SwePub - search: WFRF:(Raine R.)

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1.	Aad, G., et al. (author) 2010 swepub:Mat__t
2.	Aad, G., et al. (author) 2011 swepub:Mat__t
3.	Aad, G., et al. (author) 2010 swepub:Mat__t
4.	Aad, G., et al. (author) 2010 swepub:Mat__t
5.	2011 swepub:Mat__t
6.	Aad, G., et al. (author) 2010 swepub:Mat__t
7.	Schael, S., et al. (author) Electroweak measurements in electron positron collisions at W-boson-pair energies at LEP 2013 In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 532:4, s. 119-244 Research review (peer-reviewed)abstract Electroweak measurements performed with data taken at the electron positron collider LEP at CERN from 1995 to 2000 are reported. The combined data set considered in this report corresponds to a total luminosity of about 3 fb(-1) collected by the four LEP experiments ALEPH, DELPHI, 13 and OPAL, at centre-of-mass energies ranging from 130 GeV to 209 GeV. Combining the published results of the four LEP experiments, the measurements include total and differential cross-sections in photon-pair, fermion-pair and four-fermion production, the latter resulting from both double-resonant WW and ZZ production as well as singly resonant production. Total and differential cross-sections are measured precisely, providing a stringent test of the Standard Model at centre-of-mass energies never explored before in electron positron collisions. Final-state interaction effects in four-fermion production, such as those arising from colour reconnection and Bose Einstein correlations between the two W decay systems arising in WW production, are searched for and upper limits on the strength of possible effects are obtained. The data are used to determine fundamental properties of the W boson and the electroweak theory. Among others, the mass and width of the W boson, m(w) and Gamma(w), the branching fraction of W decays to hadrons, B(W -> had), and the trilinear gauge-boson self-couplings g(1)(Z), K-gamma and lambda(gamma), are determined to be: m(w) = 80.376 +/- 0.033 GeV Gamma(w) = 2.195 +/- 0.083 GeV B(W -> had) = 67.41 +/- 0.27% g(1)(Z) = 0.984(-0.020)(+0.018) K-gamma - 0.982 +/- 0.042 lambda(gamma) = 0.022 +/- 0.019. (C) 2013 Elsevier B.V. All rights reserved.
8.	Schael, S, et al. (author) Precision electroweak measurements on the Z resonance 2006 In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454 Research review (peer-reviewed)abstract We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
9.	Campbell, PJ, et al. (author) Pan-cancer analysis of whole genomes 2020 In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82- Journal article (peer-reviewed)abstract Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
10.	Abdesselam, A., et al. (author) Engineering for the ATLAS SemiConductor Tracker (SCT) end-cap 2008 In: Journal of Instrumentation. - 1748-0221. ; 3 Journal article (peer-reviewed)abstract The ATLAS SemiConductor Tracker (SCT) is a silicon-strip tracking detector which forms part of the ATLAS inner detector. The SCT is designed to track charged particles produced in proton-proton collisions at the Large Hadron Collider (LHC) at CERN at an energy of 14 TeV. The tracker is made up of a central barrel and two identical end-caps. The barrel contains 2112 silicon modules, while each end-cap contains 988 modules. The overall tracking performance depends not only on the intrinsic measurement precision of the modules but also on the characteristics of the whole assembly, in particular, the stability and the total material budget. This paper describes the engineering design and construction of the SCT end-caps, which are required to support mechanically the silicon modules, supply services to them and provide a suitable environment within the inner detector. Critical engineering choices are highlighted and innovative solutions are presented - these will be of interest to other builders of large-scale tracking detectors. The SCT end-caps will be fully connected at the start of 2008. Further commissioning will continue, to be ready for proton-proton collision data in 2008.
11.	Akkoyun, S., et al. (author) AGATA - Advanced GAmma Tracking Array 2012 In: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. - : Elsevier BV. - 0168-9002 .- 0167-5087 .- 1872-9576. ; 668, s. 26-58 Journal article (peer-reviewed)abstract The Advanced GAmma Tracking Array (AGATA) is a European project to develop and operate the next generation γ-ray spectrometer. AGATA is based on the technique of γ-ray energy tracking in electrically segmented high-purity germanium crystals. This technique requires the accurate determination of the energy, time and position of every interaction as a γ ray deposits its energy within the detector volume. Reconstruction of the full interaction path results in a detector with very high efficiency and excellent spectral response. The realisation of γ-ray tracking and AGATA is a result of many technical advances. These include the development of encapsulated highly segmented germanium detectors assembled in a triple cluster detector cryostat, an electronics system with fast digital sampling and a data acquisition system to process the data at a high rate. The full characterisation of the crystals was measured and compared with detector- response simulations. This enabled pulse-shape analysis algorithms, to extract energy, time and position, to be employed. In addition, tracking algorithms for event reconstruction were developed. The first phase of AGATA is now complete and operational in its first physics campaign. In the future AGATA will be moved between laboratories in Europe and operated in a series of campaigns to take advantage of the different beams and facilities available to maximise its science output. The paper reviews all the achievements made in the AGATA project including all the necessary infrastructure to operate and support the spectrometer. © 2011 Elsevier B.V. All rights reserved.
