Parton energy loss in heavy-ion collisions via direct-photon and charged-particle azimuthal correlations

Charged-particle spectra associated with direct photon (gamma(dir)) and pi(0) are measured in p + p and Au + Au collisions at center-of-mass energy root(S)(NN) = 200 GeV with the STAR detector at the Relativistic Heavy Ion Collider. A shower-shape analysis is used to partially discriminate between gamma(dir) and pi(0). Assuming no associated charged particles in the gamma(dir) direction ( near side) and small contribution from fragmentation photons (gamma(frag)), the associated charged-particle yields opposite to gamma(dir) (away side) are extracted. In central Au + Au collisions, the charged-particle yields at midrapidity (vertical bar eta vertical bar < 1) and high transverse momentum (3 < (assoc)(PT) < 16 GeV/c) associated with gamma(dir) and pi(0) (vertical bar eta vertical bar < 0.9, 8 < (trig)(PT) < 16 GeV/c) are suppressed by a factor of 3-5 compared with p + p collisions. The observed suppression of the associated charged particles is similar for gamma(dir) and pi(0) and independent of the gamma(dir) energy within uncertainties. These measurements indicate that, in the kinematic range covered and within our current experimental uncertainties, the parton energy loss shows no sensitivity to the parton initial energy, path length, or color charge.

Protein preparation, crystallization and preliminary X-ray analysis of Trypanosoma cruzi nucleoside diphosphate kinase 1

The flagellated protozoan parasite Trypanosoma cruzi is the aetiological agent of Chagas disease. Nucleoside diphosphate kinases (NDPKs) are enzymes that are involved in energy management and nucleoside balance in the cell. T. cruzi TcNDPK1, a canonical isoform, was overexpressed in Escherichia coli as an N-terminally poly-His-tagged fusion protein and crystallized. Crystals grew after 72 h in 0.2 M MgCl(2), 20% PEG 3350. Data were collected to 3.5 angstrom resolution using synchrotron X-ray radiation at the National Synchrotron Light Laboratory (Campinas, Brazil). The crystals belonged to the trigonal space group P3, with unit-cell parameters a = b = 127.84, c = 275.49 angstrom. Structure determination is under way and will provide relevant information that may lead to the first step in rational drug design for the treatment of Chagas disease.

Identification of the Schistosoma mansoni TNF-Alpha Receptor Gene and the Effect of Human TNF-Alpha on the Parasite Gene Expression Profile

Background: Schistosoma mansoni is the major causative agent of schistosomiasis. The parasite takes advantage of host signals to complete its development in the human body. Tumor necrosis factor-alpha (TNF-alpha) is a human cytokine involved in skin inflammatory responses, and although its effect on the adult parasite's metabolism and egg-laying process has been previously described, a comprehensive assessment of the TNF-alpha pathway and its downstream molecular effects is lacking. Methodology/Principal Findings: In the present work we describe a possible TNF-alpha receptor (TNFR) homolog gene in S. mansoni (SmTNFR). SmTNFR encodes a complete receptor sequence composed of 599 amino acids, and contains four cysteine-rich domains as described for TNFR members. Real-time RT-PCR experiments revealed that SmTNFR highest expression level is in cercariae, 3.5 (+/- 0.7) times higher than in adult worms. Downstream members of the known human TNF-alpha pathway were identified by an in silico analysis, revealing a possible TNF-alpha signaling pathway in the parasite. In order to simulate parasite's exposure to human cytokine during penetration of the skin, schistosomula were exposed to human TNF-alpha just 3 h after cercariae-to-schistosomula in vitro transformation, and large-scale gene expression measurements were performed with microarrays. A total of 548 genes with significantly altered expression were detected, when compared to control parasites. In addition, treatment of adult worms with TNF-alpha caused a significantly altered expression of 1857 genes. Interestingly, the set of genes altered in adults is different from that of schistosomula, with 58 genes in common, representing 3% of altered genes in adults and 11% in 3 h-old early schistosomula. Conclusions/Significance: We describe the possible molecular elements and targets involved in human TNF-alpha effect on S. mansoni, highlighting the mechanism by which recently transformed schistosomula may sense and respond to this host mediator at the site of cercarial penetration into the skin.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

Biotransformations of Substituted Phenylethanols and Acetophenones by Environmental Bacteria

Whole cells of hydrocarbon-degrading bacteria, isolated from polluted sediments in the Santos Estuary (Baixada Santista, Sao Paulo, Brazil), were able to catalyse oxidoreduction reactions with various substituted phenylethanols and acetophenones as substrates. A number of substituted phenylethanols were formed with high (>99 %) enantiomeric excess. The results of microbial oxidation of phenylethanols 2, 3, 5-7 by Acinetobacter sp. 6.4T and the reduction of acetophenones 1a-6a by Serratia marcescens 5.4T showed that the bacteria used as biocatalysts in this study present significant potential for exploitation in biotechnological processes. The reduction of prochiral acetophenones by Serratia marcescens 3.5T yielded optically active alcohols with 90-99 % enantiomeric excess, and Acinetobacter sp. 6.4T is a potential biocatalyst for the oxidation of alcohols.

