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1.
  • Richards, Stephen, et al. (author)
  • Genome Sequence of the Pea Aphid Acyrthosiphon pisum
  • 2010
  • In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
  • Journal article (peer-reviewed)abstract
    • Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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2.
  • Beal, Jacob, et al. (author)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • Journal article (peer-reviewed)abstract
    • Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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3.
  • Falster, Daniel, et al. (author)
  • AusTraits, a curated plant trait database for the Australian flora
  • 2021
  • In: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
  • Journal article (peer-reviewed)abstract
    • We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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4.
  • Gaulton, Kyle J, et al. (author)
  • Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
  • 2015
  • In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
  • Journal article (peer-reviewed)abstract
    • We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
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5.
  • Berne, Olivier, et al. (author)
  • PDRs4All : A JWST Early Release Science Program on Radiative Feedback from Massive Stars
  • 2022
  • In: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 134:1035
  • Journal article (peer-reviewed)abstract
    • Massive stars disrupt their natal molecular cloud material through radiative and mechanical feedback processes. These processes have profound effects on the evolution of interstellar matter in our Galaxy and throughout the universe, from the era of vigorous star formation at redshifts of 1-3 to the present day. The dominant feedback processes can be probed by observations of the Photo-Dissociation Regions (PDRs) where the far-ultraviolet photons of massive stars create warm regions of gas and dust in the neutral atomic and molecular gas. PDR emission provides a unique tool to study in detail the physical and chemical processes that are relevant for most of the mass in inter- and circumstellar media including diffuse clouds, proto-planetary disks, and molecular cloud surfaces, globules, planetary nebulae, and star-forming regions. PDR emission dominates the infrared (IR) spectra of star-forming galaxies. Most of the Galactic and extragalactic observations obtained with the James Webb Space Telescope (JWST) will therefore arise in PDR emission. In this paper we present an Early Release Science program using the MIRI, NIRSpec, and NIRCam instruments dedicated to the observations of an emblematic and nearby PDR: the Orion Bar. These early JWST observations will provide template data sets designed to identify key PDR characteristics in JWST observations. These data will serve to benchmark PDR models and extend them into the JWST era. We also present the Science-Enabling products that we will provide to the community. These template data sets and Science-Enabling products will guide the preparation of future proposals on star-forming regions in our Galaxy and beyond and will facilitate data analysis and interpretation of forthcoming JWST observations.
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6.
  • Brown, Brielin C., et al. (author)
  • Multiset correlation and factor analysis enables exploration of multi-omics data
  • 2023
  • In: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 3:8, s. 100359-
  • Journal article (peer-reviewed)abstract
    • Multi-omics datasets are becoming more common, necessitating better integration methods to realize their revolutionary potential. Here, we introduce multi-set correlation and factor analysis (MCFA), an unsupervised integration method tailored to the unique challenges of high-dimensional genomics data that enables fast inference of shared and private factors. We used MCFA to integrate methylation markers, protein expression, RNA expression, and metabolite levels in 614 diverse samples from the Trans-Omics for Precision Medicine/Multi-Ethnic Study of Atherosclerosis multi-omics pilot. Samples cluster strongly by ancestry in the shared space, even in the absence of genetic information, while private spaces frequently capture dataset-specific technical variation. Finally, we integrated genetic data by conducting a genome-wide association study (GWAS) of our inferred factors, observing that several factors are enriched for GWAS hits and trans-expression quantitative trait loci. Two of these factors appear to be related to metabolic disease. Our study provides a foundation and framework for further integrative analysis of ever larger multi-modal genomic datasets.
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7.
  • Aartsen, M. G., et al. (author)
  • All-flavour search for neutrinos from dark matter annihilations in the Milky Way with IceCube/DeepCore
  • 2016
  • In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 76:10
  • Journal article (peer-reviewed)abstract
    • We present the first IceCube search for a signal of dark matter annihilations in the Milky Way using all-flavour neutrino-induced particle cascades. The analysis focuses on the DeepCore sub-detector of IceCube, and uses the surrounding IceCube strings as a veto region in order to select starting events in the DeepCore volume. We use 329 live-days of data from IceCube operating in its 86-string configuration during 2011-2012. No neutrino excess is found, the final result being compatible with the background-only hypothesis. From this null result, we derive upper limits on the velocity-averaged self-annihilation cross-section, , for dark matter candidate masses ranging from 30 GeV up to 10 TeV, assuming both a cuspy and a flat-cored dark matter halo profile. For dark matter masses between 200 GeV and 10 TeV, the results improve on all previous IceCube results on , reaching a level of 10 cm s, depending on the annihilation channel assumed, for a cusped NFW profile. The analysis demonstrates that all-flavour searches are competitive with muon channel searches despite the intrinsically worse angular resolution of cascades compared to muon tracks in IceCube.
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8.
  • Aartsen, M. G., et al. (author)
  • An All-Sky Search For Three Flavors Of Neutrinos From Gamma-Ray Bursts With The Icecube Neutrino Observatory
  • 2016
  • In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 824:2
  • Journal article (peer-reviewed)abstract
    • We present the results and methodology of a search for neutrinos produced in the decay of charged pions created in interactions between protons and gamma-rays during the prompt emission of 807 gamma-ray bursts (GRBs) over the entire sky. This three-year search is the first in IceCube for shower-like Cherenkov light patterns from electron, muon, and tau neutrinos correlated with GRBs. We detect five low-significance events correlated with five GRBs. These events are consistent with the background expectation from atmospheric muons and neutrinos. The results of this search in combination with those of IceCube's four years of searches for track-like Cherenkov light patterns from muon neutrinos correlated with Northern-Hemisphere GRBs produce limits that tightly constrain current models of neutrino and ultra high energy cosmic ray production in GRB fireballs.
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9.
  • Aartsen, M. G., et al. (author)
  • Anisotropy In Cosmic-Ray Arrival Directions In The Southern Hemisphere Based On Six Years Of Data From The Icecube Detector
  • 2016
  • In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 826:2
  • Journal article (peer-reviewed)abstract
    • The IceCube Neutrino Observatory accumulated a total of 318 billion cosmic-ray-induced muon events between 2009 May and 2015 May. This data set was used for a detailed analysis of the sidereal anisotropy in the arrival directions of cosmic rays in the TeV to PeV energy range. The observed global sidereal anisotropy features large regions of relative excess and deficit, with amplitudes of the order of 10(-3) up to about 100 TeV. A decomposition of the arrival direction distribution into spherical harmonics shows that most of the power is contained in the low-multipole (l <= 4) moments. However, higher multipole components are found to be statistically significant down to an angular scale of less than 10 degrees, approaching the angular resolution of the detector. Above 100 TeV, a change in the morphology of the arrival direction distribution is observed, and the anisotropy is characterized by a wide relative deficit whose amplitude increases with primary energy up to at least 5 PeV, the highest energies currently accessible to IceCube. No time dependence of the large-and small-scale structures is observed in the period of six years covered by this analysis. The high-statistics data set reveals more details of the properties of the anisotropy and is potentially able to shed light on the various physical processes that are responsible for the complex angular structure and energy evolution.
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10.
