| 1. |
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| 2. |
- Aaltonen, T., et al.
(author)
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Combination of Tevatron Searches for the Standard Model Higgs Boson in the W+W- Decay Mode
- 2010
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 104:6, s. 061802-
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Journal article (peer-reviewed)abstract
- We combine searches by the CDF and D0 Collaborations for a Higgs boson decaying to W+W-. The data correspond to an integrated total luminosity of 4.8 (CDF) and 5.4 (D0) fb(-1) of p (p) over bar collisions at root s = 1.96 TeV at the Fermilab Tevatron collider. No excess is observed above background expectation, and resulting limits on Higgs boson production exclude a standard model Higgs boson in the mass range 162-166 GeV at the 95% C.L.
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| 3. |
- Acharya, B. S., et al.
(author)
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Introducing the CTA concept
- 2013
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In: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 43, s. 3-18
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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.
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| 4. |
- Fenstermacher, M.E., et al.
(author)
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DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
-
In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
-
Journal article (peer-reviewed)abstract
- DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
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| 5. |
- Griffin, M. J., et al.
(author)
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The Herschel-SPIRE instrument and its in-flight performance
- 2010
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518, s. L3-
-
Journal article (peer-reviewed)abstract
- The Spectral and Photometric Imaging REceiver (SPIRE), is the Herschel Space Observatory`s submillimetre camera and spectrometer. It contains a three-band imaging photometer operating at 250, 350 and 500 mu m, and an imaging Fourier-transform spectrometer (FTS) which covers simultaneously its whole operating range of 194-671 mu m (447-1550 GHz). The SPIRE detectors are arrays of feedhorn-coupled bolometers cooled to 0.3 K. The photometer has a field of view of 4' x 8', observed simultaneously in the three spectral bands. Its main operating mode is scan-mapping, whereby the field of view is scanned across the sky to achieve full spatial sampling and to cover large areas if desired. The spectrometer has an approximately circular field of view with a diameter of 2.6'. The spectral resolution can be adjusted between 1.2 and 25 GHz by changing the stroke length of the FTS scan mirror. Its main operating mode involves a fixed telescope pointing with multiple scans of the FTS mirror to acquire spectral data. For extended source measurements, multiple position offsets are implemented by means of an internal beam steering mirror to achieve the desired spatial sampling and by rastering of the telescope pointing to map areas larger than the field of view. The SPIRE instrument consists of a cold focal plane unit located inside the Herschel cryostat and warm electronics units, located on the spacecraft Service Module, for instrument control and data handling. Science data are transmitted to Earth with no on-board data compression, and processed by automatic pipelines to produce calibrated science products. The in-flight performance of the instrument matches or exceeds predictions based on pre-launch testing and modelling: the photometer sensitivity is comparable to or slightly better than estimated pre-launch, and the spectrometer sensitivity is also better by a factor of 1.5-2.
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| 6. |
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| 7. |
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| 8. |
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| 9. |
- Lee, Bruce Y., et al.
(author)
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Research gaps and opportunities in precision nutrition : an NIH workshop report
- 2022
-
In: The American journal of clinical nutrition. - : Elsevier BV. - 1938-3207 .- 0002-9165. ; 116:6, s. 1877-1900
-
Journal article (peer-reviewed)abstract
- Precision nutrition is an emerging concept that aims to develop nutrition recommendations tailored to different people's circumstances and biological characteristics. Responses to dietary change and the resulting health outcomes from consuming different diets may vary significantly between people based on interactions between their genetic backgrounds, physiology, microbiome, underlying health status, behaviors, social influences, and environmental exposures. On 11-12 January 2021, the National Institutes of Health convened a workshop entitled "Precision Nutrition: Research Gaps and Opportunities" to bring together experts to discuss the issues involved in better understanding and addressing precision nutrition. The workshop proceeded in 3 parts: part I covered many aspects of genetics and physiology that mediate the links between nutrient intake and health conditions such as cardiovascular disease, Alzheimer disease, and cancer; part II reviewed potential contributors to interindividual variability in dietary exposures and responses such as baseline nutritional status, circadian rhythm/sleep, environmental exposures, sensory properties of food, stress, inflammation, and the social determinants of health; part III presented the need for systems approaches, with new methods and technologies that can facilitate the study and implementation of precision nutrition, and workforce development needed to create a new generation of researchers. The workshop concluded that much research will be needed before more precise nutrition recommendations can be achieved. This includes better understanding and accounting for variables such as age, sex, ethnicity, medical history, genetics, and social and environmental factors. The advent of new methods and technologies and the availability of considerably more data bring tremendous opportunity. However, the field must proceed with appropriate levels of caution and make sure the factors listed above are all considered, and systems approaches and methods are incorporated. It will be important to develop and train an expanded workforce with the goal of reducing health disparities and improving precision nutritional advice for all Americans.
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| 10. |
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| 11. |
- Sigmundsson, F., et al.
