| 1. |
- McMahon, C. R., et al.
(author)
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Animal Borne Ocean Sensors - AniBOS - An Essential Component of the Global Ocean Observing System
- 2021
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In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 8
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Research review (peer-reviewed)abstract
- Marine animals equipped with biological and physical electronic sensors have produced long-term data streams on key marine environmental variables, hydrography, animal behavior and ecology. These data are an essential component of the Global Ocean Observing System (GOOS). The Animal Borne Ocean Sensors (AniBOS) network aims to coordinate the long-term collection and delivery of marine data streams, providing a complementary capability to other GOOS networks that monitor Essential Ocean Variables (EOVs), essential climate variables (ECVs) and essential biodiversity variables (EBVs). AniBOS augments observations of temperature and salinity within the upper ocean, in areas that are under-sampled, providing information that is urgently needed for an improved understanding of climate and ocean variability and for forecasting. Additionally, measurements of chlorophyll fluorescence and dissolved oxygen concentrations are emerging. The observations AniBOS provides are used widely across the research, modeling and operational oceanographic communities. High latitude, shallow coastal shelves and tropical seas have historically been sampled poorly with traditional observing platforms for many reasons including sea ice presence, limited satellite coverage and logistical costs. Animal-borne sensors are helping to fill that gap by collecting and transmitting in near real time an average of 500 temperature-salinity-depth profiles per animal annually and, when instruments are recovered (similar to 30% of instruments deployed annually, n = 103 +/- 34), up to 1,000 profiles per month in these regions. Increased observations from under-sampled regions greatly improve the accuracy and confidence in estimates of ocean state and improve studies of climate variability by delivering data that refine climate prediction estimates at regional and global scales. The GOOS Observations Coordination Group (OCG) reviews, advises on and coordinates activities across the global ocean observing networks to strengthen the effective implementation of the system. AniBOS was formally recognized in 2020 as a GOOS network. This improves our ability to observe the ocean's structure and animals that live in them more comprehensively, concomitantly improving our understanding of global ocean and climate processes for societal benefit consistent with the UN Sustainability Goals 13 and 14: Climate and Life below Water. Working within the GOOS OCG framework ensures that AniBOS is an essential component of an integrated Global Ocean Observing System.
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| 2. |
- Schoch, CL, et al.
(author)
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
- 2012
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 109:16, s. 6241-6246
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Journal article (peer-reviewed)abstract
- Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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| 3. |
- Kennicutt, M. C., et al.
(author)
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Delivering 21st century Antarctic and Southern Ocean science
- 2016
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In: Antarctic Science. - 0954-1020 .- 1365-2079. ; 28, s. 407-423
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Journal article (peer-reviewed)abstract
- © Antarctic Science Ltd 2016.The Antarctic Roadmap Challenges (ARC) project identified critical requirements to deliver high priority Antarctic research in the 21st century. The ARC project addressed the challenges of enabling technologies, facilitating access, providing logistics and infrastructure, and capitalizing on international co-operation. Technological requirements include: i) innovative automated in situ observing systems, sensors and interoperable platforms (including power demands), ii) realistic and holistic numerical models, iii) enhanced remote sensing and sensors, iv) expanded sample collection and retrieval technologies, and v) greater cyber-infrastructure to process 'big data' collection, transmission and analyses while promoting data accessibility. These technologies must be widely available, performance and reliability must be improved and technologies used elsewhere must be applied to the Antarctic. Considerable Antarctic research is field-based, making access to vital geographical targets essential. Future research will require continent- and ocean-wide environmentally responsible access to coastal and interior Antarctica and the Southern Ocean. Year-round access is indispensable. The cost of future Antarctic science is great but there are opportunities for all to participate commensurate with national resources, expertise and interests. The scope of future Antarctic research will necessitate enhanced and inventive interdisciplinary and international collaborations. The full promise of Antarctic science will only be realized if nations act together.
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| 4. |
- Boyd, P. W., et al.
(author)
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Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review
- 2018
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In: Global Change Biology. - : Wiley. - 1354-1013. ; 24:6, s. 2239-2261
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Journal article (peer-reviewed)abstract
- Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain processoriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation.