12.	Abdesselam, A., et al. (author) The ATLAS semiconductor tracker end-cap module 2007 In: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 575:3, s. 353-389 Journal article (peer-reviewed)abstract The challenges for the tracking detector systems at the LHC are unprecedented in terms of the number of channels, the required read-out speed and the expected radiation levels. The ATLAS Semiconductor Tracker. (SCT) end-caps have a total of about 3 million electronics channels each reading out every 25 ns into its own on-chip 3.3 mu s buffer. The highest anticipated dose after 10 years operation is 1.4x10(14) cm(-2) in units of 1 MeV neutron equivalent (assuming the damage factors scale with the non-ionising energy loss). The forward tracker has 1976 double-sided modules, mostly of area similar to 70 cm(2), each having 2 x 768 strips read out by six ASICs per side. The requirement to achieve an average perpendicular radiation length of 1.5% X-0, while coping with up to 7 W dissipation per module (after irradiation), leads to stringent constraints on the thermal design. The additional requirement of 1500e(-) equivalent noise charge (ENC) rising to only 1800e(-) ENC after irradiation, provides stringent design constraints on both the high-density Cu/Polyimide flex read-out circuit and the ABCD3TA read-out ASICs. Finally, the accuracy of module assembly must not compromise the 16 mu m (r phi) resolution perpendicular to the strip directions or 580 mu m radial resolution coming from the 40 mrad front-back stereo angle. A total of 2210 modules were built to the tight tolerances and specifications required for the SCT. This was 234 more than the 1976 required and represents a yield of 93%. The component flow was at times tight, but the module production rate of 40-50 per week was maintained despite this. The distributed production was not found to be a major logistical problem and it allowed additional flexibility to take advantage of where the effort was available, including any spare capacity, for building the end-cap modules. The collaboration that produced the ATLAS SCT end-cap modules kept in close contact at all times so that the effects of shortages or stoppages at different sites could be rapidly resolved.
13.	Alexandrov, Ludmil B., et al. (author) Signatures of mutational processes in human cancer 2013 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 500:7463, s. 415-421 Journal article (peer-reviewed)abstract All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
14.	Clement, E., et al. (author) Conceptual design of the AGATA 1 π array at GANIL 2017 In: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 855, s. 1-12 Journal article (peer-reviewed)abstract The Advanced GAmma Tracking Array (AGATA) has been installed at the GANIL facility, Caen-France. This setup exploits the stable and radioactive heavy-ions beams delivered by the cyclotron accelerator complex of GANIL. Additionally, it benefits from a large palette of ancillary detectors and spectrometers to address in-beam γ-ray spectroscopy of exotic nuclei. The set-up has been designed to couple AGATA with a magnetic spectrometer, charged-particle and neutron detectors, scintillators for the detection of high-energy γ rays and other devices such as a plunger to measure nuclear lifetimes. In this paper, the design and the mechanical characteristics of the set-up are described. Based on simulations, expected performances of the AGATA l π array are presented.
15.	Davies, Helen R., et al. (author) HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures 2017 In: Nature Medicine. - : Springer Science and Business Media LLC. - 1546-170X .- 1078-8956. ; 23:4, s. 517-525 Journal article (peer-reviewed)abstract Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition.
16.	Nik-Zainal, Serena, et al. (author) Landscape of somatic mutations in 560 breast cancer whole-genome sequences 2016 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54 Journal article (peer-reviewed)abstract We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
17.	Nik-Zainal, Serena, et al. (author) Mutational Processes Molding the Genomes of 21 Breast Cancers 2012 In: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 149:5, s. 979-993 Journal article (peer-reviewed)abstract All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis,'' was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed.
18.	Nik-Zainal, Serena, et al. (author) The Life History of 21 Breast Cancers 2012 In: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 149:5 Journal article (peer-reviewed)abstract Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.
