Impact of the number of fitted Debye-Waller factors on EXAFS fitting

EXAFS fit applied to asymmetric systems may imply the fit of parameters for many scattering paths. We illustrate on some examples how fitting too many independent DWs may lead to incorrect distances and mask some structural details. We question the physical meaning of the fitted DW values and we propose some ideas to avoid this problem

EXAFS Debye-Waller factors issued from Car-Parrinello molecular dynamics: Application to the fit of oxaliplatin and derivatives

One of the main pitfalls in EXAFS fitting is correlation among parameters, which can lead to unreli- able fits. The use of theoretical Debye-Waller factors (DWs) is a promising way to reduce the number of fitted parameters. When working with molecular dynamics, it is not only possible to evaluate DWs from the statistical distributions issued from the trajectory but also to estimate the distribution an- harmonicity, and to compute simulated average EXAFS spectra that can be fitted as experimental ones, in order to assess the ability of EXAFS fitting to recover information on DWs, as well as other structural and spectroscopical parameters. The case studied is oxaliplatin, a third generation anticancer drug. The structural information and the simulated average spectra were derived from a Car-Parrinello molecular dynamics (CP-MD) trajectory of a compound closely related to oxaliplatin. We present the DWs issued from this simulation and their use, by taking their theoretical absolute values (no DW fitted) or their ratios (one DW fitted). In this second approach, the fit of oxaliplatin experimental spectra leads to DWs values very close to the theoretical ones. This shows that the CP-MD trajectory provides a good representation of the distance distributions for oxaliplatin. Trans- ferability of oxaliplatin DWs, for all relevant single and multiple scattering paths, to closely related compounds is proven for the case of bis(oxalato)platinum(II) and bis(ethylene diamine)platinum(II).Ministerio de Ciencia e Innovación CTQ2011-25932Junta de Andalucía P06-FQM-0148

A genome-wide association study identifies an association between variants in EFCAB4B gene and periodontal disease in an Italian isolated population

Background and Objective: Periodontitis in one of the most prevalent dental dis- eases. Despite numerous studies have investigated its aetiopathogenetic factors, few works have focused on its genetic predisposition and most of them took into account only candidate genes. Therefore, we conducted a Genome Wide Association Study in an Italian isolated population aimed at uncovering genetic variants that pre- dispose to this disorder. Methods: Diagnosis of chronic periodontitis was made following the criteria of the American Academy of Periodontology. Patients with chronic periodontitis were grouped into different categories: slight, severe, localized and generalized. A control group composed by people without signs of periodontitis or gingivitis was defined. DNA was genotyped using 370k Illumina chips. Linear mixed model regression was used to test the association between each single nucleotide polymorphism (SNP) (in- dependent variable) and the periodontitis status (dependent variable), controlling for confounders sex, age and smoking. The genomic kinship matrix was also used as random effect. Results: Four SNPs on the gene EFCAB4B resulted significantly associated to local- ized periodontitis (P < 5 7 10 128), with the best hit on the rs242016 SNP (P = 1.5 7 10 128). Conclusions: We have identified a novel significant association between the EFCAB4B gene and localized periodontitis. These results open a new perspective in the understanding of genetic factors contributing to this common disorder

Cauchy Principal Value Contour Integral with Applications

[EN] Cauchy principal value is a standard method applied in mathematical applications by which an improper, and possibly divergent, integral is measured in a balanced way around singularities or at infinity. On the other hand, entropy prediction of systems behavior from a thermodynamic perspective commonly involves contour integrals. With the aim of facilitating the calculus of such integrals in this entropic scenario, we revisit the generalization of Cauchy principal value to complex contour integral, formalize its definition and-by using residue theory techniques-provide an useful way to evaluate them.Legua Fernandez, MP.; Sánchez Ruiz, LM. (2017). Cauchy Principal Value Contour Integral with Applications. Entropy. 19(5):1-9. doi:10.3390/e19050215S1919

Heightened immune response to autocitrullinated porphyromonas gingivalis peptidylarginine deiminase: a potential mechanism for breaching immunologic tolerance in rheumatoid arthritis

Background: Rheumatoid arthritis (RA) is characterised by autoimmunity to citrullinated proteins, and there is increasing epidemiologic evidence linking Porphyromonas gingivalis to RA. P gingivalis is apparently unique among periodontal pathogens in possessing a citrullinating enzyme, peptidylarginine deiminase (PPAD) with the potential to generate antigens driving the autoimmune response. Objectives: To examine the immune response to PPAD in patients with RA, individuals with periodontitis (PD) and controls (without arthritis), confirm PPAD autocitrullination and identify the modified arginine residues. Methods: PPAD and an inactivated mutant (C351A) were cloned and expressed and autocitrullination of both examined by immunoblotting and mass spectrometry. ELISAs using PPAD, C351A and another P gingivalis protein arginine gingipain (RgpB) were developed and antibody reactivities examined in patients with RA (n=80), individuals with PD (n=44) and controls (n=82). Results: Recombinant PPAD was a potent citrullinating enzyme. Antibodies to PPAD, but not to Rgp, were elevated in the RA sera (median 122 U/ml) compared with controls (median 70 U/ml; p&#60;0.05) and PD (median 60 U/ml; p&#60;0.01). Specificity of the anti-peptidyl citrullinated PPAD response was confirmed by the reaction of RA sera with multiple epitopes tested with synthetic citrullinated peptides spanning the PPAD molecule. The elevated antibody response to PPAD was abolished in RA sera if the C351A mutant was used on ELISA. Conclusions: The peptidyl citrulline-specific immune response to PPAD supports the hypothesis that, as a bacterial protein, it might break tolerance in RA, and could be a target for therapy