Weighted Dirac combs with pure point diffraction

A class of translation bounded complex measures, which have the form of weighted Dirac combs, on locally compact Abelian groups is investigated. Given such a Dirac comb, we are interested in its diffraction spectrum which emerges as the Fourier transform of the autocorrelation measure. We present a sufficient set of conditions to ensure that the diffraction measure is a pure point measure. Simultaneously, we establish a natural link to the theory of the cut and project formalism and to the theory of almost periodic measures. Our conditions are general enough to cover the known theory of model sets, but also to include examples such as the visible lattice points.Comment: 44 pages; several corrections and improvement

Pure point diffraction and cut and project schemes for measures: The smooth case

We present cut and project formalism based on measures and continuous weight functions of sufficiently fast decay. The emerging measures are strongly almost periodic. The corresponding dynamical systems are compact groups and homomorphic images of the underlying torus. In particular, they are strictly ergodic with pure point spectrum and continuous eigenfunctions. Their diffraction can be calculated explicitly. Our results cover and extend corresponding earlier results on dense Dirac combs and continuous weight functions with compact support. They also mark a clear difference in terms of factor maps between the case of continuous and non-continuous weight functions.Comment: 30 page

A new perturbative expansion of the time evolution operator associated with a quantum system

A novel expansion of the evolution operator associated with a -- in general, time-dependent -- perturbed quantum Hamiltonian is presented. It is shown that it has a wide range of possible realizations that can be fitted according to computational convenience or to satisfy specific requirements. As a remarkable example, the quantum Hamiltonian describing a laser-driven trapped ion is studied in detail.Comment: 32 pages; modified version with examples of my previous paper quant-ph/0404056; to appear on the J. of Optics B: Quantum and Semiclassical Optics, Special Issue on 'Optics and Squeeze Transformations after Einstein

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive

Drosophila Immunity: Analysis of PGRP-SB1 Expression, Enzymatic Activity and Function

Peptidoglycan is an essential and specific component of the bacterial cell wall and therefore is an ideal recognition signature for the immune system. Peptidoglycan recognition proteins (PGRPs) are conserved from insects to mammals and able to bind PGN (non-catalytic PGRPs) and, in some cases, to efficiently degrade it (catalytic PGRPs). In Drosophila, several non-catalytic PGRPs function as selective peptidoglycan receptors upstream of the Toll and Imd pathways, the two major signalling cascades regulating the systemic production of antimicrobial peptides. Recognition PGRPs specifically activate the Toll pathway in response to Lys-type peptidoglycan found in most Gram-positive bacteria and the Imd pathway in response to DAP-type peptidoglycan encountered in Gram-positive bacilli-type bacteria and in Gram-negative bacteria. Catalytic PGRPs on the other hand can potentially reduce the level of immune activation by scavenging peptidoglycan. In accordance with this, PGRP-LB and PGRP-SC1A/B/2 have been shown to act as negative regulators of the Imd pathway. In this study, we report a biochemical and genetic analysis of PGRP-SB1, a catalytic PGRP. Our data show that PGRP-SB1 is abundantly secreted into the hemolymph following Imd pathway activation in the fat body, and exhibits an enzymatic activity towards DAP-type polymeric peptidoglycan. We have generated a PGRP-SB1/2 null mutant by homologous recombination, but its thorough phenotypic analysis did not reveal any immune function, suggesting a subtle role or redundancy of PGRP-SB1/2 with other molecules. Possible immune functions of PGRP-SB1 are discussed

Phenolic, polysaccharidic and lipidic fractions of mushrooms from northeast Portugal: chemical compounds with antioxidant properties

Mushrooms do not constitute a significant portion of the human diet, but their consumption continues to increase due to their functional benefits and presence of bioactive compounds. Some of those compounds can be found in the phenolic, polysaccharidic and lipidic fractions of edible and inedible species. Herein, those fractions of five wild mushrooms (Coprinopsis atramentaria, Lactarius bertillonii, Lactarius vellereus, Rhodotus palmatus and Xerocomus chrysenteron) from Northeast Portugal were studied for their chemical composition and antioxidant properties. Protocatechuic, p-hydroxybenzoic, p-coumaric and cinnamic acids were found in the phenolic fraction, ramnose, xylose, fucose, arabinose, fructose, glucose, manose, mannitol, sucrose, maltose and trehalose were quantified in polysaccharidic fraction, linoleic and stearic (only in Lactarius sp.) acids, and β- and γ-tocopherols were the main compounds in the lipidic fraction. C. atramentaria and X. chrysenteron phenolic fractions gave the highest free radical scavenging activity, reducing properties and lipid peroxidation inhibition in brain homogenates, which is in agreement with its highest content in total phenolics. Furthermore, among the polysaccharidic fractions C. atramentaria also gave the highest antioxidant activity, which is accordingly with its highest total polysaccharides content and sugars obtained after hydrolysis.The authors are grateful to Fundação para a Ciência e a Tecnologia (FCT, Portugal) and COMPETE/QREN/EU (research project PTDC/AGR-ALI/110062/2009) for financial support. L. Barros (BPD/4609/2008) and S.A. Heleno (BD/70304/2010) also thank FCT, POPH-QREN and FSE. The GIP-USAL is financially supported by the Spanish Ministerio de Ciencia e Innovación through the Consolider-Ingenio 2010 Programme (FUN-C-FOOD, CSD2007-00063), and Junta de Castilla y León (Grupo de Investigación de Excelencia, GR133)

Duration of Treatment for Pseudomonas aeruginosa Bacteremia : a Retrospective Study

Introduction: There is no consensus regarding optimal duration of antibiotic therapy for Pseudomonas aeruginosa bacteremia. We aimed to evaluate the impact of short antibiotic course. Methods: We present a retrospective multicenter study including patients with P. aeruginosa bacteremia during 2009-2015. We evaluated outcomes of patients treated with short (6-10 days) versus long (11-15 days) antibiotic courses. The primary outcome was a composite of 30-day mortality or bacteremia recurrence and/or persistence. Univariate and inverse probability treatment-weighted (IPTW) adjusted multivariate analysis for the primary outcome was performed. To avoid immortal time bias, the landmark method was used. Results: We included 657 patients; 273 received a short antibiotic course and 384 a long course. There was no significant difference in baseline characteristics of patients. The composite primary outcome occurred in 61/384 patients in the long-treatment group (16%) versus 32/273 in the short-treatment group (12%) (p = 0.131). Mortality accounted for 41/384 (11%) versus 25/273 (9%) of cases, respectively. Length of hospital stay was significantly shorter in the short group [median 13 days, interquartile range (IQR) 9-21 days, versus median 15 days, IQR 11-26 days, p = 0.002]. Ten patients in the long group discontinued antibiotic therapy owing to adverse events, compared with none in the short group. On univariate and multivariate analyses, duration of therapy was not associated with the primary outcome. Conclusions: In this retrospective study, 6-10 days of antibiotic course for P. aeruginosa bacteremia were as effective as longer courses in terms of survival and recurrence. Shorter therapy was associated with reduced length of stay and less drug discontinuation