| 1. |
- Sabatini, F. M., et al.
(author)
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sPlotOpen - An environmentally balanced, open-access, global dataset of vegetation plots
- 2021
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In: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238.
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Journal article (peer-reviewed)abstract
- Motivation Assessing biodiversity status and trends in plant communities is critical for understanding, quantifying and predicting the effects of global change on ecosystems. Vegetation plots record the occurrence or abundance of all plant species co-occurring within delimited local areas. This allows species absences to be inferred, information seldom provided by existing global plant datasets. Although many vegetation plots have been recorded, most are not available to the global research community. A recent initiative, called 'sPlot', compiled the first global vegetation plot database, and continues to grow and curate it. The sPlot database, however, is extremely unbalanced spatially and environmentally, and is not open-access. Here, we address both these issues by (a) resampling the vegetation plots using several environmental variables as sampling strata and (b) securing permission from data holders of 105 local-to-regional datasets to openly release data. We thus present sPlotOpen, the largest open-access dataset of vegetation plots ever released. sPlotOpen can be used to explore global diversity at the plant community level, as ground truth data in remote sensing applications, or as a baseline for biodiversity monitoring. Main types of variable contained Vegetation plots (n = 95,104) recording cover or abundance of naturally co-occurring vascular plant species within delimited areas. sPlotOpen contains three partially overlapping resampled datasets (c. 50,000 plots each), to be used as replicates in global analyses. Besides geographical location, date, plot size, biome, elevation, slope, aspect, vegetation type, naturalness, coverage of various vegetation layers, and source dataset, plot-level data also include community-weighted means and variances of 18 plant functional traits from the TRY Plant Trait Database. Spatial location and grain Global, 0.01-40,000 m(2). Time period and grain 1888-2015, recording dates. Major taxa and level of measurement 42,677 vascular plant taxa, plot-level records. Software format Three main matrices (.csv), relationally linked.
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| 2. |
- Willerslev, E, et al.
(author)
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Fifty thousand years of arctic vegetation change and megafauna diet
- 2014
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 506:7486, s. 47-47
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Journal article (peer-reviewed)abstract
- Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
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| 3. |
- Tedersoo, Leho, et al.
(author)
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Global patterns in endemicity and vulnerability of soil fungi.
- 2022
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In: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
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Journal article (peer-reviewed)abstract
- Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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| 4. |
- Hammen, V. C., et al.
(author)
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Establishment of a cross-European field site network in the ALARM project for assessing large-scale changes in biodiversity
- 2010
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In: Environmental Monitoring & Assessment. - : Springer Science and Business Media LLC. - 1573-2959 .- 0167-6369. ; 164:1-4, s. 337-348
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Journal article (peer-reviewed)abstract
- The field site network (FSN) plays a central role in conducting joint research within all Assessing Large-scale Risks for biodiversity with tested Methods (ALARM) modules and provides a mechanism for integrating research on different topics in ALARM on the same site for measuring multiple impacts on biodiversity. The network covers most European climates and biogeographic regions, from Mediterranean through central European and boreal to subarctic. The project links databases with the European-wide field site network FSN, including geographic information system (GIS)-based information to characterise the test location for ALARM researchers for joint on-site research. Maps are provided in a standardised way and merged with other site-specific information. The application of GIS for these field sites and the information management promotes the use of the FSN for research and to disseminate the results. We conclude that ALARM FSN sites together with other research sites in Europe jointly could be used as a future backbone for research proposals.
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| 5. |
- Manni, Giovanni Li, et al.
(author)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Journal article (peer-reviewed)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 6. |
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| 7. |
- Potts, Simon G., et al.
