| 1. |
- Acharya, B. S., et al.
(author)
-
Introducing the CTA concept
- 2013
-
In: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 43, s. 3-18
-
Journal article (other academic/artistic)abstract
- The Cherenkov Telescope Array (CTA) is a new observatory for very high-energy (VHE) gamma rays. CTA has ambitions science goals, for which it is necessary to achieve full-sky coverage, to improve the sensitivity by about an order of magnitude, to span about four decades of energy, from a few tens of GeV to above 100 TeV with enhanced angular and energy resolutions over existing VHE gamma-ray observatories. An international collaboration has formed with more than 1000 members from 27 countries in Europe, Asia, Africa and North and South America. In 2010 the CTA Consortium completed a Design Study and started a three-year Preparatory Phase which leads to production readiness of CTA in 2014. In this paper we introduce the science goals and the concept of CTA, and provide an overview of the project. (C) 2013 Elsevier B.V. All rights reserved.
|
|
| 2. |
|
|
| 3. |
- Ades, M., et al.
(author)
-
Global Climate : in State of the climate in 2019
- 2020
-
In: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
-
Journal article (peer-reviewed)
|
|
| 4. |
- Ades, M., et al.
(author)
-
GLOBAL CLIMATE
- 2020
-
In: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
-
Journal article (peer-reviewed)
|
|
| 5. |
- Clark, Andrew G., et al.
(author)
-
Evolution of genes and genomes on the Drosophila phylogeny
- 2007
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
-
Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
|
|
| 6. |
- Feng, Shaohong, et al.
(author)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
|
|
| 7. |
- Griswold, Max G., et al.
(author)
-
Alcohol use and burden for 195 countries and territories, 1990-2016 : a systematic analysis for the Global Burden of Disease Study 2016
- 2018
-
In: The Lancet. - : Elsevier. - 0140-6736 .- 1474-547X. ; 392:10152, s. 1015-1035
-
Journal article (peer-reviewed)abstract
- Background: Alcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions. With our comprehensive approach to health accounting within the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (DALYs) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older.Methods: Using 694 data sources of individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use, we produced estimates of the prevalence of current drinking, abstention, the distribution of alcohol consumption among current drinkers in standard drinks daily (defined as 10 g of pure ethyl alcohol), and alcohol-attributable deaths and DALYs. We made several methodological improvements compared with previous estimates: first, we adjusted alcohol sales estimates to take into account tourist and unrecorded consumption; second, we did a new meta-analysis of relative risks for 23 health outcomes associated with alcohol use; and third, we developed a new method to quantify the level of alcohol consumption that minimises the overall risk to individual health.Findings: Globally, alcohol use was the seventh leading risk factor for both deaths and DALYs in 2016, accounting for 2.2% (95% uncertainty interval [UI] 1.5-3.0) of age-standardised female deaths and 6.8% (5.8-8.0) of age-standardised male deaths. Among the population aged 15-49 years, alcohol use was the leading risk factor globally in 2016, with 3.8% (95% UI 3.2-4-3) of female deaths and 12.2% (10.8-13-6) of male deaths attributable to alcohol use. For the population aged 15-49 years, female attributable DALYs were 2.3% (95% UI 2.0-2.6) and male attributable DALYs were 8.9% (7.8-9.9). The three leading causes of attributable deaths in this age group were tuberculosis (1.4% [95% UI 1. 0-1. 7] of total deaths), road injuries (1.2% [0.7-1.9]), and self-harm (1.1% [0.6-1.5]). For populations aged 50 years and older, cancers accounted for a large proportion of total alcohol-attributable deaths in 2016, constituting 27.1% (95% UI 21.2-33.3) of total alcohol-attributable female deaths and 18.9% (15.3-22.6) of male deaths. The level of alcohol consumption that minimised harm across health outcomes was zero (95% UI 0.0-0.8) standard drinks per week.Interpretation: Alcohol use is a leading risk factor for global disease burden and causes substantial health loss. We found that the risk of all-cause mortality, and of cancers specifically, rises with increasing levels of consumption, and the level of consumption that minimises health loss is zero. These results suggest that alcohol control policies might need to be revised worldwide, refocusing on efforts to lower overall population-level consumption.
|
|
| 8. |
|
|
| 9. |
- Andrikopoulos, Petros, et al.
