Oswaldo: A Semantic Web Enabled Approach for Identifying Open Source License Violations

Open source license violations are numerous, multifaceted, and pose significant risk to developers and companies in the form of litigation, sometimes resulting in millions in dollars in damages or settlements. Free/Libre and Open Source Licenses utilize copyright law and are written in legalese, which is often outside the scope of a developer’s expertise. Software Engineers commit violations of these licenses’ terms and conditions easily and often unknowingly. Consequently, increased knowledge, better tools, and sound processes to detect and prevent license violations are extremely important. This work is an investigation in the types of potential license violations that are committed, through direct and transitive dependency hierarchies in hundreds of thousands of real-world software projects. This thesis contributes a novel approach, entitled Oswaldo, that defines and detects three types of license conflicts: Type 1 Simple Violation, Type 2 Embedded Violations, Type 3 Compound Violations. Unidirectional compatibility/incompatibility relationships of major licenses are modelled. Ontologies and Linked Data are advantageously exploited to detect transitive violation Types 2 and 3, as well as the direct violation Type 1. This thesis also reports initial evaluations of these three types of license violations found in the Maven repository

The effects of landscape modifications on the long-term persistence of animal populations

Background: The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Methodology/Principal Findings: Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Significance: Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses

Ultracompact dwarfs in the Perseus Cluster:UCD formation via tidal stripping

We present the results of a Keck/DEIMOS survey of Ultra Compact Dwarfs (UCDs) in the Perseus Cluster core. We confirm cluster membership for 14 UCDs, with radial velocities ~5300 km s$^{-1}$. Two of these confirmed Perseus UCDs have extremely blue colours ($B-R < 0.6$ mag), reside in star forming filaments surrounding NGC 1275, and have likely formed as massive star clusters in the last ~100 Myr. We also measure a central velocity dispersion of a third, UCD13 ($\sigma_0 = 38 \pm 8$ km s$^{-1}$), the most extended UCD in our sample. We determine it to have radius $R_{e} = 85 \pm 1.1$ pc, a dynamical mass of ($2.3 \pm 0.8)\times10^{8}$ M$_{\odot}$, and a metallicity [Z/H]$= -0.52^{+0.33}_{-0.29}$ dex. UCD13 and the cluster's central galaxy, NGC 1275, have a projected separation of 30 kpc and a radial velocity difference of ~20 km s$^{-1}$. Based on its size, red colour, internal velocity dispersion, dynamical mass, metallicity and proximity to NGC 1275, we argue that UCD13 is likely the remnant nucleus of a tidally stripped dE, with this progenitor dE having $M_{B} \approx -16$ mag and mass $\sim10^{9}$ M$_{\odot}$.Comment: 9 pages, 5 figures, accepted for publication in MNRA

Hubble Space Telescope survey of the Perseus Cluster -IV: Compact stellar systems in the Perseus Cluster core and Ultra Compact Dwarf formation in star forming filaments

We present the results of the first search for Ultra Compact Dwarfs (UCDs) in the Perseus Cluster core, including the region of the cluster around the unusual Brightest Cluster Galaxy (BCG) NGC 1275. Utilising Hubble Space Telescope Advanced Camera for Surveys imaging, we identify a sample of 84 UCD candidates with half-light radii 10 pc < r_e < 57 pc out to a distance of 250 kpc from the cluster centre, covering a total survey area of ~70 armin^2. All UCDs in Perseus lie in the same size-luminosity locus seen for confirmed UCDs in other regions of the local Universe. The majority of UCDs are brighter than M_R = -10.5, and lie on an extrapolation of the red sequence followed by the Perseus Cluster dwarf elliptical population to fainter magnitudes. However, three UCD candidates in the vicinity of NGC 1275 are very blue, with colours (B-R)_0 < 0.6 implying a cessation of star formation within the past 100 Myr. Furthermore, large blue star clusters embedded in the star forming filaments are highly indicative that both proto-globular clusters (GCs) and proto-UCDs are actively forming at the present day in Perseus. We therefore suggest star forming filaments as a formation site for some UCDs, with searches necessary in other low redshift analogues of NGC 1275 necessary to test this hypothesis. We also suggest that tidal disruption of dwarf galaxies is another formation channel for UCD formation in the core of Perseus as tidal disruption is ongoing in this region as evidenced by shells around NGC 1275. Finally, UCDs may simply be massive GCs based on strong similarities in the colour trends of the two populations.Comment: 18 pages, 20 figures, 3 tables. Accepted for publication in MNRA

