| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Bernal, Ximena E., et al.
(författare)
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Empowering Latina scientists
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
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| 4. |
- dos Santos, Rodrigo Zeni, et al.
(författare)
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A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed
- 2021
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satelliteDNAs (satDNAs). These sequences are highly dynamic and tend to begenus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, similar to 140-78Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidiumgomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could b e found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
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| 5. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 6. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 7. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 8. |
- Abbasi, Rasha, et al.
(författare)
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IceCube search for neutrinos from GRB 221009A
- 2023
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Ingår i: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl.
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Konferensbidrag (refereegranskat)abstract
- GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
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| 9. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 10. |
- Akiyama, Kazunori, et al.
(författare)
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First Sagittarius A* Event Horizon Telescope Results. II. EHT and Multiwavelength Observations, Data Processing, and Calibration
- 2022
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 930:2
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Tidskriftsartikel (refereegranskat)abstract
- We present Event Horizon Telescope (EHT) 1.3 mm measurements of the radio source located at the position of the supermassive black hole Sagittarius A* (Sgr A*), collected during the 2017 April 5-11 campaign. The observations were carried out with eight facilities at six locations across the globe. Novel calibration methods are employed to account for Sgr A*'s flux variability. The majority of the 1.3 mm emission arises from horizon scales, where intrinsic structural source variability is detected on timescales of minutes to hours. The effects of interstellar scattering on the image and its variability are found to be subdominant to intrinsic source structure. The calibrated visibility amplitudes, particularly the locations of the visibility minima, are broadly consistent with a blurred ring with a diameter of similar to 50 mu as, as determined in later works in this series. Contemporaneous multiwavelength monitoring of Sgr A* was performed at 22, 43, and 86 GHz and at near-infrared and X-ray wavelengths. Several X-ray flares from Sgr A* are detected by Chandra, one at low significance jointly with Swift on 2017 April 7 and the other at higher significance jointly with NuSTAR on 2017 April 11. The brighter April 11 flare is not observed simultaneously by the EHT but is followed by a significant increase in millimeter flux variability immediately after the X-ray outburst, indicating a likely connection in the emission physics near the event horizon. We compare Sgr A*'s broadband flux during the EHT campaign to its historical spectral energy distribution and find that both the quiescent emission and flare emission are consistent with its long-term behavior.
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| 11. |
- Alves, Gustavo R., et al.
(författare)
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International Cooperation for Remote Laboratory Use
- 2018
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Ingår i: Contributions to Higher Engineering Education. - Singapore : Springer. - 9789811089176 ; , s. 1-31
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Bokkapitel (refereegranskat)abstract
- Experimenting is fundamental to the training process of all scientists and engineers. While experiments have been traditionally done inside laboratories, the emergence of Information and Communication Technologies added two alternatives accessible anytime, anywhere. These two alternatives are known as virtual and remote laboratories and are sometimes indistinguishably referred as online laboratories. Similarly to other instructional technologies, virtual and remote laboratories require some effort from teachers in integrating them into curricula, taking into consideration several factors that affect their adoption (i.e., cost) and their educational effectiveness (i.e., benefit). This chapter analyzes these two dimensions and sustains the case where only through international cooperation it is possible to serve the large number of teachers and students involved in engineering education. It presents an example in the area of electrical and electronics engineering, based on a remote laboratory named Virtual Instruments System in Reality, and it then describes how a number of European and Latin American institutions have been cooperating under the scope of an Erasmus+ project, for spreading its use in Brazil and Argentina.
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| 12. |
- Axelsson, Emil, et al.
(författare)
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Dynamic Scene Graph: Enabling Scaling, Positioning, and Navigation in the Universe
- 2017
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Ingår i: Computer graphics forum (Print). - : WILEY. - 0167-7055 .- 1467-8659. ; 36:3, s. 459-468
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we address the challenge of seamlessly visualizing astronomical data exhibiting huge scale differences in distance, size, and resolution. One of the difficulties is accurate, fast, and dynamic positioning and navigation to enable scaling over orders of magnitude, far beyond the precision of floating point arithmetic. To this end we propose a method that utilizes a dynamically assigned frame of reference to provide the highest possible numerical precision for all salient objects in a scene graph. This makes it possible to smoothly navigate and interactively render, for example, surface structures on Mars and the Milky Way simultaneously. Our work is based on an analysis of tracking and quantification of the propagation of precision errors through the computer graphics pipeline using interval arithmetic. Furthermore, we identify sources of precision degradation, leading to incorrect object positions in screen-space and z-fighting. Our proposed method operates without near and far planes while maintaining high depth precision through the use of floating point depth buffers. By providing interoperability with order-independent transparency algorithms, direct volume rendering, and stereoscopy, our approach is well suited for scientific visualization. We provide the mathematical background, a thorough description of the method, and a reference implementation.