(author)
-
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide
- 2023
-
In: Nature Communications. - 2041-1723 .- 2041-1723. ; 14:1
-
Journal article (peer-reviewed)abstract
- The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied "explainable" machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in 1,741 adult Europeans of the MetaCardis study. Here we show that next to age, kidney function is the primary variable predicting circulating TMAO, with microbiota composition and diet playing minor, albeit significant, roles. Mediation analysis suggests a causal relationship between TMAO and kidney function that we corroborate in preclinical models where TMAO exposure increases kidney scarring. Consistent with our findings, patients receiving glucose-lowering drugs with reno-protective properties have significantly lower circulating TMAO when compared to propensity-score matched control individuals. Our analyses uncover a bidirectional relationship between kidney function and TMAO that can potentially be modified by reno-protective anti-diabetic drugs and suggest a clinically actionable intervention for decreasing TMAO-associated excess cardiovascular risk.
|
|
| 10. |
- Downing, Andrea S., et al.
(author)
-
Coupled human and natural system dynamics as key to the sustainability of Lake Victoria's ecosystem services
- 2014
-
In: Ecology and Society. - 1708-3087. ; 19:4, s. 31-
-
Journal article (peer-reviewed)abstract
- East Africa's Lake Victoria provides resources and services to millions of people on the lake's shores and abroad. In particular, the lake's fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria's system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake's social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks' vulnerability to exploitation but reduce society's vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.
|
|
| 11. |
- Forslund, Sofia K., et al.
(author)
-
Combinatorial, additive and dose-dependent drug–microbiome associations
- 2021
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7889, s. 500-505
-
Journal article (peer-reviewed)abstract
- During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1–5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.
|
|
| 12. |
- Leopold, Tobias, et al.
(author)
-
Feasibility of photodetachment isobar suppression of WF5- with respect to HfF5
- 2014
-
In: International Journal of Mass Spectrometry. - : Elsevier BV. - 1387-3806 .- 1873-2798. ; 359, s. 12-18
-
Journal article (peer-reviewed)abstract
- The feasibility of using laser photodetachment as a means for isobar suppression in accelerator mass spectrometry has been investigated for the special case of HfF5-/WF5-. A method for absolute photodetachrnent cross section measurements was applied and the cross sections of tungsten pentafluoride and hafnium pentafluoride negative ions were measured. The measurements indicate that the photodetachment cross section for WF5- is at least 100 times larger than for HfF5- at the wavelength of the fourth harmonic of the Nd:YAG laser at 266 nm. The absolute cross section for WF5- at this photon energy was found to be (2.8 +/- 0.3) x 10(-18) cm(2), while an upper limit of 2 x 10(-2) cm(2) was obtained for the HfF5- cross section. The measured cross sections indicate that an optical filtering scheme for isobar suppression in accelerator mass spectrometry for the case of Hf-182 should be feasible. (C) 2013 Elsevier B.V. All rights reserved.
|
|
| 13. |
- Milham, Michael P., et al.
(author)
-
An Open Resource for Non-human Primate Imaging
- 2018
-
In: Neuron. - : Elsevier BV. - 0896-6273 .- 1097-4199. ; 100:1, s. 61-74
-
Journal article (peer-reviewed)abstract
- Non-human primate neuroimaging is a rapidly growing area of research that promises to transform and scale translational and cross-species comparative neuroscience. Unfortunately, the technological and methodological advances of the past two decades have outpaced the accrual of data, which is particularly challenging given the relatively few centers that have the necessary facilities and capabilities. The PRIMatE Data Exchange (PRIME-DE) addresses this challenge by aggregating independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI). Here, we present the rationale, design, and procedures for the PRIME-DE consortium, as well as the initial release, consisting of 25 independent data collections aggregated across 22 sites (total = 217 non-human primates). We also outline the unique pitfalls and challenges that should be considered in the analysis of non-human primate MRI datasets, including providing automated quality assessment of the contributed datasets.
|
|
| 14. |
- Molinaro, Antonio, et al.
(author)
-
Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology
- 2020
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
-
Journal article (peer-reviewed)abstract
- Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism.
|
|
| 15. |
- Mullier, Geoffrey A., et al.
(author)
-
Search for the decay of the Higgs boson to a Z boson and a light pseudoscalar particle decaying to two photons
- 2024
-
In: Physics Letters B. - : Elsevier. - 0370-2693 .- 1873-2445. ; 850
-
Journal article (peer-reviewed)abstract
- A search for the decay of the Higgs boson to a ? boson and a light, pseudoscalar particle, ?, decaying respectively to two leptons and to two photons is reported. The search uses the full LHC Run 2 proton–proton collision data at √? = 13 TeV, corresponding to 139 fb−1 collected by the ATLAS detector. This is one of the first searches for this specific decay mode of the Higgs boson, and it probes unexplored parameter space in models with axion-likeparticles (ALPs) and extended scalar sectors. The mass of the ? particle is assumed to be in the range 0.1–33 GeV. The data are analysed in two categories: a merged category where the photons from the ? decay are reconstructedin the ATLAS calorimeter as a single cluster, and a resolved category in which two separate photons are detected. The main background processes are from Standard Model ? boson production in association with photons orjets. The data are in agreement with the background predictions, and upper limits on the branching ratio of the Higgs boson decay to ?? times the branching ratio ? → ?? are derived at the 95% confidence level and theyrange from 0.08% to 2% depending on the mass of the ? particle. The results are also interpreted in the contextof ALP models.
|
|
| 16. |
|
|
| 17. |
- Abramsson, Mia L, et al.