19.	Shlien, Adam, et al. (author) Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer 2016 In: Cell Reports. - : Elsevier BV. - 2211-1247. ; 16:7, s. 2032-2046 Journal article (peer-reviewed)abstract Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation.
20.	Van de Heyning, P, et al. (author) Standards of practice in the field of hearing implants 2013 In: Cochlear implants international. - 1754-7628. ; 14 Suppl 2, s. S1-5 Journal article (peer-reviewed)
21.	Yakneen, S, et al. (author) Butler enables rapid cloud-based analysis of thousands of human genomes 2020 In: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288- Journal article (peer-reviewed)abstract We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
22.	Yakneen, S, et al. (author) Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes 2023 In: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 41:4, s. 578-578 Journal article (other academic/artistic)abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
23.	Gavilan, J, et al. (author) Quality standards for bone conduction implants 2015 In: Acta oto-laryngologica. - : Informa UK Limited. - 1651-2251 .- 0001-6489. ; 135:12, s. 1277-1285 Journal article (peer-reviewed)
24.	Glodzik, Dominik, et al. (author) A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers 2017 In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 49:3, s. 341-348 Journal article (peer-reviewed)abstract Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous-recombination-repair deficiency. Notably, these tandem-duplication hotspots were enriched in breast cancer germline susceptibility loci (odds ratio (OR) = 4.28) and breast-specific 'super-enhancer' regulatory elements (OR = 3.54). These hotspots may be sites of selective susceptibility to double-strand-break damage due to high transcriptional activity or, through incrementally increasing copy number, may be sites of secondary selective pressure. The transcriptomic consequences ranged from strong individual oncogene effects to weak but quantifiable multigene expression effects. We thus present a somatic-rearrangement mutational process affecting coding sequences and noncoding regulatory elements and contributing a continuum of driver consequences, from modest to strong effects, thereby supporting a polygenic model of cancer development.
25.	Goldkuhle, A., et al. (author) Lifetime measurements in Ti-52,Ti-54 to study shell evolution toward N=32 2019 In: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 100:5 Journal article (peer-reviewed)abstract Lifetimes of the excited states in the neutron-rich Ti-52,Ti-54 nuclei, produced in a multinucleon-transfer reaction, were measured by employing the Cologne plunger device and the recoil-distance Doppler-shift method. The experiment was performed at the Grand Accelerateur National d'Ions Lourds facility by using the Advanced Gamma Tracking Array for the gamma-ray detection, coupled to the large-acceptance variable mode spectrometer for an event-by-event particle identification. A comparison between the transition probabilities obtained from the measured lifetimes of the 2(1)(+) to 8(1)(+) yrast states in Ti-52,Ti-54 and that from the shell-model calculations based on the well-established GXPF1A, GXPF1B, and KB3G fp shell interactions support the N = 32 subshell closure. The B(E2) values for Ti-52 determined in this work are in disagreement with the known data, but are consistent with the predictions of the shell-model calculations and reduce the previously observed pronounced staggering across the even-even titanium isotopes.
26.	Rajan, G, et al. (author) Hearing preservation cochlear implantation in children: The HEARRING Group consensus and practice guide 2018 In: Cochlear implants international. - : Informa UK Limited. - 1754-7628 .- 1467-0100. ; 19:1, s. 1-13 Journal article (peer-reviewed)
27.	Reed, R. A., et al. (author) Anthology of the Development of Radiation Transport Tools as Applied to Single Event Effects 2013 In: IEEE Transactions on Nuclear Science. - : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9499 .- 1558-1578. ; 60:3, s. 1876-1911 Journal article (peer-reviewed)abstract This anthology contains contributions from eleven different groups, each developing and/or applying Monte Carlo-based radiation transport tools to simulate a variety of effects that result from energy transferred to a semiconductor material by a single particle event. The topics span from basic mechanisms for single-particle induced failures to applied tasks like developing websites to predict on-orbit single event failure rates using Monte Carlo radiation transport tools.
