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1.	Abbasi, Rasha, et al. (författare) IceCube search for neutrinos from GRB 221009A 2023 Ingår i: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl. 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.
2.	Bass, Nathan Charles, et al. (författare) Residency and movement patterns of adult Port Jackson sharks (Heterodontus portusjacksoni) at a breeding aggregation site 2021 Ingår i: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 99:4, s. 1455-1466 Tidskriftsartikel (refereegranskat)abstract Examining the movement ecology of mesopredators is fundamental to developing an understanding of their biology, ecology and behaviour, as well as the communities and ecosystems they influence. The limited research on the residency and movements of benthic marine mesopredators has primarily used visual tags, which do not allow for the efficient and accurate monitoring of individual space use. In this study, the authors investigated the residency and movement patterns of Port Jackson sharks Heterodontus portusjacksoni (Meyer 1793) at a breeding aggregation site in Jervis Bay, south-eastern Australia, using passive acoustic telemetry to further our understanding of the movement ecology of these important mesopredators. Between 2012 and 2014, individuals were tagged with acoustic transmitters, and their residency and movements within the bay were monitored for up to 4 years. H. portusjacksoni showed strong preferences for particular reefs within and between breeding seasons. Males had significantly higher residency indices at their favoured sites relative to females, suggesting that males may be engaging in territorial behaviour. Conversely, female H. portusjacksoni exhibited higher roaming indices relative to males indicating that females may move between sites to assess males. Finally, H. portusjacksoni showed temporal variation in movements between reefs with individuals typically visiting more reefs at night relative to the day, dusk and dawn corresponding with their nocturnal habits.
3.	Birney, Ewan, et al. (författare) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project 2007 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816 Tidskriftsartikel (refereegranskat)abstract We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
4.	Hill, Jason, et al. (författare) Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution 2019 Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:6 Tidskriftsartikel (refereegranskat)abstract Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.
5.	Jespersen, Nathan, et al. (författare) Systematic identification of recognition motifs for the hub protein LC8 2019 Ingår i: Life Science Alliance. - : Life Science Alliance, LLC. - 2575-1077. ; 2:4 Tidskriftsartikel (refereegranskat)abstract Hub proteins participate in cellular regulation by dynamic binding of multiple proteins within interaction networks. The hub protein LC8 reversibly interacts with more than 100 partners through a flexible pocket at its dimer interface. To explore the diversity of the LC8 partner pool, we screened for LC8 binding partners using a proteomic phage display library composed of peptides from the human proteome, which had no bias toward a known LC8 motif. Of the identified hits, we validated binding of 29 peptides using isothermal titration calorimetry. Of the 29 peptides, 19 were entirely novel, and all had the canonical TQT motif anchor. A striking observation is that numerous peptides containing the TQT anchor do not bind LC8, indicating that residues outside of the anchor facilitate LC8 interactions. Using both LC8-binding and nonbinding peptides containing the motif anchor, we developed the "LC8Pred" algorithm that identifies critical residues flanking the anchor and parses random sequences to predict LC8-binding motifs with similar to 78% accuracy. Our findings significantly expand the scope of the LC8 hub interactome.
6.	Kattge, Jens, et al. (författare) TRY plant trait database - enhanced coverage and open access 2020 Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188 Tidskriftsartikel (refereegranskat)abstract Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
7.	Lieven, Christian, et al. (författare) MEMOTE for standardized genome-scale metabolic model testing 2020 Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 38:3, s. 272-276 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
8.	Lindblad-Toh, Kerstin, et al. (författare) Genome sequence, comparative analysis and haplotype structure of the domestic dog. 2005 Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19 Tidskriftsartikel (refereegranskat)abstract Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
9.	Nallu, Sumitha, et al. (författare) The molecular genetic basis of herbivory between butterflies and their host plants 2018 Ingår i: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:9, s. 1418-1427 Tidskriftsartikel (refereegranskat)abstract Interactions between herbivorous insects and their host plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defences and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host plants. Parallel genome-wide association studies in the cabbage white butterfly, Pieris rapae, and its host plant, Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, as well as a core set of highly conserved genes in butterflies as well as their host plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of nature's most diverse taxa, butterflies and flowering plants.
10.	Newsom, Horton E., et al. (författare) Gale crater and impact processes – Curiosity’s first 364 Sols on Mars 2015 Ingår i: Icarus. - : Elsevier BV. - 0019-1035 .- 1090-2643. ; 249, s. 108-128 Tidskriftsartikel (refereegranskat)abstract Impact processes at all scales have been involved in the formation and subsequent evolution of Gale crater. Small impact craters in the vicinity of the Curiosity MSL landing site and rover traverse during the 364 Sols after landing have been studied both from orbit and the surface. Evidence for the effect of impacts on basement outcrops may include loose blocks of sandstone and conglomerate, and disrupted (fractured) sedimentary layers, which are not obviously displaced by erosion. Impact ejecta blankets are likely to be present, but in the absence of distinct glass or impact melt phases are difficult to distinguish from sedimentary/volcaniclastic breccia and conglomerate deposits. The occurrence of individual blocks with diverse petrological characteristics, including igneous textures, have been identified across the surface of Bradbury Rise, and some of these blocks may represent distal ejecta from larger craters in the vicinity of Gale. Distal ejecta may also occur in the form of impact spherules identified in the sediments and drift material. Possible examples of impactites in the form of shatter cones, shocked rocks, and ropy textured fragments of materials that may have been molten have been observed, but cannot be uniquely confirmed. Modification by aeolian processes of craters smaller than 40 m in diameter observed in this study, are indicated by erosion of crater rims, and infill of craters with aeolian and airfall dust deposits. Estimates for resurfacing suggest that craters less than 15 m in diameter may represent steady state between production and destruction. The smallest candidate impact crater observed is ∼0.6 m in diameter. The observed crater record and other data are consistent with a resurfacing rate of the order of 10 mm/Myr; considerably greater than the rate from impact cratering alone, but remarkably lower than terrestrial erosion rates.