(author)
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Segmented lateral dyke growth in a rifting event at Bardarbunga volcanic system, Iceland
- 2015
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 517:7533
-
Journal article (peer-reviewed)abstract
- Crust at many divergent plate boundaries forms primarily by the injection of vertical sheet-like dykes, some tens of kilometres long(1). Previous models of rifting events indicate either lateral dyke growth away from a feeding source, with propagation rates decreasing as the dyke lengthens(2-4), or magma flowing vertically into dykes from an underlying source(5,6), with the role of topography on the evolution of lateral dykes not clear. Here we show how a recent segmented dyke intrusion in the Bardarbunga volcanic system grew laterally for more than 45 kilometres at a variable rate, with topography influencing the direction of propagation. Barriers at the ends of each segment were overcome by the build-up of pressure in the dyke end; then a new segment formed and dyke lengthening temporarily peaked. The dyke evolution, which occurred primarily over 14 days, was revealed by propagating seismicity, ground deformation mapped by Global Positioning System(GPS), interferometric analysis of satellite radar images (InSAR), and graben formation. The strike of the dyke segments varies from an initially radial direction away from the Bardarbunga caldera, towards alignment with that expected from regional stress at the distal end. A model minimizing the combined strain and gravitational potential energy explains the propagation path. Dyke opening and seismicity focused at the most distal segment at any given time, and were simultaneous with magma source deflation and slow collapse at the Bardarbunga caldera, accompanied by a series of magnitude M > 5 earthquakes. Dyke growth was slowed down by an effusive fissure eruption near the end of the dyke. Lateral dyke growth with segment barrier breaking by pressure build-up in the dyke distal end explains how focused upwelling of magma under central volcanoes is effectively redistributed over long distances to create new upper crust at divergent plate boundaries.
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| 12. |
- Bowers, Robert M., et al.
(author)
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- 2017
-
In: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731
-
Journal article (peer-reviewed)abstract
- We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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| 13. |
- Prakash, Varsha, et al.
(author)
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Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease
- 2019
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
-
Journal article (peer-reviewed)abstract
- Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ER alpha) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
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| 14. |
- Yamauchi, M., et al.
(author)
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Plasma-neutral gas interactions in various space environments : Assessment beyond simplified approximations as a Voyage 2050 theme
- 2022
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In: Experimental astronomy. - : Springer Nature. - 0922-6435 .- 1572-9508.
-
Journal article (peer-reviewed)abstract
- In the White Paper, submitted in response to the European Space Agency (ESA) Voyage 2050 Call, we present the importance of advancing our knowledge of plasma-neutral gas interactions, and of deepening our understanding of the partially ionized environments that are ubiquitous in the upper atmospheres of planets and moons, and elsewhere in space. In future space missions, the above task requires addressing the following fundamental questions: (A) How and by how much do plasma-neutral gas interactions influence the re-distribution of externally provided energy to the composing species? (B) How and by how much do plasma-neutral gas interactions contribute toward the growth of heavy complex molecules and biomolecules? Answering these questions is an absolute prerequisite for addressing the long-standing questions of atmospheric escape, the origin of biomolecules, and their role in the evolution of planets, moons, or comets, under the influence of energy sources in the form of electromagnetic and corpuscular radiation, because low-energy ion-neutral cross-sections in space cannot be reproduced quantitatively in laboratories for conditions of satisfying, particularly, (1) low-temperatures, (2) tenuous or strong gradients or layered media, and (3) in low-gravity plasma. Measurements with a minimum core instrument package (< 15 kg) can be used to perform such investigations in many different conditions and should be included in all deep-space missions. These investigations, if specific ranges of background parameters are considered, can also be pursued for Earth, Mars, and Venus.
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| 15. |
- Arvelius, S., et al.
(author)
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Statistical study of relationships between dayside high-altitude and high-latitude O+ ion outflows, solar winds, and geomagnetic activity
- 2005
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In: Annales Geophysicae. - : Copernicus GmbH. - 0992-7689 .- 1432-0576. ; 23, s. 1909-1916
-
Journal article (peer-reviewed)abstract
- The persistent outflows of O+ ions observed by the Cluster CIS/CODIF instrument were studied statistically in the high-altitude (from 3 up to 11 RE) and high-latitude (from 70 to ~90 deg invariant latitude, ILAT) polar region. The principal results are: (1) Outflowing O+ ions with more than 1keV are observed above 10 RE geocentric distance and above 85deg ILAT location; (2) at 6-8 RE geocentric distance, the latitudinal distribution of O+ ion outflow is consistent with velocity filter dispersion from a source equatorward and below the spacecraft (e.g. the cusp/cleft); (3) however, at 8-12 RE geocentric distance the distribution of O+ outflows cannot be explained by velocity filter only. The results suggest that additional energization or acceleration processes for outflowing O+ ions occur at high altitudes and high latitudes in the dayside polar region.
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| 16. |
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| 17. |
- Dass, Randall A., et al.
