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| 2. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
- Blunden, Jessica, et al.
(författare)
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State of the Climate in 2012
- 2013
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:8, s. S1-S258
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Tidskriftsartikel (refereegranskat)abstract
- For the first time in serveral years, the El Nino-Southern Oscillation did not dominate regional climate conditions around the globe. A weak La Ni a dissipated to ENSOneutral conditions by spring, and while El Nino appeared to be emerging during summer, this phase never fully developed as sea surface temperatures in the eastern conditions. Nevertheless, other large-scale climate patterns and extreme weather events impacted various regions during the year. A negative phase of the Arctic Oscillation from mid-January to early February contributed to frigid conditions in parts of northern Africa, eastern Europe, and western Asia. A lack of rain during the 2012 wet season led to the worst drought in at least the past three decades for northeastern Brazil. Central North America also experienced one of its most severe droughts on record. The Caribbean observed a very wet dry season and it was the Sahel's wettest rainy season in 50 years. Overall, the 2012 average temperature across global land and ocean surfaces ranked among the 10 warmest years on record. The global land surface temperature alone was also among the 10 warmest on record. In the upper atmosphere, the average stratospheric temperature was record or near-record cold, depending on the dataset. After a 30-year warming trend from 1970 to 1999 for global sea surface temperatures, the period 2000-12 had little further trend. This may be linked to the prevalence of La Ni a-like conditions during the 21st century. Heat content in the upper 700 m of the ocean remained near record high levels in 2012. Net increases from 2011 to 2012 were observed at 700-m to 2000-m depth and even in the abyssal ocean below. Following sharp decreases in to the effects of La Ni a, sea levels rebounded to reach records highs in 2012. The increased hydrological cycle seen in recent years continued, with more evaporation in drier locations and more precipitation in rainy areas. In a pattern that has held since 2004, salty areas of the ocean surfaces and subsurfaces were anomalously salty on average, while fresher areas were anomalously fresh. Global tropical cyclone activity during 2012 was near average, with a total of 84 storms compared with the 1981-2010 average of 89. Similar to 2010 and 2011, the North Atlantic was the only hurricane basin that experienced above-normal activity. In this basin, Sandy brought devastation to Cuba and parts of the eastern North American seaboard. All other basins experienced either near-or below-normal tropical cyclone activity. Only three tropical cyclones reached Category 5 intensity-all in Bopha became the only storm in the historical record to produce winds greater than 130 kt south of 7 N. It was also the costliest storm to affect the Philippines and killed more than 1000 residents. Minimum Arctic sea ice extent in September and Northern Hemisphere snow cover extent in June both reached new record lows. June snow cover extent is now declining at a faster rate (-17.6% per decade) than September sea ice extent (-13.0% per decade). Permafrost temperatures reached record high values in northernmost Alaska. A new melt extent record occurred on 11-12 July on the Greenland ice sheet; 97% of the ice sheet showed some form of melt, four times greater than the average melt for this time of year. The climate in Antarctica was relatively stable overall. The largest maximum sea ice extent since records begain in 1978 was observed in September 2012. In the stratosphere, warm air led to the second smallest ozone hole in the past two decades. Even so, the springtime ozone layer above Antarctica likely will not return to its early 1980s state until about 2060. Following a slight decline associated with the global 2 emissions from fossil fuel combustion and cement production reached a record 9.5 +/- 0.5 Pg C in 2011 and a new record of 9.7 +/- 0.5 Pg C is estimated for 2012. Atmospheric CO2 concentrations increased by 2.1 ppm in 2012, to 392.6 ppm. In spring 2012, 2 concentration exceeded 400 ppm at 7 of the 13 Arctic observation sites. Globally, other greenhouse gases including methane and nitrous oxide also continued to rise in concentration and the combined effect now represents a 32% increase in radiative forcing over a 1990 baseline. Concentrations of most ozone depleting substances continued to fall.
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| 8. |
- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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| 12. |
- Hayes, A., et al.
