Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi

Random perfect lattices and the sphere packing problem

Motivated by the search for best lattice sphere packings in Euclidean spaces of large dimensions we study randomly generated perfect lattices in moderately large dimensions (up to d=19 included). Perfect lattices are relevant in the solution of the problem of lattice sphere packing, because the best lattice packing is a perfect lattice and because they can be generated easily by an algorithm. Their number however grows super-exponentially with the dimension so to get an idea of their properties we propose to study a randomized version of the algorithm and to define a random ensemble with an effective temperature in a way reminiscent of a Monte-Carlo simulation. We therefore study the distribution of packing fractions and kissing numbers of these ensembles and show how as the temperature is decreased the best know packers are easily recovered. We find that, even at infinite temperature, the typical perfect lattices are considerably denser than known families (like A_d and D_d) and we propose two hypotheses between which we cannot distinguish in this paper: one in which they improve Minkowsky's bound phi\sim 2^{-(0.84+-0.06) d}, and a competitor, in which their packing fraction decreases super-exponentially, namely phi\sim d^{-a d} but with a very small coefficient a=0.06+-0.04. We also find properties of the random walk which are suggestive of a glassy system already for moderately small dimensions. We also analyze local structure of network of perfect lattices conjecturing that this is a scale-free network in all dimensions with constant scaling exponent 2.6+-0.1.Comment: 19 pages, 22 figure

Scattering statistics of rock outcrops: Model-data comparisons and Bayesian inference using mixture distributions

The probability density function of the acoustic field amplitude scattered by the seafloor was measured in a rocky environment off the coast of Norway using a synthetic aperture sonar system, and is reported here in terms of the probability of false alarm. Interpretation of the measurements focused on finding appropriate class of statistical models (single versus two-component mixture models), and on appropriate models within these two classes. It was found that two-component mixture models performed better than single models. The two mixture models that performed the best (and had a basis in the physics of scattering) were a mixture between two K distributions, and a mixture between a Rayleigh and generalized Pareto distribution. Bayes' theorem was used to estimate the probability density function of the mixture model parameters. It was found that the K-K mixture exhibits significant correlation between its parameters. The mixture between the Rayleigh and generalized Pareto distributions also had significant parameter correlation, but also contained multiple modes. We conclude that the mixture between two K distributions is the most applicable to this dataset.Comment: 15 pages, 7 figures, Accepted to the Journal of the Acoustical Society of Americ

Least-squares inversion for density-matrix reconstruction

We propose a method for reconstruction of the density matrix from measurable time-dependent (probability) distributions of physical quantities. The applicability of the method based on least-squares inversion is - compared with other methods - very universal. It can be used to reconstruct quantum states of various systems, such as harmonic and and anharmonic oscillators including molecular vibrations in vibronic transitions and damped motion. It also enables one to take into account various specific features of experiments, such as limited sets of data and data smearing owing to limited resolution. To illustrate the method, we consider a Morse oscillator and give a comparison with other state-reconstruction methods suggested recently.Comment: 16 pages, REVTeX, 6 PS figures include

WFPC2 Observations of the Hubble Deep Field-South

The Hubble Deep Field-South observations targeted a high-galactic-latitude field near QSO J2233-606. We present WFPC2 observations of the field in four wide bandpasses centered at roughly 300, 450, 606, and 814 nm. Observations, data reduction procedures, and noise properties of the final images are discussed in detail. A catalog of sources is presented, and the number counts and color distributions of the galaxies are compared to a new catalog of the HDF-N that has been constructed in an identical manner. The two fields are qualitatively similar, with the galaxy number counts for the two fields agreeing to within 20%. The HDF-S has more candidate Lyman-break galaxies at z > 2 than the HDF-N. The star-formation rate per unit volume computed from the HDF-S, based on the UV luminosity of high-redshift candidates, is a factor of 1.9 higher than from the HDF-N at z ~ 2.7, and a factor of 1.3 higher at z ~ 4.Comment: 93 pages, 25 figures; contains very long table

Multi-model simulations of the impact of international shipping on Atmospheric Chemistry and Climate in 2000 and 2030

The global impact of shipping on atmospheric chemistry and radiative forcing, as well as the associated uncertainties, have been quantified using an ensemble of ten state-of-the-art atmospheric chemistry models and a predefined set of emission data. The analysis is performed for present-day conditions ( year 2000) and for two future ship emission scenarios. In one scenario ship emissions stabilize at 2000 levels; in the other ship emissions increase with a constant annual growth rate of 2.2% up to 2030 ( termed the "Constant Growth Scenario" (CGS)). Most other anthropogenic emissions follow the IPCC ( Intergovernmental Panel on Climate Change) SRES ( Special Report on Emission Scenarios) A2 scenario, while biomass burning and natural emissions remain at year 2000 levels. An intercomparison of the model results with observations over the Northern Hemisphere (25 degrees - 60 degrees N) oceanic regions in the lower troposphere showed that the models are capable to reproduce ozone (O-3) and nitrogen oxides (NOx= NO+ NO2) reasonably well, whereas sulphur dioxide (SO2) in the marine boundary layer is significantly underestimated. The most pronounced changes in annual mean tropospheric NO2 and sulphate columns are simulated over the Baltic and North Seas. Other significant changes occur over the North Atlantic, the Gulf of Mexico and along the main shipping lane from Europe to Asia, across the Red and Arabian Seas. Maximum contributions from shipping to annual mean near-surface O-3 are found over the North Atlantic ( 5 - 6 ppbv in 2000; up to 8 ppbv in 2030). Ship contributions to tropospheric O3 columns over the North Atlantic and Indian Oceans reach 1 DU in 2000 and up to 1.8 DU in 2030. Tropospheric O-3 forcings due to shipping are 9.8 +/- 2.0 mW/m(2) in 2000 and 13.6 +/- 2.3 mW/m(2) in 2030. Whilst increasing O-3, ship NOx simultaneously enhances hydroxyl radicals over the remote ocean, reducing the global methane lifetime by 0.13 yr in 2000, and by up to 0.17 yr in 2030, introducing a negative radiative forcing. The models show future increases in NOx and O-3 burden which scale almost linearly with increases in NOx emission totals. Increasing emissions from shipping would significantly counteract the benefits derived from reducing SO2 emissions from all other anthropogenic sources under the A2 scenario over the continents, for example in Europe. Globally, shipping contributes 3% to increases in O-3 burden between 2000 and 2030, and 4.5% to increases in sulphate under A2/CGS. However, if future ground based emissions follow a more stringent scenario, the relative importance of ship emissions will increase. Inter-model differences in the simulated O-3 contributions from ships are significantly smaller than estimated uncertainties stemming from the ship emission inventory, mainly the ship emission totals, the distribution of the emissions over the globe, and the neglect of ship plume dispersion