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| 5. |
- Hyde, Kevin D., et al.
(author)
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One stop shop: backbones trees for important phytopathogenic genera: I (2014)
- 2014
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 21-125
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Journal article (peer-reviewed)abstract
- Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
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| 6. |
- Klocker, A., et al.
(author)
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Generation of the Internal Pycnocline in the Subpolar Southern Ocean by Wintertime Sea Ice Melting
- 2023
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In: Journal of Geophysical Research-Oceans. - : American Geophysical Union (AGU). - 2169-9275 .- 2169-9291. ; 128:3
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Journal article (peer-reviewed)abstract
- The ocean's internal pycnocline is a layer of elevated stratification that separates the well-ventilated upper ocean from the more slowly renewed deep ocean. Despite its pivotal role in organizing ocean circulation, the processes governing the formation of the internal pycnocline remain little understood. Classical theories on pycnocline formation have been couched in terms of temperature and it is not clear how the theory applies in the high-latitude Southern Ocean, where stratification is dominated by salinity. Here we assess the mechanisms generating the internal pycnocline at southern high latitudes through the analysis of a high-resolution, realistic, global sea ice-ocean model. We show evidence suggesting that the internal pycnocline's formation is associated with sea ice-ocean interactions in two distinct ice-covered regions, fringing the Antarctic continental slope and the winter sea-ice edge. In both areas, winter-persistent sea-ice melt creates strong, salinity-based stratification at the base of the winter mixed layer. The resulting sheets of high stratification subsequently descend into the ocean interior at fronts of the Antarctic Circumpolar Current, and connect seamlessly to the internal pycnocline in areas further north in which pycnocline stratification is determined by temperature. Our findings thus suggest an important role of localized sea ice-ocean interactions in configuring the vertical structure of the Southern Ocean.
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| 7. |
- Portela, E., et al.
(author)
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Controls on Dense Shelf Water Formation in Four East Antarctic Polynyas
- 2022
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In: Journal of Geophysical Research: Oceans. - 2169-9275. ; 127:12
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Journal article (peer-reviewed)abstract
- Coastal polynyas are key formation regions for dense shelf water (DSW) that ultimately contributes to the ventilation of the ocean abyss. However, not all polynyas form DSW. We examine how the physiographic setting, water-mass distribution and transformation, water column stratification, and sea-ice production regulate DSW formation in four East Antarctic coastal polynyas. We use a salt budget to estimate the relative contribution of sea-ice production and lateral advection to the monthly change in salinity in each polynya. DSW forms in Mackenzie polynya due to a combination of physical features (shallow water depth and a broad continental shelf) and high sea-ice production. Sea-ice formation begins early (March) in Mackenzie polynya, counteracting fresh advection and establishing a salty mixed layer in autumn that preconditions the water column for deep convection in winter. Sea-ice production is moderate in the other three polynyas, but saline DSW is not formed (a fresh variety is formed in the Barrier polynya). In the Shackleton polynya, brine rejection during winter is insufficient to overcome the very fresh autumn mixed layer. In Vincennes Bay, a strong inflow of modified Circumpolar Deep Water stratifies the water column, hindering deep convection and DSW formation. Our study highlights that DSW formation in a given polynya depends on a complex combination of factors, some of which may be strongly altered under a changing climate, with potentially important consequences for the ventilation of the deep ocean, the global meridional overturning circulation, and the transport of ocean heat to Antarctic ice shelves.
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| 8. |
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| 9. |
- Lepage, M, et al.
(author)
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Modelling of post-irradiation events in polymer gel dosimeters
- 2001
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In: Physics in Medicine and Biology. - : IOP Publishing. - 1361-6560 .- 0031-9155. ; 46:11, s. 2827-2839
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Journal article (peer-reviewed)abstract
- The nuclear magnetic resonance (NMR) spin-spin relaxation time (T2) is related to the radiation-dependent concentration of polymer formed in polymer gel dosimeters manufactured from monomers in an aqueous gelatin matrix. Changes in T2 with time post-irradiation have been reported in the literature but their nature is not fully understood. We investigated those changes with time after irradiation using FT-Raman spectroscopy and the precise determination of T2 at high magnetic field in a polymer gel dosimeter. A model of fast exchange of magnetization taking into account ongoing gelation and strengthening of the gelatin matrix as well as the polymerization of the monomers with time is presented. Published data on the changes of T2 in gelatin gels as a function of post-manufacture time are used and fitted closely by the model presented. The same set of parameters characterizing the variations of T2 in gelatin gels and the increasing concentration of polymer determined from FT-Raman spectroscopy are used successfully in the modelling of irradiated polymer gel dosimeters. Minimal variations in T2 in an irradiated PAG dosimeter are observed after 13 h.
