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1.
  • The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
  • 2022
  • In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
  • Journal article (peer-reviewed)abstract
    • This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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2.
  • Tinetti, Giovanna, et al. (author)
  • The science of EChO
  • 2010
  • In: Proceedings of the International Astronomical Union. - 1743-9213 .- 1743-9221. ; 6:S276, s. 359-370
  • Journal article (peer-reviewed)abstract
    • The science of extra-solar planets is one of the most rapidly changing areas of astrophysics and since 1995 the number of planets known has increased by almost two orders of magnitude. A combination of ground-based surveys and dedicated space missions has resulted in 560-plus planets being detected, and over 1200 that await confirmation. NASA's Kepler mission has opened up the possibility of discovering Earth-like planets in the habitable zone around some of the 100,000 stars it is surveying during its 3 to 4-year lifetime. The new ESA's Gaia mission is expected to discover thousands of new planets around stars within 200 parsecs of the Sun. The key challenge now is moving on from discovery, important though that remains, to characterisation: what are these planets actually like, and why are they as they are In the past ten years, we have learned how to obtain the first spectra of exoplanets using transit transmission and emission spectroscopy. With the high stability of Spitzer, Hubble, and large ground-based telescopes the spectra of bright close-in massive planets can be obtained and species like water vapour, methane, carbon monoxide and dioxide have been detected. With transit science came the first tangible remote sensing of these planetary bodies and so one can start to extrapolate from what has been learnt from Solar System probes to what one might plan to learn about their faraway siblings. As we learn more about the atmospheres, surfaces and near-surfaces of these remote bodies, we will begin to build up a clearer picture of their construction, history and suitability for life. The Exoplanet Characterisation Observatory, EChO, will be the first dedicated mission to investigate the physics and chemistry of Exoplanetary Atmospheres. By characterising spectroscopically more bodies in different environments we will take detailed planetology out of the Solar System and into the Galaxy as a whole. EChO has now been selected by the European Space Agency to be assessed as one of four M3 mission candidates. © International Astronomical Union 2011.
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3.
  • Risi, Camille, et al. (author)
  • Process-evaluation of tropospheric humidity simulated by general circulation models using water vapor isotopologues : 1. Comparison between models and observations
  • 2012
  • In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 117, s. D05303-
  • Journal article (peer-reviewed)abstract
    • The goal of this study is to determine how H2O and HDO measurements in water vapor can be used to detect and diagnose biases in the representation of processes controlling tropospheric humidity in atmospheric general circulation models (GCMs). We analyze a large number of isotopic data sets (four satellite, sixteen ground-based remote-sensing, five surface in situ and three aircraft data sets) that are sensitive to different altitudes throughout the free troposphere. Despite significant differences between data sets, we identify some observed HDO/H2O characteristics that are robust across data sets and that can be used to evaluate models. We evaluate the isotopic GCM LMDZ, accounting for the effects of spatiotemporal sampling and instrument sensitivity. We find that LMDZ reproduces the spatial patterns in the lower and mid troposphere remarkably well. However, it underestimates the amplitude of seasonal variations in isotopic composition at all levels in the subtropics and in midlatitudes, and this bias is consistent across all data sets. LMDZ also underestimates the observed meridional isotopic gradient and the contrast between dry and convective tropical regions compared to satellite data sets. Comparison with six other isotope-enabled GCMs from the SWING2 project shows that biases exhibited by LMDZ are common to all models. The SWING2 GCMs show a very large spread in isotopic behavior that is not obviously related to that of humidity, suggesting water vapor isotopic measurements could be used to expose model shortcomings. In a companion paper, the isotopic differences between models are interpreted in terms of biases in the representation of processes controlling humidity.
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4.
  • Blizard, David A., et al. (author)
  • Blood pressure and heart rate QTL in mice of the B6/D2 lineage sex differences and environmental influences
  • 2009
  • In: Physiological Genomics. - : American Physiological Society. - 1094-8341 .- 1531-2267. ; 36:3, s. 158-166
  • Journal article (peer-reviewed)abstract
    • A quantitative trait locus (QTL) approach was used to define the genetic architecture underlying variation in systolic blood pressure (SBP) and heart rate (HR), measured indirectly on seven occasions by the tail cuff procedure. The tests were conducted in 395 F(2) adult mice (197 males, 198 females) derived from a cross of the C57BL/6J (B6) and DBA/2J (D2) strains and in 22 BXD recombinant-inbred (RI) strains. Interval mapping of F(2) data for the first 5 days of measurement nominated one statistically significant and one suggestive QTL for SBP on chromosomes (Chr) 4 and 14, respectively, and two statistically significant QTL for HR on Chr 1 (which was specific to female mice) and Chr 5. New suggestive QTL emerged for SBP on Chr 3 (female-specific) and 8 and for HR on Chr 11 for measurements recorded several weeks after mice had undergone stressful blood sampling procedures. The two statistically significant HR QTL were confirmed by analyses of BXD RI strain means. Male and female F(2) mice did not differ in SBP or HR but RI strain analyses showed pronounced strain-by-sex interactions and a negative genetic correlation between the two measures in both sexes. Evidence for a role for mitochondrial DNA was found for both HR and SBP. QTL for HR and SBP may differ in males and females and may be sensitive to different environmental contexts.
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5.
  • Griffith, Emily, et al. (author)
  • The Similarity of Abundance Ratio Trends and Nucleosynthetic Patterns in the Milky Way Disk and Bulge
  • 2021
  • In: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 0004-637X .- 1538-4357. ; 909:1
  • Journal article (peer-reviewed)abstract
    • We compare abundance ratio trends in a sample of similar to 11,000 Milky Way bulge stars (R-GC < 3 kpc) from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) to those of APOGEE stars in the Galactic disk (5 kpc < R-GC < 11 kpc). We divide each sample into low-Ia (high-[Mg/Fe]) and high-Ia (low-[Mg/Fe]) populations, and in each population, we examine the median trends of [X/Mg] versus [Mg/H] for elements X = Fe, O, Na, Al, Si, P, S, K, Ca, V, Cr, Mn, Co, Ni, Cu, and Ce. To remove small systematic trends of APOGEE abundances with stellar log(g), we resample the disk stars to match the log(g) distributions of the bulge data. After doing so, we find nearly identical median trends for low-Ia disk and bulge stars for all elements. High-Ia trends are similar for most elements, with noticeable (0.05-0.1 dex) differences for Mn, Na, and Co. The close agreement of abundance trends (with typical differences less than or similar to 0.03 dex) implies that similar nucleosynthetic processes enriched bulge and disk stars despite the different star formation histories and physical conditions of these regions. For example, we infer that differences in the high-mass slope of the stellar initial mass function between disk and bulge must have been less than or similar to 0.30. This agreement, and the generally small scatter about the median sequences, means that one can predict all of a bulge star's APOGEE abundances with good accuracy knowing only its measured [Mg/Fe] and [Mg/H] and the observed trends of disk stars.
