Entangled coherent-state qubits in an ion trap

We show how entangled qubits can be encoded as entangled coherent states of two-dimensional center-of-mass vibrational motion for two ions in an ion trap. The entangled qubit state is equivalent to the canonical Bell state, and we introduce a proposal for entanglement transfer from the two vibrational modes to the electronic states of the two ions in order for the Bell state to be detected by resonance fluorescence shelving methods.

The preparation and readiness for voluntary movement: a high-field event-related fMRI study of the Bereitschafts-BOLD response

Activity within motor areas of the cortex begins to increase 1 to 2 s prior to voluntary self-initiated movement (termed the Bereitschaftspotential or readiness potential). There has been much speculation and debate over the precise source of this early premovement activity as it is important for understanding the roles of higher order motor areas in the preparation and readiness for voluntary movement. In this study, we use high-field (3-T) event-related fMRI with high temporal sampling (partial brain volumes every 250 ms) to specifically examine hemodynamic response time courses during the preparation, readiness, and execution of purely self-initiated voluntary movement. Five right-handed healthy volunteers performed a rapid sequential finger-to-thumb movement performed at self-determined times (12-15 trials). Functional images for each trial were temporally aligned and the averaged time series for each subject was iteratively correlated with a canonical hemodynamic response function progressively shifted in time. This analysis method identified areas of activation without constraining hemodynamic response timing. All subjects showed activation within frontal mesial areas, including supplementary motor area (SMA) and cingulate motor areas, as well as activation in left primary sensorimotor areas. The time courses of hemodynamic responses showed a great deal of variability in shape and timing between subjects; however, four subjects clearly showed earlier relative hemodynamic responses within SMA/cingulate motor areas compared with left primary motor areas. These results provide further evidence that the SMA and cingulate motor areas are major contributors to early stage premovement activity and play an important role in the preparation and readiness for voluntary movement. (C) 2003 Elsevier Inc. All rights reserved.

Fragmentation of a Neotropical migratory fish population by a century-old dam

Loss of connectivity in impounded rivers is among the impacts imposed by dams, and mitigation measures such as fish passages might not accomplish their purpose of reestablishing an efficient bi-directional gene flow in the fish populations affected. As a consequence, fish populations remain fragmented, and a new interpopulational structure may develop, with increased risk of reduced genetic diversity and stochastic extinction. In order to evaluate the effects of the Gavio Peixoto Dam, which was constructed almost a century ago on the Jacar,-Gua double dagger u River in the Upper Parana River basin, Brazil, a comparative morphometric study was undertaken on the populations of the Neotropical migratory characid fish Salminus hilarii living up- and downstream of this dam. Population dynamics, spatial segregation, and habitat use by different age classes were monitored for 2 years. We found that segregation caused by the dam and long periods with no efficient connection by fish passages have led to fragmentation and interpopulational structuring of S. hilarii, as revealed by canonical variable analysis of morphometric features. The fish populations occupying the up- and downstream sections have succeeded in performing short-distance reproductive migrations in the main river and tributaries, have found suitable habitats for completing their life cycle, and have been able to maintain distinct small-sized populations so far.

Defective NF-kappaB Activation in Response to LPS in Type 1 Diabetes Dendritic Cells

