High refractive index of melanin in shiny occipital feathers of a bird of paradise

Male Lawes's Parotia, a bird of paradise, use the highly directional reflection of the structurally colored, brilliant-silvery occipital feathers in their courtship display. As in other birds, the structural coloration is produced by ordered melanin pigmentation. The barbules of the Parotia's occipital feathers, with thickness ~3 µm, contain 6–7 layers of densely packed melanin rodlets (diameter ~0.25 µm, length ~2 µm). The effectively ~0.2 µm thick melanin layers separated by ~0.2 µm thick keratin layers create a multilayer interference reflector. Reflectance measurements yielded peak wavelengths in the near-infrared at ~1.3 µm, i.e., far outside the visible wavelength range. With the Jamin-Lebedeff interference microscopy method recently developed for pigmented media, we here determined the refractive index of the intact barbules. We thus derived the wavelength dependence of the refractive index of the barbules' melanin to be 1.7–1.8 in the visible wavelength range. Implementing the anatomical and refractive index data in an optical multilayer model, we calculated the barbules' reflectance, transmittance and absorptance spectra, thereby confirming measured spectra

Stromal control of oncogenic traits expressed in response to the overexpression of GLI2, a pleiotropic oncogene.

Hedgehog signaling is often activated in tumors, yet it remains unclear how GLI2, a transcription factor activated by this pathway, acts as an oncogene. We show that GLI2 is a pleiotropic oncogene. The overexpression induces genomic instability and blocks differentiation, likely mediated in part by enhanced expression of the stem cell gene SOX2. GLI2 also induces transforming growth factor (TGF)B1-dependent transdifferentiation of foreskin and tongue, but not gingival fibroblasts into myofibroblasts, creating an environment permissive for invasion by keratinocytes, which are in various stages of differentiation having downregulated GLI2. Thus, upregulated GLI2 expression is sufficient to induce a number of the acquired characteristics of tumor cells; however, the stroma, in a tissue-specific manner, determines whether certain GLI2 oncogenic traits are expressed

A nonlinear structural subgrid-scale closure for compressible MHD. I. Derivation and energy dissipation properties

This is the final version. Available from AIP Publishing via the DOI in this recordCompressible magnetohydrodynamic (MHD) turbulence is ubiquitous in astrophysical phenomena ranging from the intergalactic to the stellar scales. In studying them, numerical simulations are nearly inescapable, due to the large degree of nonlinearity involved. However, the dynamical ranges of these phenomena are much larger than what is computationally accessible. In large eddy simulations (LESs), the resulting limited resolution effects are addressed explicitly by introducing to the equations of motion additional terms associated with the unresolved, subgrid-scale dynamics. This renders the system unclosed. We derive a set of nonlinear structural closures for the ideal MHD LES equations with particular emphasis on the effects of compressibility. The closures are based on a gradient expansion of the finite-resolution operator [W. K. Yeo (CUP, 1993)] and require no assumptions about the nature of the flow or magnetic field. Thus, the scope of their applicability ranges from the sub- to the hyper-sonic and -Alfvénic regimes. The closures support spectral energy cascades both up and down-scale, as well as direct transfer between kinetic and magnetic resolved and unresolved energy budgets. They implicitly take into account the local geometry, and in particular, the anisotropy of the flow. Their properties are a priori validated in Paper II [P. Grete et al., Phys. Plasmas 23, 062317 (2016)] against alternative closures available in the literature with respect to a wide range of simulation data of homogeneous and isotropic turbulence.University of GöttingenDeutsche Forschungsgemeinschaft (DFG)Max Planck Institute for Dynamics and Self-OrganizationConicyt Fondecyt: Fondo Nacional de Desarrollo Científico y TecnológicoNorth-German Supercomputing Allianc

Collaborative research and development (R&D) for climate technology transfer and uptake in developing countries: Towards a needs driven approach

While international cooperation to facilitate the transfer and uptake of climate technologies in developing countries is an ongoing part of climate policy conversations, international collaborative R&D has received comparatively little attention. Collaborative R&D, however, could be a potentially important contributor to facilitating the transfer and uptake of climate technologies in developing countries. But the complexities of international collaborative R&D options and their distributional consequences have been given little attention to date. This paper develops a systematic approach to informing future empirical research and policy analysis on this topic. Building on insights from relevant literature and analysis of empirical data based on a sample of existing international climate technology R&D initiatives, three contributions are made. First, the paper analyses the coverage of existing collaborative R&D efforts in relation to climate technologies, highlighting some important concerns, such as a lack of coverage of lower-income countries or adaptation technologies. Second, it provides a starting point for further systematic research and policy thinking via the development of a taxonomic approach for analysing collaborative designs. Finally, it matches characteristics of R&D collaborations against developing countries’ climate technology needs to provide policymakers with guidance on how to Configure R&D collaborations to meet these needs