Flow injection analysis of paracetamol using a biomimetic sensor as a sensitive and selective amperometric detector

This work describes the coupling of a biomimetic sensor to a flow injection system for the sensitive determination of paracetamol. The sensor was prepared as previously described in the literature (M. D. P. T. Sotomayor, A. Sigoli, M. R. V. Lanza, A. A. Tanaka and L. T. Kubota, J. Braz. Chem. Soc., 2008, 19, 734) by modifying a glassy carbon electrode surface with a Nafion (R) membrane doped with iron tetrapyridinoporphyrazine (FeTPyPz), a biomimetic catalyst of the P450 enzyme. The performance of the sensor for paracetamol detection was investigated and optimized in a flow injection system (FIA) using a wall jet electrochemical cell. Under optimized conditions a wide linear response range (1.0 x 10(-5) to 5.0 x 10(-2) mol L(-1)) was obtained, with a sensitivity of 2579 (+/- 129) mu A L mu mol(-1). The detection and quantification limits of the sensor for paracetamol in the FIA system were 1.0 and 3.5 mu mol L(-1), respectively. The analytical frequency was 51 samples h(-1), and over a period of five days (320 determinations) the biosensor maintained practically the same response. The system was successfully applied to paracetamol quantification in seven pharmaceutical formulations and in water samples from six rivers in Sao Paulo State, Brazil.

Morphology and biology of a new Pseudopolydora (Annelida: Spionidae) species from Brazil

Adults of Pseudopolydora rosebelae sp. nov. inhabit silty tubes on muddy bottoms in shallow water in southern Brazil, states of Sao Paulo and Rio de Janeiro. They are rare and extremely delicate, attaining 20 mm long for 55 chaetigers. The worms are distinctive by their colourful yellow and black pigmentation on the anterior part of body and palps, prominent transverse hood on the dorsal anterior edge of chaetiger 3, and lack of coloured respiratory pigment in blood. Of 12 examined individuals, all were females. Oogenesis is intraovarian; oocytes develop from chaetigers 14-15 to chaetigers 24-36. Recently laid oocytes were about 150 mu m in diameter, with embryos and developing larvae found in capsules inside female tubes in March-June. Broods comprised up to 23 capsules with 400 propagules. Capsules were joined to each other in a string and each attached by a single thin stalk to the inner wall of the tube. Larvae hatched at the 4-chaetiger stage and fed on plankton. Pelagic larvae are unique among Pseudopolydora in having large ramified mid-dorsal melanophores from chaetiger 3 onwards. Competent larvae are able to settle and metamorphose at the 15-chaetiger stage, but can remain planktonic up to 18 chaetigers. They have one pair of unpigmented ocelli and three pairs of black eyes in the prostomium, unpaired ramified mid-dorsal melanophores on chaetiger 1 and on the pygidium, ramified lateral melanophores on chaetigers 5-10, prominent yellow chromatophores in the prostomium, peristomium, on dorsal and ventral sides of chaetigers and in the pygidium. Branchiae are present on chaetigers 7-10, and gastrotrochs are arranged on chaetigers 3, 5, 7 and 12. Provisional serrated bristles are present in all notopodia, and hooks are present in neuropodia from chaetiger 8 onwards. Two pairs of provisional protonephridia are present in chaetigers 1 and 2, and adult metanephridia are present from chaetiger 4.

