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- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Galluzzi, L, et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes.
- 2009
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Ingår i: Cell death and differentiation. - : Springer Science and Business Media LLC. - 1476-5403 .- 1350-9047. ; 16:8, s. 1093-107
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Forskningsöversikt (refereegranskat)abstract
- Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous implications for the development of novel therapeutic strategies. It is, therefore, of utmost importance to standardize the experimental procedures that identify dying and dead cells in cell cultures and/or in tissues, from model organisms and/or humans, in healthy and/or pathological scenarios. Thus far, dozens of methods have been proposed to quantify cell death-related parameters. However, no guidelines exist regarding their use and interpretation, and nobody has thoroughly annotated the experimental settings for which each of these techniques is most appropriate. Here, we provide a nonexhaustive comparison of methods to detect cell death with apoptotic or nonapoptotic morphologies, their advantages and pitfalls. These guidelines are intended for investigators who study cell death, as well as for reviewers who need to constructively critique scientific reports that deal with cellular demise. Given the difficulties in determining the exact number of cells that have passed the point-of-no-return of the signaling cascades leading to cell death, we emphasize the importance of performing multiple, methodologically unrelated assays to quantify dying and dead cells.
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| 13. |
- Noorani, A, et al.
(författare)
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A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
- 2017
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 27:6, s. 902-912
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Tidskriftsartikel (refereegranskat)abstract
- The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status. Inclusion of samples collected post-chemotherapy increased the proportion of late-stage tumors. When comparing matched pre- and post-chemotherapy samples from 10 cases, the mutational signatures, copy number, and SNV mutational profiles reflect the expected heterogeneity in this disease. Analysis of SNVs in relation to allele-specific copy-number changes pinpoints the common ancestor to a point prior to chemotherapy. For cases in which pre- and post-chemotherapy samples do show substantial differences, the timing of the divergence is near-synchronous with endoreduplication. Comparison across a large prospective cohort (62 treatment-naive, 58 chemotherapy-treated samples) reveals no significant differences in the overall mutation rate, mutation signatures, specific recurrent point mutations, or copy-number events in respect to chemotherapy status. In conclusion, whole-genome sequencing of samples obtained following neoadjuvant chemotherapy is representative of the genomic landscape of esophageal adenocarcinoma. Excluding these samples reduces the material available for cataloging and introduces a bias toward the earlier stages of cancer.
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| 15. |
- Moreira, Xoaquín, et al.
(författare)
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Impacts of urbanization on insect herbivory and plant defences in oak trees
- 2019
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Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 128:1, s. 113-123
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Tidskriftsartikel (refereegranskat)abstract
- Systematic comparisons of species interactions in urban versus rural environments can improve our understanding of shifts in ecological processes due to urbanization. However, such studies are relatively uncommon and the mechanisms driving urbanization effects on species interactions (e.g. between plants and insect herbivores) remain elusive. Here we investigated the effects of urbanization on leaf herbivory by insect chewers and miners associated with the English oak Quercus robur by sampling trees in rural and urban areas throughout most of the latitudinal distribution of this species. In performing these comparisons, we also controlled for the size of the urban areas (18 cities) and gathered data on CO2 emissions. In addition, we assessed whether urbanization affected leaf chemical defences (phenolic compounds) and nutritional traits (phosphorus and nitrogen), and whether such changes correlated with herbivory levels. Urbanization significantly reduced leaf chewer damage but did not affect leaf miners. In addition, we found that leaves from urban locations had lower levels of chemical defences (condensed and hydrolysable tannins) and higher levels of nutrients (nitrogen and phosphorus) compared to leaves in rural locations. The magnitude of urbanization effects on herbivory and leaf defences was not contingent upon city size. Importantly, while the effects of urbanization on chemical defences were associated with CO2 emissions, changes in leaf chewer damage were not associated with either leaf traits or CO2 levels. These results suggest that effects of urbanization on herbivory occur through mechanisms other than changes in the plant traits measured here. Overall, our simultaneous assessment of insect herbivory, plant traits and abiotic correlates advances our understanding of the main drivers of urbanization effects on plant-herbivore interactions.
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| 16. |
- van Dijk, Laura J. A., et al.
(författare)
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Urbanization affects oak–pathogen interactions across spatial scales
- 2022
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Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 2022:1
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Tidskriftsartikel (refereegranskat)abstract
- The world is rapidly urbanizing, thereby transforming natural landscapes and changing the abundance and distribution of organisms. However, insights into the effects of urbanization on species interactions, and plant–pathogen interactions in particular, are lacking. We investigated the effects of urbanization on powdery mildew infection on Quercus robur at continental and within-city scales. At the continental scale, we compared infection levels between urban and rural areas of different-sized cities in Europe, and investigated whether plant traits, climatic variables and CO2 emissions mediated the effect of urbanization on infection levels. Within one large city (Stockholm, Sweden), we further explored whether local habitat features and spatial connectivity influenced infection levels during multiple years. At the continental scale, infection severity was consistently higher on trees in urban than rural areas, with some indication that temperature mediated this effect. Within Stockholm city, temperature had no effect, while local accumulation of leaf litter negatively affected powdery mildew incidence in one out of three years, and more connected trees had lower infection levels. This study is the first to describe the effects of urbanization on plant–pathogen interactions both within and among cities, and to uncover the potential mechanisms behind the observed patterns at each scale.