28.	Skarzynski, H, et al. (author) Towards a consensus on a hearing preservation classification system 2013 In: Acta oto-laryngologica. Supplementum. - : Informa UK Limited. - 0365-5237 .- 0001-6489 .- 1651-2251. ; 133:564, s. 3-13 Journal article (peer-reviewed)
29.	Eeraerts, Maxime, et al. (author) Synthesis of highbush blueberry pollination research reveals region-specific differences in the contributions of honeybees and wild bees 2023 In: Journal of Applied Ecology. - 0021-8901. ; 60:12, s. 2528-2539 Research review (peer-reviewed)abstract Highbush blueberry production has expanded worldwide in recent decades. To safeguard future yields, it is essential to understand if insect pollination is limiting current blueberry production and which insects contribute to pollination in different production regions. We present a systematic review including a set of meta-analyses on insect-mediated pollination in highbush blueberry. We summarize the geographic distribution of research, the abundance of different pollinator taxa and their relative pollination contributions. Using raw data from 21 studies, totalling 496 site replicates, we determine the degree of pollination service and pollen limitation (i.e. combining open pollination levels with experimental bagged and/or hand pollination treatments), as well as the contribution of honeybees and wild bees to pollination (i.e. observational, open pollination). Most studies originate from North America, focusing on only a few cultivars. Honeybees are the dominant pollinator, and wild bees are occasionally abundant. Wild bees are more efficient pollinators on a single-visit basis compared to honeybees, which increases their relative pollination contribution compared to their relative abundance. Insect-mediated pollination services increased blueberry fruit set, berry weight and seed set (R2 values: 64.8%, 75.9% and 75.2% respectively). We often detected pollen limitation, indicated by an increase in fruit set, berry weight and seed set (R2: 10.1%, 18.2% and 21.5%, respectively), with additional hand pollination. Increasing visitation of honeybees and wild bees contributed to blueberry pollination by increasing fruit set (R2: 5.4% and 3.5%), berry weight (R2: 6.5% and 2.8%) and seed set (R2: 6.4% and 3.8%) respectively. Bee contributions to fruit set and berry weight were variable across regions. Synthesis and application: A diverse community of insects, primarily bees, contributes to highbush blueberry pollination and yield. However, pollination deficits are common. The finding that both honeybees and wild bees enhance pollination highlights the possibility of adopting different management strategies that utilize honeybees, wild bees or both depending on the specific context and region. This further emphasizes the general importance of conserving pollinator health and diversity. Our synthesis highlights data gaps and areas for future research to better understand the pollination contribution of different pollinators to crops that are expanding globally.
30.	Rodriguez-Martin, B, et al. (author) Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition 2020 In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 52:3, s. 306- Journal article (peer-reviewed)abstract About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of 22 L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.
31.	Bertoldi, Bridget M., et al. (author) Pursuing the developmental aims of the triarchic model of psychopathy : Creation and validation of triarchic scales for use in the USC 2022 In: Development and psychopathology (Print). - : Cambridge University Press. - 0954-5794 .- 1469-2198. ; 34:3, s. 1088-1103 Journal article (peer-reviewed)abstract The triarchic model was advanced as an integrative, trait-based framework for investigating psychopathy using different assessment methods and across developmental periods. Recent research has shown that the triarchic traits of boldness, meanness, and disinhibition can be operationalized effectively in youth, but longitudinal research is needed to realize the model's potential to advance developmental understanding of psychopathy. We report on the creation and validation of scale measures of the triarchic traits using questionnaire items available in the University of Southern California Risk Factors for Antisocial Behavior (RFAB) project, a large-scale longitudinal study of the development of antisocial behavior that includes measures from multiple modalities (self-report, informant rating, clinical-diagnostic, task-behavioral, physiological). Using a construct-rating and psychometric refinement approach, we developed triarchic scales that showed acceptable reliability, expected intercorrelations, and good temporal stability. The scales showed theory-consistent relations with external criteria including measures of psychopathy, internalizing/externalizing psychopathology, antisocial behavior, and substance use. Findings demonstrate the viability of measuring triarchic traits in the RFAB sample, extend the known nomological network of these traits into the developmental realm, and provide a foundation for follow-up studies examining the etiology of psychopathic traits and their relations with multimodal measures of cognitive-affective function and proneness to clinical problems.
32.	Blauw, A. N., et al. (author) The use of fuzzy logic for data analysis and modelling of European harmful algal blooms: results of the HABES project 2006 In: African Journal of Marine Science. - 1814-232X. ; 28:2, s. 365-369 Journal article (peer-reviewed)abstract Fuzzy logic was applied to model blooms of Nodularia spumigena, Dinophysis spp., Alexandrium minutum, Karenia mikimotoi and Phaeocystis globosa at various European sites as part of the Harmful Algal Blooms Expert System (HABES) project. This modelling approach was useful in performing integrated analyses of interacting physical and biological factors involved in HABs. A basic knowledge of HAB formation and sufficient data are a prerequisite for successful bloom prediction.
