| 1. |
- Adloff, C, et al.
(författare)
-
A measurement of the t dependence of the helicity structure of diffractive rho meson electroproduction at HERA
- 2002
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 539:1-2, s. 25-39
-
Tidskriftsartikel (refereegranskat)abstract
- The helicity structure of the diffractive electroproduction of rho mesons, e + p --> e + rho + Y, is studied in a previously unexplored region of large four-momentum transfer squared at the proton vertex, t: 0 < t' < 3 GeV2, where t' = - min. The data used are collected with the HI detector at HERA in the kinematic domain 2.5 < Q(2) < 60 GeV2, 40 < W < 120 GeV No t dependence of the r(00)(04) spin density matrix element is found. A significant t dependent helicity non-conservation from the virtual photon to the rho meson is observed for the spin density matrix element combinations r(00)(5) + 2r(11)(5) and r(00)(1) + 2r(11)(1). These t dependences are consistently described by a perturbative QCD model based on the exchange of two gluons.
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| 2. |
- Adloff, C, et al.
(författare)
-
Diffractive photoproduction of psi(2S) mesons at HERA
- 2002
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 541:3-4, s. 251-264
-
Tidskriftsartikel (refereegranskat)abstract
- Results on diffractive photoproduction of psi(2S) mesons are presented using data collected between 1996 and 2000 with the H1 detector at the HERA ep collider. The data correspond to an integrated luminosity of 77 pb(-1). The energy dependence of the diffractive psi(2S) cross section is found to be similar to or possibly somewhat steeper than that for J/psi mesons. The dependences of the elastic and proton dissociative psi(2S) photoproduction cross sections on the squared momentum transfer t at the proton vertex are measured. The t-dependence of the elastic channel, parametrised as e(bt), yields b(el)(psi(2S)) = (4.31 +/- 0.57 +/- 0.46) GeV-2, compatible with that of the J/psi. For the proton dissociative channel the result b(pd)(psi(2S)) = (0.59 +/- 0.13 +/- 0.12) GeV-2 is 2.3 standard deviations smaller than that measured for the J/psi. With proper account of the individual wavefunctions theoretical predictions based on perturbative QCD are found to describe the measurements well. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 3. |
- Adloff, C, et al.
(författare)
-
Inelastic leptoproduction of J/psi mesons at HERA
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 25:1, s. 41-53
-
Tidskriftsartikel (refereegranskat)abstract
- The leptoproduction of J/psi mesons is studied in inelastic reactions for four momentorri transfers 2 < Q(2) < 100GeV(2). The data were taken with the H1 detector at the electron proton collider HERA and correspond to an integrated luminosity of 77 pb(-1). Single differential and double differential cross sections are measured with increased precision compared with previous analyses. New leading order calculations within the non-relativistic QCD factorisation approach including colour octet and colour singlet contributions are compared with the data and are found to give a reasonable description of most distributions. An exception is the shape of the distribution in the J/psi fractional energy. z, which deviates significantly from that of the data. Comparisons with photoproduction are made and the polarisation of the produced J/psi meson is analysed.
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| 4. |
- Adloff, C, et al.
(författare)
-
Inelastic photoproduction of J/psi mesons at HERA
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 25:1, s. 25-39
-
Tidskriftsartikel (refereegranskat)abstract
- An analysis of inelastic photoproduction of J/psi mesons is presented using data collected at the ep collider HERA corresponding to an integrated luminosity of above 80 pb(-1), Differential and double I < P-t/psi(2) < differential cross sections are measured in a wide kinematic region: 60 < W-gammap < 260 GeV, 1 p(t,psi)(2) < 60 GeV2 and 0.05 < z < 0.9. where z is the fraction of the energy of the exchanged photon transferred to the J/psi meson in the rest frame of the target proton. Cross sections at z less than or similar to 0.3 are presented for the first time. Theoretical calculations within the Colour Singlet Model at NLO for direct photon processes are shown to give a good description of the data in the medium z region (0.3 < z < 0.9) up to the highest p(t,psi)(2) values. A calculation using a k(t) factorisation approach in LO in the Colour Singlet Model is also able to describe these data. The data in the full z range are also compared to LO calculations within a non-relativistic QCD framework including colour octet and colour singlet contributions for direct and resolved photons. It seems possible to reconcile data and theory with modest contributions from colour octet processes. The polarisation of the J/psi meson is measured as a function of z and p(t,psi) and is reasonably described by the theoretical predictions.
