Centrality dependence of charged hadron and strange hadron elliptic flow from root s(NN)=200 GeVAu+Au collisions

We present STAR results on the elliptic flow upsilon(2) Of charged hadrons, strange and multistrange particles from,root s(NN) = 200 GeV Au+Au collisions at the BNL Relativistic Heavy Ion Collider (RHIC). The detailed study of the centrality dependence of upsilon(2) over a broad transverse momentum range is presented. Comparisons of different analysis methods are made in order to estimate systematic uncertainties. To discuss the nonflow effect, we have performed the first analysis Of upsilon(2) with the Lee-Yang zero method for K(S)(0) and A. In the relatively low PT region, P(T) <= 2 GeV/c, a scaling with m(T) - m is observed for identified hadrons in each centrality bin studied. However, we do not observe nu 2(p(T))) scaled by the participant eccentricity to be independent of centrality. At higher PT, 2 1 <= PT <= 6 GeV/c, V2 scales with quark number for all hadrons studied. For the multistrange hadron Omega, which does not suffer appreciable hadronic interactions, the values of upsilon(2) are consistent with both m(T) - m scaling at low p(T) and number-of-quark scaling at intermediate p(T). As a function ofcollision centrality, an increase of p(T)-integrated upsilon(2) scaled by the participant eccentricity has been observed, indicating a stronger collective flow in more central Au+Au collisions.

Mucin pattern reflects the origin of the adenocarcinoma in Barrett's esophagus: a retrospective clinical and laboratorial study

Background: Mucin immunoexpression in adenocarcinoma arising in Barrett's esophagus (BE) may indicate the carcinogenesis pathway. The aim of this study was to evaluate resected specimens of adenocarcinoma in BE for the pattern of mucins and to correlate to the histologic classification. Methods: Specimens were retrospectively collected from thirteen patients who underwent esophageal resection due to adenocarcinoma in BE. Sections were scored for the grade of intestinal metaplasia. The tissues were examined by immunohistochemistry for MUC2 and MUC5AC antibodies. Results: Eleven patients were men. The mean age was 61 years old (varied from 40 to 75 years old). The tumor size had a mean of 4.7 +/- 2.3 cm, and the extension of BE had a mean of 7.7 +/- 1.5 cm. Specialized epithelium with intestinal metaplasia was present in all adjacent mucosas. Immunohistochemistry for MUC2 showed immunoreactivity in goblet cells, while MUC5AC was extensively expressed in the columnar gastric cells, localizing to the surface epithelium and extending to a variable degree into the glandular structures in BE. Tumors were classified according to the mucins in gastric type in 7/13 (MUC5AC positive) and intestinal type in 4/13 (MUC2 positive). Two tumors did not express MUC2 or MUC5AC proteins. The pattern of mucin predominantly expressed in the adjacent epithelium was associated to the mucin expression profile in the tumors, p = 0.047. Conclusion: Barrett's esophagus adenocarcinoma shows either gastric or intestinal type pattern of mucin expression. The two types of tumors developed in Barrett's esophagus may reflect the original cell type involved in the malignant transformation.

Ultra-Deep Sequencing Reveals the microRNA Expression Pattern of the Human Stomach

Background: While microRNAs (miRNAs) play important roles in tissue differentiation and in maintaining basal physiology, little is known about the miRNA expression levels in stomach tissue. Alterations in the miRNA profile can lead to cell deregulation, which can induce neoplasia. Methodology/Principal Findings: A small RNA library of stomach tissue was sequenced using high-throughput SOLiD sequencing technology. We obtained 261,274 quality reads with perfect matches to the human miRnome, and 42% of known miRNAs were identified. Digital Gene Expression profiling (DGE) was performed based on read abundance and showed that fifteen miRNAs were highly expressed in gastric tissue. Subsequently, the expression of these miRNAs was validated in 10 healthy individuals by RT-PCR showed a significant correlation of 83.97% (P<0.05). Six miRNAs showed a low variable pattern of expression (miR-29b, miR-29c, miR-19b, miR-31, miR-148a, miR-451) and could be considered part of the expression pattern of the healthy gastric tissue. Conclusions/Significance: This study aimed to validate normal miRNA profiles of human gastric tissue to establish a reference profile for healthy individuals. Determining the regulatory processes acting in the stomach will be important in the fight against gastric cancer, which is the second-leading cause of cancer mortality worldwide.

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.

Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

Background: The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat. Results: Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA), Amazon and Cerrado (AMC), Pantanal (PAN), Northern Atlantic Forest (NAF) and Southern Atlantic Forest (SAF). The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar. Conclusions: We therefore conclude that the pattern exhibited by the common vampire bat, with marked geographical structure for a mitochondrial marker and no phylogeographic structure for nuclear markers is compatible with a historical scenario of complete isolation of refuge-like populations during the Pleistocene. The results on demographic history on this species is compatible with the Carnaval-Moritz model of Pleistocene vicariance, with demographic expansions in the southern Atlantic forest.

