From Full stopping to transparency in a holographic model of heavy ion collisions

We numerically simulate planar shock wave collisions in anti-de Sitter space as a model for heavy ion collisions of large nuclei. We uncover a crossover between two different dynamical regimes as a function of the collision energy. At low energies the shocks first stop and then explode in a manner approximately described by hydrodynamics, in close similarity with the Landau model. At high energies the receding fragments move outwards at the speed of light, with a region of negative energy density and negative longitudinal pressure trailing behind them. The rapidity distribution of the energy density at late times around midrapidity is not approximately boost invariant but Gaussian, albeit with a width that increases with the collision energy.

Sherali-Adams Relaxations and Indistinguishability in Counting Logics

Two graphs with adjacency matrices $\mathbf{A}$ and $\mathbf{B}$ are isomorphic if there exists a permutation matrix $\mathbf{P}$ for which the identity $\mathbf{P}^{\mathrm{T}} \mathbf{A} \mathbf{P} = \mathbf{B}$ holds. Multiplying through by $\mathbf{P}$ and relaxing the permutation matrix to a doubly stochastic matrix leads to the linear programming relaxation known as fractional isomorphism. We show that the levels of the Sherali--Adams (SA) hierarchy of linear programming relaxations applied to fractional isomorphism interleave in power with the levels of a well-known color-refinement heuristic for graph isomorphism called the Weisfeiler--Lehman algorithm, or, equivalently, with the levels of indistinguishability in a logic with counting quantifiers and a bounded number of variables. This tight connection has quite striking consequences. For example, it follows immediately from a deep result of Grohe in the context of logics with counting quantifiers that a fixed number of levels of SA suffice to determine isomorphism of planar and minor-free graphs. We also offer applications in both finite model theory and polyhedral combinatorics. First, we show that certain properties of graphs, such as that of having a flow circulation of a prescribed value, are definable in the infinitary logic with counting with a bounded number of variables. Second, we exploit a lower bound construction due to Cai, Fürer, and Immerman in the context of counting logics to give simple explicit instances that show that the SA relaxations of the vertex-cover and cut polytopes do not reach their integer hulls for up to $\Omega(n)$ levels, where $n$ is the number of vertices in the graph.

Comment on reversal of hypogonadotropic hypogonadism in a Chinese cohort.

The reversal of congenital hypogonadotropic hypogonadism (CHH) is a relatively recent phenomenon that has gained increasing attention over the past 10 years. Yet to date, only one prospective study has been conducted estimating that 10% (95% confidence interval [CI]: 2%-18%) of cases undergo reversal. [1] Other retrospective studies have reported rates in the range of 5%-8% [2],[3] and a recent study showed 44/308 (14%, 95% CI: 11%-19%) CHH patients underwent reversal. [4] Moreover, a time-to-event analysis in this large cohort revealed a lifetime reversal incidence of 22%. The article by Mao and colleagues presented in this issue is a meaningful contribution to our understanding of reversal as it examines the largest retrospective cohort to date. [5] Interestingly, they report the rate of reversal as 5% (95% CI: 3%-8%) in this Chinese cohort. It is difficult to reconcile the discrepancies in rates of reversibility and direct comparisons are hampered by the variable definitions employed. Using a novel definition for reversal (i.e, either endogenous testosterone (T) >270 ng dl−1 , serum T gradually increasing above 150 ng dl−1 with increased testicular volume, or normal spontaneous sperm production/normal erectile function/ejaculation), Mao and colleagues posit that testicular size and triptorelin-stimulated LH levels are reliable predictive factors for reversal. However, these cannot be considered as hard and fast rules for predicting reversal as the groups intersect - akin to the overlap observed between CHH patients and those with delayed puberty. Indeed, the fact that approximately half (44%, 95% CI: 25%-66%) of the reversal patients in the study by Mao et al.[5] were diagnosed between 17 and 19 years of age, underscores the challenge in differentiating CHH from extreme normal variants of puberty. This study further lends credence the recently reported observations that reversals may relapse. [4],[6] The notion that reversal may not be lasting highlights the vulnerability of the reproductive axis among CHH patients. While the mechanism(s) for relapse are unclear, it seems plausible that environmental, metabolic or psychiatric stressors could contribute. The factors that Mao and colleagues identify as significantly different in cases of reversal, were not informative for identifying those cases that relapsed back to a hypogonadal state. Notably, reversal has been reported in probands harboring mutations in genes underlying CHH. [1],[3],[4],[6] Unfortunately, comprehensive genetic screening on the Chinese cohort is not available. The reversal phenomenon is fascinating for its glimpse into the plasticity of the neuroendocrine control of reproduction. Future directions will almost certainly include investigation of specific genetic signatures and novel biomarkers for predicting reversal (and relapse). Yet CHH is a rare condition and to fully elucidate the biology of reversible CHH, it will be important to harmonize definitions of what constitutes a reversal, carefully phenotype patients and chart the natural history of their CHH. In this way, this unique human disease model may offer further insights into the control of human reproduction and provide opportunities to translate discoveries into enhanced approaches to improve the care and quality of life for these patients.

