| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Kim, Jae-Young, et al.
(författare)
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Event Horizon Telescope imaging of the archetypal blazar 3C 279 at an extreme 20 microarcsecond resolution
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 640
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Tidskriftsartikel (refereegranskat)abstract
- 3C 279 is an archetypal blazar with a prominent radio jet that show broadband flux density variability across the entire electromagnetic spectrum. We use an ultra-high angular resolution technique - global Very Long Baseline Interferometry (VLBI) at 1.3mm (230 GHz) - to resolve the innermost jet of 3C 279 in order to study its fine-scale morphology close to the jet base where highly variable-ray emission is thought to originate, according to various models. The source was observed during four days in April 2017 with the Event Horizon Telescope at 230 GHz, including the phased Atacama Large Millimeter/submillimeter Array, at an angular resolution of ∼20 μas (at a redshift of z = 0:536 this corresponds to ∼0:13 pc ∼ 1700 Schwarzschild radii with a black hole mass MBH = 8 × 108 M⊙). Imaging and model-fitting techniques were applied to the data to parameterize the fine-scale source structure and its variation.We find a multicomponent inner jet morphology with the northernmost component elongated perpendicular to the direction of the jet, as imaged at longer wavelengths. The elongated nuclear structure is consistent on all four observing days and across diffierent imaging methods and model-fitting techniques, and therefore appears robust. Owing to its compactness and brightness, we associate the northern nuclear structure as the VLBI "core". This morphology can be interpreted as either a broad resolved jet base or a spatially bent jet.We also find significant day-to-day variations in the closure phases, which appear most pronounced on the triangles with the longest baselines. Our analysis shows that this variation is related to a systematic change of the source structure. Two inner jet components move non-radially at apparent speeds of ∼15 c and ∼20 c (∼1:3 and ∼1:7 μas day-1, respectively), which more strongly supports the scenario of traveling shocks or instabilities in a bent, possibly rotating jet. The observed apparent speeds are also coincident with the 3C 279 large-scale jet kinematics observed at longer (cm) wavelengths, suggesting no significant jet acceleration between the 1.3mm core and the outer jet. The intrinsic brightness temperature of the jet components are ≤1010 K, a magnitude or more lower than typical values seen at ≥7mm wavelengths. The low brightness temperature and morphological complexity suggest that the core region of 3C 279 becomes optically thin at short (mm) wavelengths.
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| 3. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 4. |
- Moore, Keith J M, et al.
(författare)
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Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications
- 2021
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Ingår i: Journal of Biomolecular Techniques. - : Association of Biomolecular Resource Facilities. - 1524-0215 .- 1943-4731. ; 32:3, s. 228-275
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Forskningsöversikt (refereegranskat)abstract
- As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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| 5. |
- Lembrechts, Jonas J., et al.
(författare)
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Global maps of soil temperature
- 2022
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:9, s. 3110-3144
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Tidskriftsartikel (refereegranskat)abstract
- Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean=3.0±2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6±2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7±2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.
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| 6. |
- McPhearson, Timon, et al.
(författare)
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A social-ecological-technological systems framework for urban ecosystem services
- 2022
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Ingår i: One Earth. - : Elsevier BV. - 2590-3330 .- 2590-3322. ; 5:5, s. 505-518
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Tidskriftsartikel (refereegranskat)abstract
- As rates of urbanization and climatic change soar, decision-makers are increasingly challenged to provide innovative solutions that simultaneously address climate change impacts and risks and inclusively ensure quality of life for urban residents. Cities have turned to nature-based solutions to help address these challenges. Nature-based solutions, through the provision of ecosystem services, can yield numerous benefits for people and address multiple challenges simultaneously. Yet, efforts to mainstream nature-based solutions are impaired by the complexity of the interacting social, ecological, and technological dimensions of urban systems. This complexity must be understood and managed to ensure ecosystem-service provisioning is effective, equitable, and resilient. Here, we provide a social-ecological-technological system (SETS) framework that builds on decades of urban ecosystem services research to better understand four core challenges associated with urban nature-based solutions: multi-functionality, systemic valuation, scale mismatch of ecosystem services, and inequity and injustice. The framework illustrates the importance of coordinating natural, technological, and socio-economic systems when designing, planning, and managing urban nature-based solutions to enable optimal social-ecological outcomes.
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| 7. |
- Minzioni, Paolo, et al.