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| 13. |
- Bock, Alexander, 1985-, et al.
(författare)
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OpenSpace : A System for Astrographics
- 2020
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Ingår i: IEEE Transactions on Visualization and Computer Graphics. - : Institute of Electrical and Electronics Engineers (IEEE). - 1077-2626 .- 1941-0506. ; 26:1, s. 633-642
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Tidskriftsartikel (refereegranskat)abstract
- Human knowledge about the cosmos is rapidly increasing as instruments and simulations are generating new data supporting the formation of theory and understanding of the vastness and complexity of the universe. OpenSpace is a software system that takes on the mission of providing an integrated view of all these sources of data and supports interactive exploration of the known universe from the millimeter scale showing instruments on spacecrafts to billions of light years when visualizing the early universe. The ambition is to support research in astronomy and space exploration, science communication at museums and in planetariums as well as bringing exploratory astrographics to the class room. There is a multitude of challenges that need to be met in reaching this goal such as the data variety, multiple spatio-temporal scales, collaboration capabilities, etc. Furthermore, the system has to be flexible and modular to enable rapid prototyping and inclusion of new research results or space mission data and thereby shorten the time from discovery to dissemination. To support the different use cases the system has to be hardware agnostic and support a range of platforms and interaction paradigms. In this paper we describe how OpenSpace meets these challenges in an open source effort that is paving the path for the next generation of interactive astrographics.
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| 14. |
- Bock, Alexander, 1985-, et al.
(författare)
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TopoAngler: Interactive Topology-Based Extraction of Fishes
- 2018
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Ingår i: IEEE Transactions on Visualization and Computer Graphics. - : IEEE. - 1077-2626 .- 1941-0506. ; 24:1, s. 812-821
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Tidskriftsartikel (refereegranskat)abstract
- We present TopoAngler, a visualization framework that enables an interactive user-guided segmentation of fishes contained in a micro-CT scan. The inherent noise in the CT scan coupled with the often disconnected (and sometimes broken) skeletal structure of fishes makes an automatic segmentation of the volume impractical. To overcome this, our framework combines techniques from computational topology with an interactive visual interface, enabling the human-in-the-Ioop to effectively extract fishes from the volume. In the first step, the join tree of the input is used to create a hierarchical segmentation of the volume. Through the use of linked views, the visual interface then allows users to interactively explore this hierarchy, and gather parts of individual fishes into a coherent sub-volume, thus reconstructing entire fishes. Our framework was primarily developed for its application to CT scans of fishes, generated as part of the ScanAllFish project, through close collaboration with their lead scientist. However, we expect it to also be applicable in other biological applications where a single dataset contains multiple specimen; a common routine that is now widely followed in laboratories to increase throughput of expensive CT scanners.
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| 15. |
- Costa, Jonathas, et al.
(författare)
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Interactive Visualization of Atmospheric Effects for Celestial Bodies
- 2021
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Ingår i: IEEE Transactions on Visualization and Computer Graphics. - : IEEE COMPUTER SOC. - 1077-2626 .- 1941-0506. ; 27:2, s. 785-795
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Tidskriftsartikel (refereegranskat)abstract
- We present an atmospheric model tailored for the interactive visualization of planetary surfaces. As the exploration of the solar system is progressing with increasingly accurate missions and instruments, the faithful visualization of planetary environments is gaining increasing interest in space research, mission planning, and science communication and education. Atmospheric effects are crucial in data analysis and to provide contextual information for planetary data. Our model correctly accounts for the non-linear path of the light inside the atmosphere (in Earths case), the light absorption effects by molecules and dust particles, such as the ozone layer and the Martian dust, and a wavelength-dependent phase function for Mie scattering. The mode focuses on interactivity, versatility, and customization, and a comprehensive set of interactive controls make it possible to adapt its appearance dynamically. We demonstrate our results using Earth and Mars as examples. However, it can be readily adapted for the exploration of other atmospheres found on, for example, of exoplanets. For Earths atmosphere, we visually compare our results with pictures taken from the International Space Station and against the CIE clear sky model. The Martian atmosphere is reproduced based on available scientific data, feedback from domain experts, and is compared to images taken by the Curiosity rover. The work presented here has been implemented in the OpenSpace system, which enables interactive parameter setting and real-time feedback visualization targeting presentations in a wide range of environments, from immersive dome theaters to virtual reality headsets.
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| 16. |
- de Oliveira e Silva, Jose Claudio, et al.