(author)
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Wnt5a Signals through DVL1 to Repress Ribosomal DNA Transcription by RNA Polymerase I
- 2016
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In: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 12:8
-
Journal article (peer-reviewed)abstract
- Ribosome biogenesis is essential for cell growth and proliferation and is commonly elevated in cancer. Accordingly, numerous oncogene and tumor suppressor signaling pathways target rRNA synthesis. In breast cancer, non-canonical Wnt signaling by Wnt5a has been reported to antagonize tumor growth. Here, we show that Wnt5a rapidly represses rDNA gene transcription in breast cancer cells and generates a chromatin state with reduced transcription of rDNA by RNA polymerase I (Pol I). These effects were specifically dependent on Dishevelled1 (DVL1), which accumulates in nucleolar organizer regions (NORs) and binds to rDNA regions of the chromosome. Upon DVL1 binding, the Pol I transcription activator and deacetylase Sirtuin 7 (SIRT7) releases from rDNA loci, concomitant with disassembly of Pol I transcription machinery at the rDNA promoter. These findings reveal that Wnt5a signals through DVL1 to suppress rRNA transcription. This provides a novel mechanism for how Wnt5a exerts tumor suppressive effects and why disruption of Wnt5a signaling enhances mammary tumor growth in vivo.
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| 18. |
- Ebersole, Charles R., et al.
(author)
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Many Labs 5: Testing Pre-Data-Collection Peer Review as an Intervention to Increase Replicability
- 2020
-
In: Advances in Methods and Practices in Psychological Science. - : Sage. - 2515-2467 .- 2515-2459. ; 3:3, s. 309-331
-
Journal article (peer-reviewed)abstract
- Replication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p < .05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3-9; median total sample = 1,279.5, range = 276-3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (Delta r = .002 or .014, depending on analytic approach). The median effect size for the revised protocols (r = .05) was similar to that of the RP:P protocols (r = .04) and the original RP:P replications (r = .11), and smaller than that of the original studies (r = .37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r = .07, range = .00-.15) were 78% smaller, on average, than the original effect sizes (median r = .37, range = .19-.50).
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| 19. |
- Lui, A. T. Y., et al.
(author)
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Prelude to THEMIS tail conjunction study
- 2007
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In: Annales Geophysicae. - 0992-7689 .- 1432-0576. ; 25:4, s. 1001-1009
-
Journal article (peer-reviewed)abstract
- A close conjunction of several satellites (LANL, GOES. Polar. Geotail, and Cluster) distributed from the geostationary altitude to about 16 R-E downstream in the tail occurred during substorm activity as indicated by global auroral imaging and ground-based magnetometer data. This constellation of satellites resembles what is planned for the THEMIS (Time History of Events and Macroscopic Interactions during Substorms) mission to resolve the substorm controversy on the location of the substorm expansion onset region. In this article, we show in detail the dipolarization and dynamic changes seen by these satellites associated with two onsets of substorm intensification activity. In particular, we find that dipolarization at similar to 16 R-E downstream in the tail can occur with dawnward electric field and without plasma flow, just like some near-Earth dipolarization events reported previously. The spreading of substorm disturbances in the tail coupled with complementary ground observations indicates that the observed time sequence on the onsets of substorm disturbances favors initiation in the near-Earth region for this THEMIS-like conjunction.
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| 20. |
- Martin, David, et al.
(author)
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Defining Major Surgery: A Delphi Consensus Among European Surgical Association (ESA) Members
- 2020
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In: World Journal of Surgery. - : Springer Science and Business Media LLC. - 0364-2313 .- 1432-2323. ; 44:7, s. 2211-2219
-
Journal article (peer-reviewed)abstract
- © 2020, Société Internationale de Chirurgie. Background: Major surgery is a term frequently used but poorly defined. The aim of the present study was to reach a consensus in the definition of major surgery within a panel of expert surgeons from the European Surgical Association (ESA). Methods: A 3-round Delphi process was performed. All ESA members were invited to participate in the expert panel. In round 1, experts were inquired by open- and closed-ended questions on potential criteria to define major surgery. Results were analyzed and presented back anonymously to the panel within next rounds. Closed-ended questions in round 2 and 3 were either binary or statements to be rated on a Likert scale ranging from 1 (strong disagreement) to 5 (strong agreement). Participants were sent 3 reminders at 2-week intervals for each round. 70% of agreement was considered to indicate consensus. Results: Out of 305 ESA members, 67 (22%) answered all the 3 rounds. Significant comorbidities were the only preoperative factor retained to define major surgery (78%). Vascular clampage or organ ischemia (92%), high intraoperative blood loss (90%), high noradrenalin requirements (77%), long operative time (73%) and perioperative blood transfusion (70%) were procedure-related factors that reached consensus. Regarding postoperative factors, systemic inflammatory response (76%) and the need for intensive or intermediate care (88%) reached consensus. Consequences of major surgery were high morbidity (>30% overall) and mortality (>2%). Conclusion: ESA experts defined major surgery according to extent and complexity of the procedure, its pathophysiological consequences and consecutive clinical outcomes.