  • Aartsen, M. G., et al. (author)
  • Improved limits on dark matter annihilation in the Sun with the 79-string IceCube detector and implications for supersymmetry
  • 2016
  • In: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :4
  • Journal article (peer-reviewed)abstract
    • We present an improved event-level likelihood formalism for including neutrino telescope data in global fits to new physics. We derive limits on spin-dependent dark matter-proton scattering by employing the new formalism in a re-analysis of data from the 79-string IceCube search for dark matter annihilation in the Sun, including explicit energy information for each event. The new analysis excludes a number of models in the weak-scale minimal supersymmetric standard model (MSSM) for the first time. This work is accompanied by the public release of the 79-string IceCube data, as well as an associated computer code for applying the new likelihood to arbitrary dark matter models.
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11.
  • Aartsen, M. G., et al. (author)
  • Lowering Icecube'S Energy Threshold For Point Source Searches In The Southern Sky
  • 2016
  • In: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 824:2
  • Journal article (peer-reviewed)abstract
    • Observation of a point source of astrophysical neutrinos would be a "smoking gun" signature of a cosmic-ray accelerator. While IceCube has recently discovered a diffuse flux of astrophysical neutrinos, no localized point source has been observed. Previous IceCube searches for point sources in the southern sky were restricted by either an energy threshold above a few hundred TeV or poor neutrino angular resolution. Here we present a search for southern sky point sources with greatly improved sensitivities to neutrinos with energies below 100 TeV. By selecting charged-current nu(mu) interacting inside the detector, we reduce the atmospheric background while retaining efficiency for astrophysical neutrino-induced events reconstructed with sub-degree angular resolution. The new event sample covers three years of detector data and leads to a factor of 10 improvement in sensitivity to point sources emitting below 100 TeV in the southern sky. No statistically significant evidence of point sources was found, and upper limits are set on neutrino emission from individual sources. A posteriori analysis of the highest-energy (similar to 100 TeV) starting event in the sample found that this event alone represents a 2.8 sigma deviation from the hypothesis that the data consists only of atmospheric background.
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12.
  • Aartsen, M. G., et al. (author)
  • Neutrino oscillation studies with IceCube-DeepCore
  • 2016
  • In: Nuclear Physics B. - : Elsevier BV. - 0550-3213 .- 1873-1562. ; 908, s. 161-177
  • Journal article (peer-reviewed)abstract
    • IceCube, a gigaton-scale neutrino detector located at the South Pole, was primarily designed to search for astrophysical neutrinos with energies of PeV and higher. This goal has been achieved with the detection of the highest energy neutrinos to date. At the other end of the energy spectrum, the DeepCore extension lowers the energy threshold of the detector to approximately 10 GeV and opens the door for oscillation studies using atmospheric neutrinos. An analysis of the disappearance of these neutrinos has been completed, with the results produced being complementary with dedicated oscillation experiments. Following a review of the detector principle and performance, the method used to make these calculations, as well as the results, is detailed. Finally, the future prospects of IceCube-DeepCore and the next generation of neutrino experiments at the South Pole (IceCube-Gen2, specifically the PINGU sub-detector) are briefly discussed.
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13.
  • Aartsen, M. G., et al. (author)
  • PINGU : a vision for neutrino and particle physics at the South Pole
  • 2017
  • In: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 44:5
  • Journal article (peer-reviewed)abstract
    • The Precision IceCube Next Generation Upgrade (PINGU) is a proposed low-energy in-fill extension to the IceCube Neutrino Observatory. With detection technology modeled closely on the successful IceCube example, PINGU will provide a 6 Mton effective mass for neutrino detection with an energy threshold of a few GeV. With an unprecedented sample of over 60 000 atmospheric neutrinos per year in this energy range, PINGU will make highly competitive measurements of neutrino oscillation parameters in an energy range over an order of magnitude higher than long-baseline neutrino beam experiments. PINGU will measure the mixing parameters theta(23) and Delta m(32)(2), including the octant of theta(23) for a wide range of values, and determine the neutrino mass ordering at 3 sigma median significance within five years of operation. PINGU's high precision measurement of the rate of nu(T) appearance will provide essential tests of the unitarity of the 3 x 3 PMNS neutrino mixing matrix. PINGU will also improve the sensitivity of searches for low mass dark matter in the Sun, use neutrino tomography to directly probe the composition of the Earth's core, and improve IceCube's sensitivity to neutrinos from Galactic supernovae. Reoptimization of the PINGU design has permitted substantial reduction in both cost and logistical requirements while delivering performance nearly identical to configurations previously studied.
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14.
  • Aartsen, M. G., et al. (author)
  • Searches for Sterile Neutrinos with the IceCube Detector
  • 2016
  • In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 117:7
  • Journal article (peer-reviewed)abstract
    • The IceCube neutrino telescope at the South Pole has measured the atmospheric muon neutrino spectrum as a function of zenith angle and energy in the approximate 320 GeV to 20 TeV range, to search for the oscillation signatures of light sterile neutrinos. No evidence for anomalous nu(mu) or (nu) over bar (mu) disappearance is observed in either of two independently developed analyses, each using one year of atmospheric neutrino data. New exclusion limits are placed on the parameter space of the 3 + 1 model, in which muon antineutrinos experience a strong Mikheyev-Smirnov-Wolfenstein-resonant oscillation. The exclusion limits extend to sin(2)2 theta(24) <= 0.02 at Delta m(2) similar to 0.3 eV(2) at the 90% confidence level. The allowed region from global analysis of appearance experiments, including LSND and MiniBooNE, is excluded at approximately the 99% confidence level for the global best-fit value of vertical bar U-e4 vertical bar(2).
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15.
  • Aartsen, M. G., et al. (author)
  • The Contribution Of Fermi-2Lac Blazars To Diffuse Tev-Pev Neutrino Flux
  • 2017
  • In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 835:1
  • Journal article (peer-reviewed)abstract
    • The recent discovery of a diffuse cosmic neutrino flux extending up to PeV energies raises the question of which astrophysical sources generate this signal. Blazars are one class of extragalactic sources which may produce such high-energy neutrinos. We present a likelihood analysis searching for cumulative neutrino emission from blazars in the 2nd Fermi-LAT AGN catalog (2LAC) using IceCube neutrino data set 2009-12, which was optimized for the detection of individual sources. In contrast to those in previous searches with IceCube, the populations investigated contain up to hundreds of sources, the largest one being the entire blazar sample in the 2LAC catalog. No significant excess is observed, and upper limits for the cumulative flux from these populations are obtained. These constrain the maximum contribution of 2LAC blazars to the observed astrophysical neutrino flux to 27% or less between around 10 TeV and 2 PeV, assuming the equipartition of flavors on Earth and a single power-law spectrum with a spectral index of -2.5. We can still exclude the fact that 2LAC blazars (and their subpopulations) emit more than 50% of the observed neutrinos up to a spectral index as hard as -2.2 in the same energy range. Our result takes into account the fact that the neutrino source count distribution is unknown, and it does not assume strict proportionality of the neutrino flux to the measured 2LAC gamma-ray signal for each source. Additionally, we constrain recent models for neutrino emission by blazars.
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16.