Epidemiological associations between brachycephaly and upper respiratory tract disorders in dogs attending veterinary practices in England

Background: Brachycephalic dog breeds are increasingly common. Canine brachycephaly has been associated with upper respiratory tract (URT) disorders but reliable prevalence data remain lacking. Using primary-care veterinary clinical data, this study aimed to report the prevalence and breed-type risk factors for URT disorders in dogs. Results: The sampling frame included 170,812 dogs attending 96 primary-care veterinary clinics participating within the VetCompass Programme. Two hundred dogs were randomly selected from each of three extreme brachycephalic breed types (Bulldog, French Bulldog and Pug) and three common small-to medium sized breed types (moderate brachycephalic: Yorkshire Terrier and non-brachycephalic: Border Terrier and West Highland White Terrier). Information on all URT disorders recorded was extracted from individual patient records. Disorder prevalence was compared between groups using the chi-squared test or Fisher’s test, as appropriate. Risk factor analysis used multivariable logistic regression modelling. During the study, 83 (6.9 %) study dogs died. Extreme brachycephalic dogs (median longevity: 8.6 years, IQR: 2.4-10.8) were significantly younger at death than the moderate and non-brachycephalic group of dogs (median 12.7 years, IQR 11.1-15.0) (P \u3c 0.001). A higher proportion of deaths in extreme brachycephalic breed types were associated with URT disorders (4/24 deaths, 16.7 %) compared with the moderate and non-brachycephalic group (0/59 deaths, 0.0 %) (P = 0.001). The prevalence of having at least one URT disorder in the extreme brachycephalic group was higher (22.0 %, 95 % confidence interval (CI): 18.0-26.0) than in the moderate and non-brachycephalic group (9.7 %, 95 % CI: 7.1-12.3, P \u3c 0.001). The prevalence of URT disorders varied significantly by breed type: Bulldogs 19.5 %, French Bulldogs 20.0 %, Pugs 26.5 %, Border Terriers 9.0 %, West Highland White Terriers 7.0 % and Yorkshire Terriers 13.0 % (P \u3c 0.001). After accounting for the effects of age, bodyweight, sex, neutering and insurance, extreme brachycephalic dogs had 3.5 times (95 % CI: 2.4-5.0, P \u3c 0.001) the odds of at least one URT disorder compared with the moderate and non-brachycephalic group. Conclusions: In summary, this study reports that URT disorders are commonly diagnosed in Bulldog, French Bulldog, Pug, Border Terrier, WHWT and Yorkshire Terrier dogs attending primary-care veterinary practices in England. The three extreme brachycephalic breed types (Bulldog, French Bulldog and Pug) were relatively short-lived and predisposed to URT disorders compared with three other small-to-medium size breed types that are commonly owned (moderate brachycephalic Yorkshire Terrier and non-brachycephalic: Border Terrier and WHWT). Conclusions: In summary, this study reports that URT disorders are commonly diagnosed in Bulldog, French Bulldog, Pug, Border Terrier, WHWT and Yorkshire Terrier dogs attending primary-care veterinary practices in England. The three extreme brachycephalic breed types (Bulldog, French Bulldog and Pug) were relatively short-lived and predisposed to URT disorders compared with three other small-to-medium size breed types that are commonly owned (moderate brachycephalic Yorkshire Terrier and non-brachycephalic: Border Terrier and WHWT)

A nonlinear structural subgrid-scale closure for compressible MHD. II. A priori comparison on turbulence simulation data

This is the final version. Available from AIP Publishing via the DOI in this recordEven though compressible plasma turbulence is encountered in many astrophysical phenomena, its effect is often not well understood. Furthermore, direct numerical simulations are typically not able to reach the extreme parameters of these processes. For this reason, large-eddy simulations (LES), which only simulate large and intermediate scales directly, are employed. The smallest, unresolved scales and the interactions between small and large scales are introduced by means of a subgrid-scale (SGS) model. We propose and verify a new set of nonlinear SGS closures for future application as an SGS model in LES of compressible magnetohydrodynamics. We use 15 simulations (without explicit SGS model) of forced, isotropic, homogeneous turbulence with varying sonic Mach number Ms=0.2-20 as reference data for the most extensive a priori tests performed so far in literature. In these tests, we explicitly filter the reference data and compare the performance of the new closures against the most widely tested closures. These include eddy-viscosity and scale-similarity type closures with different normalizations. Performance indicators are correlations with the turbulent energy and cross-helicity flux, the average SGS dissipation, the topological structure and the ability to reproduce the correct magnitude and the direction of the SGS vectors. We find that only the new nonlinear closures exhibit consistently high correlations (median value > 0.8) with the data over the entire parameter space and outperform the other closures in all tests. Moreover, we show that these results are independent of resolution and chosen filter scale. Additionally, the new closures are effectively coefficient-free with a deviation of less than 20%.University of GöttingenDeutsche Forschungsgemeinschaft (DFG)Max Planck Institute for Dynamics and Self-OrganizationConicyt Fondecyt: Fondo Nacional de Desarrollo Científico y Tecnológic