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| 10. |
- Lepage, M, et al.
(author)
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The relationship between radiation-induced chemical processes and transverse relaxation times in polymer gel dosimeters
- 2001
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In: Physics in Medicine and Biology. - : IOP Publishing. - 1361-6560 .- 0031-9155. ; 46:4, s. 1061-1074
-
Journal article (peer-reviewed)abstract
- The effects of ionizing radiation in different compositions of polymer gel dosimeters are investigated using FT-Raman spectroscopy and NMR T2 relaxation times. The dosimeters are manufactured from different concentrations of comonomers (acrylamide and N,N'-methylene-bis-acrylamide) dispersed in different concentrations of an aqueous gelatin matrix. Results are analysed using a model of fast exchange of magnetization between three proton pools. The fraction of protons in each pool is determined using the known chemical composition of the dosimeter and FT-Raman spectroscopy. Based on these results, the physical and chemical processes in interplay in the dosimeters are examined in view of their effect on the changes in T2. The precipitation of growing macroradicals and the scavenging of free radicals by gelatin are used to explain the rate of polymerization. The model describes the changes in T2 as a function of the absorbed dose up to 50 Gy for the different compositions. This is expected to aid the theoretical design of new, more efficient dosimeters, since it was demonstrated that the optimum dosimeter (i.e, with the lowest dose resolution) must have a range of relaxation times which match the range of T2 values which can be determined with the lowest uncertainty using an MRI scanner.
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| 11. |
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| 12. |
- Portela, E., et al.
(author)
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Seasonal Transformation and Spatial Variability of Water Masses Within MacKenzie Polynya, Prydz Bay
- 2021
-
In: Journal of Geophysical Research: Oceans. - 2169-9275. ; 126:12
-
Journal article (peer-reviewed)abstract
- We provide a detailed description of the spatial distribution, seasonality and transformation of the main water masses within MacKenzie Polynya (MP) in Prydz Bay, East Antarctica, using data from instrumented southern elephant seals. Dense Shelf Water (DSW) formation in MP shows large spatial variability that is related to the (a) local bathymetry, (b) water column preconditioning from the presence/absence of different water masses, and (c) proximity to the Amery Ice Shelf meltwater outflow. MP exhibits sustained sea ice production and brine rejection (thus, salinity increase) from April to October. However, new DSW is only formed from June onward, when the mixed layer deepens and convection is strong enough to break the stratification set by Antarctic Surface Water above and Ice Shelf Water below. We found no evidence of DSW export from MP to Darnley polynya, as previously suggested. Rather, our observations suggest some DSW formed in Darnley Polynya may drain toward the western Prydz Bay. Then, DSW is exported offshore from Prydz Bay through the Prydz Channel. The interplay between sea ice formation, meltwater input, and sea floor topography is likely to explain why some coastal polynyas form more DSW than others, as well as the temporal variability in DSW formation within a particular polynya. © 2021. American Geophysical Union. All Rights Reserved.
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| 13. |
- Rydzewska, E., et al.
