IRMPD spectroscopy and quantum chemistry calculations on mono- and bi-metallic complexes of acetylacetonate ligands with aluminum, iron, and ruthenium ions.

Metal-ligand cluster ions are structurally characterized by means of gas-phase infrared multiple photon dissociation spectroscopy. The mass-selected complexes consist of one or two metal cations M3+ (M = Al, Fe, or Ru) and two to five anionic bidentate acetylacetonate ligands. Experimental IR spectra are compared with different density functional theory calculations, namely, PBE/TZVP, B3LYP/6-31G*, and M06/6-31+G**. Frequency analysis was also performed at different levels, namely, scaled static harmonic and unscaled static anharmonic, or with ab initio molecular dynamics simulations at the PBE/TZVP level. All methods lead to simulated spectra that fit rather well with experimental data, and the spectral red shifts of several main bands, in the 1200 cm-1-1800 cm-1 range, are sensitive to the strength of the metal-ligand interaction and to the spin state of the ion. Due to the rigidity of those complexes, first principles molecular dynamics calculations provide spectra similar to that produced by static calculations that are already able to catch the main spectral signatures using harmonic calculations at the B3LYP/6-31G* level.

Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics.

In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm(-1)), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm(-1) where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

High-Fidelity Preparation, Gates, Memory, and Readout of a Trapped-Ion Quantum Bit.

We implement all single-qubit operations with fidelities significantly above the minimum threshold required for fault-tolerant quantum computing, using a trapped-ion qubit stored in hyperfine "atomic clock" states of ^{43}Ca^{+}. We measure a combined qubit state preparation and single-shot readout fidelity of 99.93%, a memory coherence time of T_{2}^{*}=50 sec, and an average single-qubit gate fidelity of 99.9999%. These results are achieved in a room-temperature microfabricated surface trap, without the use of magnetic field shielding or dynamic decoupling techniques to overcome technical noise.

Magnetic coupling constants and vibrational frequencies by extended broken symmetry approach with hybrid functionals.

The description of the electronic structure and magnetic properties of multi-centers transition metal complexes, especially of mixed-valence compounds, still represents a challenge for density functional theory (DFT) methods. The energies and the geometries of the correctly symmetrized low-spin ground state are estimated using the Heisenberg-Dirac-van Vleck spin Hamiltonian within the extended broken symmetry method introduced by Marx and co-workers [Nair et al., J. Chem. Theory Comput. 4, 1174-1188 (2008)]. In the present work we extend the application of this technique, originally implemented using the DFT+U scheme, to the use of hybrid functionals, investigating the ground-state properties of di-iron and di-manganese compounds. The calculated magnetic coupling and vibrational properties of ferredoxin molecular models are in good agreements with experimental results and DFT+U calculations. Six different mixed-valence Mn(III)-Mn(IV) compounds have been extensively studied optimizing the geometry in low-spin, high-spin, and broken-symmetry states and with different functionals. The magnetic coupling constants calculated by the extended broken symmetry approach using B3LYP functional presents a remarkable agreement with the experimental results, revealing that the proposed methodology provides a consistent and accurate DFT approach to the electronic structure of multi-centers transition metal complexes.

Toxicity and physicochemical parameters of composts including distinct residues from agribusiness and slaughterhouse sludge.

Composting is useful for treatment of residues from agribusiness, but the potential toxicity of the final compost should be evaluated before its agricultural destination. The objective of this study was to evaluate the physicochemical characteristics and the toxicity of agribusiness residues using onion seeds as bioindicators. All tested treatments were composed by sludge from a swine slaughterhouse and sawdust. Besides the control, which included no additional materials, the other treatments included aviary bedding, rice husk and residue from tobacco industries as structuring materials. After 120 days of composting, for all treatments, the temperature inside the composting piles approached the environmental temperature, the physicochemical parameters indicated that the composts were stabilized and, except for the treatment including tobacco residues, that could be used for agriculture without impairing plant germination. Although the treatments including tobacco residues and rice husk showed evidence of cytotoxicity and genotoxicity at the beginning of the composting period, that was not observed for the treatment including aviary bedding. Such potential toxicity was not observed at the end of composting for any of the tested treatments.

Moisture content monitoring in industrial-scale composting systems using low-cost sensor-based machine learning techniques.