(författare)
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Roadmap for optofluidics
- 2017
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Ingår i: Journal of Optics. - : Institute of Physics (IOP). - 2040-8978 .- 2040-8986. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Optofluidics, nominally the research area where optics and fluidics merge, is a relatively new research field and it is only in the last decade that there has been a large increase in the number of optofluidic applications, as well as in the number of research groups, devoted to the topic. Nowadays optofluidics applications include, without being limited to, lab-on-a-chip devices, fluid-based and controlled lenses, optical sensors for fluids and for suspended particles, biosensors, imaging tools, etc. The long list of potential optofluidics applications, which have been recently demonstrated, suggests that optofluidic technologies will become more and more common in everyday life in the future, causing a significant impact on many aspects of our society. A characteristic of this research field, deriving from both its interdisciplinary origin and applications, is that in order to develop suitable solutions a combination of a deep knowledge in different fields, ranging from materials science to photonics, from microfluidics to molecular biology and biophysics, is often required. As a direct consequence, also being able to understand the long-term evolution of optofluidics research is not easy. In this article, we report several expert contributions on different topics so as to provide guidance for young scientists. At the same time, we hope that this document will also prove useful for funding institutions and stakeholders to better understand the perspectives and opportunities offered by this research field.
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| 8. |
- Wulf Hanson, Sarah, et al.
(författare)
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A global systematic analysis of the occurrence, severity, and recovery pattern of long COVID in 2020 and 2021
- 2022
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Importance: While much of the attention on the COVID-19 pandemic was directed at the daily counts of cases and those with serious disease overwhelming health services, increasingly, reports have appeared of people who experience debilitating symptoms after the initial infection. This is popularly known as long COVID.Objective: To estimate by country and territory of the number of patients affected by long COVID in 2020 and 2021, the severity of their symptoms and expected pattern of recovery.Design: We jointly analyzed ten ongoing cohort studies in ten countries for the occurrence of three major symptom clusters of long COVID among representative COVID cases. The defining symptoms of the three clusters (fatigue, cognitive problems, and shortness of breath) are explicitly mentioned in the WHO clinical case definition. For incidence of long COVID, we adopted the minimum duration after infection of three months from the WHO case definition. We pooled data from the contributing studies, two large medical record databases in the United States, and findings from 44 published studies using a Bayesian meta-regression tool. We separately estimated occurrence and pattern of recovery in patients with milder acute infections and those hospitalized. We estimated the incidence and prevalence of long COVID globally and by country in 2020 and 2021 as well as the severity-weighted prevalence using disability weights from the Global Burden of Disease study.Results: Analyses are based on detailed information for 1906 community infections and 10526 hospitalized patients from the ten collaborating cohorts, three of which included children. We added published data on 37262 community infections and 9540 hospitalized patients as well as ICD-coded medical record data concerning 1.3 million infections. Globally, in 2020 and 2021, 144.7 million (95% uncertainty interval [UI] 54.8-312.9) people suffered from any of the three symptom clusters of long COVID. This corresponds to 3.69% (1.38-7.96) of all infections. The fatigue, respiratory, and cognitive clusters occurred in 51.0% (16.9-92.4), 60.4% (18.9-89.1), and 35.4% (9.4-75.1) of long COVID cases, respectively. Those with milder acute COVID-19 cases had a quicker estimated recovery (median duration 3.99 months [IQR 3.84-4.20]) than those admitted for the acute infection (median duration 8.84 months [IQR 8.10-9.78]). At twelve months, 15.1% (10.3-21.1) continued to experience long COVID symptoms.Conclusions and relevance: The occurrence of debilitating ongoing symptoms of COVID-19 is common. Knowing how many people are affected, and for how long, is important to plan for rehabilitative services and support to return to social activities, places of learning, and the workplace when symptoms start to wane.Key Points: Question: What are the extent and nature of the most common long COVID symptoms by country in 2020 and 2021?Findings: Globally, 144.7 million people experienced one or more of three symptom clusters (fatigue; cognitive problems; and ongoing respiratory problems) of long COVID three months after infection, in 2020 and 2021. Most cases arose from milder infections. At 12 months after infection, 15.1% of these cases had not yet recovered.Meaning: The substantial number of people with long COVID are in need of rehabilitative care and support to transition back into the workplace or education when symptoms start to wane.
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| 9. |
- Wulf Hanson, Sarah, et al.
