Model reduction by separation of variables: A comparison between hierarchical model reduction and proper generalized decomposition

Hierarchical Model reduction and Proper Generalized Decomposition both exploit separation of variables to perform a model reduction. After setting the basics, we exemplify these techniques on some standard elliptic problems to highlight pros and cons of the two procedures, both from a methodological and a numerical viewpoint

Zinc ions alter morphology and chitin deposition in an ericoid fungus

A sterile mycelium PS IV, an ascomycete capable of establishing ericoid mycorrhizas, was used to investigate how zinc ions affect the cellular mechanisms of fungal growth. Asignificant reduction of the fungal biomass was observed in the presence of millimolar zinc concentrations; this mirrored conspicuous changes in hyphal morphology which led to apical swellings and increased branching in the subapical parts. Specific probes for fluorescence and electron microscopy localised chitin, the main cell wall polysaccharide, on the inner part of the fungal wall and on septa in control specimens. In Zn-treated mycelium, hyphal walls were thicker and a more intense chitin labelling was detected on the transverse walls. Aquantitative assay showed a significant increase in the amount of chitin in metal- treated hyphae

Optimising Boltzmann codes for the Planck era

High precision measurements of the Cosmic Microwave Background (CMB) anisotropies, as can be expected from the Planck satellite, will require high-accuracy theoretical predictions as well. One possible source of theoretical uncertainty is the numerical error in the output of the Boltzmann codes used to calculate angular power spectra. In this work, we carry out an extensive study of the numerical accuracy of the public Boltzmann code CAMB, and identify a set of parameters which determine the error of its output. We show that at the current default settings, the cosmological parameters extracted from data of future experiments like Planck can be biased by several tenths of a standard deviation for the six parameters of the standard Lambda-CDM model, and potentially more seriously for extended models. We perform an optimisation procedure that leads the code to achieve sufficient precision while at the same time keeping the computation time within reasonable limits. Our conclusion is that the contribution of numerical errors to the theoretical uncertainty of model predictions is well under control -- the main challenges for more accurate calculations of CMB spectra will be of an astrophysical nature instead.Comment: 13 pages, 4 figure

Widespread association between the ericoid mycorrhizal fungus Rhizoscyphus ericae and a leafy liverwort in the maritime and sub-Antarctic

A recent study identified a fungal isolate from the Antarctic leafy liverwort Cephaloziella varians as the ericoid mycorrhizal associate Rhizoscyphus ericae. However, nothing is known about the wider Antarctic distribution of R. ericae in C. varians, and inoculation experiments confirming the ability of the fungus to form coils in the liverwort are lacking. Using direct isolation and baiting with Vaccinium macrocarpon seedlings, fungi were isolated from C. varians sampled from eight sites across a 1875-km transect through sub- and maritime Antarctica. The ability of an isolate to form coils in aseptically grown C. varians was also tested. Fungi with 98–99% sequence identity to R. ericae internal transcribed spacer (ITS) region and partial large subunit ribosomal (r)DNA sequences were frequently isolated from C. varians at all sites sampled. The EF4/Fung5 primer set did not amplify small subunit rDNA from three of five R. ericae isolates, probably accounting for the reported absence of the fungus from C. varians in a previous study. Rhizoscyphus ericae was found to colonize aseptically-grown C. varians intracellularly, forming hyphal coils. This study shows that the association between R. ericae and C. varians is apparently widespread in Antarctica, and confirms that R. ericae is at least in part responsible for the formation of the coils observed in rhizoids of field-collected C. varians

A separated representation involving multiple time scales within the Proper Generalized Decomposition framework

Solutions of partial differential equations can exhibit multiple time scales. Standard discretization techniques are constrained to capture the finest scale to accurately predict the response of the system. In this paper, we provide an alternative route to circumvent prohibitive meshes arising from the necessity of capturing fine-scale behaviors. The proposed methodology is based on a time-separated representation within the standard Proper Generalized Decomposition, where the time coordinate is transformed into a multi-dimensional time through new separated coordinates, each representing one scale, while continuity is ensured in the scale coupling. For instance, when considering two different time scales, the governing Partial Differential Equation is commuted into a nonlinear system that iterates between the so-called microtime and macrotime, so that the time coordinate can be viewed as a 2D time. The macroscale effects are taken into account by means of a finite element-based macro-discretization, whereas the microscale effects are handled with unidimensional parent spaces that are replicated throughout the time domain. The resulting separated representation allows us a very fine time discretization without impacting the computational efficiency. The proposed formulation is explored and numerically verified on thermal and elastodynamic problems. © 2021, The Author(s)