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| 21. |
- Murray, Alison E., et al.
(author)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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In: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
-
Journal article (peer-reviewed)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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| 22. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Chong, S S, et al.
(author)
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Contribution of DNA sequence and CAG size to mutation frequencies of intermediate alleles for Huntington disease : evidence from single sperm analyses.
- 1997
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 6:2, s. 301-9
-
Journal article (peer-reviewed)abstract
- New mutations for Huntington disease (HD) arise from intermediate alleles (IAs) with between 29 and 35 CAG repeats that expand on transmission through the paternal germline to 36 CAGs or greater. Using single sperm analysis, we have assessed CAG mutation frequencies for four IAs in families with sporadic HD (IANM) and IAs ascertained from the general population (IAGP) by analyzing 1161 single sperm from three persons. We show that IANM are more unstable than IAGP with identical size and sequence. Furthermore, comparison of different sized IAs and IAs with different sequences between the CAG and the adjacent CCG tracts indicates that DNA sequence is a major influence on CAG stability. These studies provide estimates of the likelihood of expansion of IANM and IAGP to > or = 36 CAG repeats for these individuals. For an IA with a CAG of 35 in this family with sporadic HD, the likelihood for siblings to inherit a recurrent mutation > or = 36 CAG is approximately 10%. For IAGP of a similar size, the risk of inheriting an expanded allele of > or = 36 CAG through the paternal germline is approximately 6%. These risk estimates are higher than previously reported and provide additional information for counselling in these families. Further studies on persons with IAs will be needed to determine whether these results can be generalized to other families.
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| 28. |
- Drago, Victoria N., et al.
(author)
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Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase
- 2024
-
In: Cell Reports Physical Science. - 2666-3864. ; 5:2
-
Journal article (peer-reviewed)abstract
- Pyridoxal 5′-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
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| 29. |
- Emerson, Joanne B., et al.
(author)
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Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes
- 2021
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12
-
Journal article (peer-reviewed)abstract
- Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH4) from sediments. Ebullitive CH4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH4 emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH4-cycling microorganisms and syntrophs, were predictive of porewater CH4 concentrations. Results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to CH4 emissions in a warmer Arctic and that CH4 emission predictions may be improved by accounting for spatial variations in sediment microbiota.
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| 30. |
- Hollmann, E M, et al.
(author)
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Estimate of pre-thermal quench non-thermal electron density profile during Ar pellet shutdowns of low-density target plasmas in DIII-D
- 2021
-
In: Physics of Plasmas. - : AIP Publishing. - 1089-7674 .- 1070-664X. ; 28:7
-
Journal article (peer-reviewed)abstract
- The radial density profile of pre-thermal quench (pre-TQ) early-time non-thermal (hot) electrons is estimated by combining electron cyclotron emission and soft x-ray data during the rapid shutdown of low-density (ne≲1019m−3) DIII-D target plasmas with cryogenic argon pellet injection. This technique is mostly limited in these experiments to the pre-TQ phase and quickly loses validity during the TQ. Two different cases are studied: a high (10 keV) temperature target and a low (4 keV) temperature target. The results indicate that early-time, low-energy (∼10 keV) hot electrons form ahead of the argon pellet as it enters the plasma, affecting the pellet ablation rate; it is hypothesized that this may be caused by rapid cross field transport of argon ions ahead of the pellet or by rapid cross field transport of hot electrons. Fokker-Planck modeling of the two shots suggests that the hot electron current is quite significant during the pre-TQ phase (up to 50% of the total current). Comparison between modeled pre-TQ hot electron current and post-TQ hot electron current inferred from avalanche theory suggests that hot electron current increases during the high-temperature target TQ but decreases during the low-temperature target TQ. The uncertainties in this estimate are large; however, if true, this suggests that TQ radial loss of hot electron current could be larger than previously estimated in DIII-D.
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| 31. |
- Hong, Liang, et al.
(author)
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Structure and Dynamics of a Compact State of a Multidomain Protein, the Mercuric Ion Reductase
- 2014
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In: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 107:2, s. 393-400
-
Journal article (peer-reviewed)abstract
- The functional efficacy of colocalized, linked protein domains is dependent on linker flexibility and system compaction. However, the detailed characterization of these properties in aqueous solution presents an enduring challenge. Here, we employ a novel, to our knowledge, combination of complementary techniques, including small-angle neutron scattering, neutron spin-echo spectroscopy, and all-atom molecular dynamics and coarse-grained simulation, to identify and characterize in detail the structure and dynamics of a compact form of mercuric ion reductase (MerA), an enzyme central to bacterial mercury resistance. MerA possesses metallochaperone-like N-terminal domains (NmerA) tethered to its catalytic core domain by linkers. The NmerA domains are found to interact principally through electrostatic interactions with the core, leashed by the linkers so as to subdiffuse on the surface over an area close to the core C-terminal Hg(II)-binding cysteines. How this compact, dynamical arrangement may facilitate delivery of Hg(II) from NmerA to the core domain is discussed.
