Detailed analysis of the effects of stencil spatial variations with arbitrary high-order finite-difference Maxwell solver

Due to discretization effects and truncation to finite domains, many electromagnetic simulations present non-physical modifications of Maxwell's equations in space that may generate spurious signals affecting the overall accuracy of the result. Such modifications for instance occur when Perfectly Matched Layers (PMLs) are used at simulation domain boundaries to simulate open media. Another example is the use of arbitrary order Maxwell solver with domain decomposition technique that may under some condition involve stencil truncations at subdomain boundaries, resulting in small spurious errors that do eventually build up. In each case, a careful evaluation of the characteristics and magnitude of the errors resulting from these approximations, and their impact at any frequency and angle, requires detailed analytical and numerical studies. To this end, we present a general analytical approach that enables the evaluation of numerical discretization errors of fully three-dimensional arbitrary order finite-difference Maxwell solver, with arbitrary modification of the local stencil in the simulation domain. The analytical model is validated against simulations of domain decomposition technique and PMLs, when these are used with very high-order Maxwell solver, as well as in the infinite order limit of pseudo-spectral solvers. Results confirm that the new analytical approach enables exact predictions in each case. It also confirms that the domain decomposition technique can be used with very high-order Maxwell solver and a reasonably low number of guard cells with negligible effects on the whole accuracy of the simulation.Comment: 33 pages, 14 figure

EFFECTS OF NON-LETHAL CONCENTRATIONS OF BIOACTIVE COMPOUNDS ON PLANT-RELATED BIOFILMS

It has been estimated that at least 99 % of the world\u2019s microbial biomass exists in form of biofilm, a complex differentiated surface-associated community embedded in a self-produced polymeric matrix enabling microorganisms to develop coordinated and efficient survival strategies. Biofilm formation is a dynamic and cyclical process involving attachment, maturation and a final dispersal phase, and these steps are initiated by a variety of signals. Despite their positive effects in some cases, biofilms can be detrimental in different environmental domains since microorganisms are able to colonize almost all types of surfaces both abiotic and biotic, leading to consequences in terms of social and economic impact. These include human tissues, implantable medical devices, natural aquatic systems, plants, food and industrial lines. Once biofilm is formed, its eradication becomes difficult because its resilience to environmental stresses, disinfectants, and antimicrobial treatments. Plants support a diverse array of microorganisms that exist in form of biofilms. Even if in some cases the association with plants leads to beneficial interactions promoting plant growth, inducing plant defense mechanisms and preventing the deleterious effects of pathogenic microorganisms, in other cases they have a significant negative impact. For instance, in agriculture, plant colonization of fungi and bacteria in form of biofilm is a cause of plant diseases, affecting crop quality and productivity. Indeed, despite the planktonic growth, biofilm lifestyle improves microbial resistance to antimicrobials up to several orders of magnitude, often reducing the possibility of treating biofilm effectively. In addition, due to the worrisome consequences related to the use of these substances on human health and on their persistence in the environment, increasingly regulations are arising to limit antimicrobial application. Furthermore, in addition to the principles of integrated pest management (IPM) embraced by the worldwide legislation aims to recommend alternative approaches to the application of pesticides, an innovative approach could be the use of biocide-free bioactive compounds characterized by novel targets, unique modes of action and properties that are separate from those currently highlighted in the use of antimicrobials. Indeed, the application of non-lethal doses of bio-inspired molecules able to interfere with specific key-steps involved in the biofilm formation process has been suggested as a complementary/alternative strategy to hinder biofilm formation. In addition, this approach also lead to deprive microorganisms of their virulence factors without affecting their viability and decreasing the selection pressure for biocides resistance. In this PhD thesis, the in vitro effects of non-lethal concentrations of several bioactive compounds were evaluated on the biofilm formation of different plant-associated microorganisms. Specifically, the aim of this work was to provide new effective preventive or integrated solutions against bacterial and fungal biofilm formation. In chapter III, the methanol extracts obtained by different plant portions of three seagrass species collected in Vietnam and in India (Enhalus acoroides, Halophila ovalis and Halodule pinifolia) were investigated for their effects in mediating non-lethal interactions on sessile Escherichia coli and Candida albicans cultures taken as models of bacterial and fungal biofilms respectively. The study was focused on anti-biofilm activities of seagrass extracts, without killing cells. Seagrass extracts appeared to be more effective in deterring microbial adhesion on hydrophobic surfaces than on hydrophilic. Results revealed that E. acoroides leaf extract proved to be the most promising extract among those tested. Indeed, the selected non-lethal concentrations of E. acoroides leaf extract were found to exert an anti-biofilm effect on C. albicans and E. coli biofilm in the first phase of biofilm genesis, opening up the possibility of developing preventive strategies to hinder the adhesion of microbial cells to surfaces. The leaf extract also affected the dispersion and maturation steps in C. albicans and E. coli respectively, suggesting an important role in cell signaling processes. Methanolic extracts were characterized and major phenolic compounds were identified by MS/MS analysis, showing the unique profile of the E. acoroides leaf extract. In chapter IV, two essential oils (PK and PK-IK) derived from two cultivars of Perilla frutescens, an annual short day plant widely used in therapeutics in the traditional medicine as well as in food preparations in Asian countries. Essential oils were extracted from the leaves and were characterized. Subsequeltly, their ability to affect biofilm formation of the phytopathogenic model fungi Colletotrichum musae, Fusarium dimerum and F. oxysporum have been studied. PK and PK-IK neither inhibited fungal growth nor were they utilized as a carbon energy source. In addition, PK and PK-IK essential oils showed excellent anti-biofilm performances inhibiting conidia germination and reducing conidia adhesion. Furthermore, they revealed a magnificent anti-biofilm effect even during biofilm maturation, affecting biofilm structural development, with a reduction of dried weight, extracellular polysaccharides and proteins. In all cases PK-IK displayed better activity than PK. Thus, the anti-biofilm effects were exploited with a non-lethal mechanism. This research supported the spreading of PK and PK-IK essential oils as biocide-free agents suitable for a preventive or integrative approach for sustainable crop protection. Lastly, in chapter V, a non-lethal concentration of N-Acetylcysteine (NAC) was evaluated on the biofilm formation of Xylella fastidiosa, a phytopathogen bacterium that causes a range of economically important plant diseases worldwide and that has been recently found in Italy in olive plants, where it causes the olive quick decline syndrome (OQSD). NAC is a naturally occurring compound found in several vegetables (including garlic, onion, peppers and asparagus) and it is mostly known in clinical area, in which it is employed at lethal concentrations in the treatment of human diseases due to its ability to reduce bacterial adhesion, inhibit the production of extracellular polysaccharides and promote the dispersion of pre-formed mature biofilms. In this study, N-Acetylcysteine (NAC) was tested for its ability to affect biofilm response of X. fastidiosa CoDiRO strain, mimicking a preventive, a curative and a combination of both approaches. The not-lethal dose 0.08 mg/ml was chosen as representative of plant concentration after its application. NAC did not alter planktonic bacterial growth but promoted biofilm formation in terms of biofilm biomass (above 62 %) and matrix polysaccharides (above 53%) through a ROS-mediated mechanism. Additionally, NAC was not able to destroy X. fastidiosa biofilm when already established on the surface but rather, it was suitable to contain the biofilm infection limiting biofilm dispersal. On the contrary, a combination of both preventive and curative approach has been found promising in biofilm dissolving making it more vulnerable