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6.
  • Haas, Brian J., et al. (author)
  • Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
  • 2009
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7262, s. 393-398
  • Journal article (peer-reviewed)abstract
    • Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
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7.
  • Liu, Yuwen, et al. (author)
  • A simple, cross-linked collagen tissue substitute for corneal implantation
  • 2006
  • In: Investigative Ophthalmology and Visual Science. - : Association for Research in Vision and Ophthalmology (ARVO). - 0146-0404 .- 1552-5783. ; 47:5, s. 1869-1875
  • Journal article (peer-reviewed)abstract
    • PURPOSE. To develop a simple corneal substitute from crosslinked collagen. METHODS. Porcine type I collagen (10%, pH 5), was mixed with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and N-hydroxysuccinimide (NHS). The final homogenous solution was molded to corneal dimensions, cured, and then implanted into rabbits and minipigs by lamellar keratoplasty. The implants were followed for up to 6 months after surgery. Clinical examinations of the cornea included detailed slit lamp biomicroscopy, in vivo confocal microscopy, topography and esthesiometry for nerve function. Histopathologic examinations were also performed on rabbit corneas harvested after 6 months. RESULTS. Cross-linked collagen (refractive index, 1.35) had optical clarity superior to human corneas. Implanted into rabbit and porcine corneas, only 1 of 24 of the surgical corneas showed a slight haze at 6 months after surgery. All other implants showed no adverse reactions and remained optically clear. Topography showed a smooth surface and a profile similar to that of the contralateral nonsurgical eye. The implanted matrices promoted regeneration of corneal cells, tear film, and nerves. Touch sensitivity was restored, indicating some restoration of function. The corneas with implants showed no significant loss of thickness and demonstrated stable host- graft integration. CONCLUSIONS. Collagen can be adequately stabilized, using water soluble carbodiimides as protein cross-linking reagents, in the fabrication of corneal matrix substitutes for implantation. The simple cross-linking methodology would allow for easy fabrication of matrices for transplantation in centers where there is a shortage of corneas, or where there is need for temporary patches to repair perforations in emergency situations. Copyright © Association for Research in Vision and Ophthalmology.
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8.
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9.
  • Sha, Mahesh Kumar, et al. (author)
  • Validation of methane and carbon monoxide from Sentinel-5 Precursor using TCCON and NDACC-IRWG stations
  • 2021
  • In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 14:9, s. 6249-6304
  • Journal article (peer-reviewed)abstract
    • The Sentinel-5 Precursor (S5P) mission with the TROPOspheric Monitoring Instrument (TROPOMI) on board has been measuring solar radiation backscattered by the Earth's atmosphere and surface since its launch on 13 October 2017. In this paper, we present for the first time the S5P operational methane (CH4) and carbon monoxide (CO) products' validation results covering a period of about 3 years using global Total Carbon Column Observing Network (TCCON) and Infrared Working Group of the Network for the Detection of Atmospheric Composition Change (NDACC-IRWG) network data, accounting for a priori alignment and smoothing uncertainties in the validation, and testing the sensitivity of validation results towards the application of advanced co-location criteria. We found that the S5P standard and bias-corrected CH4 data over land surface for the recommended quality filtering fulfil the mission requirements. The systematic difference of the bias-corrected total column-averaged dry air mole fraction of methane (XCH4) data with respect to TCCON data is -0.26 +/- 0.56 % in comparison to -0.68 +/- 0.74 % for the standard XCH4 data, with a correlation of 0.6 for most stations. The bias shows a seasonal dependence. We found that the S5P CO data over all surfaces for the recommended quality filtering generally fulfil the missions requirements, with a few exceptions, which are mostly due to co-location mismatches and limited availability of data. The systematic difference between the S5P total column-averaged dry air mole fraction of carbon monoxide (XCO) and the TCCON data is on average 9.22 +/- 3.45 % (standard TCCON XCO) and 2.45 +/- 3.38 % (unscaled TCCON XCO). We found that the systematic difference between the S5P CO column and NDACC CO column (excluding two outlier stations) is on average 6.5 +/- 3.54 %. We found a correlation of above 0.9 for most TCCON and NDACC stations. The study shows the high quality of S5P CH4 and CO data by validating the products against reference global TCCON and NDACC stations covering a wide range of latitudinal bands, atmospheric conditions and surface conditions.
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10.
