Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method

In the Hamiltonian adaptive resolution simulation method (H-AdResS) it is possible to simulate coexisting atomistic (AT) and ideal gas representations of a physical system that belong to different subdomains within the simulation box. The Hamiltonian includes a field that bridges both models by smoothly switching on (off) the intermolecular potential as particles enter (leave) the AT region. In practice, external one-body forces are calculated and applied to enforce a reference density throughout the simulation box, and the resulting external potential adds up to the Hamiltonian. This procedure suggests an apparent dependence of the final Hamiltonian on the system's thermodynamic state that challenges the method's statistical mechanics consistency. In this paper, we explicitly include an external potential that depends on the switching function. Hence, we build a grand canonical potential for this inhomogeneous system to find the equivalence between H-AdResS and density functional theory (DFT). We thus verify that the external potential inducing a constant density profile is equal to the system's excess chemical potential. Given DFT's one-to-one correspondence between external potential and equilibrium density, we find that a Hamiltonian description of the system is compatible with the numerical implementation based on enforcing the reference density across the simulation box. In the second part of the manuscript, we focus on assessing our approach's convergence and computing efficiency concerning various model parameters, including sample size and solute concentrations. To this aim, we compute the excess chemical potential of water, aqueous urea solutions and Lennard-Jones (LJ) mixtures. The results' convergence and accuracy are convincing in all cases, thus emphasising the method's robustness and capabilities.

Inter and intraobserver variability in the echocardiographic measurement of vegetations in infective endocarditis

Introduction and objectives

The indication for surgery to prevent embolism in infective endocarditis includes four clinical scenarios and three different echocardiographic measurements of the maximal vegetation diameter. These cut-off points are completely arbitrary and not evidence-based. Our hypothesis is that the vegetation diameter is not an appropriate surgical criterium. The goal of the study is to analyze the inter and intra-observer variability in this measurement and to compare the surgical indications agreement based on these parameters.

Methods

Two trained echocardiographers have measured the maximal vegetation diameter by transesophageal echocardiogram in 67 consecutive patients with definite infective endocarditis in an off-line workstation. The inter- and intra-observer variability was calculated by the interclass correlation coefficient and with the Bland-Altman analysis. The relationship between the strength of agreement for the cut-off points of 10 and 15 mm was also calculated.

Results

Intra and inter-observer interclass correlation coefficient in the measurement of the maximal longitudinal diameter of the vegetations were 0.872 (0.805–0.917) and 0.757 (0.642–0.839) respectively. The strength of agreement of the intra and inter-observer analysis for the cut-off point of 10 mm were 0.674 (0.485–0.862) and 0.533 (0.327–0.759). For the cut-off point of 15 mm they were 0.696 (0.530–0.862) and 0.475 (0.270–0.679).

Conclusions

The variability in the measurements of the maximal longitudinal diameter by transesophageal echocardiogram between two experimented echocardiographers is good. Nonetheless, surgical indications based on the cut-off points recommended in the European guidelines would have changed in an unacceptable high proportion of patients. Therefore, we suggest that these indications should be revised in the light of our results.

Funding Acknowledgement

Type of funding source: None

From Soybean residue to advanced supercapacitors

Supercapacitor technology is an extremely timely area of research with fierce international competition to develop cost-effective, environmentally friendlier EC electrode materials that have real world application. Herein, nitrogen-doped carbons with large specific surface area, optimized micropore structure and surface chemistry have been prepared by means of an environmentally sound hydrothermal carbonization process using defatted soybean (i.e., Soybean meal), a widely available and cost-effective protein-rich biomass, as precursor followed by a chemical activation step. When tested as supercapacitor electrodes in aqueous electrolytes (i.e. H2SO4 and Li2SO4), they demonstrate excellent capacitive performance and robustness, with high values of specific capacitance in both gravimetric (250-260 and 176 F g(-1) in H2SO4 and Li2SO4 respectively) and volumetric (150-210 and 102 F cm(-3) in H2SO4 and Li2SO4 respectively) units, and remarkable rate capability (>60% capacitance retention at 20 A g(-1) in both media). Interestingly, when Li2SO4 is used, the voltage window is extended up to 1.7 V (in contrast to 1.1 V in H2SO4). Thus, the amount of energy stored is increased by 50% compared to H2SO4 electrolyte, enabling this environmentally sound Li2SO4-based supercapacitor to deliver ~12 Wh kg(-1) at a high power density of ~2 kW kg(-1).

