ALBERT

Beschreibung: Due to the uses of DNA profiling in criminal investigation and decision-making, it is ever more common that probabilistic information is discussed in courts. The people involved have varied backgrounds, as factfinders and lawyers are more trained in the use of non-probabilistic information, while forensic experts handle probabilistic information on a routine basis. Hence, it is important to have a good understanding of the sort of reasoning that happens in criminal cases, both probabilistic and non-probabilistic. In the present article, we report results on combining three normative reasoning frameworks from the literature: arguments, scenarios and probabilities. We discuss a hybrid model that connects arguments and scenarios, a method to probabilistically model possible scenarios in a Bayesian network, a method to extract arguments from a Bayesian network and a proposal to model arguments for and against different scenarios in standard probability theory. These results have been produced as parts of research projects on the formal and computational modelling of evidence. The present article reviews these results, shows how they are connected and where they differ, and discusses strengths and limitations.

Beschreibung: The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m 1 acp 3 ) located next to the P-site tRNA on the small subunit 18S rRNA. While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive. Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells. In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation. The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode. This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate. Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.

Beschreibung: Massive stars that have been ejected from their parent cluster and supersonically sailing away through the interstellar medium (ISM) are classified as exiled. They generate circumstellar bow-shock nebulae that can be observed. We present two-dimensional, axisymmetric hydrodynamical simulations of a representative sample of stellar wind bow shocks from Galactic OB stars in an ambient medium of densities ranging from n ISM  = 0.01 up to 10.0 cm – 3 . Independently of their location in the Galaxy, we confirm that the infrared is the most appropriated waveband to search for bow shocks from massive stars. Their spectral energy distribution is the convenient tool to analyse them since their emission does not depend on the temporary effects which could affect unstable, thin-shelled bow shocks. Our numerical models of Galactic bow shocks generated by high-mass ( 40 M ) runaway stars yield H α fluxes which could be observed by facilities such as the SuperCOSMOS H-Alpha Survey. The brightest bow-shock nebulae are produced in the denser regions of the ISM. We predict that bow shocks in the field observed at H α by means of Rayleigh-sensitive facilities are formed around stars of initial mass larger than about 20 M . Our models of bow shocks from OB stars have the emission maximum in the wavelength range 3 ≤ ≤ 50 μm which can be up to several orders of magnitude brighter than the runaway stars themselves, particularly for stars of initial mass larger than 20 M .

Beschreibung: The H.U. Sverdrupfjella is part of the high-grade Maud Belt in Dronning Maud Land (East Antarctica), which was located in a central position of the Gondwana supercontinent. Here we study high-pressure granulites from the eastern H.U. Sverdrupfjella and present a detailed reconstruction of the P–T–t history based on a combination of Zr-in-rutile and Ti-in-zircon thermometry, zircon U–Pb dating, monazite chemical dating, garnet diffusion modelling and petrological modelling. Peak metamorphic conditions of ~930°C and 1·45 GPa persisted for less than 6 Myr and were attained at 570 ± 7 Ma, embedded in a well-documented clockwise loading, heating, and decompression path. The rocks had already been rapidly exhumed to a crustal depth of ~30 km at 556 ± 7 Ma. In addition to the very short-lived ultrahigh-temperature peak, zircon preserves evidence for protracted granulite-facies conditions with temperatures above 800°C from as early as c. 590 Ma, persisting for c. 40 Myr. Constraints on prograde metamorphism are recorded in zircon and in rutile inclusions in garnet. Zr-in-rutile thermometry using rutile included in different generations of garnet is used to reconstruct the prograde P–T path, documenting burial followed by heating to ultrahigh temperatures at peak pressures. Complementary Ti zonation in prograde cores of zircon grains documents and dates heating and peak temperatures, whereas younger zircon rims show lower Ti-in-zircon temperatures and date the retrograde stages of metamorphism. Our results provide the first evidence for Neoproterozoic high-pressure granulite-facies metamorphism and ultrahigh-temperature conditions for this region. The clockwise loading–heating path and the peak P–T conditions strongly indicate that the rocks preserved in Dronning Maud Land were part of the lower plate during a continent–continent collision event related to Gondwana assembly at c. 570 Ma. The metamorphic evolution determined in this study and the correlation with similar P–T evolutions documented in adjacent terranes favour the continuation of the c. 580–560 Ma Mozambique Belt into Dronning Maud Land. Furthermore, the striking contemporaneity of the metamorphism in the different parts of central Gondwana suggests that the Coats Land Block was part of greater India prior to this collision.