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| 5. |
- Adloff, C, et al.
(författare)
-
Measurement of dijet cross sections in photoproduction at HERA
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 25:1, s. 13-23
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Tidskriftsartikel (refereegranskat)abstract
- Dijet cross sections as functions of several jet observables are measured in photoproduction using the HI detector at HERA. The data sample comprises e(+)p data with an integrated luminosity of 319 pb(-1). Jets are selected using the inclusive k(perpendicular to) algorithm with a minimum transverse energy of 25 GeV for the leading jet. The phase space covers longitudinal proton momentum fraction x(p) and photon longitudinal momentum fraction x(gamma) in the ranges 0.05 < x(p) < 0.6 and 0.1 < x(gamma) < 1. The predict ions of next-to-leading order perturbative QCD, including recent photon and proton parton densities, are found to be compatible with the data in a wide kinematical range.
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| 6. |
- Adloff, C, et al.
(författare)
-
Search for odderon-induced contributions to exclusive pi(0) photoproduction at HERA
- 2002
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 544:1-2, s. 35-43
-
Tidskriftsartikel (refereegranskat)abstract
- A search for contributions to the reaction ep --> epi(0)N* from photon-odderon fusion in the photoproduction regime at HERA is reported, at an average photon-proton centre-of-mass energy = 215 GeV. The measurement proceeds via detection of the pi(0) decay photons, a leading neutron from the N* decay, and the scattered electron. No pi(0) signal is observed and an upper limit on the cross section for the photon-odderon fusion process of sigma(gammap --> pi(0)N*) < 49 nb at the 95% confidence level is derived, integrated over the experimentally accessible range of the squared four-momentum transfer at the nucleon vertex 0.02 < < 0.3 GeV2. This excludes a recent prediction from a calculation based on a non-perturbative QCD model of a photon-odderon fusion cross section above 200 nb. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 7. |
- Adloff, C, et al.
(författare)
-
Search for QCD instanton-induced processes in deep-inelastic scattering at HERA
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 25:4, s. 495-509
-
Tidskriftsartikel (refereegranskat)abstract
- Signals of QCD instanton-induced processes are searched for in deep-inelastic scattering (DIS) at the electron-proton collider HERA in a kinematic region defined by the Bjorken-scaling variables x > 10(-3), 0.1 < y < 0.6 and photon virtualities 10 less than or similar to Q(2) < 100 GeV2. Several observables characterising hadronic final state properties of QCD instanton-induced events are exploited to identify a potentially instanton-enriched domain. While an excess of events with instanton-like topology is observed it cannot be claimed significant given the uncertainty of the standard DIS background simulation. Upper limits on the cross-section for instanton-induced processes of between 60 pb and 1000 pb are set dependent on the kinematic domain considered. The data do not exclude the cross-section predicted by instanton perturbation theory for small instanton sizes. At large instanton sizes a naive extrapolation of instanton perturbation theory yields a cross-section in the range of sensitivity of this study. Such a cross-section is not observed, in agreement with non-perturbative lattice simulations of the QCD vacuum.
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| 8. |
- Adloff, C, et al.
(författare)
-
Energy flow and rapidity gaps between jets in photoproduction at HERA
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 24:4, s. 517-527
-
Tidskriftsartikel (refereegranskat)abstract
- Dijet events in photon-proton collisions in which there is a large pseudorapidity separation, Deltaeta > 2.5 between the two highest E-T jets are studied with the H1 detector at HERA. The inclusive dijet cross sections are measured as functions of the longitudinal momentum fractions of the proton and photon which participate in the production of the jets, x(p)(jets) and x(gamma)(jets) respectively, Deltaeta, the pseudorapidity P separation between the two highest E-T jets, and E-T(gap), the total summed transverse energy between the jets. Rapidity gap events are defined as events in which E-T(gap) is less than E-T(cut), for E-T(cut) varied between jets 0.5 and 2.0 GeV. The fraction of dijet events with a rapidity gap is measured differentially in Deltaeta, x(p)(jets) and x(gamma)(jets). An excess of events with rapidity gaps at low values of E-T(cut) is observed above the expectation from standard photoproduction processes. This excess can be explained by the exchange of a strongly interacting colour singlet object between the jets.
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| 9. |
- Adloff, C, et al.