11.	Roselli, Carolina, et al. (författare) Multi-ethnic genome-wide association study for atrial fibrillation 2018 Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 50:9, s. 1225-1233 Tidskriftsartikel (refereegranskat)abstract Atrial fibrillation (AF) affects more than 33 million individuals worldwide(1) and has a complex heritability(2). We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.
12.	Schick, Ursula M, et al. (författare) Association of exome sequences with plasma C-reactive protein levels in >9000 participants. 2015 Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 24:2, s. 559-571 Tidskriftsartikel (refereegranskat)abstract C-reactive protein (CRP) concentration is a heritable systemic marker of inflammation that is associated with cardiovascular disease risk. Genome-wide association studies have identified CRP-associated common variants associated in ∼25 genes. Our aims were to apply exome sequencing to (1) assess whether the candidate loci contain rare coding variants associated with CRP levels and (2) perform an exome-wide search for rare variants in novel genes associated with CRP levels. We exome-sequenced 6050 European-Americans (EAs) and 3109 African-Americans (AAs) from the NHLBI-ESP and the CHARGE consortia, and performed association tests of sequence data with measured CRP levels. In single-variant tests across candidate loci, a novel rare (minor allele frequency = 0.16%) CRP-coding variant (rs77832441-A; p.Thr59Met) was associated with 53% lower mean CRP levels (P = 2.9 × 10(-6)). We replicated the association of rs77832441 in an exome array analysis of 11 414 EAs (P = 3.0 × 10(-15)). Despite a strong effect on CRP levels, rs77832441 was not associated with inflammation-related phenotypes including coronary heart disease. We also found evidence for an AA-specific association of APOE-ε2 rs7214 with higher CRP levels. At the exome-wide significance level (P < 5.0 × 10(-8)), we confirmed associations for reported common variants of HNF1A, CRP, IL6R and TOMM40-APOE. In gene-based tests, a burden of rare/lower frequency variation in CRP in EAs (P ≤ 6.8 × 10(-4)) and in retinoic acid receptor-related orphan receptor α (RORA) in AAs (P = 1.7 × 10(-3)) were associated with CRP levels at the candidate gene level (P < 2.0 × 10(-3)). This inquiry did not elucidate novel genes, but instead demonstrated that variants distributed across the allele frequency spectrum within candidate genes contribute to CRP levels.
13.	Schulken, Merle, et al. (författare) Strategy for the multiplicity of degrowth 2022 Ingår i: Degrowth & Strategy : How to bring about social-ecological transformation - How to bring about social-ecological transformation. - 9781906948603 - 9781906948610 - 9781906948627 ; , s. 9-34 Bokkapitel (refereegranskat)abstract This chapter starts with outlining a degrowth vision for social-ecological transformation. It then traces the existing discussion on strategy in the degrowth movement and explains why it is important to think about strategy. Its key contribution is a conceptualiation strategy, which builds on and is closely aligned with our understanding of degrowth. Finally, it introduces the book and its structure, followed by a conclusion.
14.	Sumaila, U. Rashid, et al. (författare) WTO must ban harmful fisheries subsidies 2021 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
15.	Aad, G., et al. (författare) Integrated and differential fiducial cross-section measurements for the vector boson fusion production of the Higgs boson in the H → WW* → eνμν decay channel at 13 TeV with the ATLAS detector 2023 Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 108:7 Tidskriftsartikel (refereegranskat)abstract The vector-boson production cross section for the Higgs boson decay in the H→WW*→eνμν channel is measured as a function of kinematic observables sensitive to the Higgs boson production and decay properties as well as integrated in a fiducial phase space. The analysis is performed using the proton-proton collision data collected by the ATLAS detector in Run 2 of the LHC at √s=13 TeV center-of-mass energy, corresponding to an integrated luminosity of 139 fb−1. The different flavor final state is studied by selecting an electron and a muon originating from a pair of W bosons and compatible with the Higgs boson decay. The data are corrected for the effects of detector inefficiency and resolution, and the measurements are compared with different state-of-the-art theoretical predictions. The differential cross sections are used to constrain anomalous interactions described by dimension-six operators in an effective field theory.
16.	Aad, G., et al. (författare) Measurement of the Sensitivity of Two-Particle Correlations in pp Collisions to the Presence of Hard Scatterings 2023 Ingår i: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 131:16 Tidskriftsartikel (refereegranskat)abstract A key open question in the study of multiparticle production in high-energy pp collisions is the relationship between the “ridge”—i.e., the observed azimuthal correlations between particles in the underlying event that extend over all rapidities—and hard or semihard scattering processes. In particular, it is not known whether jets or their soft fragments are correlated with particles in the underlying event. To address this question, two-particle correlations are measured in pp collisions at √s=13 TeV using data collected by the ATLAS experiment at the LHC, with an integrated luminosity of 15.8 pb−1, in two different configurations. In the first case, charged particles associated with jets are excluded from the correlation analysis, while in the second case, correlations are measured between particles within jets and charged particles from the underlying event. Second-order flow coefficients, v2, are presented as a function of event multiplicity and transverse momentum. These measurements show that excluding particles associated with jets does not affect the measured correlations. Moreover, particles associated with jets do not exhibit any significant azimuthal correlations with the underlying event, ruling out hard processes contributing to the ridge.
17.	Aad, G., et al. (författare) Observation of Single-Top-Quark Production in Association with a Photon Using the ATLAS Detector 2023 Ingår i: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 131:18 Tidskriftsartikel (refereegranskat)abstract This Letter reports the observation of single top quarks produced together with a photon, which directly probes the electroweak coupling of the top quark. The analysis uses 139 fb−1 of 13 TeV proton-proton collision data collected with the ATLAS detector at the Large Hadron Collider. Requiring a photon with transverse momentum larger than 20 GeV and within the detector acceptance, the fiducial cross section is measured to be 688±23(stat) , to be compared with the standard model prediction of at next-to-leading order in QCD.