Beschreibung: : Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency—molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. Availability and implementation: BISQUE is freely available via the web using any major web browser ( http://bisque.yulab.org/ ). Source code is available in a public GitHub repository ( https://github.com/hyulab/BISQUE ). Contact: haiyuan.yu@cornell.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Mass segregation in star clusters is often thought to indicate the onset of energy equipartition, where the most massive stars impart kinetic energy to the lower-mass stars and brown dwarfs/free-floating planets. The predicted net result of this is that the centrally concentrated massive stars should have significantly lower velocities than fast-moving low-mass objects on the periphery of the cluster. We search for energy equipartition in initially spatially and kinematically substructured N -body simulations of star clusters with N = 1500 stars, evolved for 100 Myr. In clusters that show significant mass segregation we find no differences in the proper motions or radial velocities as a function of mass. The kinetic energies of all stars decrease as the clusters relax, but the kinetic energies of the most massive stars do not decrease faster than those of lower-mass stars. These results suggest that dynamical mass segregation – which is observed in many star clusters – is not a signature of energy equipartition from two-body relaxation.

Beschreibung: Susceptibility to antibiotics is dramatically reduced when bacteria form biofilms. In clinical settings this has a profound impact on treatment of implant-associated infections, as these are characterized by biofilm formation. Current routine susceptibility testing of microorganisms from infected implants does not reflect the actual susceptibility, and the optimal antibiotic strategy for treating implant-associated infections is not established. In this study of biofilm formation in implant-associated osteomyelitis, we compared the in vitro and in vivo efficacy of selected antibiotics alone and in combination against Staphylococcus aureus. We tested vancomycin, linezolid, daptomycin and tigecycline alone and in combination with rifampicin, vancomycin, linezolid and daptomycin against S. aureus . In vitro , biofilm formation dramatically reduced susceptibility by a factor of 500–2000. In vivo , antibiotic combinations were tested in a murine model of implant-associated osteomyelitis. Mice were infected by inserting implants colonized with S. aureus trough their tibia. After 11 days, the animals were divided into different groups (five animals/group) and given 14 days of antibiotic therapy. All antibiotics resulted in a reduced bacterial load in the infected bone surrounding the implant. Overall, the most effective antibiotic combinations contained rifampicin. Combinations containing two non-rifampicin antibiotics were not more active than single drugs.

Beschreibung: RNA–RNA interactions are fast emerging as a major functional component in many newly discovered non-coding RNAs. Basepairing is believed to be a major contributor to the stability of these intermolecular interactions, much like intramolecular basepairs formed in RNA secondary structure. As such, using algorithms similar to those for predicting RNA secondary structure, computational methods have been recently developed for the prediction of RNA–RNA interactions. We provide the first comprehensive comparison comprising 14 methods that predict general intermolecular basepairs. To evaluate these, we compile an extensive data set of 54 experimentally confirmed fungal snoRNA–rRNA interactions and 102 bacterial sRNA–mRNA interactions. We test the performance accuracy of all methods, evaluating the effects of tool settings, sequence length, and multiple sequence alignment usage and quality. Our results show that—unlike for RNA secondary structure prediction—the overall best performing tools are non-comparative energy-based tools utilizing accessibility information that predict short interactions on this data set. Furthermore, we find that maintaining high accuracy across biologically different data sets and increasing input lengths remains a huge challenge, causing implications for de novo transcriptome-wide searches. Finally, we make our interaction data set publicly available for future development and benchmarking efforts.

Beschreibung: We build on a recent photometric decomposition analysis of 7506 Galaxy and Mass Assembly (GAMA) survey galaxies to derive stellar mass function fits to individual spheroid and disc component populations down to a lower mass limit of log( M * /M ) = 8. We find that the spheroid/disc mass distributions for individual galaxy morphological types are well described by single Schechter function forms. We derive estimates of the total stellar mass densities in spheroids ( spheroid = 1.24 ± 0.49 x 10 8 M  Mpc  –3 h 0.7 ) and discs ( disc = 1.20 ± 0.45 x 10 8 M  Mpc  –3 h 0.7 ), which translates to approximately 50 per cent of the local stellar mass density in spheroids and 48 per cent in discs. The remaining stellar mass is found in the dwarf ‘little blue spheroid’ class, which is not obviously similar in structure to either classical spheroid or disc populations. We also examine the variation of component mass ratios across galaxy mass and group halo mass regimes, finding the transition from spheroid to disc mass dominance occurs near galaxy stellar mass ~10 11 M and group halo mass ~10 12.5 M h –1 . We further quantify the variation in spheroid-to-total mass ratio with group halo mass for central and satellite populations as well as the radial variation of this ratio within groups.