  • Tinetti, Giovanna, et al. (author)
  • The EChO science case
  • 2015
  • In: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 40:2-3, s. 329-391
  • Journal article (peer-reviewed)abstract
    • The discovery of almost two thousand exoplanets has revealed an unexpectedly diverse planet population. We see gas giants in few-day orbits, whole multi-planet systems within the orbit of Mercury, and new populations of planets with masses between that of the Earth and Neptune-all unknown in the Solar System. Observations to date have shown that our Solar System is certainly not representative of the general population of planets in our Milky Way. The key science questions that urgently need addressing are therefore: What are exoplanets made of? Why are planets as they are? How do planetary systems work and what causes the exceptional diversity observed as compared to the Solar System? The EChO (Exoplanet Characterisation Observatory) space mission was conceived to take up the challenge to explain this diversity in terms of formation, evolution, internal structure and planet and atmospheric composition. This requires in-depth spectroscopic knowledge of the atmospheres of a large and well-defined planet sample for which precise physical, chemical and dynamical information can be obtained. In order to fulfil this ambitious scientific program, EChO was designed as a dedicated survey mission for transit and eclipse spectroscopy capable of observing a large, diverse and well-defined planet sample within its 4-year mission lifetime. The transit and eclipse spectroscopy method, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allows us to measure atmospheric signals from the planet at levels of at least 10(-4) relative to the star. This can only be achieved in conjunction with a carefully designed stable payload and satellite platform. It is also necessary to provide broad instantaneous wavelength coverage to detect as many molecular species as possible, to probe the thermal structure of the planetary atmospheres and to correct for the contaminating effects of the stellar photosphere. This requires wavelength coverage of at least 0.55 to 11 mu m with a goal of covering from 0.4 to 16 mu m. Only modest spectral resolving power is needed, with R similar to 300 for wavelengths less than 5 mu m and R similar to 30 for wavelengths greater than this. The transit spectroscopy technique means that no spatial resolution is required. A telescope collecting area of about 1 m(2) is sufficiently large to achieve the necessary spectro-photometric precision: for the Phase A study a 1.13 m(2) telescope, diffraction limited at 3 mu m has been adopted. Placing the satellite at L2 provides a cold and stable thermal environment as well as a large field of regard to allow efficient time-critical observation of targets randomly distributed over the sky. EChO has been conceived to achieve a single goal: exoplanet spectroscopy. The spectral coverage and signal-to-noise to be achieved by EChO, thanks to its high stability and dedicated design, would be a game changer by allowing atmospheric composition to be measured with unparalleled exactness: at least a factor 10 more precise and a factor 10 to 1000 more accurate than current observations. This would enable the detection of molecular abundances three orders of magnitude lower than currently possible and a fourfold increase from the handful of molecules detected to date. Combining these data with estimates of planetary bulk compositions from accurate measurements of their radii and masses would allow degeneracies associated with planetary interior modelling to be broken, giving unique insight into the interior structure and elemental abundances of these alien worlds. EChO would allow scientists to study exoplanets both as a population and as individuals. The mission can target super-Earths, Neptune-like, and Jupiter-like planets, in the very hot to temperate zones (planet temperatures of 300-3000 K) of F to M-type host stars. The EChO core science would be delivered by a three-tier survey. The EChO Chemical Census: This is a broad survey of a few-hundred exoplanets, which allows us to explore the spectroscopic and chemical diversity of the exoplanet population as a whole. The EChO Origin: This is a deep survey of a subsample of tens of exoplanets for which significantly higher signal to noise and spectral resolution spectra can be obtained to explain the origin of the exoplanet diversity (such as formation mechanisms, chemical processes, atmospheric escape). The EChO Rosetta Stones: This is an ultra-high accuracy survey targeting a subsample of select exoplanets. These will be the bright "benchmark" cases for which a large number of measurements would be taken to explore temporal variations, and to obtain two and three dimensional spatial information on the atmospheric conditions through eclipse-mapping techniques. If EChO were launched today, the exoplanets currently observed are sufficient to provide a large and diverse sample. The Chemical Census survey would consist of > 160 exoplanets with a range of planetary sizes, temperatures, orbital parameters and stellar host properties. Additionally, over the next 10 years, several new ground- and space-based transit photometric surveys and missions will come on-line (e.g. NGTS, CHEOPS, TESS, PLATO), which will specifically focus on finding bright, nearby systems. The current rapid rate of discovery would allow the target list to be further optimised in the years prior to EChO's launch and enable the atmospheric characterisation of hundreds of planets.
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11.
  • 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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12.
  • 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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13.
  • 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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14.
  • 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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15.
  • 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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16.
  • 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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17.
  • 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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18.
  • Aartsen, M. G., et al. (author)
  • Searches for relativistic magnetic monopoles in IceCube
  • 2016
  • In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 76:3
  • Journal article (peer-reviewed)abstract
    • Various extensions of the Standard Model motivate the existence of stable magnetic monopoles that could have been created during an early high-energy epoch of the Universe. These primordial magnetic monopoles would be gradually accelerated by cosmic magnetic fields and could reach high velocities that make them visible in Cherenkov detectors such as IceCube. Equivalently to electrically charged particles, magnetic monopoles produce direct and indirect Cherenkov light while traversing through matter at relativistic velocities. This paper describes searches for relativistic (nu >= 0.76 c) and mildly relativistic (nu >= 0.51 c) monopoles, each using one year of data taken in 2008/2009 and 2011/2012, respectively. No monopole candidate was detected. For a velocity above 0.51 c the monopole flux is constrained down to a level of 1.55 x 10(-18) cm(-2) s(-1) sr(-1). This is an improvement of almost two orders of magnitude over previous limits.
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19.
  • 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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20.
  • 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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21.
  • 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.
  •  
22.
  • Adrian-Martinez, S., et al. (author)
  • The First Combined Search For Neutrino Point-Sources In The Southern Hemisphere With The Antares And Icecube Neutrino Telescopes
  • 2016
  • In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 823:1
  • Journal article (peer-reviewed)abstract
    • We present the results of searches for point-like sources of neutrinos based on the first combined analysis of data from both the ANTARES and IceCube neutrino telescopes. The combination of both detectors, which differ in size and location, forms a window in the southern sky where the sensitivity to point sources improves by up to a factor of 2 compared with individual analyses. Using data recorded by ANTARES from 2007 to 2012, and by IceCube from 2008 to 2011, we search for sources of neutrino emission both across the southern sky and from a preselected list of candidate objects. No significant excess over background has been found in these searches, and flux upper limits for the candidate sources are presented for E-2.5 and E-2 power-law spectra with different energy cut-offs.
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23.