(author)
-
Charge engineering reveals the roles of ionizable side chains in electrospray ionization mass spectrometry
-
Other publication (other academic/artistic)abstract
- The role of ionizable side chains in the electrospray ionization mass spectrometry of intact proteins remains hotly debated but has not been conclusively addressed because multiple chargeable sites are present in virtually all proteins. Using engineered soluble proteins, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, whilst co-existing conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. We conclude that the sum of charges is governed solely by Coulombic terms, while their locations affect the stability of the protein in the gas phase.
|
|
| 18. |
- Abramsson, Mia L., et al.
(author)
-
Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry
- 2021
-
In: JACS Au. - : American Chemical Society (ACS). - 2691-3704. ; 1:12, s. 2385-2393
-
Journal article (peer-reviewed)abstract
- In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.
|
|
| 19. |
- Araujo, M. V., et al.
(author)
-
Lorenzetti Showers- A general-purpose framework for supporting signal reconstruction and triggering with calorimeters
- 2023
-
In: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 286
-
Journal article (peer-reviewed)abstract
- Calorimeters play an important role in high-energy physics experiments. Their design includes electronic instrumentation, signal processing chain, computing infrastructure, and also a good understanding of their response to particle showers produced by the interaction of incoming particles. This is usually supported by full simulation frameworks developed for specific experiments so that their access is restricted to the collaboration members only. Such restrictions limit the general-purpose developments that aim to propose innovative approaches to signal processing, which may include machine learning and advanced stochastic signal processing models. This work presents the Lorenzetti Showers, a general-purpose framework that mainly targets supporting novel signal reconstruction and triggering strategies using segmented calorimeter information. This framework fully incorporates developments down to the signal processing chain level (signal shaping, energy estimation, and noise mitigation techniques) to allow advanced signal processing approaches in modern calorimetry and triggering systems. The developed framework is flexible enough to be extended in different directions. For instance, it can become a tool for the phenomenology community to go beyond the usual detector design and physics process generation approaches. Program summary Program Title: Lorenzetti Showers CPC Library link to program files: https://doi .org /10 .17632 /sy64367452 .1 Developer's repository link: https://github .com /lorenzetti -hep /lorenzetti Licensing provisions: GPLv3 Programming language: Python, C++. Nature of problem: In experimental high-energy physics, simulation is essential for experiment preparation, design and interpretations of ongoing acquisitions. Especially for calorimeters, an accurate simulation that can describe detector geometry, behavior to different physics processes and signal generation close to the readout electronics and data acquisition levels is required to properly develop signal processing and computational methods. Such detectors may face very challenging demands arising from the new designs, such as pileup mitigation and noise reduction tasks under unprecedented levels. In this sense, simulation requirements continuously increase in complexity and performance, because new physics searches require large datasets and accurate modeling to experimental effects. Solution method: The Lorenzetti Showers is an integrated software framework that provides complete calorimeter information close enough to the electronic readout chain. Thus, the proposed framework allows users to access cell readout values, configurable sensor pulse-shapes, crosstalk modeling, and different energy estimation methods. It aims at supporting designs that target low or high pileup operation conditions in an easy-to-use modular structure. The developed framework is based on Pythia 8 (particle generation) and Geant4 (interactions with the calorimeter technique under analysis). An efficient data recording structure was used to allow full access to the Lorenzetti Showers outputs. In summary, the Lorenzetti Showers tool provides to the scientific community a user-friendly, flexible, user-oriented, and low-level calorimeter simulation framework. Additional comments including restrictions and unusual features: The framework current version provides the implementation of a generic segmented calorimeter (electromagnetic and hadronic sections), which may be modified by the user, if desired. It allows the generation of particles interactions using Pythia 8 (native) or any generator compatible with the HepMC format (which may be integrated using an external input file) and propagation through a user-configurable calorimeter using Geant4.
|
|
| 20. |
|
|
| 21. |
- Bitoun, R. E., et al.
(author)
-
A methodological framework for capturing marine small-scale fisheries' contributions to the sustainable development goals
- 2024
-
In: SUSTAINABILITY SCIENCE. - 1862-4065 .- 1862-4057.
