A scheme for computing surface layer turbulent fluxes from mean flow surface observations

A physical model and computational scheme are developed for generating turbulent surface stress, sensible heat flux and humidity flux from mean velocity, temperature and humidity at some fixed height in the atmospheric surface layer, where conditions at this reference level are presumed known from observations or the evolving state of a numerical atmospheric circulation model. The method is based on coupling the Monin-Obukov surface layer similarity profiles which include buoyant stability effects on mean velocity, temperature and humidity to a force-restore formulation for the evolution of surface soil temperature to yield the local values of shear stress, heat flux and surface temperature. A self-contained formulation is presented including parameterizations for solar and infrared radiant fluxes at the surface. Additional parameters needed to implement the scheme are the thermal heat capacity of the soil per unit surface area, surface aerodynamic roughness, latitude, solar declination, surface albedo, surface emissivity and atmospheric transmissivity to solar radiation

Genome sequence of enterovirus D68 from St. Louis, Missouri, USA, 2016

Enterovirus D68 (EV-D68) was rarely observed prior to a widespread outbreak in 2014. We observed its reemergence in St. Louis in 2016 and sequenced the EV-D68 genomes from two patient samples. The 2016 viruses in St. Louis differed from those we had sequenced from the 2014 outbreak but were similar to other viruses circulating nationally in 2016

Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly

Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering

The telltale heart: a non-invasive method to determine the energy expenditure of incubating Great Cormorants Phalacrocorax carbo carbo

We studied the energetics of incubating Great Cormorants Phalacrocorax carbo carbo via heart rate and respirometric measurements performed in captive and free-living animals. We applied a modified heart beat frequency (HR) monitor built for use in human athletics as well as respirometry for measurements in four captive-bred cormorants at Neumuenster Zoo, Germany. The obtained data were used to model the relationship between HR and metabolic rate (MR). The resulting correlations were MR (W kg-0.723) = 4.76 + 0.01HR (bpm) during daytime and MR (W kg-0.723) = 2.33 + 0.03HR (bpm) at night. Furthermore, the heart beat frequencies of 5 free-living, incubating cormorants at the Chausey Islands, France, were measured acoustically using artificial eggs while the activities at the nest were observed via video. HR-MR models established in the captive animals were used to determine the activity-dependent energy expenditure in these free-living cormorants. The Median MR was 5.08 W kg-0.723 at night, 6.06 W kg-0.723 while resting and sleeping during daytime, 6.20 W kg-0.723 during preening, gular flutter and unrest and 6.47 W kg-0.723 during nest building. In resting birds we found a nocturnal reduction in the energy expenditure of 16 %. Our method for measurement of heart beat frequency appears promising as a technique for determination of HR with minimal restraint to the anima

Climate mode simulation of North Atlantic polar lows in a limited area model

Polar lows are not properly resolved in global re-analyses. In order to describe the year-to-year variability and decadal trends in the formation of such mesoscale storms, atmospheric limited area models, which post-process re-analysis data, may be an appropriate tool. In this study we demonstrate the merits and potential of this approach. A series of 3-week long ensemble simulations of weather situations over the NE Atlantic with a limited area model/regional climate model (CLM) are examined. The model was driven with NCEP-NCAR re-analyses at the lateral and lower boundaries. Additionally, the spectral nudging technique was used to enforce the large-scale circulation, as given by the NCEP-NCAR reanalysis, on the simulation. The ensemble members differ by initial conditions taken from several consecutive days. In most of the cases, a polar low developed after a simulated time of about 2 weeks, that is, long after the initialization of the model calculations. The spectrally nudged version of the model is very insensitive to initial conditions. The observed polar lows were reproduced in all ensemble members. A reasonable correlation between the simulated polar low features and those derived from a satellite product (HOAPS-III) and operational high-resolution weather analyses (DWD) is found. The polar lows are considerably deepened compared to the driving NCEP-NCAR analysis, but the comparison with weather maps indicates some differences in detail. When CLM is run without the large-scale constraint of spectral nudging, considerable variability emerges across the different ensemble members and the observed polar low often does not emerge. [References: 42

The M2 internal tide simulated by a 1/10° OGCM

Using a concurrent simulation of the ocean general circulation and tides with the ° Max Planck Institute Ocean Model (MPI-OM), known as STORMTIDE, this study provides a near-global quantification of the low-mode M2 internal tides. The quantification is based on wavelengths and their near-global distributions obtained by applying spectral analysis to STORMTIDE velocities and on comparisons of the distributions with those derived by solving the Sturm–Liouville eigenvalue problem. The simulated wavelengths, with respect to both their magnitudes and their geographical distributions, compare well with those obtained by solving the eigenvalue problem, suggesting that the STORMTIDE internal waves are, to a first approximation, linear internal waves satisfying local dispersion relations. The simulated wavelengths of modes 1 and 2 range within 100–160 and 45–80 km, respectively. Their distributions reveal, to different degrees for both modes, a zonal asymmetry and a tendency of a poleward increase with stratification N and the Coriolis parameter f being responsible for these two features, respectively. Distributions of mode 1 wavelengths are found to be determined by both N and f, but those of mode 2 are mainly controlled by variations in N. Larger differences between the STORMTIDE wavelengths and those of the eigenvalue problem occur, particularly for mode 2, primarily in high-latitude oceans and the Kuroshio and Gulf Stream and their extensions

Gaussian capacity of the quantum bosonic channel with additive correlated Gaussian noise

We present an algorithm for calculation of the Gaussian classical capacity of a quantum bosonic memory channel with additive Gaussian noise. The algorithm, restricted to Gaussian input states, is applicable to all channels with noise correlations obeying certain conditions and works in the full input energy domain, beyond previous treatments of this problem. As an illustration, we study the optimal input states and capacity of a quantum memory channel with Gauss-Markov noise [J. Sch\"afer, Phys. Rev. A 80, 062313 (2009)]. We evaluate the enhancement of the transmission rate when using these optimal entangled input states by comparison with a product coherent-state encoding and find out that such a simple coherent-state encoding achieves not less than 90% of the capacity.Comment: 12+6 pages, 9 figures. Errors corrected, figures were made clearer, appendix improved and extende

Emerging view of the human virome

The human virome is the collection of all viruses that are found in or on humans, including both eukaryotic and prokaryotic viruses. Eukaryotic viruses clearly have important effects on human health, ranging from mild, self-limited acute or chronic infections to those with serious or fatal consequences. Prokaryotic viruses can also influence human health by affecting bacterial community structure and function. Therefore, definition of the virome is an important step toward understanding how microbes affect human health and disease. We review progress in virome analysis, which has been driven by advances in high-throughput, deep sequencing technology. Highlights from these studies include the association of viruses with clinical phenotypes and description of novel viruses that may be important pathogens. Together these studies indicate that analysis of the human virome is critical as we aim to understand how microbial communities influence human health and disease. Descriptions of the human virome will stimulate future work to understand how the virome affects long-term human health, immunity, and response to coinfections. Analysis of the virome ultimately may affect the treatment of patients with a variety of clinical syndromes