  • Blais, David R., et al. (author)
  • LBP and CD14 secreted in tears by the lacrimal glands modulate the LPS response of corneal epithelial cells
  • 2005
  • In: Investigative Ophthalmology and Visual Science. - : Association for Research in Vision and Ophthalmology (ARVO). - 0146-0404 .- 1552-5783. ; 46:11, s. 4235-4244
  • Journal article (peer-reviewed)abstract
    • PURPOSE. Lipopolysaccharide (LPS) is one of the most powerful bacterial virulence factors in terms of proinflammatory properties and is likely to contribute to corneal bacterial keratitis. Better understanding of the spatial expression of the LPS receptor components at the tear - corneal interface might facilitate enhanced functions of the LPS receptor complex in ocular defense against Gram-negative infections. METHODS. The expression of LPS-binding protein (LBP), CD14, toll-like receptor (TLR)-4, and MD-2 in human lacrimal glands, reflex tears, and corneal epithelia was examined by ELISA, RT-PCR, Western blot analysis, and immunofluorescence. The release of proinflammatory cytokines after the activation of primary and immortalized corneal epithelial cells with LPS and human tears was measured by ELISA. RESULTS. LBP and CD14 proteins were detected in reflex human tears. Human lacrimal glands and corneal epithelia expressed LBP, CD14, TLR4, and MD-2 mRNAs and proteins. In the corneal epithelium, LBP was mainly expressed by superficial and basal epithelial cells, whereas CD14, TLR4, and MD-2 expression were limited to the wing and basal epithelial cells. In a dose-dependant manner, tear CD14 and LBP mediated the secretion of interleukin (IL)-6 and IL-8 by corneal epithelia cells when challenged with LPS. CONCLUSIONS. Tear CD14 and LBP complemented the LPS receptor complex expressed by the corneal epithelia to trigger an immune response in the presence of LPS. The complementation of these tear and corneal immune proteins could play an important role in LPS recognition and signaling and, therefore, could modulate ocular innate immunity.
  •  
24.
  • Blumenstock, T., et al. (author)
  • Characterization and potential for reducing optical resonances in Fourier transform infrared spectrometers of the Network for the Detection of Atmospheric Composition Change (NDACC)
  • 2021
  • In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 14:2, s. 1239-1252
  • Journal article (peer-reviewed)abstract
    • Although optical components in Fourier transform infrared (FTIR) spectrometers are preferably wedged, in practice, infrared spectra typically suffer from the effects of optical resonances ("channeling") affecting the retrieval of weakly absorbing gases. This study investigates the level of channeling of each FTIR spectrometer within the Network for the Detection of Atmospheric Composition Change (NDACC). Dedicated spectra were recorded by more than 20 NDACC FTIR spectrometers using a laboratory mid-infrared source and two detectors. In the indium antimonide (InSb) detector domain (1900-5000 cm-1), we found that the amplitude of the most pronounced channeling frequency amounts to 0.1 ‰ to 2.0 ‰ of the spectral background level, with a mean of (0:68±0:48) ‰ and a median of 0.60 ‰. In the mercury cadmium telluride (HgCdTe) detector domain (700-1300 cm-1), we find even stronger effects, with the largest amplitude ranging from 0.3 ‰ to 21 ‰ with a mean of (2:45±4:50) ‰ and a median of 1.2 ‰. For both detectors, the leading channeling frequencies are 0.9 and 0.11 or 0.23 cm-1 in most spectrometers. The observed spectral frequencies of 0.11 and 0.23 cm-1 correspond to the optical thickness of the beam splitter substrate. The 0.9 cm-1 channeling is caused by the air gap in between the beam splitter and compensator plate. Since the air gap is a significant source of channeling and the corresponding amplitude differs strongly between spectrometers, we propose new beam splitters with the wedge of the air gap increased to at least 0.8. We tested the insertion of spacers in a beam splitter's air gap to demonstrate that increasing the wedge of the air gap decreases the 0.9 cm-1 channeling amplitude significantly. A wedge of the air gap of 0.8 reduces the channeling amplitude by about 50 %, while a wedge of about 2 removes the 0.9 cm-1 channeling completely. This study shows the potential for reducing channeling in the FTIR spectrometers operated by the NDACC, thereby increasing the quality of recorded spectra across the network.
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25.
  • Coutu, Daniel L, et al. (author)
  • Hierarchical scaffold design for mesenchymal stem cell-based gene therapy of hemophilia B
  • 2011
  • In: Biomaterials. - : Elsevier. - 0142-9612 .- 1878-5905. ; 32:1, s. 295-305
  • Journal article (peer-reviewed)abstract
    • Gene therapy for hemophilia B and other hereditary plasma protein deficiencies showed great promise in pre-clinical and early clinical trials. However, safety concerns about in vivo delivery of viral vectors and poor post-transplant survival of ex vivo modified cells remain key hurdles for clinical translation of gene therapy. We here describe a 3D scaffold system based on porous hydroxyapatite PLGA composites coated with biomineralized collagen 1. When combined with autologous gene-engineered factor IX (hFIX) positive mesenchymal stem cells (MSCs) and implanted in hemophilic mice, these scaffolds supported long-term engraftment and systemic protein delivery by MSCs in vivo. Optimization of the scaffolds at the macro-, micro- and nanoscales provided efficient cell delivery capacity, MSC self-renewal and osteogenesis respectively, concurrent with sustained delivery of hFIX. In conclusion, the use of gene-enhanced MSC-seeded scaffolds may be of practical use for treatment of hemophilia B and other plasma protein deficiencies.
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26.
  • Dare, Emma V., et al. (author)
  • Genipin Cross-Linked Fibrin Hydrogels for in vitro Human Articular Cartilage Tissue-Engineered Regeneration
  • 2009
  • In: Cells Tissues Organs. - : Karger. - 1422-6405 .- 1422-6421. ; 190:6, s. 313-325
  • Journal article (peer-reviewed)abstract
    • Our objective was to examine the potential of a genipin cross-linked human fibrin hydrogel system as a scaffold for articular cartilage tissue engineering. Human articular chondrocytes were incorporated into modified human fibrin gels and evaluated for mechanical properties, cell viability, gene expression, extracellular matrix production and subcutaneous biodegradation. Genipin, a naturally occurring compound used in the treatment of inflammation, was used as a cross-linker. Genipin cross-linking did not significantly affect cell viability, but significantly increased the dynamic compression and shear moduli of the hydrogel. The ratio of the change in collagen II versus collagen I expression increased more than 8-fold over 5 weeks as detected with real-time RT-PCR. Accumulation of collagen II and aggrecan in hydrogel extracellular matrix was observed after 5 weeks in cell culture. Overall, our results indicate that genipin appeared to inhibit the inflammatory reaction observed 3 weeks after subcutaneous implantation of the fibrin into rats. Therefore, genipin cross-linked fibrin hydrogels can be used as cell-compatible tissue engineering scaffolds for articular cartilage regeneration, for utility in autologous treatments that eliminate the risk of tissue rejection and viral infection.
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27.
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28.
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29.