Modeling the skin pattern of fishes

Complicated patterns showing various spatial scales have been obtained in the past by coupling Turing systems in such a way that the scales of the independent systems resonate. This produces superimposed patterns with different length scales. Here we propose a model consisting of two identical reaction-diffusion systems coupled together in such a way that one of them produces a simple Turing pattern of spots or stripes, and the other traveling wave fronts that eventually become stationary. The basic idea is to assume that one of the systems becomes fixed after some time and serves as a source of morphogens for the other system. This mechanism produces patterns very similar to the pigmentation patterns observed in different species of stingrays and other fishes. The biological mechanisms that support the realization of this model are discussed.

Cellular Renewal and Improvement of Local Cell Effector Activity in Peritoneal Cavity in Response to Infectious Stimuli

The peritoneal cavity (PerC) is a singular compartment where many cell populations reside and interact. Despite the widely adopted experimental approach of intraperitoneal (i.p.) inoculation, little is known about the behavior of the different cell populations within the PerC. To evaluate the dynamics of peritoneal macrophage (Mempty set) subsets, namely small peritoneal Mempty set (SPM) and large peritoneal Mempty set (LPM), in response to infectious stimuli, C57BL/6 mice were injected i.p. with zymosan or Trypanosoma cruzi. These conditions resulted in the marked modification of the PerC myelo-monocytic compartment characterized by the disappearance of LPM and the accumulation of SPM and monocytes. In parallel, adherent cells isolated from stimulated PerC displayed reduced staining for beta-galactosidase, a biomarker for senescence. Further, the adherent cells showed increased nitric oxide (NO) and higher frequency of IL-12-producing cells in response to subsequent LPS and IFN-gamma stimulation. Among myelo-monocytic cells, SPM rather than LPM or monocytes, appear to be the central effectors of the activated PerC; they display higher phagocytic activity and are the main source of IL-12. Thus, our data provide a first demonstration of the consequences of the dynamics between peritoneal Mempty set subpopulations by showing that substitution of LPM by a robust SPM and monocytes in response to infectious stimuli greatly improves PerC effector activity.

Nonlinear diffraction of light beams propagating in photorefractive media with embedded reflecting wire

The theory of nonlinear diffraction of intensive light beams propagating through photorefractive media is developed. Diffraction occurs on a reflecting wire embedded in the nonlinear medium at a relatively small angle with respect to the direction of the beam propagation. It is shown that this process is analogous to the generation of waves by a flow of a superfluid past an obstacle. The ""equation of state"" of such a superfluid is determined by the nonlinear properties of the medium. On the basis of this hydrodynamic analogy, the notion of the ""Mach number"" is introduced where the transverse component of the wave vector plays the role of the fluid velocity. It is found that the Mach cone separates two regions of the diffraction pattern: inside the Mach cone oblique dark solitons are generated and outside the Mach cone the region of ""optical ship waves"" (the wave pattern formed by a two-dimensional packet of linear waves) is situated. Analytical theory of the ""optical ship waves"" is developed and two-dimensional dark soliton solutions of the generalized two-dimensional nonlinear Schrodinger equation describing the light beam propagation are found. Stability of dark solitons with respect to their decay into vortices is studied and it is shown that they are stable for large enough values of the Mach number.

Elliptic and Hexadecapole Flow of Charged Hadrons in Au plus Au Collisions at root s(NN)=200 GeV

Differential measurements of the elliptic (upsilon(2)) and hexadecapole (upsilon(4)) Fourier flow coefficients are reported for charged hadrons as a function of transverse momentum (p(T)) and collision centrality or number of participant nucleons (N(part)) for Au + Au collisions at root s(NN) = 200 GeV/ The upsilon(2,4) measurements at pseudorapidity vertical bar eta vertical bar <= 0.35, obtained with four separate reaction-plane detectors positioned in the range 1.0 < vertical bar eta vertical bar < 3.9, show good agreement, indicating the absence of significant Delta eta-dependent nonflow correlations. Sizable values for upsilon(4)(p(T)) are observed with a ratio upsilon(4)(p(T), N(part))/upsilon(2)(2)(p(T), N(part)) approximate to 0.8 for 50 less than or similar to N(part) less than or similar to 200, which is compatible with the combined effects of a finite viscosity and initial eccentricity fluctuations. For N(part) greater than or similar to 200 this ratio increases up to 1.7 in the most central collisions.