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| 32. |
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| 33. |
- Kurylo, Chad M., et al.
(author)
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Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype
- 2018
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In: Cell Reports. - : CELL PRESS. - 2211-1247. ; 25:1, s. 236-248.e6
-
Journal article (peer-reviewed)abstract
- Prevailing dogma holds that ribosomes are uniform in composition and function. Here, we show that nutrient limitation-induced stress in E. coli changes the relative expression of rDNA operons to alter the rRNA composition within the actively translating ribosome pool. The most upregulated operon encodes the unique 16S rRNA, rrsH, distinguished by conserved sequence variation within the small ribosomal subunit. rrsH-bearing ribosomes affect the expression of functionally coherent gene sets and alter the levels of the RpoS sigma factor, the master regulator of the general stress response. These impacts are associated with phenotypic changes in antibiotic sensitivity, biofilm formation, and cell motility and are regulated by stress response proteins, ReIA and ReIE, as well as the metabolic enzyme and virulence-associated protein, AdhE. These findings establish that endogenously encoded, naturally occurring rRNA sequence variation can modulate ribosome function, central aspects of gene expression regulation, and cellular physiology.
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| 34. |
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| 35. |
- Parks, Michelle M., et al.
(author)
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2021-2023 Unrest and Geodetic Observations at Askja Volcano, Iceland
- 2024
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In: GEOPHYSICAL RESEARCH LETTERS. - 0094-8276 .- 1944-8007. ; 51:4
-
Journal article (peer-reviewed)abstract
- Unrest began in July 2021 at Askja volcano in the Northern Volcanic Zone (NVZ) of Iceland. Its most recent eruption, in 1961, was predominantly effusive and produced similar to 0.1 km3 lava field. The last plinian eruption at Askja occurred in 1875. Geodetic measurements between 1983 and 2021 detail subsidence of Askja, decaying in an exponential manner. At the end of July 2021, inflation was detected at Askja volcano, from GNSS observations and Sentinel-1 interferograms. The inflationary episode can be divided into two periods from the onset of inflation until September 2023. An initial period until 20 September 2021 when geodetic models suggest transfer of magma (or magmatic fluids) from within the shallowest part of the magmatic system (comprising an inflating and deflating source), potentially involving silicic magma. A following period when one source of pressure increase at shallow depth can explain the observations. Askja volcano, situated in the Northern Volcanic Zone in Iceland, has been quiet since its last eruption in 1961, with surface deformation measurements from 1983 to 2021 displaying a decaying subsidence signal within the Askja caldera. However, at the end of July 2021, the volcano began to inflate. This was detected on both GNSS and satellite observations. As of September 2023, similar to 65 cm of uplift had been measured at GNSS station OLAC. Modeling of surface deformation measurements indicates that the inflation was triggered by upward migration of melt (or magmatic fluids). At the end of July 2021, Askja volcano began to inflate-detected on both GNSS and satellite observations, ending 1983-2021 subsidence Geodetic modeling indicates upward migration of magma, feeding a magma body at an inferred depth of 2.5-3.1 km under the main Askja caldera Start of unrest was associated with magma transfer within the upper part of the system, followed by possible additional influx from depth
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| 36. |
- Parks, Matthew M., et al.
(author)
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Implications of sequence variation on the evolution of rRNA
- 2019
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In: Chromosome Research. - : Springer. - 0967-3849 .- 1573-6849. ; 27:1-2, s. 89-93
-
Research review (peer-reviewed)abstract
- The evolution of the multi-copy family of ribosomal RNA (rRNA) genes is unique in regard to its genetics and genome evolution. Paradoxically, rRNA genes are highly homogenized within and between individuals, yet they are globally distinct between species. Here, we discuss the implications for models of rRNA gene evolution in light of our recent discoveries that ribosomes bearing rRNA sequence variants can affect gene expression and physiology and that intra-individual rRNA alleles exhibit both context- and tissue-specific expression.
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| 37. |
- Parks, Matthew M., et al.
(author)
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Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression
- 2018
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In: Science Advances. - : AMER ASSOC ADVANCEMENT SCIENCE. - 2375-2548. ; 4:2
-
Journal article (peer-reviewed)abstract
- The ribosome, the integration point for protein synthesis in the cell, is conventionally considered a homogeneous molecular assembly that only passively contributes to gene expression. Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosomes molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra-and interindividual nucleotide variation in the 5S, 5.8S, 18S, and 28S ribosomal RNA (rRNA) genes of both human and mouse. Conserved rRNA sequence heterogeneities map to functional centers of the assembled ribosome, variant rRNA alleles exhibit tissue-specific expression, and ribosomes bearing variant rRNA alleles are present in the actively translating ribosome pool. These findings provide a critical framework for exploring the possibility that the expression of genomically encoded variant rRNA alleles gives rise to physically and functionally heterogeneous ribosomes that contribute to mammalian physiology and human disease.