  • Aartsen, M. G., et al. (author)
  • The IceCube Neutrino Observatory : instrumentation and online systems
  • 2017
  • In: Journal of Instrumentation. - : IOP PUBLISHING LTD. - 1748-0221. ; 12
  • Journal article (peer-reviewed)abstract
    • The IceCube Neutrino Observatory is a cubic-kilometer-scale high-energy neutrino detector built into the ice at the South Pole. Construction of IceCube, the largest neutrino detector built to date, was completed in 2011 and enabled the discovery of high-energy astrophysical neutrinos. We describe here the design, production, and calibration of the IceCube digital optical module (DOM), the cable systems, computing hardware, and our methodology for drilling and deployment. We also describe the online triggering and data filtering systems that select candidate neutrino and cosmic ray events for analysis. Due to a rigorous pre-deployment protocol, 98.4% of the DOMs in the deep ice are operating and collecting data. IceCube routinely achieves a detector uptime of 99% by emphasizing software stability and monitoring. Detector operations have been stable since construction was completed, and the detector is expected to operate at least until the end of the next decade.
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17.
  • Bojan, Alicja J., 1980, et al. (author)
  • Critical factors in cut-out complication after gamma nail treatment of proximal femoral fractures.
  • 2013
  • In: BMC musculoskeletal disorders. - : Springer Science and Business Media LLC. - 1471-2474. ; 14:1
  • Journal article (peer-reviewed)abstract
    • BACKGROUND: The most common mechanical failure in the internal fixation of trochanteric hip fractures is the cut-out of the sliding screw through the femoral head. Several factors that influence this complication have been suggested, but there is no consensus as to the relative importance of each factor.The purpose of this study was to analyse the cut-out complication with respect to the following variables: patients' age, fracture type, fracture reduction, implant positioning and implant design. METHODS: 3066 consecutive patients were treated for trochanteric fractures with Gamma Nails between 1990 and 2002 at the Centre de Traumatologie et de l`Orthopedie (CTO), Strasbourg, France. Cut-out complications were identified by reviewing all available case notes and radiographs. Subsequently, the data were analysed by a single reviewer (AJB) with focus on the studied factors. RESULTS: Seventy-one cut-out complications were found (2.3%) of the 3066 trochanteric fractures. Cut-out failure associated with avascular head necrosis, pathologic fracture, deep infection or secondary to prior failure of other implants were excluded from the study (14 cases). The remaining 57 cases (1.85 %, median age 82.6, 79% females) were believed to have a biomechanical explanation for the cut-out failure. 41 patients had a basicervical or complex fracture type. A majority of cut-outs (43 hips, 75%) had a combination of the critical factors studied; non-anatomical reduction, non-optimal lag screw position and the characteristic fracture pattern found. CONCLUSIONS: The primary cut-out rate of 1.85% was low compared with the literature. A typical cut-out complication in our study is represented by an unstable fracture involving the trochanteric and cervical regions or the combination of both, non-anatomical reduction and non-optimal screw position. Surgeons confronted with proximal femoral fractures should carefully scrutinize preoperative radiographs to assess the primary fracture geometry and fracture classification. To reduce the risk of a cut-out it is important to achieve both anatomical reduction and optimal lag screw position as these are the only two factors that can be controlled by the surgeon.
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18.
  • Brown, Caleb Marshall, et al. (author)
  • Tooth counts through growth in diapsid reptiles : implications for interpreting individual and size-related variation in the fossil record
  • 2015
  • In: Journal of Anatomy. - : Wiley. - 0021-8782 .- 1469-7580. ; 226:4, s. 322-333
  • Journal article (peer-reviewed)abstract
    • Tooth counts are commonly recorded in fossil diapsid reptiles and have been used for taxonomic and phylogenetic purposes under the assumption that differences in the number of teeth are largely explained by interspecific variation. Although phylogeny is almost certainly one of the greatest factors influencing tooth count, the relative role of intraspecific variation is difficult, and often impossible, to test in the fossil record given the sample sizes available to palaeontologists and, as such, is best investigated using extant models. Intraspecific variation (largely manifested as size-related or ontogenetic variation) in tooth counts has been examined in extant squamates (lizards and snakes) but is poorly understood in archosaurs (crocodylians and dinosaurs). Here, we document tooth count variation in two species of extant crocodylians (Alligator mississippiensis and Crocodylus porosus) as well as a large varanid lizard (Varanus komodoensis). We test the hypothesis that variation in tooth count is driven primarily by growth and thus predict significant correlations between tooth count and size, as well as differences in the frequency of deviation from the modal tooth count in the premaxilla, maxilla, and dentary. In addition to tooth counts, we also document tooth allometry in each species and compare these results with tooth count change through growth. Results reveal no correlation of tooth count with size in any element of any species examined here, with the exception of the premaxilla of C.porosus, which shows the loss of one tooth position. Based on the taxa examined here, we reject the hypothesis, as it is evident that variation in tooth count is not always significantly correlated with growth. However, growth trajectories of smaller reptilian taxa show increases in tooth counts and, although current samples are small, suggest potential correlates between tooth count trajectories and adult size. Nevertheless, interspecific variation in growth patterns underscores the importance of considering and understanding growth when constructing taxonomic and phylogenetic characters, in particular for fossil taxa where ontogenetic patterns are difficult to reconstruct.
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19.
  • Cheung, Herman H., et al. (author)
  • Monitor – Biology
  • 2004
  • In: Drug Discovery Today. - 1878-5832. ; 9:6, s. 287-290
  • Journal article (peer-reviewed)abstract
    • The hottest developments in the fields of cancer research, neuroscience, genomics and proteomics, anti-virals and more, with a pick of the key research papers in these areas.
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20.
  • Collin, David, et al. (author)
  • Added value of interpreter experience in occult and suspect hip fractures: a retrospective analysis of 254 patients.
  • 2016
  • In: Emergency Radiology. - : Springer Science and Business Media LLC. - 1438-1435 .- 1070-3004. ; 23:3, s. 229-234
  • Journal article (peer-reviewed)abstract
    • The influence of experience in categorizing suspect and occult fractures on radiography compared to MRI and clinical outcome has not been studied. The aim of this study is to evaluate the importance of experience in diagnosing normal or suspect hip radiographs compared to MRI. Primarily reported normal or suspect radiography in 254 patients with low-energy hip trauma and subsequent MRI was re-evaluated by two experienced reviewers. Primary readings and review were compared. The prevalence of fractures among normal and suspect radiographic studies was assessed. Clinical outcome was used as reference. At review of radiography, 44 fractures (17 %) were found. Significantly more fractures were found among suspect cases than among normal cases. At MRI, all 44 fractures were confirmed, and further 64 fractures were detected (25 %). MRI detected all fractures with no missed fractures revealed at follow-up. There were a significantly higher proportion of fractures at MRI among the suspect radiographic diagnoses for both the primary report and at review than among occult cases. The more experienced reviewers classified radiography examinations with higher accuracy than primary reporting general radiologists. There was almost complete agreement on MRI diagnoses.
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21.
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22.