(author)
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Developing European conservation and mitigation tools for pollination services: approaches of the STEP (Status and Trends of European Pollinators) project
- 2011
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In: Journal of Apicultural Research. - 0021-8839 .- 2078-6913. ; 50:2, s. 152-164
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Research review (peer-reviewed)abstract
- Pollinating insects form a key component of European biodiversity, and provide a vital ecosystem service to crops and wild plants. There is growing evidence of declines in both wild and domesticated pollinators, and parallel declines in plants relying upon them. The STEP project (Status and Trends of European Pollinators, 2010-2015, www.step-project.net) is documenting critical elements in the nature and extent of these declines, examining key functional traits associated with pollination deficits, and developing a Red List for some European pollinator groups. Together these activities are laying the groundwork for future pollinator monitoring programmes. STEP is also assessing the relative importance of potential drivers of pollinator declines, including climate change, habitat loss and fragmentation, agrochemicals, pathogens, alien species, light pollution, and their interactions. We are measuring the ecological and economic impacts of declining pollinator services and floral resources, including effects on wild plant populations, crop production and human nutrition. STEP is reviewing existing and potential mitigation options, and providing novel tests of their effectiveness across Europe. Our work is building upon existing and newly developed datasets and models, complemented by spatially-replicated campaigns of field research to fill gaps in current knowledge. Findings are being integrated into a policy-relevant framework to create evidence-based decision support tools. STEP is establishing communication links to a wide range of stakeholders across Europe and beyond, including policy makers, beekeepers, farmers, academics and the general public. Taken together, the STEP research programme aims to improve our understanding of the nature, causes, consequences and potential mitigation of declines in pollination services at local, national, continental and global scales.
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| 8. |
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| 9. |
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| 10. |
- Walther, Gian-Reto, et al.
(author)
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Alien species in a warmer world: risks and opportunities
- 2009
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In: Trends in Ecology & Evolution. - : Elsevier BV. - 1872-8383 .- 0169-5347. ; 24:12, s. 686-693
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Research review (peer-reviewed)abstract
- Climate change and biological invasions are key processes affecting global biodiversity, yet their effects have usually been considered separately. Here, we emphasise that global warming has enabled alien species to expand into regions in which they previously could not survive and reproduce. Based on a review of climate-mediated biological invasions of plants, invertebrates, fishes and birds, we discuss the ways in which climate change influences biological invasions. We emphasise the role of alien species in a more dynamic context of shifting species' ranges and changing communities. Under these circumstances, management practices regarding the occurrence of 'new' species could range from complete eradication to tolerance and even consideration of the 'new' species as an enrichment of local biodiversity and key elements to maintain ecosystem services.
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| 11. |
- Bajbouj, Malek, et al.
(author)
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Two-year outcome of vagus nerve stimulation in treatment-resistant depression
- 2010
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In: Journal of Clinical Psychopharmacology. - : Lippincott Williams & Wilkins. - 0271-0749 .- 1533-712X. ; 30:3, s. 273-281
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Journal article (peer-reviewed)abstract
- One of the major goals of antidepressant treatment is a sustained response and remission of depressive symptoms. Some of the previous studies of vagus nerve stimulation (VNS) have suggested antidepressant effects. Our naturalistic study assessed the efficacy and the safety of VNS in 74 European patients with therapy-resistant major depressive disorder. Psychometric measures were obtained after 3, 12, and 24 months of VNS. Mixed-model repeated-measures analysis of variance revealed a significant reduction (P < or = 0.05) at all the 3 time points in the 28-item Hamilton Rating Scale for Depression (HRSD28) score, the primary outcome measure. After 2 years, 53.1% (26/49) of the patients fulfilled the response criteria (> or =50% reduction in the HRSD28 scores from baseline) and 38.9% (19/49) fulfilled the remission criteria (HRSD28 scores < or = 10). The proportion of patients who fulfilled the remission criteria remained constant as the duration of VNS treatment increased. Voice alteration, cough, and pain were the most frequently reported adverse effects. Two patients committed suicide during the study; no other deaths were reported. No statistically significant differences were seen in the number of concomitant antidepressant medications. The results of this 2-year open-label trial suggest a clinical response and a comparatively benign adverse effect profile among patients with treatment-resistant depression.
