Blue-Light-Emitting Color Centers in High-Quality Hexagonal Boron Nitride

Light emitters in wide band gap semiconductors are of great fundamental interest and have potential as optically addressable qubits. Here we describe the discovery of a new color center in high-quality hexagonal boron nitride (h-BN) with a sharp emission line at 435 nm. The emitters are activated and deactivated by electron beam irradiation and have spectral and temporal characteristics consistent with atomic color centers weakly coupled to lattice vibrations. The emitters are conspicuously absent from commercially available h-BN and are only present in ultra-high-quality h-BN grown using a high-pressure, high-temperature Ba-B-N flux/solvent, suggesting that these emitters originate from impurities or related defects specific to this unique synthetic route. Our results imply that the light emission is activated and deactivated by electron beam manipulation of the charge state of an impurity-defect complex

Characterizing Transition-Metal Dichalcogenide Thin-Films using Hyperspectral Imaging and Machine Learning

Atomically thin polycrystalline transition-metal dichalcogenides (TMDs) are relevant to both fundamental science investigation and applications. TMD thin-films present uniquely difficult challenges to effective nanoscale crystalline characterization. Here we present a method to quickly characterize the nanocrystalline grain structure and texture of monolayer WS2 films using scanning nanobeam electron diffraction coupled with multivariate statistical analysis of the resulting data. Our analysis pipeline is highly generalizable and is a useful alternative to the time consuming, complex, and system-dependent methodology traditionally used to analyze spatially resolved electron diffraction measurements

Lithographically defined synthesis of transition metal dichalcogenides

Transition metal dichalcogenides (TMDs) promise to revolutionize optoelectronic applications. While monolayer exfoliation and vapor phase growth produce extremely high quality 2D materials, direct fabrication at wafer scale remains a significant challenge. Here, we present a method that we call ‘lateral conversion’, which enables the synthesis of patterned TMD structures, with control over the thickness down to a few layers, at lithographically predefined locations. In this method, chemical conversion of a metal-oxide film to TMD layers proceeds by diffusion of precursor propagating laterally between silica layers, resulting in structures where delicate chalcogenide films are protected from contamination or oxidation. Lithographically patterned WS2 structures were synthesized by lateral conversion and analyzed in detail by hyperspectral Raman imaging, scanning electron microscopy and transmission electron microscopy. The rate of conversion was investigated as a function of time, temperature, and thickness of the converted film. In addition, the process was extended to grow patterned MoS2, WSe2, MoSe2 structures, and to demonstrate unique WS2/SiO2 multilayer structures. We believe this method will be applicable to a variety of additional chalcogenide materials, and enable their incorporation into novel architectures and devices

How Substitutional Point Defects in Two-Dimensional WS2_2 Induce Charge Localization, Spin-Orbit Splitting, and Strain

Control of impurity concentrations in semiconducting materials is essential to device technology. Because of their intrinsic confinement, the properties of two-dimensional semiconductors such as transition metal dichalcogenides (TMDs) are more sensitive to defects than traditional bulk materials. The technological adoption of TMDs is dependent on the mitigation of deleterious defects and guided incorporation of functional foreign atoms. The first step towards impurity control is the identification of defects and assessment of their electronic properties. Here, we present a comprehensive study of point defects in monolayer tungsten disulfide (WS$_2$) grown by chemical vapor deposition (CVD) using scanning tunneling microscopy/spectroscopy, CO-tip noncontact atomic force microscopy, Kelvin probe force spectroscopy, density functional theory, and tight-binding calculations. We observe four different substitutional defects: chromium (Cr$_{\text{W}}$) and molybdenum (Mo$_{\text{W}}$) at a tungsten site, oxygen at sulfur sites in both bottom and top layers (O$_{\text{S}}$ top/bottom), as well as two negatively charged defects (CDs). Their electronic fingerprints unambiguously corroborate the defect assignment and reveal the presence or absence of in-gap defect states. The important role of charge localization, spin-orbit coupling, and strain for the formation of deep defect states observed at substitutional defects in WS$_2$ as reported here will guide future efforts of targeted defect engineering and doping of TMDs

Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammoniaoxidizer abundances in soil without drought history. To this end we conducted rain-exclusion experiments at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for potential gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia-oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Drought induced different responses at the two studied sites. At the managed meadow drought increased NH+/4 immobilization rates and NH+/4 concentrations in the soil water solution, but led to a reduction of AOA abundance compared to controls. At the abandoned site gross nitrification and NO-/3 immobilization rates decreased during drought, while AOB and AOA abundances remained stable. Rewetting had only minor, short-term effects on the parameters that had been affected by drought. Seven weeks after the end of drought no differences to control plots could be detected. Thus, our findings demonstrated that in mountain grasslands drought had distinct transient effects on soil nitrogen cycling and ammonia-oxidizers, which could have been related to a niche differentiation of AOB and AOA with increasing NH+/4 levels. However, the effect strength of drought was modulated by grassland management

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

ESR1 gene promoter region methylation in free circulating DNA and its correlation with estrogen receptor protein expression in tumor tissue in breast cancer patients

[Background] Tumor expression of estrogen receptor (ER) is an important marker of prognosis, and is predictive of response to endocrine therapy in breast cancer. Several studies have observed that epigenetic events, such methylation of cytosines and deacetylation of histones, are involved in the complex mechanisms that regulate promoter transcription. However, the exact interplay of these factors in transcription activity is not well understood. In this study, we explored the relationship between ER expression status in tumor tissue samples and the methylation of the 5′ CpG promoter region of the estrogen receptor gene (ESR1) isolated from free circulating DNA (fcDNA) in plasma samples from breast cancer patients. [Methods] Patients (n = 110) with non-metastatic breast cancer had analyses performed of ER expression (luminal phenotype in tumor tissue, by immunohistochemistry method), and the ESR1-DNA methylation status (fcDNA in plasma, by quantitative methylation specific PCR technique). [Results] Our results showed a significant association between presence of methylated ESR1 in patients with breast cancer and ER negative status in the tumor tissue (p = 0.0179). There was a trend towards a higher probability of ESR1-methylation in those phenotypes with poor prognosis i.e. 80% of triple negative patients, 60% of HER2 patients, compared to 28% and 5.9% of patients with better prognosis such as luminal A and luminal B, respectively. [Conclusion] Silencing, by methylation, of the promoter region of the ESR1 affects the expression of the estrogen receptor protein in tumors of breast cancer patients; high methylation of ESR1-DNA is associated with estrogen receptor negative status which, in turn, may be implicated in the patient’s resistance to hormonal treatment in breast cancer. As such, epigenetic markers in plasma may be of interest as new targets for anticancer therapy, especially with respect to endocrine treatment.The study was funded, in part, by a grant from the Ministerio de Educación y Ciencia (CICYT: SAF 2004–00889)