Comparative statistics of selected subgrid-scale models in large-eddy simulations of decaying, supersonic magnetohydrodynamic turbulence

This is the final version. Available from the American Physical Society via the DOI in this recordLarge-eddy simulations (LES) are a powerful tool in understanding processes that are inaccessible by direct simulations due to their complexity, for example, in the highly turbulent regime. However, their accuracy and success depends on a proper subgrid-scale (SGS) model that accounts for the unresolved scales in the simulation. We evaluate the applicability of two traditional SGS models, namely the eddy-viscosity (EV) and the scale-similarity (SS) models, and one recently proposed nonlinear (NL) SGS model in the realm of compressible magnetohydrodynamic (MHD) turbulence. Using 209 simulations of decaying, supersonic (initial sonic Mach number Ms≈3) MHD turbulence with a shock-capturing scheme and varying resolution, SGS model, and filter, we analyze the ensemble statistics of kinetic and magnetic energy spectra and structure functions. Furthermore, we compare the temporal evolution of lower- and higher-order statistical moments of the spatial distributions of kinetic and magnetic energy, vorticity, current density, and dilatation magnitudes. We find no statistical influence on the evolution of the flow by any model if grid-scale quantities are used to calculate SGS contributions. In addition, the SS models, which employ an explicit filter, have no impact in general. On the contrary, both the EV and NL models change the statistics if an explicit filter is used. For example, they slightly increase the dissipation on the smallest scales. We demonstrate that the nonlinear model improves higher-order statistics already with a small explicit filter, i.e., a three-point stencil. The results of, e.g., the structure functions or the skewness and kurtosis of the current density distribution are closer to the ones obtained from simulations at higher resolution. In addition, no additional regularization to stabilize the model is required. We conclude that the nonlinear model with a small explicit filter is suitable for application in more complex scenarios when higher-order statistics are important.University of GottingenMax-Planck-Institut MPI für Dynamik und SelbstorganisationConicyt Fondecyt: Fondo Nacional de Desarrollo Científico y TecnológicoCentro de Astrofísica y Tecnologías Afines CAT

The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 {\AA} for RHF and MP2, respectively.Comment: Revised manuscrip

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. There are more than 645,000 reported disease-relevant PPIs in the human interactome, but drugs have been developed for only 2% of these targets. The advances in PPI-focused drug discovery are highly dependent on the availability of structural data and accurate computational tools for analysis of this data. Quantum mechanical approaches are often too expensive computationally, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. FMO provides essential information for PPI drug discovery, namely, identification of key interactions formed between residues of two proteins, including their strength (in kcal/mol) and their chemical nature (electrostatic or hydrophobic). In this chapter, we have demonstrated how three different FMO-based approaches (pair interaction energy analysis (PIE analysis), subsystem analysis (SA) and analysis of protein residue networks (PRNs)) have been applied to study PPI in three protein-protein complexes

Production of a chromium Bose-Einstein condensate

The recent achievement of Bose-Einstein condensation of chromium atoms [1] has opened longed-for experimental access to a degenerate quantum gas with long-range and anisotropic interaction. Due to the large magnetic moment of chromium atoms of 6 {$\mu$}B, in contrast to other Bose- Einstein condensates (BECs), magnetic dipole-dipole interaction plays an important role in a chromium BEC. Many new physical properties of degenerate gases arising from these magnetic forces have been predicted in the past and can now be studied experimentally. Besides these phenomena, the large dipole moment leads to a breakdown of standard methods for the creation of a chromium BEC. Cooling and trapping methods had to be adapted to the special electronic structure of chromium to reach the regime of quantum degeneracy. Some of them apply generally to gases with large dipolar forces. We present here a detailed discussion of the experimental techniques which are used to create a chromium BEC and alow us to produce pure condensates with up to {$10^5$} atoms in an optical dipole trap. We also describe the methods used to determine the trapping parameters.Comment: 17 pages, 9 figure