Solid-phase synthesis of graphitic carbon nanostructures from iron and cobalt gluconates and their utilization as electrocatalyst supports

We present a novel and facile synthesis methodology for obtaining graphitic carbon structures from Fe(II) and Co(II) gluconates. The formation of graphitic carbon can be carried out in only one step by means of heat treatment of these organic salts at a temperature of 900 degrees C or 1000 degrees C under inert atmosphere. This process consists of the following steps: (a) pyrolysis of the organic gluconate and its transformation to amorphous carbon, (b) conversion of Fe(2+) and Co(2+) ions to Fe(2)O(3) and CoO and their subsequent reduction to metallic nanoparticles by the carbon and (c) conversion of a fraction of formed amorphous carbon to graphitic structures by Fe and Co nanoparticles that act as catalysts in the graphitization process. The removal of the amorphous carbon and metallic nanoparticles by means of oxidative treatment (KMnO(4) in an acid solution) allows graphitic carbon nanostructures (GCNs) to be selectively recovered. The GCNs thus obtained (i.e. nanocapsules and nanopipes) have a high crystallinity as evidenced by TEM/SAED, XRD and Raman analysis. In addition, we used these GCNs as supports for platinum nanoparticles, which were well dispersed (mean Pt size approximately 2.5-3.2 nm). Most electrocatalysts prepared in this way have a high electrocatalytical surface area, up to 90 m(2) g(-1) Pt, and exhibit high catalytic activities toward methanol electrooxidation.

Influence of first line treatment in the 5 (5yS) and 10-year (10yS) survival outcomes of patients with gastroenteropancreatic neuroendocrine tumors (GNETs): 2001–2005 Spanish task force GNET group

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Background: Data on incidence, morbidity and mortality of GNETs is limited due to the low frequency of these tumors. However this survival data is critical to design studies with new agents. Methods: Data was obtained from medical records of 262 patients with GNETs and centralized in an online registry at www.retegep.net . Among the study parameters were histology, localization, stage, diagnostic workup, 1st line and subsequent treatments, 5yS and 10yS for the whole dataset and for different stages, tumor types and 1st line systemic treatment. Results: Mean age 58, 58% male. Primary tumors: 49% Carcinoids (C), 19% non-functioning pancreatic tumors (PT), 9% insulinomas, 6% gastrinomas and 8% unknown primary. Localizations: midgut (36%), head (17%) and body of pancreas (10%). Functioning symptoms led to diagnosis in 38% of cases. 4% were associated to MEN1. Stage at diagnosis was advanced (Adv) in 46%, localised (L) in 30% and locorregional (LR) in 13% (unknown in 11%). Diagnostic workup were CT Scan (84%), Octreoscan (52%) and US (52%) and serum hormone tests (65%). Treatments for Adv disease included somatostatin analogues (SA) (47%), surgery (S) (43%), chemotherapy (CT) (35%) and interferon (IFN) (34%), embolization (7%) and radiofrequency ablation (3%). 5yS and 10yS for the whole group was 61.6% (SD: 5.2%) and 49.8% (SD: 7.7%) respectively. 5yS and 10yS for the L/LR and Adv stages were 78.1% (SD: 7.3%) and 71% (SD: 10%), and 48.9% (SD: 7.7%) and 29% (SD: 12.4%), respectively. LR PT and C had similar 5 and 10yS but Adv PT did worse than Adv C (5yS of 36.2% and 61.1%, respectively). 1st line systemic treatment for LR and Adv disease (n=90) included SA (39%), CT (34.4%), IFN (5.6%), combinations of SA+IFN (13.3%), A+CT (4.4%) and other combinations (3.3%), with a 10yS rate of 69%, 79%, 50%, 89%, 66% and 50%, respectively. Adv PT perform worse than C regardless of treatment choice. As second line systemic treatment (n=43) 30% received SA, 30% CT, 26% inmunotherapy and 14% combinations. Conclusions: An extensive use of systemic therapy and a scarce use of non-surgical LR treatments is observed in the Adv stages. Choice of 1st line systemic treatment does not seem to influence survival outcomes.

