nitrogen oxides (NOx) and frequent ammonia slip. A suggested solution for gas turbines is the use of rich-to-lean approaches, with a fuel-rich first-stage combustion, which mitigates NOx formation, followed by a lean phase for the oxidation of the remaining reactants, improving combustion efficiency. To help assess this concept, the present work investigates experimentally and computationally the combustion of ammonia/air mixtures, enriched by hydrogen (H2) for enhanced burning characteristics, in a swirl and bluff-body stabilized burner, at stoichiometric to fuel-rich conditions. Stability tests were performed for a fixed thermal input (2.8 kW), and flames of fuel/air equivalence ratios of 1.0, 1.1, and 1.2, with molar fractions of ammonia in fuel of 0.7 and 0.8, were studied. Temperature profiles along the combustor axis were measured, and flue gas measurements for NOx emissions and unburned NH3 and H2 concentrations were performed for the six studied flames. Computational simulations were performed using a chemical reactor network coupled with recent kinetic mechanisms to compare species trends and further understand the NOx formation and NH3 conversion into hydrogen, through rate of production analyses. It was found that the present laboratory combustor performed well in terms of flame stability, also generating low levels of NOx emissions in all fuel-rich conditions. H2 was detected in high concentrations in the flue gas, partially originated from ammonia dissociation, and is followed by high unburned ammonia emissions. Both H2 and NH3 emissions increase with the equivalence ratio. A secondary, spontaneous diffusion flame was observed above the combustor, proving that the flue gas may subsequently be burned. Higher fractions of hydrogen in the fuel generate more unburned ammonia but also higher H2 concentrations in the flue gas. The predictions based on a reactor network model coupled with the evaluated kinetic mechanisms presented good agreement with the experimentally observed species trends and fair agreement with species values.
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| 10. |
- Aapro, Matti, et al.
(author)
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The MAGIC survey in hormone receptor positive (HR+), HER2-negative (HER2−) breast cancer: When might multigene assays be of value?
- 2017
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In: Breast. - : Elsevier BV. - 0960-9776 .- 1532-3080. ; 33, s. 191-199
-
Journal article (peer-reviewed)abstract
- © 2017 Background A modest proportion of patients with early stage hormone receptor-positive (HR+), HER2-negative (HER2−) breast cancer benefit from adjuvant chemotherapy. Traditionally, treatment recommendations are based on clinical/pathologic criteria that are not predictive of chemotherapy benefit. Multigene assays provide prognostic and predictive information that can help to make more informed treatment decisions. The MAGIC survey evaluated international differences in treatment recommendations, how traditional parameters are used for making treatment choices, and for which patients treating physicians feel most uncertain about their decisions. Methods The MAGIC survey captured respondents' demographics, practice patterns, relevance of traditional parameters for treatment decisions, and use of or interest in using multigene assays. Using this information, a predictive model was created to simulate treatment recommendations for 672 patient profiles. Results The survey was completed by 911 respondents (879 clinicians, 32 pathologists) from 52 countries. Chemo-endocrine therapy was recommended more often than endocrine therapy alone, but there was substantial heterogeneity in treatment recommendations in 52% of the patient profiles; approximately every fourth physician provided a different treatment recommendation. The majority of physicians indicated they wanted to use multigene assays clinically. Lack of reimbursement/availability were the main reasons for non-usage. Conclusions The survey reveals substantial heterogeneity in treatment recommendations. Physicians have uncertainty in treatment recommendations in a high proportion of patients with intermediate risk features using traditional parameters. In HR+, HER2− patients with early disease the findings highlight the need for additional markers that are both prognostic and predictive of chemotherapy benefit that may support more-informed treatment decisions.
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| 11. |
- Abelev, Betty, et al.
(author)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
-
In: Journal of High Energy Physics. - 1029-8479. ; :7
-
Journal article (peer-reviewed)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 12. |
- Fonseca, Joana, et al.
