Needles in the Haystack: Identifying Individuals Present in Pooled Genomic Data

Recent publications have described and applied a novel metric that quantifies the genetic distance of an individual with respect to two population samples, and have suggested that the metric makes it possible to infer the presence of an individual of known genotype in a sample for which only the marginal allele frequencies are known. However, the assumptions, limitations, and utility of this metric remained incompletely characterized. Here we present empirical tests of the method using publicly accessible genotypes, as well as analytical investigations of the method's strengths and limitations. The results reveal that the null distribution is sensitive to the underlying assumptions, making it difficult to accurately calibrate thresholds for classifying an individual as a member of the population samples. As a result, the false-positive rates obtained in practice are considerably higher than previously believed. However, despite the metric's inadequacies for identifying the presence of an individual in a sample, our results suggest potential avenues for future research on tuning this method to problems of ancestry inference or disease prediction. By revealing both the strengths and limitations of the proposed method, we hope to elucidate situations in which this distance metric may be used in an appropriate manner. We also discuss the implications of our findings in forensics applications and in the protection of GWAS participant privacy

The order of the quantum chromodynamics transition predicted by the standard model of particle physics

We determine the nature of the QCD transition using lattice calculations for physical quark masses. Susceptibilities are extrapolated to vanishing lattice spacing for three physical volumes, the smallest and largest of which differ by a factor of five. This ensures that a true transition should result in a dramatic increase of the susceptibilities.No such behaviour is observed: our finite-size scaling analysis shows that the finite-temperature QCD transition in the hot early Universe was not a real phase transition, but an analytic crossover (involving a rapid change, as opposed to a jump, as the temperature varied). As such, it will be difficult to find experimental evidence of this transition from astronomical observations.Comment: 7 pages, 4 figure

Anomaly and a QCD-like phase diagram with massive bosonic baryons

We study a strongly coupled $Z_2$ lattice gauge theory with two flavors of quarks, invariant under an exact $\mathrm{SU}(2)\times \mathrm{SU}(2) \times \mathrm{U}_A(1) \times \mathrm{U}_B(1)$ symmetry which is the same as QCD with two flavors of quarks without an anomaly. The model also contains a coupling that can be used to break the $\mathrm{U}_A(1)$ symmetry and thus mimic the QCD anomaly. At low temperatures $T$ and small baryon chemical potential $\mu_B$ the model contains massless pions and massive bosonic baryons similar to QCD with an even number of colors. In this work we study the $T-\mu_B$ phase diagram of the model and show that it contains three phases : (1) A chirally broken phase at low $T$ and $\mu_B$, (2) a chirally symmetric baryon superfluid phase at low $T$ and high $\mu_B$, and (3) a symmetric phase at high $T$. We find that the nature of the finite temperature chiral phase transition and in particular the location of the tricritical point that seperates the first order line from the second order line is affected significantly by the anomaly.Comment: 22 pages, 16 figures, 5 tables, references adde

Biological effects of exposure to magnetic resonance imaging: an overview

The literature on biological effects of magnetic and electromagnetic fields commonly utilized in magnetic resonance imaging systems is surveyed here. After an introduction on the basic principles of magnetic resonance imaging and the electric and magnetic properties of biological tissues, the basic phenomena to understand the bio-effects are described in classical terms. Values of field strengths and frequencies commonly utilized in these diagnostic systems are reported in order to allow the integration of the specific literature on the bio-effects produced by magnetic resonance systems with the vast literature concerning the bio-effects produced by electromagnetic fields. This work gives an overview of the findings about the safety concerns of exposure to static magnetic fields, radio-frequency fields, and time varying magnetic field gradients, focusing primarily on the physics of the interactions between these electromagnetic fields and biological matter. The scientific literature is summarized, integrated, and critically analyzed with the help of authoritative reviews by recognized experts, international safety guidelines are also cited

Gated myocardial perfusion SPECT underestimates left ventricular volumes and shows high variability compared to cardiac magnetic resonance imaging -- a comparison of four different commercial automated software packages

Abstract Background We sought to compare quantification of left ventricular volumes and ejection fraction by different gated myocardial perfusion SPECT (MPS) programs with each other and to magnetic resonance (MR) imaging. Methods N = 100 patients with known or suspected coronary artery disease were examined at rest with 99 mTc-tetrofosmin gated MPS and cardiac MR imaging. Left ventricular end-diastolic volume (EDV), end-systolic volume (ESV), stroke volume (SV) and ejection fraction (EF) were obtained by analysing gated MPS data with four different programs: Quantitative Gated SPECT (QGS), GE MyoMetrix, Emory Cardiac Toolbox (ECTb) and Exini heart. Results All programs showed a mean bias compared to MR imaging of approximately -30% for EDV (-22 to -34%, p Conclusions Gated MPS, systematically underestimates left ventricular volumes by approximately 30% and shows a high variability, especially for ESV. For EF, accuracy was better, with a mean bias between -15 and 6% of EF. It may be of value to take this into consideration when determining absolute values of LV volumes and EF in a clinical setting.</p

