A Finite Model Property for Gödel Modal Logics

A new semantics with the finite model property is provided and used to establish decidability for Gödel modal logics based on (crisp or fuzzy) Kripke frames combined locally with Gödel logic. A similar methodology is also used to establish decidability, and indeed co-NP-completeness for a Gödel S5 logic that coincides with the one-variable fragment of first-order Gödel logic.

ANOVA kernels and RKHS of zero mean functions for model-based sensitivity analysis

Given a reproducing kernel Hilbert space (H,〈.,.〉)(H,〈.,.〉) of real-valued functions and a suitable measure μμ over the source space D⊂RD⊂R, we decompose HH as the sum of a subspace of centered functions for μμ and its orthogonal in HH. This decomposition leads to a special case of ANOVA kernels, for which the functional ANOVA representation of the best predictor can be elegantly derived, either in an interpolation or regularization framework. The proposed kernels appear to be particularly convenient for analyzing the effect of each (group of) variable(s) and computing sensitivity indices without recursivity.

Flow-R, a model for susceptibility mapping of debris flows and other gravitational hazards at a regional scale

The development of susceptibility maps for debris flows is of primary importance due to population pressure in hazardous zones. However, hazard assessment by process-based modelling at a regional scale is difficult due to the complex nature of the phenomenon, the variability of local controlling factors, and the uncertainty in modelling parameters. A regional assessment must consider a simplified approach that is not highly parameter dependant and that can provide zonation with minimum data requirements. A distributed empirical model has thus been developed for regional susceptibility assessments using essentially a digital elevation model (DEM). The model is called Flow-R for Flow path assessment of gravitational hazards at a Regional scale (available free of charge under http://www.flow-r.org) and has been successfully applied to different case studies in various countries with variable data quality. It provides a substantial basis for a preliminary susceptibility assessment at a regional scale. The model was also found relevant to assess other natural hazards such as rockfall, snow avalanches and floods. The model allows for automatic source area delineation, given user criteria, and for the assessment of the propagation extent based on various spreading algorithms and simple frictional laws. We developed a new spreading algorithm, an improved version of Holmgren's direction algorithm, that is less sensitive to small variations of the DEM and that is avoiding over-channelization, and so produces more realistic extents. The choices of the datasets and the algorithms are open to the user, which makes it compliant for various applications and dataset availability. Amongst the possible datasets, the DEM is the only one that is really needed for both the source area delineation and the propagation assessment; its quality is of major importance for the results accuracy. We consider a 10 m DEM resolution as a good compromise between processing time and quality of results. However, valuable results have still been obtained on the basis of lower quality DEMs with 25 m resolution.

Detailed analysis of sequence changes occurring during vlsE antigenic variation in the mouse model of Borrelia burgdorferi infection.

Lyme disease Borrelia can infect humans and animals for months to years, despite the presence of an active host immune response. The vls antigenic variation system, which expresses the surface-exposed lipoprotein VlsE, plays a major role in B. burgdorferi immune evasion. Gene conversion between vls silent cassettes and the vlsE expression site occurs at high frequency during mammalian infection, resulting in sequence variation in the VlsE product. In this study, we examined vlsE sequence variation in B. burgdorferi B31 during mouse infection by analyzing 1,399 clones isolated from bladder, heart, joint, ear, and skin tissues of mice infected for 4 to 365 days. The median number of codon changes increased progressively in C3H/HeN mice from 4 to 28 days post infection, and no clones retained the parental vlsE sequence at 28 days. In contrast, the decrease in the number of clones with the parental vlsE sequence and the increase in the number of sequence changes occurred more gradually in severe combined immunodeficiency (SCID) mice. Clones containing a stop codon were isolated, indicating that continuous expression of full-length VlsE is not required for survival in vivo; also, these clones continued to undergo vlsE recombination. Analysis of clones with apparent single recombination events indicated that recombinations into vlsE are nonselective with regard to the silent cassette utilized, as well as the length and location of the recombination event. Sequence changes as small as one base pair were common. Fifteen percent of recovered vlsE variants contained "template-independent" sequence changes, which clustered in the variable regions of vlsE. We hypothesize that the increased frequency and complexity of vlsE sequence changes observed in clones recovered from immunocompetent mice (as compared with SCID mice) is due to rapid clearance of relatively invariant clones by variable region-specific anti-VlsE antibody responses.