18.	Abazajian, Kevork, et al. (författare) CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves 2022 Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1 Tidskriftsartikel (refereegranskat)abstract CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
19.	Abbasi, R., et al. (författare) Acceptance Tests of more than 10 000 Photomultiplier Tubes for the multi-PMT Digital Optical Modules of the IceCube Upgrade 2024 Ingår i: Journal of Instrumentation. - 1748-0221. ; 19:7 Tidskriftsartikel (refereegranskat)abstract More than 10 000 photomultiplier tubes (PMTs) with a diameter of 80 mm will be installed in multi-PMT Digital Optical Modules (mDOMs) of the IceCube Upgrade. These have been tested and pre-calibrated at two sites. A throughput of more than 1000 PMTs per week with both sites was achieved with a modular design of the testing facilities and highly automated testing procedures. The testing facilities can easily be adapted to other PMTs, such that they can, e.g., be re-used for testing the PMTs for IceCube-Gen2. Single photoelectron response, high voltage dependence, time resolution, prepulse, late pulse, afterpulse probabilities, and dark rates were measured for each PMT. We describe the design of the testing facilities, the testing procedures, and the results of the acceptance tests.
20.	Abbasi, R., et al. (författare) Characterization of the astrophysical diffuse neutrino flux using starting track events in IceCube 2024 Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 2470-0010 .- 2470-0029. ; 110:2 Tidskriftsartikel (refereegranskat)abstract A measurement of the diffuse astrophysical neutrino spectrum is presented using IceCube data collected from 2011-2022 (10.3 years). We developed novel detection techniques to search for events with a contained vertex and exiting track induced by muon neutrinos undergoing a charged-current interaction. Searching for these starting track events allows us to not only more effectively reject atmospheric muons but also atmospheric neutrino backgrounds in the southern sky, opening a new window to the sub-100 TeV astrophysical neutrino sky. The event selection is constructed using a dynamic starting track veto and machine learning algorithms. We use this data to measure the astrophysical diffuse flux as a single power law flux (SPL) with a best-fit spectral index of γ=2.58-0.09+0.10 and per-flavor normalization of φper-flavorAstro=1.68-0.22+0.19×10-18×GeV-1 cm-2 s-1 sr-1 (at 100 TeV). The sensitive energy range for this dataset is 3-550 TeV under the SPL assumption. This data was also used to measure the flux under a broken power law, however we did not find any evidence of a low energy cutoff.
21.	Abbasi, R., et al. (författare) Citizen science for IceCube: Name that Neutrino 2024 Ingår i: European Physical Journal Plus. - 2190-5444. ; 139:6 Tidskriftsartikel (refereegranskat)abstract Name that Neutrino is a citizen science project where volunteers aid in classification of events for the IceCube Neutrino Observatory, an immense particle detector at the geographic South Pole. From March 2023 to September 2023, volunteers did classifications of videos produced from simulated data of both neutrino signal and background interactions. Name that Neutrino obtained more than 128,000 classifications by over 1800 registered volunteers that were compared to results obtained by a deep neural network machine-learning algorithm. Possible improvements for both Name that Neutrino and the deep neural network are discussed.
22.	Abbasi, R., et al. (författare) IceCat-1: The IceCube Event Catalog of Alert Tracks 2023 Ingår i: Astrophysical Journal, Supplement Series. - : IOP Publishing Ltd. - 1538-4365 .- 0067-0049. ; 269:1 Tidskriftsartikel (refereegranskat)abstract We present a catalog of likely astrophysical neutrino track-like events from the IceCube Neutrino Observatory. IceCube began reporting likely astrophysical neutrinos in 2016, and this system was updated in 2019. The catalog presented here includes events that were reported in real time since 2019, as well as events identified in archival data samples starting from 2011. We report 275 neutrino events from two selection channels as the first entries in the catalog, the IceCube Event Catalog of Alert Tracks, which will see ongoing extensions with additional alerts. The Gold and Bronze alert channels respectively provide neutrino candidates with a 50% and 30% probability of being astrophysical, on average assuming an astrophysical neutrino power-law energy spectral index of 2.19. For each neutrino alert, we provide the reconstructed energy, direction, false-alarm rate, probability of being astrophysical in origin, and likelihood contours describing the spatial uncertainty in the alert's reconstructed location. We also investigate a directional correlation of these neutrino events with gamma-ray and X-ray catalogs, including 4FGL, 3HWC, TeVCat, and Swift-BAT.
23.	Abbasi, R., et al. (författare) Improved modeling of in-ice particle showers for IceCube event reconstruction 2024 Ingår i: Journal of Instrumentation. - 1748-0221. ; 19:6 Tidskriftsartikel (refereegranskat)abstract The IceCube Neutrino Observatory relies on an array of photomultiplier tubes to detect Cherenkov light produced by charged particles in the South Pole ice. IceCube data analyses depend on an in-depth characterization of the glacial ice, and on novel approaches in event reconstruction that utilize fast approximations of photoelectron yields. Here, a more accurate model is derived for event reconstruction that better captures our current knowledge of ice optical properties. When evaluated on a Monte Carlo simulation set, the median angular resolution for in-ice particle showers improves by over a factor of three compared to a reconstruction based on a simplified model of the ice. The most substantial improvement is obtained when including effects of birefringence due to the polycrystalline structure of the ice. When evaluated on data classified as particle showers in the high-energy starting events sample, a significantly improved description of the events is observed.
