Spatial and frequency domain effects of defects in 1D photonic crystal

The aim of this paper is to present the analysis of influence of defects in 1D photonic crystal (PC) on the density of states and simultaneously spontaneous emission, in both spatial and frequency domains. In our investigations we use an analytic model of 1D PC with defects. Our analysis reveals how presence of a defect causes a defect mode to appear. We show that a defect in 1D PC has local character, being negligible in regions of PC situated far from the defected elementary cell. We also analyze the effect of multiple defects, which lead to photonic band gap splitting.Comment: presented at International Workshop on Physics of Photonic Crystals and Metamaterials, Brussels, Belgium, 12-13.06.200

Constant mean curvature solutions of the Einstein-scalar field constraint equations on asymptotically hyperbolic manifolds

We follow the approach employed by Y. Choquet-Bruhat, J. Isenberg and D. Pollack in the case of closed manifolds and establish existence and non-existence results for the Einstein-scalar field constraint equations on asymptotically hyperbolic manifolds.Comment: 15 page

Reverse genetics in Candida albicans predicts ARF cycling is essential for drug resistance and virulence

Peer reviewedPublisher PD

novoBreak: local assembly for breakpoint detection in cancer genomes.

We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions

A Systematic Review of Proton Therapy for the Management of Nasopharyngeal Cancer

PURPOSE: With improved technology, more patients with nasopharyngeal cancer (NPC) are receiving definitive treatment with proton therapy, which allows greater sparing of dose to normal tissues without compromising efficacy. As there is no randomized data, the purpose of this study was to systematically review the available literature on proton therapy in this setting, focusing on the toxicity endpoints. MATERIALS AND METHODS: A systematic search using PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines was conducted in 5 databases: PubMed, Embase, SCOPUS, Web of Science, and the Cochrane Central Register of Controlled Trials. A total of 491 studies were found on the topic of NPC and proton therapy. Following independent study selection by 2 investigators, 9 studies were found to have sufficient focus and relevance to be incorporated into the systematic review. RESULTS: All 9 studies were retrospective and examined only NPC patients except for one that also included paranasal sinus cancer. One study was a reirradiation study. Four studies used 3D or double scatter technique, while all others used intensity-modulated proton therapy. Oncologic outcomes were similar to intensity-modulated radiation therapy (IMRT) rates, with 2-year local and regional progression-free survival (LRFS) ranging from 84% to 100%, 2-year progression-free survival (PFS) ranging from 75% to 88.9%, and 2-year overall survival (OS) ranging from 88% to 95% in the up-front setting. Four comparison studies with IMRT found significantly lower feeding tube rates (20% versus 65%, P = .015; and 14% versus 85%, P < .001) with proton therapy as well as lower mucositis (G2 46% versus 70%, P = .019; and G3 11% versus 76%, P = .0002). All other acute and late effects were largely improved with proton therapy but not statistically significant. CONCLUSIONS: NPC patients receiving proton therapy maintain good outcomes with improved toxicity profile, likely due to sparing of dose to normal structures. Prospective studies are ongoing to better quantify the magnitude

Magnetic fluctuations and superconducting properties of CaKFe4As4 studied by 75As NMR

We report $^{75}$As nuclear magnetic resonance (NMR) studies on a new iron-based superconductor CaKFe$_4$As$_4$ with $T_{\rm c}$ = 35 K. $^{75}$As NMR spectra show two distinct lines corresponding to the As(1) and As(2) sites close to the K and Ca layers, respectively, revealing that K and Ca layers are well ordered without site inversions. We found that nuclear quadrupole frequencies $\nu_{\rm Q}$ of the As(1) and As(2) sites show an opposite temperature ($T$) dependence. Nearly $T$ independent behavior of the Knight shifts $K$ are observed in the normal state, and a sudden decrease in $K$ in the superconducting (SC) state clearly evidences spin-singlet Cooper pairs. $^{75}$As spin-lattice relaxation rates 1/$T_1$ show a power law $T$ dependence with different exponents for the two As sites. The isotropic antiferromagnetic spin fluctuations characterized by the wavevector ${\bf q}$ = ($\pi$, 0) or (0, $\pi$) in the single-iron Brillouin zone notation are revealed by 1/$T_1T$ and $K$ measurements. Such magnetic fluctuations are necessary to explain the observed temperature dependence of the $^{75}$As quadrupole frequencies, as evidenced by our first-principles calculations. In the SC state, 1/$T_1$ shows a rapid decrease below $T_{\rm c}$ without a Hebel-Slichter peak and decreases exponentially at low $T$, consistent with an $s^{\pm}$ nodeless two-gap superconductor.Comment: 9 pages, 6 figures, accepted for publication in Phys.Rev.