Moisture is a key aspect for proper composting, allowing greater efficiency and lower environmental impact. Low-cost real-time moisture determination methods are still a challenge in industrial composting processes. The aim of this study was to design a model of hardware and software that would allow self-adjustment of a low-cost capacitive moisture sensor. Samples of organic composts with distinct waste composition and from different composting stages were used. Machine learning techniques were applied for self-adjustment of the sensor. To validate the model, results obtained in a laboratory by the gravimetric method were used. The proposed model proved to be efficient and reliable in measuring moisture in compost, reaching a correlation coefficient of 0.9939 between the moisture content verified by gravimetric analysis and the prediction obtained by the Sensor Node.

Femtosecond spectroscopy probes the folding quality of antibody fragments expressed as GFP fusions in the cytoplasm.

Time-resolved femtosecond spectroscopy can improve the application of green fluorescent proteins (GFPs) as protein-folding reporters. The study of ultrafast excited-state dynamics (ESD) of GFP fused to single chain variable fragment (scFv) antibody fragments, allowed us to define and measure an empirical parameter that only depends on the folding quality (FQ) of the fusion. This method has been applied to the analysis of genetic fusions expressed in the bacterial cytoplasm and allowed us to distinguish folded and thus functional antibody fragments (high FQ) with respect to misfolded antibody fragments. Moreover, these findings were strongly correlated to the behavior of the same scFvs expressed in animal cells. This method is based on the sensitivity of the ESD to the modifications in the tertiary structure of the GFP induced by the aggregation state of the fusion partner. This approach may be applicable to the study of the FQ of polypeptides over-expressed under reducing conditions.

Metabolism of glutathione in tumour cells as evidenced by 1H MRS.

1H MRS signals of glutathione and of free glutamate were examined in samples from cultured tumour cells, namely MCF-7 from mammary carcinoma and TG98 from malignant glioma, with the aim of relating signal intensities to aspects of GSH metabolism. Spectra of cells harvested at different cell densities suggest that GSH and glu signal intensities are related to cell density and proliferation and their ratio is dependent on the activity of the gamma-glutamyl cysteine synthetase. The hypothesis is confirmed by experiments performed on cells treated with buthionine sulfoximine that inhibits the enzyme activity.

The approach by midline incision for extraperitoneal kidney transplantation.

UNLABELLED: No data are available on incisional hernia in renal transplant recipients using a midline incision. This study evaluated the incidence of abdominal wall incisional hernia, comparing two surgical approaches: midline and J-shaped incisions. METHODS: Between 1991 and 2005, 415 consecutive patients underwent renal transplantation: between 1991 and 1997, 139 patients through a lateral incision; between 1997 and 2005, 137 of 276 renal transplant patients via a midline incision, and 139 via a J-shaped incision. We evaluated the incidence of incisional herniae in these patients. Analyzed factor risks included: age, sex, body mass index, diabetes, reoperation, lymphocele, dialysis time, underlying renal disease, and immunosuppressive therapy. RESULTS: During follow-up, 15 patients of 415 transplantations were dead or lost to follow-up. Incisional herniae were identified in 12 cases of 132 (9%) between 1991 and 1997. Between 1997 and 2005 we identified 3 of 133 (2.2%) patients who underwent a midline incision and 15 of 135 (11.1%) who received a J-shaped incision (P=.005). Comparing midline and J-shaped incisions before and after 1997, the incidence reduction was significant (P=.01). Comparing the incidence among patients treated with J-shaped incision before versus after 1997, the increased incidence was insignificant (P=.6). Multivariate analysis found the most important risk factor was obesity followed by polycystic kidney disease, reoperation, wound infection, and mycophenolate mofetil therapy. CONCLUSIONS: Our data showed an advantage of a midline incision. Strategies to prevent surgical complications, such as abdominal wall relaxation and poor cosmetic results, are needed; the midline incision may be a possible alternative to address this complication.

Experimental training model of pancreas transplant.

UNLABELLED: Pancreas transplant (Ptx) is the gold standard for the treatment of type I diabetes, mainly when associated with renal failure. The number of Ptx is increasing worldwide, but in developing countries, such as Brazil, the number of centers is small and transplant surgeons need to practice the technique. METHODS: For this model, 21 pancreas harvestings were performed in patient corpses after death from extra-abdominal causes, without pancreatic disease and peritoneal or systemic infection. The vessels of the grafts were prepared on the backtable according to the usual practice in humans. The pancreas was implanted in the inferior vena cava and aorta of mixed breed dogs, with 10 exocrine-bladder drainage and 11 duodenum-ileal anastomosis. RESULTS: There were anastomotic strictures of the portal vein in dogs 1 and 2. There was no arterial stricture or large bleeding. None of the animals died until the revascularization of the graft. Dogs 2, 5, and 8 died during the exocrine anastomosis. The arterial flow was initially high, but at the end of the procedure there were thromboses of small arteries. CONCLUSION: The experimental surgical technique model is feasible, repeating the stages of clinical pancreatic transplantation and allowing the training of surgeons.

