| 1. |
- Glasbey, JC, et al.
(author)
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- 2021
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swepub:Mat__t
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| 2. |
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| 3. |
- Bravo, L, et al.
(author)
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- 2021
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swepub:Mat__t
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| 4. |
- Tabiri, S, et al.
(author)
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- 2021
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swepub:Mat__t
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| 5. |
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| 6. |
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| 7. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 8. |
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| 9. |
- Lambert, A., et al.
(author)
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Validation of the Aura Microwave Limb Sounder middle atmosphere water vapor and nitrous oxide measurements
- 2007
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In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 112:D24
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Journal article (peer-reviewed)abstract
- The quality of the version 2.2 (v2.2) middle atmosphere water vapor and nitrous oxide measurements from the Microwave Limb Sounder (MLS) on the Earth Observing System (EOS) Aura satellite is assessed. The impacts of the various sources of systematic error are estimated by a comprehensive set of retrieval simulations. Comparisons with correlative data sets from ground-based, balloon and satellite platforms operating in the UV/ visible, infrared and microwave regions of the spectrum are performed. Precision estimates are also validated, and recommendations are given on the data usage. The v2.2 H 2 O data have been improved over v1.5 by providing higher vertical resolution in the lower stratosphere and better precision above the stratopause. The single-profile precision is ∼0.2-0.3 ppmv (4-9%), and the vertical resolution is ∼3-4 km in the stratosphere. The precision and vertical resolution become worse with increasing height above the stratopause. Over the pressure range 0.1-0.01 hPa the precision degrades from 0.4 to 1.1 ppmv (6-34%), and the vertical resolution degrades to ∼12-16 km. The accuracy is estimated to be 0.2-0.5 ppmv (4-11%) for the pressure range 68-0.01 hPa. The scientifically useful range of the H 2 O data is from 316 to 0.002 hPa, although only the 82-0.002 hPa pressure range is validated here. Substantial improvement has been achieved in the v2.2 N 2 O data over v1.5 by reducing a significant low bias in the stratosphere and eliminating unrealistically high biased mixing ratios in the polar regions. The single-profile precision is ∼13-25 ppbv (7-38%), the vertical resolution is ∼4-6 km and the accuracy is estimated to be 3-70 ppbv (9-25%) for the pressure range 100-4.6 hPa. The scientifically useful range of the N 2 O data is from 100 to 1 hPa. Copyright 2007 by the American Geophysical Union.
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| 10. |
- Craig, Wendy, et al.
(author)
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Social Media Use and Cyber-Bullying: A Cross-National Analysis of Young People in 42 Countries
- 2020
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In: Journal of Adolescent Health. - : ELSEVIER SCIENCE INC. - 1054-139X .- 1879-1972. ; 66:6, s. S100-S108
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Journal article (peer-reviewed)abstract
- Purpose: Social media use (SMU) has become an intrinsic part of adolescent life. Negative consequences of SMU for adolescent health could include exposures to online forms of aggression. We explored age, gender, and cross-national differences in adolescents engagement in SMU, then relationships between SMU and victimization and the perpetration of cyber-bullying. Methods: We used data on young people aged 11-15 years (weighted n = 180,919 in 42 countries) who participated in the 2017-2018 Health Behaviour in School-aged Children study to describe engagement in the three types of SMU (intense, problematic, and talking with strangers online) by age and gender and then in the perpetration and victimization of cyber-bullying. Relationships between SMU and cyber-bullying outcomes were estimated using Poisson regression (weighted n = 166,647 from 42 countries). Results: Variations in SMU and cyber-bullying follow developmental and gender-based patterns across countries. In pooled analyses, engagement in SMU related to cyber-bullying victimization (adjusted relative risks = 1.14 [95% confidence interval (CI): 1.10-1.19] to 1.48 [95% CI: 1.42-1.55]) and perpetration (adjusted relative risk = 1.31 [95% CI: 1.26-1.36] to 1.84 [95% CI: 1.74-1.95]). These associations were stronger for cyber-perpetration versus cyber-victimization and for girls versus boys. Problematic SMU was most strongly and consistently associated with cyber-bullying, both for victimization and perpetration. Stratified analyses showed that SMU related to cyber-victimization in 19%-45% of countries and to cyber-perpetration in 38%-86% of countries. Conclusions: Accessibility to social media and its pervasive use has led to new opportunities for online aggression. The time adolescents spend on social media, engage in problematic use, and talk to strangers online each relate to cyber-bullying and merit public health intervention. Problematic use of social media poses the strongest and most consistent risk. (C) 2020 Published by Elsevier Inc. on behalf of Society for Adolescent Health and Medicine.
