A simplified minimal residual disease polymerase chain reaction method at early treatment points can stratify children with acute lymphoblastic leukemia into good and poor outcome groups

Background Minimal residual disease is an important independent prognostic factor in childhood acute lymphoblastic leukemia. The classical detection methods such as multiparameter flow cytometry and real-time quantitative polymerase chain reaction analysis are expensive, time-consuming and complex, and require considerable technical expertise. Design and Methods We analyzed 229 consecutive children with acute lymphoblastic leukemia treated according to the GBTLI-99 protocol at three different Brazilian centers. Minimal residual disease was analyzed in bone marrow samples at diagnosis and on days 14 and 28 by conventional homo/heteroduplex polymerase chain reaction using a simplified approach with consensus primers for IG and TCR gene rearrangements. Results At least one marker was detected by polymerase chain reaction in 96.4%, of the patients. By combining the minimal residual disease results obtained on days 14 and 28, three different prognostic groups were identified: minimal residual disease negative on days 14 and 28, positive on day 14/negative on day 28, and positive on both. Five-year event-free survival rates were 85%, 75.6%,, and 27.8%, respectively (p<0.0001). The same pattern of stratification held true for the group of intensively treated children. When analyzed in other subgroups of patients such as those at standard and high risk at diagnosis, those with positive B-derived CD10, patients positive for the TEL/AML1 transcript, and patients in morphological remission on a day 28 marrow, the event-free survival rate was found to be significantly lower in patients with positive minimal residual disease on day 28. Multivariate analysis demonstrated that the detection of minimal residual disease on day 28 is the most significant prognostic factor. Conclusions This simplified strategy for detection of minimal residual disease was feasible, reproducible, cheaper and simpler when compared with other methods, and allowed powerful discrimination between children with acute lymphoblastic leukemia with a good and poor outcome.

Suppression of away-side jet fragments with respect to the reaction plane in Au plus Au collisions at root s(NN)=200 GeV

Pair correlations between large transverse momentum neutral pion triggers (p(T) = 4-7 GeV/c) and charged hadron partners (p(T) = 3-7 GeV/c) in central (0%-20%) and midcentral (20%-60%) Au + Au collisions at root s(NN) = 200 GeV are presented as a function of trigger orientation with respect to the reaction plane. The particles are at larger momentum than where jet shape modifications have been observed, and the correlations are sensitive to the energy loss of partons traveling through hot densematter. An out-of-plane trigger particle produces only 26 +/- 20% of the away-side pairs that are observed opposite of an in-plane trigger particle for midcentral (20%-60%) collisions. In contrast, near-side jet fragments are consistent with no suppression or dependence on trigger orientation with respect to the reaction plane. These observations are qualitatively consistent with a picture of little near-side parton energy loss either due to surface bias or fluctuations and increased away-side parton energy loss due to a long path through the medium. The away-side suppression as a function of reaction-plane angle is shown to be sensitive to both the energy loss mechanism and the space-time evolution of heavy-ion collisions.

Transition amplitude for two-time physics

We present the transition amplitude for a particle moving in a space with two times and D space dimensions having an Sp(2, R) local symmetry and an SO(D, 2) rigid symmetry. It was obtained from the BRST-BFV quantization with a unique gauge choice. We show that by constraining the initial and final points of this amplitude to lie on some hypersurface of the D + 2 space the resulting amplitude reproduces well-known systems in lower dimensions. This work provides an alternative way to derive the effects of two-time physics where all the results come from a single transition amplitude.

Observation of Two-Source Interference in the Photoproduction Reaction AuAu -> AuAu rho(0)

In ultraperipheral relativistic heavy-ion collisions, a photon from the electromagnetic field of one nucleus can fluctuate to a quark-antiquark pair and scatter from the other nucleus, emerging as a rho(0). The rho(0) production occurs in two well-separated (median impact parameters of 20 and 40 F for the cases considered here) nuclei, so the system forms a two-source interferometer. At low transverse momenta, the two amplitudes interfere destructively, suppressing rho(0) production. Since the rho(0) decays before the production amplitudes from the two sources can overlap, the two-pion system can only be described with an entangled nonlocal wave function, and is thus an example of the Einstein-Podolsky-Rosen paradox. We observe this suppression in 200 GeV per nucleon-pair gold-gold collisions. The interference is 87%+/- 5%(stat.)+/- 8%(syst.) of the expected level. This translates into a limit on decoherence due to wave function collapse or other factors of 23% at the 90% confidence level.