An integrated approach to supply chain risk analysis

Despite the increasing attention that supply chain risk management is receiving by both researchers and practitioners, companies still lack a risk culture. Moreover, risk management approaches are either too general or require pieces of information not regularly recorded by organisations. This work develops a risk identification and analysis methodology that integrates widely adopted supply chain and risk management tools. In particular, process analysis is performed by means of the standard framework provided by the Supply Chain Operations Reference Model, the risk identification and analysis tasks are accomplished by applying the Risk Breakdown Structure and the Risk Breakdown Matrix, and the effects of risk occurrence on activities are assessed by indicators that are already measured by companies in order to monitor their performances. In such a way, the framework contributes to increase companies' awareness and communication about risk, which are essential components of the management of modern supply chains. A base case has been developed by applying the proposed approach to a hypothetical manufacturing supply chain. An in-depth validation will be carried out to improve the methodology and further demonstrate its benefits and limitations. Future research will extend the framework to include the understanding of the multiple effects of risky events on different processe

A Biochemical Genomics Screen for Substrates of Ste20p Kinase Enables the In Silico Prediction of Novel Substrates

The Ste20/PAK family is involved in many cellular processes, including the regulation of actin-based cytoskeletal dynamics and the activation of MAPK signaling pathways. Despite its numerous roles, few of its substrates have been identified. To better characterize the roles of the yeast Ste20p kinase, we developed an in vitro biochemical genomics screen to identify its substrates. When applied to 539 purified yeast proteins, the screen reported 14 targets of Ste20p phosphorylation. We used the data resulting from our screen to build an in silico predictor to identify Ste20p substrates on a proteome-wide basis. Since kinase-substrate specificity is often mediated by additional binding events at sites distal to the phosphorylation site, the predictor uses the presence/absence of multiple sequence motifs to evaluate potential substrates. Statistical validation estimates a threefold improvement in substrate recovery over random predictions, despite the lack of a single dominant motif that can characterize Ste20p phosphorylation. The set of predicted substrates significantly overrepresents elements of the genetic and physical interaction networks surrounding Ste20p, suggesting that some of the predicted substrates are in vivo targets. We validated this combined experimental and computational approach for identifying kinase substrates by confirming the in vitro phosphorylation of polarisome components Bni1p and Bud6p, thus suggesting a mechanism by which Ste20p effects polarized growth

Switchable Membrane Remodeling and Antifungal Defense by Metamorphic Chemokine XCL1

Antimicrobial peptides (AMPs) are a class of molecules which generally kill pathogens via preferential cell membrane disruption. Chemokines are a family of signaling proteins that direct immune cell migration and share a conserved α–β tertiary structure. Recently, it was found that a subset of chemokines can also function as AMPs, including CCL20, CXCL4, and XCL1. It is therefore surprising that machine learning based analysis predicts that CCL20 and CXCL4’s α-helices are membrane disruptive, while XCL1’s helix is not. XCL1, however, is the only chemokine known to be a metamorphic protein which can interconvert reversibly between two distinct native structures (a β-sheet dimer and the α–β chemokine structure). Here, we investigate XCL1’s antimicrobial mechanism of action with a focus on the role of metamorphic folding. We demonstrate that XCL1 is a molecular “Swiss army knife” that can refold into different structures for distinct context-dependent functions: whereas the α–β chemokine structure controls cell migration by binding to G-Protein Coupled Receptors (GPCRs), we find using small angle X-ray scattering (SAXS) that only the β-sheet and unfolded XCL1 structures can induce negative Gaussian curvature (NGC) in membranes, the type of curvature topologically required for membrane permeation. Moreover, the membrane remodeling activity of XCL1’s β-sheet structure is strongly dependent on membrane composition: XCL1 selectively remodels bacterial model membranes but not mammalian model membranes. Interestingly, XCL1 also permeates fungal model membranes and exhibits anti-Candida activity in vitro, in contrast to the usual mode of antifungal defense which requires Th17 mediated cell-based responses. These observations suggest that metamorphic XCL1 is capable of a versatile multimodal form of antimicrobial defense