A note about the complexity of minimizing Nesterov's smooth Chebyshev–Rosenbrock function

This short note considers and resolves the apparent contradiction between known worst-case complexity results for first- and second-order methods for solving unconstrained smooth nonconvex optimization problems and a recent note by Jarre [On Nesterov's smooth Chebyshev–Rosenbrock function, Optim. Methods Softw. (2011)] implying a very large lower bound on the number of iterations required to reach the solution's neighbourhood for a specific problem with variable dimension.     

The MORPHEUS Heterogeneous Dynamically Reconfigurable Platform

Reconfigurable computing offers a wide range of low cost and efficient solutions for embedded systems. The proper choice of the reconfigurable device, the granularity of its processing elements and its memory architecture highly depend on the type of application and their data flow. Existing solutions either offer fine grain FPGAs, which rely on a hardware synthesis flow and offer the maximum degree of flexibility, or coarser grain solutions, which are usually more suitable for a particular type of data flow and applications. In this paper, we present the MORPHEUS architecture, a versatile reconfigurable heterogeneous System-on-Chip targeting streaming applications. The presented architecture exploits different reconfigurable technologies at several computation granularities that efficiently address the different applications needs. In order to efficiently exploit the presented architecture, we implemented a complete software solution to map C applications to the reconfigurable architecture. In this paper, we describe the complete toolset and provide concrete use cases of the architecture.     

Phylogeny of trichomonads based on partial sequences of large subunit rRNA and on cladistic analysis of morphological data

Several domains of large subunit rRNA from nine trichomonad species have been sequenced. Molecular phylogenies obtained with parsimony and distance methods demonstrate the trichomonads are a monophyletic group which branches very early in the eukaryotic tree. The topology of the trees is in general agreement with traditional views on evolutionary and systematic relationships of trichomonads. A clear dichotomy is noted between the subfamily Trichomonadinae and the subfamily Tritrichomonadinae. In the latter subfamily, a second division separates the "Tritrichomonas muris-type" species from the "Tritrichomonas augusta-type" ones. Previous evolutionary schemes in which the Monocercomonadidae were regarded as the most "primitive" and the Trichomonadidae as more "evolved" are not in agreement with our molecular data. The emergence of Monocercomonas and Hypotrichomonas at the base of the Tritrichomonas lineage suggests a secondary loss of some cytoskeletal structures, the costa and undulating membrane in these genera. This is corroborated by the early branching position of Trichomitus, which possesses a costa and an undulating membrane and has usually been placed among the Trichomonadidae on the basis of cytological characters. A cladistic analysis was applied to the available morphological characters in order to produce a hierarchical grouping of the taxa reflecting their morphological diversity.     

Multiplexed-Based Assessment of DNA Damage Response to Chemotherapies Using Cell Imaging Cytometry

The current methods for measuring the DNA damage response (DDR) are relatively labor-intensive and usually based on Western blotting, flow cytometry, and/or confocal immunofluorescence analyses. They require many cells and are often limited to the assessment of a single or few proteins. Here, we used the Celigo^® image cytometer to evaluate the cell response to DNA-damaging agents based on a panel of biomarkers associated with the main DDR signaling pathways. We investigated the cytostatic or/and the cytotoxic effects of these drugs using simultaneous propidium iodide and calcein-AM staining. We also describe new dedicated multiplexed protocols to investigate the qualitative (phosphorylation) or the quantitative changes of eleven DDR markers (H2AX, DNA-PKcs, ATR, ATM, CHK1, CHK2, 53BP1, NBS1, RAD51, P53, P21). The results of our study clearly show the advantage of using this methodology because the multiplexed-based evaluation of these markers can be performed in a single experiment using the standard 384-well plate format. The analyses of multiple DDR markers together with the cell cycle status provide valuable insights into the mechanism of action of investigational drugs that induce DNA damage in a time- and cost-effective manner due to the low amounts of antibodies and reagents required.     

An Overview of the Latest Metabolomics Studies on Atopic Eczema with New Directions for Study

Atopic eczema (AE) is an inflammatory skin disorder affecting approximately 20% of children worldwide and early onset can lead to asthma and allergies. Currently, the mechanisms of the disease are not fully understood. Metabolomics, the analysis of small molecules in the skin produced by the host and microbes, opens a window to observe the mechanisms of the disease which then may lead to new drug targets for AE treatment. Here, we review the latest advances in AE metabolomics, highlighting both the lipid and non-lipid molecules, along with reviewing the metabolites currently known to reside in the skin.     