(författare)
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EMC considerations for JLRL direct lightning current measurement
- 2022
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Ingår i: 2022 36Th International Conference On Lightning Protection (ICLP 2022). - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 26-31
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Konferensbidrag (refereegranskat)abstract
- In this paper the electromagnetic compatibility (EMC) considerations made to the direct lightning current measuring system that is part of the Johannesburg Lightning Research Laboratory (JLRL) are presented. The output voltages from two series connected shunts and the sending of their analog signals downward a tower to the measuring system, makes this measuring setup particularly critical regarding immunity against the strong effects of the lightning current.
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| 17. |
- Ellqvist, Tommy, 1980-, et al.
(författare)
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Using Mediation to Achieve Provenance Interoperability
- 2008
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Ingår i: 2009 World Conference on Services - I. - : IEEE. - 9780769535357 - 9781424433803 ; , s. 398-399
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Konferensbidrag (refereegranskat)abstract
- Provenance is essential in scientific experiments. It contains information that is key to preserving the data and to determine its quality and uthorship. In complex experiments and analyses, where multiple tools are used to derive data products, provenance captured by these tools must be combined in order to determine the complete lineage of the derived products. We propose a mediator-based architecture to integrate provenance information from multiple sources, which contains two key components: a global mediated schema that is general and capable of representing provenance information represented in different models; and an expressive query interface that supports complex queries over provenance information spread over multiple different sources. We also present a case study where we show how this model was applied to integrate provenance from three provenance-enabled systems.
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| 18. |
- Ellqvist, Tommy, 1980-, et al.
(författare)
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Using Provenance to Support Real-Time Collaborative Design of Workflows
- 2008
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Ingår i: Second International Provenance and Annotation Workshop,2008. - New York : Springer. - 9783540899648 ; , s. 266-
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Konferensbidrag (refereegranskat)abstract
- Because designing workflows is a notoriously difficult task, it often requires multiple users to collaborate. In such scenarios, sharing workflow evolution provenance in a timely manner is critical. We present an environment where collaborating users can see each other’s changes in real-time. The synchronization of workflow evolution provenance is automatic, immediate, and unobtrusive, allowing users to see collaborators’ changes as they are made. This enables a richer and fuller method of collaboration. We present the interface and algorithm for the synchronization and discuss common scenarios where this mechanism has been utilized.
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| 19. |
- Etiene, Tiago, et al.
(författare)
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Verifying Volume Rendering Using Discretization Error Analysis
- 2014
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Ingår i: IEEE Transactions on Visualization and Computer Graphics. - : Institute of Electrical and Electronics Engineers (IEEE). - 1077-2626 .- 1941-0506. ; 20:1, s. 140-154
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Tidskriftsartikel (refereegranskat)abstract
- We propose an approach for verification of volume rendering correctness based on an analysis of the volume rendering integral, the basis of most DVR algorithms. With respect to the most common discretization of this continuous model (Riemann summation), we make assumptions about the impact of parameter changes on the rendered results and derive convergence curves describing the expected behavior. Specifically, we progressively refine the number of samples along the ray, the grid size, and the pixel size, and evaluate how the errors observed during refinement compare against the expected approximation errors. We derive the theoretical foundations of our verification approach, explain how to realize it in practice, and discuss its limitations. We also report the errors identified by our approach when applied to two publicly available volume rendering packages.
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| 20. |
- Ganeva, Dessislava, et al.
(författare)
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In-situ start and end of growing season dates of major European crop types from France and Bulgaria at a field level
- 2023
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Ingår i: Data in Brief. - 2352-3409. ; 51
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Tidskriftsartikel (refereegranskat)abstract
- Crop phenology data offer crucial information for crop yield estimation, agricultural management, and assessment of agroecosystems. Such information becomes more important in the context of increasing year-to-year climatic variability. The dataset provides in-situ crop phenology data (first leaves emergence and harvest date) of major European crops (wheat, corn, sunflower, rapeseed) from seventeen field study sites in Bulgaria and two in France. Additional information such as the sowing date, area of each site, coordinates, method and equipment used for phenophase data estimation, and photos of the France sites are also provided. The georeferenced ground-truth dataset provides a solid base for a better understanding of crop growth and can be used to validate the retrieval of phenological stages from remote sensing data.
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| 21. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 22. |
- Kooistra, Lammert, et al.
