A Tool for Visual Understanding of Source Code Dependencies

Many program comprehension tools use graphs to visualize and analyze source code. The main issue is that existing approaches create graphs overloaded with too much information. Graphs contain hundreds of nodes and even more edges that cross each other. Understanding these graphs and using them for a given program comprehension task is tedious, and in the worst case developers stop using the tools. In this paper we present DA4Java, a graphbased approach for visualizing and analyzing static dependencies between Java source code entities. The main contribution of DA4Java is a set of features to incrementally compose graphs and remove irrelevant nodes and edges from graphs. This leads to graphs that contain significantly fewer nodes and edges and need less effort to understand

Biogeochemistry of Norwegian cold-water coral reef sediments

Cold-water coral ecosystems may constitute a geologically significant fraction (>1%) of global carbonate production (Lindberg and Mienert, 2005). Thriving cold-water coral reefs are also considered to be hot-spots of diversity and biomass production. Nevertheless, the impacts of these ecosystems on the adjacent sediment and associated geochemical processes including carbonate preservation are poorly understood.Here we present the first data quantifying the biogeochemical processes in modern (post-glacial) cold-water coral reef sediments. This work integrates organoclastic sulfate reduction rates, multi-element pore-water profiles and solid-phase analyses of gravity cores (8 sites at two reefs) retrieved during R/V Polarstern expedition ARKXXII/1a to the mid-Norwegian cold-water coral reefs in June 2007.The reef sediments are comprised of coral fragments embedded in loose silt or clay and biogenic debris (of 0,5 to 3,2 m thickness). The base of the coral-bearing reef sediments consists of highly compacted glacial clays. High carbonate contents (up to 75 %) and low organic carbon contents (~0,5 %) characterize the reef sediments. Porewater Ca2+, Mg2+ and Sr2+ profiles indicate that on-going carbonate precipitation dominates any carbonate dissolution. Overall microbial activity in these sediments is low; measured sulfate reduction rates are less than 1 nmol S cm-3 d-1. Pore-water analyses reveal elevated Fe2+ and Mn2+ concentrations suggesting that Fe and Mn reduction occurs. This may be the result of sulfide reacting with the available reactive iron pool to form Fe-sulfides indicated by the absence of sulfide in the pore water. Fe and Mn reduction may also be attributed to dissimilatory microbial metal reduction. Iron reduction linked to microbial sulfate reduction may enhance diagenetic carbonate precipitation and coral preservation in these sediments as suggested for the older coldwater coral mound systems drilled in IODP Expedition 307 (Ferdelman et al., 2006). Extremely low methane concentrations (<0,5 µM) were found at all depths and sites along the Norwegian margin. This argues against a linkage between coral reef distribution and the appearance of hydrocarbon seepage as formulated by Hovland et al. (1998)

Carbon mineralization and carbonate preservation in modern cold-water coral reef sediments on the Norwegian shelf

Cold-water coral ecosystems are considered hot-spots of biodiversity and biomass production and may be a regionally important contributor to carbonate production. The impact of these ecosystems on biogeochemical processes and carbonate preservation in associated sediments were studied at Røst Reef and Traenadjupet Reef, two modern (post-glacial) cold-water coral reefs on the Mid-Norwegian shelf. Sulfate and iron reduction as well as carbonate dissolution and precipitation were investigated by combining pore-water geochemical profiles, steady state modeling, as well as solid phase analyses and sulfate reduction rate measurements on gravity cores of up to 3.25 m length. Low extents of sulfate depletion and dissolved inorganic carbon (DIC) production, combined with sulfate reduction rates not exceeding 3 nmol S cm−3 d−1, suggested that overall anaerobic carbon mineralization in the sediments was low. These data showed that the coral fragment-bearing siliciclastic sediments were effectively decoupled from the productive pelagic ecosystem by the complex reef surface framework. Organic matter being mineralized by sulfate reduction was calculated to consist of 57% carbon bound in CH2O groups and 43% carbon in -CH2- groups. Methane concentrations were below 1 μM, and failed to support the hypothesis of a linkage between the distribution of cold-water coral reefs and the presence of hydrocarbon seepage. Reductive iron oxide dissolution linked to microbial sulfate reduction buffered the pore-water carbonate system and inhibited acid-driven coral skeleton dissolution. A large pool of reactive iron was available leading to the formation of iron sulfide minerals. Constant pore-water Ca2+, Mg2+ and Sr2+ concentrations in most cores and decreasing Ca2+ and Sr2+ concentrations with depth in core 23–18 GC indicated diagenetic carbonate precipitation. This was consistent with the excellent preservation of buried coral fragments