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| 38. |
- Paz-Soldan, C., et al.
(author)
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Recent DIII-D advances in runaway electron measurement and model validation
- 2019
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In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:6
-
Journal article (peer-reviewed)abstract
- Novel measurements and modeling of runaway electron (RE) dynamics in DIII-D have resolved experimental discrepancies and validated predictions for ITER, improving confidence that RE avoidance and mitigation can be predictably achieved. Considering RE formation, first experimental assessments of the RE seed current demonstrates that present hot-tail theories are not yet accurate and require improved treatment of the pellet dynamics. Novel measurements of kinetic instabilities in the MHz-range have been made in the RE formation phase, with the intensity of these modes correlated with previously unexplained empirical thresholds for RE generation. Controlled RE dissipation experiments in quiescent regimes have validated RE distribution function dependencies on collisional and synchrotron damping, both in terms of distribution function shape and dissipation rates. Measurements of RE bremsstrahlung and synchrotron emission are now used in tandem to resolve energy and pitch-angle effects. A resolution to long-standing dissipation anomalies in the quiescent regime is offered by taking into account kinetic instability effects on RE phase-space dynamics. Kinetic instabilities in the 100-200 MHz range are directly observed, though modeling finds the largest dissipation arises from GHz range instabilities that are beyond the reach of existing diagnostics. Kinetic instabilities are also observed in the mature post-disruption RE plateau phase, so long as the collisional damping rate is reduced with low-Z injection. Experiments with high-Z injection find that the dissipation rate saturates with injection quantity, likely due to neutral diffusion rates being slower than vertical instability rates in DIII-D. Considering the final loss, a 0D model for first-wall Joule heating is found to be in agreement with experiment, and controlled access to RE equilibria with edge safety factor of two identifies novel dynamics brought about by large-scale kink instabilities. These dynamics are typified by fast (tens of microseconds) RE loss rates without RE beam regeneration. The above measurements and comparison with theory represent significant advances in the understanding of RE dynamics and indicate possible new opportunities for RE avoidance or mitigation via kinetic instabilities.
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| 39. |
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| 40. |
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| 41. |
- Spake, Rebecca, et al.
(author)
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Unpacking ecosystem service bundles : Towards predictive mapping of synergies and trade-offs between ecosystem services
- 2017
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In: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 47, s. 37-50
-
Journal article (peer-reviewed)abstract
- Multiple ecosystem services (ES) can respond similarly to social and ecological factors to form bundles. Identifying key social-ecological variables and understanding how they co-vary to produce these consistent sets of ES may ultimately allow the prediction and modelling of ES bundles, and thus, help us understand critical synergies and trade-offs across landscapes. Such an understanding is essential for informing better management of multi-functional landscapes and minimising costly trade-offs. However, the relative importance of different social and biophysiCal drivers of ES bundles in different types of social-ecological systems remains unclear. As such, a bottom-up understanding of the determinants of ES bundles is a critical research gap in ES and sustainability science. Here, we evaluate the current methods used in ES bundle science and synthesize these into four steps that capture the plurality of methods used to examine predictors of ES bundles. We then apply these four steps to a cross-study comparison (North and South French Alps) of relationships between social-ecological variables and ES bundles, as it is widely advocated that cross-study comparisons are necessary for achieving a general understanding of predictors of ES associations. We use the results of this case study to assess the strengths and limitations of current approaches for understanding distributions of ES bundles. We conclude that inconsistency of spatial scale remains the primary barrier for understanding and predicting ES bundles. We suggest a hypothesis-driven approach is required to predict relationships between ES, and we outline the research required for such an understanding to emerge.
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| 42. |
- Angelopoulos, V., et al.
(author)
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First Results from the THEMIS Mission
- 2008
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In: Space Science Reviews. - : Springer Science and Business Media LLC. - 0038-6308 .- 1572-9672. ; 141:1-4, s. 453-476
-
Research review (peer-reviewed)abstract
- THEMIS was launched on February 17, 2007 to determine the trigger and large-scale evolution of substorms. During the first seven months of the mission the five satellites coasted near their injection orbit to avoid differential precession in anticipation of orbit placement, which started in September 2007 and led to a commencement of the baseline mission in December 2007. During the coast phase the probes were put into a string-of-pearls configuration at 100 s of km to 2 R-E along-track separations, which provided a unique view of the magnetosphere and enabled an unprecedented dataset in anticipation of the first tail season. In this paper we describe the first THEMIS substorm observations, captured during instrument commissioning on March 23, 2007. THEMIS measured the rapid expansion of the plasma sheet at a speed that is commensurate with the simultaneous expansion of the auroras on the ground. These are the first unequivocal observations of the rapid westward expansion process in space and on the ground. Aided by the remote sensing technique at energetic particle boundaries and combined with ancillary measurements and MHD simulations, they allow determination and mapping of space currents. These measurements show the power of the THEMIS instrumentation in the tail and the radiation belts. We also present THEMIS Flux Transfer Events (FTE) observations at the magnetopause, which demonstrate the importance of multi-point observations there and the quality of the THEMIS instrumentation in that region of space.