(author)
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Adaptive Sampling of Algal Blooms Using an Autonomous Underwater Vehicle and Satellite Imagery
- 2023
-
In: 2023 IEEE Conference on Control Technology and Applications, CCTA 2023. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 638-644
-
Conference paper (peer-reviewed)abstract
- This paper proposes a method that uses satellite data to improve adaptive sampling missions. We find and track algal bloom fronts using an autonomous underwater vehicle (AUV) equipped with a sensor that measures the concentration of chlorophyll a. Chlorophyll a concentration indicates the presence of algal blooms. The proposed method learns the kernel parameters of a Gaussian process model using satellite images of chlorophyll a from previous days. The AUV estimates the chlorophyll a concentration online using locally collected data. The algal bloom front estimate is fed to the motion control algorithm. The performance of this method is evaluated through simulations using a real dataset of an algal bloom front in the Baltic. We consider a real-world scenario with sensor and localization noise and with a detailed AUV model.
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| 13. |
- Gorasso, Vanessa, et al.
(author)
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Burden of disease attributable to risk factors in European countries: a scoping literature review
- 2023
-
In: Archives of Public Health. - 0778-7367 .- 2049-3258. ; 81:1
-
Research review (peer-reviewed)abstract
- Objectives: Within the framework of the burden of disease (BoD) approach, disease and injury burden estimates attributable to risk factors are a useful guide for policy formulation and priority setting in disease prevention. Considering the important differences in methods, and their impact on burden estimates, we conducted a scoping literature review to: (1) map the BoD assessments including risk factors performed across Europe; and (2) identify the methodological choices in comparative risk assessment (CRA) and risk assessment methods. Methods: We searched multiple literature databases, including grey literature websites and targeted public health agencies websites. Results: A total of 113 studies were included in the synthesis and further divided into independent BoD assessments (54 studies) and studies linked to the Global Burden of Disease (59 papers). Our results showed that the methods used to perform CRA varied substantially across independent European BoD studies. While there were some methodological choices that were more common than others, we did not observe patterns in terms of country, year or risk factor. Each methodological choice can affect the comparability of estimates between and within countries and/or risk factors, since they might significantly influence the quantification of the attributable burden. From our analysis we observed that the use of CRA was less common for some types of risk factors and outcomes. These included environmental and occupational risk factors, which are more likely to use bottom-up approaches for health outcomes where disease envelopes may not be available. Conclusions: Our review also highlighted misreporting, the lack of uncertainty analysis and the under-investigation of causal relationships in BoD studies. Development and use of guidelines for performing and reporting BoD studies will help understand differences, avoid misinterpretations thus improving comparability among estimates.
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| 14. |
- Hoek, Gerard, et al.
(author)
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A review of exposure assessment methods for epidemiological studies of health effects related to industrially contaminated sites
- 2018
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In: Epidemiologia & Prevenzione. - : Inferenze. - 1120-9763 .- 2385-1937. ; 42:5-6, s. 21-36
-
Research review (peer-reviewed)abstract
- BACKGROUND: this paper is based upon work from COST Action ICSHNet. Health risks related to living close to industrially contaminated sites (ICSs) are a public concern. Toxicology-based risk assessment of single contaminants is the main approach to assess health risks, but epidemiological studies which investigate the relationships between exposure and health directly in the affected population have contributed important evidence. Limitations in exposure assessment have substantially contributed to uncertainty about associations found in epidemiological studies. OBJECTIVES: to examine exposure assessment methods that have been used in epidemiological studies on ICSs and to provide recommendations for improved exposure assessment in epidemiological studies by comparing exposure assessment methods in epidemiological studies and risk assessments. METHODS: after defining the multi-media framework of exposure related to ICSs, we discussed selected multi-media models applied in Europe. We provided an overview of exposure assessment in 54 epidemiological studies from a systematic review of hazardous waste sites; a systematic review of 41 epidemiological studies on incinerators and 52 additional studies on ICSs and health identified for this review. RESULTS: we identified 10 multi-media models used in Europe primarily for risk assessment. Recent models incorporated estimation of internal biomarker levels. Predictions of the models differ particularly for the routes 'indoor air inhalation' and 'vegetable consumption'. Virtually all of the 54 hazardous waste studies used proximity indicators of exposure, based on municipality or zip code of residence (28 studies) or distance to a contaminated site (25 studies). One study used human biomonitoring. In virtually all epidemiological studies, actual land use was ignored. In the 52 additional studies on contaminated sites, proximity indicators were applied in 39 studies, air pollution dispersion modelling in 6 studies, and human biomonitoring in 9 studies. Exposure assessment in epidemiological studies on incinerators included indicators (presence of source in municipality and distance to the incinerator) and air dispersion modelling. Environmental multi-media modelling methods were not applied in any of the three groups of studies. CONCLUSIONS: recommendations for refined exposure assessment in epidemiological studies included the use of more sophisticated exposure metrics instead of simple proximity indicators where feasible, as distance from a source results in misclassification of exposure as it ignores key determinants of environmental fate and transport, source characteristics, land use, and human consumption behaviour. More validation studies using personal exposure or human biomonitoring are needed to assess misclassification of exposure. Exposure assessment should take more advantage of the detailed multi-media exposure assessment procedures developed for risk assessment. The use of indicators can be substantially improved by linking definition of zones of exposure to existing knowledge of extent of dispersion. Studies should incorporate more often land use and individual behaviour.