Synthesis and SAR evaluation of coumarin derivatives as potent cannabinoid receptor agonists

We report the development and extensive structure-activity relationship evaluation of a series of modified coumarins as cannabinoid receptor ligands. In radioligand, and [S-35]GTP gamma S binding assays the CB receptor binding affinities and efficacies of the new ligands were determined. Furthermore, we used a ligand-based docking approach to validate the empirical observed results. In conclusion, several crucial structural requirements were identified. The most potent coumarins like 3-butyl-7-(1-butylcyclopentyl)-5-hydroxy-2H-chromen-2-one (36b, K-i CB2 13.7 nM, EC50 18 nM), 7-(1-butylcyclohexyl)-5-hydroxy-3-propyl-2H-chromen-2-one (39b, K-i CB2 6.5 nM, EC50 4.51 nM) showed a CB2 selective agonistic profile with low nanomolar affinities. (C) 2021 Published by Elsevier Masson SAS.Peer reviewe

Seasonal dynamics of the depth and rate of anaerobic oxidation of methane in Aarhus Bay (Denmark) sediments

A reactive-transport model has been applied to investigate the dynamics of the sulfate-methane transition zone (SMTZ) in nearshore sediments of Aarhus Bay (Denmark). The sediments are influenced by seasonal variations of temperature and particulate organic carbon (POC) deposition flux at the sediment-water interface. Initially, the model was calibrated at steady state using field data collected at two sites (M1 and M5) in December 2004, and included a dynamic gas phase which determines the depth of the SMTZ. Simulations were then performed under transient conditions of heat propagation in the porous medium, which influenced the solubility of gaseous methane, the diffusion of solutes as well as the kinetic and bioenergetic constraints on redox conditions in the system. Results revealed important variations in local rates of anaerobic oxidation of methane (AOM) over a seasonal cycle due to temperature variation. Seasonal perturbations in POC depositional flux had no influence on AOM rates but did have a strong bearing on sulfate reduction rates in the surface layers of the simulations at both stations. At M5, where the SMTZ was located 63 cm below the sediment-water interface, depth integrated AOM rates varied between 76 and 178 nmol cm-2 d-1. At M1, where the deeper SMTZ (221 cm) experienced less thermal variation, AOM rates varied relatively less (20 to 24 nmol cm-2 d-1). Furthermore, local and depth-integrated AOM rates over the year did not show a simple response to bottom water temperature but exhibited a hysteresis-type behavior related to time lags in solute transport and heat propagation. Overall, the solute concentration profiles were not very sensitive to the seasonal variability in rates or gas transport and the modeled vertical displacement of the SMTZ was limited to <1 cm at M1 and 2–3 cm at M5. The results suggest that the significantly larger apparent displacement observed in the field from repeated coring (80 cm and 16 cm at M1 and M5, respectively) must be attributed to other factors, of which spatial heterogeneity in gas transport rate appears to be the most likely

The Relative Influence of Habitat Amount and Configuration on Genetic Structure Across Multiple Spatial Scales

Despite strong interest in understanding how habitat spatial structure shapes the genetics of populations, the relative importance of habitat amount and configuration for patterns of genetic differentiation remains largely unexplored in empirical systems. In this study, we evaluate the relative influence of, and interactions among, the amount of habitat and aspects of its spatial configuration on genetic differentiation in the pitcher plant midge, Metriocnemus knabi. Larvae of this species are found exclusively within the water-filled leaves of pitcher plants (Sarracenia purpurea) in a system that is naturally patchy at multiple spatial scales (i.e., leaf, plant, cluster, peatland). Using generalized linear mixed models and multimodel inference, we estimated effects of the amount of habitat, patch size, interpatch distance, and patch isolation, measured at different spatial scales, on genetic differentiation (F ST) among larval samples from leaves within plants, plants within clusters, and clusters within peatlands. Among leaves and plants, genetic differentiation appears to be driven by female oviposition behaviors and is influenced by habitat isolation at a broad (peatland) scale. Among clusters, gene flow is spatially restricted and aspects of both the amount of habitat and configuration at the focal scale are important, as is their interaction. Our results suggest that both habitat amount and configuration can be important determinants of genetic structure and that their relative influence is scale dependent