The prescribed mean curvature equation in weakly regular domains

We show that the characterization of existence and uniqueness up to vertical translations of solutions to the prescribed mean curvature equation, originally proved by Giusti in the smooth case, holds true for domains satisfying very mild regularity assumptions. Our results apply in particular to the non-parametric solutions of the capillary problem for perfectly wetting fluids in zero gravity. Among the essential tools used in the proofs, we mention a \textit{generalized Gauss-Green theorem} based on the construction of the weak normal trace of a vector field with bounded divergence, in the spirit of classical results due to Anzellotti, and a \textit{weak Young's law} for $(\Lambda,r_{0})$-minimizers of the perimeter.Comment: 23 pages, 1 figure --- The results on the weak normal trace of vector fields have been now extended and moved in a self-contained paper available at: arXiv:1708.0139

Isomorphs in model molecular liquids

Isomorphs are curves in the phase diagram along which a number of static and dynamic quantities are invariant in reduced units. A liquid has good isomorphs if and only if it is strongly correlating, i.e., the equilibrium virial/potential energy fluctuations are more than 90% correlated in the NVT ensemble. This paper generalizes isomorphs to liquids composed of rigid molecules and study the isomorphs of two systems of small rigid molecules, the asymmetric dumbbell model and the Lewis-Wahnstrom OTP model. In particular, for both systems we find that the isochoric heat capacity, the excess entropy, the reduced molecular center-of-mass self part of the intermediate scattering function, the reduced molecular center-of-mass radial distribution function to a good approximation are invariant along an isomorph. In agreement with theory, we also find that an instantaneous change of temperature and density from an equilibrated state point to another isomorphic state point leads to no relaxation. The isomorphs of the Lewis-Wahnstrom OTP model were found to be more approximative than those of the asymmetric dumbbell model, which is consistent with the OTP model being less strongly correlating. For both models we find "master isomorphs", i.e., isomorphs have identical shape in the virial/potential energy phase diagram.Comment: 20 page

On Charge-3 Cyclic Monopoles

We determine the spectral curve of charge 3 BPS su(2) monopoles with C_3 cyclic symmetry. The symmetry means that the genus 4 spectral curve covers a (Toda) spectral curve of genus 2. A well adapted homology basis is presented enabling the theta functions and monopole data of the genus 4 curve to be given in terms of genus 2 data. The Richelot correspondence, a generalization of the arithmetic mean, is used to solve for this genus 2 curve. Results of other approaches are compared.Comment: 34 pages, 16 figures. Revision: Abstract added and a few small change

TRADEOFFs in climate effects through aircraft routing: forcing due to radiatively active gases

We have estimated impacts of alternative aviation routings on the radiative forcing. Changes in ozone and OH have been estimated in four Chemistry Transport Models (CTMs) participating in the TRADEOFF project. Radiative forcings due to ozone and methane have been calculated accordingly. In addition radiative forcing due to CO2 is estimated based on fuel consumption. Three alternative routing cases are investigated; one scenario assuming additional polar routes and two scenarios assuming aircraft cruising at higher (+2000 ft) and lower (−6000 ft) altitudes. Results from the base case in year 2000 are included as a reference. Taking first a steady state backward looking approach, adding the changes in the forcing from ozone, CO2 and CH4, the ranges of the models used in this work are −0.8 to −1.8 and 0.3 to 0.6 m Wm−2 in the lower (−6000 ft) and higher (+2000 ft) cruise levels, respectively. In relative terms, flying 6000ft lower reduces the forcing by 5–10% compared to the current flight pattern, whereas flying higher, while saving fuel and presumably flying time, increases the forcing by about 2–3%. Taking next a forward looking approach we have estimated the integrated forcing (m Wm−2 yr) over 20 and 100 years time horizons. The relative contributions from each of the three climate gases are somewhat different from the backward looking approach. The differences are moderate adopting 100 year time horizon, whereas under the 20 year horizon CO2 naturally becomes less important relatively. Thus the forcing agents impact climate differently on various time scales. Also, we have found significant differences between the models for ozone and methane. We conclude that we are not yet at a point where we can include non-CO2 effects of aviation in emission trading schemes. Nevertheless, the rerouting cases that have been studied here yield relatively small changes in the radiative forcing due to the radiatively active gases