| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 3. |
- Biurrun, Idoia, et al.
(författare)
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Benchmarking plant diversity of Palaearctic grasslands and other open habitats
- 2021
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Ingår i: Journal of Vegetation Science. - Oxford : John Wiley & Sons. - 1100-9233 .- 1654-1103. ; 32:4
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Tidskriftsartikel (refereegranskat)abstract
- Journal of Vegetation Science published by John Wiley & Sons Ltd on behalf of International Association for Vegetation Science.Aims: Understanding fine-grain diversity patterns across large spatial extents is fundamental for macroecological research and biodiversity conservation. Using the GrassPlot database, we provide benchmarks of fine-grain richness values of Palaearctic open habitats for vascular plants, bryophytes, lichens and complete vegetation (i.e., the sum of the former three groups). Location: Palaearctic biogeographic realm. Methods: We used 126,524 plots of eight standard grain sizes from the GrassPlot database: 0.0001, 0.001, 0.01, 0.1, 1, 10, 100 and 1,000 m2 and calculated the mean richness and standard deviations, as well as maximum, minimum, median, and first and third quartiles for each combination of grain size, taxonomic group, biome, region, vegetation type and phytosociological class. Results: Patterns of plant diversity in vegetation types and biomes differ across grain sizes and taxonomic groups. Overall, secondary (mostly semi-natural) grasslands and natural grasslands are the richest vegetation type. The open-access file ”GrassPlot Diversity Benchmarks” and the web tool “GrassPlot Diversity Explorer” are now available online (https://edgg.org/databases/GrasslandDiversityExplorer) and provide more insights into species richness patterns in the Palaearctic open habitats. Conclusions: The GrassPlot Diversity Benchmarks provide high-quality data on species richness in open habitat types across the Palaearctic. These benchmark data can be used in vegetation ecology, macroecology, biodiversity conservation and data quality checking. While the amount of data in the underlying GrassPlot database and their spatial coverage are smaller than in other extensive vegetation-plot databases, species recordings in GrassPlot are on average more complete, making it a valuable complementary data source in macroecology. © 2021 The Authors.
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| 4. |
- Bjurstrom, M. F., et al.
(författare)
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Differential expression of cerebrospinal fluid neuroinflammatory mediators depending on osteoarthritis pain phenotype
- 2020
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Ingår i: Pain. - : Ovid Technologies (Wolters Kluwer Health). - 1872-6623 .- 0304-3959. ; 161:9, s. 2142-2154
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Tidskriftsartikel (refereegranskat)abstract
- Neuroinflammation is implicated in the development and maintenance of persistent pain states, but there are limited data linking cerebrospinal fluid (CSF) inflammatory mediators with neurophysiological pain processes in humans. In a prospective observational study, CSF inflammatory mediators were compared between patients with osteoarthritis (OA) who were undergoing total hip arthroplasty due to disabling pain symptoms (n = 52) and pain-free comparison controls (n = 30). In OA patients only, detailed clinical examination and quantitative sensory testing were completed. Cerebrospinal fluid samples were analyzed for 10 proinflammatory mediators using Meso Scale Discovery platform. Compared to controls, OA patients had higher CSF levels of interleukin 8 (IL-8) (P = 0.002), intercellular adhesion molecule 1 (P = 0.007), and vascular cell adhesion molecule 1 (P = 0.006). Osteoarthritis patients with central sensitization possibly indicated by arm pressure pain detection threshold <250 kPa showed significantly higher CSF levels of Fms-related tyrosine kinase 1 (Flt-1) (P = 0.044) and interferon gamma-induced protein 10 (IP-10) (P = 0.024), as compared to subjects with PPDT above that threshold. In patients reporting pain numerical rating scale score >/=3/10 during peripheral venous cannulation, Flt-1 was elevated (P = 0.025), and in patients with punctate stimulus wind-up ratio >/=2, CSF monocyte chemoattractant protein 1 was higher (P = 0.011). Multiple logistic regression models showed that increased Flt-1 was associated with central sensitization, assessed by remote-site PPDT and peripheral venous cannulation pain, and monocyte chemoattractant protein-1 with temporal summation in the area of maximum pain. Multiple proinflammatory mediators measured in CSF are associated with persistent hip OA-related pain. Pain phenotype may be influenced by specific CSF neuroinflammatory profiles.