(författare)
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Estimated Global Proportions of Individuals With Persistent Fatigue, Cognitive, and Respiratory Symptom Clusters Following Symptomatic COVID-19 in 2020 and 2021
- 2022
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Ingår i: Journal of the American Medical Association (JAMA). - : American Medical Association (AMA). - 0098-7484 .- 1538-3598. ; 328:16, s. 1604-1615
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: Some individuals experience persistent symptoms after initial symptomatic SARS-CoV-2 infection (often referred to as Long COVID).OBJECTIVE: To estimate the proportion of males and females with COVID-19, younger or older than 20 years of age, who had Long COVID symptoms in 2020 and 2021 and their Long COVID symptom duration.DESIGN, SETTING, AND PARTICIPANTS: Bayesian meta-regression and pooling of 54 studies and 2 medical record databases with data for 1.2 million individuals (from 22 countries) who had symptomatic SARS-CoV-2 infection. Of the 54 studies, 44 were published and 10 were collaborating cohorts (conducted in Austria, the Faroe Islands, Germany, Iran, Italy, the Netherlands, Russia, Sweden, Switzerland, and the US). The participant data were derived from the 44 published studies (10 501 hospitalized individuals and 42 891 nonhospitalized individuals), the 10 collaborating cohort studies (10 526 and 1906), and the 2 US electronic medical record databases (250 928 and 846 046). Data collection spanned March 2020 to January 2022.EXPOSURES: Symptomatic SARS-CoV-2 infection.MAIN OUTCOMES AND MEASURES: Proportion of individuals with at least 1 of the 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after SARS-CoV-2 infection in 2020 and 2021, estimated separately for hospitalized and nonhospitalized individuals aged 20 years or older by sex and for both sexes of nonhospitalized individuals younger than 20 years of age.RESULTS: A total of 1.2 million individuals who had symptomatic SARS-CoV-2 infection were included (mean age, 4-66 years; males, 26%-88%). In the modeled estimates, 6.2% (95% uncertainty interval [UI], 2.4%-13.3%) of individuals who had symptomatic SARS-CoV-2 infection experienced at least 1 of the 3 Long COVID symptom clusters in 2020 and 2021, including 3.2% (95% UI, 0.6%-10.0%) for persistent fatigue with bodily pain or mood swings, 3.7% (95% UI, 0.9%-9.6%) for ongoing respiratory problems, and 2.2% (95% UI, 0.3%-7.6%) for cognitive problems after adjusting for health status before COVID-19, comprising an estimated 51.0% (95% UI, 16.9%-92.4%), 60.4% (95% UI, 18.9%-89.1%), and 35.4% (95% UI, 9.4%-75.1%), respectively, of Long COVID cases. The Long COVID symptom clusters were more common in women aged 20 years or older (10.6% [95% UI, 4.3%-22.2%]) 3 months after symptomatic SARS-CoV-2 infection than in men aged 20 years or older (5.4% [95% UI, 2.2%-11.7%]). Both sexes younger than 20 years of age were estimated to be affected in 2.8% (95% UI, 0.9%-7.0%) of symptomatic SARS-CoV-2 infections. The estimated mean Long COVID symptom cluster duration was 9.0 months (95% UI, 7.0-12.0 months) among hospitalized individuals and 4.0 months (95% UI, 3.6-4.6 months) among nonhospitalized individuals. Among individuals with Long COVID symptoms 3 months after symptomatic SARS-CoV-2 infection, an estimated 15.1% (95% UI, 10.3%-21.1%) continued to experience symptoms at 12 months.CONCLUSIONS AND RELEVANCE: This study presents modeled estimates of the proportion of individuals with at least 1 of 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after symptomatic SARS-CoV-2 infection.
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| 10. |
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| 11. |
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| 12. |
- Andrady, Anthony, et al.
(författare)
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Environmental effects of ozone depletion and its interaction with climate change: Progress report 2007
- 2008
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Ingår i: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-9092 .- 1474-905X. ; 7:1, s. 15-27
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Forskningsöversikt (refereegranskat)abstract
- This year theMontreal Protocol celebrates its 20th Anniversary. In September 1987, 24 countries signed the ‘Montreal Protocol on Substances that Deplete the Ozone Layer’. Today 191 countries have signed and have met strict commitments on phasing out of ozone depleting substances with the result that a 95% reduction of these substances has been achieved. The Montreal Protocol has also contributed to slowing the rate of global climate change, since most of the ozone depleting substances are also effective greenhouse gases. Even though much has been achieved, the future of the stratospheric ozone layer relies on full compliance of the Montreal Protocol by all countries for the remaining substances, including methyl bromide, as well as strict monitoring of potential risks from the production of substitute chemicals. Also the ozone depleting substances existing in banks and equipment need special attention to prevent their release to the stratosphere. Since many of the ozone depleting substances already in the atmosphere are long-lived, recovery cannot be immediate and present projections estimate a return to pre-1980 levels by 2050 to 2075. It has also been predicted that the interactions of the effects of the ozone layer and that of other climate change factors will become increasingly important.