(författare)
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A European multicentre evaluation of detection and typing methods for human enteroviruses and parechoviruses using RNA transcripts
- 2020
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Ingår i: Journal of Medical Virology. - : Wiley. - 0146-6615 .- 1096-9071. ; 92:8, s. 1065-1074
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Tidskriftsartikel (refereegranskat)abstract
- Polymerase chain reaction (PCR) detection has become the gold standard for diagnosis and typing of enterovirus (EV) and human parechovirus (HPeV) infections. Its effectiveness depends critically on using the appropriate sample types and high assay sensitivity as viral loads in cerebrospinal fluid samples from meningitis and sepsis clinical presentation can be extremely low. This study evaluated the sensitivity and specificity of currently used commercial and in-house diagnostic and typing assays. Accurately quantified RNA transcript controls were distributed to 27 diagnostic and 12 reference laboratories in 17 European countries for blinded testing. Transcripts represented the four human EV species (EV-A71, echovirus 30, coxsackie A virus 21, and EV-D68), HPeV3, and specificity controls. Reported results from 48 in-house and 15 commercial assays showed 98% detection frequencies of high copy (1000 RNA copies/5 µL) transcripts. In-house assays showed significantly greater detection frequencies of the low copy (10 copies/5 µL) EV and HPeV transcripts (81% and 86%, respectively) compared with commercial assays (56%, 50%; P = 7 × 10−5). EV-specific PCRs showed low cross-reactivity with human rhinovirus C (3 of 42 tests) and infrequent positivity in the negative control (2 of 63 tests). Most or all high copy EV and HPeV controls were successfully typed (88%, 100%) by reference laboratories, but showed reduced effectiveness for low copy controls (41%, 67%). Stabilized RNA transcripts provide an effective, logistically simple and inexpensive reagent for evaluation of diagnostic assay performance. The study provides reassurance of the performance of the many in-house assay formats used across Europe. However, it identified often substantially reduced sensitivities of commercial assays often used as point-of-care tests.
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| 17. |
- Abudurexiti, A, et al.
(författare)
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Taxonomy of the order Bunyavirales: update 2019
- 2019
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Ingår i: Archives of virology. - : Springer Science and Business Media LLC. - 1432-8798 .- 0304-8608. ; 164:7, s. 1949-1965
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Tidskriftsartikel (refereegranskat)
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| 18. |
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| 19. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 20. |
- Pearce, T. R., et al.
(författare)
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International collaboration between collections-based institutes for halting biodiversity loss and unlocking the useful properties of plants and fungi
- 2020
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Ingår i: Plants People Planet. - : Wiley. - 2572-2611. ; 2:5, s. 515-534
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Tidskriftsartikel (refereegranskat)abstract
- Societal Impact Statement The United Nations' Sustainable Development Goal (SDG) 17 calls for "strong global partnerships and cooperation" to support the other SDGs. The collections-based science community offers many examples of conservation of plant and fungal biodiversity, sharing, repatriation and aggregation of data, access to new technologies, supply of plant and fungal material, strengthening capacity of practitioners, and benefit sharing with the providers of biodiversity and genetic resources. Collaboration framed by workable multilateral treaties will increase our understanding of plant and fungal diversity, help halt biodiversity loss, and accelerate our sustainable use of plants and fungi and the exploration of their useful traits. SummaryCollections-based institutes are at the forefront of generating knowledge and understanding of plant and fungal biodiversity. Through the analysis of occurrence data, the use of modern technologies to better understand the evolutionary relationships between species and documentation of their useful properties, the work of collections-based institutes provides good models for conservation; addressing species loss and improving sustainable use of plants and fungi. Nevertheless, the pressure on the planet's plant and fungal diversity is relentless. We argue that a massive increase in the accessibility of preserved and living collections of plants and fungi is required. An increased scale of responsible exploration to both conserve and unlock the useful properties of plants and fungi is needed to deliver solutions to the many global challenges facing humanity and the planet. This article explores the role of collaborations between collections-based institutes and their partners in preventing biodiversity loss and delivering sustainable development. Drawing on examples from herbaria, agricultural and wild species genebanks, mycological collections, an international NGO, and the botanic garden community, we demonstrate how collaboration improves efficiency and impact. Collaborations can be peer to peer, institutional, governmental, national, or international, they may involve work with local communities and are frequently a combination of these. We suggest the five key benefits to collaboration and show that with trust, understanding, and mutual respect, powerful and sustainable partnerships develop. Such trust and respect are hard won, but once established, sustain a high level of commitment, enable development of shared long-term visions of success, and attract diverse funding streams.
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| 21. |
- Doherty, Walter J, et al.
