Differential Gene Expression Profiles May Differentiate Responder and Nonresponder Patients with Rheumatoid Arthritis for Methotrexate (MTX) Monotherapy and MTX plus Tumor Necrosis Factor Inhibitor Combined Therapy

Objective. We aimed to evaluate whether the differential gene expression profiles of patients with rheumatoid arthritis (RA) could distinguish responders from nonresponders to methotrexate (MTX) and, in the case of MTX nonresponders, responsiveness to MTX plus anti-tumor necrosis factor-alpha (anti-TNF) combined therapy. Methods. We evaluated 25 patients with RA taking MTX 15-20 mg/week as a monotherapy (8 responders and 17 nonresponders). All MTX nonresponders received intliximab and were reassessed after 20 weeks to evaluate their anti-TNF responsiveness using the European League Against Rheumatism response criteria. A differential gene expression analysis from peripheral blood mononuclear cells was performed in terms of hierarchical gene clustering, and an evaluation of differentially expressed genes was performed using the significance analysis of microarrays program. Results. Hierarchical gene expression clustering discriminated MTX responders from nonresponders, and MTX plus anti-TNF responders from nonresponders. The evaluation of only highly modulated genes (fold change > 1.3 or < 0.7) yielded 5 induced (4 antiapoptotic and CCL4) and 4 repressed (4 proapoptotic) genes in MTX nonresponders compared to responders. In MTX plus anti-TNF nonresponders, the CCL4, CD83, and BCL2A1 genes were induced in relation to responders. Conclusion. Study of the gene expression profiles of RA peripheral blood cells permitted differentiation of responders from nonresponders to MTX and anti-TNF. Several candidate genes in MTX non-responders (CCL4, HTRA2, PRKCD, BCL2A1, CAV1, TNIP1 CASP8AP2, MXD1, and BTG2) and 3 genes in MTX plus anti-TNF nonresponders (CCL4, CD83, and BCL2A1) were identified for further study. (First Release July 1 2012; J Rheumatol 2012;39:1524-32; doi:10.3899/jrheum.120092)

The influence of different indium-composition profiles on the electronic structure of lens-shaped InxGa1-xAs quantum dots

We present effective-mass calculations of the bound-state energy levels of electrons confined inside lens-shaped InxGa1-xAs quantum dots (QDs) embedded in a GaAs matrix, taking into account the strain as well as the In gradient inside the QDs due to the strong In segregation and In-Ga intermixing present in the InxGa1-xAs/GaAs system. In order to perform the calculations, we used a continuum model for the strain, and the QDs and wetting layer were divided into their constituting monolayers, each one with a different In concentration, to be able to produce a specific composition profile. Our results clearly show that the introduction of such effects is very important if one desires to correctly reproduce or predict the optoelectronic properties of these nanostructures.

The influence of captive breeding on the fatty acid profiles of Salminus hilarii (Characiformes: Characidae) eggs and larvae

In addition to the strong influence of the broodstock diet on the development and survival of offspring, domestication may also interfere with the larval life success. We obtained eggs from wild and domesticated Salminus hilarii females and domesticated males. Wild females were caught in the Tiete River and tributaries, and the domesticated females were born three years before the beginning of the experiment in the Ponte Nova Fish Farm. Animals from both groups were fed with the same feed to exclude feed variables. The eggs and larvae were sampled at 0, 8, 16, and 28 h after spawning (HAS), with the last sampling (28 HAS) coinciding with hatching time. After hatching, samplings proceeded at 32, 48, 66, and 96 HAS, with the last sampling (96 HAS) corresponding to the end of yolk sac consumption. Finally, the last experimental period was during the larvae exogenous feeding phase, at 102, 118, 166, and 214 HAS. Our data revealed that domestication of S. hilarii females influenced fatty acid (FA) metabolism during embryo and larva development. However, the structure of membrane phospholipid FA remained mostly stable, with changes principally in the neutral fraction. When the external conditions, mainly water and feed quality, remained constant, domestication of S. hilarii females did not significantly affect the structural FA composition but influenced the selectivity of consumption and/or storage of specific FA.

The fatty acid profiles and energetic substrates of two Nile tilapia (Oreochromis niloticus, Linnaeus) strains, Red-Stirling and Chitralada, and their hybrid

Protein and lipid content as well as the fatty acid (FA) composition of storage tissues were analysed in two varieties of Oreochromis niloticus (Red-Stirling and Chitralada) and their hybrid. The animals were maintained in cages for 11 months. The samples were taken when the animals weighed 10, 50, 100, 250 and 500 g. The results showed that changes in the metabolic processes occur during an increase in body mass in both varieties of tilapia and also their hybrid, but that these differences are not found in animals collected at the commercial weight. The protein content of the fillet and liver decreased with growth and the same protein content associated with growth was found for fillet lipid content. The genetic variety did not influence the FA profile of the fillet, but different genotypes had different hepatic FA compositions. Even with the same lipid content, the hepatocytes of Chitralada accumulated higher levels of polyunsaturated fatty acids (PUFA) n6 in triglycerides and increased C22:6n3 in the hepatocyte membranes. The higher n6PUFA content was compensated by a lower fraction of saturated FA in the hepatocyte triglycerides. The skin of Chitralada also had higher n6PUFA and C22:6n3 contents, suggesting a higher ability to deposit PUFA in the skin due to alterations in the liver synthetic pathway.