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| 13. |
- Andrady, Anthony, et al.
(författare)
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Environmental effects of ozone depletion and its interactions with climate
- 2009
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Ingår i: Photochemical and Photobiological Sciences. - 1474-9092. ; 8:1, s. 13-22
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Forskningsöversikt (refereegranskat)abstract
- After the enthusiastic celebration of the 20th Anniversary of the Montreal Protocol on Substances that Deplete the Ozone Layer in 2007, the work for the protection of the ozone layer continues. The Environmental Effects Assessment Panel is one of the three expert panels within theMontreal Protocol. This “EEAP” deals with the increase of the UV irradiance on the Earth’s surface and its effects on human health, animals, plants, biogeochemistry, air quality and materials. For the past few years, interactions of ozone depletion with climate change have also been considered. It has become clear that the environmental problems will be long-lasting. In spite of the fact that the worldwide production of ozone depleting chemicals has already been reduced by 95%, the environmental disturbances are expected to persist for about the next half a century, even if the protective work is actively continued, and completed. The latest full report was published in Photochem. Photobiol. Sci., 2007, 6, 201–332, and the last progress report in Photochem. Photobiol. Sci., 2008, 7, 15–27. The next full report on environmental effects is scheduled for the year 2010. The present progress report 2008 is one of the short interim reports, appearing annually.
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| 14. |
- Andrady, Anthony, et al.
(författare)
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Environmental effects of ozone depletion and its interactions with climate change: Progress report, 2016
- 2017
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Ingår i: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-9092 .- 1474-905X. ; 16:2, s. 107-145
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Tidskriftsartikel (refereegranskat)abstract
- The Parties to the Montreal Protocol are informed by three Panels of experts. One of these is the Environmental Effects Assessment Panel (EEAP), which deals with two focal issues. The first focus is the effects of UV radiation on human health, animals, plants, biogeochemistry, air quality, and materials. The second focus is on interactions between UV radiation and global climate change and how these may affect humans and the environment. When considering the effects of climate change, it has become clear that processes resulting in changes in stratospheric ozone are more complex than previously believed. As a result of this, human health and environmental issues will be longer-lasting and more regionally variable. Like the other Panels, the EEAPproduces a detailed report every four years; the most recent was published as a series of seven papers in 2015 (Photochem. Photobiol. Sci., 2015, 14, 1–184). In the years in between, the EEAP produces less detailed and shorter Progress Reports of the relevant scientific findings. The most recent of these was for 2015 (Photochem. Photobiol. Sci., 2016, 15, 141–147). The present Progress Report for 2016 assesses some of the highlights and new insights with regard to the interactive nature of the direct and indirect effects of UV radiation, atmospheric processes, and climate change. The more detailed Quadrennial Assessment will bemade available in 2018.
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| 15. |
- Berbés-Blázquez, Marta, et al.
(författare)
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Assessing Future Resilience, Equity, and Sustainability in Scenario Planning
- 2021
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Ingår i: Urban Book Series. - Cham : Springer International Publishing. - 2365-7588 .- 2365-757X. ; , s. 113-127
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Bokkapitel (refereegranskat)abstract
- In the absence of strong international agreements, many municipal governments are leading efforts to build resilience to climate change in general and to extreme weather events in particular. However, it is notoriously difficult to guide and activate processes of change in complex adaptive systems such as cities. Participatory scenario planning with city professionals and members of civil society provides an opportunity to coproduce positive visions of the future. Yet, not all visions are created equal. In this chapter, we introduce the Resilience, Equity, and Sustainability Qualitative (RESQ) assessment tool that we have applied to compare positive scenario visions for cities in the USA and Latin America. We use the tool to examine the visions of the two desert cities in the Urban Resilience to Extreme Events Sustainability Research Network (UREx SRN), which are Hermosillo (Mexico) and Phoenix (United States).
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| 16. |
- Berbés-Blázquez, Marta, et al.