Effects of the target spin on the reaction mechanism of the (16)O+(63)Cu system

Precise quasielastic and alpha-transfer excitation functions, at theta(lab) = 161 degrees, have been measured at energies near the Coulomb barrier for the (16)O + (63)Cu system. This is the first time reported quasielastic barrier distribution for a medium odd-A nucleus target deduced from the data. Additional elastic scattering angular distributions data available in the literature for this system were also used in the investigation of the role of several individual channels in the reaction dynamics, by comparing the data with free-parameter coupled-channels calculations. In order to do so, the nucleus-nucleus bare potential has a double-folding potential as the real component and only a very short-range imaginary potential. The quasielastic barrier distribution has been shown to be a powerful tool in this analysis at the barrier region. A high collectivity of the (63)Cu was observed, mainly due to the strong influence of its 5/2-and 7/2-states on all reaction channels investigated. A striking influence of the reorientation of the ground-state target-spin on the elastic cross sections, taken at backward angles, was also observed.

In situ infrared (FTIR) study of the mechanism of the borohydride oxidation reaction

Early reports stated that Au was a catalyst of choice for the BOR because it would yield a near complete faradaic efficiency. However, it has recently been suggested that gold could yield to some extent the heterogeneous hydrolysis of BH(4)(-),therefore lowering the electron count per BH(4)(-), especially at low potential. Actually, the blur will exist regarding the BOR mechanism on Au as long as no physical proof regarding the reaction intermediates is not put forward. In that frame, in situ physical techniques like FTIR exhibit some interest to study the BOR. Consequently, in situ infrared reflectance spectroscopy measurements (SPAIRS technique) have been performed in 1 M NaOH/1 M NaBH(4) on a gold electrode with the aim to detect the intermediate species. We monitored several bands in B-H ((nu) over bar similar to 1180,1080 and 972 cm(-1)) and B-O bond regions ((nu) over bar =1325 and similar to 1425cm(-1)), which appear sequentially as a function of the electrode polarization. These absorption bands are assigned to BH(3), BH(2) and BO(2)(-) species. At the light of the experimental results, possible initial elementary steps of the BOR on gold electrode have been proposed and discussed according to the relevant literature data.

Real-time PCR investigation on the expression of sboA and ituD genes in Bacillus spp

Aims: To investigate the expression of sboA and ituD genes among strains of Bacillus spp. at different pH and temperature. Methods and Results: Different Bacillus strains from the Amazon basin and Bacillus subtilis ATCC 19659 were investigated for the production of subtilosin A and iturin A by qRT-PCR, analysing sboA and ituD gene expression under different culture conditions. Amazonian strains presented a general gene expression level lower than B. subtilis ATCC 19659 for sboA. In contrast, when analysing the expression of ituD gene, the strains from the Amazon, particularly P40 and P45B, exhibited higher levels of expression. Changes in pH (6 and 8) and temperature (37 and 42 degrees C) caused a decrease in sboA expression, but increased ituD expression among strains from Amazonian environment. Conclusions: Temperature and pH have an important influence on the expression of genes sboA (subtilosin A) and ituD (iturin A) among Bacillus spp. The strains P40 and P45B can be useful for the production of antimicrobial peptide iturin A. Significance and Impact of the Study: Monitoring the expression of essential biosynthetic genes by qRT-PCR is a valuable tool for optimization of the production of antimicrobial peptides.

Multifractality in the random parameter model for multivariate time series

The Random Parameter model was proposed to explain the structure of the covariance matrix in problems where most, but not all, of the eigenvalues of the covariance matrix can be explained by Random Matrix Theory. In this article, we explore the scaling properties of the model, as observed in the multifractal structure of the simulated time series. We use the Wavelet Transform Modulus Maxima technique to obtain the multifractal spectrum dependence with the parameters of the model. The model shows a scaling structure compatible with the stylized facts for a reasonable choice of the parameter values. (C) 2009 Elsevier B.V. All rights reserved.

