| 1. |
- Aeschlimann, S., et al.
(author)
-
Ultrafast momentum imaging of pseudospin-flip excitations in graphene
- 2017
-
In: Physical Review B. - 2469-9969 .- 2469-9950. ; 96:2
-
Journal article (peer-reviewed)abstract
- The pseudospin of Dirac electrons in graphene manifests itself in a peculiar momentum anisotropy for photoexcited electron-hole pairs. These interband excitations are in fact forbidden along the direction of the light polarization and are maximum perpendicular to it. Here, we use time-and angle-resolved photoemission spectroscopy to investigate the resulting unconventional hot carrier dynamics, sampling carrier distributions as a function of energy, and in-plane momentum. We first show that the rapidly-established quasithermal electron distribution initially exhibits an azimuth-dependent temperature, consistent with relaxation through collinear electron-electron scattering. Azimuthal thermalization is found to occur only at longer time delays, at a rate that depends on the substrate and the static doping level. Further, we observe pronounced differences in the electron and hole dynamics in n-doped samples. By simulating the Coulomb-and phonon-mediated carrier dynamics we are able to disentangle the influence of excitation fluence, screening, and doping, and develop a microscopic picture of the carrier dynamics in photoexcited graphene. Our results clarify new aspects of hot carrier dynamics that are unique to Dirac materials, with relevance for photocontrol experiments and optoelectronic device applications.
|
|
| 2. |
- Ahlberg, Erik, et al.
(author)
-
"Vi klimatforskare stödjer Greta och skolungdomarna"
- 2019
-
In: Dagens nyheter (DN debatt). - 1101-2447.
-
Journal article (pop. science, debate, etc.)abstract
- DN DEBATT 15/3. Sedan industrialiseringens början har vi använt omkring fyra femtedelar av den mängd fossilt kol som får förbrännas för att vi ska klara Parisavtalet. Vi har bara en femtedel kvar och det är bråttom att kraftigt reducera utsläppen. Det har Greta Thunberg och de strejkande ungdomarna förstått. Därför stödjer vi deras krav, skriver 270 klimatforskare.
|
|
| 3. |
- Blum, Jurgen, et al.
(author)
-
Evidence for the formation of comet 67p/churyumov-gerasimenko through gravitational collapse of a bound clump of pebbles
- 2017
-
In: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 469, s. 755-773
-
Journal article (peer-reviewed)abstract
- The processes that led to the formation of the planetary bodies in the Solar system are still not fully understood. Using the results obtained with the comprehensive suite of instruments onboard the European Space Agency's Rosetta mission, we present evidence that comet 67P/Churyumov-Gerasimenko likely formed through the gentle gravitational collapse of a bound clump of mm-sized dust aggregates ('pebbles'), intermixed with microscopic ice particles. This formation scenario leads to a cometary make-up that is simultaneously compatible with the global porosity, homogeneity, tensile strength, thermal inertia, vertical temperature profiles, sizes and porosities of emitted dust and the steep increase in water-vapour production rate with decreasing heliocentric distance, measured by the instruments onboard the Rosetta spacecraft and the Philae lander. Our findings suggest that the pebbles observed to be abundant in protoplanetary discs around young stars provide the building material for comets and other minor bodies.
|
|
| 4. |
- Costa, Ivan G, et al.
(author)
-
Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data.
- 2007
-
In: BMC bioinformatics. - 1471-2105. ; 8 Suppl 10
-
Journal article (peer-reviewed)abstract
- Gene expression measurements during the development of the fly Drosophila melanogaster are routinely used to find functional modules of temporally co-expressed genes. Complimentary large data sets of in situ RNA hybridization images for different stages of the fly embryo elucidate the spatial expression patterns.Using a semi-supervised approach, constrained clustering with mixture models, we can find clusters of genes exhibiting spatio-temporal similarities in expression, or syn-expression. The temporal gene expression measurements are taken as primary data for which pairwise constraints are computed in an automated fashion from raw in situ images without the need for manual annotation. We investigate the influence of these pairwise constraints in the clustering and discuss the biological relevance of our results.Spatial information contributes to a detailed, biological meaningful analysis of temporal gene expression data. Semi-supervised learning provides a flexible, robust and efficient framework for integrating data sources of differing quality and abundance.
|
|
| 5. |
- Diehl, Roland, et al.
(author)
-
Early Ni-56 decay gamma rays from SN2014J suggest an unusual explosion
- 2014
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 345:6201, s. 1162-1165
-
Journal article (peer-reviewed)abstract
- Type Ia supernovae result from binary systems that include a carbon-oxygen white dwarf, and these thermonuclear explosions typically produce 0.5 solar mass of radioactive Ni-56. The Ni-56 is commonly believed to be buried deeply in the expanding supernova cloud. In SN2014J, we detected the lines at 158 and 812 kiloelectron volts from Ni-56 decay (time similar to 8.8 days) earlier than the expected several-week time scale, only similar to 20 days after the explosion and with flux levels corresponding to roughly 10% of the total expected amount of Ni-56. Some mechanism must break the spherical symmetry of the supernova and at the same time create a major amount of Ni-56 at the outskirts. A plausible explanation is that a belt of helium from the companion star is accreted by the white dwarf, where this material explodes and then triggers the supernova event.
|
|
| 6. |
- Gurwitz, Kim T., et al.
(author)
-
A framework to assess the quality and impact of bioinformatics training across ELIXIR
- 2020
-
In: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 16:7
-
Journal article (peer-reviewed)abstract
- ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course.
|
|
| 7. |
- Hafemeister, Christoph, et al.
(author)
-
Selecting oligonucleotide probes for whole-genome tiling arrays with a cross-hybridization potential.