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| 15. |
- Householder, John Ethan, et al.
(author)
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One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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In: NATURE ECOLOGY & EVOLUTION. - 2397-334X. ; 8, s. 901-911
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Journal article (peer-reviewed)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 16. |
- Luize, Bruno Garcia, et al.
(author)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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In: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699. ; 51:7, s. 1163-1184
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Journal article (peer-reviewed)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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| 17. |
- Marks, David I, et al.
(author)
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Unrelated umbilical cord blood transplant for adult acute lymphoblastic leukemia in first and second complete remission : a comparison with allografts from adult unrelated donors.
- 2014
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In: Haematologica. - : Ferrata Storti Foundation (Haematologica). - 0390-6078 .- 1592-8721. ; 99:2, s. 322-8
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Journal article (peer-reviewed)abstract
- Allogeneic hematopoietic cell transplantation has an established role in the treatment of adults with acute lymphoblastic leukemia whose survival when recipients of grafts from adult unrelated donors approaches that of recipients of grafts from sibling donors. Our aim was to determine the role of mismatched unrelated cord blood grafts in transplantation for 802 adults with acute lymphoblastic leukemia in first or second complete remission. Using Cox regression we compared outcomes after 116 mismatched single or double cord blood transplants, 546 peripheral blood progenitor cell transplants and 140 bone marrow transplants. The characteristics of the recipients and their diseases were similar except cord blood recipients were younger, more likely to be non-Caucasians and more likely to have a low white blood cell count at diagnosis. There were differences in donor-recipient human leukocyte antigen-match depending on the source of the graft. Most adult donor transplants were matched at the allele-level considering human leukocyte antigens-A, -B, -C and -DRB1. In contrast, most cord blood transplants were mismatched and considered antigen-level matching; 57% were mismatched at two loci and 29% at one locus whereas only 29% of adult donor transplants were mismatched at one locus and none at two loci. There were no differences in the 3-year probabilities of survival between recipients of cord blood (44%), matched adult donor (44%) and mismatched adult donor (43%) transplants. Cord blood transplants engrafted slower and were associated with less grade 2-4 acute but similar chronic graft-versus-host disease, relapse, and transplant-related mortality. The survival of cord blood graft recipients was similar to that of recipients of matched or mismatched unrelated adult donor grafts and so cord blood should be considered a valid alternative source of stem cells for adults with acute lymphoblastic leukemia in the absence of a matched unrelated adult donor.
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| 18. |
- Martins Dos Santos, Vitor, et al.
(author)
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Systems Biology in ELIXIR: modelling in the spotlight
- 2022
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In: F1000Research. - : F1000 Research Ltd. - 1759-796X .- 2046-1402. ; 11
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Journal article (peer-reviewed)abstract
- In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
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| 19. |
- Migliavacca, Mirco, et al.
