Principles and Implementation of an Ultrafast Transmission Electron Microscope

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 - August 2, 201

Patella malalignment, pain and patellofemoral progression: the Health ABC Study

SummaryObjectivePatellofemoral (PF) joint osteoarthritis (OA) is strongly correlated with lower extremity disability and knee pain. Risk factors for pain and structural progression in PF OA are poorly understood. Our objective was to determine the association between patella malalignment and its relation to pain severity, and PF OA disease progression.MethodsWe conducted an analysis of data from the Health ABC knee OA study. Health ABC is a community based, multi-center cohort study of 3075 Caucasian and Black men and women aged 70–79 at enrollment. Weight bearing skyline knee X-rays were obtained in a subset (595) of subjects, with and without knee pain, at year 2 and year 5 (mean follow-up 36 months). Films were read paired, and PF osteophytes (OST) and joint space narrowing (JSN) were scored on a 0–3 scale using the Osteoarthritis Research Society International atlas. We defined progression of PF OA as any increase in JSN score. Three measures of patella malalignment were made: sulcus angle; patella tilt angle; and patella subluxation medially or laterally (bisect offset). Knee symptoms were assessed using a knee specific Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) knee pain subscale. We assessed the relationship between baseline patella malalignment and pain severity (linear regression for WOMAC) and compartment specific PF OA progression (logistic regression for dichotomous outcomes). We classified continuous measures of patella alignment into quartile groups. We performed multivariable adjusted logistic regression models, including age, gender and body mass index (BMI) to assess the relation of baseline patella alignment to the occurrence of PF JSN progression using generalized estimating equations (GEE).ResultsThe subjects had a mean age 73.6 (SD 2.9), BMI 28.8 (SD 4.9), 40.3% male, and 46% were Black. Medial displacement of the patella predisposed to medial JSN progression; odds for each quartile 1, 1.2, 1.2, 2.2 (P for trend=0.03), whilst protecting from lateral JSN progression; odds for each quartile 1, 0.7, 0.6, 0.4 (P for trend=0.0004). Increasing patella tilt protected from medial JSN progression; odds for each quartile 1, 0.8, 0.5, 0.2 (P<0.0001) and trended to increasing pain severity (P=0.09).ConclusionPatella malalignment is associated with PF disease progression. Medial displacement and tilt of the patella predisposes to medial JSN progression, whilst lateral displacement is predictive of lateral JSN progression. The influence of patella malalignment has important implications since it is potentially modifiable through footwear, taping and/or knee bracing

Cosmological Parameters Degeneracies and Non-Gaussian Halo Bias

We study the impact of the cosmological parameters uncertainties on the measurements of primordial non-Gaussianity through the large-scale non-Gaussian halo bias effect. While this is not expected to be an issue for the standard LCDM model, it may not be the case for more general models that modify the large-scale shape of the power spectrum. We consider the so-called local non-Gaussianity model and forecasts from planned surveys, alone and combined with a Planck CMB prior. In particular, we consider EUCLID- and LSST-like surveys and forecast the correlations among $f_{\rm NL}$ and the running of the spectral index $\alpha_s$, the dark energy equation of state $w$, the effective sound speed of dark energy perturbations $c^2_s$, the total mass of massive neutrinos $M_\nu=\sum m_\nu$, and the number of extra relativistic degrees of freedom $N_\nu^{rel}$. Neglecting CMB information on $f_{\rm NL}$ and scales $k > 0.03 h$/Mpc, we find that, if $N_\nu^{\rm rel}$ is assumed to be known, the uncertainty on cosmological parameters increases the error on $f_{\rm NL}$ by 10 to 30% depending on the survey. Thus the $f_{\rm NL}$ constraint is remarkable robust to cosmological model uncertainties. On the other hand, if $N_\nu^{\rm rel}$ is simultaneously constrained from the data, the $f_{\rm NL}$ error increases by $\sim 80$. Finally, future surveys which provide a large sample of galaxies or galaxy clusters over a volume comparable to the Hubble volume can measure primordial non-Gaussianity of the local form with a marginalized 1--$\sigma$ error of the order $\Delta f_{\rm NL} \sim 2-5$, after combination with CMB priors for the remaining cosmological parameters. These results are competitive with CMB bispectrum constraints achievable with an ideal CMB experiment.Comment: 17 pages, 1 figure added, typos corrected, comments added, matches the published versio