33.	Bondjers, K, et al. (author) Impact of morally stressful situations on healthcare workers during the COVID-19 pandemic - an international perspective 2023 In: EUROPEAN JOURNAL OF PSYCHOTRAUMATOLOGY. - 2000-8198. ; 14 Conference paper (other academic/artistic)
34.	Collantes, Edward Ryan A., et al. (author) EFEMP1 rare variants cause familial juvenile-onset open-angle glaucoma 2022 In: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 43:2, s. 240-252 Journal article (peer-reviewed)abstract Juvenile open-angle glaucoma (JOAG) is a severe type of glaucoma with onset before age 40 and dominant inheritance. Using exome sequencing we identified 3 independent families from the Philippines with novel EFEMP1 variants (c.238A>T, p.Asn80Tyr; c.1480T>C, p.Ter494Glnext*29; and c.1429C>T, p.Arg477Cys) co-segregating with disease. Affected variant carriers (N = 34) exhibited severe disease with average age of onset of 16 years and with 76% developing blindness. To investigate functional effects, we transfected COS7 cells with vectors expressing the three novel EFEMP1 variants and showed that all three variants found in JOAG patients caused significant intracellular protein aggregation and retention compared to wild type and also compared to EFEMP1 variants associated with other ocular phenotypes including an early-onset form of macular degeneration, Malattia Leventinese/Doyne's Honeycomb retinal dystrophy. These results suggest that rare EFEMP1 coding variants can cause JOAG through a mechanism involving protein aggregation and retention, and that the extent of intracellular retention correlates with disease phenotype. This is the first report of EFEMP1 variants causing JOAG, expanding the EFEMP1 disease spectrum. Our results suggest that EFEMP1 mutations appear to be a relatively common cause of JOAG in Filipino families, an ethnically diverse population.
35.	Eeraerts, Maxime, et al. (author) Pollination deficits and their relation with insect pollinator visitation are cultivar-dependent in an entomophilous crop 2024 In: Agriculture, Ecosystems and Environment. - 0167-8809. ; 369 Journal article (peer-reviewed)abstract Insects contribute considerably to global crop pollination, with pollination deficits being documented for multiple entomophilous or pollinator-dependent crops. Different cultivars of crops are being cultivated within and across production regions, so it is essential to understand the cultivar variability of pollination deficits. Here, we used a dataset from 286 sites from multiple production regions to develop a synthesis on pollination deficits in two widely cultivated highbush blueberry cultivars, ‘Bluecrop’ and ‘Duke’. Additionally, we determined if bee visitation or bee richness reduces pollination deficits in these cultivars. On average, neither cultivar showed pollination deficits regarding fruit set. However, for ‘Bluecrop’ we found pollination deficits for berry weight and seed set, which was not the case for ‘Duke’. Increasing total bee visitation reduced pollination deficits of both berry weight and seed set for ‘Bluecrop’. More specifically, a non-linear, negative exponential model best predicted this relation between bee visitation and pollination deficits. Our results highlight that pollination deficits and responses to pollinator visitation are variable between different cultivars of a single crop, which suggests opportunities to use certain cultivars that are less dependent on insect-mediated pollination in landscapes and regions where pollination services have been compromised. In addition, the non-linear response between bee visitation and pollination deficits suggests that optimal bee visitation rates need to be determined to improve pollination management and crop yield and to support accurate economic valuations of pollination services.
36.	Fegraeus, K, et al. (author) An endothelial regulatory module links blood pressure regulation with elite athletic performance 2024 In: PLoS genetics. - 1553-7404. ; 20:6, s. e1011285- Journal article (peer-reviewed)
37.	Fegraeus, Kim, et al. (author) An endothelial regulatory module links blood pressure regulation with elite athletic performance 2024 In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 20:6 Journal article (peer-reviewed)abstract The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.