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| 5. |
- Walden, L., et al.
(författare)
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Multi-scale mapping of Australia's terrestrial and blue carbon stocks and their continental and bioregional drivers
- 2023
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Ingår i: Communications Earth & Environment. - 2662-4435. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Multi-scale spatial machine learning of soil carbon stocks in Australia's terrestrial and coastal marine ecosystems reveals eight bio-regions and their underlying subregional drivers that can help inform strategies for conservation and climate change mitigation. The soil in terrestrial and coastal blue carbon ecosystems is an important carbon sink. National carbon inventories require accurate assessments of soil carbon in these ecosystems to aid conservation, preservation, and nature-based climate change mitigation strategies. Here we harmonise measurements from Australia's terrestrial and blue carbon ecosystems and apply multi-scale machine learning to derive spatially explicit estimates of soil carbon stocks and the environmental drivers of variation. We find that climate and vegetation are the primary drivers of variation at the continental scale, while ecosystem type, terrain, clay content, mineralogy and nutrients drive subregional variations. We estimate that in the top 0-30 cm soil layer, terrestrial ecosystems hold 27.6 Gt (19.6-39.0 Gt), and blue carbon ecosystems 0.35 Gt (0.20-0.62 Gt). Tall open eucalypt and mangrove forests have the largest soil carbon content by area, while eucalypt woodlands and hummock grasslands have the largest total carbon stock due to the vast areas they occupy. Our findings suggest these are essential ecosystems for conservation, preservation, emissions avoidance, and climate change mitigation because of the additional co-benefits they provide.
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| 6. |
- 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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| 7. |
- Lundblad, Matilda, 1982, et al.
(författare)
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Epidemiological Data on LCL and PCL Injuries Over 17 Seasons in Men's Professional Soccer: The UEFA Elite Club Injury Study
- 2020
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Ingår i: Open Access Journal of Sports Medicine. - 1179-1543. ; 11, s. 105-112
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is limited epidemiological information on injury rates and injury mechanisms for lateral collateral ligament (LCL) and posterior cruciate ligament (PCL) injuries in male professional soccer. In addition, time trends and lay-off times for these injuries have not yet been determined. Aim: To determine injury rates and circumstances of LCL and PCL injuries over 17 seasons in men's professional soccer. Methods: A prospective cohort study, in which 68 professional European soccer teams were followed over 17 consecutive seasons (2001/2002 to 2017/2018). The teams' medical staff recorded player exposure and time-loss injuries. Lay-off time was reported as the median and the first and third quartile. Injury rate was defined as the number of injuries per 1000 playerhours. Results: One hundred and twenty-eight LCL and 28 PCL injuries occurred during 2,554,686 h of exposure (rate 0.05 and 0.01/1000 h, respectively). The median lay-off time for LCL injuries was 15 (Q(1)=7, Q(3)=32) days, while it was 31 days for PCL injuries (Q(1)=15, Q(3)=74). The match injury rate for LCL injuries was 11 times higher than the training injury rate (0.21 vs 0.02/1000 h, rate ratio [RR] 10.5, 95% CI 7.3 to 15.1 p<0.001) and the match injury rate for PCL injuries was 20 times higher than the training injury rate (0.056 vs 0.003/1000 h, RR 20.1, 95% CI 8.2 to 49.6, p<0.001). LCL injuries saw a significant annual decrease of approximately 3.5% (p=0.006). In total, 58% (63/108) of all LCL injuries and 54% (14/26) of all PCL injuries were related to contact mechanism. Conclusion: This study with prospectively registered data on LCL and PCL injuries in men's professional soccer shows that the median lay-off from soccer for LCL and PCL injuries is approximately 2 and 4 weeks respectively. These rare knee ligament injuries typically occur during matches and are associated with a contact injury mechanism.
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| 8. |
- Coates, Brad S., et al.
(författare)
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A draft Diabrotica virgifera virgifera genome : insights into control and host plant adaption by a major maize pest insect
- 2023
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown. Results: A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts. Conclusions: Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.
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