(författare)
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Reviews and syntheses : Remotely sensed optical time series for monitoring vegetation productivity
- 2024
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Ingår i: Biogeosciences. - 1726-4170. ; 21:2, s. 473-511
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Forskningsöversikt (refereegranskat)abstract
- Vegetation productivity is a critical indicator of global ecosystem health and is impacted by human activities and climate change. A wide range of optical sensing platforms, from ground-based to airborne and satellite, provide spatially continuous information on terrestrial vegetation status and functioning. As optical Earth observation (EO) data are usually routinely acquired, vegetation can be monitored repeatedly over time, reflecting seasonal vegetation patterns and trends in vegetation productivity metrics. Such metrics include gross primary productivity, net primary productivity, biomass, or yield. To summarize current knowledge, in this paper we systematically reviewed time series (TS) literature for assessing state-of-the-art vegetation productivity monitoring approaches for different ecosystems based on optical remote sensing (RS) data. As the integration of solar-induced fluorescence (SIF) data in vegetation productivity processing chains has emerged as a promising source, we also include this relatively recent sensor modality. We define three methodological categories to derive productivity metrics from remotely sensed TS of vegetation indices or quantitative traits: (i) trend analysis and anomaly detection, (ii) land surface phenology, and (iii) integration and assimilation of TS-derived metrics into statistical and process-based dynamic vegetation models (DVMs). Although the majority of used TS data streams originate from data acquired from satellite platforms, TS data from aircraft and unoccupied aerial vehicles have found their way into productivity monitoring studies. To facilitate processing, we provide a list of common toolboxes for inferring productivity metrics and information from TS data. We further discuss validation strategies of the RS data derived productivity metrics: (1) using in situ measured data, such as yield; (2) sensor networks of distinct sensors, including spectroradiometers, flux towers, or phenological cameras; and (3) inter-comparison of different productivity metrics. Finally, we address current challenges and propose a conceptual framework for productivity metrics derivation, including fully integrated DVMs and radiative transfer models here labelled as "Digital Twin". This novel framework meets the requirements of multiple ecosystems and enables both an improved understanding of vegetation temporal dynamics in response to climate and environmental drivers and enhances the accuracy of vegetation productivity monitoring.
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| 23. |
- Lima, Natercia, et al.
(författare)
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Do students really understand the difference between simulation and remote labs?
- 2017
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Ingår i: ACM International Conference Proceeding Series. - New York, NY, USA : Association for Computing Machinery. - 9781450353861
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Konferensbidrag (refereegranskat)abstract
- Laboratory experiments play a crucial role in engineering education as they strongly contribute to the development of important skills for the professional practice. This paper addresses a students' understanding gap between simulations and remote labs. These two resources (and namely the remote laboratory VISIR - Virtual Instrument Systems in Reality) have been commonly used on several didactical implementations, along with other didactical resources in different Engineering degrees at the Federal University of Santa Catarina and Polytechnic of Porto School of Engineering. This work, developed in the scope of the VISIR+ Project, intends to evaluate students' perceptions considering simulation and remote lab results. Quantitative and qualitative data were analyzed to better understand how deeply students realize the differences between these resources and their type of data. Preliminary results indicate that a considerable number of student's don't have a clear idea of these differences, even though sometimes they know their definition. Furthermore, this gap does not seem to differ much with the context (country, course, academic year, course content), students' final grades, teacher approach or implemented tasks. © 2017 Association for Computing Machinery.
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| 24. |
- Lin, Jasmine J., et al.
(författare)
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Motion Analytics of Trapezius Muscle Activity in an 18-Year-Old Female with Extended Upper Brachial Plexus Birth Palsy
- 2021
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Ingår i: Journal of Brachial Plexus and Peripheral Nerve Injury. - : Georg Thieme Verlag KG. - 1749-7221. ; 16:1, s. 51-55
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Tidskriftsartikel (refereegranskat)abstract
- Background: The trapezius muscle is often utilized as a muscle or nerve donor for repairing shoulder function in those with brachial plexus birth palsy (BPBP). To evaluate the native role of the trapezius in the affected limb, we demonstrate use of the Motion Browser, a novel visual analytics system to assess an adolescent with BPBP.Method: An 18-year-old female with extended upper trunk (C5-6-7) BPBP underwent bilateral upper extremity three-dimensional motion analysis with Motion Browser. Surface electromyography (EMG) from eight muscles in each limb which was recorded during six upper extremity movements, distinguishing between upper trapezius (UT) and lower trapezius (LT). The Motion Browser calculated active range of motion (AROM), compiled the EMG data into measures of muscle activity, and displayed the results in charts.Results: All movements, excluding shoulder abduction, had similar AROM in affected and unaffected limbs. In the unaffected limb, LT was more active in proximal movements of shoulder abduction, and shoulder external and internal rotations. In the affected limb, LT was more active in distal movements of forearm pronation and supination; UT was more active in shoulder abduction.Conclusion: In this female with BPBP, Motion Browser demonstrated that the native LT in the affected limb contributed to distal movements. Her results suggest that sacrificing her trapezius as a muscle or nerve donor may affect her distal functionality. Clinicians should exercise caution when considering nerve transfers in children with BPBP and consider individualized assessment of functionality before pursuing surgery.
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| 25. |
- Maasri, Alain, et al.
(författare)
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A global agenda for advancing freshwater biodiversity research
- 2022
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 25:2, s. 255-263
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Tidskriftsartikel (refereegranskat)abstract
- Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.
