A library of ab initio Raman spectra for automated identification of 2D materials

Raman spectroscopy is frequently used to identify composition, structure and layer thickness of 2D materials. Here, we describe an efficient first-principles workflow for calculating resonant first-order Raman spectra of solids within third-order perturbation theory employing a localized atomic orbital basis set. The method is used to obtain the Raman spectra of 733 different monolayers selected from the computational 2D materials database (C2DB). We benchmark the computational scheme against available experimental data for 15 known monolayers. Furthermore, we propose an automatic procedure for identifying a material based on an input experimental Raman spectrum and illustrate it for the cases of MoS$_2$ (H-phase) and WTe$_2$ (T$^\prime$-phase). The Raman spectra of all materials at different excitation frequencies and polarization configurations are freely available from the C2DB. Our comprehensive and easily accessible library of \textit{ab initio} Raman spectra should be valuable for both theoreticians and experimentalists in the field of 2D materialsComment: 17 pages, 7 figure

The impact of delirium on the prediction of in-hospital mortality in intensive care patients

Introduction: predictive models, such as acute physiology and chronic health evaluation II (APACHE-II), are widely used in intensive care units (ICUs) to estimate mortality. Although the presence of delirium is associated with a higher mortality in ICU patients, delirium is not part of the APACHE-II model. The aim of the current study was to evaluate whether delirium, present within 24 hours after ICU admission, improves the predictive value of the APACHE-II score.Methods: in a prospective cohort study 2116 adult patients admitted between February 2008 and February 2009 were screened for delirium with the confusion assessment method-ICU (CAM-ICU). Exclusion criteria were sustained coma and unable to understand Dutch. Logistic regression analysis was used to estimate the predicted probabilities in the model with and without delirium. Calibration plots and the Hosmer-Lemeshow test (HL-test) were used to assess calibration. The discriminatory power of the models was analyzed by the area under the receiver operating characteristics curve (AUC) and AUCs were compared using the Z-test.Results: 1740 patients met the inclusion criteria, of which 332 (19%) were delirious at the time of ICU admission or within 24 hours after admission. Delirium was associated with in-hospital mortality in unadjusted models, odds ratio (OR): 3.22 (95% confidence interval [CI]: 2.23 - 4.66). The OR between the APACHE-II and in-hospital mortality was 1.15 (95% CI 1.12 - 1.19) per point. The predictive accuracy of the APACHE-II did not improve after adding delirium, both in the total group as well as in the subgroup without cardiac surgery patients. The AUC of the APACHE model without delirium was 0.77 (0.73 - 0.81) and 0.78 (0.74 - 0.82) when delirium was added to the model. The z-value was 0.92 indicating no improvement in discriminative power, and the HL-test and calibration plots indicated no improvement in calibration.Conclusions: although delirium is a significant predictor of mortality in ICU patients, adding delirium as an additional variable to the APACHE-II model does not result in an improvement in its predictive estimate

Identification of genes and pathways associated with cytotoxic T lymphocyte infiltration of serous ovarian cancer

BACKGROUND: Tumour-infiltrating lymphocytes (TILs) are predictors of disease-specific survival (DSS) in ovarian cancer. It is largely unknown what factors contribute to lymphocyte recruitment. Our aim was to evaluate genes and pathways contributing to infiltration of cytotoxic T lymphocytes (CTLs) in advanced-stage serous ovarian cancer. METHODS: For this study global gene expression was compared between low TIL (n=25) and high TIL tumours (n=24). The differences in gene expression were evaluated using parametric T-testing. Selectively enriched biological pathways were identified with gene set enrichment analysis. Prognostic influence was validated in 157 late-stage serous ovarian cancer patients. Using immunohistochemistry, association of selected genes from identified pathways with CTL was validated. RESULTS: The presence of CTL was associated with 320 genes and 23 pathways (P<0.05). In addition, 54 genes and 8 pathways were also associated with DSS in our validation cohort. Immunohistochemical evaluation showed strong correlations between MHC class I and II membrane expression, parts of the antigen processing and presentation pathway, and CTL recruitment. CONCLUSION: Gene expression profiling and pathway analyses are valuable tools to obtain more understanding of tumour characteristics influencing lymphocyte recruitment in advanced-stage serous ovarian cancer. Identified genes and pathways need to be further investigated for suitability as therapeutic targets

Changes of the cosmic-ray mass composition in the 10^{14} - 10^{16} eV energy range