(författare)
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Assessing resilience, equity, and sustainability of future visions across two urban scales
- 2023
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Ingår i: Sustainability Science. - 1862-4065. ; 18:6, s. 2549-2566
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Tidskriftsartikel (refereegranskat)abstract
- Cities need to take swift action to deal with the impacts of extreme climate events. The co-production of positive visions offers the potential to not only imagine but also intervene in guiding change toward more desirable urban futures. While participatory visioning continues to be used as a tool for urban planning, there needs to be a way of comparing and evaluating future visions so that they can inform decision-making. Traditional tools for comparison tend to favor quantitative modeling, which is limited in its ability to capture nuances or normative elements of visions. In this paper, we offer a qualitative method to assess the resilience, equity, and sustainability of future urban visions and demonstrate its use by applying it to 11 visions from Phoenix, AZ. The visions were co-produced at two different governance scales: five visions were created at the village (or borough) scale, and six visions were created at the regional (or metropolitan) scale. Our analysis reveals different emphases in the mechanisms present in the visions to advance resilience, sustainability, and equity. In particular, we note that regional future visions align with a green sustainability agenda, whereas village visions focus on social issues and emphasize equity-driven approaches. The visions have implications for future trajectories, and the priorities that manifest at the two scales speak of the political nature of visioning and the need to explore how these processes may interact in complementary, synergistic, or antagonistic ways.
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| 17. |
- Bruder, Carl E G, et al.
(författare)
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Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles
- 2008
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 82:3, s. 763-71
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Tidskriftsartikel (refereegranskat)abstract
- The exploration of copy-number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic makeup between twins derived from the same zygote represent an irrefutable example of somatic mosaicism. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype by using two platforms for genome-wide CNV analyses and showed that CNVs exist within pairs in both groups. These findings have an impact on our views of genotypic and phenotypic diversity in monozygotic twins and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool for identifying disease-predisposition loci. Our results also imply that caution should be exercised when interpreting disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics.
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| 18. |
- Chester, Mikhail V., et al.
(författare)
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Sensemaking for entangled urban social, ecological, and technological systems in the Anthropocene
- 2023
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Ingår i: npj Urban Sustainability. - 2661-8001. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Our urban systems and their underlying sub-systems are designed to deliver only a narrow set of human-centered services, with little or no accounting or understanding of how actions undercut the resilience of social-ecological-technological systems (SETS). Embracing a SETS resilience perspective creates opportunities for novel approaches to adaptation and transformation in complex environments. We: i) frame urban systems through a perspective shift from control to entanglement, ii) position SETS thinking as novel sensemaking to create repertoires of responses commensurate with environmental complexity (i.e., requisite complexity), and iii) describe modes of SETS sensemaking for urban system structures and functions as basic tenets to build requisite complexity. SETS sensemaking is an undertaking to reflexively bring sustained adaptation, anticipatory futures, loose-fit design, and co-governance into organizational decision-making and to help reimagine institutional structures and processes as entangled SETS.
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| 19. |
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Collaborative Research in Language Education: Reciprocal Benefits and Challenges
- 2023
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Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)abstract
- This book focuses on the reciprocal benefits and challenges that arise from effective collaboration between the various actors in language education. Drawn from eight countries on three continents, the twelve chapters report on research carried out in a wide variety of educational contexts. For all their diversity of purpose, theme and focus, all chapters emphasize collaboration and reciprocity as central components of educational research, and they make a significant contribution to a debate that is of increasing importance to researchers, teachers, teacher educators, policymakers and funding agencies.
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| 20. |
- Erickson, Carl, et al.
(författare)
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Make Haste, Not Waste: Automated System Testing
- 2003
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Ingår i: Extreme Programming and Agile Methods. - : Springer.
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Bokkapitel (populärvet., debatt m.m.)abstract
- Haste (High-level Automated System Test Environment) represents an approach to system testing that is philosophically consistent with standard XP unit testing practices. Test code runs in the same address space as the application under test, allowing for ready examination of application state. The fundamental Haste abstractions of Story, Step, and StoryBook provide a framework to implement system tests. Utility classes simplify test development. In addition to acting as XP acceptance tests, Haste tests aid source maintenance and extension, and can play an important role in a release process. This paper describes the elements of Haste, our experience with using it to test a complex Java Swing application, and the perspective of the client for whom the application was developed. Haste is available under an open source license.