Biochemical and metabolic profiles of Trichoderma strains isolated from common bean crops in the Brazilian Cerrado, and potential antagonism against Sclerotinia sclerotiorum

Some species of Trichoderma have successfully been used in the commercial biological control of fungal pathogens, e.g., Sclerotinia sclerotiorum, an economically important pathogen of common beans (Phaseolus vulgaris L.). The objectives of the present study were (1) to provide molecular characterization of Trichoderma strains isolated from the Brazilian Cerrado; (2) to assess the metabolic profile of each strain by means of Biolog FF Microplates; and (3) to evaluate the ability of each strain to antagonize S. sclerotiorum via the production of cell wall-degrading enzymes (CWDEs), volatile antibiotics, and dual-culture tests. Among 21 isolates, we identified 42.86 % as Trichoderma asperellum, 33.33 % as Trichoderma harzianum, 14.29 % as Trichoderma tomentosum, 4.76 % as Trichoderma koningiopsis, and 4.76 % as Trichoderma erinaceum. Trichoderma asperellum showed the highest CWDE activity. However, no species secreted a specific group of CWDEs. Trichoderma asperellum 364/01, T. asperellum 483/02, and T. asperellum 356/02 exhibited high and medium specific activities for key enzymes in the mycoparasitic process, but a low capacity for antagonism. We observed no significant correlation between CWDE and antagonism, or between metabolic profile and antagonism. The diversity of Trichoderma species, and in particular of T. harzianum, was clearly reflected in their metabolic profiles. Our findings indicate that the selection of Trichoderma candidates for biological control should be based primarily on the environmental fitness of competitive isolates and the target pathogen. (C) 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Calculations of the spectral shifts and line profiles of alkaline earth atoms in liquid helium environment

Liquid configurations generated by Metropolis Monte Carlo simulations are used in time-dependent density functional theory calculations of the spectral line shifts and line profiles of the lowest lying excitation of the alkaline earth atoms, Be, Mg, Ca, Sr and Ba embedded in liquid helium. The results are in very good agreement with the available experimental data. Special attention is given to the calculated spectroscopic shift and the associated line broadening. The analysis specifies the inhomogeneous broadening of the three separate contributions due to the splitting of the s -> p transition of the alkaline earth atom in the liquid environment. (C) 2012 Elsevier B. V. All rights reserved.

Virulence Genes and Antimicrobial Resistance Profiles of Pasteurella multocida Strains Isolated from Rabbits in Brazil

Pasteurella multocida is responsible for a wide range of diseases in domestic animals. In rabbits, the agent is related to nasal discharge, pneumonia, otitis media, pyometra, orchitis, abscess, and septicemia. One hundred and forty rabbits with respiratory diseases from four rabbitries in Sao Paulo State, Brazil were evaluated for the detection of P. multocida in their nasal cavities. A total of twenty-nine animals were positive to P. multocida isolation, and 46 strains were selected and characterized by means of biochemical tests and PCR. P. multocida strains were tested for capsular type, virulence genes, and resistance profile. A total of 45.6% (21/46) of isolates belonged to capsular type A, and 54.34% (25/46) of the isolates were untypeable. None of the strains harboured toxA or pfhA genes. The frequency of the other twenty genes tested was variable, and the data generated was used to build a dendrogram, showing the relatedness of strains, which were clustered according to origin. Resistance revealed to be more common against sulfonamides and cotrimoxazole, followed by erythromycin, penicillin, and amoxicillin.

Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts

Abstract Background Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease. Methods In this study, gene expression profiles of CD34+ cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value ≤ 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts. In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value ≤ 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts. Conclusions These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34+ cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Spectral behavior of some modal soil profiles from São Paulo State, Brazil

Remote sensing has a high potential for environmental evaluation. However, a necessity exists for a better understanding of the relations between the soil attributes and spectral data. The objective of this work was to analyze the spectral behavior of some soil profiles from the region of Piracicaba, São Paulo State, using a laboratory spectroradiometer (400 to 2500 nm). The relations between the reflected electromagnetic energy and the soil physical, chemical and mineralogical attributes were analyzed, verifying the spectral variations of soil samples in depth along the profiles with their classification and discrimination. Sandy soil reflected more, presenting a spectral curve with an ascendant form, opposite to clayey soils. The 1900 nm band discriminated soil with 2:1 mineralogy from the 1:1 and oxidic soils. It was possible to detect the presence of kaolinite, gibbsite, hematite and goethite in the soils through the descriptive aspects of curves, absorption features and reflectance intensity. A relation exists between the weathering stage and spectral data. The evaluation of the superficial and subsuperficial horizon samples allowed characterizing and discriminating the analytical variability of the profile, helping to soil distinguishing and classification.

