| 1. |
- Birney, Ewan, et al.
(författare)
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
-
Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
|
|
| 2. |
- Wiedorn, Max O., et al.
(författare)
-
Megahertz serial crystallography
- 2018
-
Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a beta-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
|
|
| 3. |
|
|
| 4. |
- Chen, Mo, et al.
(författare)
-
Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol
- 2014
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:10, s. 4465-4479
-
Tidskriftsartikel (refereegranskat)abstract
- Room temperature ionic liquids (ILs) of the imidazolium family have attracted much attention during the past decade for their capability to dissolve biomass. Besides experimental work, numerous compuational studies have been concerned with the physical properties of both neat ILs and their interactions with different solutes, in particular, carbohydrates. Many classical force fields designed specifically for ILs have been found to yield viscosities that are too high for the liquid state, which has been attributed to the fact that the effective charge densities are too high due to the lack of electronic polarizability. One solution to this problem has been uniform scaling of the partial charges by a scale factor in the range 0.6-0.9, depending on model. This procedure has been shown to improve the viscosity of the models, and also to positively affect other properties, such as diffusion constants and ionic conductivity. However, less attention has been paid to how this affects the overall thermodynamics of the system, and the problems it might create when the IL models are combined with other force fields (e.g., for solutes). In the present work, we employ three widely used IL force fields to simulate 1-n-buty1-3-methyl-imidazolium chloride in both the crystal and the liquid state, as well as its binary mixture with ethanol. Two approaches are used: one in which the ionic charge is retained at its full integer value and one in which the partial charges are uniformly reduced to 85%. We investigate and calculate crystal and liquid structures, molar heat capacities, heats of fusion, self-diffusion constants, ionic conductivity, and viscosity for the neat IL, and ethanol activity as a function of ethanol concentration for the binary mixture. We show that properties of the crystal are less affected by charge scaling compared to the liquid. In the liquid state, transport properties of the neat IL are generally improved by scaling, whereas values for the heat of fusion are unaffected, and results for the heat capacity are ambiguous. Neither full nor reduced charges could reproduce experimental ethanol activities for the whole range of compositions.
|
|
| 5. |
- de Rezende, Susanna F., et al.
(författare)
-
Nullstellensatz Size-Degree Trade-offs from Reversible Pebbling
- 2019
-
Ingår i: Proceedings of the 34th Annual Computational Complexity Conference (CCC ’19). - : Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. - 9783959771160 ; , s. 18:1-18:16
-
Konferensbidrag (refereegranskat)abstract
- We establish an exactly tight relation between reversible pebblings of graphs and Nullstellensatz refutations of pebbling formulas, showing that a graph G can be reversibly pebbled in time t and space s if an only if there is a Nullstellensatz refutation of the pebbling formula over G in size t + 1 and degree s (independently of the field in which the Nullstellensatz refutation is made). We use this correspondence to prove a number of strong size-degree trade-offs for Nullstellensatz, which to the best of our knowledge are the first such results for this proof system.
|
|
| 6. |
|
|
| 7. |
- Sahlin, Jakob, et al.
(författare)
-
Transmission Line Loss Prediction Based on Linear Regression and Exchange Flow Modelling
- 2017
-
Ingår i: 2017 IEEE Manchester PowerTech, Powertech 2017. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781509042371
-
Konferensbidrag (refereegranskat)abstract
- Inaccurate line loss predictions leads to additional regulation costs for Transmission System Operators (TSOs) that place energy bids at the day-ahead market to account for these losses. This paper presents a line loss prediction model design, applicable with the TSOs forecast conditions, that can reduce additional expenditure due to inaccurate predictions. The model predicts line losses for the next day per bidding area in relation to prognosis data on electrical demand, supply, renewable energy generation and regional exchange flows. Linear regression analysis can extract these relation factors, known as line loss rates, and derive a line loss prediction with increased accuracy and precision. Required input data is available at the power exchange markets apart from future exchange flows, which instead have been modelled as an optimisation problem and predicted by linear programming. Simulations performed on the Swedish National Grid for 2015 demonstrate the models performance and adequacy for TSO application.
|
|
| 8. |
- Ödén, Jakob, et al.
(författare)
-
Technical Note : On the calculation of stopping-power ratio for stoichiometric calibration in proton therapy
- 2015
-
Ingår i: Medical physics (Lancaster). - : Wiley. - 0094-2405 .- 2473-4209. ; 42:9, s. 5252-5257
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: The quantitative effects of assumptions made in the calculation of stopping-power ratios (SPRs) are investigated, for stoichiometric CT calibration in proton therapy. The assumptions investigated include the use of the Bethe formula without correction terms, Bragg additivity, the choice of I-value for water, and the data source for elemental I-values. Methods: The predictions of the Bethe formula for SPR (no correction terms) were validated against more sophisticated calculations using the SRIM software package for 72 human tissues. A stoichiometric calibration was then performed at our hospital. SPR was calculated for the human tissues using either the assumption of simple Bragg additivity or the Seltzer-Berger rule (as used in ICRU Reports 37 and 49). In each case, the calculation was performed twice: First, by assuming the I-value of water was an experimentally based value of 78 eV (value proposed in Errata and Addenda for ICRU Report 73) and second, by recalculating the I-value theoretically. The discrepancy between predictions using ICRU elemental I-values and the commonly used tables of Janni was also investigated. Results: Errors due to neglecting the correction terms to the Bethe formula were calculated at less than 0.1% for biological tissues. Discrepancies greater than 1%, however, were estimated due to departures from simple Bragg additivity when a fixed I-value for water was imposed. When the I-value for water was calculated in a consistent manner to that for tissue, this disagreement was substantially reduced. The difference between SPR predictions when using Janni's or ICRU tables for I-values was up to 1.6%. Experimental data used for materials of relevance to proton therapy suggest that the ICRU-derived values provide somewhat more accurate results (root-mean-square-error: 0.8% versus 1.6%). Conclusions: The conclusions from this study are that (1) the Bethe formula can be safely used for SPR calculations without correction terms; (2) simple Bragg additivity can be reasonably assumed for compound materials; (3) if simple Bragg additivity is assumed, then the I-value for water should be calculated in a consistent manner to that of the tissue of interest (rather than using an experimentally derived value); (4) the ICRU Report 37 I-values may provide a better agreement with experiment than Janni's tables.
|
|