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| 21. |
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| 22. |
- Erickson, Gudrun, 1950, et al.
(författare)
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Introduction
- 2023
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Ingår i: I Erickson, G., Bardel, C., & Little, D. (eds.), Collaborative Research in Language Education: Reciprocal Benefits and Challenges. - Berlin/Boston : De Gruyter Mouton. - 1868-6362. - 9783110787535 ; , s. 1-7
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Bokkapitel (refereegranskat)
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| 23. |
- Erickson, Gudrun, 1950, et al.
(författare)
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Introduction
- 2023
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Ingår i: Collaborative Research in Language Education: Reciprocal Benefits and Challenges. - 9783110787719 ; , s. 1-7
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 24. |
- Hawthorn, F., et al.
(författare)
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TOI-836: A super-Earth and mini-Neptune transiting a nearby K-dwarf
- 2023
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 520:3, s. 3649-3668
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Tidskriftsartikel (refereegranskat)abstract
- We present the discovery of two exoplanets transiting TOI-836 (TIC 440887364) using data from TESS Sector 11 and Sector 38. TOI-836 is a bright (T = 8.5 mag), high proper motion (∼200 mas yr−1), low metallicity ([Fe/H]≈−0.28) K-dwarf with a mass of 0.68 ± 0.05 M and a radius of 0.67 ± 0.01 R. We obtain photometric follow-up observations with a variety of facilities, and we use these data sets to determine that the inner planet, TOI-836 b, is a 1.70 ± 0.07 R super-Earth in a 3.82-d orbit, placing it directly within the so-called ‘radius valley’. The outer planet, TOI-836 c, is a 2.59 ± 0.09 R mini-Neptune in an 8.60-d orbit. Radial velocity measurements reveal that TOI-836 b has a mass of 4.5 ± 0.9 M, while TOI-836 c has a mass of 9.6 ± 2.6 M. Photometric observations show Transit Timing Variations (TTVs) on the order of 20 min for TOI-836 c, although there are no detectable TTVs for TOI-836 b. The TTVs of planet TOI-836 c may be caused by an undetected exterior planet.
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| 25. |
- Jacobs, Kevin B, et al.
(författare)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Tidskriftsartikel (refereegranskat)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 26. |
- Kumar Gahlot, Dharmender, 1985-, et al.
(författare)
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Cpx-signalling facilitates Hms-dependent biofilm formation by Yersinia pseudotuberculosis
- 2022
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Ingår i: npj Biofilms and Microbiomes. - London : Nature Publishing Group. - 2055-5008. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria often reside in sessile communities called biofilms, where they adhere to a variety of surfaces and exist as aggregates in aviscous polymeric matrix. Biofilms are resistant to antimicrobial treatments, and are a major contributor to the persistence and chronicity of many bacterial infections. Herein, we determined that the CpxA-CpxR two-component system influenced the ability of enteropathogenic Yersinia pseudotuberculosis to develop biofilms. Mutant bacteria that accumulated the active CpxR~P isoform failed to form biofilms on plastic or on the surface of the Caenorhabditis elegans nematode. A failure to form biofilms on the worm surface prompted their survival when grown on the lawns of Y. pseudotuberculosis. Exopolysaccharide production by the hms loci is the major driver of biofilms formed by Yersinia. We used a number of molecular genetic approaches to demonstrate that active CpxR~P binds directly to the promoter regulatory elements of the hms loci to activate the repressors of hms expression and to repress the activators of hms expression. Consequently, active Cpx-signalling culminated in a loss of exopolysaccharide production. Hence, the development of Y. pseudotuberculosis biofilms on multiple surfaces is controlled by the Cpx-signalling, and at least inpart this occurs through repressive effects on the Hms-dependent exopolysaccharide production.
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| 27. |
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| 28. |
- Little, David, et al.