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| 11. |
- Craig, Wendy, et al.
(author)
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Social Media Use and Cyber-Bullying: A Cross-National Analysis of Young People in 42 Countries
- 2020
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In: Journal of Adolescent Health. - : Elsevier BV. - 1054-139X .- 1879-1972. ; 66:6
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Journal article (peer-reviewed)abstract
- Purpose: Social media use (SMU) has become an intrinsic part of adolescent life. Negative consequences of SMU for adolescent health could include exposures to online forms of aggression. We explored age, gender, and cross-national differences in adolescents' engagement in SMU, then relationships between SMU and victimization and the perpetration of cyber-bullying. Methods: We used data on young people aged 11–15 years (weighted n = 180,919 in 42 countries) who participated in the 2017–2018 Health Behaviour in School-aged Children study to describe engagement in the three types of SMU (intense, problematic, and talking with strangers online) by age and gender and then in the perpetration and victimization of cyber-bullying. Relationships between SMU and cyber-bullying outcomes were estimated using Poisson regression (weighted n = 166,647 from 42 countries). Results: Variations in SMU and cyber-bullying follow developmental and gender-based patterns across countries. In pooled analyses, engagement in SMU related to cyber-bullying victimization (adjusted relative risks = 1.14 [95% confidence interval (CI): 1.10–1.19] to 1.48 [95% CI: 1.42–1.55]) and perpetration (adjusted relative risk = 1.31 [95% CI: 1.26–1.36] to 1.84 [95% CI: 1.74–1.95]). These associations were stronger for cyber-perpetration versus cyber-victimization and for girls versus boys. Problematic SMU was most strongly and consistently associated with cyber-bullying, both for victimization and perpetration. Stratified analyses showed that SMU related to cyber-victimization in 19%–45% of countries and to cyber-perpetration in 38%–86% of countries. Conclusions: Accessibility to social media and its pervasive use has led to new opportunities for online aggression. The time adolescents spend on social media, engage in problematic use, and talk to strangers online each relate to cyber-bullying and merit public health intervention. Problematic use of social media poses the strongest and most consistent risk.
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| 12. |
- Cvetkovic, Vladimir, et al.
(author)
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Parameter and model sensitivities for colloid-facilitated radionuclide transport on the field scale
- 2004
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In: Water resources research. - : American Geophysical Union (AGU). - 0043-1397 .- 1944-7973. ; 40:6
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Journal article (peer-reviewed)abstract
- We investigate the potential effects of inorganic colloids on radionuclide transport in groundwater using generic sensitivity studies and an example based on the alluvial aquifer near Yucca Mountain, Nevada. Our emphasis is on kinetically controlled sorption of radionuclides on mobile and immobile colloids. Three kinetic sorption models are considered for the sensitivity analysis: bilinear, Langmuir, and linear. Plutonium is assumed to be injected into the Yucca Mountain alluvial aquifer at a constant rate and follows a random stream tube to a monitoring boundary. The linear sorption model provides a reasonable upper bound on colloid-facilitated plutonium transport for the site-specific conditions. In the absence of colloid filtration and retardation, colloids enhance the plutonium discharge by a large factor over the situation without colloids. Exchange of plutonium between solution and reversibly attached colloids makes colloid retardation relatively ineffective at reducing colloid-facilitated transport except when the retardation factor is large. Irreversible removal of colloids (filtration) is more effective than retardation at reducing colloid-facilitated transport. For fixed filtration rate the degree of attenuation depends sensitively and nonmonotonically on the rate of plutonium desorption from colloids. These results emphasize the need for accurate measurements of rates of desorption from colloids as well as in situ studies of filtration of naturally occurring colloids.
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| 13. |
- Lauwers, E., et al.
