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Sökning: WFRF:(Jönsson Henrik)

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1.
  • Jönsson, Henrik, et al. (författare)
  • Abundances of disk and bulge giants from high-resolution optical spectra I. O, Mg, Ca, and Ti in the solar neighborhood and Kepler field samples
  • 2017
  • Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 598
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. The Galactic bulge is an intriguing and significant part of our Galaxy, but it is hard to observe because it is both distant and covered by dust in the disk. Therefore, there are not many high-resolution optical spectra of bulge stars with large wavelength coverage, whose determined abundances can be compared with nearby, similarly analyzed stellar samples. Aims. We aim to determine the diagnostically important alpha elements of a sample of bulge giants using high-resolution optical spectra with large wavelength coverage. The abundances found are compared to similarly derived abundances from similar spectra of similar stars in the local thin and thick disks. In this first paper we focus on the solar neighborhood reference sample. Methods. We used spectral synthesis to derive the stellar parameters as well as the elemental abundances of both the local and bulge samples of giants. We took special care to benchmark our method of determining stellar parameters against independent measurements of effective temperatures from angular diameter measurements and surface gravities from asteroseismology. Results. In this first paper we present the method used to determine the stellar parameters and elemental abundances, evaluate them, and present the results for our local disk sample of 291 giants. Conclusions. When comparing our determined spectroscopic temperatures to those derived from angular diameter measurements, we reproduce these with a systematic difference of + 10 K and a standard deviation of 53 K. The spectroscopic gravities reproduce those determined from asteroseismology with a systematic off set of + 0.10 dex and a standard deviation of 0.12 dex. When it comes to the abundance trends, our sample of local disk giants closely follows trends found in other works analyzing solar neighborhood dwarfs, showing that the much brighter giant stars are as good abundance probes as the often used dwarfs.
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2.
  • Bhatia, Neha, et al. (författare)
  • Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality
  • 2019
  • Ingår i: eLife. - 2050-084X. ; 8
  • Tidskriftsartikel (refereegranskat)abstract
    • Dorsoventrality in leaves has been shown to depend on the pre-patterned expression of KANADI and HD-ZIPIII genes within the plant shoot apical meristem (SAM). However, it has also been proposed that asymmetric auxin levels within initiating leaves help establish leaf polarity, based in part on observations of the DII auxin sensor. By analyzing and quantifying the expression of the R2D2 auxin sensor, we find that there is no obvious asymmetry in auxin levels during Arabidopsis leaf development. We further show that the mDII control sensor also exhibits an asymmetry in expression in developing leaf primordia early on, while it becomes more symmetric at a later developmental stage as reported previously. Together with other recent findings, our results argue against the importance of auxin asymmetry in establishing leaf polarity.
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3.
  • Briat, C., et al. (författare)
  • The Conservation of Information, Towards an Axiomatized Modular Modeling Approach to Congestion Control
  • 2015
  • Ingår i: IEEE/ACM Transactions on Networking. - 1063-6692 .- 1558-2566. ; 23:3, s. 851-865
  • Tidskriftsartikel (refereegranskat)abstract
    • We derive a modular fluid-flow network congestion control model based on a law of fundamental nature in networks: the conservation of information. Network elements such as queues, users, and transmission channels and network performance indicators like sending/acknowledgment rates and delays are mathematically modeled by applying this law locally. Our contributions are twofold. First, we introduce a modular metamodel that is sufficiently generic to represent any network topology. The proposed model is composed of building blocks that implement mechanisms ignored by the existing ones, which can be recovered from exact reduction or approximation of this new model. Second, we provide a novel classification of previously proposed models in the literature and show that they are often not capable of capturing the transient behavior of the network precisely. Numerical results obtained from packet-level simulations demonstrate the accuracy of the proposed model.
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4.
  • Dautovic Bergh, Cecilia, 1972-, et al. (författare)
  • Protein S100B after cardiac surgery: An indicator of long-term anxiety?
  • 2007
  • Ingår i: Scandinavian Cardiovascular Journal. - : Informa UK Limited. - 1401-7431 .- 1651-2006. ; 41:2, s. 109-113
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives. The aim of the study was to assess long-term state and trait anxiety in cardiac surgical risk patients. Design. Thirty two patients with serum S100B > 0.3 µg/l 48 hours after cardiac surgery with cardiopulmonary bypass were matched according to age, gender, type, date and length of surgery with 35 operated patients without elevated S100B. They completed Spielberger's Anxiety Inventory (STAI). Results. Patients with elevated S100B reported more state anxiety and trait anxiety. S100B was an independent predictor of both state and trait anxiety when controlling for perioperative variables. Conclusions. Patients with elevated S100B reported more anxiety 3–6 years after cardiac surgery. A postoperative blood sample can identify risk patients and facilitate appropriate follow-up.
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5.
  • de Jong, R. S., et al. (författare)
  • 4MOST : Project overview and information for the First Call for Proposals
  • 2019
  • Ingår i: The Messenger. - : European Southern Observatory. - 0722-6691. ; 175, s. 3-11
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • We introduce the 4-metre Multi-Object Spectroscopic Telescope (4MOST), a new high-multiplex, wide-field spectroscopic survey facility under development for the four-metre-class Visible and Infrared Survey Telescope for Astronomy (VISTA) at Paranal. Its key specifications are: a large field of view (FoV) of 4.2 square degrees and a high multiplex capability, with 1624 fibres feeding two low-resolution spectrographs (R = λ/Δλ ~ 6500), and 812 fibres transferring light to the high-resolution spectrograph (R ~ 20 000). After a description of the instrument and its expected performance, a short overview is given of its operational scheme and planned 4MOST Consortium science; these aspects are covered in more detail in other articles in this edition of The Messenger. Finally, the processes, schedules, and policies concerning the selection of ESO Community Surveys are presented, commencing with a singular opportunity to submit Letters of Intent for Public Surveys during the first five years of 4MOST operations.
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6.
  • Jakobsen, Peter, et al. (författare)
  • Territorial structure: An early Marxist theorisation of geography
  • 2022
  • Ingår i: Socio-Spatial Theory in Nordic Geography : Intellectual Histories and Critical Interventions - Intellectual Histories and Critical Interventions. - Cham : Springer International Publishing. - 9783031042331 - 9783031042362 - 9783031042348 ; , s. 51-68
  • Bokkapitel (refereegranskat)abstract
    • Radical geography came only patchily to Nordic geography, and the development of theoretical Marxist geography was even sparser. But in the radical geography environment at Copenhagen University, a group of geographers in the 1970s developed a vocal and self-assured Marxist theory, which became known as the territorial-structure approach and drew its inspiration from the work of the GDR geographer Gerhard Schmidt-Renner. In this chapter we present a critical discussion of the territorial-structure approach as an example of an early theorisation of geography from a Marxist perspective. We discuss the central controversies that came to surround the approach, and we discuss the territorial-structure approach as a conscious effort to resist disciplinary specialisation and fragmentation of (human) geography. Our aim is not to resurrect the territorial-structure approach, but rather to investigate this theory as an important step towards socio-spatial theory in Nordic geography.
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7.