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| 12. |
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| 13. |
- Bogers, M., et al.
(author)
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The open innovation research landscape : established perspectives and emerging themes across different levels of analysis
- 2017
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In: Industry and Innovation. - : Routledge. - 1366-2716 .- 1469-8390. ; 24:1, s. 8-40
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Journal article (peer-reviewed)abstract
- This paper provides an overview of the main perspectives and themes emerging in research on open innovation (OI). The paper is the result of a collaborative process among several OI scholars–having a common basis in the recurrent Professional Development Workshop on ‘Researching Open Innovation’ at the Annual Meeting of the Academy of Management. In this paper, we present opportunities for future research on OI, organised at different levels of analysis. We discuss some of the contingencies at these different levels, and argue that future research needs to study OI–originally an organisational-level phenomenon–across multiple levels of analysis. While our integrative framework allows comparing, contrasting and integrating various perspectives at different levels of analysis, further theorising will be needed to advance OI research. On this basis, we propose some new research categories as well as questions for future research–particularly those that span across research domains that have so far developed in isolation.
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| 14. |
- Boyer, E, et al.
(author)
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SHREC 2011: Robust Feature Detection and Description Benchmark
- 2011
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Conference paper (peer-reviewed)abstract
- Feature-based approaches have recently become very popular in computer vision and image analysis applications, and are becoming a promising direction in shape retrieval. SHREC’11 robust feature detection and description benchmark simulates the feature detection and description stages of feature-based shape retrieval algorithms. The benchmark tests the performance of shape feature detectors and descriptors under a wide variety of transformations. The benchmark allows evaluating how algorithms cope with certain classes of transformations and strength of the transformations that can be dealt with. The present paper is a report of the SHREC’11 robust feature detection and description benchmark results.
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| 15. |
- Daru, B. H., et al.
(author)
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Widespread homogenization of plant communities in the Anthropocene
- 2021
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment of this phenomenon is lacking. Here, using a dataset of >200,000 plant species, we demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity. The timeline of most naturalisations coincides with widespread human migration within the last ~500 years, and demonstrates the profound influence humans exert on regional biotas beyond changes in species richness. © 2021, The Author(s).
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| 16. |
- Galván, Ignacio Fdez., et al.
(author)
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OpenMolcas : From Source Code to Insight
- 2019
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Journal article (peer-reviewed)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 17. |
- 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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| 18. |
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| 19. |
- Larsson, E D, et al.
(author)
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Benchmarking ANO-R basis set for multiconfigurational calculations
- 2022
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In: Electronic Structure. - : IOP Publishing. - 2516-1075. ; 4:1
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Journal article (peer-reviewed)abstract
- The selection of basis sets is very important for multiconfigurational wave function calculation, due to a balance between a desired accuracy and computational costs. Recently, the atomic natural orbital-relativistic (ANO-R) basis set was published as a suggested replacement for the ANO-RCC basis set for scalar-relativistic correlated calculations Zobel et al (2021 J. Chem. Theory Comput. 16 278-294). Benchmarking ANO-R basis set against ANO-RCC for atoms (from H to Rn) and their compounds is the goal of this study. Many of these compounds (for instance, diatomic molecules containing transition metals) have open shells, for which reason a multiconfigurational approach is necessary and was primarily used throughout this project. Performance of the ANO-R basis set in multiconfigurational calculations is similar to the ANO-RCC basis set for the ionisation potential of atoms, and the bond distance in diatomic molecules. Deficiencies are noted for atomic electron affinities and dissociation energies of fluoride diatomic molecules. ANO-R basis sets are more compact in comparison to the corresponding ANO-RCC basis sets leading to smaller computational costs, which was demonstrated by chloroiron corrole molecule as an example.
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| 20. |
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| 21. |
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| 22. |
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| 23. |
- Sator, Lea, et al.
