| 1. |
- Calogiuri, Tullia, et al.
(författare)
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Design and Construction of an Experimental Setup to Enhance Mineral Weathering through the Activity of Soil Organisms
- 2023
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Ingår i: Journal of Visualized Experiments. - : Journal of Visualized Experiments. - 1940-087X. ; :201
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Tidskriftsartikel (refereegranskat)abstract
- Enhanced weathering (EW) is an emerging carbon dioxide (CO2) removal technology that can contribute to climate change mitigation. This technology relies on accelerating the natural process of mineral weathering in soils by manipulating the abiotic variables that govern this process, in particular mineral grain size and exposure to acids dissolved in water. EW mainly aims at reducing atmospheric CO2 concentrations by enhancing inorganic carbon sequestration. Until now, knowledge of EW has been mainly gained through experiments that focused on the abiotic variables known for stimulating mineral weathering, thereby neglecting the potential influence of biotic components. While bacteria, fungi, and earthworms are known to increase mineral weathering rates, the use of soil organisms in the context of EW remains underexplored. This protocol describes the design and construction of an experimental setup developed to enhance mineral weathering rates through soil organisms while concurrently controlling abiotic conditions. The setup is designed to maximize weathering rates while maintaining soil organisms' activity. It consists of a large number of columns filled with rock powder and organic material, located in a climate chamber and with water applied via a downflow irrigation system. Columns are placed above a fridge containing jerrycans to collect the leachate. Representative results demonstrate that this setup is suitable to ensure the activity of soil organisms and quantify their effect on inorganic carbon sequestration. Challenges remain in minimizing leachate losses, ensuring homogeneous ventilation through the climate chamber, and avoiding flooding of the columns. With this setup, an innovative and promising approach is proposed to enhance mineral weathering rates through the activity of soil biota and disentangle the effect of biotic and abiotic factors as drivers of EW.
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| 2. |
- Abrahamczyk, Stefan, et al.
(författare)
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Evolution of brood-site mimicry in Madagascan Impatiens (Balsaminaceae)
- 2021
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Ingår i: Perspectives in plant ecology, evolution and systematics. - : Elsevier BV. - 1433-8319 .- 1618-0437. ; 49
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Tidskriftsartikel (refereegranskat)abstract
- The species-rich flora of Madagascar is well known for a range of unusual floral ecologies. One example is Impatiens section Trimorphopetalum with its unique combination of floral traits: small, spur-less, cup-or lip shaped, greenish or brownish flowers. So far no hypotheses on floral function or pollination of this peculiar group have been proposed. We analysed six reproductive traits in relation to pollination syndromes for 34 Madagascan Impatiens species, including 18 species of section Trimorphopetalum plus six outgroup species, in a phylogenetic framework. Further, we present pollinator observations for one additional species of Trimophopetalum. All pollination syndromes occurring in the African species are also present in Madagascan Impatiens. In addition, species of Trimorphopetalum represent two unique floral types, possibly corresponding to two different types of fly pollination. The evolution of these flower types corresponds to a strong decrease in nectar production, flower display size, pollen grain and ovule number. Autogamy is found in one derived sub-clade of the otherwise largely pollinator-dependent Trimorphopetalum. We find evidence consistent with the evolution of brood-site deception and fungus mimicry in combination with fly pollination in one clade of Trimorphopetalum and the stepwise evolution of autogamy in the second clade. The evolution of these very different reproductive strategies may have been triggered by pollinator limitation in the dense, humid forest undergrowth of Madagascar.
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| 3. |
- Appelhans, Marc S., et al.