Systematic studies of elliptic flow measurements in Au plus Au collisions at s(NN)=200 GeV

We present inclusive charged hadron elliptic flow (v(2)) measured over the pseudorapidity range vertical bar eta vertical bar < 0.35 in Au+Au collisions at s(NN)=200 GeV. Results for v(2) are presented over a broad range of transverse momentum (p(T)=0.2-8.0 GeV/c) and centrality (0-60%). To study nonflow effects that are correlations other than collective flow, as well as the fluctuations of v(2), we compare two different analysis methods: (1) the event-plane method from two independent subdetectors at forward (vertical bar eta vertical bar=3.1-3.9) and beam (vertical bar eta vertical bar>6.5) pseudorapidities and (2) the two-particle cumulant method extracted using correlations between particles detected at midrapidity. The two event-plane results are consistent within systematic uncertainties over the measured p(T) and in centrality 0-40%. There is at most a 20% difference in the v(2) between the two event-plane methods in peripheral (40-60%) collisions. The comparisons between the two-particle cumulant results and the standard event-plane measurements are discussed.

Suppression Pattern of Neutral Pions at High Transverse Momentum in Au plus Au Collisions at root S(NN)=200 GeV and Constraints on Medium Transport Coefficients

For Au + Au collisions at 200 GeV, we measure neutral pion production with good statistics for transverse momentum, p(T), up to 20 GeV/c. A fivefold suppression is found, which is essentially constant for 5 < p(T) < 20 GeV/c. Experimental uncertainties are small enough to constrain any model-dependent parametrization for the transport coefficient of the medium, e. g., <(q) over cap > in the parton quenching model. The spectral shape is similar for all collision classes, and the suppression does not saturate in Au + Au collisions.

Directed flow at midrapidity in event-by-event hydrodynamics

Fluctuations in the initial geometry of a nucleus-nucleus collision have been recently shown to result in a new type of directed flow (v(1)) that, unlike the usual directed flow, is also present at midrapidity. We compute this new v(1) versus transverse momentum and centrality for Au-Au collisions at RHIC using the hydrodynamic code NeXSPheRIO. We find that the event plane of v(1) is correlated with the angle of the initial dipole of the distribution, as predicted, though with a large dispersion. It is uncorrelated with the reaction plane. Our results are in excellent agreement with results inferred from STAR correlation data.

Importance of granular structure in the initial conditions for the elliptic flow

We show the effects of the granular structure of the initial conditions of a hydrodynamic description of high-energy nucleus-nucleus collisions on some observables, especially on the elliptic-flow parameter upsilon(2). Such a structure enhances production of isotropically distributed high-p(T) particles, making upsilon(2) smaller there. Also, it reduces upsilon(2) in the forward and backward regions where the global matter density is smaller and, therefore, where such effects become more efficacious.

Charged and strange hadron elliptic flow in Cu plus Cu collisions at root s(NN)=62.4 and 200 GeV

We present the results of an elliptic flow, v(2), analysis of Cu + Cu collisions recorded with the solenoidal tracker detector (STAR) at the BNL Relativistic Heavy Ion Collider at root s(NN) = 62.4 and 200 GeV. Elliptic flow as a function of transverse momentum, v(2)(p(T)), is reported for different collision centralities for charged hadrons h(+/-) and strangeness-ontaining hadrons K(S)(0), Lambda, Xi, and phi in the midrapidity region vertical bar eta vertical bar < 1.0. Significant reduction in systematic uncertainty of the measurement due to nonflow effects has been achieved by correlating particles at midrapidity, vertical bar eta vertical bar < 1.0, with those at forward rapidity, 2.5 < vertical bar eta vertical bar < 4.0. We also present azimuthal correlations in p + p collisions at root s = 200 GeV to help in estimating nonflow effects. To study the system-size dependence of elliptic flow, we present a detailed comparison with previously published results from Au + Au collisions at root s(NN) = 200 GeV. We observe that v(2)(p(T)) of strange hadrons has similar scaling properties as were first observed in Au + Au collisions, that is, (i) at low transverse momenta, p(T) < 2 GeV/c, v(2) scales with transverse kinetic energy, m(T) - m, and (ii) at intermediate p(T), 2 < p(T) < 4 GeV/c, it scales with the number of constituent quarks, n(q.) We have found that ideal hydrodynamic calculations fail to reproduce the centrality dependence of v(2)(p(T)) for K(S)(0) and Lambda. Eccentricity scaled v(2) values, v(2)/epsilon, are larger in more central collisions, suggesting stronger collective flow develops in more central collisions. The comparison with Au + Au collisions, which go further in density, shows that v(2)/epsilon depends on the system size, that is, the number of participants N(part). This indicates that the ideal hydrodynamic limit is not reached in Cu + Cu collisions, presumably because the assumption of thermalization is not attained.

Chaotic advection in blood flow

In this paper we argue that the effects of irregular chaotic motion of particles transported by blood can play a major role in the development of serious circulatory diseases. Vessel wall irregularities modify the flow field, changing in a nontrivial way the transport and activation of biochemically active particles. We argue that blood particle transport is often chaotic in realistic physiological conditions. We also argue that this chaotic behavior of the flow has crucial consequences for the dynamics of important processes in the blood, such as the activation of platelets which are involved in the thrombus formation.