1H MRS signals from glutathione may act as predictive markers of apoptosis in irradiated tumour cells.

Inhibition of apoptosis in tumour cells may depend on intracellular reduced glutathione (GSH) level. In this work, GSH levels were studied by (1)H MRS in MCF-7 and HeLa cells, characterised by a different radiosensitivity. Annexin-V test showed that the fraction of apoptotic HeLa cells after irradiation is much higher than in control, although MCF-7 cells did not show a significant apoptosis. MRS signals from GSH (G) show lower intensity in HeLa with respect to MCF-7 cells; the opposite is true for free glutamic acid [glu (g)]. After irradiation, the G/g ratio decreases in MCF-7, although remaining approximately constant in HeLa cells. Buthionine sulfoximine (BSO) treated MCF-7 cells show an increase in the percentage of apoptotic cells; in parallel, G/g ratio behaves as in HeLa. This study indicates that GSH level may act as predictive marker of apoptosis by irradiation.

Radiation effects in cultured tumour cells examined by 1H MRS: mobile lipids modulation and proliferative arrest.

Much attention has been devoted in the past to monitor changes of mobile lipid (ML) (1)H MRS signals in spectra of tumour cells. The purpose of this work is to exploit ML signals to provide information on cell metabolism after irradiation, comparing tumour cells characterised by different radiosensitivity and relating MRS findings to changes in cell proliferation and delays in cell cycle phases. Irradiated HeLa cells present less intense ML signals with respect to controls. The opposite is true for MCF-7 cells. A G(2) arrest is observed for both cell lines after irradiation. In HeLa cells, G(1) decreases and S phase is maintained; a sub G(1) peak is also visible. In MCF-7 cells, G(1) is decreased and S phase is strongly reduced, while no sub G(1) is present. The observed changes in ML are tentatively associated to cell cycle regulation of phospholipid synthesis. Mathematical modelling of ML variations is in progress.

Ion diffusion modelling of Fricke-agarose dosemeter gels.

In Fricke-agarose gels, an accurate determination of the spatial dose distribution is hindered by the diffusion of ferric ions. In this work, a model was developed to describe the diffusion process within gel samples of finite length and, thus, permit the reconstruction of the initial spatial distribution of the ferric ions. The temporal evolution of the ion concentration as a function of the initial concentration is derived by solving Fick's second law of diffusion in two dimensions with boundary reflections. The model was applied to magnetic resonance imaging data acquired at high spatial resolution (0.3 mm) and was found to describe accurately the observed diffusion effects.

Optical images of dose distributions in Gel-Fricke: dosimetric performances of the gel.

The purpose of this work was to examine the dosimetric performances of the radiochromic Fricke-Agarose-Xylenol Orange gel by optical measurements in order to perform dose reconstructions, in view of a future development for 3-D maps. Optical images and dose-response curves of the gel were obtained by a CCD-based device, originally designed for reading radiochromic films, that was modified to meet the optical properties of the dosemeter. With a resolution of 0.18 x 0.18 mm the optimum range of doses in which per cent uncertainty is lower than 2% was 3-10 Gy. The minimum detectable dose, estimated as the absorbed dose corresponding to 3 SD above background, was 0.1 Gy. With a resolution of 1.98 x 1.98 mm the optimum range of doses in which per cent uncertainty is lower than 2% was 0.3-10 Gy. The minimum detectable dose, estimated as the absorbed dose corresponding to 3 SD above background, was 0.015 Gy. The comparison with alanine dosemeters in the dose range 7-10 Gy showed agreement within a few per cent and the same agreement was observed for the comparison with TLD in the range 1-3 Gy.

Optical imaging of dose distributions in Fricke gels.

Ferrous-sulphate infused gels, or 'Fricke gels', encounter great interest in the field of radiation dosimetry, due to their potential for 3D radiation dose mapping. Typically, magnetic resonance (MR) relaxation rates are determined in these systems in order to derive the absorbed dose. However, when large concentration gradients are present, diffusion effects before and during the MR imaging may not be negligible. In these cases, optical techniques may represent a viable alternative. This paper describes research aimed at measuring 3D dose distributions in a Fricke-xylenol orange gel by measuring optical density with a CCD camera. This method is inexpensive and fast. A series of early experiments is described, in which optical density profiles were measured with a commercial microdensitometer for film dosimetry. The light box of the device was modified to work at 567 nm, close to the maximum absorbance of the ferric ion-xylenol orange complex. Under these conditions, the gel shows linearity with dose and high sensitivity.