Occurrence and characterization of a severe isolate of Watermelon mosaic virus from Argentina

More than 50 viruses have been reported in cucurbit crops worldwide. In Argentina, cucurbit viruses have been associated with important yield losses. The most prevalent and widespread potyvirus is Watermelon mosaic virus (WMV). WMV was detected in Argentina in all cucurbit species with high incidence. In this study, a WMV isolate (WMV 1 SDE FF) was obtained from a naturally infected squash associated with a severe outbreak on melon and squash crops in an important cucurbit growing area in Santiago del Estero province (Argentina), during a survey conducted in November 2012. The fully sequenced WMV 1 SDE FF genome consists of 10,027 nucleotides and shares 96 % nt identity and 98 % aa identity with the French isolates JF273464.1|C07–014 and EU660581.1|FMF00-LL1 of the WMV molecular group 3. Using the recombination detection program RDP4, two statistically significant recombination events were identified: event 1, an 830-nt long recombinant fragment in the putative P1 coding region, and event 2, a 4071-nt recombinant fragment detected across the HC Pro, P3 and CI coding regions. The putative parental sequences detected for event 1 were the EU660586.1| FBR04–37 (major parent) and JF273468.1|C07–284 (minor parent), both from France. Putative parental sequences for event 2 were JX079685.1| WMV-ShanXi (major parent) and HQ384216.1|Dendrobium (minor parent), from China and USA, respectively. To our knowledge, this is the first complete genome of an Argentine WMV isolate. Our results provide evidence that WMV 1 SDE FF is the causal agent of the strong outbreak reported in melon and squash fields in recent years.Inst. Patología VegetalFil: Perotto, Maria Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Celli, Marcos Giovani. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pozzi, Elizabeth Alicia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Luciani, Cecilia E. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Conci, Vilma Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Impacts to Quail Space Use and Demographics from Oil and Gas Development

Southern Texas contains some of the last relatively unfragmented habitat for northern bobwhite (Colinus virginianus; hereafter, bobwhite) and scaled quail (Callipepla squamata) in the United States. Development of the Eagle Ford Shale hydrocarbon formation in this region could negatively impact quail and their habitat. Our objective was to examine the indirect effects of oil and gas activity (traffic and noise) on bobwhite and scaled quail on 2 private ranches in southern Texas. In 2015 and 2016, we radio-marked bobwhite and scaled quail in 2 areas where oil and gas activity was occurring (disturbed treatment) and 2 areas where little oil and gas activity occurred (undisturbed treatment). We measured vehicle passages and modeled noise propagation from oil and gas infrastructure at 2 biologically relevant frequencies (250 Hz and 1,000 Hz) in our study area to quantify oil and gas disturbance and examine its effects on quail space use (site selection and home range size) and demographics (survival, nest success, and density). Bobwhite and scaled quail selected areas 0–200 m and \u3e425 m, respectively, from the primary, high-traffic roads in the disturbed treatment. In the undisturbed treatment, bobwhite and scaled quail selected areas 0–425 m and 0–300 m from primary roads, respectively. Bobwhite and scaled quail selected areas with sound levels 0–1.6 and 0–2.2 dB above ambient levels at the 250-Hz frequency level, respectively. At 1,000 Hz, bobwhite and scaled quail selected areas with sound levels 0–2 and 0–3.2 dB above ambient levels, respectively. We found no evidence that disturbance variables affected bobwhite and scaled quail home range size, survival, or density. We found bobwhite nest success decreased as sound levels (dB) at 250 Hz increased; we found no relationship between nest success and disturbance for scaled quail, possibly as they avoided major oil and gas disturbances. In calculations of the total footprint of quail habitat loss, indirect loss due to oil and gas activity needs to be considered in addition to direct loss due to conversion of rangeland to oil and gas infrastructure