(author)
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Potential human transmission of amyloid beta pathology: surveillance and risks
- 2020
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In: Lancet Neurology. - 1474-4422 .- 1474-4465. ; 19:10, s. 872-878
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Journal article (peer-reviewed)abstract
- Studies in experimental animals show transmissibility of amyloidogenic proteins associated with prion diseases, Alzheimer's disease, Parkinson's disease, and other neurodegenerative diseases. Although these data raise potential concerns for public health, convincing evidence for human iatrogenic transmission only exists for prions and amyloid beta after systemic injections of contaminated growth hormone extracts or dura mater grafts derived from cadavers. Even though these procedures are now obsolete, some reports raise the possibility of iatrogenic transmission of amyloid beta through putatively contaminated neurosurgical equipment. Iatrogenic transmission of amyloid beta might lead to amyloid deposition in the brain parenchyma and blood vessel walls, potentially resulting in cerebral amyloid angiopathy after several decades. Cerebral amyloid angiopathy can cause life-threatening brain haemorrhages; yet, there is no proof that the transmission of amyloid can also lead to Alzheimer's dementia. Large, long-term epidemiological studies and sensitive, cost-efficient tools to detect amyloid are needed to better understand any potential routes of amyloid beta transmission and to clarify whether other similar proteopathic seeds, such as tau or alpha-synuclein, can also be transferred iatrogenically.
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| 14. |
- Painter, S., et al.
(author)
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Significance of kinetics for sorption on inorganic colloids : Modeling and experiment interpretation issues
- 2002
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In: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 36:24, s. 5369-5375
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Journal article (peer-reviewed)abstract
- A two-site kinetic model for solute sorption on inorganic colloids is developed. The model quantifies linear first-order sorption on two types of sites (fast and slow) characterized by two pairs of rates (forward and reverse). We use the model to explore data requirements for long-term predictive calculations of colloid-facilitated transport and to evaluate laboratory kinetic sorption data of Lu et al.. Five batch sorption data sets are considered with plutonium as the tracer and montmorillonite, hematite, silica, and smectite as colloids. Using asymptotic results applicable on the time stale of limited duration experiments, a robust estimation procedure is developed for the fast-site partitioning coefficient K-c and the slow forward rate alpha. The estimated range of K-c is 1.1-76 L/g, and the range for a is 0.0017-0.02 1/h. The fast reverse rate k(r) is estimated in the range 0.012-0.1 1/h. Comparison of one-site and two-site sorption interpretations reveals the difficulty in, discriminating between the two models for montmorillonite and to a lesser extent for hematite. For silica and smectite, the two-site model clearly provides a better representation of the data as compared with a single site model. Kinetic data for silica are available for different colloid concentrations (0.2 g/L and 1 g/L). For the range of experimental conditions considered, a. appears to be independent of colloid concentration.
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| 15. |
- Pickett, Connor S., et al.
(author)
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Changes in the Na D-1 Absorption Components of eta Carinae Provide Clues on the Location of the Dissipating Central Occulter
- 2022
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In: Astrophysical Journal. - : Institute of Physics (IOP). - 0004-637X .- 1538-4357. ; 937:2
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Journal article (peer-reviewed)abstract
- The Na D absorption doublet in the spectrum of eta Carinae is complex, with multiple absorption features associated with the Great Eruption (1840s), the Lesser Eruption (1890s), and the interstellar clouds. The velocity profile is further complicated by the P Cygni profile originating in the system's stellar winds and blending with the He i lambda 5876 profile. The Na D profile contains a multitude of absorption components, including those at velocities of -145 km s(-1), -168 km s(-1), and +87 km s(-1), which we concentrate on in this analysis. Ground-based spectra recorded from 2008 to 2021 show significant variability of the -145 km s(-1) absorption throughout long-term observations. In the high-ionization phases of eta Carinae prior to the 2020 periastron passage, this feature disappeared completely but briefly reappeared across the 2020 periastron, along with a second absorption at -168 km s(-1). Over the past few decades, eta Carinae has been gradually brightening, which is shown to be caused by a dissipating occulter. The decreasing absorption of the -145 km s(-1) component, coupled with similar trends seen in absorptions of ultraviolet resonant lines, indicate that this central occulter was possibly a large clump associated with the Little Homunculus or another clump between the Little Homunculus and the star. We also report on a foreground absorption component at +87 km s(-1). Comparison of Na D absorption in the spectra of nearby systems demonstrates that this redshifted component likely originates in an extended foreground structure consistent with a previous ultraviolet spectral survey in the Carina Nebula.
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| 16. |
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| 17. |
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| 18. |
- Behlke, Rico, et al.
