Online Search Tool for Graphical Patterns in Electronic Band Structures

We present an online graphical pattern search tool for electronic band structure data contained within the Organic Materials Database (OMDB) available at https://omdb.diracmaterials.org/search/pattern. The tool is capable of finding user-specified graphical patterns in the collection of thousands of band structures from high-throughput ab initio calculations in the online regime. Using this tool, it only takes a few seconds to find an arbitrary graphical pattern within the ten electronic bands near the Fermi level for 26,739 organic crystals. The tool can be used to find realizations of functional materials characterized by a specific pattern in their electronic structure, for example, Dirac materials, characterized by a linear crossing of bands; topological insulators, characterized by a "Mexican hat" pattern or an effectively free electron gas, characterized by a parabolic dispersion. The source code of the developed tool is freely available at https://github.com/OrganicMaterialsDatabase/EBS-search and can be transferred to any other electronic band structure database. The approach allows for an automatic online analysis of a large collection of band structures where the amount of data makes its manual inspection impracticable.Comment: 8 pages, 8 figure

Probing the plateau-insulator quantum phase transition in the quantum Hall regime

We report quantum Hall experiments on the plateau-insulator transition in a low mobility In_{.53} Ga_{.47} As/InP heterostructure. The data for the longitudinal resistance \rho_{xx} follow an exponential law and we extract a critical exponent \kappa= .55 \pm .05 which is slightly different from the established value \kappa = .42 \pm .04 for the plateau transitions. Upon correction for inhomogeneity effects, which cause the critical conductance \sigma_{xx}^* to depend marginally on temperature, our data indicate that the plateau-plateau and plateau- insulator transitions are in the same universality class.Comment: 4 pages, 4 figures (.eps

Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties

Neo-Atlantis: The Netherlands under a 5-m sea level rise

What could happen to the Netherlands if, in 2030, the sea level starts to rise and eventually, after 100 years, a sea level of 5 m above current level would be reached? This question is addressed by studying literature, by interviewing experts in widely differing fields, and by holding an expert workshop on this question. Although most experts believe that geomorphology and current engineering skills would enable the country to largely maintain its territorial integrity, there are reasons to assume that this is not likely to happen. Social processes that precede important political decisions - such as the growth of the belief in the reality of sea level rise and the framing of such decisions in a proper political context (policy window) - evolve slowly. A flood disaster would speed up the decision-making process. The shared opinion of the experts surveyed is that eventually part of the Netherlands would be abandoned. © 2008 The Author(s)

Second site escape of a T20-dependent HIV-1 variant by a single amino acid change in the CD4 binding region of the envelope glycoprotein

BACKGROUND: We previously described the selection of a T20-dependent human immunodeficiency virus type-1 (HIV-1) variant in a patient on T20 therapy. The fusion inhibitor T20 targets the viral envelope (Env) protein by blocking a conformational switch that is critical for viral entry into the host cell. T20-dependent viral entry is the result of 2 mutations in Env (GIA-SKY), creating a protein that undergoes a premature conformational switch, and the presence of T20 prevents this premature switch and rescues viral entry. In the present study, we performed 6 independent evolution experiments with the T20-dependent HIV-1 variant in the absence of T20, with the aim to identify second site compensatory changes, which may provide new mechanistic insights into Env function and the T20-dependence mechanism. RESULTS: Escape variants with improved replication capacity appeared within 42 days in 5 evolution cultures. Strikingly, 3 cultures revealed the same single amino acid change in the CD4 binding region of Env (glycine at position 431 substituted for arginine: G431R). This mutation was sufficient to abolish the T20-dependence phenotype and restore viral replication in the absence of T20. The GIA-SKY-G431R escape variant produces an Env protein that exhibits reduced syncytia formation and reduced cell-cell fusion activity. The escape variant was more sensitive to an antibody acting on an early gp41 intermediate, suggesting that the G431R mutation helps preserve a pre-fusion Env conformation, similar to T20 action. The escape variant was also less sensitive to soluble CD4, suggesting a reduced CD4 receptor affinity. CONCLUSION: The forced evolution experiments indicate that the premature conformational switch of the T20-dependent HIV-1 Env variant (GIA-SKY) can be corrected by a second site mutation in Env (GIA-SKY-G431R) that affects the interaction with the CD4 receptor