Dendritic cells (DC) are the potent antigen presenting cells which modulate T cell responses to self or non-self antigens. DC play a significant role in the pathogenesis of autoimmune diseases, inflammation and infection, but also in the maintenance of tolerance. NF-kappaB, particularly RelB is a crucial pathway for myeloid DC differentiation and functional maturation. While the current paradigm is that mature, nuclear RelB+ DC prime T cells for immunity/autoimmunity and immature DC for tolerance, RelB-deficient mice paradoxically develop generalised systemic autoimmune inflammatory disease with myelopoiesis and splenomegaly. Previous studies suggested abnormal DC differentiation in healthy relatives of type 1 diabetes (t1dm) patients. Therefore, we compared NF- kB activation in monocyte-derived DC from t1dm and non-t1dm controls in response to LPS. While resting DC appeared normal, DC from 6 out of 7 t1dm patients but no t2dm or rheumatoid arthritis patients failed to translocate NF- kB subunits to the nucleus in response to LPS, along with a failure to up-regulate expression of cell surface CD40 and MHC class I. NF- kB subunit mRNA increased normally in t1dm DC after LPS. Both the classical or non-canonical NF- kB pathways were affected as both TNF-a and CD40 stimulation led to a similarly abnormal NF- kB response. In contrast, expression of phosphorylated p38 MAPK and pro-inflammatory cytokine production was intact. These abnormalities in NF- kB activation appear to be generally and specifically applicable at a post-translational level in t1dm, and have the capacity to profoundly influence immunoregulation in affected individuals.

Analyzing the connectivity between regions of interest: An approach based on cluster Granger causality for NRI data analysis

The identification, modeling, and analysis of interactions between nodes of neural systems in the human brain have become the aim of interest of many studies in neuroscience. The complex neural network structure and its correlations with brain functions have played a role in all areas of neuroscience, including the comprehension of cognitive and emotional processing. Indeed, understanding how information is stored, retrieved, processed, and transmitted is one of the ultimate challenges in brain research. In this context, in functional neuroimaging, connectivity analysis is a major tool for the exploration and characterization of the information flow between specialized brain regions. In most functional magnetic resonance imaging (fMRI) studies, connectivity analysis is carried out by first selecting regions of interest (ROI) and then calculating an average BOLD time series (across the voxels in each cluster). Some studies have shown that the average may not be a good choice and have suggested, as an alternative, the use of principal component analysis (PCA) to extract the principal eigen-time series from the ROI(s). In this paper, we introduce a novel approach called cluster Granger analysis (CGA) to study connectivity between ROIs. The main aim of this method was to employ multiple eigen-time series in each ROI to avoid temporal information loss during identification of Granger causality. Such information loss is inherent in averaging (e.g., to yield a single ""representative"" time series per ROI). This, in turn, may lead to a lack of power in detecting connections. The proposed approach is based on multivariate statistical analysis and integrates PCA and partial canonical correlation in a framework of Granger causality for clusters (sets) of time series. We also describe an algorithm for statistical significance testing based on bootstrapping. By using Monte Carlo simulations, we show that the proposed approach outperforms conventional Granger causality analysis (i.e., using representative time series extracted by signal averaging or first principal components estimation from ROIs). The usefulness of the CGA approach in real fMRI data is illustrated in an experiment using human faces expressing emotions. With this data set, the proposed approach suggested the presence of significantly more connections between the ROIs than were detected using a single representative time series in each ROI. (c) 2010 Elsevier Inc. All rights reserved.

Role of NFKB2 on the early myeloid differentiation of CD34+ hematopoietic stem/progenitor cells

To better understand the early events regulating lineage-specific hematopoietic differentiation, we analyzed the transcriptional profiles of CD34+ human hematopoietic stem and progenitor cells (HSPCs) subjected to differentiation stimulus. CD34+ cells were cultured for 12 and 40 h in liquid cultures with supplemented media favoring myeloid or erythroid commitment. Serial analysis of gene expression (SAGE) was employed to generate four independent libraries. By analyzing the differentially expressed regulated transcripts between the un-stimulated and the stimulated CD34+ cells, we observed a set of genes that was initially up-regulated at 12 h but were then down-regulated at 40 h, exclusively after myeloid stimulus. Among those we found transcripts for NFKB2, RELB, IL1B, LTB, LTBR, TNFRSF4, TGFB1, and IKBKA. Also, the inhibitor NFKBIA (IKBA) was more expressed at 12 h. All those transcripts code for signaling proteins of the nuclear factor kappaB pathway. NFKB2 is a subunit of the NF-kappa B transcription factor that with RELB mediates the non-canonical NF-kappa B pathway. Interference RNA (RNAi) against NFKB1, NFKB2 and control RNAi were transfected into bone marrow CD34+HSPC. The percentage and the size of the myeloid colonies derived from the CD34+ cells decreased after inhibition of NFKB2. Altogether, our results indicate that NFKB2 gene has a role in the early commitment of CD34+HSPC towards the myeloid lineage. (C) 2010 International Society of Differentiation. Published by Elsevier Ltd. All rights reserved.