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| 26. |
- Massad, Eduardo, et al.
(författare)
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Risk of symptomatic dengue for foreign visitors to the 2014 FIFA World Cup in Brazil
- 2014
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Ingår i: Memórias do instituto Oswaldo Cruz. - : FapUNIFESP (SciELO). - 0074-0276 .- 1678-8060. ; 109:3, s. 394-397
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Tidskriftsartikel (refereegranskat)abstract
- Brazil will host the FIFA World Cup™, the biggest single-event competition in the world, from June 12-July 13 2014 in 12 cities. This event will draw an estimated 600,000 international visitors. Brazil is endemic for dengue. Hence, attendees of the 2014 event are theoretically at risk for dengue. We calculated the risk of dengue acquisition to non-immune international travellers to Brazil, depending on the football match schedules, considering locations and dates of such matches for June and July 2014. We estimated the average per-capita risk and expected number of dengue cases for each host-city and each game schedule chosen based on reported dengue cases to the Brazilian Ministry of Health for the period between 2010-2013. On the average, the expected number of cases among the 600,000 foreigner tourists during the World Cup is 33, varying from 3-59. Such risk estimates will not only benefit individual travellers for adequate pre-travel preparations, but also provide valuable information for public health professionals and policy makers worldwide. Furthermore, estimates of dengue cases in international travellers during the World Cup can help to anticipate the theoretical risk for exportation of dengue into currently non-infected areas.
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| 27. |
- Mediavilla, Tomás, et al.
(författare)
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Learning-related contraction of gray matter in rodent sensorimotor cortex is associated with adaptive myelination.
- 2022
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Ingår i: eLife. - : eLife Sciences Publications. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- From observations in rodents, it has been suggested that the cellular basis of learning-dependent changes, detected using structural MRI, may be increased dendritic spine density, alterations in astrocyte volume, and adaptations within intracortical myelin. Myelin plasticity is crucial for neurological function, and active myelination is required for learning and memory. However, the dynamics of myelin plasticity and how it relates to morphometric-based measurements of structural plasticity remains unknown. We used a motor skill learning paradigm in male mice to evaluate experience-dependent brain plasticity by voxel-based morphometry (VBM) in longitudinal MRI, combined with a cross-sectional immunohistochemical investigation. Whole-brain VBM revealed nonlinear decreases in gray matter volume (GMV) juxtaposed to nonlinear increases in white matter volume (WMV) within GM that were best modeled by an asymptotic time course. Using an atlas-based cortical mask, we found nonlinear changes with learning in primary and secondary motor areas and in somatosensory cortex. Analysis of cross-sectional myelin immunoreactivity in forelimb somatosensory cortex confirmed an increase in myelin immunoreactivity followed by a return towards baseline levels. Further investigations using quantitative confocal microscopy confirmed these changes specifically to the length density of myelinated axons. The absence of significant histological changes in cortical thickness suggests that nonlinear morphometric changes are likely due to changes in intracortical myelin for which morphometric WMV in somatosensory cortex significantly correlated with myelin immunoreactivity. Together, these observations indicate a nonlinear increase of intracortical myelin during learning and support the hypothesis that myelin is a component of structural changes observed by VBM during learning.
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| 28. |
- Metra, Marco, et al.
(författare)
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y Effects of Serelaxin in Patients with Acute Heart Failure
- 2019
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Ingår i: New England Journal of Medicine. - : MASSACHUSETTS MEDICAL SOC. - 0028-4793 .- 1533-4406. ; 381:8, s. 716-726
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundSerelaxin is a recombinant form of human relaxin-2, a vasodilator hormone that contributes to cardiovascular and renal adaptations during pregnancy. Previous studies have suggested that treatment with serelaxin may result in relief of symptoms and in better outcomes in patients with acute heart failure. MethodsIn this multicenter, double-blind, placebo-controlled, event-driven trial, we enrolled patients who were hospitalized for acute heart failure and had dyspnea, vascular congestion on chest radiography, increased plasma concentrations of natriuretic peptides, mild-to-moderate renal insufficiency, and a systolic blood pressure of at least 125 mm Hg, and we randomly assigned them within 16 hours after presentation to receive either a 48-hour intravenous infusion of serelaxin (30 mu g per kilogram of body weight per day) or placebo, in addition to standard care. The two primary end points were death from cardiovascular causes at 180 days and worsening heart failure at 5 days.ResultsA total of 6545 patients were included in the intention-to-treat analysis. At day 180, death from cardiovascular causes had occurred in 285 of the 3274 patients (8.7%) in the serelaxin group and in 290 of the 3271 patients (8.9%) in the placebo group (hazard ratio, 0.98; 95% confidence interval [CI], 0.83 to 1.15; P=0.77). At day 5, worsening heart failure had occurred in 227 patients (6.9%) in the serelaxin group and in 252 (7.7%) in the placebo group (hazard ratio, 0.89; 95% CI, 0.75 to 1.07; P=0.19). There were no significant differences between the groups in the incidence of death from any cause at 180 days, the incidence of death from cardiovascular causes or rehospitalization for heart failure or renal failure at 180 days, or the length of the index hospital stay. The incidence of adverse events was similar in the two groups.ConclusionsIn this trial involving patients who were hospitalized for acute heart failure, an infusion of serelaxin did not result in a lower incidence of death from cardiovascular causes at 180 days or worsening heart failure at 5 days than placebo. (Funded by Novartis Pharma; RELAX-AHF-2 ClinicalTrials.gov number, NCT01870778.) In a randomized trial, 6545 patients with acute heart failure were assigned to either serelaxin or placebo in addition to standard care. There were no significant differences between the two groups in the incidence of death from cardiovascular causes at 180 days or worsening heart failure at 5 days.