Modified Fluoroquinolones as Antimicrobial Compounds Targeting Chlamydia trachomatis

Chlamydia trachomatis causes the most common sexually transmitted bacterial infection and trachoma, an eye infection. Untreated infections can lead to sequelae, such as infertility and ectopic pregnancy in women and blindness. We previously enhanced the antichlamydial activity of the fluoroquinolone ciprofloxacin by grafting a metal chelating moiety onto it. In the present study, we pursued this pharmacomodulation and obtained nanomolar active molecules (EC₅₀) against this pathogen. This gain in activity prompted us to evaluate the antibacterial activity of this family of molecules against other pathogenic bacteria, such as Neisseria gonorrhoeae and bacteria from the ESKAPE group. The results show that the novel molecules have selectively improved activity against C. trachomatis and demonstrate how the antichlamydial effect of fluoroquinolones can be enhanced.     

Characterization of a Cutibacterium acnes Camp Factor 1-Related Peptide as a New TLR-2 Modulator in In Vitro and Ex Vivo Models of Inflammation

Cutibacterium acnes (C. acnes) has been implicated in inflammatory acne where highly mutated Christie–Atkins–Munch–Petersen factor (CAMP)1 displays strong toll like receptor (TLR)-2 binding activity. Using specific antibodies, we showed that CAMP1 production was independent of C. acnes phylotype and involved in the induction of inflammation. We confirmed that TLR-2 bound both mutated and non-mutated recombinant CAMP1, and peptide array analysis showed that seven peptides (A14, A15, B1, B2, B3, C1 and C3) were involved in TLR-2 binding, located on the same side of the three-dimensional structure of CAMP1. Both mutated and non-mutated recombinant CAMP1 proteins induced the production of C-X-C motif chemokine ligand interleukin (CXCL)8/(IL)-8 in vitro in keratinocytes and that of granulocyte macrophage-colony stimulating factor (GM-CSF), tumor necrosis factor (TNF)-α, IL-1β and IL-10 in ex vivo human skin explants. Only A14, B1 and B2 inhibited the production of CXCL8/IL-8 by keratinocytes and that of (GM-CSF), TNF-α, IL-1β and IL-10 in human skin explants stimulated with rCAMP1 and C. acnes. Following pretreatment with B2, RNA sequencing on skin explants identified the 10 genes displaying the strongest differential expression as IL6, TNF, CXCL1, CXCL2, CXCL3, CXCL8, IL-1β, chemokine ligand (CCL)2, CCL4 and colony stimulating factor (CSF)2. We, thus, identified a new CAMP1-derived peptide as a TLR-2 modulator likely to be a good candidate for clinical evaluation.     

Control of food spoilage fungi by ethanol

This review discusses the effects of ethanol on the inhibition of growth and germination of fungi and on the inactivation of fungal spores. After a brief survey on the impact of spoilage fungi on the economy and food quality, the major applications of ethanol in controlling fruit decay and extending the shelf-life of food products are reviewed. Many parameters including minimum inhibitory concentration (MIC) and D-values for various moulds are included. The thermodynamic relationship between the liquid phase and the headspace and the mode of action of ethanol on fungi are explained. Due to their promising use as a fumigant, special attention is paid to ethanol vapours.     

Comparing the streaming of FGS encoded video at different aggregation levels: frame,GoP, and scene

Fine granularity scalability (FGS), a new coding technique that has recently been added to the MPEG‐4 video coding standard, allows for the flexible scaling of each individual video frame at very fine granularity. This flexibility makes FGS video very well suited for rate‐distortion optimized streaming mechanisms, which minimize the distortion (i.e. maximize the quality) of the streamed video by transmitting the optimal number of bits for each individual frame. The per‐frame optimization of the transmission schedule, however, puts a significant computational burden on video servers and intermediate streaming gateways. In this paper we investigate the rate‐distortion optimized streaming at different video frame aggregation levels. We find that compared to the optimization for each individual video frame, optimization at the level of video scenes reduces the computational effort dramatically, while reducing the video quality only very slightly. Copyright © 2005 John Wiley & Sons, Ltd.