  • Jönsson, Henrik, et al. (författare)
  • Controversial significance of early S100B levels after cardiac surgery
  • 2004
  • Ingår i: BMC Neurology. - : Springer Science and Business Media LLC. - 1471-2377. ; 4:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundThe brain-derived protein S100B has been shown to be a useful marker of brain injury of different etiologies. Cognitive dysfunction after cardiac surgery using cardiopulmonary bypass has been reported to occur in up to 70% of patients. In this study we tried to evaluate S100B as a marker for cognitive dysfunction after coronary bypass surgery with cardiopulmonary bypass in a model where the inflow of S100B from shed mediastinal blood was corrected for.Methods56 patients scheduled for coronary artery bypass grafting underwent prospective neuropsychological testing. The test scores were standardized and an impairment index was constructed. S100B was sampled at the end of surgery, hourly for the first 6 hours, and then 8, 10, 15, 24 and 48 hours after surgery. None of the patients received autotransfusion.ResultsIn simple linear analysis, no significant relation was found between S100B levels and neuropsychological outcome. In a backwards stepwise regression analysis the three variables, S100B levels at the end of cardiopulmonary bypass, S100B levels 1 hour later and the age of the patients were found to explain part of the neuropsychological deterioration (r = 0.49, p < 0.005).ConclusionsIn this study we found that S100B levels 1 hour after surgery seem to be the most informative. Our attempt to control the increased levels of S100B caused by contamination from the surgical field did not yield different results. We conclude that the clinical value of S100B as a predictive measurement of postoperative cognitive dysfunction after cardiac surgery is limited.
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8.
  • Larsen, Henrik Gutzon, et al. (författare)
  • Sublimated expansionism? Living space ideas in Nordic small-state geopolitics
  • 2022
  • Ingår i: Socio-Spatial Theory in Nordic Geography : Intellectual Histories and Critical Interventions - Intellectual Histories and Critical Interventions. - Cham : Springer International Publishing. - 9783031042331 - 9783031042362 - 9783031042348 ; , s. 15-30
  • Bokkapitel (refereegranskat)abstract
    • In intellectual histories of geography as well as in international relations, geopolitics is usually the business of great powers, understood as the expansion of hard power through territorial control. However, the existence of a ‘Geopolitik of the weak’ has also been theorised, premised on the ability of smaller states – such as the Nordic countries – to secure their survival through a wider range of policy instruments. In this chapter, we analyse key themes in the work of two Nordic geographical thinkers deeply concerned with the place and status of their home countries in the era of high modernity – Rudolf Kjellén and Gudmund Hatt. Relying upon their scholarly works as well as relevant public debates circa 1905–1945, we trace the ‘small-state geopoliticking’ of Hatt and Kjellén, identifying three key characteristics of their style of small-state geopolitics: (1) determinism is qualified by voluntarism; (2) space is complemented by future; and (3) external expansion is sublimated into internal progress. In its reconceptualisation of living space as primarily concerned with existential survival as premised upon future progress, rather than outward-oriented territorial expansion, small-state geopolitics emerges as a highly situated, somewhat quaint but nonetheless significant element in Nordic theorising of geography.
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9.
  • Smiljanic, R., et al. (författare)
  • The Gaia-ESO Survey: The analysis of high-resolution UVES spectra of FGK-type stars
  • 2014
  • Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 570
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. The ongoing Gaia-ESO Public Spectroscopic Survey is using FLAMES at the VLT to obtain high-quality medium-resolution Giraffe spectra for about 10(5) stars and high-resolution UVES spectra for about 5000 stars. With UVES, the Survey has already observed 1447 FGK-type stars. Aims. These UVES spectra are analyzed in parallel by several state-of-the-art methodologies. Our aim is to present how these analyses were implemented, to discuss their results, and to describe how a final recommended parameter scale is defined. We also discuss the precision (method-to-method dispersion) and accuracy (biases with respect to the reference values) of the final parameters. These results are part of the Gaia-ESO second internal release and will be part of its first public release of advanced data products. Methods. The final parameter scale is tied to the scale defined by the Gaia benchmark stars, a set of stars with fundamental atmospheric parameters. In addition, a set of open and globular clusters is used to evaluate the physical soundness of the results. Each of the implemented methodologies is judged against the benchmark stars to define weights in three different regions of the parameter space. The final recommended results are the weighted medians of those from the individual methods. Results. The recommended results successfully reproduce the atmospheric parameters of the benchmark stars and the expected T-eff-log g relation of the calibrating clusters. Atmospheric parameters and abundances have been determined for 1301 FGK-type stars observed with UVES. The median of the method-to-method dispersion of the atmospheric parameters is 55K for T-eff, 0.13dex for log g and 0.07 dex for [Fe/H]. Systematic biases are estimated to be between 50-100 K for T-eff, 0.10-0.25 dex for log g and 0.05-0.10 dex for [Fe/H]. Abundances for 24 elements were derived: C, N, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, Nd, and Eu. The typical method-to-method dispersion of the abundances varies between 0.10 and 0.20 dex. Conclusions. The Gaia-ESO sample of high-resolution spectra of FGK-type stars will be among the largest of its kind analyzed in a homogeneous way. The extensive list of elemental abundances derived in these stars will enable significant advances in the areas of stellar evolution and Milky Way formation and evolution.
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10.
  • Thorsbro, B., et al. (författare)
  • Evidence against Anomalous Compositions for Giants in the Galactic Nuclear Star Cluster
  • 2018
  • Ingår i: Astrophysical Journal. - : Bibliopolis, Edizioni di Filosofia e Scienze. - 0004-637X .- 1538-4357. ; 866:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Very strong Sc I lines have recently been found in cool M giants in the Nuclear Star Cluster (NSC) in the Galactic center. Interpreting these as anomalously high scandium abundances in the Galactic center would imply a unique enhancement signature and chemical evolution history for NSCs, and a potential test for models of chemical enrichment in these objects. We present high resolution K-band spectra (NIRSPEC/Keck II) of cool M giants situated in the solar neighborhood and compare them with spectra of M giants in the NSC. We clearly identify strong Sc I lines in our solar neighborhood sample as well as in the NSC sample. The strong Sc I lines in M giants are therefore not unique to stars in the NSC and we argue that the strong lines are a property of the line formation process that currently escapes accurate theoretical modeling. We further conclude that for giant stars with effective temperatures below approximately 3800 K these Sc I lines should not be used for deriving the scandium abundances in any astrophysical environment until we better understand how these lines are formed. We also discuss the lines of vanadium, titanium, and yttrium identified in the spectra, which demonstrate a similar striking increase in strength below 3500 K effective temperature.
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11.
  • Åhl, Henrik, et al. (författare)
  • High-Throughput 3D Phenotyping of Plant Shoot Apical Meristems From Tissue-Resolution Data
  • 2022
  • Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Confocal imaging is a well-established method for investigating plant phenotypes on the tissue and organ level. However, many differences are difficult to assess by visual inspection and researchers rely extensively on ad hoc manual quantification techniques and qualitative assessment. Here we present a method for quantitatively phenotyping large samples of plant tissue morphologies using triangulated isosurfaces. We successfully demonstrate the applicability of the approach using confocal imaging of aerial organs in Arabidopsis thaliana. Automatic identification of flower primordia using the surface curvature as an indication of outgrowth allows for high-throughput quantification of divergence angles and further analysis of individual flowers. We demonstrate the throughput of our method by quantifying geometric features of 1065 flower primordia from 172 plants, comparing auxin transport mutants to wild type. Additionally, we find that a paraboloid provides a simple geometric parameterisation of the shoot inflorescence domain with few parameters. We utilise parameterisation methods to provide a computational comparison of the shoot apex defined by a fluorescent reporter of the central zone marker gene CLAVATA3 with the apex defined by the paraboloid. Finally, we analyse the impact of mutations which alter mechanical properties on inflorescence dome curvature and compare the results with auxin transport mutants. Our results suggest that region-specific expression domains of genes regulating cell wall biosynthesis and local auxin transport can be important in maintaining the wildtype tissue shape. Altogether, our results indicate a general approach to parameterise and quantify plant development in 3D, which is applicable also in cases where data resolution is limited, and cell segmentation not possible. This enables researchers to address fundamental questions of plant development by quantitative phenotyping with high throughput, consistency and reproducibility.