  • Fairfield, Heather, et al. (author)
  • Mutation discovery in mice by whole exome sequencing
  • 2011
  • In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 12:9, s. R86-
  • Journal article (peer-reviewed)abstract
    • We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we show that whole exome sequencing is a robust approach for discovery of putative mutations, irrespective of strain background. We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis.
  •  
30.
  • Ferm, Martin, et al. (author)
  • Comparison of different techniques to measure ammonia emission after manure application
  • 2000
  • Reports (other academic/artistic)abstract
    • Manure application leads to a number of different environmental problems, as ammonia emission, leaching and nitrous oxide emission. The environmental aspects are on local, regional and global scales. New methods for manure applications have to be developed in order to mitigate the problems. During the developing of these methods, measurements of the nitrogen exchange with the atmosphere has to be performed. For this purpose suitable and reliable measuring techniques are needed. A number of methods to measure the NH3 exchange were therefore tested in parallel. Ammonia emission after band spreading of pig slurry on a young wheat crop was measured using five different techniques. Three variants of the gradient technique were used. The techniques were: i) concentration gradients measured over short periods using FTIR spectroscopy were multiplied with the diffusitivity determined by an aerodynamic method, ii) FTIR gradient with the diffusitivity estimated using a trace gas release, iii) integrating gradient technique in which the wind speed weighted average concentration profile was multiplied with the average diffusitivity, iv) A mass balance technique in which the horizontal flux of ammonia entering and leaving the field was measured, v) a chamber technique in which the emission was calculated from the mass transfer coefficient, ambient, and equilibrium concentrations. The results agreed within ca 25 % with one exception for the chamber technique
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31.
  • Griffith, Frank, et al. (author)
  • Communicating the ideas and attitudes of spying in film music : a social semiotic approach
  • 2014
  • In: Sign System Studies. - : Tartu University Press. - 1406-4243 .- 1736-7409. ; 42:1, s. 72-97
  • Journal article (peer-reviewed)abstract
    • Taking the example of two 1960s popular spy films this paper explores how social semiotics can make a contribution to the analysis of film music. Following other scholars who have sought to create inventories of sound meanings to help us break down the way that music communicates, this paper explores how we can draw on the principles of Hallidayan functional grammar to present an inventory of meaning potentials in sound. This provides one useful way to describe the semiotic resources available to composers to allow them to communicate quite specific ideas, attitudes and identities through combinations of different sounds and sound qualities, by presenting them as systems of meaning rather than as lists of connotations. Here we apply this to the different uses of music and sound in Dr No and The Ipcress Files which allows us to show how we can reveal different ideologies of spying.
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32.
  • Griffith, May, et al. (author)
  • Artificial human corneas - Scaffolds for transplantation and host regeneration
  • 2002
  • In: Cornea. - : Lippincott, Williams andamp; Wilkins. - 0277-3740 .- 1536-4798. ; 21:7, s. S54-S61
  • Journal article (peer-reviewed)abstract
    • Purpose. To review the development of artificial corneas (prostheses and tissue equivalents) for transplantation, and to provide recent updates on our tissue-engineered replacement corneas. Methods. Modified natural polymers and synthetic polymers were screened for their potential to replace damaged portions of the human cornea or the entire corneal thickness. These polymers, combined with cells derived from each of the three main corneal layers or stem cells, were used to develop artificial corneas. Functional testing was performed in vitro. Trials of biocompatibility and immune and inflammatory reactions were performed by implanting the most promising polymers into rabbit corneas. Results. Collagen-based biopolymers, combined with synthetic crosslinkers or copolymers, formed effective scaffolds for developing prototype artificial corneas that could be used as tissue replacements in the future. We have previously developed an artificial cornea that mimicked key morphologic and functional properties of the human cornea. The addition of synthetic polymers increased its toughness as it retained transparency and low light scattering, making the matrix scaffold more suitable for transplantation. These new composites were implanted into rabbits without causing any acute inflammation or immune response. We have also fabricated full-thickness composites that can be fully sutured. However, the long-term effects of these artificial corneas need to be evaluated. Conclusions. Novel tissue-engineered corneas that comprise composites of natural and synthetic biopolymers together with corneal cell lines or stem cells will, in the future, replace portions of the cornea that are damaged. Our results provide a basis for the development of both implantable temporary and permanent corneal replacements.
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33.
  • Griffith, May, et al. (author)
  • Vision Enhancing Ophthalmic Devices and Related Methods and Compositions
  • 2005
  • Patent (pop. science, debate, etc.)abstract
    • Devices, methods, and compositions for improving vision or treating diseases, disorders or injury of the eye are described. Ophthalmic devices, such as corneal onlays, corneal inlays, and full-thickness corneal implants, are made of a material that is effective in facilitating nerve growth through or over the device. The material may include an amount of collagen greater than 1% (w/w), such as between about 10% (w/w) and about 30% (w/w). The material may include collagen polymers and/or a second biopolymer or water-soluble synthetic polymer cross-linked using EDC/NHS chemistry. The material may additionally comprise a synthetic polymer. The devices are placed into an eye to correct or improve the vision of an individual or to treat a disease, disorder or injury of an eye of an individual.
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34.
  • Griffith, Simon C., et al. (author)
  • Variation in reproductive success across captive populations: Methodological differences, potential biases and opportunities
  • 2017
  • In: Ethology. - : Wiley. - 1439-0310 .- 0179-1613. ; 123:1, s. 1-29
  • Journal article (peer-reviewed)abstract
    • Our understanding of fundamental organismal biology has been disproportionately influenced by studies of a relatively small number of ‘model’ species extensively studied in captivity. Laboratory populations of model species are commonly subject to a number of forms of past and current selection that may affect experimental outcomes. Here, we examine these processes and their outcomes in one of the most widely used vertebrate species in the laboratory – the zebra finch (Taeniopygia guttata). This important model species is used for research across a broad range of fields, partly due to the ease with which it can be bred in captivity. However despite this perceived amenability, we demonstrate extensive variation in the success with which different laboratories and studies bred their subjects, and overall only 64% of all females that were given the opportunity, bred successfully in the laboratory. We identify and review several environmental, husbandry, life-history and behavioural factors that potentially contribute to this variation. The variation in reproductive success across individuals could lead to biases in experimental outcomes and drive some of the heterogeneity in research outcomes across studies. The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency.
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35.