  • Collin, David (author)
  • Imaging of hip trauma - occult, suspect and concomitant fractures
  • 2016
  • Doctoral thesis (other academic/artistic)abstract
    • Background: Between one and nine percent of all hip fractures are occult or suspect and further examinations with computed tomography (CT) and/or magnetic resonance imaging (MRI) are vital for further handling. Statistically robust conclusions have not been previously reported. Aims: To evaluate the extent to which the observer agreement (reliability) differs between different modalities and different observers; if high reliability for CT in the study cases reflects the actual fracture status (accuracy): if occult and suspect fractures are different entities and if experience influences the diagnostics; if exclusively pelvic fractures after low-energy trauma to the hip frequently occur and to what extent concomitant hip and pelvic fractures co-exist. Methods and Material: Patients with normal or suspect radiographs and with subsequent examination with CT and/or MRI were reviewed and scored by four observers with varying radiological experience. Statistical analyses were performed with linear weighted kappa (κ) statistics and chi-square tests. Results: Observer agreements for all interpreters were high for CT and MRI but the accuracy for CT was inferior to MRI – in the study cases. There was a higher rate of fractures among suspect than among occult cases, both at review of radiography and at MRI. At MRI there were frequent concomitant hip and pelvic fractures as well as exclusively pelvic fractures. Conclusions: Occult and suspect fractures are different entities. Experience improves the diagnostic performance for both radiography and CT but is of less importance for fracture diagnosis with MRI. The reliability of CT for an experienced reviewer is high but does not necessarily correlate with high accuracy in the study population. Exclusively pelvic fractures at MRI are common after hip trauma. Hip and pelvic fractures are not mutually exclusive.
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23.
  • Collin, David, et al. (author)
  • Observer variation for radiography, computed tomography, and magnetic resonance imaging of occult hip fractures
  • 2011
  • In: Acta Radiologica. - : SAGE Publications. - 1600-0455 .- 0284-1851. ; 52:8, s. 871-874
  • Journal article (peer-reviewed)abstract
    • Background: Conventional radiography is insufficient for diagnosis in a small but not unimportant number of hip fractures, and secondary imaging with computed tomography (CT) or magnetic resonance imaging (MRI) is warranted. There are no convincing observer variation studies performed for conventional radiography or CT in occult fractures, and no large materials for MRI. Purpose: To assess observer variation in radiography, CT and MRI of suspected occult, non-displaced hip fractures, and to evaluate to what extent observer experience or patient age may influence observer performance. Material and Methods: A total of 375 patients after hip trauma where radiography was followed by CT or MRI to evaluate a suspected occult hip fracture were collected retrospectively from two imaging centers. After scoring by three observers with varying degrees of radiologic experience, observer variation was assessed by using linear weighted kappa statistics. Results: For radiography, agreements between the three observers were moderate to substantial for intracapsular fractures, with kappa values in the ranges of 0.56-0.66. Kappa values were substantial for extracapsular fractures, in the ranges of 0.69-0.72. With increasing professional experience, fewer fractures were classified as equivocal at radiography. For CT and MRI, observer agreements were similar and almost perfect, with kappa values in the ranges of 0.85-0.97 and 0.93-0.97. Conclusion: There were almost perfect observer agreements for CT and MRI in diagnosing non-displaced, occult hip fractures. Observer agreements for radiography were moderate to substantial, and observer experience influenced agreement only at radiography.
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24.
  • Collin, David, et al. (author)
  • Prevalence of exclusively and concomitant pelvic fractures at magnetic resonance imaging of suspect and occult hip fractures.
  • 2015
  • In: Emergency Radiology. - : Springer Science and Business Media LLC. - 1438-1435 .- 1070-3004.
  • Journal article (peer-reviewed)abstract
    • Pelvic fractures may occur together with hip fractures as a result of low energy trauma. It is unclear whether they do require special attention. There are conflicting results in the literature about the prevalence of both concomitant hip and pelvic fractures as well as exclusive pelvic fractures. It has been reported that hip fractures and obturator ring fractures are mutually exclusive. To retrospectively analyze the prevalence of exclusively pelvic as well as concomitant hip and pelvic fractures in patients examined with MRI after low-energy trauma in elderly. During 9 years, 316 elderly patients had been examined with MRI for suspected or occult hip fracture after a fall. A fracture was diagnosed when MRI showed focal signal abnormalities in the subcortical bone marrow, with or without disruption of adjacent cortices. One observer reviewed all studies. A second observer verified all studies with hip fractures. Follow-up was available for all but two patients that died prior to hip surgery. The prevalence of concomitant pelvic and femoral neck or trochanteric fractures was statistically compared using chi-squared test for categorical variables. Hip fractures were found in 161 (51 %) patients of which 29 (9 %) had concomitant pelvic fractures. There were exclusively pelvic fractures in 82 (26 %) patients of which 65 (79 %) were on the traumatized side only. In 73 patients, there were no fractures. Occult or suspected hip fractures are not infrequently associated with pelvic fractures. Exclusively pelvic fractures are not uncommon.
  •  
25.
  • Cooper, David K. C., et al. (author)
  • First update of the International Xenotransplantation Association consensus statement on conditions for undertaking clinical trials of porcine islet products in type 1 diabetes - Chapter 4 : pre-clinical efficacy and complication data required to justify a clinical trial
  • 2016
  • In: Xenotransplantation. - : Wiley. - 0908-665X .- 1399-3089. ; 23:1, s. 46-52
  • Journal article (peer-reviewed)abstract
    • In 2009, the International Xenotransplantation Association (IXA) published a consensus document that provided guidelines and recommendations (not regulations) for those contemplating clinical trials of porcine islet transplantation. These guidelines included the IXA's opinion on what constituted rigorous pre-clinical studies using the most relevant animal models and were based on non-human primate testing. We now report our discussion following a careful review of the 2009 guidelines as they relate to pre-clinical testing. In summary, we do not believe there is a need to greatly modify the conclusions and recommendations of the original consensus document. Pre-clinical studies should be sufficiently rigorous to provide optimism that a clinical trial is likely to be safe and has a realistic chance of success, but need not be so demanding that success might only be achieved by very prolonged experimentation, as this would not be in the interests of patients whose quality of life might benefit immensely from a successful islet xenotransplant. We believe these guidelines will be of benefit to both investigators planning a clinical trial and to institutions and regulatory authorities considering a proposal for a clinical trial. In addition, we suggest consideration should be given to establishing an IXA Clinical Trial Advisory Committee that would be available to advise (but not regulate) researchers considering initiating a clinical trial of xenotransplantation.
  •  
26.
  • Davidsson, Josef, et al. (author)
  • Array-based genotype-phenotype correlation in a case of supernumerary ring chromosome 12
  • 2008
  • In: Clinical Genetics. - : Wiley. - 0009-9163. ; 73:1, s. 44-49
  • Journal article (peer-reviewed)abstract
    • Supernumerary ring chromosomes (SRC) account for approximately 10% of prenatal marker chromosomes and 60% of these SRCs are associated with an abnormal phenotype of the patient carrying them. SRCs have, with few exceptions, not been characterized at the molecular genetic level. Here, we present the first case of a SRC 12 thoroughly investigated with tiling resolution array-based comparative genomic hybridization (array CGH); multicolor, centromere, subtelomeric and whole chromosome painting fluorescence in situ hybridization. In addition, to be able to correlate phenotypic manifestations with a possible pathogenetic outcome of the SRC 12, we retrospectively compared and reviewed all 14 cases of SRC 12 reported, including our present case. Our analyses revealed that the SRC comprised 25.53-46.40 Mb of chromosome 12, a region known to harbor 47 annotated genes of which nine were of putative pathogenetic relevance. Reviewing the previously described cases of SRC 12, we could not establish any specific recurrent features associated with this type of SRC. This most probably reflects heterogeneity in break-point distribution among the reported cases, resulting in differently sized ring chromosomes and hence varying phenotypic traits of the patients. Detailed genomic evaluation, by array CGH or similar techniques may thus be of importance to predict the clinical course in individual cases.