Kalibrointimenetelmä planaaristen siirtojohtojen mittaamiseen

Tässä diplomityössä tutkittiin TRL-kalibroinnin käyttämistä tasomaisten siirtojohtojen sähköisten parametrien määrittämisessä taajuusalueella 0,3 – 12 GHz. Työssä perehdyttiin TRL-kalibroinnin käyttämiseen piirianalysaattorilla toteutettujen mittauksien mittauskalibrointiin sekä kalibrointiin tarvittavien kalibrointistandardien mitoittamiseen. Kalibrointistandardit suunniteltiin ja toteutettiin sekä mikroliuska- että liuskajohdoille, joiden toiminnallisuutta tarkasteltiin sekä taajuustason että aikatason mittausten avulla. Työssä perehdyttiin myös kalibrointistandardien liityntärajapinnan suunniteluun ja toteuttamiseen. Saatujen tulosten perusteella voitiin osoittaa mikroliuskajohtokitin soveltuvan hyvin mittauskalibroinnin toteuttamiseen tarkoissa mittaussovelluksissa.

MorphoGraphX: A platform for quantifying morphogenesis in 4D.

Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX ( www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.

Tailoring the surface density of silicon nanocrystals embedded in SiOx single layers

In this article, we explore the possibility of modifying the silicon nanocrystal areal density in SiOx single layers, while keeping constant their size. For this purpose, a set of SiOx monolayers with controlled thickness between two thick SiO2 layers has been fabricated, for four different compositions (x=1, 1.25, 1.5, or 1.75). The structural properties of the SiO x single layers have been analyzed by transmission electron microscopy (TEM) in planar view geometry. Energy-filtered TEM images revealed an almost constant Si-cluster size and a slight increase in the cluster areal density as the silicon content increases in the layers, while high resolution TEM images show that the size of the Si crystalline precipitates largely decreases as the SiO x stoichiometry approaches that of SiO2. The crystalline fraction was evaluated by combining the results from both techniques, finding a crystallinity reduction from 75% to 40%, for x = 1 and 1.75, respectively. Complementary photoluminescence measurements corroborate the precipitation of Si-nanocrystals with excellent emission properties for layers with the largest amount of excess silicon. The integrated emission from the nanoaggregates perfectly scales with their crystalline state, with no detectable emission for crystalline fractions below 40%. The combination of the structural and luminescence observations suggests that small Si precipitates are submitted to a higher compressive local stress applied by the SiO2 matrix that could inhibit the phase separation and, in turn, promotes the creation of nonradiative paths.

Sähköisen ja optisen signaalin käyttö samalla piirilevyllä

Työssä tutkittiin sähköisen ja optisen signaalin siirtoa samalla piirilevyllä. Optisen siirtotien komponentit ja niiden toiminta esiteltiin teoriakappaleessa. Valosignaalin vaimentumisilmiö selitettiin pääasiassa johtuvan absorption ja sironnan vaikutuksesta. Sironnan ja absorption vaikutusta valokuidussa käytettävään aallonpituusalueeseen tutkittiin ja esiteltiin valon yleisin modulaatiomenetelmä WDM. Työssä esiteltiin myös dispersion aiheuttama aikahajonta. Optisen signaalin siirrossa piirilevyllä keskityttiin valokanava- ja free-space-siirtoon. Valokanavamateriaalin vaikutusta heijastuksiin optisessa tiedonsiirrossa piirilevyllä tutkittiin. Nykyisten piirilevyjen tuotantomenetelmien käytön mahdollisuutta valokanavapiirilevyn valmistuksessa tutkittiin eri materiaaleille. Moduulien sisäisten tiedonsiirtoteiden integroinnin yleistymistä tulevaisuudessa perusteltiin. Lopuksi työssä esiteltiin kolme uutta keksintöä liittyen optiseen tiedonsiirtoon. Tarkoituksena oli esittää alan moninaisuutta ja uusien sovellusten mahdollisuuksia.

Correcting surface coil excitation inhomogeneities in single-shot SPEN MRI.