(author)
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Semiempirical modeling of abiotic and biotic factors controlling ecosystem respiration across eddy covariance sites
- 2011
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In: Global Change Biology. - : Wiley. - 1354-1013. ; 17:1, s. 390-409
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Journal article (peer-reviewed)abstract
- In this study we examined ecosystem respiration (R-ECO) data from 104 sites belonging to FLUXNET, the global network of eddy covariance flux measurements. The goal was to identify the main factors involved in the variability of R-ECO: temporally and between sites as affected by climate, vegetation structure and plant functional type (PFT) (evergreen needleleaf, grasslands, etc.). We demonstrated that a model using only climate drivers as predictors of R-ECO failed to describe part of the temporal variability in the data and that the dependency on gross primary production (GPP) needed to be included as an additional driver of R-ECO. The maximum seasonal leaf area index (LAI(MAX)) had an additional effect that explained the spatial variability of reference respiration (the respiration at reference temperature T-ref=15 degrees C, without stimulation introduced by photosynthetic activity and without water limitations), with a statistically significant linear relationship (r2=0.52, P < 0.001, n=104) even within each PFT. Besides LAI(MAX), we found that reference respiration may be explained partially by total soil carbon content (SoilC). For undisturbed temperate and boreal forests a negative control of total nitrogen deposition (N-depo) on reference respiration was also identified. We developed a new semiempirical model incorporating abiotic factors (climate), recent productivity (daily GPP), general site productivity and canopy structure (LAI(MAX)) which performed well in predicting the spatio-temporal variability of R-ECO, explaining > 70% of the variance for most vegetation types. Exceptions include tropical and Mediterranean broadleaf forests and deciduous broadleaf forests. Part of the variability in respiration that could not be described by our model may be attributed to a series of factors, including phenology in deciduous broadleaf forests and management practices in grasslands and croplands.
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| 20. |
- Mir, Zahid Mohammad, et al.
(author)
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Numerical and Experimental Analysis of Self-Protection in Reinforced Concrete due to Application of Mg–Al–NO2 Layered Double Hydroxides
- 2020
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In: Advanced Engineering Materials. - : Wiley-VCH Verlag. - 1438-1656 .- 1527-2648.
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Journal article (peer-reviewed)abstract
- Concrete possesses an intrinsic chloride binding capacity. Chloride ions from the environment bind with the hydrated cementitious phases in the form of bound chlorides. The contribution of chemically bound chlorides toward increasing the service life of concrete structures is vital as they help in slowing down the chloride diffusion in the concrete thereby delaying reinforcement depassivation. The authors attempt to increase the chloride binding capacity of concrete by adding a small amount of Mg–Al–NO2 layered double hydroxides (LDHs) with the objective to delay reinforcement corrosion and by this to considerably extend the service life of concrete structures situated in harsh environments. This study presents numerical and experimental analysis of the action of LDH in concrete. Formation factor is used to determine the effective chloride diffusion coefficient. In addition, the chloride binding isotherms together with Poisson–Nernst–Planck equations are used to model the chloride ingress. A comparable chloride binding is observed for concrete with and without Mg–Al–NO2, depicting only a slight chloride uptake by Mg–Al–NO2. Further investigations are conducted to understand this behavior by studying the stability and chloride entrapping capacity Mg–Al–NO2 in concrete. © 2020 The Authors.
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| 21. |
- Oskyrko, Oleksandra, et al.
(author)
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The possible origin of the common wall lizard, Podarcis muralis (Laurenti, 1768) in Ukraine
- 2020
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In: Herpetozoa. - 1013-4425. ; 33, s. 87-93
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Research review (peer-reviewed)abstract
- The phylogenetic relationships and possible origin of a putative non-native population of Podarcis muralis in Ukraine were assessed based on sequences of the mitochondrial gene cytochrome b. Phylogenetic analysis showed that the Ukrainian lizards belong to two distinct mitochondrial lineages (haplogroups), both occurring within the Central Balkan clade, which includes most of central and south-eastern European populations. From overall three detected Ukrainian haplotypes, one haplotype share same genetic signal with the hyplotype from the locality Bjala (Bulgaria), the other two are unique for Ukrainian population. Two of haplotypes correspond with haplogroup covering large geographic region of Bulgaria, Serbia, and Romania. These results reinforce previous findings that the species has the ability to establish new populations out of its native range. While most introductions to Germany and Britain have been deliberate, it appears likely that human transport of goods via the Danube river of goods is responsible for the range expansion into Ukraine.