(författare)
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Molecular ordering in monolayers of an alkyl-Substituted perylene-bisimide dye by attenuated total reflectance ultraviolet-visible spectroscopy
- 2005
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Ingår i: Applied Spectroscopy. - : SAGE Publications. - 0003-7028 .- 1943-3530. ; 59:10, s. 1248-1256
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Tidskriftsartikel (refereegranskat)abstract
- Surface-relative orientational parameters were determined for monolayer films of N, N'-ditridecylperylenetetracarboxylic dianhydridediimide (C 13-PTCDI) in terms of the relative electronic transition dipole strengths, providing a three-dimensional view of the absorption dipole distribution. In order to obtain a macroscopically ordered film, C 13-PTCDI was deposited by (1) horizontal Langmuir-Blodgett (LB) transfer onto methyl- and phenyl-silanized glass, and (2) vapor deposition onto oriented films of poly(tetrafluoroethylene) (PTFE) on glass. Films of LB-deposited C13-PTCDI were found to be completely Isotropic prior to annealing. After annealing, these films remained isotropic in the plane of the substrate while the out-of-plane anisotropy was significantly enhanced. In contrast, films of C13-PTCDI vapor deposited onto oriented poly(tetrafluoroethylene) (PTFE)-modified substrates yielded films with a high degree of both in- and out-of-plane anisotropy. Atomic force microscopy (AFM) images of both the LB- and vapor-deposited films show substantial differences in film morphology and long-range order. These results demonstrate that molecular orientation in C13-PTCDI films can be controlled by varying substrate surface chemistry and post-deposition processing. © 2005 Society for Applied Spectroscopy.
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| 22. |
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| 23. |
- Shellock, R. J., et al.
(författare)
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Building leaders for the UN Ocean Science Decade : a guide to supporting early career women researchers within academic marine research institutions
- 2023
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Ingår i: ICES Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; 80:1, s. 56-75
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Tidskriftsartikel (refereegranskat)abstract
- Diverse and inclusive marine research is paramount to addressing ocean sustainability challenges in the 21st century, as envisioned by the UN Decade of Ocean Science for Sustainable Development. Despite increasing efforts to diversify ocean science, women continue to face barriers at various stages of their career, which inhibits their progression to leadership within academic institutions. In this perspective, we draw on the collective experiences of thirty-four global women leaders, bolstered by a narrative review, to identify practical strategies and actions that will help empower early career women researchers to become the leaders of tomorrow. We propose five strategies: (i) create a more inclusive culture, (ii) ensure early and equitable career development opportunities for women ECRs, (iii) ensure equitable access to funding for women ECRs, (iv) offer mentoring opportunities and, (v) create flexible, family-friendly environments. Transformational, meaningful, and lasting change will only be achieved through commitment and collaborative action across various scales and by multiple stakeholders.
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| 24. |
- Simmonds, P, et al.
(författare)
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Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes
- 2005
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Ingår i: Hepatology. - : Ovid Technologies (Wolters Kluwer Health). - 1527-3350 .- 0270-9139. ; 42:4, s. 962-973
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Tidskriftsartikel (refereegranskat)abstract
- International standardization and coordination of the nomenclature of variants of hepatitis C virus (HCV) is increasingly needed as more is discovered about the scale of HCV-related liver disease and important biological and antigenic differences that exist between variants. A group of scientists expert in the field of HCV genetic variability, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re-examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised criteria for the assignment of new genotypes as they are discovered in the future. A comprehensive listing of all currently classified variants of HCV incorporates a number of agreed genotype and subtype name reassignments to create consistency in nomenclature. The paper also contains consensus proposals for the classification of new variants into genotypes and subtypes, which recognizes and incorporates new knowledge of HCV genetic diversity and epidemiology. A proposal was made that HCV variants be classified into 6 genotypes (representing the 6 genetic groups defined by phylogenetic analysis). Subtype name assignment will be either confirmed or provisional, depending on the availability of complete or partial nucleotide sequence data, or remain unassigned where fewer than 3 examples of a new subtype have been described. In conclusion, these proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment-of-new genotypes and subtypes in the future.
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| 26. |
- Bennecke, E, et al.
(författare)
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Early Genital Surgery in Disorders/Differences of Sex Development: Patients' Perspectives
- 2021
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Ingår i: Archives of sexual behavior. - : Springer Science and Business Media LLC. - 1573-2800 .- 0004-0002. ; 50:3, s. 913-923
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Tidskriftsartikel (refereegranskat)abstract
- Controversy continues over a proposed moratorium on elective genital surgery in childhood for disorders/differences of sex development (DSD). Empirical evidence on patient preference is needed to inform decision-making. We conducted a multicentre survey by cross-sectional questionnaire in 14 specialized clinics in six European countries. The sample comprised 459 individuals (≥ 16 years) with a DSD diagnosis, including individuals with congenital adrenal hyperplasia (CAH) (n = 192), XY DSD with prenatal androgen effect (A) (n = 150), and without (nA) (n = 117). Main outcome measures were level of agreement with given statements regarding genital surgery, including clitoris reduction, vaginoplasty, and hypospadias repair. A total of 66% of individuals with CAH and 60% of those with XY DSD-A thought that infancy or childhood were the appropriate age for genital surgery. Females with XY DSD were divided on this issue and tended to prefer vaginoplasty at a later age (XY DSD-A 39%, XY DSD-nA 32%). A total of 47% of males preferred early hypospadias surgery. Only 12% (CAH), 11% (XY DSD-A), and 21% (XY DSD-nA) thought they would have been better off without any surgery in childhood or adolescence. Individuals who had early genital surgery were more likely to approve of it. Outcome data failed to support a general moratorium on early elective genital surgery. Participant perspectives varied considerably by diagnostic category, gender, history of surgery, and contact with support groups. Case-by-case decision-making is better suited to grasping the ethical complexity of the issues at stake.Trial registration: German Clinical Trials Register DRKS00006072.