38.	Giménez-García, Angel, et al. (author) Pollination supply models from a local to global scale 2023 In: Web Ecology. - 1399-1183. ; 23:2, s. 99-129 Journal article (peer-reviewed)abstract Ecological intensification has been embraced with great interest by the academic sector but is still rarely taken up by farmers because monitoring the state of different ecological functions is not straightforward. Modelling tools can represent a more accessible alternative of measuring ecological functions, which could help promote their use amongst farmers and other decision-makers. In the case of crop pollination, modelling has traditionally followed either a mechanistic or a data-driven approach. Mechanistic models simulate the habitat preferences and foraging behaviour of pollinators, while data-driven models associate georeferenced variables with real observations. Here, we test these two approaches to predict pollination supply and validate these predictions using data from a newly released global dataset on pollinator visitation rates to different crops. We use one of the most extensively used models for the mechanistic approach, while for the data-driven approach, we select from among a comprehensive set of state-of-The-Art machine-learning models. Moreover, we explore a mixed approach, where data-derived inputs, rather than expert assessment, inform the mechanistic model. We find that, at a global scale, machine-learning models work best, offering a rank correlation coefficient between predictions and observations of pollinator visitation rates of 0.56. In turn, the mechanistic model works moderately well at a global scale for wild bees other than bumblebees. Biomes characterized by temperate or Mediterranean forests show a better agreement between mechanistic model predictions and observations, probably due to more comprehensive ecological knowledge and therefore better parameterization of input variables for these biomes. This study highlights the challenges of transferring input variables across multiple biomes, as expected given the different composition of species in different biomes. Our results provide clear guidance on which pollination supply models perform best at different spatial scales-the first step towards bridging the stakeholder-Academia gap in modelling ecosystem service delivery under ecological intensification.
39.	Kabath, Petr, et al. (author) TOI-2046b, TOI-1181b, and TOI-1516b, three new hot Jupiters from TESS: planets orbiting a young star, a subgiant, and a normal star 2022 In: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 513:4, s. 5955-5972 Journal article (peer-reviewed)abstract We present the confirmation and characterization of three hot Jupiters, TOI-118 lb, TOI-1516b, and TOI-2046b, discovered by the "NESS space mission. The reported hot Jupiters have orbital periods between 1.4 and 2.05 d. The masses of the three planets are 1.18 +/- 0.14 Mj, 3.16 +/- 0.12 Mj, and 2.30 +/- 0.28 Mj, for TOI-1181b, TOI-1516b, and TOI-2046b, respectively. The stellar host of TOI-1181b is a F9IV star, whereas TOI-1516b and TOI-2046b orbit F main sequence host stars. The ages of the first two systems are in the range of 2-5 Gyrs. However, TOI-2046 is among the few youngest known planetary systems hosting a hot Jupiter, with an age estimate of 100-400 Myrs. The main instruments used for the radial velocity follow-up of these three planets are located at OndIejov, Tautenburg, and McDonald Observatory, and all three are mounted on 2-3 m aperture telescopes, demonstrating that mid-aperture telescope networks can play a substantial role in the follow-up of gas giants discovered by TESS and in the future by PLATO.
40.	McNamee, Sara E., et al. (author) Distribution, occurrence and biotoxin composition of the main shellfish toxin producing microalgae within European waters : A comparison of methods of analysis 2016 In: Harmful Algae. - : Elsevier BV. - 1568-9883 .- 1878-1470. ; 55, s. 112-120 Journal article (peer-reviewed)abstract Harmful algal blooms (HABs) are a natural global phenomena emerging in severity and extent. Incidents have many economic, ecological and human health impacts. Monitoring and providing early warning of toxic HABs are critical for protecting public health. Current monitoring programmes include measuring the number of toxic phytoplankton cells in the water and biotoxin levels in shellfish tissue. As these efforts are demanding and labour intensive, methods which improve the efficiency are essential. This study compares the utilisation of a multitoxin surface plasmon resonance (multitoxin SPR) biosensor with enzyme-linked immunosorbent assay (ELISA) and analytical methods such as high performance liquid chromatography with fluorescence detection (HPLC-FLD) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for toxic HAB monitoring efforts in Europe. Seawater samples (n = 256) from European waters, collected 2009-2011, were analysed for biotoxins: saxitoxin and analogues, okadaic acid and dinophysistoxins 1/2 (VDU /DTX2) and domoic acid responsible for paralytic shellfish poisoning (PSP), diarrheic shellfish poisoning (DSP) and amnesic shellfish poisoning (ASP), respectively. Biotoxins were detected mainly in samples from Spain and Ireland. France and Norway appeared to have the lowest number of toxic samples. Both the multitoxin SPR biosensor and the RNA microarray were more sensitive at detecting toxic HABs than standard light microscopy phytoplankton monitoring. Correlations between each of the detection methods were performed with the overall agreement, based on statistical 2 x 2 comparison tables, between each testing platform ranging between 32% and 74% for all three toxin families illustrating that one individual testing method may not be an ideal solution. An efficient early warning monitoring system for the detection of toxic HABs could therefore be achieved by combining both the multitoxin SPR biosensor and RNA microarray. (C) 2016 Elsevier B.V. All rights reserved.