(författare)
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Age and historical biogeography of the pantropically distributed Spathelioideae (Rutaceae, Sapindales)
- 2012
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 39:7, s. 1235-1250
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Tidskriftsartikel (refereegranskat)abstract
- Aim The family Rutaceae (rue family) is the largest within the eudicot order Sapindales and is distributed mainly in the tropical and subtropical regions of both the New World and the Old World, with a few genera in temperate zones. The main objective of this study is to present molecular dating and biogeographical analyses of the subfamily Spathelioideae, the earliest branching clade (which includes eight extant genera), to interpret the temporal and spatial origins of this group, ascertaining possible vicariant patterns and dispersal routes and inferring diversification rates through time. Location Pantropics. Methods A dataset comprising a complete taxon sampling at generic level (83.3% at species level) of Spathelioideae was used for a Bayesian molecular dating analysis (beast). Four fossil calibration points and an age constraint for Sapindales were applied. An ancestral area reconstruction analysis utilizing the dispersalextinctioncladogenesis model and diversification rate analyses was conducted. Results Dating analyses indicate that Rutaceae and Spathelioideae are probably of Late Cretaceous origin, after which Spathelioideae split into a Neotropical and a Palaeotropical lineage. The Palaeotropical taxa have their origin inferred in Africa, with postulated dispersal events to the Mediterranean, the Canary Islands, Madagascar and Southeast Asia. The lineages within Spathelioideae evolved at a relatively constant diversification rate. However, abrupt changes in diversification rates are inferred from the beginning of the Miocene and during the Pliocene/Pleistocene. Main conclusions The geographical origin of Spathelioideae probably lies in Africa. The existence of a Neotropical lineage may be the result of a dispersal event at a time in the Late Cretaceous when South America and Africa were still quite close to each other (assuming that our age estimates are close to the actual ages), or by Gondwanan vicariance (assuming that our age estimates provide minimal ages only). Separation of land masses caused by sea level changes during the Pliocene and Pleistocene may have been triggers for speciation in the Caribbean genus Spathelia.
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| 4. |
- De Block, Petra, et al.
(författare)
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Molecular phylogenetics and generic assessment in the tribe Pavetteae (Rubiaceae)
- 2015
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Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 64:1, s. 79-95
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Tidskriftsartikel (refereegranskat)abstract
- This is the first phylogenetic study focused on the Pavetteae, one of the most species-rich and morphologically diverse tribes within the coffee family (Rubiaceae). Fifteen of the 17 currently recognized genera, represented by 85 taxa, were sequenced for rps16, trnT-F and ITS and analysed using Bayesian inference and maximum likelihood methods. The monophyly of the Pavetteae is confirmed. Four major lineages are identified, but their phylogenetic relationships are not fully resolved. The continental African genera Rutidea, Nichallea and Tennantia, the Madagascan genera Homollea and Robbrechtia, and the paleotropical genus Pavetta are monophyletic. Other genera are paraphyletic in their current circumscriptions and the following changes are made: Homolliella is placed in synonymy with Paracephaelis, and Coleactina and Dictyandra with Leptactina, resulting in four new combinations. The large paleotropical genus Tarenna is shown not to be monophyletic. In the future, the name Tarenna should not be used for continental African species. Most of these could be transferred to the hitherto monospecific genus Cladoceras, but other species might constitute altogether new genera. The relationship between the monophyletic Asian-Pacific and Madagascan Tarenna species remains unclear. The phylogeny of the Madagascan genera of the Pavetteae is largely unresolved and the largest Madagascar-centred genus Coptosperma was not recovered as monophyletic. The low resolution for the Madagascan taxa can be considered as an indication of rapid radiation. Further molecular and morphological studies are necessary to clarify the phylogeny of the Pavetteae, especially regarding the African Tarenna species and the Madagascan genera of the tribe.
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| 5. |
- De Block, Petra, et al.