  •  
27.
  • De Greef, Julien, et al. (author)
  • Risk factors for Nocardia infection among allogeneic hematopoietic cell transplant recipients : A case-control study of the Infectious Diseases Working Party of the European Society for Blood and Marrow Transplantation
  • 2024
  • In: Journal of Infection. - : Elsevier. - 0163-4453 .- 1532-2742. ; 88:6
  • Journal article (peer-reviewed)abstract
    • ObjectivesNocardiosis is a rare but life-threatening infection after hematopoietic cell transplantation (HCT). We aimed at identifying risk factors for nocardiosis after allogeneic HCT and clarifying the effect of trimethoprim-sulfamethoxazole prophylaxis on its occurrence.MethodsWe performed a retrospective multicenter case-control study of patients diagnosed with nocardiosis after allogeneic HCT between January 2000 and December 2018. For each case, two controls were matched by center, transplant date, and age group. Multivariable analysis was conducted using conditional logistic regression to identify potential risk factors for nocardiosis. Kaplan-Meier survival curves of cases and controls were compared using log-rank tests.ResultsSixty-four cases and 128 controls were included. Nocardiosis occurred at a median of 9 months after allogeneic HCT (interquartile range: 5–18). After adjustment for potential confounders in a multivariable model, Nocardia infection was associated with tacrolimus use (adjusted odds ratio [aOR] 9.9, 95 % confidence interval [95 % CI]: 1.6–62.7), lymphocyte count < 500/µL (aOR 8.9, 95 % CI: 2.3–34.7), male sex (aOR 8.1, 95 % CI: 2.1–31.5), recent use of systemic corticosteroids (aOR 7.9, 95 % CI: 2.2–28.2), and recent CMV infection (aOR 4.3, 95 % CI: 1.2–15.9). Conversely, use of trimethoprim-sulfamethoxazole prophylaxis was associated with a significantly decreased risk of nocardiosis (aOR 0.2, 95 % CI: 0.1–0.8). HCT recipients who developed nocardiosis had a significantly decreased survival, as compared with controls (12-month survival: 58 % and 90 %, respectively; p < 0.0001).ConclusionsWe identified six factors independently associated with the occurrence of nocardiosis among allogeneic HCT recipients. In particular, trimethoprim-sulfamethoxazole prophylaxis was found to protect against nocardiosis.
  •  
28.
  • Delker, Collin J., et al. (author)
  • 1/f Noise Sources in Dual-Gated Indium Arsenide Nanowire Transistors
  • 2012
  • In: IEEE Transactions on Electron Devices. - 0018-9383. ; 59:7, s. 1980-1987
  • Journal article (peer-reviewed)abstract
    • 1/f noise is studied in dual-gated InAs nanowire transistors consisting of an omega top gate with high-k atomic layer deposited dielectric and silicon dioxide to substrate back gate. Noise spectra at varying gate bias combinations are compared from devices with differing top-gate lengths to separate the noise contributions of the top-gated channel from the ungated access portion, including the metal-nanowire contacts. For a given device geometry, it is possible to bias the device into four different regimes where the resistance and the noise amplitude can each be independently dominated by either the channel or the access/contact regions. When the device is fully in the on state, the access/contact regions dominate both resistance and noise. When the device is operating near or below threshold, the channel dominates resistance and noise. For the lowest amount of overall 1/f noise, most of the nanowire should be covered by the top gate, minimizing the access region length.
  •  
29.
  • Geijer, Mats, et al. (author)
  • Bone bruise, lipohemarthrosis, and joint effusion in CT of non-displaced hip fracture.
  • 2012
  • In: Acta radiologica (Stockholm, Sweden : 1987). - : SAGE Publications. - 1600-0455 .- 0284-1851. ; 53:2, s. 197-202
  • Journal article (peer-reviewed)abstract
    • BackgroundA suspected occult hip fracture after normal radiography is not uncommon in an elderly person after a fall. Despite a lack of robust validation in the literature, computed tomography (CT) is often used as secondary imaging.PurposeTo assess the frequency and clinical utility of non-cortical skeletal and soft tissue lesions as ancillary fracture signs in CT diagnosis of occult hip fractures.Material and MethodsAll fracture signs (cortical and trabecular fractures, bone bruise, joint effusion, and lipohemarthrosis) were recorded in 231 hip low-energy trauma cases with CT performed after normal or equivocal radiography in two trauma centers.ResultsThere were no fracture signs in 110 patients. Twelve of these had a joint effusion. In 121 patients with 46 cervical hip fractures and 75 trochanteric fractures one or more fracture signs were present. Cortical fractures were found in 115 patients. Bone bruise was found in 119 patients, joint effusion in 35, and lipohemarthrosis in 20 patients.ConclusionAncillary signs such as bone bruise and lipohemarthrosis can strengthen and sometimes indicate the diagnosis in CT of occult hip fractures. Joint effusion is a non-specific sign.
  •  
30.
  •  
31.
  • Hart, Nathan S., et al. (author)
  • Visual Opsin Diversity in Sharks and Rays
  • 2020
  • In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 37:3, s. 811-827
  • Journal article (peer-reviewed)abstract
    • The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.
  •  
32.
  • Heath, Victoria, et al. (author)
  • Monitor – biology
  • 2004
  • In: Drug Discovery Today. - 1878-5832. ; 9:15, s. 678-681
  • Journal article (peer-reviewed)abstract
    • The hottest developments in the fields of cancer research, neuroscience, genomics and proteomics, anti-virals and more, with a pick of the key research papers in these areas.
  •  
33.
  • Kervarrec, Thibault, et al. (author)
  • Digital Papillary Adenocarcinoma in Nonacral Skin : Clinicopathologic and Genetic Characterization of 5 Cases
  • 2023
  • In: American Journal of Surgical Pathology. - 0147-5185. ; 47:10, s. 1077-1084
  • Journal article (peer-reviewed)abstract
    • Digital papillary adenocarcinoma (DPA) is a rare sweat gland neoplasm that has exceptionally been reported outside acral locations. Recently, human papillomavirus 42 was identified as the main oncogenic driver of DPA. Herein, we report 5 tumors arising in extra-Acral locations predominantly in the female anogenital skin. Four patients were female and 1 patient was male. The mean age at the diagnosis time was 65 years (range: 55 to 82 y). Tumors were located on the vulva (n=3), perianal area (n=1), and forearm (n=1). Histologically, all tumors were lobular and mainly solid and composed of sheets of cells with rare focal papillae and frequent glandular structures in a "back-To-back" pattern and lined by atypical basophilic cells. Immunohistochemistry showed diffuse positivity for SOX10. Epithelial membrane antigen and carcinoembryonic antigen highlighted the luminal cells and staining for p63 and p40 revealed a consistent and continuous myoepithelial component around glandular structures. Follow-up was available in 3 cases (mean duration: 12 mo [range: 8 to 16 mo]). One patient developed local recurrence and 1 experienced regional lymph node metastases. HPV Capture Next-generation sequencing revealed the presence of the HPV42 genome in all samples. Viral reads distributions were compatible in the 5 cases with an episomal nature of the viral genome, with a recurrent deletion in the E1 and/or E2 open reading frames. In conclusion, this study demonstrates that digital DPA may rarely present in nonacral locations mainly in the female anogenital area, usually with a more solid pattern as compared with those cases presenting on the digits and it is also associated with HPV42.