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| 28. |
- Mariani, S., et al.
(författare)
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North Sea herring population structure revealed by microsatellite analysis
- 2005
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Ingår i: Marine Ecology-Progress Series. - 0171-8630. ; 303, s. 245-257
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Tidskriftsartikel (refereegranskat)abstract
- The Atlantic herring Clupea harengus has played a pivotal role in the formulation of ideas relating to population structuring in marine fishes, yet considerable uncertainty remains as to the extent to which phenotypic and genetic differentiation coincide in such a highly mobile species. In this study, we examined genetic population structure across the major herring spawning aggregations in the North Sea and adjacent waters over 2 years, 2002 and 2003. We analysed 1660 spawning individuals across 9 microsatellite loci. Data were analysed using several approaches, taking into account the effect of location, year-class and sex, as well as pooling all individuals together, making no assumption as to the number of populations present in the data set. The results suggest the presence of a genetically homogeneous unit off Northern Scotland, and a temporally stable pattern of isolation by distance determined predominantly by the divergence of the English Channel samples and, in 2003, by the Norwegian spring spawners. Our data suggest that the current view of North Sea herring as a unit-stock might be adequate, but confirm the considerable degree of demographic independence of the herring populations in the English Channel. Despite major recent population collapses, genetic data indicated no evidence of bottlenecks affecting the genetic diversity of extant North Sea herring populations. Finally, despite evidence of weak population structuring, we discuss the risks of underestimating population differentiation in marine fish of large population sizes, and with reference to herring population history and dynamics, we attempt to reconcile the existing theories on herring population structure.
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| 29. |
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| 30. |
- Ruzzante, D. E., et al.
(författare)
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Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring
- 2006
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Ingår i: Proceedings of the Royal Society B-Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 273:1593, s. 1459-1464
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Tidskriftsartikel (refereegranskat)abstract
- The existence of biologically differentiated populations has been credited with a major role in conferring sustainability and in buffering overall productivity of anadromous fish population complexes where evidence for spatial structure is uncontroversial. Here, we describe evidence of correlated genetic and life history (spawning season linked to spawning location) differentiation in an abundant and highly migratory pelagic fish, Atlantic herring, Clupea harengus, in the North Sea (NS) and adjacent areas. The existence of genetically and phenotypically diverse stocks in this region despite intense seasonal mixing strongly implicates natal homing in this species. Based on information from genetic markers and otolith morphology, we estimate the proportional contribution by NS, Skagerrak (SKG) and Kattegat and western Baltic (WBS) fish to mixed aggregations targeted by the NS fishery. We use these estimates to identify spatial and temporal differences in life history (migratory behaviour) and habitat use among genetically differentiated migratory populations that mix seasonally. Our study suggests the existence of more complex patterns of intraspecific diversity than was previously recognized. Sustainability may be compromised if such complex patterns are reduced through generalized management (e.g. area closures) that overlooks population differences in spatial use throughout the life cycle.
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| 31. |
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| 32. |
- Simmonds, P., et al.
(författare)
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Recommendations for the nomenclature of enteroviruses and rhinoviruses
- 2020
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Ingår i: Archives of Virology. - : Springer. - 0304-8608 .- 1432-8798. ; 165, s. 793-797
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Tidskriftsartikel (refereegranskat)abstract
- Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as "coxsackieviruses", "polioviruses" and "echoviruses", which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.
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| 33. |
- Smith, D. B., et al.
(författare)
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Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A)
- 2020
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Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 101:7, s. 692-698
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Tidskriftsartikel (refereegranskat)abstract
- In this recommendation, we update our 2016 table of reference sequences of subtypes of hepatitis E virus (HEV; species Orthohepevirus A, family Hepeviridae) for which complete genome sequences are available (Smith et al., 2016). This takes into account subsequent publications describing novel viruses and additional proposals for subtype names; there are now eight genotypes and 36 subtypes. Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV.
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