- 2011
-
In: IEEE/ACM transactions on computational biology and bioinformatics. - 1557-9964. ; 8:6, s. 1642-52
-
Journal article (peer-reviewed)abstract
- For designing oligonucleotide tiling arrays popular, current methods still rely on simple criteria like Hamming distance or longest common factors, neglecting base stacking effects which strongly contribute to binding energies. Consequently, probes are often prone to cross-hybridization which reduces the signal-to-noise ratio and complicates downstream analysis. We propose the first computationally efficient method using hybridization energy to identify specific oligonucleotide probes. Our Cross-Hybridization Potential (CHP) is computed with a Nearest Neighbor Alignment, which efficiently estimates a lower bound for the Gibbs free energy of the duplex formed by two DNA sequences of bounded length. It is derived from our simplified reformulation of t-gap insertion-deletion-like metrics. The computations are accelerated by a filter using weighted ungapped q-grams to arrive at seeds. The computation of the CHP is implemented in our software OSProbes, available under the GPL, which computes sets of viable probe candidates. The user can choose a trade-off between running time and quality of probes selected. We obtain very favorable results in comparison with prior approaches with respect to specificity and sensitivity for cross-hybridization and genome coverage with high-specificity probes. The combination of OSProbes and our Tileomatic method, which computes optimal tiling paths from candidate sets, yields globally optimal tiling arrays, balancing probe distance, hybridization conditions, and uniqueness of hybridization.
|
|
| 8. |
- Heggarty, Paul, et al.
(author)
-
Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages
- 2023
-
In: Science. - 0036-8075 .- 1095-9203. ; 381:6656
-
Journal article (peer-reviewed)abstract
- Languages of the Indo-European family are spoken by almost half of the world’s population, but their origins and patterns of spread are disputed. Heggarty et al. present a database of 109 modern and 52 time-calibrated historical Indo-European languages, which they analyzed with models of Bayesian phylogenetic inference. Their results suggest an emergence of Indo-European languages around 8000 years before present. This is a deeper root date than previously thought, and it fits with an initial origin south of the Caucasus followed by a branch northward into the Steppe region. These findings lead to a “hybrid hypothesis” that reconciles current linguistic and ancient DNA evidence from both the eastern Fertile Crescent (as a primary source) and the steppe (as a secondary homeland).
|
|
| 9. |
|
|
| 10. |
- Nakatani, Yoshio, et al.
(author)
-
Role of Alanine Racemase Mutations in Mycobacterium tuberculosis D-Cycloserine Resistance
- 2017
-
In: Antimicrobial Agents and Chemotherapy. - : AMER SOC MICROBIOLOGY. - 0066-4804 .- 1098-6596. ; 61:12
-
Journal article (peer-reviewed)abstract
- A screening of more than 1,500 drug-resistant strains of Mycobacterium tuberculosis revealed evolutionary patterns characteristic of positive selection for three alanine racemase (Alr) mutations. We investigated these mutations using molecular modeling, in vitro MIC testing, as well as direct measurements of enzymatic activity, which demonstrated that these mutations likely confer resistance to D-cycloserine.
|
|
| 11. |
- Rungsarityotin, Wasinee, et al.
(author)
-
Identifying protein complexes directly from high-throughput TAP data with Markov random fields.
- 2007
-
In: BMC bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8
-
Journal article (peer-reviewed)abstract
- Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rely on a two-step process. First, they construct an interaction graph from the data, predominantly using heuristics, and subsequently cluster its vertices to identify protein complexes.We propose a model-based identification of protein complexes directly from the experimental observations. Our model of protein complexes based on Markov random fields explicitly incorporates false negative and false positive errors and exhibits a high robustness to noise. A model-based quality score for the resulting clusters allows us to identify reliable predictions in the complete data set. Comparisons with prior work on reference data sets shows favorable results, particularly for larger unfiltered data sets. Additional information on predictions, including the source code under the GNU Public License can be found at http://algorithmics.molgen.mpg.de/Static/Supplements/ProteinComplexes.We can identify complexes in the data obtained from high-throughput experiments without prior elimination of proteins or weak interactions. The few parameters of our model, which does not rely on heuristics, can be estimated using maximum likelihood without a reference data set. This is particularly important for protein complex studies in organisms that do not have an established reference frame of known protein complexes.
|
|
| 12. |
- Schliep, Alexander, 1967, et al.
(author)
-
Efficient algorithms for the computational design of optimal tiling arrays.
- 2008
-
In: IEEE/ACM transactions on computational biology and bioinformatics. - 1557-9964. ; 5:4, s. 557-67
-
Journal article (peer-reviewed)abstract
- The representation of a genome by oligonucleotide probes is a prerequisite for the analysis of many of its basic properties, such as transcription factor binding sites, chromosomal breakpoints, gene expression of known genes and detection of novel genes, in particular those coding for small RNAs. An ideal representation would consist of a high density set of oligonucleotides with similar melting temperatures that do not cross-hybridize with other regions of the genome and are equidistantly spaced. The implementation of such design is typically called a tiling array or genome array. We formulate the minimal cost tiling path problem for the selection of oligonucleotides from a set of candidates. Computing the selection of probes requires multi-criterion optimization, which we cast into a shortest path problem. Standard algorithms running in linear time allow us to compute globally optimal tiling paths from millions of candidate oligonucleotides on a standard desktop computer for most problem variants. The solutions to this multi-criterion optimization are spatially adaptive to the problem instance. Our formulation incorporates experimental constraints with respect to specific regions of interest and trade offs between hybridization parameters, probe quality and tiling density easily. A web application is available at http://tileomatic.org.
|
|
