Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members.

HIV +Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4 +T cells with resistance specific to R5-tropic HIV, reversed after introduction of ccr5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4 +T cells of these EC/VCs had lower ccr2 and ccr5 RNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of ccr2 and ccr5, despite having more accessible chromatin by ATAC-seq. Other nearby genes were also down-regulated, over a region of ~500 kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with ccr2/ccr5 down-regulation, suggesting that the phenotype is heritable

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal (2019), doi:10.1038/s41396-019-0373-4.The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich

Statistical Theory for Incoherent Light Propagation in Nonlinear Media

A novel statistical approach based on the Wigner transform is proposed for the description of partially incoherent optical wave dynamics in nonlinear media. An evolution equation for the Wigner transform is derived from a nonlinear Schrodinger equation with arbitrary nonlinearity. It is shown that random phase fluctuations of an incoherent plane wave lead to a Landau-like damping effect, which can stabilize the modulational instability. In the limit of the geometrical optics approximation, incoherent, localized, and stationary wave-fields are shown to exist for a wide class of nonlinear media.Comment: 4 pages, REVTeX4. Submitted to Physical Review E. Revised manuscrip

Schubert calculus of Richardson varieties stable under spherical Levi subgroups

We observe that the expansion in the basis of Schubert cycles for $H^*(G/B)$ of the class of a Richardson variety stable under a spherical Levi subgroup is described by a theorem of Brion. Using this observation, along with a combinatorial model of the poset of certain symmetric subgroup orbit closures, we give positive combinatorial descriptions of certain Schubert structure constants on the full flag variety in type $A$. Namely, we describe $c_{u,v}^w$ when $u$ and $v$ are inverse to Grassmannian permutations with unique descents at $p$ and $q$, respectively. We offer some conjectures for similar rules in types $B$ and $D$, associated to Richardson varieties stable under spherical Levi subgroups of SO(2n+1,\C) and SO(2n,\C), respectively.Comment: Section 4 significantly shortened, and other minor changes made as suggested by referees. Final version, to appear in Journal of Algebraic Combinatoric

Quantum Particles Constrained on Cylindrical Surfaces with Non-constant Diameter

We present a theoretical formulation of the one-electron problem constrained on the surface of a cylindrical tubule with varying diameter. Because of the cylindrical symmetry, we may reduce the problem to a one-dimensional equation for each angular momentum quantum number $m$ along the cylindrical axis. The geometrical properties of the surface determine the electronic structures through the geometry dependent term in the equation. Magnetic fields parallel to the axis can readily be incorporated. Our formulation is applied to simple examples such as the catenoid and the sinusoidal tubules. The existence of bound states as well as the band structures, which are induced geometrically, for these surfaces are shown. To show that the electronic structures can be altered significantly by applying a magnetic field, Aharonov-Bohm effects in these examples are demonstrated.Comment: 7 pages, 7 figures, submitted to J. Phys. Soc. Jp

Orbital Kondo effect in carbon nanotubes

Progress in the fabrication of nanometer-scale electronic devices is opening new opportunities to uncover the deepest aspects of the Kondo effect, one of the paradigmatic phenomena in the physics of strongly correlated electrons. Artificial single-impurity Kondo systems have been realized in various nanostructures, including semiconductor quantum dots, carbon nanotubes and individual molecules. The Kondo effect is usually regarded as a spin-related phenomenon, namely the coherent exchange of the spin between a localized state and a Fermi sea of electrons. In principle, however, the role of the spin could be replaced by other degrees of freedom, such as an orbital quantum number. Here we demonstrate that the unique electronic structure of carbon nanotubes enables the observation of a purely orbital Kondo effect. We use a magnetic field to tune spin-polarized states into orbital degeneracy and conclude that the orbital quantum number is conserved during tunneling. When orbital and spin degeneracies are simultaneously present, we observe a strongly enhanced Kondo effect, with a multiple splitting of the Kondo resonance at finite field and predicted to obey a so-called SU(4) symmetry.Comment: 26 pages, including 4+2 figure