No significant financial relationships to disclose.

Comparison of benefit to sugarcane plant growth and 15N2 incorporation following inoculation of sterile plants with Acetobacter diazotrophicus wild-type and Nif- mutants strains

The ability of the nitrogen-fixing bacterial endophyte Acetobacter diazotrophicus strain PAl5 to enhance the growth of sugarcane SP70-1143 was evaluated in the growth chamber, greenhouse, and field by comparing plants inoculated with wild-type and Nif mutant MAd3A in two independent experiments. The wild-type and Nif mutant strains colonized sugarcane plants equally and persisted in mature plants. In N-deficient conditions, sugarcane plants inoculated with A. diazotrophicus PAl5 generally grew better and had a higher total N content 60 days after planting than did plants inoculated with mutant MAd3A or uninoculated plants. These results indicate that the transfer of fixed N from A. diazotrophicus to sugarcane might be a significant mechanism for plant growth promotion in this association. When N was not limiting, growth enhancement was observed in plants inoculated with either wild-type or Nif- mutants, suggesting the additional effect of a plant growth promoting factor provided by A. diazotrophicus. A 15N2 incorporation experiment demonstrated that A. diazotrophicus wild-type strains actively fixed N2 inside sugarcane plants, whereas the Nif- mutants did not.

Characterization of a major cluster of nif, fix, and associated genes in a sugarcane endophyte, Acetobacter diazotrophicus

A major 30.5-kb cluster of nif and associated genes of Acetobacter diazotrophicus (syn. Gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. This cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. Northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. The overall arrangement of genes is most like that of the nif-fix cluster in Azospirillum brasilense, while the individual gene products are more similar to those in species of Rhizobiaceae or in Rhodobacter capsulatus.

Anisakis simplex: a cause of intestinal pseudo-obstruction

OBJECTIVE

the ingestion of Anisakis simplex larvae may lead to the appearance of gastrointestinal symptoms. However, the number of reported cases of parasitization by Anisakis in Spain is lower than would be expected in a country with the second-highest fish consumption per inhabitant in the world, particularly since fish is often eaten raw or only slightly cooked. We suggest that the incidence of anisakiasis in Spain would be higher if complementary studies were used in all patients suspected of having anisakiasis.

METHODS

we studied 6 patients with a diagnosis of intestinal obstruction who frequently ate fish. Skin prick tests with seafood, inhalant allergen and Anisakis extracts were done. Total and specific IgE against Anisakis larvae were tested with a CAP system radioimmunoassay and immunoblot assays. Oral challenge tests with frozen larvae were also used.

RESULTS

a positive skin prick result and high levels of total and specific IgE were found in all patients. The results of immunoblot assays for IgE did not show a consistent pattern, but a group of several low (14-18 kDa) and intermediate molecular weight antigens (30-50 kDa) were found in all patients. All patients tolerated the oral challenge test well.

CONCLUSIONS

in our patients with intestinal pseudo-obstruction and a history of frequent fish eating, the clinical and laboratory findings were suggestive of parasitization by Anisakis simplex larvae as the cause of the obstruction. Such complementary studies should be used whenever there is a suspicion of anisakiasis. The results of the oral provocation test show that the intake of dead larvae does not induce clinical parasitization.