41.	Papaemmanuil, E, et al. (author) Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts 2011 In: The New England journal of medicine. - 1533-4406. ; 365:15, s. 1384-1395 Journal article (peer-reviewed)
42.	Raine, T, et al. (author) Trends in corticosteroid (CS) use over time and following diagnosis in patients with Inflammatory Bowel Disease (IBD), using IBM® MarketScan® 2022 In: JOURNAL OF CROHNS & COLITIS. - 1873-9946. ; 16, s. I454-I455 Conference paper (other academic/artistic)
43.	Raine, T, et al. (author) Trends in corticosteroid (CS) use over time and following diagnosis in patients with Inflammatory Bowel Disease (IBD), using IBM (R) MarketScan (R) 2022 In: JOURNAL OF CROHNS & COLITIS. - 1873-9946. ; 16, s. I454-I455 Conference paper (other academic/artistic)
44.	Rääf, Christopher, et al. (author) Ecological half-time and effective dose from Chernobyl debris and from nuclear weapons fallout of Cs-137 as measured in different Swedish populations 2006 In: HEALTH PHYSICS. - 0017-9078 .- 1538-5159. ; 90:5, s. 446-458 Journal article (peer-reviewed)
45.	Rääf, Christopher, et al. (author) Transfer of (137)Cs from Chernobyl debris and nuclear weapons fallout to different Swedish population groups. 2006 In: Science of the Total Environment. - : Elsevier BV. - 1879-1026 .- 0048-9697. ; 367:Feb 24, s. 324-340 Journal article (peer-reviewed)abstract Data from measurements on the body burden Of (CS)-C-134, Cs-137 and K-40 in various Swedish populations between 1959 and 2001 has been compiled into a national database. The compilation is a co-operation between the Departments of Radiation Physics in Malmo and Goteborg, the National Radiation Protection Authority (SSI) and the Swedish Defense Research Agency (FOI). In a previous study the effective ecological half time and the associated effective dose to various Swedish populations due to internal contamination of Cs-134 and Cs-137 have been assessed using the database. In this study values of human body burden have been combined with data on the local and regional ground deposition of fallout from nuclear weapons tests (only Cs-137) and Chernobyl debris (both Cs-134 and (CS)-C-137), which have enabled estimates of the radioecological transfer in the studied populations. The assessment of the database shows that the transfer of radiocesium from Chernobyl fallout to humans varies considerably between various populations in Sweden. In terms of committed effective dose over a 70 y period from internal contamination per unit activity deposition, the general (predominantly urban) Swedish population obtains 20-30 mu Sv/kBq m(-2). Four categories of populations exhibit higher radioecological transfer than the general population; i.) reindeer herders (similar to 700 mu Sv/kBq m(-2)), ii.) hunters in the counties dominated by forest vegetation (similar to 100 mu Sv/kBq m(-2)), iii.) rural non-farming populations living in sub-arctic areas (40-150 mu Sv/kBq m(-2)), and iv.) farmers (similar to 50 mu Sv/kBq m(-2)). Two important factors determine the aggregate transfer from ground deposition to man; i.) dietary habits (intakes of foodstuff originating from natural and semi-natural ecosystems), and ii.) inclination to follow the recommended food restriction by the authorities. The transfer to the general population is considerably lower (similar to a factor of 3) for the Chernobyl fallout than during the 1960s and 70s, which is partly explained by a higher awareness of the pathways of radiocaesium to man both by the public and by the regulating authorities, and by the time-pattern of the nuclear weapons fallout during the growth season in Sweden. (c) 2005 Elsevier B.V. All rights reserved.
46.	Skuladottir, GV, et al. (author) Long term orexigenic effect of a novel melanocortin 4 receptor selectiveantagonist. 1999 In: Br J Pharmacol. ; 126, s. 27- Journal article (peer-reviewed)
47.	Tran, Quang H., et al. (author) TOI-1670 b and c: An Inner Sub-Neptune with an Outer Warm Jupiter Unlikely to Have Originated from High-eccentricity Migration 2022 In: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 163:5 Journal article (peer-reviewed)abstract We report the discovery of two transiting planets around the bright (V = 9.9 mag) main-sequence F7 star TOI-1670 by the Transiting Exoplanet Survey Satellite. TOI-1670 b is a sub-Neptune (R-b = 2.06(-0.15)(+0.19) R-circle plus) on a 10.9 day orbit, and TOI-1670 c is a warm Jupiter (R-c= 0.987(-0.025)(+0.025) R-Jup) on a 40.7 day orbit. Using radial velocity observations gathered with the Tull Coude Spectrograph on the Harlan J. Smith telescope and HARPS-N on the Telescopio Nazionale Galileo, we find a planet mass of M-c = 0.63(-0.08)(+0.09) M(Jup )for the outer warm Jupiter, implying a mean density of rho(c) = 0.81(-0.11)(+0.13) g cm(-3). The inner sub-Neptune is undetected in our radial velocity data (M-b < 0.13 M-Jup at the 99% confidence level). Multiplanet systems like TOI-1670 hosting an outer warm Jupiter on a nearly circular orbit (l(e) = 0.09(-0.04)(+0.05)) and one or more inner coplanar planets are more consistent with "gentle" formation mechanisms such as disk migration or in situ formation rather than high-eccentricity migration. Of the 11 known systems with a warm Jupiter and a smaller inner companion, eight (73%) are near a low-order mean-motion resonance, which can be a signature of migration. TOI-1670 joins two other systems (27% of this subsample) with period commensurabilities greater than 3, a common feature of in situ formation or halted inward migration. TOI-1670 and the handful of similar systems support a diversity of formation pathways for warm Jupiters.