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34.
  • Kielty, Collin L., et al. (author)
  • The Pristine survey - XII. Gemini-GRACES chemo-dynamical study of newly discovered extremely metal-poor stars in the Galaxy
  • 2021
  • In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 506:1, s. 1438-1461
  • Journal article (peer-reviewed)abstract
    • High-resolution optical spectra of 30 metal-poor stars selected from the Pristine survey are presented, based on observations taken with the Gemini Observatory GRACES spectrograph. Stellar parameters Teff and log g are determined using a Gaia DR2 colour–temperature calibration and surface gravity from the Stefan–Boltzmann equation. GRACES spectra are used to determine chemical abundances (or upper limits) for 20 elements (Li, O, Na, Mg, K, Ca, Ti, Sc, Cr, Mn, Fe, Ni, Cu, Zn, Y, Zr, Ba, La, Nd, Eu). These stars are confirmed to be metal-poor ([Fe/H] < −2.5), with higher precision than from earlier medium-resolution analyses. The chemistry for most targets is similar to other extremely metal-poor stars in the Galactic halo. Three stars near [Fe/H] = −3.0 have unusually low Ca and high Mg, suggestive of contributions from few SN II where alpha-element formation through hydrostatic nucleosynthesis was more efficient. Three new carbon-enhanced metal-poor (CEMP) stars are also identified (two CEMP-s and one potential CEMP-no star) when our chemical abundances are combined with carbon from previous medium-resolution analyses. The GRACES spectra also provide precision radial velocities (σRV ≤ 0.2 km s−1) for dynamical orbit calculations with the Gaia DR2 proper motions. Most of our targets are dynamically associated with the Galactic halo; however, five stars with [Fe/H] < −3 have planar-like orbits, including one retrograde star. Another five stars are dynamically consistent with the Gaia-Sequoia accretion event; three have typical halo [α/Fe] ratios for their metallicities, whereas two are [Mg/Fe]-deficient, and one is a new CEMP-s candidate. These results are discussed in terms of the formation and early chemical evolution of the Galaxy.
  •  
35.
  • Lorentsson, Robert, 1969, et al. (author)
  • Investigation of the Impact of Defective Ultrasound Transducers on Clinical Image Quality in Grayscale 2-D Still Images.
  • 2023
  • In: Ultrasound in medicine & biology. - 0301-5629 .- 1879-291X. ; 49:9, s. 2126-2133
  • Journal article (peer-reviewed)abstract
    • There are several studies that show high defect rates of transducers in clinical use. The purpose of the present study was to investigate whether image quality and the risk for misdiagnosis is affected by using defective transducers.Four defective transducers with varying degrees of defect severity, still in clinical use, were selected. Forty artifact-affected clinical images from each transducer were compared with images acquired from fully functional transducers, of the same model, in an observer study where four experienced radiologists rated each of the 320 images. The rating tasks included if the artifacts were detectable, if the possible artifacts might affect the diagnosis, how well structural details were reproduced and, finally, an assessment of overall image quality.The artifacts in the images were detectable for three of the four transducers (p < 0.05), and in 121 of 640 assessments of the images from the defective transducers the observers were confident that the artifacts could affect the diagnosis. All four faulty transducers were assessed to have decreased ability to resolve structural details (p < 0.05), and three of the four transducers were assessed to have worse overall image quality (p < 0.05).The present study shows that image quality and the risk of misdiagnosis can be affected by using defective transducers. This highlights the importance of frequent quality control of the transducers to avoid decreased image quality and even misdiagnosis.
  •  
36.
  • Pozina, Galia, et al. (author)
  • Phase identification in γ- and κ-alumina coatings by cathodoluminescence
  • 2009
  • In: Scripta Materialia. - : Elsevier BV. - 1359-6462 .- 1872-8456. ; 61:4, s. 379-382
  • Journal article (peer-reviewed)abstract
    • Cathodoluminescence (CL) properties were studied for metastable γ- and κ-Al2O3 coatings for cutting tool inserts. The alumina films demonstrate a strong CL, with peak energies depending on the Al2O3 polymorphs. The phase transformation caused by heat treatment is shown to correlate with strong CL modification in the annealed coatings. Spatially resolved CL is found to be a powerful nondestructive technique for identification of different alumina phases on the microscopic level. The corresponding optical properties of γ- and κ-Al2O3 are discussed.
  •  
37.
  • Sansone, Mikael, et al. (author)
  • Outcome of hip arthroscopy in patients with mild to moderate osteoarthritis-A prospective study.
  • 2016
  • In: Journal of hip preservation surgery. - : Oxford University Press (OUP). - 2054-8397. ; 3:1, s. 61-7
  • Journal article (peer-reviewed)abstract
    • Osteoarthritis (OA) of the hip is a common cause of hip pain. The arthroscopic management of patients with femoro-acetabular impingement (FAI) has been reported to yield good outcomes. The purpose of this study was to report on outcome following the arthroscopic treatment of patients with FAI in the presence of mild to moderate OA. Seventy-five patients undergoing arthroscopic surgery for FAI, all with preoperative radiological signs of mild to moderate OA were prospectively included in this study. A 2-year follow-up, using web-based patient-reported outcome measures, including the International Hip Outcome Tool (iHOT-12), Copenhagen Hip and Groin Outcome (HAGOS), EQ-5D, Hip Sports Activity Scale (HSAS) for physical activity level and a visual analogue scale (VAS) for overall hip function, was performed, complemented by a radiographic evaluation. At follow-up (mean 26 months, SD 5), five patients (7%) had undergone total hip arthroplasty, leaving 70 patients for the analysis. Preoperative scores compared with those obtained at the 2-year follow-up revealed significant improvements (P<0.0001) for all measured outcomes; the iHOT-12 (42 versus 65), VAS for global hip function (48 versus 68), HSAS (2.5 versus 3), EQ5D index (0.62 versus 0.76), EQ VAS (69 versus 75) and different HAGOS subscales (54 versus 72, 47 versus 67, 56 versus 75, 40 versus 61, 33 versus 56, 31 versus 55). At follow-up, 56 (82%) patients reported that they was satisfied with the outcome of surgery. Arthroscopic treatment for patients with FAI in the presence of mild to moderate OA resulted in statistically significant and clinically relevant improvements in outcome measures related to pain, symptoms, function, physical activity level and quality of life in the majority of patients.
  •  
38.