An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (10pJ/word on-die to 10,000pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use more and more cores on each compute nodes ("fat nodes") that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignement constraints and avoids gather/scatter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of $\times 2$ to $\times 2.5$ speed-up in double precision for particle shape factor of order $1$ to $3$. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles).Comment: 36 pages, 5 figure

Interleukin-1β Mediates Metalloproteinase-Dependent Renal Cell Carcinoma Tumor Cell Invasion through the Activation of CCAAT Enhancer Binding Protein β

Effective treatment of metastatic renal cell carcinoma (RCC) remains a major medical concern, as these tumors are refractory to standard therapies and prognosis is poor. Although molecularly targeted therapies have shown some promise in the treatment of this disease, advanced RCC tumors often develop resistance to these drugs. Dissecting the molecular mechanisms underlying the progression to advanced disease is necessary to design alternative and improved treatment strategies. Tumor-associated macrophages (TAMs) found in aggressive RCC tumors produce a variety of inflammatory cytokines, including interleukin-1 b (IL-1b). Moreover, the presence of TAMs and high serum levels of IL-1b in RCC patients correlate with advanced disease. We hypothesized that IL-1b in the tumor microenvironment promotes the development of aggressive RCC tumors by directing affecting tumor epithelial cells. To address this, we investigated the role of IL-1b in mediating RCC tumor cell invasion as a measure of tumor progression. We report that IL-1b induced tumor cell invasion of RCC cells through a process that was dependent on the activity of matrix metalloproteinases (MMPs) and was independent of migration rate. Specifically, IL-1b induced the expression of MMP-1, MMP-3, MMP-10, and MT1-MMP in a mechanism dependent on IL-1b activation of the transcription factor CCAAT enhancer binding protein b (CEBP b). Consistent with its role in MMP gene expression, CEBP b knockdown significantly reduced invasion, but not migration, of RCC tumor cells. These results identify the IL-1b /CEBP b/MMP pathway as a putative target in the design of anti-metastatic therapies for the treatment of advanced RCC

Adoption and Implementation of the Surgical Safety Checklist: Improving Safety in an Italian Teaching Hospital

Although it is known that clinical risk management tools such as the Surgical Checklist lead to greater safety for patients and protection for the operators, clinical risk management units have much work to do to implement and spread the use of quality health care tools

Resonant, broadband and highly efficient optical frequency conversion in semiconductor nanowire gratings at visible and UV wavelengths

Using a hydrodynamic approach we examine bulk- and surface-induced second and third harmonic generation from semiconductor nanowire gratings having a resonant nonlinearity in the absorption region. We demonstrate resonant, broadband and highly efficient optical frequency conversion: contrary to conventional wisdom, we show that harmonic generation can take full advantage of resonant nonlinearities in a spectral range where nonlinear optical coefficients are boosted well beyond what is achievable in the transparent, long-wavelength, non-resonant regime. Using femtosecond pulses with approximately 500 MW/cm2 peak power density, we predict third harmonic conversion efficiencies of approximately 1% in a silicon nanowire array, at nearly any desired UV or visible wavelength, including the range of negative dielectric constant. We also predict surface second harmonic conversion efficiencies of order 0.01%, depending on the electronic effective mass, bistable behavior of the signals as a result of a reshaped resonance, and the onset fifth order nonlinear effects. These remarkable findings, arising from the combined effects of nonlinear resonance dispersion, field localization, and phase-locking, could significantly extend the operational spectral bandwidth of silicon photonics, and strongly suggest that neither linear absorption nor skin depth should be motivating factors to exclude either semiconductors or metals from the list of useful or practical nonlinear materials in any spectral range.Comment: 12 pages, 4 figure