Changes of the cosmic-ray mass composition at the `knee' of the cosmic-ray flux spectrum near 10^{15} eV energy are investigated using data from ten Cosmic Ray Tracking (CRT) detectors and the HEGRA air-shower array on La Palma, Canary Islands. The analysis is based on the angular distribution of muons in air showers. Results can be easily expressed in terms of of primary cosmic rays. We find a rise of below 10^{15} eV, consistent with direct measurements. Simple cosmic-ray composition models are presented which are fully consistent with our results as well as the JACEE flux and composition measurements and the flux measurements of the Tibet AS-gamma collaboration.Comment: 22 pages, 11 Postscript figures, 2 tables. Accepted for publication in Astroparticle Physic

A Promiscuous DNA Packaging Machine from Bacteriophage T4

Packaged viral genome can be removed from bacteriophage T4 capsid and the capsid refilled with any double-stranded DNA, single or multiple molecules, using a powerful ATP-fueled DNA packaging machine

Evolution of Microstructure and Texture during Warm Rolling Of a Duplex Steel

The effect of warm rolling on the evolution of microstructure and texture in a duplex stainless steel (DSS) was investigated. For this purpose, a DSS steel was warm rolled up to 90 pct reduction in thickness at 498 K, 698 K, and 898 K (225 °C, 425 °C, and 625 °C). The microstructure with an alternate arrangement of deformed ferrite and austenite bands was observed after warm rolling; however, the microstructure after 90 pct warm rolling at 498 K and 898 K (225 °C and 625 °C) was more lamellar and uniform as compared to the rather fragmented and inhomogeneous structure observed after 90 pct warm rolling at 698 K (425 °C). The texture of ferrite in warm-rolled DSS was characterized by the presence of the RD (〈011〉//RD) and ND (〈111〉//ND) fibers. However, the texture of ferrite in DSS warm rolled at 698 K (425 °C) was distinctly different having much higher fraction of the RD-fiber components than that of the ND-fiber components. The texture and microstructural differences in ferrite in DSS warm rolled at different temperatures could be explained by the interaction of carbon atoms with dislocations. In contrast, the austenite in DSS warm rolled at different temperatures consistently showed pure metal- or copper-type deformation texture which was attributed to the increase in stacking fault energy at the warm-rolling temperatures. It was concluded that the evolution of microstructure and texture of the two constituent phases in DSS was greatly affected by the temperature of warm rolling, but not significantly by the presence of the other phas

Inclusive V0V^0 Production Cross Sections from 920 GeV Fixed Target Proton-Nucleus Collisions

Inclusive differential cross sections $d\sigma_{pA}/dx_F$ and $d\sigma_{pA}/dp_t^2$ for the production of \kzeros, \lambdazero, and \antilambda particles are measured at HERA in proton-induced reactions on C, Al, Ti, and W targets. The incident beam energy is 920 GeV, corresponding to $\sqrt {s} = 41.6$ GeV in the proton-nucleon system. The ratios of differential cross sections \rklpa and \rllpa are measured to be $6.2\pm 0.5$ and $0.66\pm 0.07$, respectively, for \xf $\approx-0.06$. No significant dependence upon the target material is observed. Within errors, the slopes of the transverse momentum distributions $d\sigma_{pA}/dp_t^2$ also show no significant dependence upon the target material. The dependence of the extrapolated total cross sections $\sigma_{pA}$ on the atomic mass $A$ of the target material is discussed, and the deduced cross sections per nucleon $\sigma_{pN}$ are compared with results obtained at other energies.Comment: 17 pages, 7 figures, 5 table

Molecular Interactions between Prions as Seeds and Recombinant Prion Proteins as Substrates Resemble the Biological Interspecies Barrier In Vitro

Prion diseases like Creutzfeldt-Jakob disease in humans, Scrapie in sheep or bovine spongiform encephalopathy are fatal neurodegenerative diseases, which can be of sporadic, genetic, or infectious origin. Prion diseases are transmissible between different species, however, with a variable species barrier. The key event of prion amplification is the conversion of the cellular isoform of the prion protein (PrPC) into the pathogenic isoform (PrPSc). We developed a sodiumdodecylsulfate-based PrP conversion system that induces amyloid fibril formation from soluble α-helical structured recombinant PrP (recPrP). This approach was extended applying pre-purified PrPSc as seeds which accelerate fibrillization of recPrP. In the present study we investigated the interspecies coherence of prion disease. Therefore we used PrPSc from different species like Syrian hamster, cattle, mouse and sheep and seeded fibrillization of recPrP from the same or other species to mimic in vitro the natural species barrier. We could show that the in vitro system of seeded fibrillization is in accordance with what is known from the naturally occurring species barriers