Impact of ultrafast electronic damage in single particle x-ray imaging experiments

In single particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces electronic dynamics on the femtosecond time scale in the system, which can reduce the contrast of the obtained diffraction patterns and adds an isotropic background. We quantify the degradation of the diffraction pattern from ultrafast electronic damage by performing simulations on a biological sample exposed to x-ray pulses with different parameters. We find that the contrast is substantially reduced and the background is considerably strong only if almost all electrons are removed from their parent atoms. This happens at fluences of at least one order of magnitude larger than provided at currently available XFEL sources.Comment: 15 pages, 3 figures submitted to PR

Narration and Focalization : A Cognitivist and an Unnaturalist, Made Strange

Any new narratological theory faces the test of being applicable to much-analyzedclassics of prose fiction and of yielding new insights into narratives that have served as textbook examples of narrative strategies for decades. This essay is a constructed dialogue between imaginary narratologists who are paradigmatic proponents of two schools of thought in postclassical narratology: the cognitive and the unnatural. The two narratologists juxtapose their respective concepts and methodologies in an analysis of William Golding's late modernist classic The Inheritors, especially the narrative dynamics of "alien" Neanderthal focalization versus "naturalizing" Homo sapiens narration. Ultimately, The Inheritors reminds the cognitivist of how language-bound the readerly effects of estrangement and integration in internal focalization can be. Conversely, the same novel serves as an example for the unnaturalist of the paradoxical necessity for perceptual and emotional familiarization in our attempts to understand fundamental alterity. The parameters of cognitive and unnatural narratology may seem divergent at the outset, but in this essay their representatives find a common ground in an estranging reading of the enactive immersion in The Inheritors. Here the extraordinary embodiedness of the Neanderthal focalization is a key to a literary-allegorical reading of the Neanderthal mind as imagined by Golding. This reading, accomplished through a constructed debate between two paradigms, reflects the actual positions of the authors of this essay: Makela and Polvinen are both proponents of an approach that acknowledges the inherent syntheticity and linguistic overdeterminedness of a literary narrative as well as its "natural" enactivist pull toward bodily immersion.Peer reviewe

A Bigraph Relational Model

In this paper, we present a model based on relations for bigraphical reactive systems [Milner09]. Its defining characteristics are that validity and reaction relations are captured as traces in a multi-set rewriting system. The relational model is derived from Milner's graphical definition and directly amenable to implementation.Comment: In Proceedings LFMTP 2011, arXiv:1110.668

Retrospective Analysis on the Efficacy, Safety and Treatment Failure Group of Sitagliptin for Mean 10-Month Duration

BackgroundTo investigate the clinical results of sitagliptin (SITA) and the characteristics of the treatment failure group or of low responders to SITA.MethodsA retrospective study of type 2 diabetic patients reviewed 99 cases, including 12 treatment failure cases, who stopped SITA because of worsening patients' condition, and 87 cases, who continued treatment over five visits (total 9.9±10.1 months) after receiving the prescription of SITA from December 2008 to June 2009. Subjects were classified as five groups administered SITA as an initial combination with metformin (MET), add-on to metformin or sulfonylurea, and switching from sulfonylurea or thiazolidinedione. The changes in HbA1c level from the first to last visit (ΔHbA1c) in treatment maintenance group were subanalyzed.ResultsThe HbA1c level was significantly reduced in four groups, including initial coadministration of SITA with metformin (ΔHbA1c=-1.1%, P<0.001), add-on to MET (ΔHbA1c=-0.6%, P=0.017), add-on to sulfonylurea (ΔHbA1c=-0.5%, P<0.001), and switching from thiazolidinedione (ΔHbA1c=-0.3%, P=0.013). SITA was noninferior to sulfonlyurea (ΔHbA1c=-0.2%, P=0.63). There was no significant adverse effect. The treatment failure group had a longer diabeties duration (P=0.008), higher HbA1c (P=0.001) and fasting plasma glucose (P=0.003) compared to the maintenance group. Subanalysis on the tertiles of ΔHbA1c showed that low-response to SITA (tertile 1) was associated with a longer diabetes duration (P=0.009) and lower HbA1c (P<0.001).ConclusionSITA was effective and safe for use in Korean type 2 diabetic patients. However, its clinical responses and long-term benefit-harm profile is yet to be established

Theory of x-ray absorption by laser-dressed atoms

An ab initio theory is devised for the x-ray photoabsorption cross section of atoms in the field of a moderately intense optical laser (800nm, 10^13 W/cm^2). The laser dresses the core-excited atomic states, which introduces a dependence of the cross section on the angle between the polarization vectors of the two linearly polarized radiation sources. We use the Hartree-Fock-Slater approximation to describe the atomic many-particle problem in conjunction with a nonrelativistic quantum-electrodynamic approach to treat the photon-electron interaction. The continuum wave functions of ejected electrons are treated with a complex absorbing potential that is derived from smooth exterior complex scaling. The solution to the two-color (x-ray plus laser) problem is discussed in terms of a direct diagonalization of the complex symmetric matrix representation of the Hamiltonian. Alternative treatments with time-independent and time-dependent non-Hermitian perturbation theories are presented that exploit the weak interaction strength between x rays and atoms. We apply the theory to study the photoabsorption cross section of krypton atoms near the K edge. A pronounced modification of the cross section is found in the presence of the optical laser.Comment: 13 pages, 3 figures, 1 table, RevTeX4, corrected typoe