(author)
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Age at identification, prevalence and general health of children with autism: Observational study of a whole country population
- 2019
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In: Bmj Open. - : BMJ. - 2044-6055. ; 9:7
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Journal article (peer-reviewed)abstract
- Objectives: Reported childhood prevalence of autism varies considerably between studies and over time, and general health status has been little investigated. We aimed to investigate contemporary prevalence of reported autism by age, and general health status of children/young people with and without autism. Design: Secondary analysis of Scotland's Census, 2011 data. Cross-sectional study. Setting: General population of Scotland. Participants: All children (n=916 331) and young people (n=632 488) in Scotland. Main outcome measures: Number (%) of children/young people reported to have autism and their general health status; prevalence of autism; prevalence of poor health (fair, bad and very bad health); odds ratios (95% confidence intervals) of autism predicting poor health, adjusted for age and gender and OR for age and gender in predicting poor health within the population with reported autism. Results: Autism was reported for 17 348/916 331 (1.9%) children aged 0-15, and 7715/632 488 (1.2%) young people aged 16-24. The rate increased to age 11 in boys and age 10 in girls, reflecting age at diagnosis. Prevalence was 2.8% at age 10 (4.4% for boys; 1.1% for girls), and 2.9% at age 11 (4.5% for boys; 1.1% for girls). 22.0% of children and 25.5% of young people with autism reported poor health, compared with 2.0% and 4.4% without autism. Autism had OR=11.3 (11.0 to 11.7) in predicting poor health. Autistic females had poorer health than autistic males, OR=1.6 (1.5 to 1.8). Conclusion: Accurate information on the proportion of autistic children and their health status is essential plan appropriate prevention and intervention measures and provide resources for those who may put demand on services designed for autistic people. © 2019 Author(s).
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| 14. |
- Rydzewska, E., et al.
(author)
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General health of adults with autism spectrum disorders - A whole country population cross-sectional study
- 2019
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In: Research in Autism Spectrum Disorders. - : Elsevier BV. - 1750-9467. ; 60, s. 59-66
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Journal article (peer-reviewed)abstract
- Background: General health status in adult populations with autism spectrum disorders has been little studied. We aimed to investigate general health status and predictors of poor health in adults with autism spectrum disorders compared with other adults. Method: Whole country data were drawn from Scotland's Census, 2011. We calculated and compared the frequencies of health status in adults with and without autism spectrum disorders. We then used logistic regressions to calculate odds ratios (OR) with 95% confidence intervals (95% CI) of autism predicting poor general health in the whole population, adjusted for age and gender, and OR (95% CI) of age and gender predicting poor general health within the autism spectrum disorders population. Results: Autism spectrum disorders were reported for 6649/3,746,584 (0.2%) adults aged 25 + years, of whom 46.8% (N = 3111) had poor general health, compared with 23.7% (N = 887,878) of other people. Poor health was common across the entire lifecourse for adults with autism spectrum disorders. Autism had OR = 5.1 (4.9-5.4, 95% CI) for predicting poor general health, or OR = 7.5 (6.9-8.2, 95% CI) when the interaction with age was included. Poorer health was more common at older age, and for women. Conclusions: Poor general health merits attention across the full lifecourse for adults with autism. Health practitioners need to be alert to the burden of potential health problems to seek them out to be addressed, and so the health agenda can turn towards potential mechanisms for prevention and better support for adults who may call upon services for people with autism.
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| 15. |
- Rydzewska, E., et al.
(author)
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Prevalence of long-term health conditions in adults with autism: observational study of a whole country population
- 2018
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In: BMJ Open. - : BMJ. - 2044-6055. ; 8:8
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Journal article (peer-reviewed)abstract
- Objectives To investigate the prevalence of comorbid mental health conditions and physical disabilities in a whole country population of adults aged 25+ withand without reported autism. Design Secondary analysis of Scotland's Census, 2011 data. Cross-sectional study. Participants 94% of Scotland's population, including 6649/3 746 584 adults aged 25+ reportedto have autism. Main outcome measures Prevalence of six comorbidities: deafness or partial hearing loss, blindness or partial sight loss, intellectual disabilities, mental health conditions, physical disability and other condition; ORs (95% CI) of autism predicting these comorbidities, adjusted for age and gender; and OR for age and gender in predicting comorbidities within the population with reported autism. Results Comorbidities were common: deafness/hearing loss17.5%; blindness/sight loss12.1%; intellectual disabilities29.4%; mental health conditions33.0%; physical disability30.7%; other condition34.1%. Autism statistically predicted all of the conditions: OR 3.3 (95% CI 3.1 to 3.6) for deafness or partial hearing loss, OR 8.5 (95% CI 7.9 to 9.2) for blindness or partial sight loss, OR 94.6 (95% CI 89.4 to 100.0) for intellectual disabilities, OR 8.6 (95% CI 8.2 to 9.0) for mental health conditions, OR 6.2 (95% CI 5.8 to 6.6) for physical disability and OR 2.6 (95% CI 2.5 to 2.8) for other condition. Contrary to findings within the general population, female gender predicted all conditions within the population with reported autism, including intellectual disabilities (OR=1.4). Conclusions Clinicians need heightened awareness of comorbidities in adults with autism to improve detection and suitable care, especially given the added complexity of assessment in this population and the fact that hearing and visual impairments may cause additional difficulties with reciprocal communication which are also a feature of autism; hence posing further challenges in assessment.