24.	Abbasi, R., et al. (författare) Measurement of atmospheric neutrino mixing with improved IceCube DeepCore calibration and data processing 2023 Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 108:1 Tidskriftsartikel (refereegranskat)abstract We describe a new data sample of IceCube DeepCore and report on the latest measurement of atmospheric neutrino oscillations obtained with data recorded between 2011-2019. The sample includes significant improvements in data calibration, detector simulation, and data processing, and the analysis benefits from a sophisticated treatment of systematic uncertainties, with significantly greater level of detail since our last study. By measuring the relative fluxes of neutrino flavors as a function of their reconstructed energies and arrival directions we constrain the atmospheric neutrino mixing parameters to be sin2θ23=0.51±0.05 and Δm322=2.41±0.07×10-3 eV2, assuming a normal mass ordering. The errors include both statistical and systematic uncertainties. The resulting 40% reduction in the error of both parameters with respect to our previous result makes this the most precise measurement of oscillation parameters using atmospheric neutrinos. Our results are also compatible and complementary to those obtained using neutrino beams from accelerators, which are obtained at lower neutrino energies and are subject to different sources of uncertainties.
25.	Abbasi, R., et al. (författare) Observation of seasonal variations of the flux of high-energy atmospheric neutrinos with IceCube 2023 Ingår i: European Physical Journal C. - : Springer. - 1434-6044 .- 1434-6052. ; 83:9 Tidskriftsartikel (refereegranskat)abstract Atmospheric muon neutrinos are produced by meson decays in cosmic-ray-induced air showers. The flux depends on meteorological quantities such as the air temperature, which affects the density of air. Competition between decay and re-interaction of those mesons in the first particle production generations gives rise to a higher neutrino flux when the air density in the stratosphere is lower, corresponding to a higher temperature. A measurement of a temperature dependence of the atmospheric νμ flux provides a novel method for constraining hadronic interaction models of air showers. It is particularly sensitive to the production of kaons. Studying this temperature dependence for the first time requires a large sample of high-energy neutrinos as well as a detailed understanding of atmospheric properties. We report the significant (>10σ) observation of a correlation between the rate of more than 260,000 neutrinos, detected by IceCube between 2012 and 2018, and atmospheric temperatures of the stratosphere, measured by the Atmospheric Infrared Sounder (AIRS) instrument aboard NASA’s AQUA satellite. For the observed 10 % seasonal change of effective atmospheric temperature we measure a 3.5(3) % change in the muon neutrino flux. This observed correlation deviates by about 2-3 standard deviations from the expected correlation of 4.3 % as obtained from theoretical predictions under the assumption of various hadronic interaction models.
26.	Abbasi, R., et al. (författare) Search for 10-1000 GeV Neutrinos from Gamma-Ray Bursts with IceCube 2024 Ingår i: Astrophysical Journal. - : Institute of Physics (IOP). - 1538-4357 .- 0004-637X. ; 964:2 Tidskriftsartikel (refereegranskat)abstract We present the results of a search for 10-1000 GeV neutrinos from 2268 gamma-ray bursts (GRBs) over 8 yr of IceCube-DeepCore data. This work probes burst physics below the photosphere where electromagnetic radiation cannot escape. Neutrinos of tens of giga electronvolts are predicted in sub-photospheric collision of free-streaming neutrons with bulk-jet protons. In a first analysis, we searched for the most significant neutrino-GRB coincidence using six overlapping time windows centered on the prompt phase of each GRB. In a second analysis, we conducted a search for a group of GRBs, each individually too weak to be detectable, but potentially significant when combined. No evidence of neutrino emission is found for either analysis. The most significant neutrino coincidence is for Fermi-GBM GRB bn 140807500, with a p-value of 0.097 corrected for all trials. The binomial test used to search for a group of GRBs had a p-value of 0.65 after all trial corrections. The binomial test found a group consisting only of GRB bn 140807500 and no additional GRBs. The neutrino limits of this work complement those obtained by IceCube at tera electronvolt to peta electronvolt energies. We compare our findings for the large set of GRBs as well as GRB 221009A to the sub-photospheric neutron-proton collision model and find that GRB 221009A provides the most constraining limit on baryon loading. For a jet Lorentz factor of 300 (800), the baryon loading on GRB 221009A is lower than 3.85 (2.13) at a 90% confidence level.
27.	Abbasi, R., et al. (författare) Search for Galactic Core-collapse Supernovae in a Decade of Data Taken with the IceCube Neutrino Observatory 2024 Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 1538-4357 .- 0004-637X. ; 961:1 Tidskriftsartikel (refereegranskat)abstract The IceCube Neutrino Observatory has been continuously taking data to search for O(0.5–10) s long neutrino bursts since 2007. Even if a Galactic core-collapse supernova is optically obscured or collapses to a black hole instead of exploding, it will be detectable via the O(10) MeV neutrino burst emitted during the collapse. We discuss a search for such events covering the time between 2008 April 17 and 2019 December 31. Considering the average data taking and analysis uptime of 91.7% after all selection cuts, this is equivalent to 10.735 yr of continuous data taking. In order to test the most conservative neutrino production scenario, the selection cuts were optimized for a model based on an 8.8 solar mass progenitor collapsing to an O–Ne–Mg core. Conservative assumptions on the effects of neutrino oscillations in the exploding star were made. The final selection cut was set to ensure that the probability to detect such a supernova within the Milky Way exceeds 99%. No such neutrino burst was found in the data after performing a blind analysis. Hence, a 90% C.L. upper limit on the rate of core-collapse supernovae out to distances of ≈25 kpc was determined to be 0.23 yr−1. For the more distant Magellanic Clouds, only high neutrino luminosity supernovae will be detectable by IceCube, unless external information on the burst time is available. We determined a model-independent limit by parameterizing the dependence on the neutrino luminosity and the energy spectrum.