Lignin phenols used to infer organic matter sources to Sepetiba Bay - RJ, Brasil

Lignin phenols were measured in the sediments of Sepitiba Bay, Rio de Janeiro, Brazil and in bedload sediments and suspended sediments of the four major fluvial inputs to the bay: Sao Francisco and Guandu Channels and the Guarda and Cacao Rivers. Fluvial suspended lignin yields (Sigma 8 3.5-14.6 mgC 10 g dw(-1)) vary little between the wet and dry seasons and are poorly correlated with fluvial chlorophyll concentrations (0.8-50.2 mu gC L(-1)). Despite current land use practices that favor grassland agriculture or industrial uses, fluvial lignin compositions are dominated by a degraded leaf-sourced material. The exception is the Guarda River, which has a slight influence from grasses. The Lignin Phenol Vegetation Index, coupled with acid/aldehyde and 3.5 Db/V ratios, indicate that degraded leaf-derived phenols are also the primary preserved lignin component in the bay. The presence of fringe Typha sp. and Spartina sp. grass beds surrounding portions of the Bay are not reflected in the lignin signature. Instead, lignin entering the bay appears to reflect the erosion of soils containing a degraded signature from the former Atlantic rain forest that once dominated the watershed, instead of containing a significant signature derived from current agricultural uses. A three-component mixing model using the LPVI, atomic N:C ratios, and stable carbon isotopes (which range between -26.8 and -21.8 parts per thousand) supports the hypothesis that fluvial inputs to the bay are dominated by planktonic matter (78% of the input), with lignin dominated by leaf (14% of the input) over grass (6%). Sediments are composed of a roughly 50-50 mixture of autochthonous material and terrigenous material, with lignin being primarily sourced from leaf. (C) 2010 Elsevier Ltd. All rights reserved.

A flow injection procedure based on solenoid micro-pumps for spectrophotometric determination of free glycerol in biodiesel

A flow system designed with solenoid micro-pumps is proposed for fast and greener spectrophotometric determination of free glycerol in biodiesel. Glycerol was extracted from samples without using organic solvents. The determination involves glycerol oxidation by periodate, yielding formaldehyde followed by formation of the colored (3,5-diacetil-1,4-dihidrolutidine) product upon reaction with acetylacetone. The coefficient of variation, sampling rate and detection limit were estimated as 1.5% (20.0 mg L(-1) glycerol, n =10), 34 h(-1), and 1.0 mg L(-1) (99.7% confidence level), respectively. A linear response was observed from 5 to 50 mg L(-1), with reagent consumption estimated as 345 mu g of KIO(4) and 15 mg of acetylacetone per determination. The procedure was successfully applied to the analysis of biodiesel samples and the results agreed with the batch reference method at the 95% confidence level. (C) 2010 Elsevier B.V. All rights reserved.

Sequential spectrofluorimetric determination of free and total glycerol in biodiesel in a multicommuted flow system

A new procedure for spectrofluorimetric determination of free and total glycerol in biodiesel samples is presented. It is based on the oxidation of glycerol by periodate, forming formaldehyde, which reacts with acetylacetone, producing the luminescent 3,5-diacetyl-1,4-dihydrolutidine. A flow system with solenoid micro-pumps is proposed for solution handling. Free glycerol was extracted off-line from biodiesel samples with water, and total glycerol was converted to free glycerol by saponification with sodium ethylate under sonication. For free glycerol, a linear response was observed from 5 to 70 mg L(-1) with a detection limit of 0.5 mg L(-1), which corresponds to 2 mg kg(-1) in biodiesel. The coefficient of variation was 0.9% (20 mg L(-1), n = 10). For total glycerol, samples were diluted on-line, and the linear response range was 25 to 300 mg L(-1). The detection limit was 1.4 mg L(-1) (2.8 mg kg(-1) in biodiesel) with a coefficient of variation of 1.4% (200 mg L(-1), n = 10). The sampling rate was ca. 35 samples h(-1) and the procedure was applied to determination of free and total glycerol in biodiesel samples from soybean, cottonseed, and castor beans.

Liquid-liquid microextraction without phase separation in a multicommuted flow system for diltiazem determination in pharmaceuticals

Liquid-liquid microextraction without phase segmentation was implemented in a multicommuted flow system for determination of the anti-hypertensive diltiazem. The procedure was based on ion pair formation between the drug and the dye bromothymol blue at pH 3.5. The detection was performed without phase separation in a glass tube coupled to a fiber-optics spectrophotometer. The total volume of chloroform was reduced to 50 mu L in comparison with 10 mL consumed in batch. A linear response was observed between 9 and 120 mu mol L(-1), with a detection limit of 0.9 mu mol L(-1) (99.7% confidence level). The coefficient of variation (n = 10), sampling rate and extraction efficiency were estimated as 0.6%, 78 determinations per hour and 61%, respectively. About 30 mu g of bromothymol blue was consumed and the waste volume was 380 mu L per determination. The results for pharmaceutical samples agreed with those obtained by the reference procedure at the 95% confidence level. (C) 2011 Elsevier B.V. All rights reserved.