Tetanus toxin impairs accessory and secretory functions in interferon-gamma-treated murine macrophages

Tetanus neurotoxin (TT), a product of microbial origin, acts as a zinc endopeptidase on vesicle-associated membrane proteins (VAMP). We have demonstrated that TT displays inhibitory effects on secretory and accessory functions in the murine macrophage (Mphi) cell line GG2EE. Nitric oxide (NO) secretion was decreased when interferon (IFN)-gamma-pretreated GG2EE Mphis were coincubated with a fungal costimulus (SMP200) and TT. When heat-inactivated TT was used this effect was not evident. The TT-mediated phenomenon was dose-dependent and specific since, under the same experimental conditions, it did not affect interleukin-6 or tumor necrosis factor-alpha secretion. Furthermore, IFN-gamma-induced major histocompatibility complex class II molecule expression and GG2EE accessory function, assessed by SMP200-stimulated lymphoproliferation, were also inhibited by TT. Such inhibition was incomplete, in line with our previous results showing that TT partially cleaves VAMP proteins in murine Mφ.

Autacoids mediate coronary vasoconstriction induced by nitric oxide synthesis inhibition

Inhibition of nitric oxide (NO) synthesis results in coronary vasoconstriction. Using a Langendorff rat heart preparation, we tested the hypothesis that this vasoconstriction is caused by the unopposed effect of the autacoids prostaglandin H2 (PGH2) or thromboxane A2 (TxA2) or both through a mechanism that involves oxygen free radicals. The vasoconstriction induced by NO synthesis inhibition was studied with two different NO synthase inhibitors, N(omega)-nitro-L-arginine methyl ester (L-NAME) and N(omega)-monomethyl-L-arginine (L-NMMA). We found that the decrease in coronary flow (CF) induced by L-NAME (from 19.3 +/- 0.9 to 13.2 +/- 0.9 ml/min; p < 0.001) and L-NMMA (from 20.1 +/- 0.4 to 15.0 +/- 0.3 ml/min; p < 0.001) was completely blocked by the cyclooxygenase inhibitor indomethacin. A different cyclooxygenase inhibitor (ibuprofen), a PGH2/TxA2-receptor antagonist (SQ29548), and a TxA2 synthase inhibitor (CGS 13080) also completely abolished the vasoconstrictor effect of L-NAME, suggesting that this vasoconstriction is mediated by TxA2. Two different scavengers of superoxide radical anions (O2-), the enzyme superoxide dismutase (SOD) and a cell-permeable SOD mimic, 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (Tempol), also blocked the vasoconstriction induced by NO synthesis inhibition. In contrast, catalase, which inactivates hydrogen peroxide (H2O2), failed to do so, indicating that O2- is needed for the vasoconstrictor effect of L-NAME, whereas H2O2 is not. To determine whether O2- acts on the conversion of PGH2 to TxA2 or at the receptor or postreceptor level, we studied whether the vasoconstriction induced by exogenous PGH2 or the TxA2 receptor agonist U46619 is blocked by scavengers of O2-. CF decreased by 50% with PGH2 (from 21 +/- 2.1 to 10.6 +/- 5.8 ml/min; p < 0.01), and this decrease was abolished by SOD and Tempol but not catalase. However, SOD had no effect on the vasoconstriction induced by U46619, which decreased CF by 45% (from 17.3 +/- 2.5 to 9.5 +/- 1.8 ml/min; p < 0.01). In addition, PGH2 increased the release of TxB2 (the stable metabolite of TxA2) in the coronary effluent (from 5.1 +/- 1.2 to 136.1 +/- 11.8 pg/ml/min). The release of TxB2 was significantly lower in hearts treated with SOD (76.8 +/- 14.2 pg/ml/min) and CGS (65.7 +/- 13.9 pg/ml/min). We conclude that the coronary vasoconstriction induced by inhibition of NO synthesis is the result of the unopposed effect of the autacoid TxA2 through activation of its receptor, and that O2- is necessary for conversion of PGH2 to TxA2.