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12.
  • Abolfathi, Bela, et al. (författare)
  • The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
  • 2018
  • Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
  • Tidskriftsartikel (refereegranskat)abstract
    • The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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13.
  • Aguado, D. S., et al. (författare)
  • The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
  • 2019
  • Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
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14.
  • Ahlström, Stina, et al. (författare)
  • Characteristics of post-mortem beta-hydroxybutyrate-positivet cases : A retrospective study on age, sex and BMI in 1407 forensic autopsies
  • 2021
  • Ingår i: Forensic Science International. - : Elsevier BV. - 0379-0738 .- 1872-6283. ; 325
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundPost-mortem biochemistry, including the analysis of beta-hydroxybutyrate (BHB), is increasingly employed in forensic medicine, especially in conditions such as diabetes and chronic alcoholism. However, not much is known about the associations between age, body mass index (BMI), and sex and BHB concentrations in ketoacidotic conditions.AimTo retrospectively study the association between age, BMI and sex in several conditions, such as diabetic ketoacidosis (DKA), alcoholic ketoacidosis (AKA), and elevated post-mortem BHB concentrations.Methods1407 forensic autopsy cases analysed for BHB were grouped by diagnosis: DKA, AKA, HHS [hyperosmolar hyperglycaemic state], acidosis NOS [not otherwise specified], or hypothermia. Age, sex, BMI and the concentrations of blood alcohol, vitreous glucose and blood BHB were recorded.ResultsCases of AKA and DKA were most numerous (184 and 156, respectively). In DKA and in its male subgroup, cases with severe ketosis (BHB>1000 µg/g) were younger and had a lower BMI than those with moderate ketosis (BHB 250–1000 µg/g) and controls (P<0.001). In DKA and in its female subgroup, cases with moderate ketosis cases were older (P = 0.0218 and P = 0.0083) than controls. In AKA and in its male subgroup, cases with severe ketosis had a lower BMI than those with moderate ketosis (P = 0.0391 and P = 0.0469) and controls (P<0.001). Cases with moderate ketosis had a lower BMI than controls (P<0.001).ConclusionsBHB concentration is associated with BMI in DKA and AKA, and with both BMI and age in DKA. Constitutional factors should, therefore, be considered in potential AKA and DKA cases.
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15.
  • Ahlström, Stina, et al. (författare)
  • The Importance of BHB Testing on the Post-Mortem Diagnosis of Ketoacidosis
  • 2022
  • Ingår i: Biomolecules. - : MDPI. - 2218-273X. ; 12:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Although beta-hydroxybutyrate (BHB) analysis has proved its importance in forensic pathology, its effects on cause-of-death diagnostics are unaddressed. Therefore, this study aims at evaluating the effects of BHB analysis on the number of deaths by DKA (diabetes ketoacidosis), AKA (alcoholic ketoacidosis), HHS (hyperosmolar hyperglycaemic state), hypothermia, diabetes, alcoholism, and acidosis NOS (not otherwise specified). All 2900 deaths from 2013 through 2019 in which BHB was analysed at the National Board of Forensic Medicine, and 1069 DKA, AKA, HHS, hypothermia, diabetes, alcoholism, and acidosis cases without BHB analysis were included. The prevalence of BHB-positive cases for each cause of death, and trends and proportions of different BHB concentrations, were investigated. The number of BHB analyses/year increased from 13 to 1417. AKA increased from three to 66 and acidosis from one to 20. The deaths from alcoholism, DKA, and hypothermia remained stable. It is unclear why death from alcoholism remained stable while AKA increased. The increase in unspecific acidosis deaths raises the question why a more specific diagnosis had not been used. In conclusion, BHB analysis is instrumental in detecting AKA and acidosis. The scientific basis for the diagnosis of DKA and hypothermia improved, but the number of cases did not change.
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16.
  • Ahrenberg, Lars, 1948-, et al. (författare)
  • Studying Disability Related Terms with Swe-Clarin Resources
  • 2019
  • Konferensbidrag (refereegranskat)abstract
    • In Swedish, as in other languages, the words used to refer to disabilities and people with disabilities are manifold. Recommendations as to which terms to use have been changed several times over the last hundred years. In this exploratory paper we have used textual resources provided by Swe-Clarin to study such changes quantitatively. We demonstrate that old and new recommendations co-exist for long periods of time, and that usage sometimes converges.
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17.
  • Ahumada, Romina, et al. (författare)
  • The 16th Data Release of the Sloan Digital Sky Surveys : First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra
  • 2020
  • Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 249:1
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17).
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18.
  • Anderson, Henrik, et al. (författare)
  • Quartz crystal microbalance sensor design : I. Experimental study of sensor response and performance
  • 2007
  • Ingår i: Sensors and actuators. B, Chemical. - : Elsevier BV. - 0925-4005 .- 1873-3077. ; 123:1, s. 27-34
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper investigates a novel quartz crystal microbalance (QCM) biosensor with a small and rectangular flow cell along with a correspondingly shaped crystal electrode. The sensor was evaluated with impedance analysis and compared to standard circular sensor crystals and sensor crystals with small circular electrodes. Comparative QCM measurements on an antibody–antigen interaction system were carried out on the rectangular and standard circular sensor systems. Impedance analysis and subsequent data extraction of the three different sensor crystals showed that the smaller sensors had significantly higher Q-values in air, but that liquid load on the electrodes lowered the Q-values radically for all crystals. Under liquid load, Q-values for the standard circular and the rectangular sensors were similar whereas the Q-value for the small circular sensor was 50% higher. QCM experiments showed that the QCM system with rectangular crystal electrodes was fully functional in a liquid environment. The rectangular system showed higher and more rapid responses for series of antibody injections, albeit at a higher noise level than the standard system. The study elucidates a significant potential for improvement of sensor performance by optimising the sensor electrode size and shape together with the flow cell geometry.
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19.
  • Andersson, Alexandra, et al. (författare)
  • Comparison of diafiltration and size-exclusion chromatography to recover hemicelluloses from process water from thermomechanical pulping of spruce
  • 2007
  • Ingår i: Applied Biochemistry and Biotechnology. - : Springer Science and Business Media LLC. - 1559-0291 .- 0273-2289. ; 137:1-12, s. 971-983
  • Tidskriftsartikel (refereegranskat)abstract
    • Hemicelluloses constitute one of the most abundant renewable resources on earth. To increase their utilization, the isolation of hemicelluloses from industrial biomass side-streams would be beneficial. A method was investigated to isolate hemicelluloses from process water from a thermomechanical pulp mill. The method consists of three steps: removal of solids by microfiltration, preconcentration of the hemicelluloses by ultrafiltration, and purification by either size-exclusion chromatography (SEC) or diafiltration. The purpose of the final purification step is to separate hemicelluloses from small oligosaccharides, monosaccharides, and salts. The ratio between galactose, glucose, and mannose in oligo- and polysaccharides after preconcentration was 0.8: 1: 2.8, which is similar to that found in galactoglucomannan. Continuous diafiltration was performed using a composite fluoro polymer membrane with cutoff of 1000 Da. After diafiltration with four diavolumes the purity of the hemicelluloses was 77% (gram oligo- and polysaccharides/gram total dissolved solids) and the recovery was 87%. Purification by SEC was performed with 5, 20, and 40% sample loadings, respectively and a flow rate of 12 or 25 mL/min (9 or 19 cm/h). The purity of hemicelluloses after SEC was approx 82%, and the recovery was above 99%. The optimal sample load and flow rate were 20% and 25 mL/min, respectively. The process water from thermomechanical pulping of spruce is inexpensive. Thus, the recovery of hemicelluloses is not of main importance. If the purity of 77%, obtained with diafiltration, is sufficient for the utilization of the hemicelluloses, diafiltration probably offers a less expensive alternative in this application.