Macronutrients in Marandu Palisade Grass as Influenced by Lime, Slag, and Nitrogen Fertilization

Soil acidity is one of the main limiting factors for the growth of pasture grasses in Brazilian soils. In addition to lime, slag can be used to correct soil acidity and help plants to absorb nutrients in adequate amounts. The objective of this experiment was to evaluate, under greenhouse conditions, the effects of slag and lime plus nitrogen (N) on marandu palisade grass plants` nutritional status as well as the absorption of macronutrients submitted to two cuts. The treatments consisted of two corrective materials (slag and lime), three corrective material rates (0.81, 1.61, and 3.22 g dm-3 of ECaCO3), three N rates (75, 150, and 300 mg dm-3) plus a control treatment, with four replications. Macronutrient contents in the forage plants were found to be present in adequate levels. The mean value of N accumulated in the shoot was 40.1 mg per plant, phosphorus (P) was 4.6 mg per plant, potassium (K) was 38.6 mg per plant, calcium (Ca) was 7.3 mg per plant, magnesium (Mg) was 6.7 mg per plant, and sulfur (S) was 3.5 mg per plant at the first cut. At the second cut, the nutrient accumulations values were N 50.8 mg per plant, P 6.3 mg per plant, K 20.7 mg per plant, Ca 21.6 mg per plant, Mg 24.0 mg per plant, and S 4.7 mg per plant. Macronutrients accumulation in the shoot of grass increased with the addition of both the correctives as well as the N rates.

Microsatellite Polymorphisms in Cassava Landraces from the Cerrado Biome, Mato Grosso do Sul, Brazil

Using nine microsatellite loci, we investigated genetic structure and diversity in 83 Brazilian cassava accessions, including several landraces, in the Cerrado biome in Mato Grosso do Sul, Brazil. All nine loci were polymorphic, averaging 6.00 alleles per locus. Treating each of seven municipalities as a cassava group or population, they averaged 3.5 alleles per locus, with 97% polymorphic loci, high values for observed heterozygosity (0.32) and gene diversity (0.56). Total genetic variability was high (0.668), and most of this genetic variability was concentrated within municipalities (0.577). Cluster and structure analyses divided accessions into two major clusters or populations (K = 2). Also, a significant genetic versus geographic correlation was found (r = 0.4567; P < 0.0260). Migratory routes in the Cerrado are considered main contributors to the region`s high cassava diversity and spatial genetic structure, amplifying interactions between traditional farmers and the evolutionary dynamics of this crop.

Severe Lactic Acidosis Treated With Prolonged Hemodiafiltration in a Disseminated Histoplasmosis

Infections with Histoplasma are rarely seen in immunocompromized patients. We report the case of a renal transplant recipient who presented with disseminated histoplasmosis 3.5 years after transplant He presented severe lactic acidosis (LA), sepsis complicated by circulatory failure, renal failure, and liver dysfunction. We describe the successful use of continuous venovenous hemodiafiltration (CVVHDF) with regional citrate anticoagulation, treatment that stabilized our patient until infectious focus was identified and treated. The lactate was decreasing, concomitant with hemodynamic improvement, with reduction and suspension of the norepinephrine. The serum lactate level normalized 52 hours after CVVHDF initiated (from 28.9 to 2.2 mmol/L). Continuous renal replacement therapy was safely applied and can be recommended as an efficient method on adjuvant treatment of hyperlactatemia. ASAIO Journal 2009; 55:123-125.

Understanding Pain and Quality of Life for Patients With Chronic Venous Ulcers

Aim. To identify the impact of pain on quality of life (QOL) of patients with chronic venous ulcers. Methods. A cross-sectional study was performed on 40 outpatients with chronic venous ulcers who were recruited at one outpatient care center in Sao Paulo, Brazil. WHOQOL-Bref was used to assess QOL, the McGill Pain Questionnarie-Short Form (MPQ) to identify pain characteristics, and an 11-point numerical pain rating scale to measure pain intensity. Kruskall-Wallis or ANOVA test, with post-hoc correction (Tukey test) was applied to compare groups. Multiple linear regression models were used. Results. The mean age of the patients was 67 +/- 11 years (range, 39-95 years), and 26 (65%) were women. The prevalence of pain was 90%, with worst pain mean intensity of 6.2 +/- 3.5. Severe pain was the most prevalent (21 patients, 52.5%). Pain most frequently reported was sensory-discriminative and evaluate in quality. Pain was significantly and negatively correlated with physical (PY), environmental (EV), and overall QOL. Compared to a no-pain group, those with pain had lower overall QOL. On multiple analyses, pain remained as a predictor of overall QOL (beta = -0.73, P = 0.03) and was also predictive of social QOL, whereas pain did not have any impact on physical, emotional, or social relationships QOL (beta = -3.85, P = 0.00) when adjusted for age, number, duration and frequency of wounds, pain dimension (MPQ), partnership, and economic status. Conclusion. To improve QOL of out-patients with chronic venous ulcers, the qualities and the intensity of pain must be considered differently.