Genetically determined heterogeneity of lung disease in a mouse model of airway mucus obstruction

Mucus clearance is an important airway innate defense mechanism. Airway-targeted overexpression of the epithelial Na(+) channel β-subunit [encoded by sodium channel nonvoltage gated 1, beta subunit (Scnn1b)] in mice [Scnn1b-transgenic (Tg) mice] increases transepithelial Na(+) absorption and dehydrates the airway surface, which produces key features of human obstructive lung diseases, including mucus obstruction, inflammation, and air-space enlargement. Because the first Scnn1b-Tg mice were generated on a mixed background, the impact of genetic background on disease phenotype in Scnn1b-Tg mice is unknown. To explore this issue, congenic Scnn1b-Tg mice strains were generated on C57BL/6N, C3H/HeN, BALB/cJ, and FVB/NJ backgrounds. All strains exhibited a two- to threefold increase in tracheal epithelial Na(+) absorption, and all developed airway mucus obstruction, inflammation, and air-space enlargement. However, there were striking differences in neonatal survival, ranging from 5 to 80% (FVB/NJvariable Clara cell necrotic degeneration in neonatal intrapulmonary airways and a variable incidence of pulmonary hemorrhage and lung atelectasis. The spontaneous occurrence of a high surviving BALB/cJ line, which exhibited delayed onset of Na(+) hyperabsorption, provided evidence that: 1) air-space enlargement and postnatal death were only present when Na(+) hyperabsorption occurred early, and 2) inflammation and mucus obstruction developed whenever Na(+) hyperabsorption was expressed. In summary, the genetic context and timing of airway innate immune dysfunction critically determines lung disease phenotype. These mouse strains may be useful to identify key modifier genes and pathways.

Detailed analysis of sequence changes occurring during vlsE antigenic variation in the mouse model of Borrelia burgdorferi infection.

Lyme disease Borrelia can infect humans and animals for months to years, despite the presence of an active host immune response. The vls antigenic variation system, which expresses the surface-exposed lipoprotein VlsE, plays a major role in B. burgdorferi immune evasion. Gene conversion between vls silent cassettes and the vlsE expression site occurs at high frequency during mammalian infection, resulting in sequence variation in the VlsE product. In this study, we examined vlsE sequence variation in B. burgdorferi B31 during mouse infection by analyzing 1,399 clones isolated from bladder, heart, joint, ear, and skin tissues of mice infected for 4 to 365 days. The median number of codon changes increased progressively in C3H/HeN mice from 4 to 28 days post infection, and no clones retained the parental vlsE sequence at 28 days. In contrast, the decrease in the number of clones with the parental vlsE sequence and the increase in the number of sequence changes occurred more gradually in severe combined immunodeficiency (SCID) mice. Clones containing a stop codon were isolated, indicating that continuous expression of full-length VlsE is not required for survival in vivo; also, these clones continued to undergo vlsE recombination. Analysis of clones with apparent single recombination events indicated that recombinations into vlsE are nonselective with regard to the silent cassette utilized, as well as the length and location of the recombination event. Sequence changes as small as one base pair were common. Fifteen percent of recovered vlsE variants contained "template-independent" sequence changes, which clustered in the variable regions of vlsE. We hypothesize that the increased frequency and complexity of vlsE sequence changes observed in clones recovered from immunocompetent mice (as compared with SCID mice) is due to rapid clearance of relatively invariant clones by variable region-specific anti-VlsE antibody responses.

A Model Study of the Seasonal Circulation in the Gulf of Maine

The Princeton Ocean Model is used to study the circulation in the Gulf of Maine and its seasonal transition in response to wind, surface heat flux, river discharge, and the M-2 tide. The model has an orthogonal-curvature linear grid in the horizontal with variable spacing from 3 km nearshore to 7 km offshore and 19 levels in the vertical. It is initialized and forced at the open boundary with model results from the East Coast Forecast System. The first experiment is forced by monthly climatological wind and heat flux from the Comprehensive Ocean Atmosphere Data Set; discharges from the Saint John, Penobscot, Kennebec, and Merrimack Rivers are added in the second experiment; the semidiurnal lunar tide (M-2) is included as part of the open boundary forcing in the third experiment. It is found that the surface heat flux plays an important role in regulating the annual cycle of the circulation in the Gulf of Maine. The spinup of the cyclonic circulation between April and June is likely caused by the differential heating between the interior gulf and the exterior shelf/slope region. From June to December the cyclonic circulation continues to strengthen, but gradually shrinks in size. When winter cooling erodes the stratification, the cyclonic circulation penetrates deeper into the water column. The circulation quickly spins down from December to February as most of the energy is consumed by bottom friction. While inclusion of river discharge changes details of the circulation pattern, the annual evolution of the circulation is largely unaffected. On the other hand, inclusion of the tide results in not only the anticyclonic circulation on Georges Bank but also modifications to the seasonal circulation.