Variance based weighting of multisensory head rotation signals for verticality perception

We tested the hypothesis that the brain uses a variance-based weighting of multisensory cues to estimate head rotation to perceive which way is up. The hypothesis predicts that the known bias in perceived vertical, which occurs when the visual environment is rotated in a vertical-plane, will be reduced by the addition of visual noise. Ten healthy participants sat head-fixed in front of a vertical screen presenting an annulus filled with coloured dots, which could rotate clockwise or counter-clockwise at six angular velocities (1, 2, 4, 6, 8, 16°/s) and with six levels of noise (0, 25, 50, 60, 75, 80%). Participants were required to keep a central bar vertical by rotating a hand-held dial. Continuous adjustments of the bar were required to counteract low-amplitude low-frequency noise that was added to the bar's angular position. During visual rotation, the bias in verticality perception increased over time to reach an asymptotic value. Increases in visual rotation velocity significantly increased this bias, while the addition of visual noise significantly reduced it, but did not affect perception of visual rotation velocity. The biasing phenomena were reproduced by a model that uses a multisensory variance-weighted estimate of head rotation velocity combined with a gravito-inertial acceleration signal (GIA) from the vestibular otoliths. The time-dependent asymptotic behaviour depends on internal feedback loops that act to pull the brain's estimate of gravity direction towards the GIA signal. The model's prediction of our experimental data furthers our understanding of the neural processes underlying human verticality perception

Variable effects of exposure to formulated microbicides on antibiotic susceptibility in firmicutes and proteobacteria

Microbicides are broad-spectrum antimicrobial agents that generally interact with multiple pharmacological targets. While they are widely deployed in disinfectant, antiseptic, and preservative formulations, data relating to their potential to select for microbicide or antibiotic resistance have been generated mainly by testing the compounds in much simpler aqueous solutions. In the current investigation, antibiotic susceptibility was determined for bacteria that had previously exhibited decreased microbicide susceptibility following repeated exposure to microbicides either in formulation with sequestrants and surfactants or in simple aqueous solution. Statistically significant increases in antibiotic susceptibility occurred for 12% of bacteria after exposure to microbicides in formulation and 20% of bacteria after exposure to microbicides in aqueous solutions, while 22% became significantly less susceptible to the antibiotics, regardless of formulation. Of the combinations of a bacterium and an antibiotic for which British Society for Antimicrobial Chemotherapy breakpoints are available, none became resistant. Linear modeling taking into account phylogeny, microbicide, antibiotic, and formulation identified small but significant effects of formulation that varied depending on the bacterium and microbicide. Adaptation to formulated benzalkonium chloride in particular was more likely to increase antibiotic susceptibility than adaptation to the simple aqueous solution. In conclusion, bacterial adaptation through repeated microbicide exposure was associated with both increases and decreases in antibiotic susceptibility. Formulation of the microbicide to which the bacteria had previously adapted had an identifiable effect on antibiotic susceptibility, but it effect was typically small relative to the differences observed among microbicides. Susceptibility changes resulting in resistance were not observed. IMPORTANCE The safety of certain microbicide applications has been questioned due to the possibility that microbicide exposure could select for microbicide and antibiotic resistance. Evidence that this may happen is based mainly on in vitro experiments where bacteria have been exposed to microbicides in aqueous solution. Microbicides are, however, normally deployed in products formulated with surfactants, sequestrants, and other compounds. While this may influence the frequency and extent of susceptibility changes, few studies reported in the literature have assessed this. In the current investigation, therefore, we have investigated changes in antibiotic susceptibility in bacteria which exhibited decreased microbicide susceptibility following repeated exposure to microbicides in simple aqueous solutions and in formulation. We report that the microbicide formulation had an identifiable effect on antibiotic susceptibility, but it was typically small relative to the differences observed among microbicides. We did not observe susceptibility changes resulting in resistance