28.	Abbasi, R., et al. (författare) Search for neutrino lines from dark matter annihilation and decay with IceCube 2023 Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 108:10 Tidskriftsartikel (refereegranskat)abstract Dark matter particles in the Galactic Center and halo can annihilate or decay into a pair of neutrinos producing a monochromatic flux of neutrinos. The spectral feature of this signal is unique and it is not expected from any astrophysical production mechanism. Its observation would constitute a dark matter smoking gun signal. We performed the first dedicated search with a neutrino telescope for such signal, by looking at both the angular and energy information of the neutrino events. To this end, a total of five years of IceCube's DeepCore data has been used to test dark matter masses ranging from 10 GeV to 40 TeV. No significant neutrino excess was found and upper limits on the annihilation cross section, as well as lower limits on the dark matter lifetime, were set. The limits reached are of the order of 10-24 cm3/s for an annihilation and up to 1027 s for decaying dark matter. Using the same data sample we also derive limits for dark matter annihilation or decay into a pair of Standard Model charged particles.
29.	Abdoullaye, Doukary, et al. (författare) Permanent genetic resources added to molecular ecology resources database 1 August 2009 - 30 September 2009 2010 Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:1, s. 232-236 Tidskriftsartikel (refereegranskat)abstract This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.
30.	Aben, Ralf C. H., et al. (författare) Cross continental increase in methane ebullition under climate change 2017 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8 Tidskriftsartikel (refereegranskat)abstract Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature-ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 degrees C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6-20% per 1 degrees C increase), contributing to global warming.
31.	Abolfathi, Bela, et al. (författare) The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment 2018 Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2 Tidskriftsartikel (refereegranskat)abstract The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
32.	Abrahamson, Dor, et al. (författare) Moving Forward: In Search of Synergy Across Diverse Views on the Role of Physical Movement in Design for STEM Education 2018 Ingår i: Rethinking Learning in the Digital Age: Making the Learning Sciences Count, 13th International Conference of the Learning Sciences (ICLS) 2018, Volume 2. - : International Society of the Learning Sciences.. - 1573-4552. - 9781732467217 Konferensbidrag (refereegranskat)abstract Inspired by the current embodiment turn in the cognitive sciences, researchers of STEM teaching and learning have been evaluating implications of this turn for educational theory and practice. But whereas design researchers have been developing domain-specific theories that implicate the role of physical movement in conceptual learning, the field has yet to agree on a conceptually coherent and empirically validated framework for leveraging and shaping students’ capacity for physical movement as a socio–cognitive educational resource. This symposium thus convenes to ask, “What is movement in relation to concepts such that we can design for learning?” To stimulate discussion, we highlight an emerging tension across a set of innovative technological designs with respect to the framing question of whether students should discover an activity’s targeted movement forms themselves or that these forms should be cued directly. Our content domains span mathematics (proportions, geometry), physics, chemistry, and ecological system dynamics (predator–prey, bees).
33.	Acuña, Ulyana Muñoz, et al. (författare) Activity in MCF-7 Estrogen-sensitive Breast Cancer Cells of Capsicodendrin from Cinnamosma fragrans 2021 Ingår i: Anticancer Research. - : International Institute of Anticancer Research. - 0250-7005 .- 1791-7530. ; 41:12, s. 5935-5944 Tidskriftsartikel (refereegranskat)abstract Background/Aim: Effect of capsicodendrin on the NF-KB pathway was studied in MCF-7 cancer cells. Materials and Methods: The transcription factor assay was used to screen for NF-KB activity. The effect on IKK beta, ICAM-1, and caspase-7 were studied using western blot. Caspase-1 was studied using Promega Caspase-Glo (R) assay. Reactive oxygen species (ROS) were detected using the fluorescent probe DCFH-DA. The potentiometric dye JC-1 was used to assess mitochondrial membrane potential (Delta psi m) and the cell cycle was examined using a fluorescence-activated cell sorter. Results: NF-kappa B p65 inhibitory effect was IC50=8.6 mu M and cytotoxic activity was IC50=7.5 mu M. The upstream IKK and the downstream ICAM-1 were down-regulated. Sub G1-phase population increased to 81% after 12 h of treatment with capsicodendrin (10 mu M) and there was no loss of Delta psi M. Conclusion: Increased levels of intracellular ROS promoted activity of caspase-1 and induced cell death in MCF-7 cells. Capsicodendrin may be a future anticancer agent that prevents the progression of metastatic breast cancer.
34.	Ade, Peter, et al. (författare) The Simons Observatory : science goals and forecasts 2019 Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2 Tidskriftsartikel (refereegranskat)abstract The Simons Observatory (SO) is a new cosmic microwave background experiment being built on Cerro Toco in Chile, due to begin observations in the early 2020s. We describe the scientific goals of the experiment, motivate the design, and forecast its performance. SO will measure the temperature and polarization anisotropy of the cosmic microwave background in six frequency bands centered at: 27, 39, 93, 145, 225 and 280 GHz. The initial con figuration of SO will have three small-aperture 0.5-m telescopes and one large-aperture 6-m telescope, with a total of 60,000 cryogenic bolometers. Our key science goals are to characterize the primordial perturbations, measure the number of relativistic species and the mass of neutrinos, test for deviations from a cosmological constant, improve our understanding of galaxy evolution, and constrain the duration of reionization. The small aperture telescopes will target the largest angular scales observable from Chile, mapping approximate to 10% of the sky to a white noise level of 2 mu K-arcmin in combined 93 and 145 GHz bands, to measure the primordial tensor-to-scalar ratio, r, at a target level of sigma(r) = 0.003. The large aperture telescope will map approximate to 40% of the sky at arcminute angular resolution to an expected white noise level of 6 mu K-arcmin in combined 93 and 145 GHz bands, overlapping with the majority of the Large Synoptic Survey Telescope sky region and partially with the Dark Energy Spectroscopic Instrument. With up to an order of magnitude lower polarization noise than maps from the Planck satellite, the high-resolution sky maps will constrain cosmological parameters derived from the damping tail, gravitational lensing of the microwave background, the primordial bispectrum, and the thermal and kinematic Sunyaev-Zel'dovich effects, and will aid in delensing the large-angle polarization signal to measure the tensor-to-scalar ratio. The survey will also provide a legacy catalog of 16,000 galaxy clusters and more than 20,000 extragalactic sources.