  • Sestito, Federico, et al. (author)
  • The Pristine survey – X. A large population of low-metallicity stars permeates the Galactic disc
  • 2020
  • In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966 .- 1745-3925 .- 1745-3933. ; 497:1, s. L7-L12
  • Journal article (peer-reviewed)abstract
    • The orbits of the least chemically enriched stars open a window on the formation of our Galaxy when it was still in its infancy. The common picture is that these low-metallicity stars are distributed as an isotropic, pressure-supported component since these stars were either accreted from the early building blocks of the assembling Milky Way (MW), or were later brought by the accretion of faint dwarf galaxies. Combining the metallicities and radial velocities from the Pristine and LAMOST surveys and Gaia DR2 parallaxes and proper motions for an unprecedented large and unbiased sample of 1027 very metal poor stars at [Fe/H] ≤ −2.5 dex, we show that this picture is incomplete. We find that 31 per cent of the stars that currently reside spatially in the disc (⁠|Z|≤3kpc⁠) do not venture outside of the disc plane throughout their orbit. Moreover, this sample shows strong statistical evidence (at the 5.0σ level) of asymmetry in their kinematics, favouring prograde motion. The discovery of this population implies that a significant fraction of stars with iron abundances [Fe/H] ≤ −2.5 dex merged into, formed within, or formed concurrently with the MW disc and that the history of the disc was quiet enough to allow them to retain their disc-like orbital properties, challenging theoretical and cosmological models.
  •  
39.
  • Spitzer, Eric, et al. (author)
  • Monitor – biology
  • 2004
  • In: Drug Discovery Today. - 1878-5832. ; 9:21, s. 941-943
  • Journal article (peer-reviewed)abstract
    • The hottest developments in the fields of cancer research, neuroscience, genomics and proteomics, anti-virals and more, with a pick of the key research papers in these areas.
  •  
40.
  • Trinh, David, 1981-, et al. (author)
  • Coated Insert
  • 2006
  • Patent (pop. science, debate, etc.)
  •  
41.
  • Trinh, David Huy, 1981-, et al. (author)
  • Nanocomposite Al2O3-ZrO2 thin films grown by reactive dual radio-frequency magnetron sputtering
  • 2008
  • In: Thin Solid Films. - : Elsevier. - 0040-6090 .- 1879-2731. ; 516:15, s. 4977-4982
  • Journal article (peer-reviewed)abstract
    • Crystalline alumina–zirconia nanocomposites have been synthesized at 450 °C and 750 °C with reactive magnetron sputtering using radio-frequency power supplies. The composition of the films ranged from pure alumina to pure zirconia as measured by ion beam techniques. Microstructural characterization showed the presence of monoclinic zirconia in the pure zirconia films and γ-alumina in the pure alumina films while the nanocomposites contained either an amorphous compound, γ-alumina, cubic zirconia or a mixture of these. The grain size was 5 nm for the nanocomposite compared to larger grains in the pure oxide films. Electron energy loss spectroscopy showed a clear progression from the pure alumina to the pure zirconia.
  •  
42.
  • Trinh, David Huy, 1981- (author)
  • Nanocrystalline Alumina-Zirconia Thin Films Grown by Magnetron Sputtering
  • 2008
  • Doctoral thesis (other academic/artistic)abstract
    • Alumina-zirconia thin films have been deposited using dual magnetron sputtering. Film growth was performed at relatively low-to-medium temperatures, ranging from ~300°C to 810 °C. Different substrates were applied, including silicon (100), and industrially relevant materials, such as WC-Co hardmetal. Both radio-frequency sputtering and direct-current magnetron sputtering were utilised to achieve a range of film compositions. The influence of sputtering target was investigated; both ceramics and metals were used as sputtering sources. Microstructural characterisation was performed with a range of electron microscopy and x-ray diffraction techniques which show that the pure zirconia was deposited in the monoclinic phase. Reduced mobility of depositing species, as in the case of direct-current sputtering, yielded preferred crystallographic orientation in the {100} directions. The initial nucleation layer consisted of the metastable tetragonal zirconia phase. This phase could be grown over film thicknesses ~1 μm through the addition of ~3 at.% Al under similar low mobility conditions. For cases of higher mobility, as obtained through radio-frequency sputtering, the metastable cubic zirconia phase formed in the film bulk for alumina-zirconia nanocomposites. A combination of two mechanisms is suggested for the stabilisation of metastable zirconia phases: oxygen-deficiency and aluminium segregations with resultant restraint on the zirconia lattice. The sputter deposition process was investigated through energy resolved mass spectrometry in the case of radio-frequency sputtering; the sputter deposition flux contained a mixture of metallic ions, metaloxygen clusters, and oxygen ions. The presence of metal-oxygen clusters was found to be important in oxygen-stoichiometry and thus the phase selection of the resultant film. The energy distributions were similar when comparing sputtering from ceramic and metallic targets. A mass-balance model has also been developed for the transport phenomena and reactions of particles in reactive sputtering of two targets in a two-gas scenario for the alumina-zirconia system. Addition of nitrogen to the working gas was found to eliminate the hysteresis in the target poisoning for oxygen reactive sputtering. The higher reactivity of oxygen contributed to a higher oxygen content in resultant films compared to the oxygen content in the oxy-nitride working gas. The model was thus shown to be successful for tuning depositions in the alumina-zirconia oxy-nitride system.
  •  
43.
  • Trinh, David Huy, et al. (author)
  • Radio frequency dual magnetron sputtering deposition and characterization of nanocomposite Al2O3-ZrO2 thin films
  • 2006
  • In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : American Vacuum Society. - 0734-2101 .- 1520-8559. ; 24:2, s. 309-316
  • Journal article (peer-reviewed)abstract
    • Radio frequency magnetron sputtering from oxide targets has been used to synthesize crystalline alumina–zirconia nanocomposites at a relatively low temperature of 450  °C. Films of different compositions have been deposited ranging from pure zirconia to pure alumina, the compositions being measured with Rutherford backscattering and elastic recoil detection analysis. X-ray diffraction studies show the presence of the monoclinic zirconia phase in pure zirconia films. Addition of alumina into the film results in the growth of the cubic zirconia phase and amorphous alumina. No crystalline alumina was detected in either the composite or the pure alumina film. The microstructure of the films as studied by high resolution electron microscopy and scanning transmission electron microscopy shows a columnar growth mode in both the pure zirconia and nanocomposite films, but reveals differences in the intracolumnar structure. For the nanocomposite small equiaxed grains, ~5  nm in size, are found at the base of the columns at the interface with the substrate. An amorphous tissue of alumina was present between the small crystallites in the case of the nanocomposite.
  •  
44.
  •  
45.
  • Trinh, David, et al. (author)
  • Phase transformation in kappa- and gamma-Al2O3 coatings on cutting tool inserts
  • 2009
  • In: Surface & Coatings Technology. - : Elsevier BV. - 0257-8972 .- 1879-3347. ; 203:12, s. 1682-1688
  • Journal article (peer-reviewed)abstract
    • The phase transformation in as-deposited, metastable kappa- and gamma-alumina coatings on cutting inserts has been studied by a combination of X-ray diffraction, scanning electron microscopy and cathodoluminescence. In the case of kappa-alumina, mechanical forces during metal cutting lower the transformation temperature of the metastable phases to the thermodynamically stable alpha-alumina phase from 1050 degrees C to 930 degrees C. This is the reason why that coating has a similar performance during metal cutting when compared to the stable ce-alumina phase. The transformation temperature in gamma-alumina coated cutting tools is found to be as low as 950-975 degrees C. Cathodoluminescence (CL) has been demonstrated as a possible method for differentiation between the various alumina phases. Specifically, both kappa- and gamma-alumina films have revealed a strong room temperature CL with different peak energies depending on the phase. CL of the metastable alumina coatings annealed at the transformation temperatures corresponds to the stable alpha-alumina phase.