A 3D view of dwarf galaxies with Gaia and VLT/FLAMES: I. The Sculptor dwarf spheroidal

We present a new homogeneous survey of VLT/FLAMES LR8 line-of-sight radial velocities (vlos) for 1604 resolved red giant branch stars in the Sculptor dwarf spheroidal galaxy. In addition, we provide reliable Ca II triplet metallicities, [Fe/H], for 1339 of these stars. From this combination of new observations (2257 individual spectra) with ESO archival data (2389 spectra), we obtain the largest and most complete sample of vlos and [Fe/H] measurements for individual stars in any dwarf galaxy. Our sample includes VLT/FLAMES LR8 spectra for ∼55% of the red giant branch stars at G 70% of the brightest stars, G < 18.75. Our spectroscopic velocities are combined with Gaia DR3 proper motions and parallax measurements for a new and more precise membership analysis. We look again at the global characteristics of Sculptor, deriving a mean metallicity of h[Fe/H]i = −1.82 ± 0.45 and a mean line-of-sight velocity of hvlosi = +111.2 ± 0.25 km s−1 . There is a clear metallicity gradient in Sculptor, −0.7deg dex−1 , with the most metal-rich population being the most centrally concentrated. Furthermore, the most metal-poor population in Sculptor, [Fe/H] < −2.5, appears to show kinematic properties distinct from the rest of the stellar population. Finally, we combine our results with the exquisite Gaia DR3 multi-colour photometry to further investigate the colour-magnitude diagram of the resolved stellar population in Sculptor. Our detailed analysis shows a similar global picture as previous studies, but with much more precise detail, revealing that Sculptor has more complex properties than previously thought. This survey emphasises the role of the stellar spectroscopy technique and this galaxy as a benchmark system for modelling galaxy formation and evolution on small scales

Biomass and morphology of fine roots in temperate broad-leaved forests differing in tree species diversity: is there evidence of below-ground overyielding?

Biodiversity effects on ecosystem functioning in forests have only recently attracted increasing attention. The vast majority of studies in forests have focused on above-ground responses to differences in tree species diversity, while systematic analyses of the effects of biodiversity on root systems are virtually non-existent. By investigating the fine root systems in 12 temperate deciduous forest stands in Central Europe, we tested the hypotheses that (1) stand fine root biomass increases with tree diversity, and (2) ‘below-ground overyielding’ of species-rich stands in terms of fine root biomass is the consequence of spatial niche segregation of the roots of different species. The selected stands represent a gradient in tree species diversity on similar bedrock from almost pure beech forests to medium-diverse forests built by beech, ash, and lime, and highly-diverse stands dominated by beech, ash, lime, maple, and hornbeam. We investigated fine root biomass and necromass at 24 profiles per stand and analyzed species differences in fine root morphology by microscopic analysis. Fine root biomass ranged from 440 to 480 g m−2 in the species-poor to species-rich stands, with 63–77% being concentrated in the upper 20 cm of the soil. In contradiction to our two hypotheses, the differences in tree species diversity affected neither stand fine root biomass nor vertical root distribution patterns. Fine root morphology showed marked distinctions between species, but these root morphological differences did not lead to significant differences in fine root surface area or root tip number on a stand area basis. Moreover, differences in species composition of the stands did not alter fine root morphology of the species. We conclude that ‘below-ground overyielding’ in terms of fine root biomass does not occur in the species-rich stands, which is most likely caused by the absence of significant spatial segregation of the root systems of these late-successional species