Spontaneous noise reduction in a strongly cooperative reaction model

Noise characteristics of a simple multiparticle reaction model were investigated. The model can describe strongly cooperative reactions and is defined as follows. Particles A react in clusters of size k and each reaction forms a product molecule P. The back reaction is also allowed, and each cluster can dissociate into k reactants A. To describe a situation where the reaction is part of a pathway, the system is made open by assuming that particles A are injected and that particles P decay. This is a continuation study. The model is studied by using the same technique as employed previously, the pair approach reaction noise estimator (PARNES) method. Several new issues have been addressed. (i) In the previous work closeness to the Poisson distribution was used as a noise measure. In this work a more traditional noise measure, the ratio of the variance and the mean, was used to analyze stochastic features of the problem. (ii) The dependence of the new noise measure on k has been analyzed in detail, with an emphasis of investigating reactions with large k values. (iii) The previous study focused on understanding time-dependent issues, while this study focuses on describing the equilibrium state of the system. (iv) An exact solution (published elsewhere), available for closed system only, was used to re-investigate the validity of the PARNES method for describing reactions with large k. It was found that the PARNES method cannot describe fine details of the noise characteristics of such reactions.     

Escherichia coli peptide binding protein OppA has a preference for positively charged peptides

The Escherichia coli peptide binding protein OppA is an essential component of the oligopeptide transporter Opp. Based on studies on its orthologue from Salmonella typhimurium, it has been proposed that OppA binds peptides between two and five amino acids long, with no apparent sequence selectivity. Here, we studied peptide binding to E. coli OppA directly and show that the protein has an unexpected preference for basic peptides. OppA was expressed in the periplasm, where it bound to available peptides. The protein was purified in complex with tightly bound peptides. The crystal structure (up to 2.0 Å) of OppA liganded with the peptides indicated that the protein has a preference for peptides containing a lysine. Mass spectrometry analysis of the bound peptides showed that peptides between two and five amino acids long bind to the protein and indeed hinted at a preference for positively charged peptides. The preference of OppA for peptides with basic residues, in particular lysines, was corroborated by binding studies with peptides of defined sequence using isothermal titration calorimetry and intrinsic protein fluorescence titration. The protein bound tripeptides and tetrapeptides containing positively charged residues with high affinity, whereas related peptides without lysines/arginines were bound with low affinity. A structure of OppA in an open conformation in the absence of ligands was also determined to 2.0 Å, revealing that the initial binding site displays a negative surface charge, consistent with the observed preference for positively charged peptides. Taken together, E. coli OppA appears to have a preference for basic peptides.     

Novel insights into interactions between mitochondria and xanthine oxidase in acute cardiac volume overload

Xanthine oxidoreductase (XOR) is increased in the left ventricle (LV) of humans with volume overload (VO), and mitochondrial inhibition of the respiratory chain occurs in animal models of VO. Because mitochondria are both a source and a target of reactive oxygen and nitrogen species, we hypothesized that activation of XOR and mitochondrial dysfunction are interdependent. To test this we used the aortocaval fistula (ACF) rat model of VO and a simulation of the stretch response in isolated adult cardiomyocytes with and without the inhibitor of XOR, allopurinol, or the mitochondrially targeted antioxidant MitoQ. Xanthine oxidase (XO) activity was increased in cardiomyocytes from ACF vs sham rats (24h) without an increase in XO protein. A twofold increase in LV end-diastolic pressure/wall stress and a decrease in LV systolic elastance with ACF were improved when allopurinol treatment (100mg/kg) was started at ACF induction. Subsarcolemmal State 3 mitochondrial respiration was significantly decreased in ACF and normalized by allopurinol. Cardiomyocytes subjected to 3h cyclical stretch resulted in an increase in XO activity and mitochondrial swelling, which was prevented by allopurinol or MitoQ pretreatment. These studies establish an early interplay between cardiomyocyte XO activation and bioenergetic dysfunction that may provide a new target that prevents progression to heart failure in VO.     

Horizontal or vertical photobioreactors? How to improve microalgae photosynthetic efficiency

The productivity of a vertical outdoor photobioreactor was quantitatively assessed and compared to a horizontal reactor. Daily light cycles in southern Spain were simulated and applied to grow the microalgae Chlorella sorokiniana in a flat panel photobioreactor.The maximal irradiance around noon differs from 400 μmol photons m⁻² s⁻¹ in the vertical position to 1800 μmol photons m⁻² s⁻¹ in the horizontal position. The highest volumetric productivity was achieved in the simulated horizontal position, 4 g kg culture⁻¹ d⁻¹. The highest photosynthetic efficiency was found for the vertical simulation, 1.3 g of biomass produced per mol of PAR photons supplied, which compares favorably to the horizontal position (0.85 g mol⁻¹) and to the theoretical maximal yield (1.8 g mol⁻¹). These results prove that productivity per unit of ground area could be greatly enhanced by placing the photobioreactors vertically.     

