| 1. |
- Aravind, P. V., et al.
(författare)
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Negative emissions at negative cost-an opportunity for a scalable niche
- 2022
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Ingår i: Frontiers in Energy Research. - : Frontiers Media SA. - 2296-598X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- In the face of the rapidly dwindling carbon budgets, negative emission technologies are widely suggested as required to stabilize the Earth's climate. However, finding cost-effective, socially acceptable, and politically achievable means to enable such technologies remains a challenge. We propose solutions based on negative emission technologies to facilitate wealth creation for the stakeholders while helping to mitigate climate change. This paper comes up with suggestions and guidelines on significantly increasing carbon sequestration in coffee farms. A coffee and jackfruit agroforestry-based case study is presented along with an array of technical interventions, having a special focus on bioenergy and biochar, potentially leading to "negative emissions at negative cost. " The strategies for integrating food production with soil and water management, fuel production, adoption of renewable energy systems and timber management are outlined. The emphasis is on combining biological and engineering sciences to devise a practically viable niche that is easy to adopt, adapt and scale up for the communities and regions to achieve net negative emissions. The concerns expressed in the recent literature on the implementation of emission reduction and negative emission technologies are briefly presented. The novel opportunities to alleviate these concerns arising from our proposed interventions are then pointed out. Our analysis indicates that 1 ha coffee jackfruit-based agroforestry can additionally sequester around 10 tonnes of CO2-eq and lead to an income enhancement of up to 3,000-4,000 Euros in comparison to unshaded coffee. Finally, the global outlook for an easily adoptable nature-based approach is presented, suggesting an opportunity to implement revenue-generating negative emission technologies on a gigatonne scale. We anticipate that our approach presented in the paper results in increased attention to the development of practically viable science and technology-based interventions in order to support the speeding up of climate change mitigation efforts.
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| 2. |
- Christmas, Matthew, et al.
(författare)
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Evolutionary constraint and innovation across hundreds of placental mammals
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6643
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Tidskriftsartikel (refereegranskat)abstract
- Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (similar to 10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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| 3. |
- In ’t Veld, Sjors G.J.G., et al.
(författare)
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Detection and localization of early- and late-stage cancers using platelet RNA
- 2022
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Ingår i: Cancer Cell. - : Elsevier. - 1535-6108 .- 1878-3686. ; 40:9, s. 999-1009.e6
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Tidskriftsartikel (refereegranskat)abstract
- Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.
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| 4. |
- Javal, Marion, et al.
(författare)
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A preliminary assessment of the physiological and morphological correlates of beetle aggression in an emerging sugarcane pest, Cacosceles newmannii ( Thomson, 1877) (Coleoptera: Cerambycidae)
- 2022
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Ingår i: African Entomology. - : ENTOMOLOGICAL SOC SOUTHERN AFRICA. - 1021-3589 .- 2224-8854. ; 30
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the morphological and physiological correlates of competitive behaviours can provide important insights into the ecology of competition, home range size and resource consumption. Here we first estimated and defined sexual dimorphism in a poorly studied African cerambycid species, Cacosceles newmannii (Thomson, 1877). We then assessed morphological and physiological attributes of male beetles in relation to their fighting behaviour. Suites of morphological and energetic measurements were carried out on adult males, the latter before and after male-male interactions. Aggressive behaviour and the outcomes of male fighting trials were assessed under controlled conditions. The species is highly sexually dimorphic in relation to mandible size. During male-male interactions, a continuum of behaviours with an increasing risk of injury and metabolic cost was observed. Grasping was prolonged in males with larger fighting apparatus, who also tended to use more energy during the encounter than males displaying other behaviours. Our results indicate that the mandible size in C. newmannii serves as an honest signal of fighting ability in this species. Additionally, energetic assessments in preparation for fighting, costs during a fight, and persistence of metabolic costs postfighting may be useful for understanding the relative fitness costs of competition.
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| 5. |
- Lähteenaro, Meri, et al.
(författare)
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Phylogenomic species delimitation of the twisted-winged parasite genus Stylops (Strepsiptera)
- 2024
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Ingår i: Systematic Entomology. - : John Wiley & Sons. - 0307-6970 .- 1365-3113. ; 49:2, s. 294-313
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Tidskriftsartikel (refereegranskat)abstract
- The twisted-winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life-history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole-genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host-parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general.
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| 6. |
- Lähteenaro, Meri, et al.
(författare)
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Phylogenomic species delimitation of the twisted-winged parasite genus Stylops (Strepsiptera)
- 2024
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Ingår i: Systematic Entomology. - 0307-6970 .- 1365-3113. ; 49:2, s. 294-313
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Tidskriftsartikel (refereegranskat)abstract
- The twisted-winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life-history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole-genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host–parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general.
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| 7. |
- Smit, Chantelle, et al.
