Canard-like phenomena in piecewise-smooth Van der Pol systems

We show that a nonlinear, piecewise-smooth, planar dynamical system can exhibit canard phenomena. Canard solutions and explosion in nonlinear, piecewise-smooth systems can be qualitatively more similar to the phenomena in smooth systems than piecewise-linear systems, since the nonlinearity allows for canards to transition from small cycles to canards ``with heads." The canards are born of a bifurcation that occurs as the slow-nullcline coincides with the splitting manifold. However, there are conditions under which this bifurcation leads to a phenomenon called super-explosion, the instantaneous transition from a globally attracting periodic orbit to relaxations oscillations. Also, we demonstrate that the bifurcation---whether leading to canards or super-explosion---can be subcritical.Comment: 17 pages, 11 figure

An unstructured CD-grid variational formulation for sea ice dynamics

For the numerical simulation of earth system models, Arakawa grids are largely employed. A quadrilateral mesh is assumed for their classical definition, and different types of grids are identified depending on the location of the discretized quantities. The B-grid has both velocity components at the center of a cell, the C-grid places the velocity components on the edges in a staggered fashion, and the D-grid is a ninety-degree rotation of a C-grid. Historically, B-grid formulations of sea ice dynamics have been dominant because they have matched the grid type used by ocean models. In recent years, as ocean models have increasingly progressed to C-grids, sea ice models have followed suit on quadrilateral meshes, but few if any implementations of unstructured C-grid sea ice models have been developed. In this work, we present an unstructured CD-grid type formulation of the elastic-viscous-plastic rheology, where the velocity unknowns are located at the edges, rather than at the vertices, as in the B-grid. The notion of a CD-grid has been recently introduced and assumes that the velocity components are co-located at the edges. The mesh cells in our analysis have $n$ sides, with $n$ greater than or equal to four. Numerical results are included to investigate the features of the proposed method. Our framework of choice is the Model for Prediction Across Scales (MPAS) within E3SM, the climate model of the U.S. Department of Energy, although our approach is general and could be applied to other models as well. While MPAS-Seaice is currently defined on a B-grid, MPAS-Ocean runs on a C-grid, hence interpolation operators are heavily used when coupled simulations are performed. The discretization introduced here aims at transitioning the dynamics of MPAS-Seaice to a CD-grid, to ultimately facilitate improved coupling with MPAS-Ocean and reduce numerical errors associated with this communication

Biosafety Research for Non-Target Organism Risk Assessment of RNAi-Based GE Plants

RNA interference, or RNAi, refers to a set of biological processes that make use of conserved cellular machinery to silence genes. Although there are several variations in the source and mechanism, they are all triggered by double stranded RNA (dsRNA) which is processed by a protein complex into small, single stranded RNA, referred to as small interfering RNAs (siRNA) with complementarity to sequences in genes targeted for silencing. The use of the RNAi mechanism to develop new traits in plants has fueled a discussion about the environmental safety of the technology for these applications, and this was the subject of a symposium session at the 13th ISBGMO in Cape Town, South Africa. This paper continues that discussion by proposing research areas that may be beneficial for future environmental risk assessments of RNAi-based genetically modified plants, with a particular focus on non-target organism assessment

Oceanographic setting and short-timescale environmental variability at an Arctic seamount sponge ground

Mass occurrences of large sponges, or ‘sponge grounds’, are found globally in a range of oceanographic settings. Interest in these grounds is growing because of their ecological importance as hotspots of biodiversity, their role in biogeochemical cycling and bentho-pelagic coupling, the biotechnological potential of their constituent sponges, and their perceived vulnerability to physical disturbance and environmental change. Little is known about the environmental conditions required for sponges to persist and for grounds to form, and very few studies have explicitly characterised and interpreted the importance of oceanographic conditions. Here, results are presented of the first observational oceanographic campaign at a known sponge ground on the Schultz Massif Seamount (SMS; Arctic Mid-Ocean Ridge, Greenland / Norwegian Seas). The campaign consisted of water column profiling and short-term deployment of a benthic lander. It was supported by multibeam echosounder bathymetry and remotely operated vehicle video surveys. The seamount summit hosted several environmental factors potentially beneficial to sponges. It occurred within relatively nutrient-rich waters and was regularly flushed from above with slightly warmer, oxygen-enriched Norwegian Arctic Intermediate Water. It was exposed to elevated suspended particulate matter levels and oscillating currents (with diurnal tidal frequency) likely to enhance food supply and prevent smothering of the sponges by sedimentation. Elevated chlorophyll a concentration was observed in lenses above the summit, which may indicate particle retention by seamount-scale circulation patterns. High sponge density and diversity observed on the summit is likely explained by the combination of several beneficial factors, the coincidence of which at the summit arises from interaction between seamount geomorphology, hydrodynamic regime, and water column structure. Neighbouring seamounts along the mid-ocean ridge are likely to present similarly complex oceanographic settings and, as with the SMS, associated sponge ground ecosystems may therefore be sensitive to changes over a particularly broad range of abiotic factor