Contuse lesion of the rat spinal cord of moderate intensity leads to a higher time-dependent secondary neurodegeneration than severe one - An open-window for experimental neuroprotective interventions

Secondary neurodegeneration takes place in the surrounding tissue of spinal cord trauma and modifies substantially the prognosis, considering the small diameter of its transversal axis. We analyzed neuronal and glial responses in rat spinal cord after different degree of contusion promoted by the NYU Impactor. Rats were submitted to vertebrae laminectomy and received moderate or severe contusions. Control animals were sham operated. After 7 and 30 days post surgery, stereological analysis of Nissl staining cellular profiles showed a time progression of the lesion volume after moderate injury, but not after severe injury. The number of neurons was not altered cranial to injury. However, same degree of diminution was seen in the caudal cord 30 days after both severe and moderate injuries. Microdensitometric image analysis demonstrated a microglial reaction in the white matter 30 days after a moderate contusion and showed a widespread astroglial reaction in the white and gray matters 7 days after both severities. Astroglial activation lasted close to lesion and in areas related to Wallerian degeneration. Data showed a more protracted secondary degeneration in rat spinal cord after mild contusion, which offered an opportunity for neuroprotective approaches. Temporal and regional glial responses corroborated to diverse glial cell function in lesioned spinal cord. (C) 2007 Elsevier Ltd. All rights reserved.

Prediction of Crude Oil Properties and Chemical Composition by Means of Steady-State and Time-Resolved Fluorescence

Steady-state and time-resolved fluorescence measurements are reported for several crude oils and their saturates, aromatics, resins, and asphaltenes (SARA) fractions (saturates, aromatics and resins), isolated from maltene after pentane precipitation of the asphaltenes. There is a clear relationship between the American Petroleum Institute (API) grade of the crude oils and their fluorescence emission intensity and maxima. Dilution of the crude oil samples with cyclohexane results in a significant increase of emission intensity and a blue shift, which is a clear indication of the presence of energy-transfer processes between the emissive chromophores present in the crude oil. Both the fluorescence spectra and the mean fluorescence lifetimes of the three SARA fractions and their mixtures indicate that the aromatics and resins are the major contributors to the emission of crude oils. Total synchronous fluorescence scan (TSFS) spectral maps are preferable to steady-state fluorescence spectra for discriminating between the fractions, making TSFS maps a particularly interesting choice for the development of fluorescence-based methods for the characterization and classification of crude oils. More detailed studies, using a much wider range of excitation and emission wavelengths, are necessary to determine the utility of time-resolved fluorescence (TRF) data for this purpose. Preliminary models constructed using TSFS spectra from 21 crude oil samples show a very good correlation (R(2) > 0.88) between the calculated and measured values of API and the SARA fraction concentrations. The use of models based on a fast fluorescence measurement may thus be an alternative to tedious and time-consuming chemical analysis in refineries.

Performance analysis of a single-user MISO ultra-wideband time reversal system with DFE

This paper presents an analysis of the performance of a baseband multiple-input single-output (MISO) time reversal ultra-wideband system (TR-UWB) incorporating a symbol spaced decision feedback equalizer (DFE). A semi-analytical performance analysis based on a Gaussian approach is considered, which matched well with simulation results, even for the DFE case. The channel model adopted is based on the IEEE 802.15.3a model, considering correlated shadowing across antenna elements. In order to provide a more realistic analysis, channel estimation errors are considered for the design of the TR filter. A guideline for the choice of equalizer length is provided. The results show that the system`s performance improves with an increase in the number of transmit antennas and when a symbol spaced equalizer is used with a relatively small number of taps compared to the number of resolvable paths in the channel impulse response. Moreover, it is possible to conclude that due to the time reversal scheme, the error propagation in the DFE does not play a role in the system`s performance.

On the Filtering Problem for Continuous-Time Markov Jump Linear Systems with no Observation of the Markov Chain

We consider in this paper the optimal stationary dynamic linear filtering problem for continuous-time linear systems subject to Markovian jumps in the parameters (LSMJP) and additive noise (Wiener process). It is assumed that only an output of the system is available and therefore the values of the jump parameter are not accessible. It is a well known fact that in this setting the optimal nonlinear filter is infinite dimensional, which makes the linear filtering a natural numerically, treatable choice. The goal is to design a dynamic linear filter such that the closed loop system is mean square stable and minimizes the stationary expected value of the mean square estimation error. It is shown that an explicit analytical solution to this optimal filtering problem is obtained from the stationary solution associated to a certain Riccati equation. It is also shown that the problem can be formulated using a linear matrix inequalities (LMI) approach, which can be extended to consider convex polytopic uncertainties on the parameters of the possible modes of operation of the system and on the transition rate matrix of the Markov process. As far as the authors are aware of this is the first time that this stationary filtering problem (exact and robust versions) for LSMJP with no knowledge of the Markov jump parameters is considered in the literature. Finally, we illustrate the results with an example.