The interaction of histone H3 with histone H4 and with other histones studied by 19F nuclear magnetic resonance.

The behaviour, upon variations in ionic strength, pH and temperature of 19F nuclear nuclear magnetic resonance signals of the trifluoroacetonylated derivative of histone H3 is compared with those of the H3-H4 complex and of the Hv fraction (an equimolar mixture of H2A, H2B, H3 and h4). The line width of the 19F-labelled histone H3 signals increases with ionic strength or pH, an effect consistent with aggregation of the protein. In the case of H3-H4 complex or Hv the line width decreases at intermediate ionic strengths (0.1-0.25 M NaCl). This effect is interpreted as the consequence of the formation of a well defined structure with ionic strength. At high salt concentrations the line width increases as a consequence of the final rigid quaternary structure or of the formation of higher aggregates.

Changes in cell volume and internal sodium concentration in HeLa cells during exponential growth and following lonidamine treatment.

Cell volumes decreased in HeLa cells as a function of time after seeding during exponential growth. Cell volume distributions revealed the presence of two cell populations in all stages of growth. When cells approached confluence, the ratio of the two populations abruptly shifted towards that characterised by the smallest volume. Percentages of G1-, S- and G2 + M-phase cells were also measured and it was found that G1 frequency increased as a function of cell density during exponential growth. Intracellular sodium concentration, [Na]i was monitored by 23Na NMR in the presence of 5 mM dysprosium (III) tripolyphosphate. [Na]i increased from 22.8 to 59.0 mM in cells from the second to the seventh day after seeding. Treatment with lonidamine, an antitumoral drug that it is known to slow down cell growth by affecting aerobic glycolysis, produced a complete block of cell progression after a few days of treatment. The progression of cell volume distributions towards smaller volumes and the increase in internal sodium concentration as a function of time after seeding were also affected by the drug. These phenomena were related to the existence of a subpopulation of mitotically inactive G1-phase cells during exponential growth, pointing out that a density-dependent cellular mechanism regulates the cell cycling in HeLa cells.

Water and potassium dynamics inside the KcsA K(+) channel.

Molecular dynamics simulations and electrostatic modeling are used to investigate structural and dynamical properties of the potassium ions and of water molecules inside the KcsA channel immersed in a membrane-mimetic environment. Two potassium ions, initially located in the selectivity filter binding sites, maintain their position during 2 ns of dynamics. A third potassium ion is very mobile in the water-filled cavity. The protein appears engineered so as to polarize water molecules inside the channel cavity. The resulting water induced dipole and the positively charged potassium ion within the cavity are the key ingredients for stabilizing the two K(+) ions in the binding sites. These two ions experience single file movements upon removal of the potassium in the cavity, confirming the role of the latter in ion transport through the channel.

Effect of lipophilic vitamins on the erythrocyte membrane. 31P NMR and fluorescence studies.

Structural changes induced by the fat-soluble vitamins A, D3, E and K1 in natural membranes were studied by 31P NMR and fluorescence anisotropy on erythrocyte ghosts; the occurrence of cell fusion following vitamin addition was detected by optical microscopy of intact cells. Vitamins A, E and K1, which produce cell fusion, also induce the formation of configurational phases other than the bilayer and increase, at a different extent for the different vitamins, membrane fluidity. Vitamin D3, on the contrary, induces aggregation without fusion, paralleled by bilayer phase stabilization and microviscosity increase. A correlation between fusion phenomena and structural variations in the bilayer organization is therefore suggested.

Characterization of vesicles, containing an acylated oligopeptide, released by human colon adenocarcinoma cells. NMR and biochemical studies.

RNA-containing vesicles, recovered from the supernatant of high-density cell samples of human colon carcinoma, produce a high-resolution 1H NMR spectrum of lipids characterized by isotropic tumbling; these vesicles contain large amounts of triglycerides and cholesterol esters. Both findings have strict analogies to what is displayed by the proteolipid complexes isolated from the sera of tumor-bearing patients [(1985) Proc. Natl. Acad. Sci. USA 82, 3455-3459; (1986) FEBS Lett. 203, 164-168]. Lipid analysis and enzymatic tests indicate that these vesicles are selected micromaps of plasma membranes, analogous to those that can be recovered from culture media in which tumor cells are grown [(1985) Dev. Biol. 3, 33-57]. Peculiar lipids, an acylated oligopeptide and a modified phospholipid, are also present in the vesicles.