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20.
  • André-Jönsson, Henrik, 1968- (författare)
  • Indexing strategies for time series data
  • 2002
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Traditionally, databases have stored textual data and have been used to store administrative information. The computers used. and more specifically the storage available, have been neither large enough nor fast enough to allow databases to be used for more technical applications. In recent years these two bottlenecks have started to di sappear and there is an increasing interest in using databases to store non-textual data like sensor measurements or other types of process-related data. In a database a sequence of sensor measurements can be represented as a time series. The database can then be queried to find, for instance, subsequences, extrema points, or the points in time at which the time series had a specific value. To make this search efficient, indexing methods are required. Finding appropriate indexing methods is the focus of this thesis.There are two major problems with existing time series indexing strategies: the size of the index structures and the lack of general indexing strategies that are application independent. These problems have been thoroughly researched and solved in the case of text indexing files. We have examined the extent to which text indexing methods can be used for indexing time series.A method for transforming time series into text sequences has been investigated. An investigation was then made on how text indexing methods can be applied on these text sequences. We have examined two well known text indexing methods: the signature files and the B-tree. A study has been made on how these methods can be modified so that they can be used to index time series. We have also developed two new index structures, the signature tree and paged trie structures. For each index structure we have constructed cost and size models. resulting in comparisons between the different approaches.Our tests indicate that the indexing method we have developed. together with the B-tree structure. produces good results. It is possible to search for and find sub-sequences of very large time series efficiently.The thesis also discusses what future issues will have to be investigated for these techniques to be usable in a control system relying on time-series indexing to identify control modes.
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21.
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22.
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23.
  • Atalay, B., et al. (författare)
  • MCDHF and RCI calculations of energy levels, lifetimes, and transition rates in Si III and Si IV
  • 2019
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 631
  • Tidskriftsartikel (refereegranskat)abstract
    • We present extensive multiconfiguration Dirac-Hartree-Fock and relativistic configuration interaction calculations including 106 states in doubly ionized silicon (Si III) and 45 states in triply ionized silicon (Si IV), which are important for astrophysical determination of plasma properties in different objects. These calculations represents an important extension and improvement of earlier calculations especially for Si III. The calculations are in good agreement with available experiments for excitation energies, transition properties, and lifetimes. Important deviations from the NIST-database for a selection of perturbed Rydberg series are discussed in detail.
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24.
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25.
  • Bengtsson, Henrik, et al. (författare)
  • Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
  • 2004
  • Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the microarray scanner and the image analysis software. Results: By scanning the same spotted oligonucleotide microarray at different photomultiplier tube (PMT) gains, we have identified a channel-specific bias present in two-channel microarray data. For the scanners analyzed it was in the range of 15 - 25 ( out of 65,535). The observed bias was very stable between subsequent scans of the same array although the PMT gain was greatly adjusted. This indicates that the bias does not originate from a step preceding the scanner detector parts. The bias varies slightly between arrays. When comparing estimates based on data from the same array, but from different scanners, we have found that different scanners introduce different amounts of bias. So do various image analysis methods. We propose a scanning protocol and a constrained affine model that allows us to identify and estimate the bias in each channel. Backward transformation removes the bias and brings the channels to the same scale. The result is that systematic effects such as intensity dependent log-ratios are removed, but also that signal densities become much more similar. The average scan, which has a larger dynamical range and greater signal-to-noise ratio than individual scans, can then be obtained. Conclusions: The study shows that microarray scanners may introduce a significant bias in each channel. Such biases have to be calibrated for, otherwise systematic effects such as intensity dependent log-ratios will be observed. The proposed scanning protocol and calibration method is simple to use and is useful for evaluating scanner biases or for obtaining calibrated measurements with extended dynamical range and better precision. The cross-platform R package aroma, which implements all described methods, is available for free from http://www.maths.lth.se/ bioinformatics/.
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26.
  • Bengtsson, Staffan, et al. (författare)
  • Brandskyddsteknisk projektering
  • 2005
  • Ingår i: Brandskyddshandboken - En handbok för projektering av brandskydd i byggnader. - 1402-3504. ; , s. 21-49
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)
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27.
  • Bergh, Cecilia, et al. (författare)
  • In the eye of both patient and spouse: memory is poor 1 to 2 years after coronary bypass and angioplasty.
  • 2002
  • Ingår i: Annals of Thoracic Surgery. - 1552-6259. ; 74:3, s. 689-693
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The study aimed to investigate patient and spouse perception of cognitive functioning 1 to 2 years after coronary artery bypass grafting. METHODS: Seventy-six married patients who had undergone coronary artery bypass grafting were selected and sex- and age-matched with 75 concurrent married patients who had undergone percutaneous transluminal coronary angioplasty. Couples received a letter of explanation and then completed telephone interviews. Forty-seven questions assessed memory, concentration, general health, social functioning, and emotional state. Response choices were: improved, unchanged, or deteriorated function after coronary artery bypass grafting/percutaneous transluminal coronary angioplasty. RESULTS: Patients who had undergone coronary artery bypass grafting did not differ in subjective ratings on any measure from patients who had undergone percutaneous transluminal coronary angioplasty. There were no differences between spouses in the respective groups; spouse ratings also did not differ from patient ratings. Only in memory function did patients and spouses report a postprocedural decline. CONCLUSIONS: No subjective differences were found in patients who had undergone either coronary artery bypass grafting or percutaneous transluminal coronary angioplasty. Spouse ratings agreed with each other and with patient ratings. Positive correlations were found between the questionnaire factors, suggesting that perceived health and well-being are associated with subjective cognition.
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28.
  • Bergh, Cecilia, 1972-, et al. (författare)
  • In the eye of both patient and spouse: memory is poor 1 to 2 years after coronary bypass and angioplasty
  • 2002
  • Ingår i: Annals of Thoracic Surgery. - : Elsevier BV. - 0003-4975 .- 1552-6259. ; 74:3, s. 689-693
  • Tidskriftsartikel (refereegranskat)abstract
    • Background. The study aimed to investigate patient and spouse perception of cognitive functioning 1 to 2 years after coronary artery bypass grafting.Methods. Seventy-six married patients who had undergone coronary artery bypass grafting were selected and sex- and age-matched with 75 concurrent married patients who had undergone percutaneous transluminal coronary angioplasty. Couples received a letter of explanation and then completed telephone interviews. Forty-seven questions assessed memory, concentration, general health, social functioning, and emotional state. Response choices were: improved, unchanged, or deteriorated function after coronary artery bypass grafting/percutaneous transluminal coronary angioplasty.Results. Patients who had undergone coronary artery bypass grafting did not differ in subjective ratings on any measure from patients who had undergone percutaneous transluminal coronary angioplasty. There were no differences between spouses in the respective groups; spouse ratings also did not differ from patient ratings. Only in memory function did patients and spouses report a postprocedural decline.Conclusions. No subjective differences were found in patients who had undergone either coronary artery bypass grafting or percutaneous transluminal coronary angioplasty. Spouse ratings agreed with each other and with patient ratings. Positive correlations were found between the questionnaire factors, suggesting that perceived health and well-being are associated with subjective cognition.