(författare)
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Tarennella, a new Pavetteae (Rubiaceae) genus from eastern Madagascar
- 2021
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Ingår i: Plant Ecology and Evolution. - : Agentschap Plantentuin Meise. - 2032-3913 .- 2032-3921. ; 154:1, s. 87-110
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Tidskriftsartikel (refereegranskat)abstract
- Background – This contribution is part of an ongoing study on the taxonomy and the phylogenetic relationships of the Malagasy representatives of the tribe Pavetteae (Rubiaceae).Material and methods – Taxonomic methods follow normal practice of herbarium taxonomy. A molecular study using the plastid markers rps16, trnT-F, petD, and accD-psa1, the nuclear ribosomal marker ITS and the nuclear MADS-box gene marker PI was executed.Key results – Five new species are described from littoral, lowland, or mid-elevation humid forests in eastern Madagascar. They are characterized by compact inflorescences with small, sessile flowers, a densely pubescent style, large placentas with 2–3 immersed ovules, seeds with a small, superficial hilum not surrounded by a thickened annulus, and pollen grains with supratectal elements. The phylogenetic tree, which included three of the five new species, showed an unresolved backbone but high support for distal nodes grouping species. The new species form a distinct monophyletic clade among the other Malagasy Pavetteae genera and are recognised at genus level under the name Tarennella. Provisional IUCN Red List assessments show that Tarennella homolleana is Vulnerable, T. cordatifolia and T. sanguinea are Endangered, T. puberula is Critically Endangered, and T. coronata is Critically Endangered (Possibly Extinct).
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| 6. |
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| 7. |
- Hendriks, Kasper P., et al.
(författare)
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Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
- 2023
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 33:19, s. 4052-4068
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Tidskriftsartikel (refereegranskat)abstract
- The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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| 8. |
- Janssens, Rosanne, et al.
(författare)
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Opportunities and challenges for the inclusion of patient preferences in the medical product life cycle: a systematic review
- 2019
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Ingår i: BMC Medical Informatics and Decision Making. - : Springer Science and Business Media LLC. - 1472-6947.
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Tidskriftsartikel (refereegranskat)abstract
- Background: The inclusion of patient preferences (PP) in the medical product life cycle is a topic of growing interest to stakeholders such as academics, Health Technology Assessment (HTA) bodies, reimbursement agencies, industry, patients, physicians and regulators. This review aimed to understand the potential roles, reasons for using PP and the expectations, concerns and requirements associated with PP in industry processes, regulatory benefitrisk assessment (BRA) and marketing authorization (MA), and HTA and reimbursement decision-making. Methods: A systematic review of peer-reviewed and grey literature published between January 2011 and March 2018 was performed. Consulted databases were EconLit, Embase, Guidelines International Network, PsycINFO and PubMed. A two-step strategy was used to select literature. Literature was analyzed using NVivo (QSR international). Results: From 1015 initially identified documents, 72 were included. Most were written from an academic perspective (61%) and focused on PP in BRA/MA and/or HTA/reimbursement (73%). Using PP to improve understanding of patients’ valuations of treatment outcomes, patients’ benefit-risk trade-offs and preference heterogeneity were roles identified in all three decision-making contexts. Reasons for using PP relate to the unique insights and position of patients and the positive effect of including PP on the quality of the decision-making process. Concerns shared across decision-making contexts included methodological questions concerning the validity, reliability and cognitive burden of preference methods. In order to use PP, general, operational and quality requirements were identified, including recognition of the importance of PP and ensuring patient understanding in PP studies. Conclusions: Despite the array of opportunities and added value of using PP throughout the different steps of the MPLC identified in this review, their inclusion in decision-making is hampered by methodological challenges and lack of specific guidance on how to tackle these challenges when undertaking PP studies. To support the development of such guidance, more best practice PP studies and PP studies investigating the methodological issues identified in this review are critically needed.
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| 9. |
- Janssens, Rosanne, et al.