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| 29. |
- Ponticelli, Francesco, et al.
(författare)
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Safety and efficacy of coronary sinus narrowing in chronic refractory angina: Insights from the RESOURCE study.
- 2021
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Ingår i: International journal of cardiology. - : Elsevier BV. - 1874-1754 .- 0167-5273. ; 337, s. 29-37
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Tidskriftsartikel (refereegranskat)abstract
- Refractory angina (RA) is considered the end-stage of coronary artery disease, and often has no interventional treatment options. Coronary sinus Reducer (CSR) is a recent addition to the therapeutic arsenal, but its efficacy has only been evaluated on small populations. The RESOURCE registry provides further insights into this therapy.The RESOURCE is an observational, retrospective registry that includes 658 patients with RA from 20 centers in Europe, United Kingdom and Israel. Prespecified endpoints were the amelioration of anginal symptoms evaluated with the Canadian Cardiovascular Society (CCS) score, the rates of procedural success and complications, and MACEs as composite of all-cause mortality, acute coronary syndromes, and stroke.At a median follow-up of 502days (IQR 225-1091) after CSR implantation, 39.7% of patients improved by ≥2 CCS classes (primary endpoint), and 76% by ≥1 class. Procedural success was achieved in 96.7% of attempts, with 3% of procedures aborted mostly for unsuitable coronary sinus anatomy. Any complication occurred in 5.7% of procedures, but never required bailout surgery nor resulted in intra- or periprocedural death or myocardial infarction. One patient developed periprocedural stroke after inadvertent carotid artery puncture. At the last available follow-up, overall mortality and MACE were 10.4% and 14.6% respectively. At one, three and five years, mortality rate at Kaplan-Meier analysis was 4%, 13.7%, and 23.4% respectively.CSR implantation is safe and reduces angina in patients with refractory angina.
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| 30. |
- Saba, Marcelo, et al.
(författare)
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The study of lightning strikes to common buildings in Brazil
- 2016
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Konferensbidrag (refereegranskat)abstract
- Most of what is known about the electric current of downward flashes and striking distance of lightning protection systems come from information gathered on tall towers. There are no observational data of lightning attachment to common structures or buildings (under 60 m) that are present in almost every city. In order to study lightning strikes to common buildings, several instruments were installed in and around two identical buildings located in São Paulo city, Brazil. This paper describes the setup of electric field sensors, current transformers, X-ray sensors, high-speed video and standard video cameras. Some of the data already obtained in its first two months of operation are also shown.
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| 31. |
- Serrano-Freitas, Erica A., et al.
(författare)
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Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes
- 2020
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Ingår i: Molecular Genetics and Genomics. - : SPRINGER HEIDELBERG. - 1617-4615 .- 1617-4623. ; 295:1, s. 195-207
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Tidskriftsartikel (refereegranskat)abstract
- The origin of supernumerary (B) chromosomes is clearly conditioned by their ancestry from the standard (A) chromosomes. Sequence similarity between A and B chromosomes is thus crucial to determine B chromosome origin. For this purpose, we compare here the DNA sequences from A and B chromosomes in the characid fish Characidium gomesi using two main approaches. First, we found 59 satellite DNA (satDNA) families constituting the satellitome of this species and performed FISH analysis for 18 of them. This showed the presence of six satDNAs on the B chromosome: one shared with sex chromosomes and autosomes, two shared with sex chromosomes, one shared with autosomes and two being B-specific. This indicated that B chromosomes most likely arose from the sex chromosomes. Our second approach consisted of the analysis of five repetitive DNA families: 18S and 5S ribosomal DNA (rDNA), the H3 histone gene, U2 snDNA and the most abundant satDNA (CgoSat01-184) on DNA obtained from microdissected B chromosomes and from B-lacking genomes. PCR and sequence analysis of these repetitive sequences was successful for three of them (5S rDNA, H3 histone gene and CgoSat01-184), and sequence comparison revealed that DNA sequences obtained from the B chromosomes displayed higher identity with C. gomesi genomic DNA than with those obtained from other Characidium species. Taken together, our results support the intraspecific origin of B chromosomes in C. gomesi and point to sex chromosomes as B chromosome ancestors, which raises interesting prospects for future joint research on the genetic content of sex and B chromosomes in this species.