BASP1 interacts with estrogen receptor α and modifies the tamoxifen response

AbstractTamoxifen binds to oestrogen receptor α (ERα) to elicit distinct responses that vary by cell/tissue type and status, but the factors that determine these differential effects are unknown. Here we report that the transcriptional corepressor BASP1 interacts with ERα and in breast cancer cells, this interaction is enhanced by tamoxifen. We find that BASP1 acts as a major selectivity factor in the transcriptional response of breast cancer cells to tamoxifen. In all, 40% of the genes that are regulated by tamoxifen in breast cancer cells are BASP1 dependent, including several genes that are associated with tamoxifen resistance. BASP1 elicits tumour-suppressor activity in breast cancer cells and enhances the antitumourigenic effects of tamoxifen treatment. Moreover, BASP1 is expressed in breast cancer tissue and is associated with increased patient survival. Our data have identified BASP1 as an ERα cofactor that has a central role in the transcriptional and antitumourigenic effects of tamoxifen.</jats:p

Regulation of genes affecting body size and innate immunity by the DBL-1/BMP-like pathway in Caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>Bone morphogenetic proteins (BMPs) are members of the conserved transforming growth factor β (TGFβ superfamily, and play many developmental and homeostatic roles. In <it>C. elegans</it>, a BMP-like pathway, the DBL-1 pathway, controls body size and is involved in innate immunity. How these functions are carried out, though, and what most of the downstream targets of this pathway are, remain unknown.</p> <p>Results</p> <p>We performed a microarray analysis and compared expression profiles of animals lacking the SMA-6 DBL-1 receptor, which decreases pathway signaling, with animals that overexpress DBL-1 ligand, which increases pathway signaling. Consistent with a role for DBL-1 in control of body size, we find positive regulation by DBL-1 of genes involved in physical structure, protein synthesis and degradation, and metabolism. However, cell cycle genes were mostly absent from our results. We also identified genes in a <it>hedgehog</it>-related pathway, which may comprise a secondary signaling pathway downstream of DBL-1 that controls body size. In addition, DBL-1 signaling up-regulates pro-innate immunity genes. We identified a reporter for DBL-1 signaling, which is normally repressed but is up-regulated when DBL-1 signaling is reduced.</p> <p>Conclusions</p> <p>Our results indicate that body size in <it>C. elegans </it>is controlled in part by regulation of metabolic processes as well as protein synthesis and degradation. This supports the growing body of evidence that suggests cell size is linked to metabolism. Furthermore, this study discovered a possible role for <it>hedgehog</it>-related pathways in transmitting the BMP-like signal from the hypodermis, where the core DBL-1 pathway components are required, to other tissues in the animal. We also identified the up-regulation of genes involved in innate immunity, clarifying the role of DBL-1 in innate immunity. One of the highly regulated genes is expressed at very low levels in wild-type animals, but is strongly up-regulated in Sma/Mab mutants, making it a useful reporter for DBL-1/BMP-like signaling in <it>C. elegans</it>.</p

Enhanced Cellular Immunity in Shrimp (Litopenaeus vannamei) after ‘Vaccination’

It has long been viewed that invertebrates rely exclusively upon a wide variety of innate mechanisms for protection from disease and parasite invasion and lack any specific acquired immune mechanisms comparable to those of vertebrates. Recent findings, however, suggest certain invertebrates may be able to mount some form of specific immunity, termed ‘specific immune priming’, although the mechanism of this is not fully understood (see Textbox S1). In our initial experiments, either formalin-inactivated Vibrio harveyi or sterile saline were injected into the main body cavity (haemocoel) of juvenile shrimp (Litopenaeus vannamei). Haemocytes (blood cells) from V. harveyi-injected shrimp were collected 7 days later and incubated with a 1∶1 mix of V. harveyi and an unrelated Gram positive bacterium, Bacillus subtilis. Haemocytes from ‘vaccinated’ shrimp showed elevated levels of phagocytosis of V. harveyi, but not B. subtilis, compared with those from saline-injected (non-immunised) animals. The increased phagocytic activity was characterised by a significant increase in the percentage of phagocytic cells. When shrimp were injected with B. subtilis rather than vibrio, there was no significant increase in the phagocytic activity of haemocytes from these animals in comparison to the non-immunised (saline injected) controls. Whole haemolymph (blood) from either ‘immunised’ or non-immunised’ shrimp was shown to display innate humoral antibacterial activity against V. harveyi that was absent against B. subtilis. However, there was no difference in the potency of antibacterial activity between V. harveyi-injected shrimp and control (saline injected) animals showing that ‘vaccination’ has no effect on this component of the shrimp's immune system. These results imply that the cellular immune system of shrimp, particularly phagocytosis, is capable of a degree of specificity and shows the phenomenon of ‘immune priming’ reported by other workers. However, in agreement with other studies, this phenomenon is not universal to all potential pathogens

Revisiting the washout period in the incident user study design: why 6–12 months may not be sufficient

The purpose of this study was to describe how washout period duration affects the size and accuracy of retrospective incident user cohorts