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29.
  • Bergström, Lena, et al. (författare)
  • Klimatförändringar och biologisk mångfald : Slutsatser från IPCC och IPBES i ett svenskt perspektiv.
  • 2020
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • De stora miljö- och samhällsproblemen kommer inte ensamma. De är sammankopplade på olika sätt. Detta innebär utmaningar men ger också möjligheter att utveckla åtgärder och lösningar. Det gäller både för klimatfrågan och frågan om att motverka förlusten av biologisk mångfald och ekosystem. Kunskapens betydelse för att hantera dessa och andra aspekter är ovärderlig, såväl kring specifika frågeställningar som kring omständigheter och förutsättningar för åtgärdsarbetet.Den här kunskapssammanställningen har gjorts av forskare från Lunds universitet och Sveriges lantbruksuniversitet på uppdrag av Naturvårdsverket och SMHI. Forskarna har tagit avstamp i de omfattande kunskapsutvärderingar som gjorts av den mellanstatliga klimatpanelen (IPCC) och den mellanstatliga plattformen för biologisk mångfald (IPBES). Slutsatserna från IPCC och IPBES sätts i ett svenskt perspektiv, bland annat genom utvalda exempel vilka fungerar som aktuella illustrationer av hur klimatförändringar påverkar biologisk mångfald och ekosystem i Sverige.
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30.
  • Berndtsson, Ronny, et al. (författare)
  • Drivers of changing urban flood risk : A framework for action
  • 2019
  • Ingår i: Journal of Environmental Management. - : Elsevier. - 0301-4797 .- 1095-8630. ; 240, s. 47-56
  • Tidskriftsartikel (refereegranskat)abstract
    • This study focuses on drivers for changing urban flood risk. We suggest a framework for guiding climate change adaptation action concerning flood risk and manageability in cities. The identified key drivers of changing flood hazard and vulnerability are used to provide an overview of each driver's impact on flood risk and manageability at the city level. We find that identified drivers for urban flood risk can be grouped in three different priority areas with different time horizon. The first group has high impact but is manageable at city level. Typical drivers in this group are related to the physical environment such as decreasing permeability and unresponsive engineering. The second group of drivers is represented by public awareness and individual willingness to participate and urbanization and urban sprawl. These drivers may be important and are manageable for the cities and they involve both short-term and long-term measures. The third group of drivers is related to policy and long-term changes. This group is represented by economic growth and increasing values at risk, climate change, and increasing complexity of society. They have all high impact but low manageability. Managing these drivers needs to be done in a longer time perspective, e.g., by developing long-term policies and exchange of ideas.
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31.
  • Betancourt, Lazaro Hiram, et al. (författare)
  • Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
  • 2019
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.
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32.
  • Bhatia, Neha, et al. (författare)
  • Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis
  • 2016
  • Ingår i: Current Biology. - : Elsevier BV. - 1879-0445 .- 0960-9822. ; 26:23, s. 3202-3208
  • Tidskriftsartikel (refereegranskat)abstract
    • The periodic formation of plant organs such as leaves and flowers gives rise to intricate patterns that have fascinated biologists and mathematicians alike for hundreds of years [1]. The plant hormone auxin plays a central role in establishing these patterns by promoting organ formation at sites where it accumulates due to its polar, cell-to-cell transport [2-6]. Although experimental evidence as well as modeling suggest that feedback from auxin to its transport direction may help specify phyllotactic patterns [7-12], the nature of this feedback remains unclear [13]. Here we reveal that polarization of the auxin efflux carrier PIN-FORMED 1 (PIN1) is regulated by the auxin response transcription factor MONOPTEROS (MP) [14]. We find that in the shoot, cell polarity patterns follow MP expression, which in turn follows auxin distribution patterns. By perturbing MP activity both globally and locally, we show that localized MP activity is necessary for the generation of polarity convergence patterns and that localized MP expression is sufficient to instruct PIN1 polarity directions non-cell autonomously, toward MP-expressing cells. By expressing MP in the epidermis of mp mutants, we further show that although MP activity in a single-cell layer is sufficient to promote polarity convergence patterns, MP in sub-epidermal tissues helps anchor these polarity patterns to the underlying cells. Overall, our findings reveal a patterning module in plants that determines organ position by orienting transport of the hormone auxin toward cells with high levels of MP-mediated auxin signaling. We propose that this feedback process acts broadly to generate periodic plant architectures.
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33.
  • Bijavara Seshashayana, Shilpa, et al. (författare)
  • Stellar Population Astrophysics (SPA) with TNG
  • 2024
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 683
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. The age, evolution, and chemical properties of the Galactic disk can be effectively ascertained using open clusters. Within the large program Stellar Populations Astrophysics at the Telescopio Nazionale Galileo, we specifically focused on stars in open clusters, to investigate various astrophysical topics, from the chemical content of very young systems to the abundance patterns of lesser studied intermediate-age and old open clusters.Aims. We investigate the astrophysically interesting element fluorine (F), which has an uncertain and intriguing cosmic origin. We also determine the abundance of cerium (Ce), as F abundance is expected to correlate with the s-process elements. We intend to determine the trend of F abundance across the Galactic disk as a function of metallicity and age. This will offer insights into Galactic chemical evolution models, potentially enhancing our comprehension of this element’s cosmic origin.Methods. High-resolution near-infrared spectra were obtained using the GIANO-B spectrograph. The Python version of Spectroscopy Made Easy (PySME), was used to derive atmospheric parameters and abundances. The stellar parameters were determined using OH, CN, and CO molecular lines along with Fe I lines. The F and Ce abundances were inferred using two K-band HF lines (λλ 2.28, 2.33 µm) and two atomic H-band lines (λλ 1.66, and 1.71 µm), respectively.Results. Of all the clusters in our sample, only King 11 had not been previously studied through medium- to high-resolution spectroscopy, and our stellar parameter and metallicity findings align well with those documented in the literature. We have successfully inferred F and Ce abundances in all seven open clusters and probed the radial and age distributions of abundance ratios. This paper presents the first F Galactic radial abundance gradient. Our results are also compared with literature estimates and with Galactic chemical evolution models that have been generated using different F production channels.Conclusions. Our results indicate a constant, solar pattern in the [F/Fe] ratios across clusters of different ages, supporting the latest findings that fluorine levels do not exhibit any secondary behavior for stars with solar or above-solar metallicity. However, an exception to this trend is seen in NGC 6791, a metal-rich, ancient cluster whose chemical composition is distinct due to its enhanced fluorine abundance. This anomaly strengthens the hypothesis that NGC 6791 originated in the inner regions of the Galaxy before migrating to its present position. By comparing our sample stars with the predictions of Galactic chemical evolution models, we came to the conclusion that both asymptotic giant branch stars and massive stars, including a fraction of fast rotators that increase with decreasing metallicity, are needed to explain the cosmic origin of F.
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34.