Given their high sensitivity and ability to limit the field of view (FOV), surface coils are often used in magnetic resonance spectroscopy (MRS) and imaging (MRI). A major downside of surface coils is their inherent radiofrequency (RF) B1 heterogeneity across the FOV, decreasing with increasing distance from the coil and giving rise to image distortions due to non-uniform spatial responses. A robust way to compensate for B1 inhomogeneities is to employ adiabatic inversion pulses, yet these are not well adapted to all imaging sequences - including to single-shot approaches like echo planar imaging (EPI). Hybrid spatiotemporal encoding (SPEN) sequences relying on frequency-swept pulses provide another ultrafast MRI alternative, that could help solve this problem thanks to their built-in heterogeneous spatial manipulations. This study explores how this intrinsic SPEN-based spatial discrimination, could be used to compensate for the B1 inhomogeneities inherent to surface coils. Experiments carried out in both phantoms and in vivo rat brains demonstrate that, by suitably modulating the amplitude of a SPEN chirp pulse that progressively excites the spins in a direction normal to the coil, it is possible to compensate for the RF transmit inhomogeneities and thus improve sensitivity and image fidelity.

Fusion weld metal solidification:Continuum from weld interface to centerline

We present a brief résumé of the history of solidification research and key factors affecting the solidification of fusion welds. There is a general agreement of the basic solidification theory, albeit differing - even confusing - nomenclatures do exist, and Cases 2 and 3 (the Chalmers' basic boundary conditions for solidification, categorized by Savage as Cases) are variably emphasized. Model Frame, a tool helping to model the continuum of fusion weld solidification from start to end, is proposed. It incorporates the general solidification models, of which the pertinent ones are selected for the actual modeling. The basic models are the main solidification Cases 1…4. These discrete Cases are joined with Sub-Cases: models of Pfann, Flemings and others, bringing needed Sub-Case variables into the model. Model Frame depicts a grain growing from the weld interface to its centerline. Besides modeling, the Model Frame supports education and academic debate. The new mathematical modeling techniques will extend its use into multi-dimensional modeling, introducing new variables and increasing the modeling accuracy. We propose a model: melting/solidification-model (M/S-model) - predicting the solute profile at the start of the solidification of a fusion weld. This Case 3-based Sub-Case takes into account the melting stage, the solute back-diffusion in the solid, and the growth rate acceleration typical to fusion welds. We propose - based on works of Rutter & Chalmers, David & Vitek and our experimental results on copper - that NEGS-EGS-transition is not associated only with cellular-dendritic-transition. Solidification is studied experimentally on pure and doped copper with welding speed range from 0 to 200 cm/min, with one test at 3000 cm/min. Found were only planar and cellular structures, no dendrites - columnar or equiaxed. Cell sub structures: rows of cubic elements we call "cubelettes", "cell-bands" and "micro-cells", as well as an anomalous crack morphology "crack-eye", were detected, as well as microscopic hot crack nucleus we call "grain-lag cracks", caused by a grain slightly lagging behind its neighbors in arrival to the weld centerline. Varestraint test and R-test revealed a change of crack morphologies from centerline cracks to grainand cell boundary cracks with an increasing welding speed. High speed made the cracks invisible to bare eye and hardly detectable with light microscope, while electron microscope often revealed networks of fine micro-cracks.

Effect of the surface charge discretization on electric double layers. A Monte Carlo simulation study

The structure of the electric double layer in contact with discrete and continuously charged planar surfaces is studied within the framework of the primitive model through Monte Carlo simulations. Three different discretization models are considered together with the case of uniform distribution. The effect of discreteness is analyzed in terms of charge density profiles. For point surface groups,a complete equivalence with the situation of uniformly distributed charge is found if profiles are exclusively analyzed as a function of the distance to the charged surface. However, some differences are observed moving parallel to the surface. Significant discrepancies with approaches that do not account for discreteness are reported if charge sites of finite size placed on the surface are considered.

Simulation-based evaluation of susceptibility distortion correction methods in diffusion MRI for connectivity analysis

Connectivity analysis on diffusion MRI data of the whole- brain suffers from distortions caused by the standard echo- planar imaging acquisition strategies. These images show characteristic geometrical deformations and signal destruction that are an important drawback limiting the success of tractography algorithms. Several retrospective correction techniques are readily available. In this work, we use a digital phantom designed for the evaluation of connectivity pipelines. We subject the phantom to a âeurooetheoretically correctâeuro and plausible deformation that resembles the artifact under investigation. We correct data back, with three standard methodologies (namely fieldmap-based, reversed encoding-based, and registration- based). Finally, we rank the methods based on their geometrical accuracy, the dropout compensation, and their impact on the resulting connectivity matrices.