-
Journal article (peer-reviewed)abstract
- Small-scale fisheries (SSF) receive increasing international attention for landing around 40% of global marine fisheries catches and employing millions of people globally. Their contributions to food security and poverty alleviation, especially in developing countries, make it relevant to consider them when discussing sustainable development goals (SDGs). Achieving SDGs by supporting SSF means understanding fisheries in their broader context, from the health of marine ecosystems to social and economic features such as employment, public health, culture, and the effects of global change. Social-ecological relationships in SSF are complex and poorly understood, thus challenging the identification of policies that could improve and preserve the contributions of SSF to sustainable development. Here, we developed an expert-based rapid appraisal framework to identify and characterize the relationships between SSF and SDGs. The framework serves as a diagnostic tool for identifying strengths and gaps in SSF potential in enhancing SDG achievement in data-limited situations. Our structured approach extends beyond SDG 14 and target 14.b, offering insights into SSF's contributions to 11 other SDGs. As a proof of concept, we illustrate the approach and its potential contributions in two case studies in Madagascar. The method effectively captured the multiple dimensions of the SSF through the SDG lens, providing a contextually relevant understanding of how global UN goals can be achieved locally. Further research is needed to define mechanisms for aggregating and reporting the multiple, case-specific contributions of SSF to monitor progress toward the SDGs at national and global levels.
|
|
| 22. |
- Chernykh, Denis, et al.
(author)
-
NEW ACOUSTICAL TECHNIQUE TO QUANTIFY METHANE EBULLITION IN SEDIMENT WATER COLUMN : A CASE STUDY IN THE LAPTEV SEA, THE ARCTIC OCEAN
- 2018
-
In: Bulletin of the Tomsk Polytechnic University - Geo Assets Engineering. - : National Research Tomsk Polytechnic University. - 2500-1019. ; 329:11, s. 153-167
-
Journal article (peer-reviewed)abstract
- The relevance of the research is caused by the need to develop a scientifically based approach to quantitative estimation of bubble transfer of methane and other gases based on acoustic techniques, which allow reliable estimate of methane flow from the bubble unloading areas by sound locators and submarine sonars. The main aim of the research is to investigate the possible application of an acoustical technique based on acoustic scattering in bubble plumes vs the acoustical technique based on calibration which was applied to quantify in situ sonar observations; to show that both techniques can be used for a quantification of methane ebullition in the bottom-water column system. Objects: gas flares or seeps - the emanations of gas in the form of rising bubbles from the seabottom, which form stable regions of their increased concentration in the water column. Methods: modification of acoustical techniques based on acoustic scattering in bubble plumes and on ist calibration which was applied by authors to quantify in situ single sonar observations. Results. We demonstrate a first attempt to use acoustical techniques based on (1) acoustic scattering in bubble plumes vs acoustical technique based on (2) calibration which was applied to quantify in situ sonar observations. It has been shown that both techniques can be used for a quatitative express-evaluation of methane ebullition in the bottom-water system in any aquatic ecosystem including seas, lakes, and rivers, while the first acoustical technique gives the bubble efflux values -20 % lower then the second acoustical technique.
|
|
| 23. |
|
|
| 24. |
- Feigin, Valery L, et al.
(author)
-
Global, Regional, and Country-Specific Lifetime Risks of Stroke, 1990 and 2016.
- 2018
-
In: The New England journal of medicine. - 1533-4406 .- 0028-4793. ; 379:25, s. 2429-2437
-
Journal article (peer-reviewed)abstract
- The lifetime risk of stroke has been calculated in a limited number of selected populations. We sought to estimate the lifetime risk of stroke at the regional, country, and global level using data from a comprehensive study of the prevalence of major diseases.We used the Global Burden of Disease (GBD) Study 2016 estimates of stroke incidence and the competing risks of death from any cause other than stroke to calculate the cumulative lifetime risks of first stroke, ischemic stroke, or hemorrhagic stroke among adults 25 years of age or older. Estimates of the lifetime risks in the years 1990 and 2016 were compared. Countries were categorized into quintiles of the sociodemographic index (SDI) used in the GBD Study, and the risks were compared across quintiles. Comparisons were made with the use of point estimates and uncertainty intervals representing the 2.5th and 97.5th percentiles around the estimate.The estimated global lifetime risk of stroke from the age of 25 years onward was 24.9% (95% uncertainty interval, 23.5 to 26.2); the risk among men was 24.7% (95% uncertainty interval, 23.3 to 26.0), and the risk among women was 25.1% (95% uncertainty interval, 23.7 to 26.5). The risk of ischemic stroke was 18.3%, and the risk of hemorrhagic stroke was 8.2%. In high-SDI, high-middle-SDI, and low-SDI countries, the estimated lifetime risk of stroke was 23.5%, 31.1% (highest risk), and 13.2% (lowest risk), respectively; the 95% uncertainty intervals did not overlap between these categories. The highest estimated lifetime risks of stroke according to GBD region were in East Asia (38.8%), Central Europe (31.7%), and Eastern Europe (31.6%), and the lowest risk was in eastern sub-Saharan Africa (11.8%). The mean global lifetime risk of stroke increased from 22.8% in 1990 to 24.9% in 2016, a relative increase of 8.9% (95% uncertainty interval, 6.2 to 11.5); the competing risk of death from any cause other than stroke was considered in this calculation.In 2016, the global lifetime risk of stroke from the age of 25 years onward was approximately 25% among both men and women. There was geographic variation in the lifetime risk of stroke, with the highest risks in East Asia, Central Europe, and Eastern Europe. (Funded by the Bill and Melinda Gates Foundation.).