Analysis of the Ontogenetic Variation in the Venom Proteome/Peptidome of Bothrops jararaca Reveals Different Strategies to Deal with Prey

Previous studies have demonstrated that the pharmacological activities displayed by Bothrops jararaca venom undergo a significant ontogenetic shift. Variation in the venom proteome is a well-documented phenomenon; however, variation in the venom peptidome is poorly understood. We report a comparative proteomic and peptidomic analysis of venoms from newborn and adult specimens of B. jararaca and correlate it with the evaluation of important venom features. We demonstrate that newborn and adult venoms have similar hemorrhagic activities, while the adult venom has a slightly higher lethal activity in mice; however, the newborn venom is extremely more potent to kill chicks. The coagulant activity of newborn venom upon human plasma is 10 times higher than that of adult venom. These differences were clearly reflected in their different profiles of SDS-PAGE, gelatin zimography, immunostaining using specific antibodies, glycosylation pattern, and concanavalin A-binding proteins. Furthermore, we report for the first time the analysis of the peptide fraction of newborn and adult venoms by MALDI-TOF mass spectrometry and LC-MS/MS, which revealed different contents of peptides, while the bradykinin potentiating peptides (BPPs) showed rather similar profiles and were detected in the venoms showing their canonical sequences and also novel sequences corresponding to BPPs processed from their precursor protein at sites so far not described. As a result of these studies, we demonstrated that the ontogenetic shift in diet, from ectothermic prey in early life to endothermic prey in adulthood, and in animal size are associated with changes in the venom proteome in B. jararaca species.

WNT-5A, but not matrix metalloproteinase 3 or beta-catenin protein, expression is related to early stages of lip carcinogenesis

Background: Oncogenic Wnt/beta-catenin signaling occurs in numerous types of cancers, but little is known about the role of the Wnt protein family member, WNT-5A, in lip carcinogenesis. The aim of this study was to investigate WNT-5A, beta-catenin, and matrix metalloproteinase (MMP)-3 protein expression in actinic cheilitis (AC), and lip squamous cell carcinoma (LSCC). Methods: Twenty-one cases of AC, and fifty-one cases of LSCC were analyzed, with normal lip mucosa used as a control. Qualitative and semi-quantitative analyses of WNT-5A, beta-catenin, and MMP-3 immunostaining pattern and cellular distribution were performed. Results: WNT-5A was observed in more than 50% of the cells, scattered in all layers of AC, in contrast to the absence of immunostaining in normal lip mucosa. AC presented a higher level of WNT-5A expression than LSCC (P = 0.0289, Fisher test), while MMP-3 immunoexpression was statistically more significant in LSCC than in AC (P = 0.0285, Fisher test). Immunolabeling of beta-catenin protein was differentially distributed between samples; the majority of AC cases (61.90%) demonstrated a membranous-cytoplasmic pattern, while a considerable number of LSCC cases (29.41%) revealed a cytoplasmic pattern, instead of the usual membranous pattern. Conclusions: The present results suggest that WNT-5A may be an important marker during initial events of AC malignant transformation, in which non-canonical and canonical Wnt/beta-catenin signaling pathways could be involved. Additionally, WNT-5A might recruit other events in LSCC, such as MMP-3 protein synthesis, as its presence is increased in established malignant processes without beta-catenin dependency.

