Interaction of Na+ Ion With the Solvated Gramicidin A Transmembrane Channel

A 6-12-1 atom-atom pair potential for the interaction of a Na+ion with gramicidin A (GA) has been derived from ab initio SCF calculations on the intermolecular interaction energies between one Na+ion and GA molecular fragments. This potential has been used to obtain iso-energy maps, which in turn provide an energy profile of the Na+ion in the GA channel. We have applied this potential in Monte Carlo simulations in order to obtain i) the number of water molecules which can be placed inside the GA channel and ii) the hydration structures of the GA channel in the presence of one Na+ion

Interaction of Na+ Ion With the Solvated Gramicidin A Transmembrane Channel

A 6-12-1 atom-atom pair potential for the interaction of a Na+ion with gramicidin A (GA) has been derived from ab initio SCF calculations on the intermolecular interaction energies between one Na+ion and GA molecular fragments. This potential has been used to obtain iso-energy maps, which in turn provide an energy profile of the Na+ion in the GA channel. We have applied this potential in Monte Carlo simulations in order to obtain i) the number of water molecules which can be placed inside the GA channel and ii) the hydration structures of the GA channel in the presence of one Na+ion

Sodium bis-(2-ethylhexyl) sulfosuccinate sepf-aggregation in vacuo: Molecular Dynamics simulation

Molecular dynamics (MD) simulations were conducted for systems in vacuo consisting of n AOT anions (bis(2-ethylhexyl)sulfosuccinate ions) and n 1 or n Na+ ions up to n = 20. For n = 15, positively charged systems with Li+, K+, and Cs+ cations were also considered. All systems were observed to form reverse micelle-like aggregates whose centre is occupied by cations and polar heads in a very compact solid-like way, while globally the aggregate has the form of an elongated and rather flat ellipsoid. Various types of statistical analyses were carried out on the systems to enlighten structural and dynamical properties including gyration radius, atomic pair correlation functions, atomic B-factor and moment of inertia tensor. For completeness and comparison the stability of reverse micelle is tested in the case of neutral n = 20 system in CCl4 solution

Molecular dynamics simulation of aqueous solutions of 26-unit segments of p(NIPAAm) and of p(NIPAAm) "doped" with amino acid based comonomers

We have performed 75-ns molecular dynamics (MD) simulations of aqueous solutions of a 26-unit NIPAAm oligomer at two temperatures, 302 and 315 K, below and above the experimentally determined lower critical solution temperature (LCST) of p(NIPAAm). We have been able to show that at 315 K the oligomer assumes a compact form, while it keeps a more extended form at 302 K. A similar behavior has been demonstrated for a similar NIPAAm oligomer, where two units had been substituted by methacryloyl-l-valine (MAVA) comonomers, one of them being charged and one neutral. For another analogous oligomer, where the same units had been substituted by methacryloyl-l-leucine (MALEU) comonomers, no transition from the extended to the more compact conformation has been found within the same simulation time. Statistical analysis of the trajectories indicates that this transition is related to the dynamics of the oligomer backbone, and to the formation of intramolecular hydrogen bonds and water-bridges between distant units of the solute. In the MAVA case, we have also evidenced an important role of the neutral MAVA comonomer in stabilizing the compact coiled structure. In the MALEU case, the corresponding comonomer is not equally efficacious and, possibly, is even hindering the readjustment of the oligomer backbone. Finally the self-diffusion coefficient of water molecules surrounding the oligomers at the two temperatures for selected relevant times is observed to characteristically depend on the distance from the solute molecules

Invasive pneumococcal disease in tuscany region, Italy, 2016–2017: Integrating multiple data sources to investigate underreporting

Invasive pneumococcal disease (IPD) is a vaccine-preventable disease characterized by the presence of Streptococcus pneumoniae in normally sterile sites. Since 2007, Italy has implemented an IPD national surveillance system (IPD-NSS). This system suffers from high rates of underreporting. To estimate the level of underreporting of IPD in 2016–2017 in Tuscany (Italy), we integrated data from IPD-NSS and two other regional data sources, i.e., Tuscany regional microbiological surveillance (Microbiological Surveillance and Antibiotic Resistance in Tuscany, SMART) and hospitalization discharge records (HDRs). We collected (1) notifications to IPD-NSS, (2) SMART records positive for S. pneumoniae from normally sterile sites, and (3) hospitalization records with IPD-related International Classification of Diseases, Ninth Revision, Clinical Modification (ICD9) codes in discharge diagnoses. We performed data linkage of the three sources to obtain a combined surveillance system (CSS). Using the CSS, we calculated the completeness of the three sources and performed a three-source log-linear capture–recapture analysis to estimate total IPD underreporting. In total, 127 IPD cases were identified from IPD-NSS, 320 were identified from SMART, and 658 were identified from HDRs. After data linkage, a total of 904 unique cases were detected. The average yearly CSS notification rate was 12.1/100,000 inhabitants. Completeness was 14.0% for IPD-NSS, 35.4% for SMART, and 72.8% for HDRs. The capture–recapture analysis suggested a total estimate of 3419 cases of IPD (95% confidence interval (CI): 1364–5474), corresponding to an underreporting rate of 73.7% (95% CI: 34.0–83.6) for CSS. This study shows substantial underreporting in the Tuscany IPD surveillance system. Integration of available data sources may be a useful approach to complement notification-based surveillance and provide decision-makers with better information to plan effective control strategies against IPD

Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks

© 2021 The Authors. Several experimental studies indicated that large conformational changes, including partial domain unfolding, have a role in the functional mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription factors. Recently, single-molecule atomic force microscopy (AFM) revealed two distinct pathways for the mechanical unfolding of the ARNT PAS-B. In this work we used steered molecular dynamics simulations to gain new insights into this process at an atomistic level. To reconstruct and classify pathways sampled in multiple simulations, we designed an original approach based on the use of self-organizing maps (SOMs). This led us to identify two types of unfolding pathways for the ARNT PAS-B, which are in good agreement with the AFM findings. Analysis of average forces mapped on the SOM revealed a stable conformation of the PAS-B along one pathway, which represents a possible structural model for the intermediate state detected by AFM. The approach here proposed will facilitate the study of other signal transmission mechanisms involving the folding/unfolding of PAS domains.National Institutes of Environmental Health Sciences (R01-ES007685); Leverhulme Trust (RPG-2017-222)

Hospital clinical pathways for children affected by juvenile idiopathic arthritis

BACKGROUND: Juvenile idiopathic arthritis (JIA) is the most common pediatric chronic rheumatic disease, which requires constant follow-up over the years, due to relapses during its progression. To maintain a good quality of life, it is important to limit admissions as far as possible. With the development of a Diagnostic Therapeutic Assistance Pathway (DTAP), we aim to select patients with suitable clinical conditions to be moved from routine hospital management to day care or outpatient treatment, evaluating the number of patients to whom this would apply. METHODS: Monocentric study regarding admissions for JIA between 2014 and 2016 in a Pediatric Unit of a university hospital in Milan. Through an analysis of the medical records, relevant information was extracted and collected in a Microsoft™ Excel database; starting from the data collected during the first year, a DTAP was prepared for patients with active arthritis and appropriate clinical conditions. RESULTS: The study includes data from 223 JIA hospitalization cases involving 127 patients. Applying DTAP criteria, 32% patients would have avoided admissions and 23% would have been admitted less frequently. The data concerning the activities of the Unit for JIA patients showed a relevant drop in the number of hospitalizations since 2015, from 89 in 2014 to 66 and 68 in 2015 and 2016 respectively. CONCLUSION: The opportunity offered by DTAP, has suggested feasible changes in hospitalization management and it's use would promote the possibility of treating the children without hospitalization, or minimizing it. In conclusion DTAP application is a priority for the continuous improvement of clinical practice and quality of life for patients and their families

Hospital clinical pathways for children affected by juvenile idiopathic arthritis

BACKGROUND: Juvenile idiopathic arthritis (JIA) is the most common pediatric chronic rheumatic disease, which requires constant follow-up over the years, due to relapses during its progression. To maintain a good quality of life, it is important to limit admissions as far as possible. With the development of a Diagnostic Therapeutic Assistance Pathway (DTAP), we aim to select patients with suitable clinical conditions to be moved from routine hospital management to day care or outpatient treatment, evaluating the number of patients to whom this would apply. METHODS: Monocentric study regarding admissions for JIA between 2014 and 2016 in a Pediatric Unit of a university hospital in Milan. Through an analysis of the medical records, relevant information was extracted and collected in a Microsoft\u2122 Excel database; starting from the data collected during the first year, a DTAP was prepared for patients with active arthritis and appropriate clinical conditions. RESULTS: The study includes data from 223 JIA hospitalization cases involving 127 patients. Applying DTAP criteria, 32% patients would have avoided admissions and 23% would have been admitted less frequently. The data concerning the activities of the Unit for JIA patients showed a relevant drop in the number of hospitalizations since 2015, from 89 in 2014 to 66 and 68 in 2015 and 2016 respectively. CONCLUSION: The opportunity offered by DTAP, has suggested feasible changes in hospitalization management and it's use would promote the possibility of treating the children without hospitalization, or minimizing it. In conclusion DTAP application is a priority for the continuous improvement of clinical practice and quality of life for patients and their families

Serum oncostatin M at baseline predicts mucosal healing in Crohn's disease patients treated with infliximab

Background: Oncostatin M is upregulated in Crohn's disease inflamed intestinal mucosa, and has been suggested as a promising biomarker to predict responsiveness to anti-TNF therapy in patients with inflammatory bowel diseases. Aim: To evaluate the suitability of serum oncostatin M as a predictive marker of response to infliximab in Crohn's disease. Methods: We included patients treated with infliximab monotherapy. All patients underwent colonoscopy at week 54 to evaluate mucosal healing. Serum oncostatin M and faecal calprotectin were measured at baseline and after 14 weeks of treatment. Mann-Whitney test was used to evaluate correlation of oncostatin M and faecal calprotectin at baseline and week 14 with mucosal healing at week 54. Their accuracy in predicting mucosal healing was assessed by area under the curve (AUC). Results: In a cohort of 45 included patients, 27 displayed mucosal healing. At both baseline and week 14, oncostatin M levels were significantly lower in patients with mucosal healing than in patients not achieving this endpoint (P < 0.001). Faecal calprotectin levels at week 14 were lower also in responders than nonresponders (P < 0.001). Oncostatin M values at baseline and week 14 were significantly associated (Spearman correlation = 0.92, P < 0.001). The diagnostic accuracy of oncostatin M at baseline in predicting mucosal healing (AUC = 0.91) was greater than faecal calprotectin (AUC = 0.51, P < 0.001). Conclusion: These results suggest that oncostatin M can predict the outcome of infliximab treatment. Compared with faecal calprotectin, the predictive capability of oncostatin M was appreciable at baseline, thus indicating oncostatin M as a promising biomarker for driving therapeutic choices in Crohn's disease