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| 43. |
- Clifford, DB, et al.
(author)
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Rituximab-associated progressive multifocal leukoencephalopathy in rheumatoid arthritis
- 2011
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In: Archives of neurology. - : American Medical Association (AMA). - 1538-3687 .- 0003-9942. ; 68:9, s. 1156-1164
-
Journal article (peer-reviewed)abstract
- To describe the development of progressive multifocal leukoencephalopathy (PML) in patients with rheumatoid arthritis (RA) treated with rituximab.DesignCase study.SettingClinical care for patients with rheumatologic diseases. Most were referred to academic centers for care after diagnosis (Washington University, St Louis, Missouri; Karolinska Insitute, Stockholm, Sweden; and Royal Melbourne Hospital, Melbourne, Australia) while one was cared for in a neurology practice in Dallas, Texas, with consultation by an academic neurovirologist from the University of Colorado in Denver.PatientsFour patients developing PML in the setting of rituximab therapy for RA.InterventionRituximab therapy.Main Outcome MeasuresClinical and pathological observations.ResultsFour patients from an estimated population of 129 000 exposed to rituximab therapy for RA are reported in whom PML developed after administration of this drug. All were women older than 50 years, commonly with Sjögren syndrome and a history of treatment for joint disease ranging from 3 to 14 years. One case had no prior biologic and minimal immunosuppressive therapy. Progressive multifocal leukoencephalopathy presented as a progressive neurological disorder, with diagnosis confirmed by detection of JC virus DNA in the cerebrospinal fluid or brain biopsy specimen. Two patients died in less than 1 year from PML diagnosis, while 2 remain alive after treatment withdrawal. Magnetic resonance scans and tissue evaluation confirmed the frequent development of inflammatory PML during the course of the disease.ConclusionThese cases suggest an increased risk, about 1 case per 25 000 individuals, of PML in patients with RA being treated with rituximab. Inflammatory PML may occur in this setting even while CD20 counts remain low.
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| 44. |
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| 45. |
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| 46. |
- Germany, G A, et al.
(author)
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Remote determination of auroral energy characteristics during substorm activity
- 1997
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In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 24, s. 995-998
-
Journal article (peer-reviewed)abstract
- Ultraviolet auroral images from the Ultraviolet Imager (UVI) onboard the POLAR satellite can be used as quantitative remote diagnostics of the auroral regions, yielding estimates of incident energy characteristics, compositional changes, and other higher order data products. Here incident energy estimates derived from UVI are compared with in situ measurements of the same parameters from an overflight by the DMSP F12 satellite coincident with the UVI image times during substorm activity occurring on May 19, 1996. This event was simultaneously observed by WIND, GEOTAIL, INTERBALL, DMSP and NOAA spacecraft as well as by POLAR.
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| 47. |
- Gorini, Giacomo, et al.
(author)
-
Engagement of monocytes, NK cells, and CD4(+) Th1 cells by ALVAC-SIV vaccination results in a decreased risk of SIVmac251 vaginal acquisition
- 2020
-
In: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 16:3
-
Journal article (peer-reviewed)abstract
- The ALVAC-HIV/gp120/alum regimen tested in 8,197 human volunteers (61.4% males, 38.6% females) in the RV144 trial decreased the risk of HIV infection similarly in both sexes. The ALVAC-SIV/gp120/alum vaccine also reduced the risk of intrarectal SIVmac251 acquisition in both female and male vaccinated macaques at an average of 44% per exposure. In the current work, we tested whether this vaccine modality could also reduce the risk of intravaginal SIVmac251 exposure. In order to detect correlates of risk, we administered the virus by the intravaginal route and tested another vaccine regimen based on the vaccinia derivative poxvirus NYVAC in parallel. We demonstrate here that the ALVAC-SIV/gp120/alum regimen decreases the risk of vaginal SIVmac251 acquisition (50% vaccine efficacy) and, importantly, we confirmed that subsets of monocytes and CD4(+) T cells are correlates of risk of acquisition. In addition, we uncovered cytotoxic vaginal NKG2A(+) cells and gut-homing alpha(4)beta(7) positive plasmablasts as novel correlates of risk of intravaginal virus acquisition. In contrast, NYVAC-SIV vaccination induced high levels of activated T cells and did not protect against SIVmac251 acquisition. We examined the contrasting immune responses to better understand the correlate of protection and found that the unique ability of ALVAC-SIV to activate early interferon responses and the inflammasome during priming differentiates the two poxvirus vectors. This work demonstrates the reproducibility of the efficacy observed in the ALVAC-based regimen and defines novel correlates of risk in the rigorous SIVmac251 macaque model, establishing a benchmark for future improvement of this vaccine approach. The recombinant Canarypox ALVAC-HIV/gp120/alum vaccine regimen