|
|
| 25. |
- Filmer, E. K., et al.
(author)
-
Combination of Searches for Resonant Higgs Boson Pair Production Using Formula Presented Collisions at Formula Presented with the ATLAS Detector
- 2024
-
In: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 132:23
-
Journal article (peer-reviewed)abstract
- A combination of searches for a new resonance decaying into a Higgs boson pair is presented, using up to Formula Presented of Formula Presented collision data at Formula Presented recorded with the ATLAS detector at the LHC. The combination includes searches performed in three decay channels: Formula Presented, Formula Presented, and Formula Presented. No excess above the expected Standard Model background is observed and upper limits are set at the 95% confidence level on the production cross section of Higgs boson pairs originating from the decay of a narrow scalar resonance with mass in the range 251 GeV-5 TeV. The observed (expected) limits are in the range 0.96-600 fb (1.2-390 fb). The limits are interpreted in the type-I two-Higgs-doublet model and the minimal supersymmetric standard model, and constrain parameter space not previously excluded by other searches.
|
|
| 26. |
- Filmer, E. K., et al.
(author)
-
Measurement of jet substructure in boosted Formula Presented events with the ATLAS detector using Formula Presented of 13 TeV Formula Presented collisions
- 2024
-
In: Physical Review D. - : American Physical Society (APS). - 2470-0010 .- 2470-0029. ; 109:11
-
Journal article (peer-reviewed)abstract
- Measurements of the substructure of top-quark jets are presented, using Formula Presented of 13 TeV Formula Presented collision data recorded with the ATLAS detector at the LHC. Top-quark jets reconstructed with the anti-Formula Presented algorithm with a radius parameter Formula Presented are selected in top-quark pair (Formula Presented) events where one top quark decays semileptonically and the other hadronically, or where both top quarks decay hadronically. The top-quark jets are required to have transverse momentum Formula Presented, yielding large samples of data events with jet Formula Presented values between 350 and 600 GeV. One- and two-dimensional differential cross sections for eight substructure variables, defined using only the charged components of the jets, are measured in a particle-level phase space by correcting for the smearing and acceptance effects induced by the detector. The differential cross sections are compared with the predictions of several Monte Carlo simulations in which top-quark pair-production quantum chromodynamic matrix-element calculations at next-to-leading-order precision in the strong coupling constant Formula Presented are passed to leading-order parton shower and hadronization generators. The Monte Carlo predictions for measures of the broadness, and also the two-body structure, of the top-quark jets are found to be in good agreement with the measurements, while variables sensitive to the three-body structure of the top-quark jets exhibit some tension with the measured distributions.
|
|
| 27. |
- Filmer, E. K., et al.
(author)
-
Search for pair production of higgsinos in events with two Higgs bosons and missing transverse momentum in Formula Presented Formula Presented collisions at the ATLAS experiment
- 2024
-
In: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 109:11
-
Journal article (peer-reviewed)abstract
- This paper presents a search for pair production of higgsinos, the supersymmetric partners of the Higgs bosons, in scenarios with gauge-mediated supersymmetry breaking. Each higgsino is assumed to decay into a Higgs boson and a nearly massless gravitino. The search targets events where each Higgs boson decays into Formula Presented, leading to a reconstructed final state with at least three energetic Formula Presented-jets and missing transverse momentum. Two complementary analysis channels are used, with each channel specifically targeting either low or high values of the higgsino mass. The low-mass (high-mass) channel exploits Formula Presented of Formula Presented data collected by the ATLAS detector during Run 2 of the Large Hadron Collider. No significant excess above the Standard Model prediction is found. At 95% confidence level, masses between 130 GeV and 940 GeV are excluded for higgsinos decaying exclusively into Higgs bosons and gravitinos. Exclusion limits as a function of the higgsino decay branching ratio to a Higgs boson are also reported.
|
|
| 28. |
- Filmer, E. K., et al.