Onset of magnetism in B2 transition metals aluminides

Ab initio calculation results for the electronic structure of disordered bcc Fe(x)Al(1-x) (0.4<x<0.75), Co(x)Al(1-x) and Ni(x)Al(1-x) (x=0.4; 0.5; 0.6) alloys near the 1:1 stoichiometry, as well as of the ordered B2 (FeAl, CoAl, NiAl) phases with point defects are presented. The calculations were performed using the coherent potential approximation within the Korringa-Kohn-Rostoker method (KKR-CPA) for the disordered case and the tight-binding linear muffin-tin orbital (TB-LMTO) method for the intermetallic compounds. We studied in particular the onset of magnetism in Fe-Al and Co-Al systems as a function of the defect structure. We found the appearance of large local magnetic moments associated with the transition metal (TM) antisite defect in FeAl and CoAl compounds, in agreement with the experimental findings. Moreover, we found that any vacancies on both sublattices enhance the magnetic moments via reducing the charge transfer to a TM atom. Disordered Fe-Al alloys are ferromagnetically ordered for the whole range of composition studied, whereas Co-Al becomes magnetic only for Co concentration >0.5.Comment: 11 pages with 9 embedded postscript figures, to be published in Phys.Rev.

Fertility, Living Arrangements, Care and Mobility

There are four main interconnecting themes around which the contributions in this book are based. This introductory chapter aims to establish the broad context for the chapters that follow by discussing each of the themes. It does so by setting these themes within the overarching demographic challenge of the twenty-first century – demographic ageing. Each chapter is introduced in the context of the specific theme to which it primarily relates and there is a summary of the data sets used by the contributors to illustrate the wide range of cross-sectional and longitudinal data analysed

14-3-3epsilon contributes to tumour suppression in laryngeal carcinoma by affecting apoptosis and invasion

<p>Abstract</p> <p>Background</p> <p>14-3-3epsilon regulates a wide range of biological processes, including cell cycle control, proliferation, and apoptosis, and plays a significant role in neurogenesis and the formation of malignant tumours. However, the exact function and regulatory mechanism of 14-3-3epsilon in carcinogenesis have not been elucidated.</p> <p>Methods</p> <p>The expression of <it>14-3-3epsilon </it>was assessed by RT-PCR and western blotting. The invasiveness and viability of Hep-2 cells were determined by the transwell migration assay and MTT assay, respectively. Cell cycle and apoptosis of Hep-2 cells were detected by flow cytometry.</p> <p>Results</p> <p>The mRNA and protein expression of <it>14-3-3epsilon </it>in larynx squamous cell carcinoma (LSCC) tissues were significantly lower than those in clear surgical margin tissues. Statistical analysis showed that the 14-3-3epsilon protein level in metastatic lymph nodes was lower than that in paired tumour tissues. In addition, the protein level of 14-3-3epsilon in stage III or IV tumours was significantly lower than that in stage I or II tumours. Compared with control Hep-2 cells, the percentages of viable cells in the 14-3-3epsilon-GFP and negative control GFP groups were 36.68 ± 14.09% and 71.68 ± 12.10%, respectively. The proportions of S phase were 22.47 ± 3.36%, 28.17 ± 3.97% and 46.15 ± 6.82%, and the apoptotic sub-G1 populations were 1.23 ± 1.02%, 2.92 ± 1.59% and 13.72 ± 3.89% in the control, negative control GFP and 14-3-3epsilon-GFP groups, respectively. The percentages of the apoptotic cells were 0.84 ± 0.25%, 1.08 ± 0.24% and 2.93 ± 0.13% in the control, negative control GFP and 14-3-3epsilon-GFP groups, respectively. The numbers of cells that penetrated the filter membrane in the control, negative control GFP and 14-3-3epsilon-GFP groups were 20.65 ± 1.94, 17.63 ± 1.04 and 9.1 ± 0.24, respectively, indicating significant differences among the different groups.</p> <p>Conclusions</p> <p>Decreased expression of <it>14-3-3epsilon </it>in LSCC tissues contributes to the initiation and progression of LSCC. <it>14-3-3epsilon </it>can promote apoptosis and inhibit the invasiveness of LSCC.</p