(författare)
-
Measurement of inclusive jet cross-sections in deep-inelastic ep scattering at HERA
- 2002
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 542:3-4, s. 193-206
-
Tidskriftsartikel (refereegranskat)abstract
- A measurement of inclusive jet cross-sections in deep-inelastic ep scattering at HERA is presented based on data with an integrated luminosity of 21.1 pb(-1). The measurement is performed for photon virtualities Q(2) between 5 and 100 GeV2, differentially in Q(2), in the jet transverse energy E-T, in E-T(2)/Q(2) and in the pseudorapidity eta(lab). With the renormalization scale mu(R) = E-T, perturbative QCD calculations in next-to-leading order (NLO) give a good description of the data in most of the phase space. Significant discrepancies are observed only for jets in the proton beam direction with ET below 20 GeV and Q2 below 20 GeV2. This corresponds to the region in which NLO corrections are largest and further improvement of the calculations is thus of particular interest.
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| 10. |
- Adloff, C, et al.
(författare)
-
Search for excited neutrinos at HERA
- 2002
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 525:1-2, s. 9-16
-
Tidskriftsartikel (refereegranskat)abstract
- We present a search for excited neutrinos using e(-) p data taken by the H1 experiment at HERA at a center-of-mass energy of 318 GeV with an integrated luminosity of 15 pb(-1). No evidence for excited neutrino production is found. Mass dependent exclusion limits are determined for the ratio of the coupling to the compositeness scale, f/Lambda, independently of the relative couplings to the SU(2) and U(1) gauge bosons. These limits extend the excluded region to higher masses than has been possible in previous searches at other colliders.
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| 11. |
- Adloff, C, et al.
(författare)
-
Measurement of D*(+/-) meson production and F-2(c) in deep-inelastic scattering at HERA
- 2002
-
Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 528:3-4, s. 199-214
-
Tidskriftsartikel (refereegranskat)abstract
- The inclusive production of D*+/-(2010) mesons in deep-inelastic scattering is studied with the HI detector at HERA. In the kinematic region 1 < Q(2) < 100 GeV2 and 0.05 < y < 0.7 an e(+) p cross section for inclusive D*+/- meson production of 8.50 +/- 0.42(stat.)(-100)(+1.21)(syst.) nb is measured in the visible range p(tD*) > 1.5 GeV and eta(D*) < 1.5. Single and double differential inclusive D*+/- meson cross sections are compared to perturbative QCD calculations in two different evolution schemes, The charm contribution to the proton structure, F-c(2)(x, Q(2)), is determined by extrapolating the visible charm cross section to the full phase space. This contribution is found to rise from about 10% at Q(2) = 1.5 GeV2 to more than 25% at Q(2) = 60 GeV2 corresponding to x values ranging from 5 x 10(-5) to 3 x 10(-3). (C) 2002 Elsevier Science B.V. All rights reserved.
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| 12. |
- Adloff, C, et al.
(författare)
-
Measurement of dijet electroproduction at small jet separation
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 24:1, s. 33-41
-
Tidskriftsartikel (refereegranskat)abstract
- Deep-inelastic scattering data in the range 150 < Q(2) < 35000 GeV2 are used to investigate the minimum jet separation necessary to allow accurate description of the rate of dijet production using next-to-leading order perturbative QCD calculations. The required jet separation is found to be small, allowing about 1/3 of DIS data to be classified as dijet, as opposed to approximately 1/10 with more typical jet analyses. A number of precision measurements made using this dijet sample are well described by the calculations. The data are also described by the combination of leading order matrix elements and parton showers, as implemented in the QCD based Monte Carlo model RAPGAP.
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| 13. |
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| 14. |
- Ainsworth, Elizabeth A., et al.
(författare)
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Next generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world
- 2008
-
Ingår i: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 31:9, s. 1317-1324
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Tidskriftsartikel (refereegranskat)abstract
- A rising global population and demand for protein-rich diets are increasing pressure to maximize agricultural productivity. Rising atmospheric [CO2] is altering global temperature and precipitation patterns, which challenges agricultural productivity. While rising [CO2] provides a unique opportunity to increase the productivity of C-3 crops, average yield stimulation observed to date is well below potential gains. Thus, there is room for improving productivity. However, only a fraction of available germplasm of crops has been tested for CO2 responsiveness. Yield is a complex phenotypic trait determined by the interactions of a genotype with the environment. Selection of promising genotypes and characterization of response mechanisms will only be effective if crop improvement and systems biology approaches are closely linked to production environments, that is, on the farm within major growing regions. Free air CO2 enrichment (FACE) experiments can provide the platform upon which to conduct genetic screening and elucidate the inheritance and mechanisms that underlie genotypic differences in productivity under elevated [CO2]. We propose a new generation of large-scale, low-cost per unit area FACE experiments to identify the most CO2-responsive genotypes and provide starting lines for future breeding programmes. This is necessary if we are to realize the potential for yield gains in the future.