(author)
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Overdiagnosis of COPD in Subjects With Unobstructed Spirometry A BOLD Analysis
- 2019
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In: Chest. - : Elsevier BV. - 0012-3692 .- 1931-3543. ; 156:2, s. 277-288
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Journal article (peer-reviewed)abstract
- BACKGROUND: There are several reports on underdiagnosis of COPD, while little is known about COPD overdiagnosis and overtreatment. We describe the overdiagnosis and the prevalence of spirometrically defined false positive COPD, as well as their relationship with overtreatment across 23 population samples in 20 countries participating in the BOLD Study between 2003 and 2012.METHODS: A false positive diagnosis of COPD was considered when participants reported a doctor's diagnosis of COPD, but postbronchodilator spirometry was unobstructed (FEV1/FVC > LLN). Additional analyses were performed using the fixed ratio criterion (FEV1/FVC < 0.7).RESULTS: Among 16,177 participants, 919 (5.7%) reported a previous medical diagnosis of COPD. Postbronchodilator spirometry was unobstructed in 569 subjects (61.9%): false positive COPD. A similar rate of overdiagnosis was seen when using the fixed ratio criterion (55.3%). In a subgroup analysis excluding participants who reported a diagnosis of "chronic bronchitis" or "emphysema" (n = 220), 37.7% had no airflow limitation. The site-specific prevalence of false positive COPD varied greatly, from 1.9% in low- to middle-income countries to 4.9% in high-income countries. In multivariate analysis, overdiagnosis was more common among women, and was associated with higher education; former and current smoking; the presence of wheeze, cough, and phlegm; and concomitant medical diagnosis of asthma or heart disease. Among the subjects with false positive COPD, 45.7% reported current use of respiratory medication. Excluding patients with reported asthma, 34.4% of those with normal spirometry still used a respiratory medication.CONCLUSIONS: False positive COPD is frequent. This might expose nonobstructed subjects to possible adverse effects of respiratory medication.
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| 24. |
- Schlaepfer, T E, et al.
(author)
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Vagus nerve stimulation for depression: Efficacy and safety in a European study.
- 2008
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In: Psychological Medicine. - 0033-2917 .- 1469-8978. ; 38:5, s. 651-661
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Journal article (peer-reviewed)abstract
- Background: Vagus nerve stimulation (VNS) therapy is associated with a decrease in seizure frequency in partial-onset seizure patients. Initial trials suggest that it may be an effective treatment, with few side-effects, for intractable depression. Method: An open, uncontrolled European multi-centre study (D03) of VNS therapy was conducted, in addition to stable pharmacotherapy, in 74 patients with treatment-resistant depression (TRD). Treatment remained unchanged for the first 3 months; in the subsequent 9 months, medications and VNS dosing parameters were altered as indicated clinically. Results: The baseline 28-item Hamilton Depression Rating Scale (HAMD-28) score averaged 34. After 3 months of VNS, response rates (≥50% reduction in baseline scores) reached 37% and remission rates (HAMD-28 score <10) 17%. Response rates increased to 53% after 1 year of VNS, and remission rates reached 33%. Response was defined as sustained if no relapse occurred during the first year of VNS after response onset; 44% of patients met these criteria. Median time to response was 9 months. Most frequent side-effects were voice alteration (63% at 3 months of stimulation) and coughing (23%). Conclusions: VNS therapy was effective in reducing severity of depression; efficacy increased over time. Efficacy ratings were in the same range as those previously reported from a USA study using a similar protocol; at 12 months, reduction of symptom severity was significantly higher in the European sample. This might be explained by a small but significant difference in the baseline HAMD-28 score and the lower number of treatments in the current episode in the European study.
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| 25. |
- Schweiger, Oliver, et al.