(författare)
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Metabolic responses to starvation and feeding contribute to the invasiveness of an emerging pest insect
- 2021
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Ingår i: Journal of insect physiology. - : Elsevier BV. - 0022-1910 .- 1879-1611. ; 128
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Tidskriftsartikel (refereegranskat)abstract
- Metabolic rate, and the flexibility thereof, is a complex trait involving several inter-linked variables that can influence animal energetics, behavior, and ultimately, fitness. Metabolic traits respond readily to ambient temperature variation, in some cases increasing relative or absolute energetic costs, while in other cases, depending on the organism's metabolic and behavioral responses to changing conditions, resulting in substantial energy savings. To gain insight into the rapid recent emergence of the indigenous South African longhorn beetle Cacosceles newmannii as a crop pest in sugarcane, a better understanding of its metabolic rate, feeding response, digestion times, and aerobic scope is required, in conjunction with any behavioral responses to food availability or limitation thereof. Here, we therefore experimentally determined metabolic rate, estimated indirectly as CO2 production using flow-through respirometry, in starved, fasted, and fed C. newmannii larvae, at 20 degrees C and 30 degrees C. We estimated multiple parameters of metabolic rate (starved, standard, active, and maximum metabolic rates) as well as aerobic scope (AS), specific dynamic action (SDA), and the percentage time active during respirometry trials. Additionally, in individuals that showed cyclic or discontinuous gas exchange patterns, we compared rate, volume, and duration of cycles, and how these were influenced by temperature. Standard and active metabolic rate, and AS and SDA were significantly higher in the larvae measured at 30 degrees C than those measured at 20 degrees C. By contrast, starved and maximum metabolic rates and percentage time active were unaffected by temperature. At rest and after digestion was complete, 35% of larvae showed cyclic gas exchange at both temperatures; 5% and 15% showed continuous gas exchange at 20 degrees C and 30 degrees C respectively, and 10% and 0% showed discontinuous gas exchange at 20 degrees C and 30 degrees C respectively. We propose that the ability of C. newmannii larvae to survive extended periods of resource limitation, combined with a rapid ability to process food upon securing resources, even at cooler conditions that would normally suppress digestion in tropical insects, may have contributed to their ability to feed on diverse low energy resources typical of their host plants, and become pests of, and thrive on, a high energy host plant like sugarcane.
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| 8. |
- Smit, Marloes A., et al.
(författare)
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Deep learning based tumor–stroma ratio scoring in colon cancer correlates with microscopic assessment
- 2023
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Ingår i: Journal of Pathology Informatics. - : Elsevier B.V.. - 2229-5089 .- 2153-3539. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: The amount of stroma within the primary tumor is a prognostic parameter for colon cancer patients. This phenomenon can be assessed using the tumor–stroma ratio (TSR), which classifies tumors in stroma-low (≤50% stroma) and stroma-high (>50% stroma). Although the reproducibility for TSR determination is good, improvement might be expected from automation. The aim of this study was to investigate whether the scoring of the TSR in a semi- and fully automated method using deep learning algorithms is feasible. Methods: A series of 75 colon cancer slides were selected from a trial series of the UNITED study. For the standard determination of the TSR, 3 observers scored the histological slides. Next, the slides were digitized, color normalized, and the stroma percentages were scored using semi- and fully automated deep learning algorithms. Correlations were determined using intraclass correlation coefficients (ICCs) and Spearman rank correlations. Results: 37 (49%) cases were classified as stroma-low and 38 (51%) as stroma-high by visual estimation. A high level of concordance between the 3 observers was reached, with ICCs of 0.91, 0.89, and 0.94 (all P < .001). Between visual and semi-automated assessment the ICC was 0.78 (95% CI 0.23–0.91, P-value 0.005), with a Spearman correlation of 0.88 (P < .001). Spearman correlation coefficients above 0.70 (N=3) were observed for visual estimation versus the fully automated scoring procedures. Conclusion: Good correlations were observed between standard visual TSR determination and semi- and fully automated TSR scores. At this point, visual examination has the highest observer agreement, but semi-automated scoring could be helpful to support pathologists. © 2023 The Authors
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| 9. |
- Waeijen-Smit, Kiki, et al.
(författare)
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Global mortality and readmission rates following COPD exacerbation-related hospitalisation : a meta-analysis of 65 945 individual patients
- 2024
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Ingår i: ERJ Open Research. - : European Respiratory Society. - 2312-0541. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Exacerbations of COPD (ECOPD) have a major impact on patients and healthcare systems across the world. Precise estimates of the global burden of ECOPD on mortality and hospital readmission are needed to inform policy makers and aid preventive strategies to mitigate this burden. The aims of the present study were to explore global in-hospital mortality, post-discharge mortality and hospital readmission rates after ECOPD-related hospitalisation using an individual patient data meta-analysis (IPDMA) design. Methods A systematic review was performed identifying studies that reported in-hospital mortality, postdischarge mortality and hospital readmission rates following ECOPD-related hospitalisation. Data analyses were conducted using a one-stage random-effects meta-analysis model. This study was conducted and reported in accordance with the PRISMA-IPD statement. Results Data of 65 945 individual patients with COPD were analysed. The pooled in-hospital mortality rate was 6.2%, pooled 30-, 90- and 365-day post-discharge mortality rates were 1.8%, 5.5% and 10.9%, respectively, and pooled 30-, 90- and 365-day hospital readmission rates were 7.1%, 12.6% and 32.1%, respectively, with noticeable variability between studies and countries. Strongest predictors of mortality and hospital readmission included noninvasive mechanical ventilation and a history of two or more ECOPD-related hospitalisations < 12 months prior to the index event. Conclusions This IPDMA stresses the poor outcomes and high heterogeneity of ECOPD-related hospitalisation across the world. Whilst global standardisation of the management and follow-up of ECOPD-related hospitalisation should be at the heart of future implementation research, policy makers should focus on reimbursing evidence-based therapies that decrease (recurrent) ECOPD.
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