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| 32. |
- Silva Barbosa Linck, Glaucia Kelly, et al.
(författare)
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The Influence of Tactile Perception on Classification of Bone Tissue at Dental Implant Insertion
- 2016
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Ingår i: Clinical Implant Dentistry and Related Research. - : John Wiley & Sons. - 1523-0899 .- 1708-8208. ; 18:3, s. 601-608
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Tidskriftsartikel (refereegranskat)abstract
- Background: Various ways of using the Lekholm and Zarb (L&Z) classification have added to the lack of scientific evidence of the effectiveness of this clinical method in the evaluation of implant treatment. Purpose: The study aims to assess subjective jawbone classifications in patients referred for implant treatment, using L&Z classification with and without surgeon&s hand perception at implant insertion. The association between bone type classifications and quantitative parameters of primary implant stability was also assessed. Materials and Methods: One hundred thirty-five implants were inserted using conventional loading protocol. Three surgeons classified bone quality at implant sites using two methods: one based on periapical and panoramic images (modified L&Z) and one based on the same images associated with the surgeon&s tactile perception during drilling (original L&Z). Peak insertion torque and implant stability quotient (ISQ) were recorded. Results: The modified and original L&Z were strongly correlated (rho = 0.79; p < .001); Wilcoxon signed-rank test showed no significant difference in the distribution of bone type classification between pairs using the two methods (p = .538). Spearman correlation tested the association between primary stability parameters and bone type classifications (-0.34 to -0.57 [p < .001]). Conclusions: Tactile surgical perception has a minor influence on rating of subjective bone type for dental implant treatment using the L&Z classification.
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| 33. |
- Teixeira, Fabio, et al.
(författare)
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The Intuitive Human Interaction to Activate the Wetsuit Heating System
- 2016
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Ingår i: HCI International 2016. - Cham : Springer. - 9783319405421 - 9783319405414 ; , s. 546-551
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Konferensbidrag (refereegranskat)abstract
- The design process to create a wetsuit with heating system is shown in this paper. The wetsuit concept was inspired by characteristics of amphibians, so it was proposed a product that provides freedom of movement and adaptability into several environments. An intuitive interface without buttons or display based on human body language was created to activate the heating system of a wetsuit.
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| 34. |
- Van Den Berg, F. D., et al.
(författare)
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In-line Characterisation of Microstructure and Mechanical Properties in the Manufacturing of Steel Strip for the Purpose of Product Uniformity Control
- 2016
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Ingår i: DGZfP-Proceedings BB 158. - 9783940283788
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Konferensbidrag (refereegranskat)abstract
- The uniformity of the microstructure of steel strip over the entire coil length and between different coils of the same grade is key to stable and consistent material behaviour in steel manufacturers’ proprietary processes, like rolling and levelling, and customers’ processes, like pressing and deep-drawing. In particular for high-strength steels, like dual phase and complex phase steels, the microstructure is very sensitive to processing variations resulting in a potentially larger spread in the mechanical properties of the product. In July 2013, a large European consortium consisting of 15 institutes started an RFCS [1] – funded project called “Product Uniformity Control” (PUC) with the primary objective to achieve enhanced and sustained product uniformity of steel strip by improved interpretation of data from inline measurement methods that aim 2 for real-time and non-destructive characterisation of microstructure and technomechanical parameters. Commonly, these techniques are based on electromagnetic (EM) or ultrasonic (US) measurement principles, which are favoured because of their non-destructive and potentially contact-free nature. To improve the techniques for inline materials characterisation, the PUC consortium takes a systematic approach to investigate the interrelations between mechanical properties -- microstructural parameters -- EM & US properties -- inline measurement thereof. The studies involve dedicated laboratory experiments, modelling of the EM and US properties of steel, modelling of inline measurement setups and statistical analysis of data from inline measurement systems. The synthesis of these activities should result in improved, model-based, calibrations and finally in a broader deployment and integration of the inline material characterisation techniques in steel manufacturing, adding value to the product and enhancing the process efficiency throughout the production chain from hot-rolling to finishing. This paper outlines the project approach, highlights interconnecting modelling and experimental research work, and demonstrates first results. Various contributions being presented at this WCNDT conference originate from the collaborative activities of this PUC project.