Regulation of Phytoplankton Carbon to Chlorophyll Ratio By Light, Nutrients and Temperature in the Equatorial Pacific Ocean: A Basin-Scale Model

The complex effects of light, nutrients and temperature lead to a variable carbon to chlorophyll (C:Chl) ratio in phytoplankton cells. Using field data collected in the Equatorial Pacific, we derived a new dynamic model with a non-steady C:Chl ratio as a function of irradiance, nitrate, iron, and temperature. The dynamic model is implemented into a basin-scale ocean circulation-biogeochemistry model and tested in the Equatorial Pacific Ocean. The model reproduces well the general features of phytoplankton dynamics in this region. For instance, the simulated deep chlorophyll maximum (DCM) is much deeper in the western warm pool (similar to 100 m) than in the Eastern Equatorial Pacific (similar to 50 m). The model also shows the ability to reproduce chlorophyll, including not only the zonal, meridional and vertical variations, but also the interannual variability. This modeling study demonstrates that combination of nitrate and iron regulates the spatial and temporal variations in the phytoplankton C:Chl ratio in the Equatorial Pacific. Sensitivity simulations suggest that nitrate is mainly responsible for the high C:Chl ratio in the western warm pool while iron is responsible for the frontal features in the C:Chl ratio between the warm pool and the upwelling region. In addition, iron plays a dominant role in regulating the spatial and temporal variations of the C:Chl ratio in the Central and Eastern Equatorial Pacific. While temperature has a relatively small effect on the C:Chl ratio, light is primarily responsible for the vertical decrease of phytoplankton C:Chl ratio in the euphotic zone.

A Model Study of the Circulation in the Pearl River Estuary (PRE) and Its Adjacent Coastal Waters: 1. Simulations and Comparison with Observations

The Princeton Ocean Model is used to study the circulation features in the Pearl River Estuary and their responses to tide, river discharge, wind, and heat flux in the winter dry and summer wet seasons. The model has an orthogonal curvilinear grid in the horizontal plane with variable spacing from 0.5 km in the estuary to 1 km on the shelf and 15 sigma levels in the vertical direction. The initial conditions and the subtidal open boundary forcing are obtained from an associated larger-scale model of the northern South China Sea. Buoyancy forcing uses the climatological monthly heat fluxes and river discharges, and both the climatological monthly wind and the realistic wind are used in the sensitivity experiments. The tidal forcing is represented by sinusoidal functions with the observed amplitudes and phases. In this paper, the simulated tide is first examined. The simulated seasonal distributions of the salinity, as well as the temporal variations of the salinity and velocity over a tidal cycle are described and then compared with the in situ survey data from July 1999 and January 2000. The model successfully reproduces the main hydrodynamic processes, such as the stratification, mixing, frontal dynamics, summer upwelling, two-layer gravitational circulation, etc., and the distributions of hydrodynamic parameters in the Pearl River Estuary and coastal waters for both the winter and the summer season.

Plasticity to wind is modular and genetically variable in Arabidopsis thaliana

Thigmomorphogenesis, the characteristic phenotypic changes by which plants react to mechanical stress, is a widespread and probably adaptive type of phenotypic plasticity. However, little is known about its genetic basis and population variation. Here, we examine genetic variation for thigmomorphogenesis within and among natural populations of the model system Arabidopsis thaliana. Offspring from 17 field-collected European populations was subjected to three levels of mechanical stress exerted by wind. Overall, plants were remarkably tolerant to mechanical stress. Even high wind speed did not significantly alter the correlation structure among phenotypic traits. However, wind significantly affected plant growth and phenology, and there was genetic variation for some aspects of plasticity to wind among A. thaliana populations. Our most interesting finding was that phenotypic traits were organized into three distinct and to a large degree statistically independent covariance modules associated with plant size, phenology, and growth form, respectively. These phenotypic modules differed in their responsiveness to wind, in the degree of genetic variability for plasticity, and in the extent to which plasticity affected fitness. It is likely, therefore, that thigmomorphogenesis in this species evolves quasi-independently in different phenotypic modules.