was the first to significantly decrease the risk of HIV acquisition in humans, with equal effectiveness in both males and females. Similarly, an equivalent SIV-based ALVAC vaccine regimen decreased the risk of virus acquisition in Indian rhesus macaques of both sexes following intrarectal exposure to low doses of SIVmac251. Here, we demonstrate that the ALVAC-SIV/gp120/alum vaccine is also efficacious in female Chinese rhesus macaques following intravaginal exposure to low doses of SIVmac251 and we confirm that CD14(+) classical monocytes are a strong correlate of decreased risk of virus acquisition. Furthermore, we demonstrate that the frequency of CD14(+) cells and/or their gene expression correlates with blood Type 1 CD4(+) T helper cells, alpha(4)beta(+)(7) plasmablasts, and vaginal cytocidal NKG2A(+) cells. To better understand the correlate of protection, we contrasted the ALVAC-SIV vaccine with a NYVAC-based SIV/gp120 regimen that used the identical immunogen. We found that NYVAC-SIV induced higher immune activation via CD4(+)Ki67(+)CD38(+) and CD4(+)Ki67(+)alpha(4)beta(+)(7) T cells, higher SIV envelope-specific IFN-gamma producing cells, equivalent ADCC, and did not decrease the risk of SIVmac251 acquisition. Using the systems biology approach, we demonstrate that specific expression profiles of plasmablasts, NKG2A(+) cells, and monocytes elicited by the ALVAC-based regimen correlated with decreased risk of virus acquisition.
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| 48. |
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| 49. |
- Lassen, Kristoffer, et al.
(author)
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Guidelines for perioperative care for pancreaticoduodenectomy : enhanced recovery after surgery (ERAS®) society recommendations
- 2013
-
In: World Journal of Surgery. - : Springer. - 0364-2313 .- 1432-2323. ; 37:2, s. 240-258
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Protocols for enhanced recovery provide comprehensive and evidence-based guidelines for best perioperative care. Protocol implementation may reduce complication rates and enhance functional recovery and, as a result of this, also reduce length-of-stay in hospital. There is no comprehensive framework available for pancreaticoduodenectomy.METHODS: An international working group constructed within the Enhanced Recovery After Surgery (ERAS(®)) Society constructed a comprehensive and evidence-based framework for best perioperative care for pancreaticoduodenectomy patients. Data were retrieved from standard databases and personal archives. Evidence and recommendations were classified according to the GRADE system and reached through consensus in the group. The quality of evidence was rated "high", "moderate", "low" or "very low". Recommendations were graded as "strong" or "weak".RESULTS: Comprehensive guidelines are presented. Available evidence is summarised and recommendations given for 27 care items. The quality of evidence varies substantially and further research is needed for many issues to improve the strength of evidence and grade of recommendations.CONCLUSIONS: The present evidence-based guidelines provide the necessary platform upon which to base a unified protocol for perioperative care for pancreaticoduodenectomy. A unified protocol allows for comparison between centres and across national borders. It facilitates multi-institutional prospective cohort registries and adequately powered randomised trials.
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| 50. |
- Lassen, Kristoffer, et al.
(author)
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Guidelines for perioperative care for pancreaticoduodenectomy : enhanced recovery after surgery (ERAS®) society recommendations
- 2012
-
In: Clinical Nutrition. - Amsterdam, Netherlands : Elsevier. - 0261-5614 .- 1532-1983. ; 31:6, s. 817-830
-
Journal article (peer-reviewed)abstract
- Background & Aims: Protocols for enhanced recovery provide comprehensive and evidence-based guidelines for best perioperative care. Protocol implementation may reduce complication rates and enhance functional recovery and, as a result of this, also reduce length-of-stay in hospital. There is no comprehensive framework available for pancreaticoduodenectomy.Methods: An international working group constructed within the Enhanced Recovery After Surgery (ERAS®) Society constructed a comprehensive and evidence-based framework for best perioperative care for pancreaticoduodenectomy patients. Data were retrieved from standard databases and personal archives. Evidence and recommendations were classified according to the GRADE system and reached through consensus in the group. The quality of evidence was rated "high", "moderate", "low" or "very low". Recommendations were graded as "strong" or "weak".Results: Comprehensive guidelines are presented. Available evidence is summarised and recommendations given for 27 care items. The quality of evidence varies substantially and further research is needed for many issues to improve the strength of evidence and grade of recommendations.Conclusions: The present evidence-based guidelines provide the necessary platform upon which to base a unified protocol for perioperative care for pancreaticoduodenectomy. A unified protocol allows for comparison between centres and across national borders. It facilitates multi-institutional prospective cohort registries and adequately powered randomised trials.
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