Quantification of Listeria monocytogenes in minimally processed leafy vegetables using a combined method based on enrichment and 16S rRNA real-time PCR

Modern lifestyle markedly changed eating habits worldwide, with an increasing demand for ready-to-eat foods, such as minimally processed fruits and leafy greens. Packaging and storage conditions of those products may favor the growth of psychrotrophic bacteria, including the pathogen Listeria monocytogenes. In this work, minimally processed leafy vegetables samples (n = 162) from retail market from Ribeirao Preto, Sao Paulo, Brazil, were tested for the presence or absence of Listeria spp. by the immunoassay Listeria Rapid Test, Oxoid. Two L. monocytogenes positive and six artificially contaminated samples of minimally processed leafy vegetables were evaluated by the Most Probable Number (MPN) with detection by classical culture method and also culture method combined with real-time PCR (RTi-PCR) for 16S rRNA genes of L monocytogenes. Positive MPN enrichment tubes were analyzed by RTi-PCR with primers specific for L. monocytogenes using the commercial preparation ABSOLUTET (TM) QPCR SYBR (R) Green Mix (ABgene, UK). Real-time PCR assay presented good exclusivity and inclusivity results and no statistical significant difference was found in comparison with the conventional culture method (p < 0.05). Moreover, RTi-PCR was fist and easy to perform, with MPN results obtained in ca. 48 h for RTi-PCR in comparison to 7 days for conventional method. (C) 2009 Elsevier Ltd. All rights reserved.

The effect of diabetic neuropathy and previous foot ulceration in EMG and ground reaction forces during gait

Background. We aimed at investigating the influence of diabetic neuropathy and previous history of plantar ulcers on electromyography (EMG) of the thigh and calf and on vertical ground reaction forces during gait. Methods. This study involved 45 adults divided into three groups: a control group (n = 16), diabetic neuropathic group (n = 19) and diabetic neuropathic group with previous history of plantar ulceration (it = 10). EMG of the right vastus lateralis, lateral gastrocnemius and tibialis anterior were studied during the stance phase. The peaks and time of peak occurrence were determined and a co-activation index between tibialis anterior and lateral gastrocnemius. In order to represent the effect of the changes in EMG, the first and second peaks and the minimum value of the vertical ground reaction force were also determined. Inter-group comparisons of the electromyographical and ground reaction forces variables were made using three MANCOVA (peaks and times of EMG and peaks of force) and one ANCOVA (co-activation index). Findings. The ulcerated group presented a delayed in the time of the lateral gastrocnemius and vastus lateralis peak occurrence in comparison to control`s. The lateral gastrocnemius delay may be related to the lower second vertical peak in diabetic subjects. However, the delay of the vastus lateralis did not cause any significant change on the first vertical peak. Interpretations. The vastus lateralis and lateral gastrocnemius delay demonstrate that ulcerated diabetic neuropathic patients have a motor deficit that could compromise their ability to walk, which was partially confirmed by changes on ground reaction forces during the push-off phase. (c) 2007 Elsevier Ltd. All rights reserved.

miRNA analysis of prostate cancer by quantitative real time PCR: Comparison between formalin-fixed paraffin embedded and fresh-frozen tissue

Objective: Micro RNA (miRNA) is a class of small noncoding RNA that plays a major role in the regulation of gene expression, which has been related to cancer behavior. The possibility of analyzing miRNA from the archives of pathology laboratories is exciting, as it allows for large retrospective studies. Formalin is the most common fixative used in the surgical pathology routine, and its promotion of nucleic acid degradation is well known. Our aim is to compare miRNA profiles from formalin-fixed paraffin embedded (FFPE) tissues with fresh-frozen prostate cancer tissues. Methods: The expression of 14 miRNAs was determined by quantitative real time polymerase chain reaction (qRT-PCR) in 5 paired fresh-frozen and FFPE tissues, which were representative of prostate carcinoma. Results: There was a very good correlation of the miRNA expression of miR-let7c and miR-32 between the fresh-frozen and FFPE tissues, with Pearson`s correlation coefficients of 0.927 (P = 0.023) and 0.960 (P = 0.010), respectively. For the remaining miRNAs, the correlation was good with Spearman correlation coefficient of 0.638 (P < 0.001). Conclusion: Analysis of miRNAs from routinely processed and stored FFPE prostate tissue is feasible for some miRNAs using qRT-PCR. Further studies should be conducted to confirm the reliability of using stock tissues for miRNA expression determination. (C) 2011 Elsevier Inc. All rights reserved.