  • Birkhofer, Klaus, et al. (författare)
  • A framework to identify indicator species for ecosystem services in agricultural landscapes
  • 2018
  • Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 91, s. 278-286
  • Tidskriftsartikel (refereegranskat)abstract
    • Improving our understanding of the relationships between biodiversity and the delivery of ecosystem services is crucial for the development of sustainable agriculture. We introduce a novel framework that is based on the identification of indicator species for single or multiple ecosystem services across taxonomic groups based on indicator species analyses. We utilize multi-species community data (unlike previous single species approaches) without giving up information about the identity of species in our framework (unlike previous species richness approaches). We compiled a comprehensive community dataset including abundances of 683 invertebrate, vertebrate and plant species to identify indicator species that were either positively or negatively related to biological control, diversity of red-listed species or crop yield in agricultural landscapes in southern Sweden. Our results demonstrate that some taxonomic groups include significantly higher percentages of indicator species for these ecosystem services. Spider communities for example included a higher percentage of significant positive indicator species for biological control than ground or rove beetle communities. Bundles of indicator species for the analysed ecosystem service potentials usually included species that could be linked to the respective ecosystem service based on their functional role in local communities. Several of these species are conspicuous enough to be monitored by trained amateurs and could be used in bundles that are either crucial for the provision of individual ecosystem services or indicate agricultural landscapes with high value for red-listed species or crop yields. The use of bundles of characteristic indicator species for the simultaneous assessment of ecosystem services may reduce the amount of labour, time and cost in future assessments. In addition, future analysis using our framework in other ecosystems or with other subsets of ecosystem services and taxonomic groups will improve our understanding of service-providing species in local communities. In any case, expert knowledge is needed to select species from the identified subsets of significant indicator species and these species should be validated by existing data or additional sampling prior to being used for ecosystem service monitoring.
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35.
  • Birkhofer, Klaus, et al. (författare)
  • Relationships between multiple biodiversity components and ecosystem services along a landscape complexity gradient
  • 2018
  • Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 218, s. 247-253
  • Tidskriftsartikel (refereegranskat)abstract
    • The assessment of effects of anthropogenic disturbance on biodiversity (BD) and ecosystem services (ES) and their relationships are key priorities of the Intergovernmental Panel for Biodiversity and Ecosystem Services. Agricultural landscapes and their associated BD provide multiple ES and it is crucial to understand how relationships between ES and BD components change along gradients of landscape complexity. In this study, we related eight ES potentials to the species richness of five invertebrate, vertebrate and plant taxonomic groups in cereal farming systems. The landscape complexity gradient ranged from areas dominated by annually tilled arable land to areas with high proportions of unfertilized, non-rotational pastures and uncultivated field borders. We show that after accounting for landscape complexity relationships between yield and bird richness or biological control became more positive, but relationships between bird richness and biological control became less positive. The relationship between bird and plant richness turned from positive to negative. Multidiversity (overall biodiversity), was positively related to landscape complexity, whereas multifunctionality (overall ES provision), was not significantly related to either one of these. Our results suggest that multidiversity can be promoted by increasing landscape complexity; however; we found no support for a simultaneous increase of several individual ES, BD components or multifunctionality. These results challenge the assumption that bio-diversity-friendly landscape management will always simultaneously promote multiple ES in agricultural landscapes. Future studies need to verify this pattern by using multi-year data, larger sets of ES and BD components and a study design that is appropriate to address larger spatial scales and relationships in several regions.
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36.
  • Blanton, Michael R., et al. (författare)
  • Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
  • 2017
  • Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
  • Tidskriftsartikel (refereegranskat)abstract
    • We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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37.
  • Bonfanti, Alessandra, et al. (författare)
  • Stiffness transitions in new walls post-cell division differ between Marchantia polymorpha gemmae and Arabidopsis thaliana leaves
  • 2023
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424. ; 120:41
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant morphogenesis is governed by the mechanics of the cell wall—a stiff and thin polymeric box that encloses the cells. The cell wall is a highly dynamic composite material. New cell walls are added during cell division. As the cells continue to grow, the properties of cell walls are modulated to undergo significant changes in shape and size without breakage. Spatial and temporal variations in cell wall mechanical properties have been observed. However, how they relate to cell division remains an outstanding question. Here, we combine time-lapse imaging with local mechanical measurements via atomic force microscopy to systematically map the cell wall’s age and growth, with their stiffness. We make use of two systems, Marchantia polymorpha gemmae, and Arabidopsis thaliana leaves. We first characterize the growth and cell division of M. polymorpha gemmae. We then demonstrate that cell division in M. polymorpha gemmae results in the generation of a temporary stiffer and slower-growing new wall. In contrast, this transient phenomenon is absent in A. thaliana leaves. We provide evidence that this different temporal behavior has a direct impact on the local cell geometry via changes in the junction angle. These results are expected to pave the way for developing more realistic plant morphogenetic models and to advance the study into the impact of cell division on tissue growth.
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38.
  • Borg, J., et al. (författare)
  • Contribution of non-genetic factors to dopamine and serotonin receptor availability in the adult human brain
  • 2016
  • Ingår i: Molecular Psychiatry. - London, United Kingdom : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 51, s. 879-879
  • Tidskriftsartikel (refereegranskat)abstract
    • The dopamine (DA) and serotonin (5-HT) neurotransmission systems are of fundamental importance for normal brain function and serve as targets for treatment of major neuropsychiatric disorders. Despite central interest for these neurotransmission systems in psychiatry research, little is known about the regulation of receptor and transporter density levels. This lack of knowledge obscures interpretation of differences in protein availability reported in psychiatric patients. In this study, we used positron emission tomography (PET) in a twin design to estimate the relative contribution of genetic and environmental factors, respectively, on dopaminergic and serotonergic markers in the living human brain. Eleven monozygotic and 10 dizygotic healthy male twin pairs were examined with PET and [(11)C]raclopride binding to the D2- and D3-dopamine receptor and [(11)C]WAY100635 binding to the serotonin 5-HT1A receptor. Heritability, shared environmental effects and individual-specific non-shared effects were estimated for regional D2/3 and 5-HT1A receptor availability in projection areas. We found a major contribution of genetic factors (0.67) on individual variability in striatal D2/3 receptor binding and a major contribution of environmental factors (pairwise shared and unique individual; 0.70-0.75) on neocortical 5-HT1A receptor binding. Our findings indicate that individual variation in neuroreceptor availability in the adult brain is the end point of a nature-nurture interplay, and call for increased efforts to identify not only the genetic but also the environmental factors that influence neurotransmission in health and disease.
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39.
  • Boström, Marja L., et al. (författare)
  • A specific, highly enriching and "green" method for hollow fiber liquid phase microextraction of ionizable pharmaceuticals from fish tissue
  • 2014
  • Ingår i: Analytical Methods. - : Royal Society of Chemistry (RSC). - 1759-9660. ; 6:15, s. 6031-6037
  • Tidskriftsartikel (refereegranskat)abstract
    • Ionizable pharmaceuticals are a class of emerging contaminants that pose a challenge to analytical chemistry due to their low environmental concentrations. To measure such low concentrations in organism tissue, e.g. fish muscle, specific extraction techniques minimizing co-extraction and interference alongside providing high enrichment of the compounds are needed. In this study we present a technique using hollow fiber liquid phase microextraction which is selective and highly enriching due to a pH gradient across a selective membrane, trapping ions in the extract. Microextraction minimizes the use of organic solvents, thereby making the technique "green". We used high volume pharmaceuticals for method development, specifically, the weak acids ketoprofen, naproxen, diclofenac and ibuprofen, and the weak bases fluoxetine and sertraline. Lyophilized tissue extraction gave higher enrichment than fresh tissue extraction and concentration enrichment factors ranged from 1900 to 3000 times. Method detection limits with the analysis instruments used in this study were for ketoprofen, 0.23 ng g(-1) fish tissue; naproxen, 0.32 ng g(-1) fish tissue; diclofenac, 0.12 ng g(-1) fish tissue; ibuprofen, 0.34 ng g-1 fish tissue; fluoxetine, 13 ng g-1. fish tissue and sertraline, 23 ng g(-1) fish tissue. All analytes were successfully detected in tissue from fish exposed live via spiked water. The resulting extraction parameters shown in this study suggest the developed technique to be a useful work up method for extensive environmental data collection as well as for toxicokinetic studies.