48.	Van de Heyning, P, et al. (author) The reliability of hearing implants: report on the type and incidence of cochlear implant failures 2020 In: Cochlear implants international. - : Informa UK Limited. - 1754-7628 .- 1467-0100. ; 21:4, s. 228-237 Journal article (peer-reviewed)
49.	Westra, Edze R, et al. (author) H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO 2010 In: Molecular Microbiology. - : Wiley. - 0950-382X .- 1365-2958. ; 77:6, s. 1380-1393 Journal article (peer-reviewed)abstract The recently discovered prokaryotic CRISPR/Cas defence system provides immunity against viral infections and plasmid conjugation. It has been demonstrated that in Escherichia coli transcription of the Cascade genes (casABCDE) and to some extent the CRISPR array is repressed by heat-stable nucleoid-structuring (H-NS) protein, a global transcriptional repressor. Here we elaborate on the control of the E. coli CRISPR/Cas system, and study the effect on CRISPR-based anti-viral immunity. Transformation of wild-type E. coli K12 with CRISPR spacers that are complementary to phage Lambda does not lead to detectable protection against Lambda infection. However, when an H-NS mutant of E. coli K12 is transformed with the same anti-Lambda CRISPR, this does result in reduced sensitivity to phage infection. In addition, it is demonstrated that LeuO, a LysR-type transcription factor, binds to two sites flanking the casA promoter and the H-NS nucleation site, resulting in derepression of casABCDE12 transcription. Overexpression of LeuO in E. coli K12 containing an anti-Lambda CRISPR leads to an enhanced protection against phage infection. This study demonstrates that in E. coli H-NS and LeuO are antagonistic regulators of CRISPR-based immunity.
50.	Wijn, Stan R.W., et al. (author) Arthroscopic partial meniscectomy for the degenerative meniscus tear : a comparison of patients included in RCTs and prospective cohort studies 2023 In: Acta Orthopaedica. - 1745-3674. ; 94, s. 570-576 Journal article (peer-reviewed)abstract Background and purpose — Concerns exist regarding the generalizability of results from randomized controlled trials (RCTs) evaluating arthroscopic partial meniscectomy (APM) to treat degenerative meniscus tears. It has been suggested that study populations are not representative of subjects selected for surgery in daily clinical practice. There-fore, we aimed to compare patients included in trials and prospective cohort studies that received APM for a degenerative meniscus tear. Patients and methods — Individual participant data from 4 RCTs and 2 cohort studies undergoing APM were collected. 1,970 patients were analyzed: 605 patients included in RCTs and 1,365 included in the cohorts. We compared patient and disease characteristics, knee pain, overall knee function, and health-related quality of life at baseline between the RCT and cohort groups using standardized differences, ratios comparing the variance of continuous covariates, and graphical methods such as quantile–quantile plots, side-by-side boxplots, and non-parametric density plots. Results — Differences between RCT and the cohort were observed primarily in age (younger patients in the cohort; standardized difference: 0.32) and disease severity, with the RCT group having more severe symptoms (standardized difference: 0.38). While knee pain, overall knee function, and quality of life generally showed minimal differences between the 2 groups, it is noteworthy that the largest observed difference was in knee pain, where the cohort group scored 7 points worse (95% confidence interval 5–9, standardized difference: 0.29). Conclusion — Patients in RCTs were largely representative of those in cohort studies regarding baseline scores, though variations in age and disease severity were observed. Younger patients with less severe osteoarthritis were more common in the cohort; however, trial participants still appear to be broadly representative of the target population.

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