Who Earns More and Why? A Multiple Mediation Model from Personality to Salary

Purpose The purpose of this study was to investigate multiple indirect Big Five personality influences on professionals’ annual salary while considering relevant mediators. These are the motivational variables of occupational self-efficacy and career-advancement goals, and the work status variable of contractual work hours. The motivational and work status variables were conceptualized as serial mediators (Big Five → occupational self-efficacy/career-advancement goals → contractual work hours → annual salary). Design/Methodology/Approach We realized a 4 year longitudinal survey study with 432 participants and three points of measurement. We assessed personality prior to the mediators and the mediators prior to annual salary. Findings Results showed that except for openness the other Big Five personality traits exerted indirect influences on annual salary. Career-advancement goals mediated influences of conscientiousness (+), extraversion (+), and agreeableness (−). Occupational self-efficacy mediated influences of neuroticism (–) and conscientiousness (+). Because the influence of occupational self-efficacy on annual salary was fully mediated by contractual work hours, indirect personality influences via occupational self-efficacy always included contractual work hours in a serial mediation. Implications These findings underline the importance of distal personality traits for career success. They give further insights into direct and indirect relationships between personality, goal content, self-efficacy beliefs, and an individual’s career progress. Originality/Value Previous research predominantly investigated direct Big Five influences on salary, and it analyzed cross-sectional data. This study is one of the first to investigate multiple indirect Big Five influences on salary in a longitudinal design. The findings support process-oriented theories of personality influences on career outcomes.

Investigation of retinal morphology alterations using spectral domain optical coherence tomography in a mouse model of retinal branch and central retinal vein occlusion.

Retinal vein occlusion is a leading cause of visual impairment. Experimental models of this condition based on laser photocoagulation of retinal veins have been described and extensively exploited in mammals and larger rodents such as the rat. However, few reports exist on the use of this paradigm in the mouse. The objective of this study was to investigate a model of branch and central retinal vein occlusion in the mouse and characterize in vivo longitudinal retinal morphology alterations using spectral domain optical coherence tomography. Retinal veins were experimentally occluded using laser photocoagulation after intravenous application of Rose Bengal, a photo-activator dye enhancing thrombus formation. Depending on the number of veins occluded, variable amounts of capillary dropout were seen on fluorescein angiography. Vascular endothelial growth factor levels were markedly elevated early and peaked at day one. Retinal thickness measurements with spectral domain optical coherence tomography showed significant swelling (p<0.001) compared to baseline, followed by gradual thinning plateauing two weeks after the experimental intervention (p<0.001). Histological findings at day seven correlated with spectral domain optical coherence tomography imaging. The inner layers were predominantly affected by degeneration with the outer nuclear layer and the photoreceptor outer segments largely preserved. The application of this retinal vein occlusion model in the mouse carries several advantages over its use in other larger species, such as access to a vast range of genetically modified animals. Retinal changes after experimental retinal vein occlusion in this mouse model can be non-invasively quantified by spectral domain optical coherence tomography, and may be used to monitor effects of potential therapeutic interventions.

Transient Earth system responses to cumulative carbon dioxide emissions: linearities, uncertainties, and probabilities in an observation-constrained model ensemble

