Nuclear quantum effects in ab initio dynamics: theory and experiments for lithium imide

Owing to their small mass, hydrogen atoms exhibit strong quantum behavior even at room temperature. Including these effects in first principles calculations is challenging, because of the huge computational effort required by conventional techniques. Here we present the first ab-initio application of a recently-developed stochastic scheme, which allows to approximate nuclear quantum effects inexpensively. The proton momentum distribution of lithium imide, a material of interest for hydrogen storage, was experimentally measured by inelastic neutron scattering experiments and compared with the outcome of quantum thermostatted ab initio dynamics. We obtain favorable agreement between theory and experiments for this purely quantum mechanical property, thereby demonstrating that it is possible to improve the modelling of complex hydrogen-containing materials without additional computational effort

Current exposure of Italian women of reproductive age to PFOS and PFOA: a human biomonitoring study

Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) concentrations were determined in serum samples collected in 2011-2012 from 549 nulliparous Italian women of reproductive age who resided in six different Italian Regions. Assessment of exposure to perfluorinated compounds was part of a large human biomonitoring study (Project Life Plus "Womenbiopop") that aimed at examining the exposure of women of reproductive age to priority organic pollutants. The median concentrations of PFOS and PFOA were 2.43, and 1.55ngg-1, respectively. Significant differences in the concentrations of both compounds were observed among the six Regions. Women from central Italy had the highest levels of both compounds, followed by women from northern Italy, and southern Italy. No differences in the PFOS concentrations were found between women from urban/industrial areas and women from rural areas, whereas the levels of PFOA were significantly higher in women residing in urban/industrial areas than in women residing in rural areas. Taken together, the observed concentrations confirm that the overall exposure of the Italian population is among the lowest observed in industrialized countries. A downward temporal trend in exposure was observed for both compounds when comparing the results from the present study with those assessed in a study conducted in 2008

Diverse Temperate Bacteriophage Carriage in Clostridium difficile 027 Strains

The hypervirulent Clostridium difficile ribotype 027 can be classified into subtypes, but it unknown if these differ in terms of severity of C. difficile infection (CDI). Genomic studies of C. difficile 027 strains have established that they are rich in mobile genetic elements including prophages. This study combined physiological studies, electron microscopy analysis and molecular biology to determine the potential role of temperate bacteriophages in disease and diversity of C. difficile 027.We induced prophages from 91 clinical C. difficile 027 isolates and used transmission electron microscopy and pulsed-field gel electrophoresis to characterise the bacteriophages present. We established a correlation between phage morphology and subtype. Morphologically distinct tailed bacteriophages belonging to Myoviridae and Siphoviridae were identified in 63 and three isolates, respectively. Dual phage carriage was observed in four isolates. In addition, there were inducible phage tail-like particles (PT-LPs) in all isolates. The capacity of two antibiotics mitomycin C and norfloxacin to induce prophages was compared and it was shown that they induced specific prophages from C. difficile isolates. A PCR assay targeting the capsid gene of the myoviruses was designed to examine molecular diversity of C. difficile myoviruses. Phylogenetic analysis of the capsid gene sequences from eight ribotypes showed that all sequences found in the ribotype 027 isolates were identical and distinct from other C. difficile ribotypes and other bacteria species.A diverse set of temperate bacteriophages are associated with C. difficile 027. The observed correlation between phage carriage and the subtypes suggests that temperate bacteriophages contribute to the diversity of C. difficile 027 and may play a role in severity of disease associated with this ribotype. The capsid gene can be used as a tool to identify C. difficile myoviruses present within bacterial genomes

Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens

Salmonella is a food-borne pathogen often linked to poultry sources, causing gastrointestinal infections in humans, with the numbers of multidrug resistant (MDR) isolates increasing globally. To gain insight into the genomic diversity of common serovars and their potential contribution to disease, we characterized antimicrobial resistance genes, and virulence factors encoded in 88 UK and 55 Thai isolates from poultry; the presence of virulence genes was detected through an extensive virulence determinants database compiled in this study. Long-read sequencing of three MDR isolates, each from a different serovar, was used to explore the links between virulence and resistance. To augment current control methods, we determined the sensitivity of isolates to 22 previously characterized Salmonella bacteriophages. Of the 17 serovars included, Salmonella Typhimurium and its monophasic variants were the most common, followed by S. Enteritidis, S. Mbandaka, and S. Virchow. Phylogenetic analysis of Typhumurium and monophasic variants showed poultry isolates were generally distinct from pigs. Resistance to sulfamethoxazole and ciprofloxacin was highest in isolates from the UK and Thailand, respectively, with 14–15% of all isolates being MDR. We noted that >90% of MDR isolates were likely to carry virulence genes as diverse as the srjF, lpfD, fhuA, and stc operons. Long-read sequencing revealed the presence of global epidemic MDR clones in our dataset, indicating they are possibly widespread in poultry. The clones included MDR ST198 S. Kentucky, harboring a Salmonella Genomic Island-1 (SGI)-K, European ST34 S. 1,4,[5],12:i:-, harboring SGI-4 and mercury-resistance genes, and a S. 1,4,12:i:- isolate from the Spanish clone harboring an MDR-plasmid. Testing of all isolates against a panel of bacteriophages showed variable sensitivity to phages, with STW-77 found to be the most effective. STW-77 lysed 37.76% of the isolates, including serovars important for human clinical infections: S. Enteritidis (80.95%), S. Typhimurium (66.67%), S. 1,4,[5],12:i:- (83.3%), and S. 1,4,12: i:- (71.43%). Therefore, our study revealed that combining genomics and phage sensitivity assays is promising for accurately identifying and providing biocontrols for Salmonella to prevent its dissemination in poultry flocks and through the food chain to cause infections in humans

Design optimization of waveguide bends in photonic crystals

In this paper, a fast and robust optimization scheme is presented and applied to the optimal design of planar photonic crystals. It is based on a parallel hybrid (stochastic-deterministic) algorithm coupled to a semi-analytic solution of full Maxwell equations by multiple scattering technique. The numerical results of the optimal design of different waveguide bends are presented

Fragility assessment of unreinforced masonry walls undergoing earthquake-induced local failure mechanisms

Damage observations from strong earthquakes show that unreinforced masonry buildings have exhibited recurrent local failure mechanisms and constitute a serious life-safety hazard. This contribution is aimed at evaluating the fragility functions for unreinforced masonry walls in the presence of local failure mechanisms induced by out-of plane loading The out-of-plane response consists of the overturning of the entire or apart of the wall insufficiently connected to the rest of the structure. The wall can be idealized as a number of rigid bodies undergoing rocking motion. They are assumed to undergo one-sided rocking or vertical spanning strip wall displacing as an assembly of a coupled rigid body. In this study, we use a set of 44 ground motions from earthquake events that occurred in Italy from 1972 to 2017. For any given wall undergoing a specific collapse mechanism, the probability of collapse is evaluated through a Multiple Stripe Analysis (MSA). Then, a fragility curve is fitted to the MSA datapoints. The procedure outlined may be extended to obtain typological fragility functions as a combination of the fragility curves corresponding to the various mechanisms analyzed. A preliminary application of the procedure to the historical centre of Ferrara, Italy, is described

Impact of Phage CDHS-1 on the Transcription, Physiology and Pathogenicity of a <i>Clostridioides difficile</i> Ribotype 027 Strain, R20291

All known Clostridioides difficile phages encode integrases rendering them potentially able to lyse or lysogenise bacterial strains. Here, we observed the infection of the siphovirus, CDHS-1 on a ribotype 027 strain, R20291 and determined the phage and bacterial gene expression profiles, and impacts of phage infection on bacterial physiology and pathogenicity. Using RNA-seq and RT-qPCR we analysed transcriptomic changes during early, mid-log and late phases of phage replication at an MOI of 10. The phage has a 20 min latent period, takes 80 min to lyse cells and a burst size of ~37. All phage genes are highly expressed during at least one time point. The Cro/C1-transcriptional regulator, ssDNA binding protein and helicase are expressed early, the holin is expressed during the mid-log phase and structural proteins are expressed from mid-log to late phase. Most bacterial genes, particularly the metabolism and toxin production/regulatory genes, were downregulated from early phage replication. Phage-resistant strains and lysogens showed reduced virulence during Galleria mellonella colonization as ascertained by the larval survival and expression of growth (10), reproduction (2) and infection (2) marker genes. These data suggest that phage infection both reduces colonization and negatively impacts bacterial pathogenicity, providing encouraging data to support the development of this phage for therapy to treat C. difficile infection