Mocarts: a lightweight radiation transport simulator for easy handling of complex sensing geometries

In functional neuroimaging (fNIRS), elaborated sensing geometries pairing multiple light sources and detectors arranged over the tissue surface are needed. A variety of software tools for probing forward models of radiation transport in tissue exist, but their handling of sensing geometries and specification of complex tissue architectures is, most times, cumbersome. In this work, we introduce a lightweight simulator, Monte Carlo Radiation Transport Simulator (MOCARTS) that attends these demands for simplifying specification of tissue architectures and complex sensing geometries. An object-oriented architecture facilitates such goal. The simulator core is evolved from the Monte Carlo Multi-Layer (mcml) tool but extended to support multi-channel simulations. Verification against mcml yields negligible error (RMSE~4-10e-9) over a photon trajectory. Full simulations show concurrent validity of the proposed tool. Finally, the ability of the new software to simulate multi-channel sensing geometries and to define biological tissue models in an intuitive nested-hierarchy way are exemplified

Investigating the biological properties of carbohydrate derived fulvic acid (CHD-FA) as a potential novel therapy for the management of oral biofilm infections.

Background: A number of oral diseases, including periodontitis, derive from microbial biofilms and are associated with increased antimicrobial resistance. Despite the widespread use of mouthwashes being used as adjunctive measures to control these biofilms, their prolonged use is not recommended due to various side effects. Therefore, alternative broad-spectrum antimicrobials that minimise these effects are highly sought after. Carbohydrate derived fulvic acid (CHD-FA) is an organic acid which has previously demonstrated to be microbiocidal against Candida albicans biofilms, therefore, the aims of this study were to evaluate the antibacterial activity of CHD-FA against orally derived biofilms and to investigate adjunctive biological effects.<p></p> Methods: Minimum inhibitory concentrations were evaluated for CHD-FA and chlorhexidine (CHX) against a range of oral bacteria using standardised microdilution testing for planktonic and sessile. Scanning electron microscopy was also employed to visualise changes in oral biofilms after antimicrobial treatment. Cytotoxicity of these compounds was assessed against oral epithelial cells, and the effect of CHD-FA on host inflammatory markers was assessed by measuring mRNA and protein expression.<p></p> Results: CHD-FA was highly active against all of the oral bacteria tested, including Porphyromonas gingivalis, with a sessile minimum inhibitory concentration of 0.5%. This concentration was shown to kill multi-species biofilms by approximately 90%, levels comparable to that of chlorhexidine (CHX). In a mammalian cell culture model, pretreatment of epithelial cells with buffered CHD-FA was shown to significantly down-regulate key inflammatory mediators, including interleukin-8 (IL-8), after stimulation with a multi-species biofilm.<p></p> Conclusions: Overall, CHD-FA was shown to possess broad-spectrum antibacterial activity, with a supplementary function of being able to down-regulate inflammation. These properties offer an attractive spectrum of function from a naturally derived compound, which could be used as an alternative topical treatment strategy for oral biofilm diseases. Further studies in vitro and in vivo are required to determine the precise mechanism by which CHD-FA modulates the host immune response.<p></p&gt

Mass hierarchy, mass gap and corrections to Newton's law on thick branes with Poincare symmetry

We consider a scalar thick brane configuration arising in a 5D theory of gravity coupled to a self-interacting scalar field in a Riemannian manifold. We start from known classical solutions of the corresponding field equations and elaborate on the physics of the transverse traceless modes of linear fluctuations of the classical background, which obey a Schroedinger-like equation. We further consider two special cases in which this equation can be solved analytically for any massive mode with m^2>0, in contrast with numerical approaches, allowing us to study in closed form the massive spectrum of Kaluza-Klein (KK) excitations and to compute the corrections to Newton's law in the thin brane limit. In the first case we consider a solution with a mass gap in the spectrum of KK fluctuations with two bound states - the massless 4D graviton free of tachyonic instabilities and a massive KK excitation - as well as a tower of continuous massive KK modes which obey a Legendre equation. The mass gap is defined by the inverse of the brane thickness, allowing us to get rid of the potentially dangerous multiplicity of arbitrarily light KK modes. It is shown that due to this lucky circumstance, the solution of the mass hierarchy problem is much simpler and transparent than in the (thin) Randall-Sundrum (RS) two-brane configuration. In the second case we present a smooth version of the RS model with a single massless bound state, which accounts for the 4D graviton, and a sector of continuous fluctuation modes with no mass gap, which obey a confluent Heun equation in the Ince limit. (The latter seems to have physical applications for the first time within braneworld models). For this solution the mass hierarchy problem is solved as in the Lykken-Randall model and the model is completely free of naked singularities.Comment: 25 pages in latex, no figures, content changed, corrections to Newton's law included for smooth version of RS model and an author adde

CD98hc facilitates B cell proliferation and adaptive humoral immunity.

The proliferation of antigen-specific lymphocytes and resulting clonal expansion are essential for adaptive immunity. We report here that B cell-specific deletion of the heavy chain of CD98 (CD98hc) resulted in lower antibody responses due to total suppression of B cell proliferation and subsequent plasma cell formation. Deletion of CD98hc did not impair early B cell activation but did inhibit later activation of the mitogen-activated protein kinase Erk1/2 and downregulation of the cell cycle inhibitor p27. Reconstitution of CD98hc-deficient B cells with CD98hc mutants showed that the integrin-binding domain of CD98hc was required for B cell proliferation but that the amino acid-transport function of CD98hc was dispensable for this. Thus, CD98hc supports integrin-dependent rapid proliferation of B cells. We propose that the advantage of adaptive immunity favored the appearance of CD98hc in vertebrates

Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline

Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality

Chitin Modulates Innate Immune Responses of Keratinocytes

Chitin, after cellulose the second most abundant polysaccharide in nature, is an essential component of exoskeletons of crabs, shrimps and insects and protects these organisms from harsh conditions in their environment. Unexpectedly, chitin has been found to activate innate immune cells and to elicit murine airway inflammation. The skin represents the outer barrier of the human host defense and is in frequent contact with chitin-bearing organisms, such as house-dust mites or flies. The effects of chitin on keratinocytes, however, are poorly understood. We hypothesized that chitin stimulates keratinocytes and thereby modulates the innate immune response of the skin. Here we show that chitin is bioactive on primary and immortalized keratinocytes by triggering production of pro-inflammatory cytokines and chemokines. Chitin stimulation further induced the expression of the Toll-like receptor (TLR) TLR4 on keratinocytes at mRNA and protein level. Chitin-induced effects were mainly abrogated when TLR2 was blocked, suggesting that TLR2 senses chitin on keratinocytes. We speculate that chitin-bearing organisms modulate the innate immune response towards pathogens by upregulating secretion of cytokines and chemokines and expression of MyD88-associated TLRs, two major components of innate immunity. The clinical relevance of this mechanism remains to be defined

Differential Glucose-Regulation of MicroRNAs in Pancreatic Islets of Non-Obese Type 2 Diabetes Model Goto-Kakizaki Rat

The Goto-Kakizaki (GK) rat is a well-studied non-obese spontaneous type 2 diabetes (T2D) animal model characterized by impaired glucose-stimulated insulin secretion (GSIS) in the pancreatic beta cells. MicroRNAs (miRNAs) are short regulatory RNAs involved in many fundamental biological processes. We aim to identify miRNAs that are differentially-expressed in the pancreatic islets of the GK rats and investigate both their short- and long term glucose-dependence during glucose-stimulatory conditions