The sensitivity of BAO Dark Energy Constraints to General Isocurvature Perturbations

Baryon Acoustic Oscillation (BAO) surveys will be a leading method for addressing the dark energy challenge in the next decade. We explore in detail the effect of allowing for small amplitude admixtures of general isocurvature perturbations in addition to the dominant adiabatic mode. We find that non-adiabatic initial conditions leave the sound speed unchanged but instead excite different harmonics. These harmonics couple differently to Silk damping, altering the form and evolution of acoustic waves in the baryon-photon fluid prior to decoupling. This modifies not only the scale on which the sound waves imprint onto the baryon distribution, which is used as the standard ruler in BAO surveys, but also the shape, width and height of the BAO peak. We discuss these effects in detail and show how more general initial conditions impact our interpretation of cosmological data in dark energy studies. We find that the inclusion of these additional isocurvature modes leads to an increase in the Dark Energy Task Force Figure of merit by 140% and 60% for the BOSS and ADEPT experiments respectively when considered in conjunction with Planck data. We also show that the incorrect assumption of adiabaticity has the potential to bias our estimates of the dark energy parameters by $3\sigma$ ($1\sigma$) for a single correlated isocurvature mode, and up to $8\sigma$ ($3\sigma$) for three correlated isocurvature modes in the case of the BOSS (ADEPT) experiment. We find that the use of the large scale structure data in conjunction with CMB data improves our ability to measure the contributions of different modes to the initial conditions by as much as 100% for certain modes in the fully correlated case.Comment: 20 pages, 17 figure

The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Self-consistent Green's function approaches

We present the fundamental techniques and working equations of many-body Green's function theory for calculating ground state properties and the spectral strength. Green's function methods closely relate to other polynomial scaling approaches discussed in chapters 8 and 10. However, here we aim directly at a global view of the many-fermion structure. We derive the working equations for calculating many-body propagators, using both the Algebraic Diagrammatic Construction technique and the self-consistent formalism at finite temperature. Their implementation is discussed, as well as the inclusion of three-nucleon interactions. The self-consistency feature is essential to guarantee thermodynamic consistency. The pairing and neutron matter models introduced in previous chapters are solved and compared with the other methods in this book.Comment: 58 pages, 14 figures, Submitted to Lect. Notes Phys., "An advanced course in computational nuclear physics: Bridging the scales from quarks to neutron stars", M. Hjorth-Jensen, M. P. Lombardo, U. van Kolck, Editor

Constraining primordial non-Gaussianity with cosmological weak lensing: shear and flexion

We examine the cosmological constraining power of future large-scale weak lensing surveys on the model of \emph{Euclid}, with particular reference to primordial non-Gaussianity. Our analysis considers several different estimators of the projected matter power spectrum, based on both shear and flexion, for which we review the covariances and Fisher matrices. The bounds provided by cosmic shear alone for the local bispectrum shape, marginalized over $\sigma_8$, are at the level of $\Delta f_\mathrm{NL} \sim 100$. We consider three additional bispectrum shapes, for which the cosmic shear constraints range from $\Delta f_\mathrm{NL}\sim 340$ (equilateral shape) up to $\Delta f_\mathrm{NL}\sim 500$ (orthogonal shape). The competitiveness of cosmic flexion constraints against cosmic shear ones depends on the galaxy intrinsic flexion noise, that is still virtually unconstrained. Adopting the very high value that has been occasionally used in the literature results in the flexion contribution being basically negligible with respect to the shear one, and for realistic configurations the former does not improve significantly the constraining power of the latter. Since the flexion noise decreases with decreasing scale, by extending the analysis up to $\ell_\mathrm{max} = 20,000$ cosmic flexion, while being still subdominant, improves the shear constraints by $\sim 10$ when added. However on such small scales the highly non-linear clustering of matter and the impact of baryonic physics make any error estimation uncertain. By considering lower, and possibly more realistic, values of the flexion intrinsic shape noise results in flexion constraining power being a factor of $\sim 2$ better than that of shear, and the bounds on $\sigma_8$ and $f_\mathrm{NL}$ being improved by a factor of $\sim 3$ upon their combination. (abridged)Comment: 30 pages, 4 figures, 4 tables. To appear on JCA

