| 1. |
- Grüning, Björn, et al.
(author)
-
Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
-
Other publication (other academic/artistic)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
|
|
| 2. |
- Schafmayer, Clemens, et al.
(author)
-
Genome-wide association analysis of diverticular disease points towards neuromuscular, connective tissue and epithelial pathomechanisms
- 2019
-
In: Gut. - : BMJ. - 0017-5749 .- 1468-3288. ; 68:5, s. 854-865
-
Journal article (peer-reviewed)abstract
- Objective Diverticular disease is a common complex disorder characterised by mucosal outpouchings of the colonic wall that manifests through complications such as diverticulitis, perforation and bleeding. We report the to date largest genome-wide association study (GWAS) to identify genetic risk factors for diverticular disease. Design Discovery GWAS analysis was performed on UK Biobank imputed genotypes using 31 964 cases and 419 135 controls of European descent. Associations were replicated in a European sample of 3893 cases and 2829 diverticula-free controls and evaluated for risk contribution to diverticulitis and uncomplicated diverticulosis. Transcripts at top 20 replicating loci were analysed by real-time quatitative PCR in preparations of the mucosal, submucosal and muscular layer of colon. The localisation of expressed protein at selected loci was investigated by immunohistochemistry. Results We discovered 48 risk loci, of which 12 are novel, with genome-wide significance and consistent OR in the replication sample. Nominal replication (p< 0.05) was observed for 27 loci, and additional 8 in meta-analysis with a population-based cohort. The most significant novel risk variant rs9960286 is located near CTAGE1 with a p value of 2.3x10-10 and 0.002 (OR allelic = 1.14 (95% CI 1.05 to 1.24)) in the replication analysis. Four loci showed stronger effects for diverticulitis, PHGR1 (OR 1.32, 95% CI 1.12 to 1.56), FAM155A-2 (OR 1.21, 95% CI 1.04 to 1.42), CALCB (OR 1.17, 95% CI 1.03 to 1.33) and S100A10 (OR 1.17, 95% CI 1.03 to 1.33). Conclusion I n silico analyses point to diverticulosis primarily as a disorder of intestinal neuromuscular function and of impaired connective fibre support, while an additional diverticulitis risk might be conferred by epithelial dysfunction.
|
|
| 3. |
|
|
| 4. |
- Menkveld, Albert J., et al.
(author)
-
Nonstandard Errors
- 2024
-
In: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
-
Journal article (peer-reviewed)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
|
|
| 5. |
-
- 2019
-
Journal article (peer-reviewed)
|
|
| 6. |
- Haziza, Frédéric, et al.
(author)
-
Pointer Race Freedom
- 2016
-
In: Verification, Model Checking, And Abstract Interpretation, VMCAI 2016. - Berlin, Heidelberg : Springer. - 9783662491225 - 9783662491218 ; , s. 393-412
-
Conference paper (peer-reviewed)abstract
- We propose a novel notion of pointer race for concurrent programs manipulating a shared heap. A pointer race is an access to a memory address which was freed, and it is out of the accessor's control whether or not the cell has been re-allocated. We establish two results. (1) Under the assumption of pointer race freedom, it is sound to verify a program running under explicit memory management as if it was running with garbage collection. (2) Even the requirement of pointer race freedom itself can be verified under the garbage-collected semantics. We then prove analogues of the theorems for a stronger notion of pointer race needed to cope with performance-critical code purposely using racy comparisons and even racy dereferences of pointers. As a practical contribution, we apply our results to optimize a thread-modular analysis under explicit memory management. Our experiments confirm a speedup of up to two orders of magnitude.
|
|
| 7. |
- Lee, Wai Tung, et al.
(author)
-
Polarisation Development at the European Spallation Source
- 2023
-
In: EPJ Web of Conferences. - 2100-014X. ; 286, s. 03004-03004
-
Journal article (peer-reviewed)abstract
- To meet the ever-increasing user demand, eleven of the fifteen European Spallation Source (ESS) instruments under construction aim to offer polarised neutrons for user experiments. They include an imaging instrument, a SANS instruments, two reflectometers, three diffractometers, and four spectrometers. In conjunction with in-kind contributions and instrumentation grants, the ESS Polarisation Project will support the incorporation of polarisation analysis on eight of the eleven instruments. The project aims to deliver polarised neutrons for first-science experiments as instruments enter operation. Different polariser and polarisation analyser techniques will be available to accommodate the specifics of experiments on a given instrument. Polarised 3He neutron spin filter using either Metastable Optical Pumping (MEOP) or Spin-Exchange Optical Pumping (SEOP) techniques will provide shared-use equipment among many instruments, with SEOP’s main application being in situ beam-polarisation. Several instruments will also use polarising-supermirror devices. To provide wide-bandwidth spin-flipping capability to the time-of-flight instruments, Adiabatic Fast Passage (AFP) neutron spin flippers, also known as gradient-field radiofrequency spin flippers will be the main method of choice. Devices based on the same AFP principle will also be used to flip 3He nuclear spins. We are constructing our first 3He polariser setup, including field coils to produce highly uniform magnetic field. Monte Carlo simulations are being done for the supermirror polarisers. To ensure science-focused development, we are working with university partners in doing scientific experiments with polarised neutrons. These are some of the activities developing polarisation analysis for ESS instruments in our project.
|
|
| 8. |
- Saini, Apurve, et al.