(author)
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Multiple stressors on biotic interactions: how climate change and alien species interact to affect pollination
- 2010
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In: Biological Reviews. - 1469-185X .- 1464-7931. ; 85:4, s. 777-795
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Research review (peer-reviewed)abstract
- Global change may substantially affect biodiversity and ecosystem functioning but little is known about its effects on essential biotic interactions. Since different environmental drivers rarely act in isolation it is important to consider interactive effects. Here, we focus on how two key drivers of anthropogenic environmental change, climate change and the introduction of alien species, affect plant-pollinator interactions. Based on a literature survey we identify climatically sensitive aspects of species interactions, assess potential effects of climate change on these mechanisms, and derive hypotheses that may form the basis of future research. We find that both climate change and alien species will ultimately lead to the creation of novel communities. In these communities certain interactions may no longer occur while there will also be potential for the emergence of new relationships. Alien species can both partly compensate for the often negative effects of climate change but also amplify them in some cases. Since potential positive effects are often restricted to generalist interactions among species, climate change and alien species in combination can result in significant threats to more specialist interactions involving native species.
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| 29. |
- Wasof, Safaa, et al.
(author)
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Disjunct populations of European vascular plant species keep the same climatic niches
- 2015
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In: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 24:12, s. 1401-1412
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Journal article (peer-reviewed)abstract
- Aim Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been separated for thousands of years. Location European Alps and Fennoscandia. Methods Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly disjunct populations and 358 species having either a contiguous or a patchy distribution with distant populations. First, we used species distribution modelling to test for a region effect on each species' climatic niche. Second, we quantified niche overlap and shifts in niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) within a bi-dimensional climatic space. Results Only one species (3%) of the 31 species with strictly disjunct populations and 58 species (16%) of the 358 species with distant populations showed a region effect on their climatic niche. Niche overlap was higher for species with strictly disjunct populations than for species with distant populations and highest for arctic-alpine species. Climatic niches were, on average, wider and located towards warmer and wetter conditions in the Alps. Main conclusion Climatic niches seem to be generally conserved between populations that are separated between the Alps and Fennoscandia and have probably been so for 10,000-15,000 years. Therefore, the basic assumption of species distribution models that a species' climatic niche is constant in space and time-at least on time scales 104 years or less-seems to be largely valid for arctic-alpine plants.
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| 30. |
- Zheng, TH, et al.
(author)
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Genome-wide analysis of 944 133 individuals provides insights into the etiology of haemorrhoidal disease
- 2021
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In: Gut. - : BMJ. - 1468-3288 .- 0017-5749. ; 70:8, s. 1538-1549
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Journal article (peer-reviewed)abstract
- Haemorrhoidal disease (HEM) affects a large and silently suffering fraction of the population but its aetiology, including suspected genetic predisposition, is poorly understood. We report the first genome-wide association study (GWAS) meta-analysis to identify genetic risk factors for HEM to date.DesignWe conducted a GWAS meta-analysis of 218 920 patients with HEM and 725 213 controls of European ancestry. Using GWAS summary statistics, we performed multiple genetic correlation analyses between HEM and other traits as well as calculated HEM polygenic risk scores (PRS) and evaluated their translational potential in independent datasets. Using functional annotation of GWAS results, we identified HEM candidate genes, which differential expression and coexpression in HEM tissues were evaluated employing RNA-seq analyses. The localisation of expressed proteins at selected loci was investigated by immunohistochemistry.ResultsWe demonstrate modest heritability and genetic correlation of HEM with several other diseases from the GI, neuroaffective and cardiovascular domains. HEM PRS validated in 180 435 individuals from independent datasets allowed the identification of those at risk and correlated with younger age of onset and recurrent surgery. We identified 102 independent HEM risk loci harbouring genes whose expression is enriched in blood vessels and GI tissues, and in pathways associated with smooth muscles, epithelial and endothelial development and morphogenesis. Network transcriptomic analyses highlighted HEM gene coexpression modules that are relevant to the development and integrity of the musculoskeletal and epidermal systems, and the organisation of the extracellular matrix.ConclusionHEM has a genetic component that predisposes to smooth muscle, epithelial and connective tissue dysfunction.
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