(författare)
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Learner Identity, Learner Agency, and the Assessment of Language Proficiency: Some Reflections Prompted by the Common European Framework of Reference for Languages
- 2015
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Ingår i: Annual Review of Applied Linguistics. - 0267-1905. ; 35, s. 120-139
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Tidskriftsartikel (refereegranskat)abstract
- This article starts from the assumption that education is a process of “people shaping” designed to help learners extend and perhaps in some ways modify their identity while exploiting and developing their agency. This view is harmonious with the approach to language education that the Council of Europe has developed since the 1970s, and especially with its early commitment to learner autonomy and self-assessment. The approach adopted by the Common European Framework of Reference for Languages: Learning, teaching, assessment (CEFR) to the description of language proficiency clearly implicates the user-learner's identity and agency, which are also central to the CEFR's companion piece, the European Language Portfolio (ELP), in which self-assessment plays a key role. The article proposes that taken together, the CEFR and the ELP imply an assessment culture in which learning and assessment are reciprocally integrated. From the perspective thus established, the authors review some current trends in language assessment and their potential impact on learner identity and learner agency, focusing in turn on self-assessment, peer assessment, teacher assessment, and large-scale testing and assessment. The article concludes by arguing that although recent developments in language assessment pay significantly more attention to the learner than was previously the case, a great deal of work remains to be done to further increase the engagement of learner agency in processes of self-assessment and peer assessment and to align them with other forms of assessment.
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| 29. |
- Little, David, et al.
(författare)
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The role of assessment in the language education of immigrants and refugees
- 2017
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Ingår i: Workshop at the 16th International Conference of the Greek Applied Linguistics Association; Thessaloniki, 7 October 2017.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The assessment of immigrants’ and refugees’ developing proficiency in the language of schooling will play a central role in whatever measures are taken nationally and locally to provide them with an education that promotes equity and social inclusion. The purpose of this symposium (maximum enrolment 45) is to raise awareness, stimulate networking, and encourage participants to think of designing and launching small-scale collaborative projects. The symposium will be divided into three sessions, each of which will include work in small groups. The first session will consider the relation between teaching, learning and assessment from the perspective of the Common European Framework of Reference for Languages (CEFR) and introduce the tools developed by Integrate Ireland Language and Training on the basis of the CEFR’s descriptive scheme and proficiency levels. The second session will consider the two basic functions of assessment, to enhance learning and promote equity, and will address aims, constructs, methods, agency, and consequences: aspects of language testing and assessment related to the questions Why?, What?, How?, Who?, and And…? The third session will describe how assessment is used in Scoil Bhríde: to elicit information about how and what pupils are learning, to identify and affirm learning that has taken place, and to provide support for future learning. The symposium will conclude by briefly relating assessment at school to a larger picture, describing a Swedish national programme that maps the competences of newly arrived immigrant children and teenagers in a number of domains.
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| 30. |
- Longhini, Alberta, et al.
(författare)
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EDO-Net : Learning Elastic Properties of Deformable Objects from Graph Dynamics
- 2023
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Ingår i: Proceedings - ICRA 2023. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 3875-3881
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Konferensbidrag (refereegranskat)abstract
- We study the problem of learning graph dynamics of deformable objects that generalizes to unknown physical properties. Our key insight is to leverage a latent representation of elastic physical properties of cloth-like deformable objects that can be extracted, for example, from a pulling interaction. In this paper we propose EDO-Net (Elastic Deformable Object - Net), a model of graph dynamics trained on a large variety of samples with different elastic properties that does not rely on ground-truth labels of the properties. EDO-Net jointly learns an adaptation module, and a forward-dynamics module. The former is responsible for extracting a latent representation of the physical properties of the object, while the latter leverages the latent representation to predict future states of cloth-like objects represented as graphs. We evaluate EDO-Net both in simulation and real world, assessing its capabilities of: 1) generalizing to unknown physical properties, 2) transferring the learned representation to new downstream tasks.
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| 31. |
- Longhini, Alberta, et al.
(författare)
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Elastic Context : Encoding Elasticity for Data-driven Models of Textiles
- 2023
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Ingår i: Proceedings - ICRA 2023. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 1764-1770
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Konferensbidrag (refereegranskat)abstract
- Physical interaction with textiles, such as assistivedressing or household tasks, requires advanced dexterous skills.The complexity of textile behavior during stretching and pullingis influenced by the material properties of the yarn and bythe textile’s construction technique, which are often unknownin real-world settings. Moreover, identification of physicalproperties of textiles through sensing commonly available onrobotic platforms remains an open problem. To address this,we introduce Elastic Context (EC), a method to encode theelasticity of textiles using stress-strain curves adapted fromtextile engineering for robotic applications. We employ EC tolearn generalized elastic behaviors of textiles and examine theeffect of EC dimension on accurate force modeling of real-worldnon-linear elastic behaviors.
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| 32. |
- Muscarella, Robert, et al.
(författare)
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A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data
- 2014
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:11
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Tidskriftsartikel (refereegranskat)abstract
- Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.
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| 33. |
- Poplawski, Andrzej B., et al.