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| 20. |
- Gonzalez, Grecia M., et al.
(författare)
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Structure of the Escherichia coli ProQ RNA-binding protein
- 2017
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Ingår i: RNA. - : COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. - 1355-8382 .- 1469-9001. ; 23:5, s. 696-711
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Tidskriftsartikel (refereegranskat)abstract
- The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia call ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.
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| 21. |
- Tedersoo, L., et al.
(författare)
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Towards a co-crediting system for carbon and biodiversity
- 2023
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Ingår i: Plants People Planet. - 2572-2611. ; 6:1, s. 18-28
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Tidskriftsartikel (refereegranskat)abstract
- Societal Impact StatementHumankind is facing both climate and biodiversity crises. This article proposes the foundations of a scheme that offers tradable credits for combined aboveground and soil carbon and biodiversity. Multidiversity-as estimated based on high-throughput molecular identification of soil meiofauna, fungi, bacteria, protists, plants and other organisms shedding DNA into soil, complemented by acoustic and video analyses of aboveground macrobiota-offers a cost-effective method that captures much of the terrestrial biodiversity. Such a voluntary crediting system would increase the quality of carbon projects and contribute funding for delivering the Kunming-Montreal Global Biodiversity Framework. Carbon crediting and land offsets for biodiversity protection have been developed to tackle the challenges of increasing greenhouse gas emissions and the loss of global biodiversity. Unfortunately, these two mechanisms are not optimal when considered separately. Focusing solely on carbon capture-the primary goal of most carbon-focused crediting and offsetting commitments-often results in the establishment of non-native, fast-growing monocultures that negatively affect biodiversity and soil-related ecosystem services. Soil contributes a vast proportion of global biodiversity and contains traces of aboveground organisms. Here, we outline a carbon and biodiversity co-crediting scheme based on the multi-kingdom molecular and carbon analyses of soil samples, along with remote sensing estimation of aboveground carbon as well as video and acoustic analyses-based monitoring of aboveground macroorganisms. Combined, such a co-crediting scheme could help halt biodiversity loss by incentivising industry and governments to account for biodiversity in carbon sequestration projects more rigorously, explicitly and equitably than they currently do. In most cases, this would help prioritise protection before restoration and help promote more socially and environmentally sustainable land stewardship towards a 'nature positive' future.
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| 23. |
- Winning, Tracey, et al.
(författare)
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Evidence-based care and the curriculum
- 2008
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Ingår i: European journal of dental education. - : Wiley. - 1396-5883 .- 1600-0579. ; 12:Suppl 1, s. 48-63
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Forskningsöversikt (övrigt vetenskapligt/konstnärligt)abstract
- An evidence-based (EB) approach has been a significant driver in reforming healthcare over the past two decades. This change has extended across a broad range of health professions, including oral healthcare. A key element in achieving an EB approach to oral healthcare is educating our practitioners, both current and future. This involves providing opportunities integrated within simulated and actual clinical settings for practitioners to learn and apply the principles and processes of evidence-based oral healthcare (EBOHC). Therefore, the focus of this discussion will be on ways in which EBOHC and associated research activities can be implemented into curricula, with the aim of improving patient care. This paper will initially define the scope of EBOHC and research, what these involve, why they are important, and issues that we need to manage when implementing EBOHC. This will be followed by a discussion of factors that enable successful implementation of EBOHC and research into curricula. The paper concludes with suggestions on the future of EBOHC and research in curricula. Key recommendations related to curricula include strengthening of the culture of a scientific approach to education and oral healthcare provision; complete integration of EBOHC into the curriculum at all levels; and faculty development to implement EBOHC based on their needs and evidence of effective approaches. Key recommendations to support implementation and maintenance of EBOHC include recognition and funding for high-quality systematic reviews and development of associated methodologies relevant for global environments; building global capacity of EBOHC researchers; research into improving translation of effective interventions into education and healthcare practice, including patient-reported outcomes, safety and harms, understanding and incorporation of patient values into EB decision-making, economic evaluation research specific to oral healthcare and effective methods for changing practitioner (faculty) behaviours; and extend access to synthesized research in 'user friendly' formats and languages tailored to meet users' needs. Realizing these recommendations may help to improve access to effective healthcare as a basic human right.
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