(author)
-
Layering of magnetic nanoparticles at amorphous magnetic templates with perpendicular anisotropy
- 2020
-
In: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 16:33, s. 7676-7684
-
Journal article (peer-reviewed)abstract
- We reveal the assembly of magnetite nanoparticles of sizes 5 nm, 15 nm and 25 nm from dilute water-based ferrofluids onto an amorphous magnetic template with out-of-plane anisotropy. From neutron reflectometry experiments we extract density profiles and show that the particles self-assemble into layers at the magnetic surface. The layers are extremely stable against cleaning and rinsing of the substrate. The density of the layers is determined by and increases with the remanent magnetic moment of the particles.
|
|
| 9. |
- Wiesmaier, Sebastian, et al.
(author)
-
Magmatic Differentiation in the Teide–Pico Viejo Succession : Isotope Analysis as a Key to Deciphering the Origin of Phonolite Magma
- 2013
-
In: Teide Volcano. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783642258923 - 9783642258930 ; , s. 173-190
-
Book chapter (peer-reviewed)abstract
- In Tenerife, lavas of the recent Teide–Pico Viejo central complex show a marked bimodality in composition from initially mafic lava (200–30 ka) to highly differentiated phonolite (30–0 ka). Groundmass Sr–Nd–Pb–O and feldspar 18O data demonstrate open system behaviour for the petrogenesis of Teide–Pico Viejo felsic lavas, but contamination by ocean sediment can be excluded due to the low 206Pb/204Pb ratios of North Atlantic sediment. Isotope mixing hyperbolae require an assimilant of predominantly felsic composition for the Teide–Pico Viejo succession. Unsystematic and heterogeneous variation of 18O in fresh and unaltered feldspars across the Teide–Pico Viejo succession indicates magmatic addition of diverse 18O assimilants, best matched by nepheline syenites that occur as fresh and altered lithic blocks in voluminous pre-Teide ignimbrite deposits. Rare earth element modelling indicates that nepheline syenite needs to be melted in bulk to form a suitable end-member composition. Energy-Constrained Assimilation Fractional Crystallisation (EC-AFC) modelling reproduces the bulk of the succession, which implies that the petrogenesis of Teide–Pico Viejo lavas is governed by the coupled assimilation of nepheline syenite during fractional crystallisation. The most differentiated (and most radiogenic) lava computes to >97.8 % assimilant, likely represented by a nepheline syenite bulk melt that formed by underplating with juvenile mafic material. These recent research developments therefore recognise a wider variability of magmatic differentiation processes at Teide–Pico Viejo than previously considered.
|
|
| 10. |
- Wiesmaier, Sebastian, et al.
(author)
-
Open-system processes in the differentiation of mafic magma in the Teide-Pico Viejo succession, Tenerife
- 2013
-
In: Journal of the Geological Society. - : Geological Society of London. - 0016-7649 .- 2041-479X. ; 170:3, s. 557-570
-
Journal article (peer-reviewed)abstract
- Oceanic island basalts are commonly thought to differentiate by fractional crystallization, yet closed-system fractionation models have so far failed to reproduce major and trace element variations observed in mafic lavas from the Teide-Pico Viejo stratovolcano complex on Tenerife. Here, new high-precision plagioclase trace element data are fed into such a fractionation model. The results confirm that fractionation of phenocrysts found in the lavas does not reproduce trace element variations, in particular enrichment of Sr and Zr observed in the Teide-Pico Viejo mafic suite. This enrichment of Sr and Zr is tested by an energy-constrained recharge, assimilation and fractional crystallization (EC-RAFC) model at high T and low Lambda T intervals, consistent with previously determined magma storage beneath Tenerife at sub-Moho depths. Published mineral-melt equilibrium relations using the plagioclase anorthite content (0.4 < X-An < 0.8) constrain the temperature during differentiation. Gabbroic xenoliths found in Tenerife lavas are assumed as contaminant. Enrichment of Sr and Zr in the Teide mafic suite is reproduced by this combined assimilation and fractional crystallization model, as assimilation causes higher degrees of enrichment in incompatible trace elements than is possible by crystal fractionation alone. Recycling of plutonic roots may thus have significantly enriched trace elements in the primitive lavas of the Teide-Pico Viejo succession.
|
|