Impurity-assisted tunneling in graphene

The electric conductance of a strip of undoped graphene increases in the presence of a disorder potential, which is smooth on atomic scales. The phenomenon is attributed to impurity-assisted resonant tunneling of massless Dirac fermions. Employing the transfer matrix approach we demonstrate the resonant character of the conductivity enhancement in the presence of a single impurity. We also calculate the two-terminal conductivity for the model with one-dimensional fluctuations of disorder potential by a mapping onto a problem of Anderson localization.Comment: 6 pages, 3 figures, final version, typos corrected, references adde

FLT3 mutations in Early T-Cell Precursor ALL characterize a stem cell like leukemia and imply the clinical use of tyrosine kinase inhibitors

Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) has been identified as high-risk subgroup of acute T-lymphoblastic leukemia (T-ALL) with a high rate of FLT3-mutations in adults. To unravel the underlying pathomechanisms and the clinical course we assessed molecular alterations and clinical characteristics in a large cohort of ETP-ALL (n = 68) in comparison to non-ETP T-ALL adult patients. Interestingly, we found a high rate of FLT3-mutations in ETP-ALL samples (n = 24, 35%). Furthermore, FLT3 mutated ETP-ALL was characterized by a specific immunophenotype (CD2+/CD5-/CD13+/CD33-), a distinct gene expression pattern (aberrant expression of IGFBP7, WT1, GATA3) and mutational status (absence of NOTCH1 mutations and a low frequency, 21%, of clonal TCR rearrangements). The observed low GATA3 expression and high WT1 expression in combination with lack of NOTCH1 mutations and a low rate of TCR rearrangements point to a leukemic transformation at the pluripotent prothymocyte stage in FLT3 mutated ETP-ALL. The clinical outcome in ETP-ALL patients was poor, but encouraging in those patients with allogeneic stem cell transplantation (3-year OS: 74%). To further explore the efficacy of targeted therapies, we demonstrate that T-ALL cell lines transfected with FLT3 expression constructs were particularly sensitive to tyrosine kinase inhibitors. In conclusion, FLT3 mutated ETP-ALL defines a molecular distinct stem cell like leukemic subtype. These data warrant clinical studies with the implementation of FLT3 inhibitors in addition to early allogeneic stem cell transplantation for this high risk subgroup

Ballistic Josephson junctions in edge-contacted graphene

Hybrid graphene-superconductor devices have attracted much attention since the early days of graphene research. So far, these studies have been limited to the case of diffusive transport through graphene with poorly defined and modest quality graphene-superconductor interfaces, usually combined with small critical magnetic fields of the superconducting electrodes. Here we report graphene based Josephson junctions with one-dimensional edge contacts of Molybdenum Rhenium. The contacts exhibit a well defined, transparent interface to the graphene, have a critical magnetic field of 8 Tesla at 4 Kelvin and the graphene has a high quality due to its encapsulation in hexagonal boron nitride. This allows us to study and exploit graphene Josephson junctions in a new regime, characterized by ballistic transport. We find that the critical current oscillates with the carrier density due to phase coherent interference of the electrons and holes that carry the supercurrent caused by the formation of a Fabry-P\'{e}rot cavity. Furthermore, relatively large supercurrents are observed over unprecedented long distances of up to 1.5 $\mu$m. Finally, in the quantum Hall regime we observe broken symmetry states while the contacts remain superconducting. These achievements open up new avenues to exploit the Dirac nature of graphene in interaction with the superconducting state.Comment: Updated version after peer review. Includes supplementary material and ancillary file with source code for tight binding simulation

Explaining spatial variation in housing construction activity in Turkey

In Turkey, there has been a strong policy narrative that has emphasized the importance of construction activity as a driver of economic growth. This has given shape to a central state-led policy regime that has sought to ensure that planners and other urban policy makers develop plans and strategies that support construction activity. Against this backdrop, and a recent history of uneven spatial development, this paper seeks to understand what this policy imperative might mean for housing construction activity in different provinces. It seeks to reflect on both the relationship between the state and the market, and the interaction between state policies, economic drivers and levels of construction activity. The evidence presented in the paper suggests that uneven spatial development might be explained in different ways in different provinces. Although, in many cases, patterns of construction activity are consistent with economic fundamentals, there are important exceptions in some regions where arguably activity levels are at odds with prior expectations