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| 35. |
- Vera-Agullo, Jose, et al.
(författare)
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Durability of concrete caissons made in floating docks
- 2015
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Ingår i: Concrete 2015. - : Institute of Australia. - 9781943847709 ; , s. 894-903
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Konferensbidrag (refereegranskat)abstract
- ACCIONA Infrastructure, a Spanish contractor, uses the caisson method for the construction ofbreakwater structures. One of its floating docks, Kugira, is one of the largest of its kind in the world and itcan produce concrete caissons measuring 70 m long by 36 m wide and 35 m high. Concrete caissonsmade in floating docks are gradually immersed in sea water as they are built; thus, the set concrete isexposed to sea water at a very early stage, within 18 to 48 hours after casting in sliding formwork. In orderto study the durability of slag concrete using this construction method, the properties of concrete exposedto sea water at a very young age have been tested. Specimens were exposed to artificial sea water by theponding method at different ages (16h, 1, 2, 3, 7 and 28 days) for a period of 6, 18 and 36 (analysispending) months. The following properties were measured and compared with unexposed specimens:compressive strength, water and oxygen permeability, pore size distribution, migration coefficient DNT492and chloride profiles. After 6 and 18 months ponding, lower chloride contents were measured for thespecimens exposed to sea water after 28 days curing compared to those exposed at early ages.However, this difference significantly decreases within a small depth from the exposed surface. Also themigration coefficient DNT492 decreases significantly with the increase of the age of the concrete. Withregards to water and oxygen permeability, no significant differences were found. In this paper, a summaryof all these works is presented.Apart from this laboratory analysis, real scale tests were performed at site with the aim to increasedurability by the addition of nanosilica particles. The characterization of these real scale tests are alsodescribed and discussed in this paper.
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| 36. |
- Williams, Francis, et al.
(författare)
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Unwind: Interactive Fish Straightening
- 2020
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Ingår i: PROCEEDINGS OF THE 2020 CHI CONFERENCE ON HUMAN FACTORS IN COMPUTING SYSTEMS (CHI20). - New York, NY, USA : ASSOC COMPUTING MACHINERY. - 9781450367080
-
Konferensbidrag (refereegranskat)abstract
- The ScanAllFish project is a large-scale effort to scan all the worlds 33,100 known species of fishes. It has already generated thousands of volumetric CT scans of fish species which are available on open access platforms such as the Open Science Framework. To achieve a scanning rate required for a project of this magnitude, many specimens are grouped together into a single tube and scanned all at once. The resulting data contain many fish which are often bent and twisted to fit into the scanner. Our system, Unwind, is a novel interactive visualization and processing tool which extracts, unbends, and untwists volumetric images of fish with minimal user interaction. Our approach enables scientists to interactively unwarp these volumes to remove the undesired torque and bending using a piecewise-linear skeleton extracted by averaging iso-surfaces of a harmonic function connecting the head and tail of each fish. The result is a volumetric dataset of a individual, straight fish in a canonical pose defined by the marine biologist expert user. We have developed Unwind in collaboration with a team of marine biologists: Our system has been deployed in their labs, and is presently being used for dataset construction, biomechanical analysis, and the generation of figures for scientific publication.
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| 37. |
- Zerbinato de Andrade Silva, Duilio Mazzoni, et al.
(författare)
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Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish
- 2021
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Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Eukaryote genomes frequently harbor supernumerary B chromosomes in addition to the "standard" A chromosome set. B chromosomes are thought to arise as byproducts of genome rearrangements and have mostly been considered intraspecific oddities. However, their evolutionary transcendence beyond species level has remained untested.Results: Here we reveal that the large metacentric B chromosomes reported in several fish species of the genus Astyanax arose in a common ancestor at least 4 million years ago. We generated transcriptomes of A. scabripinnis and A. paranae 0B and 1B individuals and used these assemblies as a reference for mapping all gDNA and RNA libraries to quantify coverage differences between B-lacking and B-carrying genomes. We show that the B chromosomes of A. scabripinnis and A. paranae share 19 protein-coding genes, of which 14 and 11 were also present in the B chromosomes of A. bockmanni and A. fasciatus, respectively. Our search for B-specific single-nucleotide polymorphisms (SNPs) identified the presence of B-derived transcripts in B-carrying ovaries, 80% of which belonged to nobox, a gene involved in oogenesis regulation. Importantly, the B chromosome nobox paralog is expressed >30x more than the A chromosome paralog. This indicates that the normal regulation of this gene is altered in B-carrying females, which could potentially facilitate B inheritance at higher rates than Mendelian law prediction.Conclusions: Taken together, our results demonstrate the long-term survival of B chromosomes despite their lack of regular pairing and segregation during meiosis and that they can endure episodes of population divergence leading to species formation.
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