A comparative analysis of Acuros XB and the analytical anisotropic algorithm for volumetric modulation arc therapy

BackgroundThis study aimed to verify the dosimetric impact of Acuros XB (AXB) (AXB, Varian Medical Systems Palo Alto CA, USA), a two model-based algorithm, in comparison with Anisotropic Analytical Algorithm (AAA ) calculations for prostate, head and neck and lung cancer treatment by volumetric modulated arc therapy (VMAT ), without primary modification to AA. At present, the well-known and validated AA algorithm is clinically used in our department for VMAT treatments of different pathologies. AXB could replace it without extra measurements. The treatment result and accuracy of the dose delivered depend on the dose calculation algorithm.Materials and methodNinety-five complex VMAT plans for different pathologies were generated using the Eclipse version 15.0.4 treatment planning system (TPS). The dose distributions were calculated using AA and AXB (dose-to-water, AXB_w and dose-to-medium, AXB_m), with the same plan parameters for all VMAT plans. The dosimetric parameters were calculated for each planning target volume (PTV) and involved organs at risk (OA R). The patient specific quality assurance of all VMAT plans has been verified by Octavius^®-4D phantom for different algorithms.ResultsThe relative differences among AA, AXB_w and AXB_m, with respect to prostate, head and neck were less than 1% for PTV D_95%. However, PTV D_95% calculated by AA tended to be overestimated, with a relative dose difference of 3.23% in the case of lung treatment. The absolute mean values of the relative differences were 1.1 ± 1.2% and 2.0 ± 1.2%, when comparing between AXB_w and AA, AXB_m and AA, respectively. The gamma pass rate was observed to exceed 97.4% and 99.4% for the measured and calculated doses in most cases of the volumetric 3D analysis for AA and AXB_m, respectively.ConclusionThis study suggests that the dose calculated to medium using AXB_m algorithm is better than AAA and it could be used clinically. Switching the dose calculation algorithm from AA to AXB does not require extra measurements.     

Thermoregulation and water balance in fat-tailed sheep and Kacang goat under sunlight exposure and water restriction in a hot and dry area

The objective of this study was to analyze differences in thermoregulation and water balance under conditions of heat load and water restriction between fat-tailed sheep (S) and Kacang goats (G). The daily intakes of food and water, daily outputs of urine and feces, rectal temperature, respiration rates, hematocrit values and plasma volumes of five shorn S and five G were determined over 10 days of four consecutive experimental conditions: (1) indoor--unrestricted water; (2) indoor--restricted water; (3) 10 h sunlight exposure--unrestricted water; and (4) 10 h sunlight exposure--restricted water. There was a 6- to 7-day adjustment period between two consecutive conditions. The study was conducted during the dry season. The animals were placed in individual cages, fed chopped native grass ad libitum and had free access to a urea-molasses multi-nutrient block. Under sunlight exposure with unrestricted water availability, S and G record an increase in the maximum rectal temperatures from 39.2°C to 40.2°C and from 39.9°C to 41.8°C, respectively. The thermoregulatory strategy used by S for maintaining a lower rectal temperature mostly depends on increasing the respiration rate as the main cooling mechanism. On the other hand, G apparently used sweating as the predominant mechanism for cooling. Moreover, G seemed to be more tolerable to higher heat storage and body temperature than S with a significant increase in plasma volume (P<0.01), and this may be beneficial to the animals for the prevention of water loss. Under restricted water condition in either indoor or outdoor environment, both species decreased their plasma volume significantly, but rectal temperatures were relatively maintained. In all experimental conditions, the daily total water exchanges (ml/kg0.82 per day) of S were significantly higher than G (P<0.01). However, when the percentages of the total daily water exchange were considered, the water lost through urination (38% to 39%), defecation (11% to 14%) and evaporation (46% to 49%) by S and G was not significantly different. Therefore, the results from this study clearly showed that S and G have different homeostatic strategies for the regulation of body temperature and fluid to cope with heat load and water restriction. These differences may have an important impact on the production management of S and G.     

Aqueous two phase extraction of invertase from baker's yeast: Effect of process parameters on partitioning

Invertase (β-d-fructofuronoside fructohydrolase) is an industrially important enzyme useful for the hydrolysis of sucrose. The potential of aqueous two phase extraction for the isolation and purification of invertase from crude baker's yeast is explored. Influence of the process parameters such as type of phase forming salts, PEG molecular weight, concentration of salt and polymer, tie line length and volume ratio on partitioning of invertase was studied. PEG 3350/magnesium sulphate system was found most suitable for the extraction which has resulted in favorable pH (5 ± 0.2) for the enzyme extraction. Polymer and salt concentration were found to significantly affect the degree of purification and enzyme recovery of invertase. The purity of ∼8.81 fold was obtained compared to crude extract with recovery of 77% at the standardized process conditions. Overall results demonstrated the feasibility of aqueous two phase extraction for the isolation and purification of invertase without the need of multiple steps.     