(author)
-
Search for singly produced vectorlike top partners in multilepton final states with Formula Presented of Formula Presented collision data at Formula Presented with the ATLAS detector
- 2024
-
In: Physical Review D. - : American Physical Society (APS). - 2470-0010 .- 2470-0029. ; 109:11
-
Journal article (peer-reviewed)abstract
- A search for the single production of a vectorlike top partner (Formula Presented) with mass greater than 1 TeV decaying into a Formula Presented boson and a top quark is presented, using the full Run 2 dataset corresponding to Formula Presented of Formula Presented collisions at Formula Presented, collected in 2015-2018 with the ATLAS detector at the Large Hadron Collider. The targeted final state is characterized by the presence of a pair of electrons or muons with opposite-sign charges which form a Formula Presented-boson candidate, as well as by the presence of Formula Presented-tagged jets and forward jets. Events with exactly two or at least three leptons are categorized into two independently optimized analysis channels. No significant excess above the background expectation is observed and the results from the two channels are statistically combined to set exclusion limits at 95% confidence level on the masses and couplings of Formula Presented. The results are interpreted in several benchmark scenarios to set limits on the mass and universal coupling strength (Formula Presented) of the vectorlike quark. For singlet Formula Presented quarks, Formula Presented values between 0.22 and 0.64 are excluded for masses between 1000 and 1975 GeV. For Formula Presented quarks in the doublet scenario, where the production cross section is much lower, Formula Presented values between 0.54 and 0.88 are excluded for masses between 1000 and 1425 GeV.
|
|
| 29. |
- Hammond, Philip S., et al.
(author)
-
Cetacean abundance and distribution in European Atlantic shelf waters to inform conservation and management
- 2013
-
In: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 164, s. 107-122
-
Journal article (peer-reviewed)abstract
- The European Union (EU) Habitats Directive requires Member States to monitor and maintain at favourable conservation status those species identified to be in need of protection, including all cetaceans. In July 2005 we surveyed the entire EU Atlantic continental shelf to generate robust estimates of abundance for harbour porpoise and other cetacean species. The survey used line transect sampling methods and purpose built data collection equipment designed to minimise bias in estimates of abundance. Shipboard transects covered 19,725 km in sea conditions <= Beaufort 4 in an area of 1,005,743 km(2). Aerial transects covered 15,802 km in good/moderate conditions (<= Beaufort 3) in an area of 364,371 km(2). Thirteen cetacean species were recorded; abundance was estimated for harbour porpoise (375,358; CV = 0.197), bottlenose dolphin (16,485; CV = 0.422), white-beaked dolphin (16,536; CV = 0.303), short-beaked common dolphin (56,221; CV = 0.234) and minke whale (18,958; CV = 0.347). Abundance in 2005 was similar to that estimated in July 1994 for harbour porpoise, white-beaked dolphin and minke whale in a comparable area. However, model-based density surfaces showed a marked difference in harbour porpoise distribution between 1994 and 2005. Our results allow EU Member States to discharge their responsibilities under the Habitats Directive and inform other international organisations concerning the assessment of conservation status of cetaceans and the impact of bycatch at a large spatial scale. The lack of evidence for a change in harbour porpoise abundance in EU waters as a whole does not exclude the possibility of an impact of bycatch in some areas. Monitoring bycatch and estimation of abundance continue to be essential. (C) 2013 The Authors.
|
|
| 30. |
- Hayrapetyan, A., et al.
(author)
-
Combination of Measurements of the Top Quark Mass from Data Collected by the ATLAS and CMS Experiments at Formula Presented and 8 TeV
- 2024
-
In: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 132:26
-
Journal article (peer-reviewed)abstract
- A combination of fifteen top quark mass measurements performed by the ATLAS and CMS experiments at the LHC is presented. The datasets used correspond to an integrated luminosity of up to 5 and Formula Presented of proton-proton collisions at center-of-mass energies of 7 and 8 TeV, respectively. The combination includes measurements in top quark pair events that exploit both the semileptonic and hadronic decays of the top quark, and a measurement using events enriched in single top quark production via the electroweak Formula Presented channel. The combination accounts for the correlations between measurements and achieves an improvement in the total uncertainty of 31% relative to the most precise input measurement. The result is Formula Presented, with a total uncertainty of 0.33 GeV.
|
|
| 31. |
- Herper, Heike C., et al.
