Monthly resolved modelled oceanic emissions of carbonyl sulfide and carbon disulfide for the period 2000–2019

Carbonyl sulfide (OCS) is the most abundant, long-lived sulphur gas in the atmosphere and a major supplier of sulfur to the stratospheric sulfate aerosol layer. The short-lived gas carbon disulfide (CS2) is oxidized to OCS and constitutes a major indirect source to the atmospheric OCS budget. The atmospheric budget of OCS is not well constrained due to a large missing source needed to compensate for substantial evidence that was provided for significantly higher sinks. Oceanic emissions are associated with major uncertainties. Here we provide a first, monthly resolved ocean emission inventory of both gases for the period 2000–2019 (available at https://doi.org/10.5281/zenodo.4297010) (Lennartz et al., 2020a). Emissions are calculated with a numerical box model (resolution 2.8° × 2.8° at equator, T42 grid) for the surface mixed layer. We find that interannual variability in OCS emissions is smaller than seasonal variability, and is mainly driven by variations in chromophoric dissolved organic matter (CDOM), which influences both photochemical and light-independent production. A comparison with a global database of more than 2500 measurements reveals overall good agreement. Emissions of CS2 constitute a larger sulfur source to the atmosphere than OCS, and equally show interannual variability connected to variability of CDOM. The emission estimate of CS2 is associated with higher uncertainties, as process understanding of the marine cycling of CS2 is incomplete. We encourage the use of the data provided here as input for atmospheric modelling studies to further assess the atmospheric OCS budget and the role of OCS in climate

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

The interplay of Hrd3 and the molecular chaperone system ensures efficient degradation of malfolded secretory proteins

Misfolded proteins of the secretory pathway are extracted from the endoplasmic reticulum (ER), polyubiquitylated by a protein complex termed the Hmg-CoA reductase degradation ligase (HRD-ligase) and degraded by cytosolic 26S proteasomes. This process is termed ER-associated protein degradation (ERAD). We previously showed that the membrane protein Der1, which is a subunit of the HRD-ligase, is involved in the export of aberrant polypeptides from the ER. Unexpectedly, we also uncovered a close spatial proximity of Der1 and the substrate receptor Hrd3 in the ER lumen. We report here on a mutant Hrd3KR, which is selectively defective for ERAD of soluble proteins. Hrd3KR displays subtle structural changes that affect its positioning toward Der1. Furthermore, increased quantities of the ER-resident Hsp70 type chaperone Kar2 and the Hsp40 type cochaperone Scj1 bind to Hrd3KR. Noteworthy, deletion of SCJ1 impairs ERAD of model substrates and causes the accumulation of client proteins at Hrd3. Our data imply a function of Scj1 in the removal of malfolded proteins from the receptor Hrd3, which facilitates their delivery to downstream acting components like Der1

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

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

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

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

Excited-State Effective Masses in Lattice QCD

We apply black-box methods, i.e. where the performance of the method does not depend upon initial guesses, to extract excited-state energies from Euclidean-time hadron correlation functions. In particular, we extend the widely used effective-mass method to incorporate multiple correlation functions and produce effective mass estimates for multiple excited states. In general, these excited-state effective masses will be determined by finding the roots of some polynomial. We demonstrate the method using sample lattice data to determine excited-state energies of the nucleon and compare the results to other energy-level finding techniques.Comment: 18 pages, 6 figure

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