Loss of alveolar membrane diffusing capacity and pulmonary capillary blood volume in pulmonary arterial hypertension

Background

Reduced gas transfer in patients with pulmonary arterial hypertension (PAH) is traditionally attributed to remodeling and progressive loss of pulmonary arterial vasculature that results in decreased capillary blood volume available for gas exchange.

Methods

We tested this hypothesis by determination of lung diffusing capacity (DL) and its components, the alveolar capillary membrane diffusing capacity (D_m) and lung capillary blood volume (V_c) in 28 individuals with PAH in comparison to 41 healthy individuals, and in 19 PAH patients over time. Using single breath simultaneous measure of diffusion of carbon monoxide (DL_CO) and nitric oxide (DL_NO), DL and D_m were respectively determined, and V_c calculated. D_m and V_c were evaluated over time in relation to standard clinical indicators of disease severity, including brain natriuretic peptide (BNP), 6-minute walk distance (6MWD) and right ventricular systolic pressure (RVSP) by echocardiography.

Results

Both DL_CO and DL_NO were reduced in PAH as compared to controls and the lower DL in PAH was due to loss of both D_m and V_c (all p < 0.01). While DL_CO of PAH patients did not change over time, DL_NO decreased by 24 ml/min/mmHg/year (p = 0.01). Consequently, D_m decreased and V_c tended to increase over time, which led to deterioration of the D_m/V_c ratio, a measure of alveolar-capillary membrane functional efficiency without changes in clinical markers.

Conclusions

The findings indicate that lower than normal gas transfer in PAH is due to loss of both D_m and V_c, but that deterioration of D_m/V_c over time is related to worsening membrane diffusion.     

Measurement of primary tumor volume by PET–CT to evaluate risk of mediastinal nodal involvement in NSCLC patients with clinically negative N2 lymph nodes

Aim

The study aimed to determine a prognostic value of primary tumor volume measured on the basis of integrated positron emission tomography–computerized tomography (PET–CT) in terms of mediastinal nodal metastases (N2) prediction in non-small-cell lung cancer (NSCLC) patients with PET–CT N2 negative lymph nodes.

Methods

The records of 70 potentially operable NSCLC patients treated with surgical resection were analyzed. All patients underwent diagnostic, preoperative PET–CT, which was the basis for tumor volume calculations as well as the evaluation of N2 nodes status. The logistic regression analysis was employed to determine correlation between mediastinal nodal involvement and volume of primary tumor (izoSUV2.5 volume), that is the volume of primary tumor inside SUV 2.5 line, tumor histology, location (peripheral vs. central), hilar node status.

Results

A statistically significant correlation between mediastinal node involvement and izoSUV2.5 volume, tumor histology, locations peripheral vs. central and hilar node status was found. The risk of mediastinal lymph node metastasis is 24% for tumor volume of 100 cm³ and increases up to 40% for tumor volume of 360 cm³. An increase of tumor volume by 1 cm³ increases the risk of lymph node disease by 0.3%. Tumor histology adenocarcinoma vs. squamous cell carcinoma increases the risk of mediastinal lymph node involvement by 195%, location central vs. peripheral by 68% and hilar node involvement by 166%.

Conclusions

The study demonstrates that izoSUV2.5 volume of primary tumor may be considered as a prognostic factor in NSCLC patients, since it strongly correlates with mediastinal lymph node pathological status. This correlation is modified by primary tumor location, histology and hilar node involvement.     

Comparison of dosimetric variation between prostate IMRT and VMAT due to patient's weight loss: Patient and phantom study

Aim

This study compared the dosimetric impact between prostate IMRT and VMAT due to patient''s weight loss.

Background

Dosimetric variation due to change of patient''s body contour is difficult to predict in prostate IMRT and VMAT, since a large number of small and irregular segmental fields is used in the delivery.

Materials and methods

Five patients with prostate volumes ranging from 32.0 to 86.5 cm³ and a heterogeneous pelvis phantom were used for prostate IMRT and VMAT plans using the same set of dose–volume constraints. Doses in IMRT and VMAT plans were recalculated with the patient''s and phantom''s body contour reduced by 0.5–2 cm to mimic size reduction. Dose coverage/criteria of the PTV and CTV and critical organs (rectum, bladder and femoral heads) were compared between IMRT and VMAT.

Results

In IMRT plans, increases of the D99% for the PTV and CTV were equal to 4.0 ± 0.1% per cm of reduced depth, which were higher than those in VMAT plans (2.7 ± 0.24% per cm). Moreover, increases of the D30% of the rectum and bladder per reduced depth in IMRT plans (4.0 ± 0.2% per cm and 3.5 ± 0.5% per cm) were higher than those of VMAT (2.2 ± 0.2% per cm and 2.0 ± 0.6% per cm). This was also true for the increase of the D5% for the right femoral head in a patient or phantom with size reduction due to weight loss.

Conclusions

VMAT would be preferred to IMRT in prostate radiotherapy, when a patient has potential to suffer from weight loss during the treatment.