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40.
  • Bozorg, Behruz, et al. (författare)
  • A continuous growth model for plant tissue
  • 2016
  • Ingår i: Physical Biology. - : IOP Publishing. - 1478-3975. ; 13:6, s. 065002-065002
  • Tidskriftsartikel (refereegranskat)abstract
    • Morphogenesis in plants and animals involves large irreversible deformations. In plants, the response of the cell wall material to internal and external forces is determined by its mechanical properties. An appropriate model for plant tissue growth must include key features such as anisotropic and heterogeneous elasticity and cell dependent evaluation of mechanical variables such as turgor pressure, stress and strain. In addition, a growth model needs to cope with cell divisions as a necessary part of the growth process. Here we develop such a growth model, which is capable of employing not only mechanical signals but also morphogen signals for regulating growth. The model is based on a continuous equation for updating the resting configuration of the tissue. Simultaneously, material properties can be updated at a different time scale. We test the stability of our model by measuring convergence of growth results for a tissue under the same mechanical and material conditions but with different spatial discretization. The model is able to maintain a strain field in the tissue during re-meshing, which is of particular importance for modeling cell division. We confirm the accuracy of our estimations in two and three-dimensional simulations, and show that residual stresses are less prominent if strain or stress is included as input signal to growth. The approach results in a model implementation that can be used to compare different growth hypotheses, while keeping residual stresses and other mechanical variables updated and available for feeding back to the growth and material properties.
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41.
  • Bozorg, Behruz, et al. (författare)
  • Stress and strain provide positional and directional cues in development.
  • 2014
  • Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-7358. ; 10:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The morphogenesis of organs necessarily involves mechanical interactions and changes in mechanical properties of a tissue. A long standing question is how such changes are directed on a cellular scale while being coordinated at a tissular scale. Growing evidence suggests that mechanical cues are participating in the control of growth and morphogenesis during development. We introduce a mechanical model that represents the deposition of cellulose fibers in primary plant walls. In the model both the degree of material anisotropy and the anisotropy direction are regulated by stress anisotropy. We show that the finite element shell model and the simpler triangular biquadratic springs approach provide equally adequate descriptions of cell mechanics in tissue pressure simulations of the epidermis. In a growing organ, where circumferentially organized fibers act as a main controller of longitudinal growth, we show that the fiber direction can be correlated with both the maximal stress direction and the direction orthogonal to the maximal strain direction. However, when dynamic updates of the fiber direction are introduced, the mechanical stress provides a robust directional cue for the circumferential organization of the fibers, whereas the orthogonal to maximal strain model leads to an unstable situation where the fibers reorient longitudinally. Our investigation of the more complex shape and growth patterns in the shoot apical meristem where new organs are initiated shows that a stress based feedback on fiber directions is capable of reproducing the main features of in vivo cellulose fiber directions, deformations and material properties in different regions of the shoot. In particular, we show that this purely mechanical model can create radially distinct regions such that cells expand slowly and isotropically in the central zone while cells at the periphery expand more quickly and in the radial direction, which is a well established growth pattern in the meristem.
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42.
  • Braybrook, Siobhan A, et al. (författare)
  • Shifting foundations: the mechanical cell wall and development.
  • 2016
  • Ingår i: Current Opinion in Plant Biology. - : Elsevier BV. - 1369-5266. ; 29, s. 115-120
  • Forskningsöversikt (refereegranskat)abstract
    • The cell wall has long been acknowledged as an important physical mediator of growth in plants. Recent experimental and modelling work has brought the importance of cell wall mechanics into the forefront again. These data have challenged existing dogmas that relate cell wall structure to cell/organ growth, that uncouple elasticity from extensibility, and those which treat the cell wall as a passive and non-stressed material. Within this review we describe experiments and models which have changed the ways in which we view the mechanical cell wall, leading to new hypotheses and research avenues. It has become increasingly apparent that while we often wish to simplify our systems, we now require more complex multi-scale experiments and models in order to gain further insight into growth mechanics. We are currently experiencing an exciting and challenging shift in the foundations of our understanding of cell wall mechanics in growth and development.
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43.
  • Briat, Corentin, et al. (författare)
  • An axiomatic fluid-flow model for congestion control analysis
  • 2011
  • Ingår i: 2011 50th IEEE Conference on Decision and Control andEuropean Control Conference (CDC-ECC). ; , s. 3122-3129
  • Konferensbidrag (refereegranskat)abstract
    • An axiomatic model for congestion control isderived. The proposed four axioms serve as a basis for theconstruction of models for the network elements. It is shownthat, under some assumptions, some models of the literature canbe recovered. A single-buffer/multiple-users topology is finallyderived and studied for illustration.
  •  
44.
  • Briat, Corentin, et al. (författare)
  • Nonlinear state-dependent delay modeling and stability analysis of internet congestion control
  • 2010
  • Ingår i: 49TH IEEE CONFERENCE ON DECISION AND CONTROL (CDC). - 9781424477463 ; , s. 1484-1491
  • Konferensbidrag (refereegranskat)abstract
    • It is shown that the queuing delay involved in the congestion control algorithm is state-dependent and does not depend on the current time. Then, using an accurate formulation for buffers, networks with arbitrary topologies can be built. At equilibrium, our model reduces to the widely used setup by Paganini et al. Using this model, the delay-derivative is analyzed and it is proved that the delay time-derivative does not exceed one for the considered topologies. It is then shown that the considered congestion control algorithm globally stabilizes a delay-free single buffer network. Finally, using a specific linearization result for systems with state-dependent delays from Cooke and Huang, we show the local stability of the single bottleneck network.
  •  
45.
  • Busquets, Rosa, et al. (författare)
  • Biomonitoring of Dietary Heterocyclic Amines and Metabolites in Urine by Liquid Phase Microextraction: 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a Possible Biomarker of Exposure to Dietary PhIP
  • 2013
  • Ingår i: Chemical Research in Toxicology. - : American Chemical Society (ACS). - 1520-5010 .- 0893-228X. ; 26:2, s. 233-240
  • Tidskriftsartikel (refereegranskat)abstract
    • Heterocyclic amines (HCAs) are mutagenic/carcinogenic compounds formed at ng/g levels during frying meat or fish. The effect of the normal intake of dietary HCAs in humans and their involvement in the etiology of cancer are currently unknown. In this work, a new extraction method, liquid phase microextraction (LPME) with hollow fibers, and LC-MS/MS have been used for the first time to determine HCAs and metabolites in nonspiked human urine following a single meal of chicken cooked at 180 degrees C for 6 min. The total intake of HCAs was estimated to be 6 mu g, of which 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) accounted for about 1 mu g. The concentrations of PhIP in nonhydrolyzed urine samples ranged from 11.7 to 59.4 pg/g. The total amount of PhIP in urine ranged between 9.3 and 21.1 ng, which corresponds to 0.91-2.1% of the ingested PhIP. In addition, the urine levels of 4'-OH-PhIP (2-amino-1-methyl-6-(4'-hydroxy)phenylimidazo[4,5-b]pyridine) and 5-OH-PhIP (2-amino-1-methyl-6-(5-hydroxy)phenylimidazo[4,5-b]pyridine) also showed a narrow variation between the samples. The analysis of urine samples after acid hydrolysis did not give additional information but showed a notable increase in norharman in some cases. The obtained results suggest PhIP in urine as a possible biomarker of exposure to HCAs and the LPME and LC-MS/MS method as an appropriate strategy to biomonitor HCAs in urine.