(author)
-
Magnetic properties of NdFe11Ti and YFe11Ti, from experiment and theory
- 2023
-
In: Acta Materialia. - : Elsevier. - 1359-6454 .- 1873-2453. ; 242
-
Journal article (peer-reviewed)abstract
- NdFe11Ti and YFe11Ti serve as prototypes for rare-earth (RE) lean or REfree magnets with the ThMn12-type structure. Although NdFe11Ti has been studied for a long time the origin of its complex magnetism at low temperature is so far not well-understood. We present a comprehensive theoretical and experimental study of the magnetic properties of NdFe11Ti and RE-free YFe11Ti to elucidate the influence of the 4f electrons. The partially localized 4 f electrons of Nd are the driving force behind the complex behavior of the magnetocrystalline anisotropy which changes from cone to uniaxial above 170 dK. The spontaneous magnetization and the five leading anisotropy constants were determined from high-quality single crystal samples over a wide temperature range using field dependencies of magnetization measured along the principle crystallographic directions. The experimental data are compared with density functional theory combined with a Hartree-Fock correction (+U) and an approximate dynamical mean-field theory.
|
|
| 32. |
- Kaldmäe, Margit, et al.
(author)
-
A “spindle and thread” mechanism unblocks p53 translation by modulating N-terminal disorder
- 2022
-
In: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 30:5, s. 733-742, e1-e7
-
Journal article (peer-reviewed)abstract
- Disordered proteins pose a major challenge to structural biology. A prominent example is the tumor suppressor p53, whose low expression levels and poor conformational stability hamper the development of cancer therapeutics. All these characteristics make it a prime example of “life on the edge of solubility.” Here, we investigate whether these features can be modulated by fusing the protein to a highly soluble spider silk domain (NT∗). The chimeric protein displays highly efficient translation and is fully active in human cancer cells. Biophysical characterization reveals a compact conformation, with the disordered transactivation domain of p53 wrapped around the NT∗ domain. We conclude that interactions with NT∗ help to unblock translation of the proline-rich disordered region of p53. Expression of partially disordered cancer targets is similarly enhanced by NT∗. In summary, we demonstrate that inducing co-translational folding via a molecular “spindle and thread” mechanism unblocks protein translation in vitro.
|
|
| 33. |
- Liti, Gianni, et al.
(author)
-
Population genomics of domestic and wild yeasts.
- 2009
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 458:7236, s. 337-41
-
Journal article (peer-reviewed)abstract
- Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
|
|
| 34. |
- Piening, B. D., et al.
(author)
-
Integrative Personal Omics Profiles during Periods of Weight Gain and Loss
- 2018
-
In: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 6:2
-
Journal article (peer-reviewed)abstract
- Advances in omics technologies now allow an unprecedented level of phenotyping for human diseases, including obesity, in which individual responses to excess weight are heterogeneous and unpredictable. To aid the development of better understanding of these phenotypes, we performed a controlled longitudinal weight perturbation study combining multiple omics strategies (genomics, transcriptomics, multiple proteomics assays, metabolomics, and microbiomics) during periods of weight gain and loss in humans. Results demonstrated that: (1) weight gain is associated with the activation of strong inflammatory and hypertrophic cardiomyopathy signatures in blood; (2) although weight loss reverses some changes, a number of signatures persist, indicative of long-term physiologic changes; (3) we observed omics signatures associated with insulin resistance that may serve as novel diagnostics; (4) specific biomolecules were highly individualized and stable in response to perturbations, potentially representing stable personalized markers. Most data are available open access and serve as a valuable resource for the community.
|
|
| 35. |
- Sahin, Cagla, et al.
(author)
-
Ion mobility-mass spectrometry shows stepwise protein unfolding under alkaline conditions
- 2021
-
In: Chemical Communications. - : Royal Society of Chemistry. - 1359-7345 .- 1364-548X. ; 57:12, s. 1450-1453
-
Journal article (peer-reviewed)abstract
- Although native mass spectrometry is widely applied to monitor chemical or thermal protein denaturation, it is not clear to what extent it can inform about alkali-induced unfolding. Here, we probe the relationship between solution- and gas-phase structures of proteins under alkaline conditions. Native ion mobility-mass spectrometry reveals that globular proteins are destabilized rather than globally unfolded, which is supported by solution studies, providing detailed insights into alkali-induced unfolding events. Our results pave the way for new applications of MS to monitor structures and interactions of proteins at high pH.
|
|
| 36. |
- Sahin, Cagla, et al.