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| 15. |
- Calfapietra, Carlo, et al.
(författare)
-
Challenges in elevated CO2 experiments on forests
- 2010
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Ingår i: Trends in Plant Science. - : Elsevier BV. - 1360-1385. ; 15:1, s. 5-10
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Forskningsöversikt (refereegranskat)abstract
- Current forest Free Air CO2 Enrichment (FACE) experiments are reaching completion. Therefore, it is time to define the scientific goals and priorities of future experimental facilities. In this opinion article, we discuss the following three overarching issues (i) What are the most urgent scientific questions and how can they be addressed? (ii) What forest ecosystems should be investigated? (iii) Which other climate change factors should be coupled with elevated CO2 concentrations in future experiments to better predict the effects of climate change? Plantations and natural forests can have conflicting purposes for high productivity and environmental protection. However, in both cases the assessment of carbon balance and how this will be affected by elevated CO2 concentrations and the interacting climate change factors is the most pressing priority for future experiments.
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| 16. |
- Hakkarainen, M, et al.
(författare)
-
The clinical picture of ERCC6L2 disease: from bone marrow failure to acute leukemia
- 2023
-
Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 141:23, s. 2853-2866
-
Tidskriftsartikel (refereegranskat)abstract
- Biallelic germline ERCC6L2 variants strongly predispose to bone marrow failure (BMF) and myeloid malignancies characterized by somatic TP53-mutated clones and erythroid predominance. We present a series of 52 subjects (35 families) with ERCC6L2 biallelic germline variants collected retrospectively in 11 centers globally, including follow-up of 1165 person-years. At initial investigations, 32 individuals were diagnosed with BMF and 15 with a hematological malignancy (HM). Subjects presented with 19 different variants across ERCC6L2, and we identified a founder mutation c.1424delT in the Finnish patients. The median age of subjects at baseline was 18 years (range 2-65). Changes in complete blood count (CBC) were mild despite severe bone marrow hypoplasia and somatic TP53 mutations, with no significant difference between subjects with or without (HM). Signs of a progressive disease were increasing TP53 variant allele frequency, dysplasia in megakaryocytes and/or erythroid lineage, and erythroid predominance in bone marrow morphology. The median age at onset of HM was 37.0 years (95% CI: 31.5-42.5; range 12-65). Overall survival (OS) at 3 years was 95% (95% CI: 85-100) and 19% (95% CI: 0-39) for patients with BMF and HM, respectively. Patients with myelodysplastic syndrome or acute myeloid leukemia with mutated TP53 undergoing hematopoietic stem cell transplantation had a poor outcome: 3-year OS is 28% (95% CI: 0-61). Our results demonstrate the importance of early recognition and active surveillance of patients with biallelic germline ERCC6L2 variants.
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| 17. |
- Mikkelsen, T N, et al.
(författare)
-
Experimental design of multifactor climate change experiments with elevated CO2, warming and drought: the CLIMAITE project
- 2008
-
Ingår i: Functional Ecology. - : Wiley. - 1365-2435 .- 0269-8463. ; 22:1, s. 185-195
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Tidskriftsartikel (refereegranskat)abstract
- Recent findings indicate that the interactions among CO2, temperature and water can be substantial, and that the combined effects on the biological systems of several factors may not be predicted from experiments with one or a few factors. Therefore realistic multifactorial experiments involving a larger set of main factors are needed. We describe a new Danish climate change-related field scale experiment, CLIMAITE, in a heath/grassland ecosystem. CLIMAITE is a full factorial combination of elevated CO2, elevated temperature and prolonged summer drought. The manipulations are intended to mimic anticipated major environmental changes at the site by year 2075 as closely as possible. The impacts on ecosystem processes and functioning (at ecophysiological levels, through responses by individuals and communities to ecosystem-level responses) are investigated simultaneously. The increase of [CO2] closely corresponds with the scenarios for year 2075, while the warming treatment is at the lower end of the predictions and seems to be the most difficult treatment to increase without unwanted side effects on the other variables. The drought treatment follows predictions of increased frequency of drought periods in summer. The combination of the treatments does not create new unwanted side effects on the treatments relative to the treatments alone.
