Electron dynamics in topological insulator based semiconductor-metal interfaces (topological p-n interface based on Bi2Se3 class)

Single-Dirac-cone topological insulators (TI) are the first experimentally discovered class of three dimensional topologically ordered electronic systems, and feature robust, massless spin-helical conducting surface states that appear at any interface between a topological insulator and normal matter that lacks the topological insulator ordering. This topologically defined surface environment has been theoretically identified as a promising platform for observing a wide range of new physical phenomena, and possesses ideal properties for advanced electronics such as spin-polarized conductivity and suppressed scattering. A key missing step in enabling these applications is to understand how topologically ordered electrons respond to the interfaces and surface structures that constitute a device. Here we explore this question by using the surface deposition of cathode (Cu/In/Fe) and anode materials (NO$_2$) and control of bulk doping in Bi$_2$Se$_3$ from P-type to N-type charge transport regimes to generate a range of topological insulator interface scenarios that are fundamental to device development. The interplay of conventional semiconductor junction physics and three dimensional topological electronic order is observed to generate novel junction behaviors that go beyond the doped-insulator paradigm of conventional semiconductor devices and greatly alter the known spin-orbit interface phenomenon of Rashba splitting. Our measurements for the first time reveal new classes of diode-like configurations that can create a gap in the interface electron density near a topological Dirac point and systematically modify the topological surface state Dirac velocity, allowing far reaching control of spin-textured helical Dirac electrons inside the interface and creating advantages for TI superconductors as a Majorana fermion platform over spin-orbit semiconductors.Comment: 14 pages, 4 Figure

Optical evidence of surface state suppression in Bi based topological insulators

A key challenge in condensed matter research is the optimization of topological insulator (TI) compounds for the study and future application of their unique surface states. Truly insulating bulk states would allow the exploitation of predicted surface state properties, such as protection from backscattering, dissipationless spin-polarized currents, and the emergence of novel particles. Towards this end, major progress was recently made with the introduction of highly resistive Bi$_2$Te$_2$Se, in which surface state conductance and quantum oscillations are observed at low temperatures. Nevertheless, an unresolved and pivotal question remains: while room temperature ARPES studies reveal clear evidence of TI surface states, their observation in transport experiments is limited to low temperatures. A better understanding of this surface state suppression at elevated temperatures is of fundamental interest, and crucial for pushing the boundary of device applications towards room-temperature operation. In this work, we simultaneously measure TI bulk and surface states via temperature dependent optical spectroscopy, in conjunction with transport and ARPES measurements. We find evidence of coherent surface state transport at low temperatures, and propose that phonon mediated coupling between bulk and surface states suppresses surface conductance as temperature rises.Comment: 13 pages, 10 figure

IκBβ acts to inhibit and activate gene expression during the inflammatory response

The activation of pro-inflammatory gene programs by nuclear factor-κB (NF-κB) is primarily regulated through cytoplasmic sequestration of NF-κB by the inhibitor of κB (IκB) family of proteins1. IκBβ, a major isoform of IκB, can sequester NF-κB in the cytoplasm2, although its biological role remains unclear. Although cells lacking IκBβ have been reported3, 4, in vivo studies have been limited and suggested redundancy between IκBα and IκBβ5. Like IκBα, IκBβ is also inducibly degraded; however, upon stimulation by lipopolysaccharide (LPS), it is degraded slowly and re-synthesized as a hypophosphorylated form that can be detected in the nucleus6, 7, 8, 9, 10, 11. The crystal structure of IκBβ bound to p65 suggested this complex might bind DNA12. In vitro, hypophosphorylated IκBβ can bind DNA with p65 and c-Rel, and the DNA-bound NF-κB:IκBβ complexes are resistant to IκBα, suggesting hypophosphorylated, nuclear IκBβ may prolong the expression of certain genes9, 10, 11. Here we report that in vivo IκBβ serves both to inhibit and facilitate the inflammatory response. IκBβ degradation releases NF-κB dimers which upregulate pro-inflammatory target genes such as tumour necrosis factor-α (TNF-α). Surprisingly, absence of IκBβ results in a dramatic reduction of TNF-α in response to LPS even though activation of NF-κB is normal. The inhibition of TNF-α messenger RNA (mRNA) expression correlates with the absence of nuclear, hypophosphorylated-IκBβ bound to p65:c-Rel heterodimers at a specific κB site on the TNF-α promoter. Therefore IκBβ acts through p65:c-Rel dimers to maintain prolonged expression of TNF-α. As a result, IκBβ^(−/−) mice are resistant to LPS-induced septic shock and collagen-induced arthritis. Blocking IκBβ might be a promising new strategy for selectively inhibiting the chronic phase of TNF-α production during the inflammatory response