(författare)
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Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression
- 2010
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 18:5, s. 560-568
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Tidskriftsartikel (refereegranskat)abstract
- Breast cancer is a major cause of morbidity and mortality in women and its metastatic spread is the principal reason behind the fatal outcome. Metastasis-related research of breast cancer is however underdeveloped when compared with the abundant literature on primary tumors. We applied an unexplored approach comparing at high resolution the genomic profiles of primary tumors and synchronous axillary lymph node metastases from 13 patients with breast cancer. Overall, primary tumors displayed 20% higher number of aberrations than metastases. In all but two patients, we detected in total 157 statistically significant differences between primary lesions and matched metastases. We further observed differences that can be linked to metastatic disease and there was also an overlapping pattern of changes between different patients. Many of the differences described here have been previously linked to poor patient survival, suggesting that this is a viable approach toward finding biomarkers for disease progression and definition of new targets useful for development of anticancer drugs. Frequent genetic differences between primary tumors and metastases in breast cancer also question, at least to some extent, the role of primary tumors as a surrogate subject of study for the systemic disease. European Journal of Human Genetics (2010) 18, 560-568; doi:10.1038/ejhg.2009.230; published online 6 January 2010
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| 34. |
- Rodriguez-Ayllon, Maria, et al.
(författare)
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Role of Physical Activity and Sedentary Behavior in the Mental Health of Preschoolers, Children and Adolescents: A Systematic Review and Meta-Analysis
- 2019
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Ingår i: Sports Medicine. - : ADIS INT LTD. - 0112-1642 .- 1179-2035. ; 49:9, s. 1383-1410
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Forskningsöversikt (refereegranskat)abstract
- Background Evidence suggests that participation in physical activity may support young peoples current and future mental health. Although previous reviews have examined the relationship between physical activity and a range of mental health outcomes in children and adolescents, due to the large increase in published studies there is a need for an update and quantitative synthesis of effects. Objectives The objectives of this study were to determine the effect of physical activity interventions on mental health outcomes by conducting a systematic review and meta-analysis, and to systematically synthesize the observational evidence (both longitudinal and cross-sectional studies) regarding the associations between physical activity and sedentary behavior and mental health in preschoolers (2-5 years of age), children (6-11 years of age) and adolescents (12-18 years of age). Methods A systematic search of the PubMed and Web of Science electronic databases was performed from January 2013 to April 2018, by two independent researchers. Meta-analyses were performed to examine the effect of physical activity on mental health outcomes in randomized controlled trials (RCTs) and non-RCTs (i.e. quasi-experimental studies). A narrative synthesis of observational studies was conducted. Studies were included if they included physical activity or sedentary behavior data and at least one psychological ill-being (i.e. depression, anxiety, stress or negative affect) or psychological well-being (i.e. self-esteem, self-concept, self-efficacy, self-image, positive affect, optimism, happiness and satisfaction with life) outcome in preschoolers, children or adolescents. Results A total of 114 original articles met all the eligibility criteria and were included in the review (4 RCTs, 14 non-RCTs, 28 prospective longitudinal studies and 68 cross-sectional studies). Of the 18 intervention studies, 12 (3 RCTs and 9 non-RCTs) were included in the meta-analysis. There was a small but significant overall effect of physical activity on mental health in children and adolescents aged 6-18 years (effect size 0.173, 95% confidence interval 0.106-0.239, p amp;lt; 0.001, percentage of total variability attributed to between-study heterogeneity [I-2] = 11.3%). When the analyses were performed separately for children and adolescents, the results were significant for adolescents but not for children. Longitudinal and cross-sectional studies demonstrated significant associations between physical activity and lower levels of psychological ill-being (i.e. depression, stress, negative affect, and total psychological distress) and greater psychological well-being (i.e. self-image, satisfaction with life and happiness, and psychological well-being). Furthermore, significant associations were found between greater amounts of sedentary behavior and both increased psychological ill-being (i.e. depression) and lower psychological well-being (i.e. satisfaction with life and happiness) in children and adolescents. Evidence on preschoolers was nearly non-existent. Conclusions Findings from the meta-analysis suggest that physical activity interventions can improve adolescents mental health, but additional studies are needed to confirm the effects of physical activity on childrens mental health. Findings from observational studies suggest that promoting physical activity and decreasing sedentary behavior might protect mental health in children and adolescents. PROSPERO Registration Number: CRD42017060373.
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