Theory of pseudomodes in quantum optical processes

This paper deals with non-Markovian behavior in atomic systems coupled to a structured reservoir of quantum electromagnetic field modes, with particular relevance to atoms interacting with the field in high-Q cavities or photonic band-gap materials. In cases such as the former, we show that the pseudomode theory for single-quantum reservoir excitations can be obtained by applying the Fano diagonalization method to a system in which the atomic transitions are coupled to a discrete set of (cavity) quasimodes, which in turn are coupled to a continuum set of (external) quasimodes with slowly varying coupling constants and continuum mode density. Each pseudomode can be identified with a discrete quasimode, which gives structure to the actual reservoir of true modes via the expressions for the equivalent atom-true mode coupling constants. The quasimode theory enables cases of multiple excitation of the reservoir to now be treated via Markovian master equations for the atom-discrete quasimode system. Applications of the theory to one, two, and many discrete quasimodes are made. For a simple photonic band-gap model, where the reservoir structure is associated with the true mode density rather than the coupling constants, the single quantum excitation case appears to be equivalent to a case with two discrete quasimodes.

Non-Markovian quantum optical processes and pseudomodes

Non-Markovian behaviour in atomic systems coupled to a structured reservoir of quantum EM field modes, such as in high Q cavities, is treated using a quasimode description, and the pseudo mode theory for single quantum reservoir excitations is obtained via Fano diagonalisation. The atomic transitions are coupled to a discrete set of (cavity) quasimodes, which are also coupled to a continuum set of (external) quasimodes with slowly varying coupling constants. Each pseudomode corresponds to a cavity quasimode, and the original reservoir structure is obtained in expressions for the equivalent atom-true mode coupling constants. Cases of multiple excitation of the reservoir are now treatable via Markovian master equations for the atom-discrete quasimode system.

Optimal input states and feedback for interferometric phase estimation

We derive optimal N-photon two-mode input states for interferometric phase measurements. Under canonical measurements the phase variance scales as N-2 for these states, as compared to N-1 or N-1/2 for states considered bq previous authors. We prove, that it is not possible to realize the canonical measurement by counting photons in the outputs of the interferometer, even if an adjustable auxiliary phase shift is allowed in the interferometer. However. we introduce a feedback algorithm based on Bayesian inference to control this auxiliary phase shift. This makes the measurement close to a canonical one, with a phase variance scaling slightly above N-2. With no feedback, the best result (given that the phase to be measured is completely unknown) is a scaling of N-1. For optimal input states having up to four photons, our feedback scheme is the best possible one, but for higher photon numbers more complicated schemes perform marginally better.

Quasimode theory of quantum optical processes in photonic band gap materials

This paper deals with atomic systems coupled to a structured reservoir of quantum EM field modes, with particular relevance to atoms interacting with the field in photonic band gap materials. The case of high Q cavities has been treated elsewhere using Fano diagonalization based on a quasimode approach, showing that the cavity quasimodes are responsible for pseudomodes introduced to treat non-Markovian behaviour. The paper considers a simple model of a photonic band gap case, where the spatially dependent permittivity consists of a constant term plus a small spatially periodic term that leads to a narrow band gap in the spectrum of mode frequencies. Most treatments of photonic band gap materials are based on the true modes, obtained numerically by solving the Helmholtz equation for the actual spatially periodic permittivity. Here the field modes are first treated in terms of a simpler quasimode approach, in which the quasimodes are plane waves associated with the constant permittivity term. Couplings between the quasimodes occur owing to the small periodic term in the permittivity, with selection rules for the coupled modes being related to the reciprocal lattice vectors. This produces a field Hamiltonian in quasimode form. A matrix diagonalization method may be applied to relate true mode annihilation operators to those for quasimodes. The atomic transitions are coupled to all the quasimodes, and the true mode atom-EM field coupling constants (one-photon Rabi frequencies) are related to those for the quasimodes and also expressions are obtained for the true mode density. The results for the one-photon Rabi frequencies differ from those assumed in other work. Expressions for atomic decay rates are obtained using the Fermi Golden rule, although these are valid only well away from the band gaps.