Spatially Resolved Stellar Spectroscopy of the Ultra-diffuse Galaxy Dragonfly 44. III. Evidence for an Unexpected Star-Formation History

We use the Keck Cosmic Web Imager integral-field unit spectrograph to: 1) measure the global stellar population parameters for the ultra-diffuse galaxy (UDG) Dragonfly 44 (DF44) to much higher precision than previously possible for any UDG, and 2) for the first time measure spatially-resolved stellar population parameters of a UDG. We find that DF44 falls below the mass--metallicity relation established by canonical dwarf galaxies both in and beyond the Local Group. We measure a flat radial age gradient ($m_{\rm age} \sim +0.01_{-0.08}^{+0.07}$ log Gyr kpc$^{-1}$) and a flat-to-positive metallicity gradient ($m_{\rm [Fe/H]} \sim +0.08_{-0.11}^{+0.11}$ dex kpc$^{-1}$), which are inconsistent with the gradients measured in similarly pressure-supported dwarf galaxies. We also measure a flat-to-negative [Mg/Fe] gradient ($m_{\rm [Mg/Fe]} \sim -0.18_{-0.17}^{+0.17}$ dex kpc$^{-1}$) such that the central $1.5$ kpc of DF44 has stellar population parameters comparable to metal-poor globular clusters. Overall, DF44 does not have internal properties similar to other dwarf galaxies and is inconsistent with it having been puffed up through a prolonged, bursty star-formation history, as suggested by some simulations. Rather, the evidence indicates that DF44 experienced an intense epoch of "inside-out" star formation and then quenched early and catastrophically, such that star-formation was cut off more quickly than in canonical dwarf galaxies.Comment: Accepted to Ap

The SLUGGS Survey: Calcium Triplet-based Spectroscopic Metallicities for Over 900 Globular Clusters

Although the colour distribution of globular clusters in massive galaxies is well known to be bimodal, the spectroscopic metallicity distribution has been measured in only a few galaxies. After redefining the calcium triplet index-metallicity relation, we use our relation to derive the metallicity of 903 globular clusters in 11 early-type galaxies. This is the largest sample of spectroscopic globular cluster metallicities yet assembled. We compare these metallicities with those derived from Lick indices finding good agreement. In 6 of the 8 galaxies with sufficient numbers of high quality spectra we find bimodality in the spectroscopic metallicity distribution. Our results imply that most massive early-type galaxies have bimodal metallicity, as well as colour, distributions. This bimodality suggests that most massive galaxies early-type galaxies experienced two periods of star formation.Comment: 23 pages, 13 figures. Accepted for publication in MNRAS. For more information about the SLUGGS Survey please see http://sluggs.swin.edu.a

Progress in achieving quantitative classification of psychopathology

Shortcomings of approaches to classifying psychopathology based on expert consensus have given rise to contemporary efforts to classify psychopathology quantitatively. In this paper, we review progress in achieving a quantitative and empirical classification of psychopathology. A substantial empirical literature indicates that psychopathology is generally more dimensional than categorical. When the discreteness versus continuity of psychopathology is treated as a research question, as opposed to being decided as a matter of tradition, the evidence clearly supports the hypothesis of continuity. In addition, a related body of literature shows how psychopathology dimensions can be arranged in a hierarchy, ranging from very broad "spectrum level" dimensions, to specific and narrow clusters of symptoms. In this way, a quantitative approach solves the "problem of comorbidity" by explicitly modeling patterns of co-occurrence among signs and symptoms within a detailed and variegated hierarchy of dimensional concepts with direct clinical utility. Indeed, extensive evidence pertaining to the dimensional and hierarchical structure of psychopathology has led to the formation of the Hierarchical Taxonomy of Psychopathology (HiTOP) Consortium. This is a group of 70 investigators working together to study empirical classification of psychopathology. In this paper, we describe the aims and current foci of the HiTOP Consortium. These aims pertain to continued research on the empirical organization of psychopathology; the connection between personality and psychopathology; the utility of empirically based psychopathology constructs in both research and the clinic; and the development of novel and comprehensive models and corresponding assessment instruments for psychopathology constructs derived from an empirical approach