  • Halat, David M., et al. (author)
  • Natural abundance solid-state S-33 NMR study of NbS3: applications for battery conversion electrodes
  • 2019
  • In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1364-548X .- 1359-7345. ; 55:84, s. 12687-12690
  • Journal article (peer-reviewed)abstract
    • We report ultra-wideline, high-field natural abundance solid-state S-33 NMR spectra of the Li-ion battery conversion electrode NbS3, the first S-33 NMR study of a compound containing disulfide (S-2(2-)) units. The large quadrupolar coupling parameters (C-Q approximate to 31 MHz) are consistent with values obtained from DFT calculations, and the spectra provide evidence for the linear Peierls distortion that doubles the number of S-33 sites.
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36.
  • He, Min, et al. (author)
  • Artificial Polymeric Scaffolds as Extracellular Matrix Substitutes for Autologous Conjunctival Goblet Cell Expansion
  • 2016
  • In: Investigative Ophthalmology and Visual Science. - : ASSOC RESEARCH VISION OPHTHALMOLOGY INC. - 0146-0404 .- 1552-5783. ; 57:14, s. 6134-6146
  • Journal article (peer-reviewed)abstract
    • PURPOSE. We fabricated and investigated polymeric scaffolds that can substitute for the conjunctival extracellular matrix to provide a substrate for autologous expansion of human conjunctival goblet cells in culture. METHODS. We fabricated two hydrogels and two silk films: (1) recombinant human collagen (RHC) hydrogel, (2) recombinant human collagen 2-methacryloylxyethyl phosphorylcholine (RHC-MPC) hydrogel, (3) arginine-glycine-aspartic acid (RGD) modified silk, and (4) poly-D-lysine (PDL) coated silk, and four electrospun scaffolds: (1) collagen, (2) poly(acrylic acid) (PAA), (3) poly(caprolactone) (PCL), and (4) poly(vinyl alcohol) (PVA). Coverslips and polyethylene terephthalate (PET) were used for comparison. Human conjunctival explants were cultured on scaffolds for 9 to 15 days. Cell viability, outgrowth area, and the percentage of cells expressing markers for stratified squamous epithelial cells (cytokeratin 4) and goblet cells (cytokeratin 7) were determined. RESULTS. Most of cells grown on all scaffolds were viable except for PCL in which only 3.6 +/- 2.2% of the cells were viable. No cells attached to PVA scaffold. The outgrowth was greatest on PDL-silk and PET. Outgrowth was smallest on PCL. All cells were CK7-positive on RHCMPC while 84.7 +/- 6.9% of cells expressed CK7 on PDL-silk. For PCL, 87.10 +/- 3.17% of cells were CK7-positive compared to PET where 67.10 +/- 12.08% of cells were CK7-positive cells. CONCLUSIONS. Biopolymer substrates in the form of hydrogels and silk films provided for better adherence, proliferation, and differentiation than the electrospun scaffolds and could be used for conjunctival goblet cell expansion for eventual transplantation once undifferentiated and stratified squamous cells are included. Useful polymer scaffold design characteristics have emerged from this study.
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37.
  • Hoban, Sean, et al. (author)
  • Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible
  • 2021
  • In: BioScience. - : Oxford University Press (OUP). - 0006-3568 .- 1525-3244. ; 71:9, s. 964-976
  • Journal article (peer-reviewed)abstract
    • Global conservation policy and action have largely neglected protecting and monitoring genetic diversity-one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species' adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.
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38.
  • Kozak Ljunggren, Monika, et al. (author)
  • Effect of Surgical Technique on Corneal Implant Performance.
  • 2014
  • In: Translational Vision Science & Technology. - : Association for Research in Vision and Ophthalmology (ARVO). - 2164-2591. ; 3:2
  • Journal article (peer-reviewed)abstract
    • PURPOSE: Our aim was to determine the effect of a surgical technique on biomaterial implant performance, specifically graft retention.METHODS: Twelve mini pigs were implanted with cell-free, 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide (EDC)/N-hydroxysuccinimide (NHS) cross-linked recombinant human collagen type III (RHCIII) hydrogels as substitutes for donor corneal allografts using overlying sutures with or without human amniotic membrane (HAM) versus interrupted sutures with HAM. The effects of the retention method were compared as well as the effects of collagen concentration (13.7% to 15% RHCIII).RESULTS: All implanted corneas showed initial haze that cleared with time, resulting in corneas with optical clarity matching those of untreated controls. Biochemical analysis showed that by 12 months post operation, the initial RHCIII implants had been completely remodeled, as type I collagen, was the major collagenous protein detected, whereas no RHCIII could be detected. Histological analysis showed all implanted corneas exhibited regeneration of epithelial and stromal layers as well as nerves, along with touch sensitivity and tear production. Most neovascularization was seen in corneas stabilized by interrupted sutures.CONCLUSIONS: This showed that the surgical technique used does have a significant effect on the overall performance of corneal implants, overlying sutures caused less vascularization than interrupted sutures.TRANSLATIONAL RELEVANCE: Understanding the significance of the suturing technique can aid the selection of the most appropriate procedure when implanting artificial corneal substitutes. The same degree of regeneration, despite a higher collagen content indicates that future material development can progress toward stronger, more resistant implants.
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39.
  • Lambrechts, Marcel M., et al. (author)
  • The design of artificial nestboxes for the study of secondary hole-nesting birds: a review of methodological inconsistencies and potential biases
  • 2010
  • In: Acta Ornithologica. - 0001-6454 .- 1734-8471. ; 45:1, s. 1-26
  • Journal article (peer-reviewed)abstract
    • The widespread use of artificial nestboxes has led to significant advances in our knowledge of the ecology, behaviour and physiology of cavity nesting birds, especially small passerines Nestboxes have made it easier to perform routine monitoring and experimental manipulation of eggs or nestlings, and also repeatedly to capture, identify and manipulate the parents However, when comparing results across study sites the use of nestboxes may also Introduce a potentially significant confounding variable in the form of differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained However, the use of nestboxes may also introduce an unconsidered and potentially significant confounding variable clue to differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained Here we review to what extent the characteristics of artificial nestboxes (e g size, shape, construction material, colour) are documented in the 'methods' sections of publications involving hole-nesting passerine birds using natural or excavated cavities or artificial nestboxes for reproduction and roosting Despite explicit previous recommendations that authors describe in detail the characteristics of the nestboxes used, we found that the description of nestbox characteristics in most recent publications remains poor and insufficient We therefore list the types of descriptive data that should be included in the methods sections of relevant manuscripts and justify this by discussing how variation in nestbox characteristics can affect or confound conclusions from nestbox studies We also propose several recommendations to improve the reliability and usefulness of research based on long-term studies of any secondary hole-nesting species using artificial nestboxes for breeding or roosting.