Radiation-induced DNA damage as a function of hydration. II. Base damage from electron-loss centers

The induction of base damage products in gamma-irradiated DNA, hydrated between 2.5 and 32.8 moles of water per mole of nucleotide (tau), was investigated using the gas chromatography/mass spectrometry-selected ion monitoring technique. In general, the yields of the measured base damage products were found to be dependent on the extent of the hydration when the DNA was irradiated under nitrogen. At low hydrations (tau < or = 13), the highest yields of the measured products were found for 7,8-dihydro-8-oxo-guanine, 5,6-dihydrothymine and, to a lesser extent, 2,6-diamino-4-oxo-5-formamidopyrimidine, products which are consistent with the base radicals found in low-temperature ESR studies. At higher hydrations (tau < or = 13), changes in DNA conformation and an increase in the attack of bulk water radicals on DNA play a significant role in the formation of radiation-induced DNA base damage products. Additional findings in our study include: (1) the sum of the yields of the products formed from electron-loss centers is greater than the sum of the yields of the products formed from electron-gain centers, indicating that there might be other electron-gain products which have not been identified; (2) the combined yield for the base damage products and the release of unaltered bases at tau < or = 13 is constant, implying that radiation damage in the tightly bound water molecules of the primary hydration layer causes DNA damage (quasi-direct effect) that is similar to the damage caused by direct ionization of the DNA (direct effect); and (3) the yields of the individual base damage products that were formed from electron-loss centers can be modeled on the basis of both the known reactions that lead to the formation of the initial charged base radicals in irradiated DNA, and the known reactions that involve the conversion of these initial DNA radicals into their respective nonradical end products.

Insulin requirements and residual beta-cell function 12 months after concluding immunotherapy in type I diabetic patients treated with combined azathioprine and thymostimulin administration for one year

An increase in clinical and functional remissions with immunosuppression, as well as abnormal T-cell function, in Type I diabetic patients has been reported in the early stages of diabetes. A controlled trial with azathioprine and thymostimulin in separate and combined administration was performed in 45 recently diagnosed Type I diabetic patients. Phenotyping of the T-lymphocyte subsets, levels of CD25 positive cells and interleukin-2 production by patients' lymphocytes, as well as remission rate and stimulated C-peptide levels, were serially assessed. Remission was defined as mean weekly glycemic profiles less than or equal to 7 mmole/l, serial HbA1 values in the normal range and no insulin requirements for at least 2 consecutive months. At 3,6,9 and 12 months of immunotherapy, remission occurred respectively in 0%, 8.3%, 16.6% and 0% of the conventionally treated diabetic controls and in 42.8%, 50%, 42.8% and 36.2% of the subjects submitted to combined azathioprine and thymostimulin administration. Patients receiving azathioprine or thymostimulin alone did not achieve better remission rates than controls. C-peptide levels were significantly higher (above 0.6 pmol/ml) in patients with remission than in those not in remission (P less than 0.02) throughout the trial. Excessive interleukin-2 production in recently diagnosed diabetics returned to normal levels in patients in remission. In the group receiving combined therapy, 38.5%, 25% and 23% were still in clinical remission at 6, 9 and 12 months after drug withdrawal. Twelve months after stopping treatment, patients who had remitted exhibited significantly lower insulin requirements and greater endogenous insulin secretion than those who had not remitted; the former also maintained near normal glycemic control. No side effects were detected except mild and transient leucopenia in a reduced number of patients receiving azathioprine. Remission was related to the time of beginning immunotherapy after the onset of diabetes (17.1 +/- 7 vs 42.5 +/- 15 days; P less than 0.01) and to age (17.7 +/- 5.6 vs 13 +/- 7 years; P less than 0.05). Interleukin-2 production seems to be negatively associated with clinical remission in the early stages of diabetes. Results suggest a complementary effect of the drugs used in this study that may enhance long-term remission in recently diagnosed Type I diabetic patients.