Validation of nonlinear PCA

Linear principal component analysis (PCA) can be extended to a nonlinear PCA by using artificial neural networks. But the benefit of curved components requires a careful control of the model complexity. Moreover, standard techniques for model selection, including cross-validation and more generally the use of an independent test set, fail when applied to nonlinear PCA because of its inherent unsupervised characteristics. This paper presents a new approach for validating the complexity of nonlinear PCA models by using the error in missing data estimation as a criterion for model selection. It is motivated by the idea that only the model of optimal complexity is able to predict missing values with the highest accuracy. While standard test set validation usually favours over-fitted nonlinear PCA models, the proposed model validation approach correctly selects the optimal model complexity.Comment: 12 pages, 5 figure

Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages.

Escherichia coli is the leading cause of urinary tract infection, one of the most common bacterial infections in humans. Despite this, a genomic perspective is lacking regarding the phylogenetic distribution of isolates associated with different clinical syndromes. Here, we present a large-scale phylogenomic analysis of a spatiotemporally and clinically diverse set of 907 E. coli isolates, including 722 uropathogenic E. coli (UPEC) isolates. A genome-wide association approach identifies the (P-fimbriae-encoding) papGII locus as the key feature distinguishing invasive UPEC, defined as isolates associated with severe UTI, i.e., kidney infection (pyelonephritis) or urinary-source bacteremia, from non-invasive UPEC, defined as isolates associated with asymptomatic bacteriuria or bladder infection (cystitis). Within the E. coli population, distinct invasive UPEC lineages emerged through repeated horizontal acquisition of diverse papGII-containing pathogenicity islands. Our findings elucidate the molecular determinants of severe UTI and have implications for the early detection of this pathogen

Comparison of Short-Term Estrogenicity Tests for Identification of Hormone-Disrupting Chemicals

The aim of this study was to compare results obtained by eight different short-term assays of estrogenlike actions of chemicals conducted in 10 different laboratories in five countries. Twenty chemicals were selected to represent direct-acting estrogens, compounds with estrogenic metabolites, estrogenic antagonists, and a known cytotoxic agent. Also included in the test panel were 17β-estradiol as a positive control and ethanol as solvent control. The test compounds were coded before distribution. Test methods included direct binding to the estrogen receptor (ER), proliferation of MCF-7 cells, transient reporter gene expression in MCF-7 cells, reporter gene expression in yeast strains stably transfected with the human ER and an estrogen-responsive reporter gene, and vitellogenin production in juvenile rainbow trout. 17β-Estradiol, 17α-ethynyl estradiol, and diethylstilbestrol induced a strong estrogenic response in all test systems. Colchicine caused cytotoxicity only. Bisphenol A induced an estrogenic response in all assays. The results obtained for the remaining test compounds—tamoxifen, ICI 182.780, testosterone, bisphenol A dimethacrylate, 4-n-octylphenol, 4-n-nonylphenol, nonylphenol dodecylethoxylate, butylbenzylphthalate, dibutylphthalate, methoxychlor, o,p′-DDT, p,p′-DDE, endosulfan, chlomequat chloride, and ethanol—varied among the assays. The results demonstrate that careful standardization is necessary to obtain a reasonable degree of reproducibility. Also, similar methods vary in their sensitivity to estrogenic compounds. Thus, short-term tests are useful for screening purposes, but the methods must be further validated by additional interlaboratory and interassay comparisons to document the reliability of the methods

Epstein-Barr Virus and p16INK4A Methylation in Squamous Cell Carcinoma and Precancerous Lesions of the Cervix Uteri

Methylation of p16 is an important mechanism in cervical carcinogenesis. However, the relationship between cervical squamous cell carcinoma (SCC) and Epstein-Barr virus (EBV) remains controversial. Here, we explored whether EBV infection and/or p16 gene inactivation would play any role in cervical carcinogenesis. Eighty-two specimens included 41 invasive SCCs, 30 cervical intraepithelial neoplasm (CIN; CIN 1, 11 cases, CIN II, 3 cases, CIN III 16 cases) and 11 nonneoplastic cervices. EBV was detected by polymerase chain reaction (PCR) for EBNA-1 and in situ hybridization for EBER-1. The p16 methylation-status and the expression of p16 protein were studied by methylation-specific PCR and immunohistochemistry, respectively. The materials were divided into four groups: 1) nonneoplastic cervices, 2) CIN I, 3) CIN II-III and 4) invasive SCCs. p16 methylation and p16 immunoexpressions increased in CIN and invasive SCCs than nonneoplastic tissue. p16-methylation and p16-immunoreactivities were higher in the EBV-positive group (p=0.009, p<0.001) than in the EBV-negative group. EBV was detected more frequently in CIN and SCCs than nonneoplastic cervices. In conclusion, a correlation between p16 methylation, p16 immunoreactivity and the detection of EBV strongly suggested that the cooperation of EBV and p16 gene may play a synergic effect on cell cycle deregulation