Performance and radial distribution profiles of a variable flow rate sprinkler developed for precision irrigation

Variable rate sprinklers (VRS) have been developed to promote localized water application of irrigated areas. In Precision Irrigation, VRS permits better control of flow adjustment and, at the same time, provides satisfactory radial distribution profiles for various pressures and flow rates are really necessary. The objective of this work was to evaluate the performance and radial distribution profiles of a developed VRS which varies the nozzle cross sectional area by moving a pin in or out using a stepper motor. Field tests were performed under different conditions of service pressure, rotation angles imposed on the pin and flow rate which resulted in maximal water throw radiuses ranging from 7.30 to 10.38 m. In the experiments in which the service pressure remained constant, the maximal throw radius varied from 7.96 to 8.91 m. Averages were used of repetitions performed under conditions without wind or with winds less than 1.3 m s-1. The VRS with the four stream deflector resulted in greater water application throw radius compared to the six stream deflector. However, the six stream deflector had greater precipitation intensities, as well as better distribution. Thus, selection of the deflector to be utilized should be based on project requirements, respecting the difference in the obtained results. With a small opening of the nozzle, the VRS produced small water droplets that visually presented applicability for foliar chemigation. Regarding the comparison between the estimated and observed flow rates, the stepper motor produced excellent results.

Testing phenomenological and theoretical models of dark matter density profiles with galaxy clusters

We use the stacked gravitational lensingmass profile of four high-mass (M 1015M ) galaxy clusters around z≈0.3 from Umetsu et al. to fit density profiles of phenomenological [Navarro– Frenk–White (NFW), Einasto, S´ersic, Stadel, Baltz–Marshall–Oguri (BMO) and Hernquist] and theoretical (non-singular Isothermal Sphere, DARKexp and Kang & He) models of the dark matter distribution. We account for large-scale structure effects, including a two-halo term in the analysis.We find that the BMO model provides the best fit to the data as measured by the reduced χ2. It is followed by the Stadel profile, the generalized NFW profile with a free inner slope and by the Einasto profile. The NFW model provides the best fit if we neglect the two-halo term, in agreement with results from Umetsu et al. Among the theoretical profiles, the DARKexp model with a single form parameter has the best performance, very close to that of the BMO profile. This may indicate a connection between this theoretical model and the phenomenology of dark matter haloes, shedding light on the dynamical basis of empirical profiles which emerge from numerical simulations.

PRoSPer: perceptual similarity queries in medical CBIR systems through user profiles

In this paper, we present a novel approach to perform similarity queries over medical images, maintaining the semantics of a given query posted by the user. Content-based image retrieval systems relying on relevance feedback techniques usually request the users to label relevant/irrelevant images. Thus, we present a highly effective strategy to survey user profiles, taking advantage of such labeling to implicitly gather the user perceptual similarity. The profiles maintain the settings desired for each user, allowing tuning of the similarity assessment, which encompasses the dynamic change of the distance function employed through an interactive process. Experiments on medical images show that the method is effective and can improve the decision making process during analysis.

Lipid and glucose profiles of dairy buffaloes during lactation and dry period

The purpose of this study was to analyze the influence of lactation and dry period in the constituents of lipid and glucose metabolism of buffaloes. One hundred forty-seven samples of serum and plasma were collected between November 2009 and July 2010, from properties raising Murrah, Mediterranean and crossbred buffaloes, located in the State of Sao Paulo, Brazil. Biochemical analysis was obtained by determining the contents of serum cholesterol, triglycerides, beta-hydroxybutyrate (β-HBO), non-esterified fatty acids (NEFA) and plasma glucose. Values for arithmetic mean and standard error mean were calculated using the SAS procedure, version 9.2. Tests for normality of residuals and homogeneity of variances were performed using the SAS Guide Data Analysis. Data were analyzed by ANOVA using the SAS procedure Glimmix. The group information (Lactation), Farm and Age were used in the statistical models. Means of groups were compared using Least Square Means (LSMeans) of SAS, where significant difference was observed at P ≤ 0.05. It was possible to conclude that buffaloes during peak lactation need to metabolize body reserves to supplement the lower amounts of bloodstream lipids, when they remain in negative energy balance. In the dry period, there were significant changes in the lipid profile, characterized by decrease of nutritional requirements, with consequent improvement in the general conditions of the animals.