35.	Adler, Jan-Olof, et al. (författare) The upgraded photon tagging facility at the MAX IV Laboratory 2013 Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 715, s. 1-10 Tidskriftsartikel (refereegranskat)abstract A description is given of the upgraded photon tagging facility at the MAX IV Laboratory. Two magnetic spectrometers are used to momentum analyze post-bremsstrahlung electrons. The tagged photon range extends from 10 to 180 MeV with an energy resolution of about 300 keV. The system has been operated at rates up to 4 x 10(6) photons s(-1) MeV (-1). Different diagnostic tools are described as well as the experimental program.
36.	Aebersold, Ruedi, et al. (författare) How many human proteoforms are there? 2018 Ingår i: Nature Chemical Biology. - : NATURE PUBLISHING GROUP. - 1552-4450 .- 1552-4469. ; 14:3, s. 206-214 Tidskriftsartikel (refereegranskat)abstract Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA-and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.
37.	af Edholm, Kristoffer, 1985- (författare) Ascetic poetry in ancient India : The ideal renouncer and the path to liberation, according to independent verses in early Brahmanic, Buddhist, and Jaina literature 2024 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract The dissertation identifies the ideal renouncer and the path to liberation on the basis of nearly 3500 “independent verses”, i.e. one-strophe stanzas (gāthās, ślokas), in early Brahmanic, Buddhist, and Jaina literature, including Mahābhārata, Suttanipāta, Dhammapada, Saṃyuttanikāya, Uttarajjhayaṇa, Sūyagaḍa, Isibhāsiyāiṃ, and other texts. It is argued that this genre of poetry is important for our knowledge about the ascetic milieu in Northern India around the 5th century BCE.Verses from the three traditions are compared with one another, the verse-material is compared with selected texts belonging to other genres, and the literature is placed in its historical context. Attention is given to vocabulary, formulas, similes, and recurrent themes. Hypotheses about the early history of the renouncer-traditions are tested against the verse-material.Part 1 discusses aim, theory, method, terminology, previous studies, earliness and authenticity of the verses, origins and characteristics of the genre, and relevant texts. Part 2 treats the debated origins of emancipatory askesis, brāhmaṇa and śramaṇa, authority and founder-figures, and female ascetics. Part 3 proceeds along an ideal path to liberation: from reasons for giving up mundane pursuits, to going forth into homelessness, practise of austerity, itinerancy, solitude, seclusion, mendicancy, purification, non-harm, restraint, heroic overcoming of obstacles, and meditation, to attainment of gnosis and awakening, and finally liberation from saṃsāra. Part 4 is the conclusion. The Appendices contain the entire verse-material, as well as defining sentences in final pādas, shared whole verses, and key-terms.It is concluded that in the three verse-corpora one can identify a shared outlook, which is world-rejecting, autocentric, and telos-oriented, and a shared renouncer-ideal, which is male, heroic, and austere. The same outlook and ideal are found in narrative accounts about Śākyamuni, Mahāvīra, and others who attain the highest goal. Differences between the three traditions concern mainly the use of certain terms, formulas, and similes, less so doctrine, but the differences are not reducible to a divide between Brahmanic and Buddhist/Jaina.Generally speaking, each tradition has composed its own verses that promote a renouncer-ideal and a path to liberation, rather than having borrowed verses from another tradition or from a common source. The many similarities between the three traditions are primarily due to their common origin in the ascetic milieu, in which the one-strophe gāthā was an established literary medium for making authoritative statements.It is argued that the shared outlook and ideal were established before the introduction of two-step ordination, nuns’ order, fourfold community, devotion to an exalted founder-figure, and the building of monasteries. The verse-content points to a rural environment and a stratified society rooted in late Vedic culture. The renunciant movement of the 5th century BCE can be seen as the culmination of a centuries-old ascetic tradition in ancient India.
38.	Aguado, D. S., et al. (författare) The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library 2019 Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2 Tidskriftsartikel (refereegranskat)abstract Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
39.	Agyemang, Alex Adusei, et al. (författare) Cell-free oxidized hemoglobin drives reactive oxygen species production and pro-inflammation in an immature primary rat mixed glial cell culture 2021 Ingår i: Journal of Neuroinflammation. - : Springer Science and Business Media LLC. - 1742-2094. ; 18:1 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Germinal matrix intraventricular hemorrhage (GM-IVH) is associated with deposition of redox active cell-free hemoglobin (Hb), derived from hemorrhagic cerebrospinal fluid (CSF), in the cerebrum and cerebellum. In a recent study, using a preterm rabbit pup model of IVH, intraventricularly administered haptoglobin (Hp), a cell-free Hb scavenger, partially reversed the damaging effects observed following IVH. Together, this suggests that cell-free Hb is central in the pathophysiology of the injury to the immature brain following GM-IVH. An increased understanding of the causal pathways and metabolites involved in eliciting the damaging response following hemorrhage is essential for the continued development and implementation of neuroprotective treatments of GM-IVH in preterm infant.METHODS: We exposed immature primary rat mixed glial cells to hemorrhagic CSF obtained from preterm human infants with IVH (containing a mixture of Hb-metabolites) or to a range of pure Hb-metabolites, incl. oxidized Hb (mainly metHb with iron in Fe3+), oxyHb (mainly Fe2+), or low equivalents of heme, with or without co-administration with human Hp (a mixture of isotype 2-2/2-1). Following exposure, cellular response, reactive oxygen species (ROS) generation, secretion and expression of pro-inflammatory cytokines and oxidative markers were evaluated.RESULTS: Exposure of the glial cells to hemorrhagic CSF as well as oxidized Hb, but not oxyHb, resulted in a significantly increased rate of ROS production that positively correlated with the rate of production of pro-inflammatory and oxidative markers. Congruently, exposure to oxidized Hb caused a disintegration of the polygonal cytoskeletal structure of the glial cells in addition to upregulation of F-actin proteins in microglial cells. Co-administration of Hp partially reversed the damaging response of hemorrhagic CSF and oxidized Hb.CONCLUSION: Exposure of mixed glial cells to oxidized Hb initiates a pro-inflammatory and oxidative response with cytoskeletal disintegration. Early administration of Hp, aiming to minimize the spontaneous autoxidation of cell-free oxyHb and liberation of heme, may provide a therapeutic benefit in preterm infant with GM-IVH.