(author)
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Solitary structures associated with short large-amplitude magnetic structures (SLAMS) upstream of the Earth's quasi-parallel bow shock
- 2004
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In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 31:16
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Journal article (peer-reviewed)abstract
- [1] For the first time, solitary waves (SWs) have been observed within short large-amplitude magnetic structures (SLAMS) upstream of the Earth's quasi-parallel bow shock. The SWs often occur as bipolar pulses in the electric field data and move parallel to the background magnetic field at velocities of v = 400–1200 km/s. They have peak-to-peak amplitudes in the parallel electric field of up to E′∥ = 65 mV/m and parallel scale sizes of L∥ ∼ 10 λD. The bipolar solitary waves exhibit negative potential structures of ∣Φ∥∣ = 0.4–2.2 V, i.e., eΦ∥/kTe ∼ 0.1. None of the theories commonly used to describe SWs adequately address these negative potential structures moving at velocities above the ion thermal speed in a weakly magnetized plasma.
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| 19. |
- Conn, Jonathan G.M., et al.
(author)
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Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models
- 2023
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In: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 63:4, s. 1099-1113
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Journal article (peer-reviewed)abstract
- Accurate methods to predict solubility from molecular structure are highly sought after in the chemical sciences. To assess the state of the art, the American Chemical Society organized a "Second Solubility Challenge"in 2019, in which competitors were invited to submit blinded predictions of the solubilities of 132 drug-like molecules. In the first part of this article, we describe the development of two models that were submitted to the Blind Challenge in 2019 but which have not previously been reported. These models were based on computationally inexpensive molecular descriptors and traditional machine learning algorithms and were trained on a relatively small data set of 300 molecules. In the second part of the article, to test the hypothesis that predictions would improve with more advanced algorithms and higher volumes of training data, we compare these original predictions with those made after the deadline using deep learning models trained on larger solubility data sets consisting of 2999 and 5697 molecules. The results show that there are several algorithms that are able to obtain near state-of-the-art performance on the solubility challenge data sets, with the best model, a graph convolutional neural network, resulting in an RMSE of 0.86 log units. Critical analysis of the models reveals systematic differences between the performance of models using certain feature sets and training data sets. The results suggest that careful selection of high quality training data from relevant regions of chemical space is critical for prediction accuracy but that other methodological issues remain problematic for machine learning solubility models, such as the difficulty in modeling complex chemical spaces from sparse training data sets.
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| 20. |
- Cui, Daqing, et al.
(author)
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Immobilization of radionuclides on iron canister material at simulated near-field conditions
- 2009
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In: Scientific Basis for Nuclear Waste Management XXXII. - Warrendale, Pa : Materials Research Society. - 9781605110967 ; 1124
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Conference paper (peer-reviewed)abstract
- This work is a continuation of a long-term spent fuel leaching and radionuclides immobilization (by iron canister) experiment under simulated near-field conditions, in deoxygenated 2 mM NaHCO3 solution with 1 Gy/h γ irradiation. The corrosion of iron canister material was investigated by electrochemical and microanalytical methods. Significant amounts of radionuclides (U, Np, Tc, Sr) were found to be immobilized on the corrosion layer of iron canister material by using SEM-WDS and SIMS methods. The observation is useful for bettering our understanding of near-field chemical processes at earlier canister failure conditions.
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| 21. |
- Damineli, Augusto, et al.
(author)
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The Long-term Spectral Changes of Eta Carinae : Are they Caused by a Dissipating Occulter as Indicated by CMFGEN Models?
- 2023
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In: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 0004-637X .- 1538-4357. ; 954
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Journal article (peer-reviewed)abstract
- Eta Carinae (η Car) exhibits a unique set of P Cygni profiles with both broad and narrow components. Over many decades, the spectrum has changed-there has been an increase in observed continuum fluxes and a decrease in Fe II and H I emission-line equivalent widths. The spectrum is evolving toward that of a P Cygni star such as P Cygni itself and HDE 316285. The spectral evolution has been attributed to intrinsic variations such as a decrease in the mass-loss rate of the primary star or differential evolution in a latitudinal-dependent stellar wind. However, intrinsic wind changes conflict with three observational results: the steady long-term bolometric luminosity; the repeating X-ray light curve over the binary period; and the constancy of the dust-scattered spectrum from the Homunculus. We extend previous work that showed a secular strengthening of P Cygni absorptions by adding more orbital cycles to overcome temporary instabilities and by examining more atomic transitions. CMFGEN modeling of the primary wind shows that a time-decreasing mass-loss rate is not the best explanation for the observations. However, models with a small dissipating absorber in our line of sight can explain both the increase in brightness and changes in the emission and P Cygni absorption profiles. If the spectral evolution is caused by the dissipating circumstellar medium, and not by intrinsic changes in the binary, the dynamical timescale to recover from the Great Eruption is much less than a century, different from previous suggestions.