  •  
46.
  • VanBuren, Collin S., et al. (author)
  • Head size, weaponry, and cervical adaptation : Testing craniocervical evolutionary hypotheses in Ceratopsia
  • 2015
  • In: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 69:7, s. 1728-1744
  • Research review (peer-reviewed)abstract
    • The anterior cervical vertebrae form the skeletal connection between the cranial and postcranial skeletons in higher tetrapods. As a result, the morphology of the atlas-axis complex is likely to be shaped by selection pressures acting on either the head or neck. The neoceratopsian (Reptilia:Dinosauria) syncervical represents one of the most highly modified atlas-axis regions in vertebrates, being formed by the complete coalescence of the three most anterior cervical vertebrae. In ceratopsids, the syncervical has been hypothesized to be an adaptation to support a massive skull, or to act as a buttress during intraspecific head-to-head combat. Here, we test these functional/adaptive hypotheses within a phylogenetic framework and critically examine the previously proposed methods for quantifying relative head size in the fossil record for the first time. Results indicate that neither the evolution of cranial weaponry nor large head size correlates with the origin of cervical fusion in ceratopsians, and we, therefore, reject both adaptive hypotheses for the origin of the syncervical. Anterior cervical fusion has evolved independently in a number of amniote clades, and further research on extant groups with this peculiar anatomy is needed to understand the evolutionary basis for cervical fusion in Neoceratopsia.
  •  
47.
  • Venn, Kim A., et al. (author)
  • The Pristine survey – IX. CFHT ESPaDOnS spectroscopic analysis of 115 bright metal-poor candidate stars
  • 2020
  • In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 492:3, s. 3241-3262
  • Journal article (peer-reviewed)abstract
    • A chemo-dynamical analysis of 115 metal-poor candidate stars selected from the narrow band Pristine photometric survey is presented based on CFHT high-resolution ESPaDOnS spectroscopy, We have discovered 28 new bright (V < 15) stars with I Fe/H] <-2,5 and 5 with 1Fe/11-11 <-3.0 for success rates of 40 (28/70) and 19 per cent (5/27), respectively. A detailed model atmosphere analysis is carried out for the 28 new metal-poor stars. Stellar parameters were determined from SDSS photometric colours, Gala DR2 parallaxes, MESA/MIST stellar isochrones, and the initial Pristine survey metallicities, following a Bayesian inference method, Chemical abundances are determined for 10 elements (Na, Mg, Ca, Sc, Ti, Cr, Fe, Ni, Y, and Ba), Most stars show chemical abundance patterns that are similar to the normal metal-poor stars in the Galactic halo; however, we also report the discoveries of a new r-process-rich star, a new CF.MP-s candidate with I Y/Ba 0, and a metal-poor star with very low I Mg/Fe I, The kinematics and orbits for all of the highly probable metal-poor candidates are determined by combining our precision radial velocities with Gaia DR2 proper motions. Some stars show unusual kinematics for their chemistries, including planar orbits, unbound orbits, and highly elliptical orbits that plunge deeply into the Galactic bulge (Rperi < 0.5 kpc); also, eight stars have orbital energies and actions consistent with the Gaia-Enceladus accretion event. This paper contributes to our understanding of the complex chemo-dynamics of the metal-poor Galaxy, and increases the number of known bright metal-poor stars available for detailed nucleosynthetic studies.
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48.
  • Vestin, Fredrik, et al. (author)
  • Rotational coherent anti-Stokes Raman spectroscopy (CARS) applied to thermometry in high-pressure hydrocarbon flames
  • 2008
  • In: Combustion and Flame. - : Elsevier BV. - 0010-2180. ; 154:1-2, s. 143-152
  • Journal article (peer-reviewed)abstract
    • Dual-broadband rotational coherent anti-Stokes Raman spectroscopy (DB-RCARS) has been investigated for thermometry under high-pressure and high-temperature conditions, in the product gas of fuel-lean hydrocarbon flames up to 1 MPa. Initial calibration measurements made in nitrogen, oxygen, and air, at pressures up to 1.55 MPa and temperatures up to 1800 K, showed good agreement between experimental and theoretical spectra. In the high-pressure flames, high-quality single-shot spectra were recorded in which nitrogen lines dominated, and peaks from CO2 and O-2 were also visible. A spectral model including the species N-2, CO2, and O-2, as well as the best available Raman linewidth models for flame thermometry, were used to evaluate the experimental spectra. Experimental problems as well as considerations related to the spectral evaluation are discussed. This work demonstrates the significant potential of DB-RCARS thermometry for applications in high-pressure and high-temperature environments.
  •  
49.
  • Wagner, R., et al. (author)
  • Design of an optimized nested-mirror neutron reflector for a NNBAR experiment
  • 2023
  • In: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 1051
  • Journal article (peer-reviewed)abstract
    • The NNBAR experiment for the European Spallation Source will search for free neutrons converting to antineutrons with an expected sensitivity improvement of three orders of magnitude compared to the last such search. This paper describes both the simulations of a key component for the experiment, the neutron optical reflector and the expected gains in sensitivity.
  •  
50.
  • Warrington, Rachael E., et al. (author)
  • Visual opsin expression and morphological characterization of retinal photoreceptors in the pouched lamprey (Geotria australis, Gray)
  • 2021
  • In: Journal of Comparative Neurology. - : John Wiley & Sons. - 0021-9967 .- 1096-9861. ; 529:9, s. 2265-2282
  • Journal article (peer-reviewed)abstract
    • Lampreys are extant members of the agnathan (jawless) vertebrates that diverged ~500 million years ago, during a critical stage of vertebrate evolution when image‐forming eyes first emerged. Among lamprey species assessed thus far, the retina of the southern hemisphere pouched lamprey, Geotria australis, is unique, in that it possesses morphologically distinct photoreceptors and expresses five visual photopigments. This study focused on determining the number of different photoreceptors present in the retina of G. australis and whether each cell type expresses a single opsin class. Five photoreceptor subtypes were identified based on ultrastructure and differential expression of one of each of the five different visual opsin classes (lws, sws1, sws2, rh1, and rh2) known to be expressed in the retina. This suggests, therefore, that the retina of G. australis possesses five spectrally and morphologically distinct photoreceptors, with the potential for complex color vision. Each photoreceptor subtype was shown to have a specific spatial distribution in the retina, which is potentially associated with changes in spectral radiance across different lines of sight. These results suggest that there have been strong selection pressures for G. australis to maintain broad spectral sensitivity for the brightly lit surface waters that this species inhabits during its marine phase. These findings provide important insights into the functional anatomy of the early vertebrate retina and the selection pressures that may have led to the evolution of complex color vision.
  •  
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