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| 22. |
- Perfecto-Avalos, Yocanxóchitl, et al.
(author)
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Denaturing high-performance liquid chromatography and principal component analysis for identification of DNA point mutations in breast cancer and lymphoma samples
- 2018
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In: Journal of Chemometrics. - : Wiley. - 0886-9383. ; 32:10
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Journal article (peer-reviewed)abstract
- Abstract DNA mutations are identified by techniques that use the knowledge of the wild-type DNA sequence and its mutated variant. The involved analytic methods must be accurate, rapid, and sustainable, if a clinical application is pursued. High-performance liquid chromatography under denaturing conditions is a useful technique to screen mutations. Denaturing high-performance liquid chromatography resultant chromatograms are suitable for feature extraction analysis with multivariate methods such as principal component analysis. In this work, principal component analysis was applied to analyze the chromatograms from 3 different genes. Fragments with verified wild-type sequence were used as reference and samples with sequence unknown were tested. A statistical characterization based on Tukey’s boxplot equation of principal component scores allowed us to analyze the distance distribution between reference and sample clusters to establish a classification criterion: an outlier could represent a mutated sample, and a typical value could be a wild-type sample. Identified outliers were further analyzed by sequencing and proved to carry a mutation. From 72 datasets with a total of 4258 injections, we successfully assessed the classification criterion, identifying mutated samples in lymphoma and breast cancer patients with ratio of prediction Gmean = [0.89, 1.00]. Compared with sequencing analysis, this procedure reduced time and costs.
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| 23. |
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| 24. |
- Quaglia, Federica, et al.
(author)
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DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation
- 2022
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:D1, s. D480-D487
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Journal article (peer-reviewed)abstract
- The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
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| 25. |
- Rocha, A., et al.
(author)
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Optimal AUV trajectory planning and execution control for maritime pollution incident response
- 2021
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In: Oceans Conference Record (IEEE). - : Institute of Electrical and Electronics Engineers Inc..
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Conference paper (peer-reviewed)abstract
- Marine pollution incidents can have a huge impact on different ecosystems, with unpredictable short- and long-term consequences. Once the pollutant is detected, it is critical to quickly understand its characteristics so that authorities can lay out an adequate response. In parallel to the time- and cost-constrained traditional operational means, this paper suggests the use of AUVs for the sampling procedures of marine pollution incidents, to increase the speed and efficiency of operations. A new software architecture is developed, integrating trajectory optimization for AUVs into a software toolchain that allows human operators to plan, simulate, and control multiple vehicles deployments. A method to optimize AUVs deployment position and time is also presented. The overall architecture is simulated using high-resolution hydrodynamic data from the Ria de Aveiro lagoon and the adjacent coastal area, in Aveiro, Portugal.
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| 26. |
- Sartelli, Massimo, et al.
(author)
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Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action
- 2023
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In: WORLD JOURNAL OF EMERGENCY SURGERY. - 1749-7922. ; 18:1
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Research review (peer-reviewed)abstract
- Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.
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| 27. |
- Shome, Sayane, et al.
(author)
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Global network of computational biology communities : ISCB's Regional Student Groups breaking barriers
- 2019
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In: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 8
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Journal article (peer-reviewed)abstract
- Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: "Nurture the new generation of computational biologists".
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| 28. |
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| 29. |
- ter Steege, Hans, et al.
(author)
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Mapping density, diversity and species-richness of the Amazon tree flora
- 2023
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In: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1
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Journal article (peer-reviewed)abstract
- Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution. A study mapping the tree species richness in Amazonian forests shows that soil type exerts a strong effect on species richness, probably caused by the areas of these forest types. Cumulative water deficit, tree density and temperature seasonality affect species richness at a regional scale.
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