(author)
-
Ion mobility-mass spectrometry shows stepwise protein unfolding under alkaline conditions
- 2021
-
In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 57:12, s. 1450-1453
-
Journal article (peer-reviewed)abstract
- Although native mass spectrometry is widely applied to monitor chemical or thermal protein denaturation, it is not clear to what extent it can inform about alkali-induced unfolding. Here, we probe the relationship between solution- and gas-phase structures of proteins under alkaline conditions. Native ion mobility-mass spectrometry reveals that globular proteins are destabilized rather than globally unfolded, which is supported by solution studies, providing detailed insights into alkali-induced unfolding events. Our results pave the way for new applications of MS to monitor structures and interactions of proteins at high pH.
|
|
| 37. |
- Vincent, Theresa, et al.
(author)
-
A SNAIL1–SMAD3/4 transcriptional repressor complex promotes TGF‑β mediated epithelial–mesenchymal transition
- 2009
-
In: Nature Cell Biology. - : Springer Science and Business Media LLC. - 1465-7392 .- 1476-4679. ; 11:8, s. 943-950
-
Journal article (peer-reviewed)abstract
- Epithelial-mesenchymal transition (EMT) is essential for organogenesis and is triggered during carcinoma progression to an invasive state. Transforming growth factor-β (TGF-β) cooperates with signalling pathways, such as Ras and Wnt, to induce EMT, but the molecular mechanisms are not clear. Here, we report that SMAD3 and SMAD4 interact and form a complex with SNAIL1, a transcriptional repressor and promoter of EMT. The SNAIL1-SMAD3/4 complex was targeted to the gene promoters of CAR, a tight-junction protein, and E-cadherin during TGF-β-driven EMT in breast epithelial cells. SNAIL1 and SMAD3/4 acted as co-repressors of CAR, occludin, claudin-3 and E-cadherin promoters in transfected cells. Conversely, co-silencing of SNAIL1 and SMAD4 by siRNA inhibited repression of CAR and occludin during EMT. Moreover, loss of CAR and E-cadherin correlated with nuclear co-expression of SNAIL1 and SMAD3/4 in a mouse model of breast carcinoma and at the invasive fronts of human breast cancer. We propose that activation of a SNAIL1-SMAD3/4 transcriptional complex represents a mechanism of gene repression during EMT.
|
|
| 38. |
- Zamani, Leila, et al.
(author)
-
Discrimination among IgG1-Κ monoclonal antibodies produced by two cell lines using charge state distributions in nanoESI-TOF mass spectra
- 2009
-
In: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 20:6, s. 1030-1036
-
Journal article (peer-reviewed)abstract
- Charge state distributions (CSDs) of proteins in nanoESI mass spectra are affected by the instrumental settings and experimental conditions, in addition to the conformations of the proteins in the analyzed solutions. In the presented study, instrumental and experimental parameters-the desolvation gas flow rate, temperature, pH, buffer (ammonium acetate), and organic modifier (methanol) concentrations-were optimized according to a reduced central composite face experimental design to maximize the separation of CSDs of monoclonal IgG1-kappa antibodies produced by two production systems (CHO and GS-NS0 cell lines). Principal component analysis and Fisher linear discriminant analysis were then used to reduce the dimensions of the acquired dataset and quantify the separation of the protein classes, respectively. The results show that the IgG1-kappa molecules produced by the two production systems can be clearly distinguished using the described approach, which could be readily applied to other proteins and production systems.
|
|
| 39. |
- Zhang, Wuyong, et al.
(author)
-
Coordinative Stabilization of Single Bismuth Sites in a Carbon-Nitrogen Matrix to Generate Atom-Efficient Catalysts for Electrochemical Nitrate Reduction to Ammonia
- 2023
-
In: Advanced Science. - : John Wiley & Sons. - 2198-3844. ; 10:28
-
Journal article (peer-reviewed)abstract
- Electrochemical nitrate reduction to ammonia powered by renewable electricity is not only a promising alternative to the established energy-intense and non-ecofriendly Haber-Bosch reaction for ammonia generation but also a future contributor to the ever-more important denitrification schemes. Nevertheless, this reaction is still impeded by the lack of understanding for the underlying reaction mechanism on the molecular scale which is necessary for the rational design of active, selective, and stable electrocatalysts. Herein, a novel single-site bismuth catalyst (Bi-N-C) for nitrate electroreduction is reported to produce ammonia with maximum Faradaic efficiency of 88.7% and at a high rate of 1.38 mg h(-1) mg(cat)(-1) at -0.35 V versus reversible hydrogen electrode (RHE). The active center (described as BiN2C2) is uncovered by detailed structural analysis. Coupled density functional theory calculations are applied to analyze the reaction mechanism and potential rate-limiting steps for nitrate reduction based on the BiN2C2 model. The findings highlight the importance of model catalysts to utilize the potential of nitrate reduction as a new-generation nitrogen-management technology based on the construction of efficient active sites.
|
|