Added value of SPECT/CT in addition to whole-body scintigraphy augmented with prone lateral views in patients with well-differentiated thyroid carcinoma

Purpose: We aimed to determine the impact of SPECT/CT performed in addition to whole-­‐body scintigraphy augmented with prone lateral views in patients with well-­‐differentiated thyroid carcinoma. Methods and Materials: This retrospective study included 141 patients (87 female, 54 male, mean age 47 years) with well-­‐differentiated thyroid carcinoma (105 papillary, 31 follicular, 1 Hürthle cell and 4 poorly differentiated) treated with radioiodine therapy (1000-7400 MBq). Patients were referred for either first postsurgical therapy (n=76) or further treatment (n=65). Two nuclear medicine physicians interpreted the scans in consensus (first whole-­‐body scintigraphy with prone lateral view, then SPECT/CT) reporting abnormal iodine uptake in the thyroid bed, lymph nodes and distant metastasis. The corresponding ATA risk score was calculated for each patient before and after SPECT/CT, as well as change in disease extension Results: The analysis showed a difference between scintigraphy and SPECT/CT in n=17 lesions in 14 patients (9.9%): 12 were described as suspicious on scintigraphy and could be considered as benign on SPECT/CT (3 corresponded to local iodine uptake, 6 to lymph nodes metastases and 3 to distant metastases). The others 5 corresponded to metastases (4 lymph nodes and 1 distant) that were not seen on whole-­‐body scintigraphy augmented with prone lateral views. In 10 of 141 (7.1%) patients, we observed a change in ATA risk stratification, with a risk increase in 4 of them (2.8%). Conclusion: SPECT/CT allowed detecting 5 focal lesions missed on planar scintigraphy, and to precise benignity of 12 suspicious lesions on planar scintigraphy. Moreover, SPECT/CT improved the risk stratification in 10 patients with a significant change in the patient management

Reconstruction and analysis of surface variation using photometric stereo

In many industrial applications, accurate and fast surface reconstruction is essential for quality control. Variation in surface finishing parameters, such as surface roughness, can reflect defects in a manufacturing process, non-optimal product operational efficiency, and reduced life expectancy of the product. This thesis considers reconstruction and analysis of high-frequency variation, that is roughness, on planar surfaces. Standard roughness measures in industry are calculated from surface topography. A fast and non-contact method to obtain surface topography is to apply photometric stereo in the estimation of surface gradients and to reconstruct the surface by integrating the gradient fields. Alternatively, visual methods, such as statistical measures, fractal dimension and distance transforms, can be used to characterize surface roughness directly from gray-scale images. In this thesis, the accuracy of distance transforms, statistical measures, and fractal dimension are evaluated in the estimation of surface roughness from gray-scale images and topographies. The results are contrasted to standard industry roughness measures. In distance transforms, the key idea is that distance values calculated along a highly varying surface are greater than distances calculated along a smoother surface. Statistical measures and fractal dimension are common surface roughness measures. In the experiments, skewness and variance of brightness distribution, fractal dimension, and distance transforms exhibited strong linear correlations to standard industry roughness measures. One of the key strengths of photometric stereo method is the acquisition of higher frequency variation of surfaces. In this thesis, the reconstruction of planar high-frequency varying surfaces is studied in the presence of imaging noise and blur. Two Wiener filterbased methods are proposed of which one is optimal in the sense of surface power spectral density given the spectral properties of the imaging noise and blur. Experiments show that the proposed methods preserve the inherent high-frequency variation in the reconstructed surfaces, whereas traditional reconstruction methods typically handle incorrect measurements by smoothing, which dampens the high-frequency variation.

Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos

A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitude of the free energy obtained from this simulation did not permit us to conclude that urea is non-planar in water.

Simulations of 3D Stripixel Detectors

Large Hadron Collider (LHC) is the main particle accelerator at CERN. LHC is created with main goal to search elementary particles and help science investigate our universe. Radiation in LHC is caused by charged particles circular acceleration, therefore detectors tracing particles in existed severe conditions during the experiments must be radiation tolerant. Moreover, further upgrade of luminosity (up to 1035 cm-2s-1) requires development of particle detector’s structure. This work is dedicated to show the new type 3D stripixel detector with serious structural improvement. The new type of radiation-hard detector has a three-dimensional (3D) array of the p+ and n+ electrodes that penetrate into the detector bulk. The electrons and holes are then collected at oppositely biased electrodes. Proposed 3D stripixel detector demonstrates that full depletion voltage is lower that that for planar detectors. Low depletion voltage is one of the main advantages because only depleted part of the device is active are. Because of small spacing between electrodes, charge collection distances are smaller which results in high speed of the detector’s response. In this work is also briefly discussed dual-column type detectors, meaning consisting both n+ and p+ type columnar electrodes in its structure, and was declared that dual-column detectors show better electric filed distribution then single sided radiation detectors. The dead space or in other words low electric field region in significantly suppressed. Simulations were carried out by using Atlas device simulation software. As a simulation results in this work are represented the electric field distribution under different bias voltages.