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40.
  • Li, Fengfu, et al. (author)
  • Cellular and nerve regeneration within a biosynthetic extracellular matrix for corneal transplantation
  • 2003
  • In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences; 1999. - 0027-8424 .- 1091-6490. ; 100:26, s. 15346-15351
  • Journal article (peer-reviewed)abstract
    • Our objective was to determine whether key properties of extracellular matrix (ECM) macromolecules can be replicated within tissue-engineered biosynthetic matrices to influence cellular properties and behavior. To achieve this, hydrated collagen and N-isopropylacrylamide copolymer-based ECMs were fabricated and tested on a corneal model. The structural and immunological simplicity of the cornea and importance of its extensive innervation for optimal functioning makes it an ideal test model. In addition, corneal failure is a clinically significant problem. Matrices were therefore designed to have the optical clarity and the proper dimensions, curvature, and biomechanical properties for use as corneal tissue replacements in transplantation. In vitro studies demonstrated that grafting of the laminin adhesion pentapeptide motif, YIGSR, to the hydrogels promoted epithelial stratification and neurite in-growth. Implants into pigs corneas demonstrated successful in vivo regeneration of host corneal epithelium, stroma, and nerves. In particular, functional nerves were observed to rapidly regenerate in implants. By comparison, nerve regeneration in allograft controls was too slow to be observed during the experimental period, consistent with the behavior of human cornea transplants. Other corneal substitutes have been produced and tested, but here we report an implantable matrix that performs as a physiologically functional tissue substitute and not simply as a prosthetic device. These biosynthetic ECM replacements should have applicability to many areas of tissue engineering and regenerative medicine, especially where nerve function is required.
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41.
  • Li, Fengfu, et al. (author)
  • Corneal implantation with collagen-copolymer matrices
  • 2005
  • In: Key Engineering Materials. - : Trans Tech Publications. - 1013-9826 .- 1662-9795. ; 288-289, s. 389-392
  • Journal article (peer-reviewed)abstract
    • A transparent matrix composed of collagen and poly(N, N-dimethylacrylamide-coacryloxysuccimide), 8mm in diameter and 350 mu m thick was implanted into pigs corneas using the lamellar keratoplasty (LKP) technique. No adverse immune or inflammatory reaction was observed during 4 month implantation period. Regenerated nerve filaments were observed in the subepithelial region and stroma by confacal microscopy. The endothelium of the operated eye was not touched by LKP and remained similar to that of the contra lateral (not operated) eye. The implant remained transparent over the four-month post-operative period, and clinical topography showed reconstitution of a smooth cornea surface. These preliminary results indicated that a new, functional cornea was re-established from the implanted biosynthetic matrix. This bio-synthetic matrix may have applications in other tissue engineering areas,, especially where innervation is important.
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42.
  • McTiernan, Christopher D., et al. (author)
  • LiQD Cornea: Pro-regeneration collagen mimetics as patches and alternatives to corneal transplantation
  • 2020
  • In: Science Advances. - : AMER ASSOC ADVANCEMENT SCIENCE. - 2375-2548. ; 6:25
  • Journal article (peer-reviewed)abstract
    • Transplantation with donor corneas is the mainstay for treating corneal blindness, but a severe worldwide shortage necessitates the development of other treatment options. Corneal perforation from infection or inflammation is sealed with cyanoacrylate glue. However, the resulting cytotoxicity requires transplantation. LiQD Cornea is an alternative to conventional corneal transplantation and sealants. It is a cell-free, liquid hydrogel matrix for corneal regeneration, comprising short collagen-like peptides conjugated with polyethylene glycol and mixed with fibrinogen to promote adhesion within tissue defects. Gelation occurs spontaneously at body temperature within 5 min. Light exposure is not required-particularly advantageous because patients with corneal inflammation are typically photophobic. The self-assembling, fully defined, synthetic collagen analog is much less costly than human recombinant collagen and reduces the risk of immune rejection associated with xenogeneic materials. In situ gelation potentially allows for clinical application in outpatient clinics instead of operating theaters, maximizing practicality, and minimizing health care costs.
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43.
  • Nokhbeh, M. Reza, et al. (author)
  • Enterovirus 70 binds to different glycoconjugates containing alpha 2,3-linked sialic acid on different cell lines
  • 2005
  • In: Journal of Virology. - : American Society for Microbiology. - 0022-538X .- 1098-5514. ; 79:11, s. 7087-7094
  • Journal article (peer-reviewed)abstract
    • Enterovirus 70 (EV70), the causative agent of acute hemorrhagic conjunctivitis, exhibits a restricted tropism for conjunctival and corneal cells in vivo but infects a wide spectrum of mammalian cells in culture. Previously, we demonstrated that human CD55 is a receptor for EV70 on HeLa cells but that EV70 also binds to sialic acid-containing receptors on a variety of other human cell lines. Virus recognition of sialic acid attached to underlying glycans by a particular glycosidic linkage may contribute to host range, tissue tropism, and pathogenesis. Therefore, we tested the possibility that EV70 binds to andalpha; 2,3-linked sialic acid, like other viruses associated with ocular infections. Through the use of linkage-specific sialidases, sialyltransferases, and lectins, we show that EV70 recognizes andalpha; 2,3-linked sialic acid on human corneal epithelial cells and on U-937 cells. Virus attachment to both cell lines is CD55 independent and sensitive to benzyl N-acetyl-andalpha;-D-galactosaminide, an inhibitor of O-linked glycosylation. Virus binding to corneal cells, but not U-937 cells, is inhibited by proteinase K, but not by phosphatidylinositol-specific phospholipase C treatment. These results are consistent with the idea that a major EV70 receptor on corneal epithelial cells is an O-glycosylated, non-glycosyl phosphatidylinositol-anchored membrane glycoprotein containing andalpha; 2,3-linked sialic acid, while sialylated receptors on U-937 cells are not proteinaceous.