  •  
46.
  • Busquets, Rosa, et al. (författare)
  • Hollow fibre-supported liquid membrane extraction and LC-MS/MS detection for the analysis of heterocyclic amines in urine samples
  • 2009
  • Ingår i: Molecular Nutrition and Food Research. - : Wiley. - 1613-4133 .- 1613-4125. ; 53:12, s. 1496-1504
  • Tidskriftsartikel (refereegranskat)abstract
    • Heterocyclic amines (HCAs) are potent mutagens/carcinogens to which humans are frequently exposed through the consumption of cooked meat and fish food. The effect of normal intake of HCAs and their role in the aetiology of human cancer is unknown. To some extent, limitations of the existing analytical methods in monitoring the low levels of HCAs in biological samples have hindered obtaining conclusive results. In this study, a method for the analysis of HCAs in human urine has been studied to detect HCAs and metabolites at levels resulting from consumption of food cooked at ordinary conditions. The analytical method consisted of extraction and clean-Lip by the novel technique liquid-phase microextraction combined with LC-MS/MS. The effect of pH during the extraction and hydrolysis step was examined. High sensitivity was achieved when the extraction was performed in raw urine adjusted to pH 5.5, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine being detected from 2 pg/g urine, levels comparable with a normal exposure. Good reproducibility and repeat-ability was obtained for 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline, below 9% using isotopic dilution. The performance of the method on 9H-pyrido[3,4-b]indole, 2-amino-1-methyl-6-(4'-hydroxyphenyl)imidazo[4,5-b]pyridine and 2-amino-1-methyl-6-(5-hydroxy)phenylimidazo[4,5-b]pyridine was also studied.
  •  
47.
  • Cabrita, Rita, et al. (författare)
  • Tertiary lymphoid structures improve immunotherapy and survival in melanoma
  • 2020
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 577:7791, s. 561-565
  • Tidskriftsartikel (refereegranskat)abstract
    • Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable tumour control and result in the long-term survival of patients with advanced cancers1. Current predictive biomarkers for therapy response include high levels of intratumour immunological activity, a high tumour mutational burden and specific characteristics of the gut microbiota2,3. Although the role of T cells in antitumour responses has thoroughly been studied, other immune cells remain insufficiently explored. Here we use clinical samples of metastatic melanomas to investigate the role of B cells in antitumour responses, and find that the co-occurrence of tumour-associated CD8+ T cells and CD20+ B cells is associated with improved survival, independently of other clinical variables. Immunofluorescence staining of CXCR5 and CXCL13 in combination with CD20 reveals the formation of tertiary lymphoid structures in these CD8+CD20+ tumours. We derived a gene signature associated with tertiary lymphoid structures, which predicted clinical outcomes in cohorts of patients treated with immune checkpoint blockade. Furthermore, B-cell-rich tumours were accompanied by increased levels of TCF7+ naive and/or memory T cells. This was corroborated by digital spatial-profiling data, in which T cells in tumours without tertiary lymphoid structures had a dysfunctional molecular phenotype. Our results indicate that tertiary lymphoid structures have a key role in the immune microenvironment in melanoma, by conferring distinct T cell phenotypes. Therapeutic strategies to induce the formation of tertiary lymphoid structures should be explored to improve responses to cancer immunotherapy.
  •  
48.
  • Cabrita, Rita, et al. (författare)
  • Tertiary lymphoid structures improve immunotherapy and survival in melanoma.
  • 2020
  • Ingår i: Nature. - : Nature Publishing Group. - 1476-4687 .- 0028-0836. ; 577:7791, s. 561-565
  • Tidskriftsartikel (refereegranskat)abstract
    • Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable tumour control and result in the long-term survival of patients with advanced cancers1. Current predictive biomarkers for therapy response include high levels of intratumour immunological activity, a high tumour mutational burden and specific characteristics of the gut microbiota2,3. Although the role of T cells in antitumour responses has thoroughly been studied, other immune cells remain insufficiently explored. Here we use clinical samples of metastatic melanomas to investigate the role of B cells in antitumour responses, and find that the co-occurrence of tumour-associated CD8+ T cells and CD20+ B cells is associated with improved survival, independently of other clinical variables. Immunofluorescence staining of CXCR5 and CXCL13 in combination with CD20 reveals the formation of tertiary lymphoid structures in these CD8+CD20+ tumours. We derived a gene signature associated with tertiary lymphoid structures, which predicted clinical outcomes in cohorts of patients treated with immune checkpoint blockade. Furthermore, B-cell-rich tumours were accompanied by increased levels of TCF7+ naive and/or memory T cells. This was corroborated by digital spatial-profiling data, in which T cells in tumours without tertiary lymphoid structures had a dysfunctional molecular phenotype. Our results indicate that tertiary lymphoid structures have a key role in the immune microenvironment in melanoma, by conferring distinct T cell phenotypes. Therapeutic strategies to induce the formation of tertiary lymphoid structures should be explored to improve responses to cancer immunotherapy.
  •  
49.
  • Cabrita, Rita, et al. (författare)
  • The Role of PTEN Loss in Immune Escape, Melanoma Prognosis and Therapy Response
  • 2020
  • Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 12:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Checkpoint blockade therapies have changed the clinical management of metastatic melanoma patients considerably, showing survival benefits. Despite the clinical success, not all patients respond to treatment or they develop resistance. Although there are several treatment predictive biomarkers, understanding therapy resistance and the mechanisms of tumor immune evasion is crucial to increase the frequency of patients benefiting from treatment. The PTEN gene is thought to promote immune evasion and is frequently mutated in cancer and melanoma. Another feature of melanoma tumors that may affect the capacity of escaping T-cell recognition is melanoma cell dedifferentiation characterized by decreased expression of the microphtalmia-associated transcription factor (MITF) gene. In this study, we have explored the role of PTEN in prognosis, therapy response, and immune escape in the context of MITF expression using immunostaining and genomic data from a large cohort of metastatic melanoma. We confirmed in our cohort that PTEN alterations promote immune evasion highlighted by decreased frequency of T-cell infiltration in such tumors, resulting in a worse patient survival. More importantly, our results suggest that dedifferentiated PTEN negative melanoma tumors have poor patient outcome, no T-cell infiltration, and transcriptional properties rendering them resistant to targeted- and immuno-therapy.
  •  
50.
  • Caggiano, Monica Pia, et al. (författare)
  • Cell type boundaries organize plant development
  • 2017
  • Ingår i: eLife. - 2050-084X.
  • Tidskriftsartikel (refereegranskat)abstract
    • In plants the dorsoventral boundary of leaves defines an axis of symmetry through thecentre of the organ separating the top (dorsal) and bottom (ventral) tissues. Although thepositioning of this boundary is critical for leaf morphogenesis, how the boundary is established andhow it influences development remains unclear. Using live-imaging and perturbation experimentswe show that leaf orientation, morphology and position are pre-patterned by HD-ZIPIII and KANgene expression in the shoot, leading to a model in which dorsoventral genes coordinate toregulate plant development by localizing auxin response between their expression domains.However we also find that auxin levels feedback on dorsoventral patterning by spatially organizingHD-ZIPIII and KAN expression in the shoot periphery. By demonstrating that the regulation ofthese genes by auxin also governs their response to wounds, our results also provide aparsimonious explanation for the influence of wounds on leaf dorsoventrality.
  •  
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