On the Effect of Nb on the Microstructure and Properties of Next Generation Polycrystalline Powder Metallurgy Ni-Based Superalloys

Abstract The effect of Nb on the properties and microstructure of two novel powder metallurgy (P/M) Ni-based superalloys was evaluated, and the results critically compared with the Rolls-Royce alloy RR1000. The Nb-containing alloy was found to exhibit improved tensile and creep properties as well as superior oxidation resistance compared with both RR1000 and the Nb-free variant tested. The beneficial effect of Nb on the tensile and creep properties was due to the microstructures obtained following the post-solution heat treatments, which led to a higher γ′ volume fraction and a finer tertiary γ′ distribution. In addition, an increase in the anti-phase-boundary energy of the γ′ phase is also expected with the addition of Nb, further contributing to the strength of the material. However, these modifications in the γ′ distribution detrimentally affect the dwell fatigue crack-growth behavior of the material, although this behavior can be improved through modified heat treatments. The oxidation resistance of the Nb-containing alloy was also enhanced as Nb is believed to accelerate the formation of a defect-free Cr2O3 scale. Overall, both developmental alloys, with and without the addition of Nb, were found to exhibit superior properties than RR1000.This work was supported by the Rolls-Royce/EPSRC Strategic Partnership under EP/H022309/1, EP/H500375/1 and EP/ M005607/1

Inhibitor of Kappa B Epsilon (IκBε) Is a Non-Redundant Regulator of c-Rel-Dependent Gene Expression in Murine T and B Cells

Inhibitors of kappa B (IκBs) -α, -β and -ε effect selective regulation of specific nuclear factor of kappa B (NF-κB) dimers according to cell lineage, differentiation state or stimulus, in a manner that is not yet precisely defined. Lymphocyte antigen receptor ligation leads to degradation of all three IκBs but activation only of subsets of NF-κB-dependent genes, including those regulated by c-Rel, such as anti-apoptotic CD40 and BAFF-R on B cells, and interleukin-2 (IL-2) in T cells. We report that pre-culture of a mouse T cell line with tumour necrosis factor-α (TNF) inhibits IL-2 gene expression at the level of transcription through suppressive effects on NF-κB, AP-1 and NFAT transcription factor expression and function. Selective upregulation of IκBε and suppressed nuclear translocation of c-Rel were very marked in TNF-treated, compared to control cells, whether activated via T cell receptor (TCR) pathway or TNF receptor. IκBε associated with newly synthesised c-Rel in activated cells and, in contrast to IκBα and -β, showed enhanced association with p65/c-Rel in TNF-treated cells relative to controls. Studies in IκBε-deficient mice revealed that basal nuclear expression and nuclear translocation of c-Rel at early time-points of receptor ligation were higher in IκBε−/− T and B cells, compared to wild-type. IκBε−/− mice exhibited increased lymph node cellularity and enhanced basal thymidine incorporation by lymphoid cells ex vivo. IκBε−/− T cell blasts were primed for IL-2 expression, relative to wild-type. IκBε−/− splenic B cells showed enhanced survival ex vivo, compared to wild-type, and survival correlated with basal expression of CD40 and induced expression of CD40 and BAFF-R. Enhanced basal nuclear translocation of c-Rel, and upregulation of BAFF-R and CD40 occurred despite increased IκBα expression in IκBε−/− B cells. The data imply that regulation of these c-Rel-dependent lymphoid responses is a non-redundant function of IκBε

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p