(författare)
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Patient Preferences for Multiple Myeloma Treatments: A Multinational Qualitative Study
- 2021
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Ingår i: Frontiers in Medicine. - : Frontiers Media SA. - 2296-858X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Investigational and marketed drugs for the treatment of multiple myeloma (MM) are associated with a range of characteristics and uncertainties regarding long term side-effects and efficacy. This raises questions about what matters most to patients living with this disease. This study aimed to understand which characteristics MM patients find most important, and hence should be included as attributes and levels in a subsequent quantitative preference survey among MM patients.Methods: This qualitative study involved: (i) a scoping literature review, (ii) discussions with MM patients (n = 24) in Belgium, Finland, Romania, and Spain using Nominal Group Technique, (iii) a qualitative thematic analysis including multi-stakeholder discussions.Results: MM patients voiced significant expectations and hopes that treatments would extend their lives and reduce their cancer signs and symptoms. Participants however raised concerns about life-threatening side-effects that could cause permanent organ damage. Bone fractures and debilitating neuropathic effects (such as chronic tingling sensations) were highlighted as major issues reducing patients' independence and mobility. Patients discussed the negative impact of the following symptoms and side-effects on their daily activities: thinking problems, increased susceptibility to infections, reduced energy, pain, emotional problems, and vision problems. MM patients were concerned with uncertainties regarding the durability of positive treatment outcomes, and the cause, severity, and duration of their symptoms and side-effects. Patients feared short-term positive treatment responses complicated by permanent, severe side-effects and symptoms.Conclusions: This study gained an in-depth understanding of the treatment and disease-related characteristics and types of attribute levels (severity, duration) that are most important to MM patients. Results from this study argue in favor of MM drug development and individual treatment decision-making that focuses not only on extending patients' lives but also on addressing those symptoms and side-effects that significantly impact MM patients' quality of life. This study underscores a need for transparent communication toward MM patients about MM treatment outcomes and uncertainties regarding their long-term efficacy and safety. Finally, this study may help drug developers and decision-makers understand which treatment outcomes and uncertainties are most important to MM patients and therefore should be incorporated in MM drug development, evaluation, and clinical practice.
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| 10. |
- Janssens, Rosanne, et al.
(författare)
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Patient Preferences in the Medical Product Life Cycle : What do Stakeholders Think? Semi-Structured Qualitative Interviews in Europe and the USA
- 2019
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Ingår i: Patient. - : Springer Science and Business Media LLC. - 1178-1653 .- 1178-1661. ; 12:5, s. 513-526
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundPatient preferences (PP), which are investigated in PP studies using qualitative or quantitative methods, are a growing area of interest to the following stakeholders involved in the medical product lifecycle: academics, health technology assessment bodies, payers, industry, patients, physicians, and regulators. However, the use of PP in decisions along the medical product lifecycle remains limited. As the adoption of PP heavily relies on these stakeholders, knowledge of their perceptions of PP is critical.ObjectiveThis study aimed to characterize stakeholders’ attitudes, needs, and concerns with respect to PP in decision making along the medical product lifecycle.MethodsSemi-structured interviews (n = 143) were conducted with academics (n = 24), health technology assessment/payer representatives (n = 24), industry representatives (n = 24), patients, caregivers and patient representatives (n = 24), physicians (n = 24), and regulators (n = 23) from seven European countries and the USA. Interviews were conducted between April and August 2017. The framework method was used to organize the data and identify themes and key findings in each interviewed stakeholder group.ResultsInterviewees reported being unfamiliar (43%), moderately familiar (42%), or very familiar (15%) with preference methods and studies. Interviewees across stakeholder groups generally supported the idea of using PP in the medical product lifecycle but expressed mixed opinions about the feasibility and impact of using PP in decision making. Interviewees from all stakeholder groups stressed the importance of increasing stakeholders’ understanding of the concept of PP and preference methods and ensuring patients’ understanding of the questions asked in PP studies. Key concerns and needs in each interviewed stakeholder group were as follows: (1) academics: investigating the validity, reliability, reproducibility, and generalizability of preference methods; (2) health technology assessment/payer representatives: developing quality criteria for evaluating PP studies and gaining insights into how to weigh them in reimbursement/payer decision making; (3) industry representatives: obtaining guidance on PP studies and recognition on the importance of PP from decision makers; (4) patients, caregivers, and patient representatives: providing an incentive and adequate information towards patients when participating in PP studies; (5) physicians: avoiding bias as a result of commercial agendas in PP studies and clarifying how to deal with subjective and emotional elements when measuring PP; and (6) regulators: avoiding the misuse of PP study results to overrule the traditional efficacy and safety criteria used for marketing authorization and obtaining robust PP study results.ConclusionsDespite the interest all interviewed stakeholder groups reported in PP, the effective use of PP in decision making across the medical product lifecycle is currently hampered by a lack of standardization and consensus on how to both measure and use PP.
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