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| 22. |
- Deng, X. H., et al.
(author)
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Dynamics and waves near multiple magnetic null points in reconnection diffusion region
- 2009
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In: Journal of Geophysical Research. - : Blackwell Publishing. - 0148-0227 .- 2156-2202. ; 114:7
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Journal article (peer-reviewed)abstract
- Identifying the magnetic structure in the region where the magnetic field lines break and how reconnection happens is crucial to improving our understanding of three-dimensional reconnection. Here we show the in situ observation of magnetic null structures in the diffusion region, the dynamics, and the associated waves. Possible spiral null pair has been identified near the diffusion region. There is a close relation among the null points, the bipolar signature of the Z component of the magnetic field, and enhancement of the flux of energetic electrons up to 100 keV. Near the null structures, whistler-mode waves were identified by both the polarity and the power law of the spectrum of electric and magnetic fields. It is found that the angle between the fans of the nulls is quite close to the theoretically estimated maximum value of the group-velocity cone angle for the whistler wave regime of reconnection.
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| 23. |
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| 24. |
- Green, C., et al.
(author)
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A Horizon Scan to Support Chemical Pollution-Related Policymaking for Sustainable and Climate-Resilient Economies
- 2023
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In: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 42:6, s. 1212-1228
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Journal article (peer-reviewed)abstract
- While chemicals are vital to modern society through materials, agriculture, textiles, new technology, medicines, and consumer goods, their use is not without risks. Unfortunately, our resources seem inadequate to address the breadth of chemical challenges to the environment and human health. Therefore, it is important we use our intelligence and knowledge wisely to prepare for what lies ahead. The present study used a Delphi-style approach to horizon-scan future chemical threats that need to be considered in the setting of chemicals and environmental policy, which involved a multidisciplinary, multisectoral, and multinational panel of 25 scientists and practitioners (mainly from the United Kingdom, Europe, and other industrialized nations) in a three-stage process. Fifteen issues were shortlisted (from a nominated list of 48), considered by the panel to hold global relevance. The issues span from the need for new chemical manufacturing (including transitioning to non-fossil-fuel feedstocks); challenges from novel materials, food imports, landfills, and tire wear; and opportunities from artificial intelligence, greater data transparency, and the weight-of-evidence approach. The 15 issues can be divided into three classes: new perspectives on historic but insufficiently appreciated chemicals/issues, new or relatively new products and their associated industries, and thinking through approaches we can use to meet these challenges. Chemicals are one threat among many that influence the environment and human health, and interlinkages with wider issues such as climate change and how we mitigate these were clear in this exercise. The horizon scan highlights the value of thinking broadly and consulting widely, considering systems approaches to ensure that interventions appreciate synergies and avoid harmful trade-offs in other areas. We recommend further collaboration between researchers, industry, regulators, and policymakers to perform horizon scanning to inform policymaking, to develop our ability to meet these challenges, and especially to extend the approach to consider also concerns from countries with developing economies. Environ Toxicol Chem 2023;00:1-17. (c) 2023 Crown copyright and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article is published with the permission of the Controller of HMSO and the King's Printer for Scotland.
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| 25. |
- Klein, Daniel B., Adjungerad professor
(author)
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What 21st-Century Works Will Merit a Close Reading in 2050? : Second Tranche of Responses
- 2021
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In: Econ Journal Watch. - : Econ Journal Watch. - 1933-527X. ; 18:1, s. 164-191
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Journal article (pop. science, debate, etc.)abstract
- Adam Smith applied the expression “never to be forgotten” to two thinkers he knew personally, born more than 300 years ago, and those two thinkers are not yet forgotten.We undertook the present query in 2020, looking a mere 30 years ahead. What 21st-century works will merit a close reading in 2050? That is the question asked of Econ Journal Watch authors (specifically: those who authored material in sections other than the Comments section of the journal). The previous issue of this journal provided responses from authors with last names beginning A through K (link). Here we present nineteen responses from authors L through Z.
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