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| 16. |
- Silvano, Alessandro, et al.
(author)
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Observing Antarctic Bottom Water in the Southern Ocean
- 2023
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In: Frontiers in Marine Science. - 2296-7745. ; 10
-
Research review (peer-reviewed)abstract
- Dense, cold waters formed on Antarctic continental shelves descend along the Antarctic continental margin, where they mix with other Southern Ocean waters to form Antarctic Bottom Water (AABW). AABW then spreads into the deepest parts of all major ocean basins, isolating heat and carbon from the atmosphere for centuries. Despite AABW's key role in regulating Earth's climate on long time scales and in recording Southern Ocean conditions, AABW remains poorly observed. This lack of observational data is mostly due to two factors. First, AABW originates on the Antarctic continental shelf and slope where in situ measurements are limited and ocean observations by satellites are hampered by persistent sea ice cover and long periods of darkness in winter. Second, north of the Antarctic continental slope, AABW is found below approximately 2 km depth, where in situ observations are also scarce and satellites cannot provide direct measurements. Here, we review progress made during the past decades in observing AABW. We describe 1) long-term monitoring obtained by moorings, by ship-based surveys, and beneath ice shelves through bore holes; 2) the recent development of autonomous observing tools in coastal Antarctic and deep ocean systems; and 3) alternative approaches including data assimilation models and satellite-derived proxies. The variety of approaches is beginning to transform our understanding of AABW, including its formation processes, temporal variability, and contribution to the lower limb of the global ocean meridional overturning circulation. In particular, these observations highlight the key role played by winds, sea ice, and the Antarctic Ice Sheet in AABW-related processes. We conclude by discussing future avenues for observing and understanding AABW, impressing the need for a sustained and coordinated observing system.
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| 17. |
- Thunnissen, Erik, et al.
(author)
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The challenge of NSCLC diagnosis and predictive analysis on small samples. Practical approach of a working group
- 2012
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In: Lung Cancer. - : Elsevier BV. - 1872-8332 .- 0169-5002. ; 76:1, s. 1-18
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Research review (peer-reviewed)abstract
- Until recently, the division of pulmonary carcinomas into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) was adequate for therapy selection. Due to the emergence of new treatment options subtyping of NSCLC and predictive testing have become mandatory. A practical approach to the new requirements involving interaction between pulmonologist, oncologist and molecular pathology to optimize patient care is described. The diagnosis of lung cancer involves (i) the identification and complete classification of malignancy, (ii) immunohistochemistry is used to predict the likely NSCLC subtype (squamous cell vs. adenocarcinoma), as in small diagnostic samples specific subtyping is frequently on morphological grounds alone not feasible (NSCLC-NOS), (iii) molecular testing. To allow the extended diagnostic and predictive examination (i) tissue sampling should be maximized whenever feasible and deemed clinically safe, reducing the need for re-biopsy for additional studies and (ii) tissue handling, processing and sectioning should be optimized. Complex diagnostic algorithms are emerging, which will require close dialogue and understanding between pulmonologists and others who are closely involved in tissue acquisition, pathologists and oncologists who will ultimately, with the patient, make treatment decisions. Personalized medicine not only means the choice of treatment tailored to the individual patient, but also reflects the need to consider how investigative and diagnostic strategies must also be planned according to individual tumour characteristics. (C) 2011 Elsevier Ireland Ltd. All rights reserved.
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