Constraining Primordial Non-Gaussianity with High-Redshift Probes

We present an analysis of the constraints on the amplitude of primordial non-Gaussianity of local type described by the dimensionless parameter $f_{\rm NL}$. These constraints are set by the auto-correlation functions (ACFs) of two large scale structure probes, the radio sources from NRAO VLA Sky Survey (NVSS) and the quasar catalogue of Sloan Digital Sky Survey Release Six (SDSS DR6 QSOs), as well as by their cross-correlation functions (CCFs) with the cosmic microwave background (CMB) temperature map (Integrated Sachs-Wolfe effect). Several systematic effects that may affect the observational estimates of the ACFs and of the CCFs are investigated and conservatively accounted for. Our approach exploits the large-scale scale-dependence of the non-Gaussian halo bias. The derived constraints on {$f_{\rm NL}$} coming from the NVSS CCF and from the QSO ACF and CCF are weaker than those previously obtained from the NVSS ACF, but still consistent with them. Finally, we obtain the constraints on $f_{\rm NL}=53\pm25$ ($1\,\sigma$) and $f_{\rm NL}=58\pm24$ ($1\,\sigma$) from NVSS data and SDSS DR6 QSO data, respectively.Comment: 16 pages, 8 figures, 1 table, Accepted for publication on JCA

Measuring the neutrino mass from future wide galaxy cluster catalogues

We present forecast errors on a wide range of cosmological parameters obtained from a photometric cluster catalogue of a future wide-field Euclid-like survey. We focus in particular on the total neutrino mass as constrained by a combination of the galaxy cluster number counts and correlation function. For the latter we consider only the shape information and the Baryon Acoustic Oscillations (BAO), while marginalising over the spectral amplitude and the redshift space distortions. In addition to the cosmological parameters of the standard LCDM+nu model we also consider a non-vanishing curvature, and two parameters describing a redshift evolution for the dark energy equation of state. For completeness, we also marginalise over a set of "nuisance" parameters, representing the uncertainties on the cluster mass determination. We find that combining cluster counts with power spectrum information greatly improves the constraining power of each probe taken individually, with errors on cosmological parameters being reduced by up to an order of magnitude. In particular, the best improvements are for the parameters defining the dynamical evolution of dark energy, where cluster counts break degeneracies. Moreover, the resulting error on neutrino mass is at the level of \sigma(M_\nu)\sim 0.9 eV, comparable with that derived from present Ly-alpha forest measurements and Cosmic Microwave background (CMB) data in the framework of a non-flat Universe. Further adopting Planck priors and reducing the number of free parameters to a LCDM+nu cosmology allows to place constraints on the total neutrino mass of \sigma(M_\nu) \sim 0.08 eV, close to the lower bound enforced by neutrino oscillation experiments. [abridged]Comment: 25 pages, 2 figures, 2 tables, matches the JCAP accepted versio

Measurement of charged particle multiplicities in pppp collisions at s=7{\sqrt{s} =7}TeV in the forward region

The charged particle production in proton-proton collisions is studied with the LHCb detector at a centre-of-mass energy of ${\sqrt{s} =7}$TeV in different intervals of pseudorapidity $\eta$. The charged particles are reconstructed close to the interaction region in the vertex detector, which provides high reconstruction efficiency in the $\eta$ ranges $-2.5<\eta<-2.0$ and $2.0<\eta<4.5$. The data were taken with a minimum bias trigger, only requiring one or more reconstructed tracks in the vertex detector. By selecting an event sample with at least one track with a transverse momentum greater than 1 GeV/c a hard QCD subsample is investigated. Several event generators are compared with the data; none are able to describe fully the multiplicity distributions or the charged particle density distribution as a function of $\eta$. In general, the models underestimate the charged particle production