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| 18. |
- Alneberg, Johannes, et al.
(författare)
-
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.
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| 19. |
- Alneberg, Johannes, et al.
(författare)
-
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
-
Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
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| 20. |
- Alneberg, Johannes, et al.
(författare)
-
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes
- 2020
-
Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 3:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
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| 21. |
- Alneberg, Johannes, et al.
(författare)
-
Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic microorganism are key drivers of global biogeochemical cycles and form the basis of aquatic food webs. However, there is still much left to be learned about these organisms and their interaction within specific environments, such as the Baltic Sea. Crucial information for such an understanding can be found within the genome sequences of organisms within the microbial community.In this study, the previous set of Baltic Sea clusters, constructed by Hugert et al., is greatly expanded using a large set of metagenomic samples, spanning the environmental gradients of the Baltic Sea. In total, 124 samples were individually assembled and binned to obtain 2,032 Metagenome Assembled Genomes (MAGs), clustered into 353 prokaryotic and 14 eukaryotic species- level clusters. The prokaryotic genomes were widely distributed over the prokaryotic tree of life, representing 20 different phyla, while the eukaryotic genomes were mostly limited to the division of Chlorophyta. The large number of reconstructed genomes allowed us to identify key factors determining the quality of the genome reconstructions.The Baltic Sea is heavily influenced of human activities of which we might not see the full implications. The genomes reported within this study will greatly aid further studies in our strive for an understanding of the Baltic Sea microbial ecosystem.
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| 22. |
- Grubisic, Lorena M., et al.
(författare)
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Lake bacterioplankton dynamics over diurnal timescales
- 2017
-
Ingår i: Freshwater Biology. - : Blackwell Publishing. - 0046-5070 .- 1365-2427. ; 62:1, s. 191-204
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Tidskriftsartikel (refereegranskat)abstract
- 1. Planktonic bacterial community dynamics over short timescales can be of great importance for food webs and ecosystem functioning but are rarely described when microbial community and composition are assessed. To study the significance of such dynamics we sampled the surface water at the deepest point of a mesotrophic lake (Lake Erken, Sweden) every third hour over two days. 2. By combining 454 pyrosequencing of 16S rRNA genes with bromodeoxyuridine immunocapturing of DNA, replicating populations were identified and compared to the community retrieved from total DNA samples. This comparison revealed a significant difference between the actively replicating and total community. 3. The high-frequency diurnal sampling was compared to a year-long survey conducted in the same lake in order to compare the diurnal and seasonal variation in bacterioplankton community composition. At the diurnal-scale, the variation was significantly higher in the replicating than in the total community. However, variation in both active and total diurnal community was significantly lower than the variation in the seasonal total community. 4. Our analysis revealed pronounced short-term dynamics of individual bacterial populations uncoupled from the diurnal light cycle. For example, the proliferating fraction of the most abundant bacterial tribe (LD12) followed a cyclic pattern that covaried with viral abundance. This implies that environmental factors other than light may act as important drivers of microbial community composition, at least in mesotrophic Lake Erken.
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| 23. |
- Hakkarainen, M, et al.
(författare)
-
The clinical picture of ERCC6L2 disease: from bone marrow failure to acute leukemia
- 2023
-
Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 141:23, s. 2853-2866
-
Tidskriftsartikel (refereegranskat)abstract
- Biallelic germline ERCC6L2 variants strongly predispose to bone marrow failure (BMF) and myeloid malignancies characterized by somatic TP53-mutated clones and erythroid predominance. We present a series of 52 subjects (35 families) with ERCC6L2 biallelic germline variants collected retrospectively in 11 centers globally, including follow-up of 1165 person-years. At initial investigations, 32 individuals were diagnosed with BMF and 15 with a hematological malignancy (HM). Subjects presented with 19 different variants across ERCC6L2, and we identified a founder mutation c.1424delT in the Finnish patients. The median age of subjects at baseline was 18 years (range 2-65). Changes in complete blood count (CBC) were mild despite severe bone marrow hypoplasia and somatic TP53 mutations, with no significant difference between subjects with or without (HM). Signs of a progressive disease were increasing TP53 variant allele frequency, dysplasia in megakaryocytes and/or erythroid lineage, and erythroid predominance in bone marrow morphology. The median age at onset of HM was 37.0 years (95% CI: 31.5-42.5; range 12-65). Overall survival (OS) at 3 years was 95% (95% CI: 85-100) and 19% (95% CI: 0-39) for patients with BMF and HM, respectively. Patients with myelodysplastic syndrome or acute myeloid leukemia with mutated TP53 undergoing hematopoietic stem cell transplantation had a poor outcome: 3-year OS is 28% (95% CI: 0-61). Our results demonstrate the importance of early recognition and active surveillance of patients with biallelic germline ERCC6L2 variants.