40.	Ahmed, Md Estak, et al. (författare) A Bidirectional Bioinspired [FeFe]-Hydrogenase Model 2022 Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:8, s. 3614-3625 Tidskriftsartikel (refereegranskat)abstract With the price-competitiveness of solar and wind power, hydrogen technologies may be game changers for a cleaner, defossilized, and sustainable energy future. H-2 can indeed be produced in electrolyzers from water, stored for long periods, and converted back into power, on demand, in fuel cells. The feasibility of the latter process critically depends on the discovery of cheap and efficient catalysts able to replace platinum group metals at the anode and cathode of fuel cells. Bioinspiration can be key for designing such alternative catalysts. Here we show that a novel class of iron-based catalysts inspired from the active site of [FeFe]-hydrogenase behave as unprecedented bidirectional electrocatalysts for interconverting H-2 and protons efficiently under near-neutral aqueous conditions. Such bioinspired catalysts have been implemented at the anode of a functional membrane-less H-2/O-2 fuel cell device.
41.	Ahmed, Syed Ishtiaque, et al. (författare) Citational justice and the politics of knowledge production 2022 Ingår i: interactions. - : Association for Computing Machinery (ACM). - 1072-5520 .- 1558-3449. ; 29:5, s. 78-82 Tidskriftsartikel (refereegranskat)abstract Citation is how we acknowledge our debt to those who came before; those who helped us find our way when the way was obscured because we deviated from the paths we were told to follow. Sara Ahmed reminds us that just citational practices recognize the knowledge contributions of less dominant, routinely overlooked voices. Pursuing citational justice, then, entails moving away from individualistic views of authorship and toward a shared, reciprocal understanding of how knowledge is produced. Drawing from our experiences working within HCI, we extend an invitation for a just citational practice—one that makes space for the diversity of human experience and recognizes that human-computer interactions must be responsive to cultural and geographic differences. We outline parts of our ongoing conversations as a collective to motivate a careful citation practice across our field, interrogating how we can best honor one another’s ideas and labor without alienation or appropriation.
42.	Ahmed, Sairah, et al. (författare) Impact of type of reduced-intensity conditioning regimen on the outcomes of allogeneic haematopoietic cell transplantation in classical Hodgkin lymphoma 2020 Ingår i: British Journal of Haematology. - : WILEY. - 0007-1048 .- 1365-2141. ; 190:4, s. 573-582 Tidskriftsartikel (refereegranskat)abstract Reduced-intensity conditioning (RIC) allogeneic haematopoietic cell transplantation (allo-HCT) is a curative option for select relapsed/refractory Hodgkin lymphoma (HL) patients; however, there are sparse data to support superiority of any particular conditioning regimen. We analyzed 492 adult patients undergoing human leucocyte antigen (HLA)-matched sibling or unrelated donor allo-HCT for HL between 2008 and 2016, utilizing RIC with either fludarabine/busulfan (Flu/Bu), fludarabine/melphalan (Flu/Mel140) or fludarabine/cyclophosphamide (Flu/Cy). Multivariable regression analysis was performed using a significance level of <0 center dot 01. There were no significant differences between regimens in risk for non-relapse mortality (NRM) (P = 0 center dot 54), relapse/progression (P = 0 center dot 02) or progression-free survival (PFS) (P = 0 center dot 14). Flu/Cy conditioning was associated with decreased risk of mortality in the first 11 months after allo-HCT (HR = 0 center dot 28; 95% CI = 0 center dot 10-0 center dot 73; P = 0 center dot 009), but beyond 11 months post allo-HCT it was associated with a significantly higher risk of mortality, (HR = 2 center dot 46; 95% CI = 0 center dot 1.32-4 center dot 61; P = 0 center dot 005). Four-year adjusted overall survival (OS) was similar across regimens at 62% for Flu/Bu, 59% for Flu/Mel140 and 55% for Flu/Cy (P = 0 center dot 64), respectively. These data confirm the choice of RIC for allo-HCT in HL does not influence risk of relapse, NRM or PFS. Although no OS benefit was seen between Flu/Bu and Flu/Mel 140; Flu/Cy was associated with a significantly higher risk of mortality beyond 11 months from allo-HCT (possibly due to late NRM events).
43.	Ahmed, Shahnawaz, 1995, et al. (författare) Implicit differentiation of variational quantum algorithms 2022 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract Several quantities important in condensed matter physics, quantum information, and quantum chemistry, as well as quantities required in meta-optimization of machine learning algorithms, can be expressed as gradients of implicitly defined functions of the parameters characterizing the system. Here, we show how to leverage implicit differentiation for gradient computation through variational quantum algorithms and explore applications in condensed matter physics, quantum machine learning, and quantum information. A function defined implicitly as the solution of a quantum algorithm, e.g., a variationally obtained ground- or steady-state, can be automatically differentiated using implicit differentiation while being agnostic to how the solution is computed. We apply this notion to the evaluation of physical quantities in condensed matter physics such as generalized susceptibilities studied through a variational quantum algorithm. Moreover, we develop two additional applications of implicit differentiation -- hyperparameter optimization in a quantum machine learning algorithm, and the variational construction of entangled quantum states based on a gradient-based maximization of a geometric measure of entanglement. Our work ties together several types of gradient calculations that can be computed using variational quantum circuits in a general way without relying on tedious analytic derivations, or approximate finite-difference methods.