Close packed transitions in slit-shaped pores: Density functional theory study of methane adsorption capacity in carbon

An important feature of improving lattice gas models and classical isotherms is the incorporation of a pore size dependent capacity, which has hitherto been overlooked. In this paper, we develop a model for predicting the temperature dependent variation in capacity with pore size. The model is based on the analysis of a lattice gas model using a density functional theory approach at the close packed limit. Fluid-fluid and solid-fluid interactions are modeled by the Lennard-Jones 12-6 potential and Steele's 10-4-3, potential respectively. The capacity of methane in a slit-shaped carbon pore is calculated from the characteristic parameters of the unit cell, which are extracted by minimizing the grand potential of the unit cell. The capacities predicted by the proposed model are in good agreement with those obtained from grand canonical Monte Carlo simulation, for pores that can accommodate up to three adsorbed layers. Single particle and pair distributions exhibit characteristic features that correspond to the sequence of buckling and rhombic transitions that occur as the slit pore width is increased. The model provides a useful tool to model continuous variation in the microstructure of an adsorbed phase, namely buckling and rhombic transitions, with increasing pore width. (C) 2002 American Institute of Physics.

Modeling of phase equilibrium and vapor adsorption on carbon black based on a combination of a lattice theory and equation of state

A thermodynamic approach is developed in this paper to describe the behavior of a subcritical fluid in the neighborhood of vapor-liquid interface and close to a graphite surface. The fluid is modeled as a system of parallel molecular layers. The Helmholtz free energy of the fluid is expressed as the sum of the intrinsic Helmholtz free energies of separate layers and the potential energy of their mutual interactions calculated by the 10-4 potential. This Helmholtz free energy is described by an equation of state (such as the Bender or Peng-Robinson equation), which allows us a convenient means to obtain the intrinsic Helmholtz free energy of each molecular layer as a function of its two-dimensional density. All molecular layers of the bulk fluid are in mechanical equilibrium corresponding to the minimum of the total potential energy. In the case of adsorption the external potential exerted by the graphite layers is added to the free energy. The state of the interface zone between the liquid and the vapor phases or the state of the adsorbed phase is determined by the minimum of the grand potential. In the case of phase equilibrium the approach leads to the distribution of density and pressure over the transition zone. The interrelation between the collision diameter and the potential well depth was determined by the surface tension. It was shown that the distance between neighboring molecular layers substantially changes in the vapor-liquid transition zone and in the adsorbed phase with loading. The approach is considered in this paper for the case of adsorption of argon and nitrogen on carbon black. In both cases an excellent agreement with the experimental data was achieved without additional assumptions and fitting parameters, except for the fluid-solid potential well depth. The approach has far-reaching consequences and can be readily extended to the model of adsorption in slit pores of carbonaceous materials and to the analysis of multicomponent adsorption systems. (C) 2002 Elsevier Science (USA).

Adsorption in slit-like pores of activated carbons: Improvement of the Horvath and Kawazoe method

Anew thermodynamic approach has been developed in this paper to analyze adsorption in slitlike pores. The equilibrium is described by two thermodynamic conditions: the Helmholtz free energy must be minimal, and the grand potential functional at that minimum must be negative. This approach has led to local isotherms that describe adsorption in the form of a single layer or two layers near the pore walls. In narrow pores local isotherms have one step that could be either very sharp but continuous or discontinuous benchlike for a definite range of pore width. The latter reflects a so-called 0 --> 1 monolayer transition. In relatively wide pores, local isotherms have two steps, of which the first step corresponds to the appearance of two layers near the pore walls, while the second step corresponds to the filling of the space between these layers. All features of local isotherms are in agreement with the results obtained from the density functional theory and Monte Carlo simulations. The approach is used for determining pore size distributions of carbon materials. We illustrate this with the benzene adsorption data on activated carbon at 20, 50, and 80 degreesC, argon adsorption on activated carbon Norit ROX at 87.3 K, and nitrogen adsorption on activated carbon Norit R1 at 77.3 K.