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| 24. |
- Holmstrup, Martin, et al.
(författare)
-
Long-term and realistic global change manipulations had low impact on diversity of soil biota in temperate heathland
- 2017
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- In a dry heathland ecosystem we manipulated temperature (warming), precipitation (drought) and atmospheric concentration of CO2 in a full-factorial experiment in order to investigate changes in below-ground biodiversity as a result of future climate change. We investigated the responses in community diversity of nematodes, enchytraeids, collembolans and oribatid mites at two and eight years of manipulations. We used a structural equation modelling (SEM) approach analyzing the three manipulations, soil moisture and temperature, and seven soil biological and chemical ariables. The analysis revealed a persistent and positive effect of elevated CO2 on litter C:N ratio. After two years of treatment, the fungi to bacteria ratio was increased by warming, and the diversities within oribatid mites, collembolans and nematode groups were all affected by elevated CO2 mediated through increased litter C:N ratio. After eight years of treatment, however, the CO2-increased litter C:N ratio did not influence the diversity in any of the four fauna groups. The number of significant correlations between treatments, food source quality, and soil biota diversities was reduced from six to three after two and eight years, respectively. These results suggest a remarkable resilience within the soil biota against global climate change treatments in the long term.
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| 25. |
- Mascher, Martin, et al.
(författare)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Tidskriftsartikel (refereegranskat)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 26. |
- Mates, L, et al.
(författare)
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Comparative analysis of the mouse and human genes (Matn2 and MATN2) for matrilin-2, a filament-forming protein widely distributed in extracellular matrices
- 2002
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Ingår i: Matrix Biology. - 1569-1802. ; 21:2, s. 163-174
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Tidskriftsartikel (refereegranskat)abstract
- We previously identified matrilin-2 (MATN2), the largest member of the novel family of matrilins. These filament-forming adapter proteins expressed in a distinct, but partially overlapping, pattern in all tissues were implicated in the organization of the extracellular matrix. Matrilin-2 functions in a great variety of tissues. Here, we present the genomic organization of the highly conserved mouse and human MATN2 loci, which cover > 100 kb and 167.167 kb genomic regions, respectively, and are composed of 19 exons. RT-PCR analysis revealed that alternative transcripts with identical protein coding regions are transcribed from two promoters in both species. The upstream, housekeeping type promoter is functional in all tissues and cell types tested. The activity of the downstream, TATA-like promoter preceded with putative motifs for the homeobox transcription factor PRRX2 is restricted to embryonic fibroblasts and certain cell lines. The oligomerization module is split by an U12-type AT-AC intron found in conserved position in all four matrilin genes. We assigned Matn2 to mouse chromosome 15, linked to Trhr and Sntb1 in a region synthenic to human chromosome 8q22-24.
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| 27. |
- McGinn, Steven, et al.
(författare)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Forskningsöversikt (refereegranskat)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 28. |
- Pan, Jiaxin, et al.
(författare)
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Operando dynamics of trapped carriers in perovskite solar cells observed via infrared optical activation spectroscopy
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Conventional spectroscopies are not sufficiently selective to comprehensively understand the behaviour of trapped carriers in perovskite solar cells, particularly under their working conditions. Here we use infrared optical activation spectroscopy (i.e., pump-push-photocurrent), to observe the properties and real-time dynamics of trapped carriers within operando perovskite solar cells. We compare behaviour differences of trapped holes in pristine and surface-passivated FA(0.99)Cs(0.01)PbI(3) devices using a combination of quasi-steady-state and nanosecond time-resolved pump-push-photocurrent, as well as kinetic and drift-diffusion models. We find a two-step trap-filling process: the rapid filling (similar to 10 ns) of low-density traps in the bulk of perovskite, followed by the slower filling (similar to 100 ns) of high-density traps at the perovskite/hole transport material interface. Surface passivation by n-octylammonium iodide dramatically reduces the number of trap states (similar to 50 times), improving the device performance substantially. Moreover, the activation energy (similar to 280 meV) of the dominant hole traps remains similar with and without surface passivation.
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| 29. |
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