Information on the relationship between cumulative fossil CO2 emissions and multiple climate targets is essential to design emission mitigation and climate adaptation strategies. In this study, the transient response of a climate or environmental variable per trillion tonnes of CO2 emissions, termed TRE, is quantified for a set of impact-relevant climate variables and from a large set of multi-forcing scenarios extended to year 2300 towards stabilization. An  ∼ 1000-member ensemble of the Bern3D-LPJ carbon–climate model is applied and model outcomes are constrained by 26 physical and biogeochemical observational data sets in a Bayesian, Monte Carlo-type framework. Uncertainties in TRE estimates include both scenario uncertainty and model response uncertainty. Cumulative fossil emissions of 1000 Gt C result in a global mean surface air temperature change of 1.9 °C (68 % confidence interval (c.i.): 1.3 to 2.7 °C), a decrease in surface ocean pH of 0.19 (0.18 to 0.22), and a steric sea level rise of 20 cm (13 to 27 cm until 2300). Linearity between cumulative emissions and transient response is high for pH and reasonably high for surface air and sea surface temperatures, but less pronounced for changes in Atlantic meridional overturning, Southern Ocean and tropical surface water saturation with respect to biogenic structures of calcium carbonate, and carbon stocks in soils. The constrained model ensemble is also applied to determine the response to a pulse-like emission and in idealized CO2-only simulations. The transient climate response is constrained, primarily by long-term ocean heat observations, to 1.7 °C (68 % c.i.: 1.3 to 2.2 °C) and the equilibrium climate sensitivity to 2.9 °C (2.0 to 4.2 °C). This is consistent with results by CMIP5 models but inconsistent with recent studies that relied on short-term air temperature data affected by natural climate variability.

Continuous eclogite melting and variable refertilisation in upwelling heterogeneous mantle

Large-scale tectonic processes introduce a range of crustal lithologies into the Earth's mantle. These lithologies have been implicated as sources of compositional heterogeneity in mantle-derived magmas. The model being explored here assumes the presence of widely dispersed fragments of residual eclogite (derived from recycled oceanic crust), stretched and stirred by convection in the mantle. Here we show with an experimental study that these residual eclogites continuously melt during upwelling of such heterogeneous mantle and we characterize the melting reactions and compositional changes in the residue minerals. The chemical exchange between these partial melts and more refractory peridotite leads to a variably metasomatised mantle. Re-melting of these metasomatised peridotite lithologies at given pressures and temperatures results in diverse melt compositions, which may contribute to the observed heterogeneity of oceanic basalt suites. We also show that heterogeneous upwelling mantle is subject to diverse local freezing, hybridization and carbonate-carbon-silicate redox reactions along a mantle adiabat.

Variable phenotypic expressivity in inbred retinal degeneration mouse lines: A comparative study of C3H/HeOu and FVB/N rd1 mice

PURPOSE Recent advances in optogenetics and gene therapy have led to promising new treatment strategies for blindness caused by retinal photoreceptor loss. Preclinical studies often rely on the retinal degeneration 1 (rd1 or Pde6b(rd1)) retinitis pigmentosa (RP) mouse model. The rd1 founder mutation is present in more than 100 actively used mouse lines. Since secondary genetic traits are well-known to modify the phenotypic progression of photoreceptor degeneration in animal models and human patients with RP, negligence of the genetic background in the rd1 mouse model is unwarranted. Moreover, the success of various potential therapies, including optogenetic gene therapy and prosthetic implants, depends on the progress of retinal degeneration, which might differ between rd1 mice. To examine the prospect of phenotypic expressivity in the rd1 mouse model, we compared the progress of retinal degeneration in two common rd1 lines, C3H/HeOu and FVB/N. METHODS We followed retinal degeneration over 24 weeks in FVB/N, C3H/HeOu, and congenic Pde6b(+) seeing mouse lines, using a range of experimental techniques including extracellular recordings from retinal ganglion cells, PCR quantification of cone opsin and Pde6b transcripts, in vivo flash electroretinogram (ERG), and behavioral optokinetic reflex (OKR) recordings. RESULTS We demonstrated a substantial difference in the speed of retinal degeneration and accompanying loss of visual function between the two rd1 lines. Photoreceptor degeneration and loss of vision were faster with an earlier onset in the FVB/N mice compared to C3H/HeOu mice, whereas the performance of the Pde6b(+) mice did not differ significantly in any of the tests. By postnatal week 4, the FVB/N mice expressed significantly less cone opsin and Pde6b mRNA and had neither ERG nor OKR responses. At 12 weeks of age, the retinal ganglion cells of the FVB/N mice had lost all light responses. In contrast, 4-week-old C3H/HeOu mice still had ERG and OKR responses, and we still recorded light responses from C3H/HeOu retinal ganglion cells until the age of 24 weeks. These results show that genetic background plays an important role in the rd1 mouse pathology. CONCLUSIONS Analogous to human RP, the mouse genetic background strongly influences the rd1 phenotype. Thus, different rd1 mouse lines may follow different timelines of retinal degeneration, making exact knowledge of genetic background imperative in all studies that use rd1 models.