44.	Aigine Cultural Research Center, ., et al. (författare) Map of events in Pishpek uezd from July 4th to August 23rd in 1916. 2020 Annan publikation (karta/atlas) (övrigt vetenskapligt/konstnärligt)abstract The map was created within the project "Mobilizing academic communities in Central Asia to produce new knowledge about the 1916 Uprising, and to build shared academic platforms for exchanging and disseminating knowledge about ethnically or/and politically sensitive topics".Open access digital publication.
45.	Ajawatanawong, Pravech, et al. (författare) SeqFIRE : a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments 2012 Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 40:W1, s. W340-W347 Tidskriftsartikel (refereegranskat)abstract Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.
46.	Akhter, Shirin, et al. (författare) Transcriptome studies of the early cone-setting acrocona mutant provide evidence for a functional conservation of the age-dependent flowering pathway between angiosperms and gymnosperms. Annan publikation (övrigt vetenskapligt/konstnärligt)abstract All seed plants go through a juvenile period before they initiate seed- and pollen-bearing organs and reproduce. Reproductive phase-change is well characterized in angiosperm model species, but much less well described in gymnosperms. Here, we utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies; a representative of the gymnosperm lineage. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. By sequence analysis of mRNA and microRNA transcripts, we demonstrate that orthologous components of the Age-dependent flowering pathway are active at the time of cone initiation. We show that a member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL7, is active in reproductive meristems, whereas a putative negative regulator of PaSPL7, microRNA156 is upregulated in vegetative meristem. By allele-specific assembly, we also identify a short nucleotide polymorphism (SNP) in the miRNA156 binding of PaSPL7. By genotyping a segregating population of inbred acrocona trees, we show a clear co-segregation between the early cone-setting phenotype and trees homozygous for the SNP. Hence, the data presented demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating cone-setting in the conifer P. abies.
47.	Albury, Nathan, et al. (författare) Cultural heritage is a child's right, so let's celebrate International Mother Language Day 2018 Annan publikation (populärvet., debatt m.m.)
48.	Alcorn, J, et al. (författare) Basic instrumentation for Hall A at Jefferson Lab 2004 Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 522:3, s. 294-346 Tidskriftsartikel (refereegranskat)abstract The instrumentation in Hall A at the Thomas Jefferson National Accelerator Facility was designed to study electro-and photo-induced reactions at very high luminosity and good momentum and angular resolution for at least one of the reaction products. The central components of Hall A are two identical high resolution spectrometers, which allow the vertical drift chambers in the focal plane to provide a momentum resolution of better than 2 x 10(-4). A variety of Cherenkov counters, scintillators and lead-glass calorimeters provide excellent particle identification. The facility has been operated successfully at a luminosity well in excess of 10(38) CM-2 s(-1). The research program is aimed at a variety of subjects, including nucleon structure functions, nucleon form factors and properties of the nuclear medium. (C) 2003 Elsevier B.V. All rights reserved.
49.	Alegria Zufía, Javier, Ph.D. 1992- (författare) Picophytoplankton seasonal dynamics in the Baltic Sea 2022 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Picophytoplankton (<2 μm diameter) is a diverse group of picocyanobacterial and photosynthetic picoeukaryotes (PPE).Picophytoplankton contribute significantly to total phytoplankton biomassand can dominate primary production in oceans, lakes and estuaries. In the estuarine Baltic Sea, the composition of picophytoplankton is linked to the north to south salinity gradient but knowledge of the seasonal dynamics interms of abundance, biomass and diversity is largely unknown. This thesis investigated the in situ dynamics, bottom up and top down controls of picocyanobacteria (SYN; consisting of primarily Synechococcus and Cyanobium among other genuses) and PPE at two sampling stations, one coastal and one offshore. Monitoring data over three years (2018-2020) showed high biomass contribution across all seasons. Picocyanobacterial peak abundances occurred from spring to summer at the coastal station and in late-summer to autumn at the offshore station (up to 4.7 × 105 cells mL-1).Differentiation of pigment populations showed that phycoerythrin rich(PE)-SYN was the main contributor to SYN abundances except at the coastalstation during summer, when PE-SYN and phycocyanin rich (PC)-SYN had equal contributions. PPE peak abundances occurred during late summer to autumn (up to 1.1 × 105 cells mL-1 cells ml-1). Temperature was linked topicophytoplankton growth and abundance, with PE-SYN, PCSYN and PPEadapted to different temperature ranges. Temperature also affected SYNnitrogen preference: SYN was nitrogen limited during early summer and at>15°C there was a preference for ammonium over nitrate. Clade A/B dominated the SYN community, except during summer at the coastal station when low nitrate and warm temperatures promoted S5.2 dominance. Grazing was observed to control SYN and PPE abundances and had an effect on the SYN community structure. Identification and laboratory experiments of key Synechococcus strains using a range of salinity, temperature and light conditions provided important insights into the physiological diversity of co-occurring ecotypes and links to the SYN dynamics that were observed in the field. In summary, this thesis provided novel information of picophytoplankton dynamics and community structure in the Baltic Sea. The results show that picophytoplankton play a relevant role in Baltic Sea and shows the importance of monitoring programs to understand picophytoplankton dynamics.
50.	Aleksich, Mariya, et al. (författare) XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates 2023 Ingår i: Journal of the American Chemical Society. - 0002-7863. ; 145:31, s. 17042-17055 Tidskriftsartikel (refereegranskat)abstract New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

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