An Alternative Interpretation of Recent ARPES Measurements on TiSe2

Recently there has been a renewed interest in the charge density wave transition of TiSe2, fuelled by the possibility that this transition may be driven by the formation of an excitonic insulator or even an excitonic condensate. We show here that the recent ARPES measurements on TiSe2 can also be interpreted in terms of an alternative scenario, in which the transition is due to a combination of Jahn-Teller effects and exciton formation. The hybrid exciton-phonons which cause the CDW formation interpolate between a purely structural and a purely electronic type of transition. Above the transition temperature, the electron-phonon coupling becomes ineffective but a finite mean-field density of excitons remains and gives rise to the observed diffuse ARPES signals.Comment: 4 pages, 2 figure

Real-world indoor mobility with simulated prosthetic vision:The benefits and feasibility of contour-based scene simplification at different phosphene resolutions

Contains fulltext : 246314.pdf (Publisher’s version ) (Open Access)Neuroprosthetic implants are a promising technology for restoring some form of vision in people with visual impairments via electrical neurostimulation in the visual pathway. Although an artificially generated prosthetic percept is relatively limited compared with normal vision, it may provide some elementary perception of the surroundings, re-enabling daily living functionality. For mobility in particular, various studies have investigated the benefits of visual neuroprosthetics in a simulated prosthetic vision paradigm with varying outcomes. The previous literature suggests that scene simplification via image processing, and particularly contour extraction, may potentially improve the mobility performance in a virtual environment. In the current simulation study with sighted participants, we explore both the theoretically attainable benefits of strict scene simplification in an indoor environment by controlling the environmental complexity, as well as the practically achieved improvement with a deep learning-based surface boundary detection implementation compared with traditional edge detection. A simulated electrode resolution of 26 x 26 was found to provide sufficient information for mobility in a simple environment. Our results suggest that, for a lower number of implanted electrodes, the removal of background textures and within-surface gradients may be beneficial in theory. However, the deep learning-based implementation for surface boundary detection did not improve mobility performance in the current study. Furthermore, our findings indicate that, for a greater number of electrodes, the removal of within-surface gradients and background textures may deteriorate, rather than improve, mobility. Therefore, finding a balanced amount of scene simplification requires a careful tradeoff between informativity and interpretability that may depend on the number of implanted electrodes.14 p

The Chitobiose-Binding Protein, DasA, Acts as a Link between Chitin Utilization and Morphogenesis in Streptomyces Coelicolor

Streptomycetes are mycelial soil bacteria that undergo a developmental programme that leads to sporulating aerial hyphae. As soil-dwelling bacteria, streptomycetes rely primarily on natural polymers such as cellulose, xylan and chitin for the colonization of their environmental niche and therefore these polysaccharides may play a critical role in monitoring the global nutritional status of the environment. In this work we analysed the role of DasA, the sugar-binding component of the chitobiose ATP-binding cassette transport system, in informing the cell of environmental conditions, and its role in the onset of development and in ensuring correct sporulation. The chromosomal interruption of dasA resulted in a carbon-source-dependent vegetative arrest phenotype, and we identified a second DasR-dependent sugar transporter, in addition to the N-acetylglucosamine phosphotransferase system (PTS(GlcNAc)), that relates primary metabolism to development. Under conditions that allowed sporulation, highly aberrant spores with many prematurely produced germ tubes were observed. While GlcNAc locks streptomycetes in the vegetative state, a high extracellular concentration of the GlcNAc polymer chitin has no effect on development. The striking distinction is due to a difference in the transporters responsible for the import of GlcNAc, which enters via the PTS, and of chitin, which enters as the hydrolytic product chitobiose (GlcNAc(2)) through the DasABC transporter. A model explaining the role of these two essentially different transport systems in the control of development is provided

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10x Metagenomics

Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotyp

Functional analysis identifies damaging CHEK2 missense variants associated with increased cancer risk.

Heterozygous carriers of germline loss-of-function variants in the tumor suppressor gene checkpoint kinase 2 (CHEK2) are at an increased risk for developing breast and other cancers. While truncating variants in CHEK2 are known to be pathogenic, the interpretation of missense variants of uncertain significance (VUS) is challenging. Consequently, many VUS remain unclassified both functionally and clinically. Here we describe a mouse embryonic stem (mES) cell-based system to quantitatively determine the functional impact of 50 missense VUS in human CHEK2. By assessing the activity of human CHK2 to phosphorylate one of its main targets, Kap1, in Chek2 knockout mES cells, 31 missense VUS in CHEK2 impaired protein function to a similar extent as truncating variants, and 9 CHEK2 missense VUS resulted in intermediate functional defects. Mechanistically, most VUS impaired CHK2 kinase function by causing protein instability or by impairing activation through (auto)phosphorylation. Quantitative results showed that the degree of CHK2 kinase dysfunction correlates with an increased risk for breast cancer. Both damaging CHEK2 variants as a group (OR 2,23; 95% CI 1,62-3,07; pG/p.D162G, was also identified, which co-segregated with familial prostate cancer. Altogether, these functional assays efficiently and reliably identified VUS in CHEK2 that associate with cancer

The influence of BRAF and KRAS mutation status on the association between aspirin use and survival after colon cancer diagnosis

Background: Use of aspirin after diagnosis of colon cancer has been associated with improved survival. Identification of cancer subtypes that respond to aspirin treatment may help develop personalized treatment regimens. The aim of this study was to investigate the influence of BRAF and KRAS mutation status on the association between aspirin use and overall survival after colon cancer diagnosis. Methods: A random selection of 599 patients with colon cancer were analyzed, selected from the Eindhoven Cancer Registry, and BRAF and KRAS mutation status was determined. Data on aspirin use (80 mg) were obtained from the PHARMO Database Network. Parametric survival models with exponential (Poisson) distribution were used. Results: Aspirin use after colon cancer diagnosis was associated with improved overall survival in wild-type BRAF tumors, adjusted rate ratio (RR) of 0.60 (95% CI 0.44-0.83). In contrast, aspirin use in BRAF mutated tumors was not associated with an improved survival (RR 1.11, 95% CI 0.57-2.16). P-value for interaction was non-significant. KRAS mutational status did not differentiate in the association between aspirin use and survival. Conclusion: Low-dose aspirin use after colon cancer diagnosis was associated with improved survival in BRAF wild-type tumors only. However, the large confidence interval of the rate ratio for the use of aspirin in patients with BRAF mutation does not rule out a possible benefit. These results preclude BRAF and KRAS mutation status to be used as a marker for individualized treatment with aspirin, if aspirin becomes regular adjuvant treatment for colon cancer patients in the future

Emergence of coherence in the charge-density wave state of 2H-NbSe2_2

A charge-density wave (CDW) state has a broken symmetry described by a complex order parameter with an amplitude and a phase. The conventional view, based on clean, weak-coupling systems, is that a finite amplitude and long-range phase coherence set in simultaneously at the CDW transition temperature T$_{cdw}$. Here we investigate, using photoemission, X-ray scattering and scanning tunneling microscopy, the canonical CDW compound 2H-NbSe$_2$ intercalated with Mn and Co, and show that the conventional view is untenable. We find that, either at high temperature or at large intercalation, CDW order becomes short-ranged with a well-defined amplitude that impacts the electronic dispersion, giving rise to an energy gap. The phase transition at T$_{cdw}$ marks the onset of long-range order with global phase coherence, leading to sharp electronic excitations. Our observations emphasize the importance of phase fluctuations in strongly coupled CDW systems and provide insights into the significance of phase incoherence in `pseudogap' states.Comment: main manuscript plus supplementary informatio