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44.
  • Ron-Doitch, Sapir, et al. (author)
  • Reduced cytotoxicity and enhanced bioactivity of cationic antimicrobial peptides liposomes in cell cultures and 3D epidermis model against HSV
  • 2016
  • In: Journal of Controlled Release. - : ELSEVIER SCIENCE BV. - 0168-3659 .- 1873-4995. ; 229, s. 163-171
  • Journal article (peer-reviewed)abstract
    • Cationic antimicrobial peptides (AMPs) are part of the innate immunity, and act against a wide variety of pathogenic microorganisms by perturbation of the microorganisms plasma membrane. Although attractive for clinical applications, these agents suffer from limited stability and activity in vivo, as well as non-specific interaction with host biological membranes, leading to cytotoxic adverse effects. We hypothesized that encapsulation of AMPs within liposomes could result in reduced cytotoxicity, and with enhanced stability as well as bioactivity against herpes simplex virus 1 (HSV-1). We formulated nano-sized liposomal formulations of LL-37 and indolicidin, and their physicochemical properties, cellular uptake, in vitro cytotoxicity and antiviral efficacy have been determined. Lower cytotoxicity of LL-37 liposomes was found in comparison to indolicidin liposomes attributed to the superior physicochemical properties, and to the different degree of interaction with the liposomal membrane. The disc-like shaped LL-37 liposomes (106.8 +/- 10.1 nm, shelf-life stability of N1 year) were taken up more rapidly and to a significantly higher extent than the free peptide by human keratinocyte cell line (HaCaT), remained intact within the cells, followed by release of the active peptide within the cytoplasm and migration of the vesicles lipids to the plasma membrane. LL-37 liposomes were found significantly less toxic than both the free agent and liposomal indolicidin. In the new 3D epidermis model (immortalized primary keratinocytes) liposomal LL-37 treatment (N20 mu M), but not free LL-37, efficiently protected the epidermis, inhibiting HSV-1 infection. This positive antiviral effect was obtained with no cytotoxicity even at very high concentrations (400 mu M). Thus, the antiviral activity of encapsulated LL-37 was significantly improved, expanding its therapeutic window. Liposomal LL-37 appears to be a promising delivery system for HSV therapy. (C) 2016 Elsevier B.V. All rights reserved.
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45.
  • Simpson, Fiona C., et al. (author)
  • Collagen analogs with phosphorylcholine are inflammation-suppressing scaffolds for corneal regeneration from alkali burns in mini-pigs
  • 2021
  • In: Communications Biology. - : Nature Research. - 2399-3642. ; 4:1
  • Journal article (peer-reviewed)abstract
    • The long-term survival of biomaterial implants is often hampered by surgery-induced inflammation that can lead to graft failure. Considering that most corneas receiving grafts are either pathological or inflamed before implantation, the risk of rejection is heightened. Here, we show that bioengineered, fully synthetic, and robust corneal implants can be manufactured from a collagen analog (collagen-like peptide-polyethylene glycol hybrid, CLP-PEG) and inflammation-suppressing polymeric 2-methacryloyloxyethyl phosphorylcholine (MPC) when stabilized with the triazine-based crosslinker 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride. The resulting CLP-PEG-MPC implants led to reduced corneal swelling, haze, and neovascularization in comparison to CLP-PEG only implants when grafted into a mini-pig cornea alkali burn model of inflammation over 12 months. Implants incorporating MPC allowed for faster nerve regeneration and recovery of corneal sensation. CLP-PEG-MPC implants appear to be at a more advanced stage of regeneration than the CLP-PEG only implants, as evidenced by the presence of higher amounts of cornea-specific type V collagen, and a corresponding decrease in the presence of extracellular vesicles and exosomes in the corneal stroma, in keeping with the amounts present in healthy, unoperated corneas. Simpson, McTiernan et al. develop fully synthetic corneal implants. The resulting CLP-PEG-MPC implants show reduced corneal swelling, haze, and neovascularization compared to CLP-PEG only implants when grafted into a mini-pig cornea alkali burn model of inflammation over 12 months. This study suggests the superiority of CLP-PEG-MPC implants over the CLP-PEG only implants.
  •  
46.
  • Tinetti, G., et al. (author)
  • A chemical survey of exoplanets with ARIEL
  • 2018
  • In: Experimental Astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 46:1, s. 135-209
  • Journal article (peer-reviewed)abstract
    • Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.
  •  
47.
  • Weinberg, David H., et al. (author)
  • Chemical Cartography with APOGEE : Mapping Disk Populations with a 2-process Model and Residual Abundances
  • 2022
  • In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 260:2, s. 1-46
  • Journal article (peer-reviewed)abstract
    • We apply a novel statistical analysis to measurements of 16 elemental abundances in 34,410 Milky Way disk stars from the final data release (DR17) of APOGEE-2. Building on recent work, we fit median abundance ratio trends [X/Mg] versus [Mg/H] with a 2-process model, which decomposes abundance patterns into a "prompt" component tracing core-collapse supernovae and a "delayed" component tracing Type Ia supernovae. For each sample star, we fit the amplitudes of these two components, then compute the residuals Delta[X/H] from this two-parameter fit. The rms residuals range from similar to 0.01-0.03 dex for the most precisely measured APOGEE abundances to similar to 0.1 dex for Na, V, and Ce. The correlations of residuals reveal a complex underlying structure, including a correlated element group comprised of Ca, Na, Al, K, Cr, and Ce and a separate group comprised of Ni, V, Mn, and Co. Selecting stars poorly fit by the 2-process model reveals a rich variety of physical outliers and sometimes subtle measurement errors. Residual abundances allow for the comparison of populations controlled for differences in metallicity and [alpha/Fe]. Relative to the main disk (R = 3-13 kpc), we find nearly identical abundance patterns in the outer disk (R = 15-17 kpc), 0.05-0.2 dex depressions of multiple elements in LMC and Gaia Sausage/Enceladus stars, and wild deviations (0.4-1 dex) of multiple elements in omega Cen. The residual abundance analysis opens new opportunities for discovering chemically distinctive stars and stellar populations, for empirically constraining nucleosynthetic yields, and for testing chemical evolution models that include stochasticity in the production and redistribution of elements.
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