The gradient flow running coupling with twisted boundary conditions

We study the gradient flow for Yang-Mills theories with twisted boundary conditions. The perturbative behavior of the energy density $\langle E(t)\rangle$ is used to define a running coupling at a scale given by the linear size of the finite volume box. We compute the non-perturbative running of the pure gauge $SU(2)$ coupling constant and conclude that the technique is well suited for further applications due to the relatively mild cutoff effects of the step scaling function and the high numerical precision that can be achieved in lattice simulations. We also comment on the inclusion of matter fields.Comment: 27 pages. LaTe

Antiglucocorticoid RU38486 reduces net protein catabolism in experimental acute renal failure

BACKGROUND: In acute renal failure, a pronounced net protein catabolism occurs that has long been associated with corticoid action. By competitively blocking the glucocorticoid receptor with the potent antiglucocorticoid RU 38486, the present study addressed the question to what extent does corticoid action specific to uremia cause the observed muscle degradation, and does inhibition of glucocorticoid action reduce the protein wasting? METHODS: RU 38486 was administered in a dose of 50 mg/kg/24 h for 48 h after operation to fasted bilaterally nephrectomized (BNX) male adult Wistar rats and sham operated (SHAM) controls. Protein turnover was evaluated by high performance liquid chromatography (HPLC) of amino acid efflux in sera from isolated perfused hindquarters of animals treated with RU 38486 versus untreated controls. RESULTS: Administration of RU 38486 reduces the total amino acid efflux (TAAE) by 18.6% in SHAM and 15.6% in BNX and efflux of the indicator of net protein turnover, phenylalanine (Phe) by 33.3% in SHAM and 13% in BNX animals as compared to the equally operated, but untreated animals. However, the significantly higher protein degradation observed in BNX (0.6 ± 0.2 nmol/min/g muscle) versus SHAM (0.2 ± 0.1 nmol/min/g muscle) rats, as demonstrated by the marker of myofribrillar proteolytic rate, 3-Methylhistidine (3 MH) remains unaffected by administration of RU 38486 (0.5 ± 0.1 v. 0.2 ± 0.1 nmol/min/g muscle in BNX v. SHAM). CONCLUSION: RU 38486 does not act on changes of muscular protein turnover specific to uremia but reduces the effect of stress- stimulated elevated corticosterone secretion arising from surgery and fasting. A potentially beneficial effect against stress- induced catabolism in severe illness can be postulated that merits further study

The Curious Adventure of the Ultrahigh Energy Cosmic Rays

These lectures discuss the mysteries involving the production and extragalactic propagation of ultrahigh energy cosmic rays and suggested possible solutions.Comment: Lectures given at the D. Chalonge Euroschool, Erice, Italy, November 2000, 25 pages, 7 ps figs., expanded revision with color fig.

Very Cold Gas and Dark Matter

We have recently proposed a new candidate for baryonic dark matter: very cold molecular gas, in near-isothermal equilibrium with the cosmic background radiation at 2.73 K. The cold gas, of quasi-primordial abundances, is condensed in a fractal structure, resembling the hierarchical structure of the detected interstellar medium. We present some perspectives of detecting this very cold gas, either directly or indirectly. The H$_2$ molecule has an "ultrafine" structure, due to the interaction between the rotation-induced magnetic moment and the nuclear spins. But the lines fall in the km domain, and are very weak. The best opportunity might be the UV absorption of H$_2$ in front of quasars. The unexpected cold dust component, revealed by the COBE/FIRAS submillimetric results, could also be due to this very cold H$_2$ gas, through collision-induced radiation, or solid H$_2$ grains or snowflakes. The $\gamma$-ray distribution, much more radially extended than the supernovae at the origin of cosmic rays acceleration, also points towards and extended gas distribution.Comment: 16 pages, Latex pages, crckapb macro, 3 postscript figures, uuencoded compressed tar file. To be published in the proceeedings of the "Dust-Morphology" conference, Johannesburg, 22-26 January, 1996, D. Block (ed.), (Kluwer Dordrecht