Exact location of dopants below the Si(001):H surface from scanning tunnelling microscopy and density functional theory

Control of dopants in silicon remains the most important approach to tailoring the properties of electronic materials for integrated circuits, with Group V impurities the most important n-type dopants. At the same time, silicon is finding new applications in coherent quantum devices, thanks to the magnetically quiet environment it provides for the impurity orbitals. The ionization energies and the shape of the dopant orbitals depend on the surfaces and interfaces with which they interact. The location of the dopant and local environment effects will therefore determine the functionality of both future quantum information processors and next-generation semiconductor devices. Here we match observed dopant wavefunctions from low-temperature scanning tunnelling microscopy (STM) to images simulated from first-principles density functional theory (DFT) calculations. By this combination of experiment and theory we precisely determine the substitutional sites of neutral As dopants between 5 and 15A below the Si(001):H surface. In the process we gain a full understanding of the interaction of the donor-electron state with the surface, and hence of the transition between the bulk dopant (with its delocalised hydrogenic orbital) and the previously studied dopants in the surface layer.Comment: 12 pages; accepted for publication in Phys. Rev.

Lignin repolymerisation in spruce autohydrolysis pretreatment increases cellulase deactivation

This study presents a modified autohydrolysis pretreatment which helps to overcome the recalcitrance of softwood for enzymatic hydrolysis of its cellulose. Autohydrolysis pretreatments of spruce wood were performed with 2-naphthol, which prevents lignin repolymerisation reactions, thereby increasing the enzymatic digestibility of cellulose by up to 64%. The negative influence of repolymerised lignin structures on enzymatic hydrolysis was confirmed by the addition of resorcinol in autohydrolysis, which is known to promote repolymerisation reactions and decreased the biomass digestibility. Several analyses were performed to study the underlying mechanism of this effect on hydrolysis, indicating that cellulolytic enzymes are adsorbed and deactivated especially by repolymerised lignin structures, which accounts for the high differences in biomass digestibility. It was shown that lignin repolymerisation significantly increases its specific surface area through modification of the lignin nanostructure, which is supposed to increase the unproductive binding of enzymes

Local and global feature aggregation for accurate epithelial cell classification using graph attention mechanisms in histopathology images

In digital pathology, cell-level tissue analyses are widely used to better understand tissue composition and structure. Publicly available datasets and models for cell detection and classification in colorectal cancer exist but lack the differentiation of normal and malignant epithelial cells that are important to perform prior to any downstream cell-based analysis. This classification task is particularly difficult due to the high intra-class variability of neoplastic cells. To tackle this, we present here a new method that uses graph-based node classification to take advantage of both local cell features and global tissue architecture to perform accurate epithelial cell classification. The proposed method demonstrated excellent performance on F1 score (PanNuke: 1.0, TCGA: 0.98) and performed significantly better than conventional computer vision methods (PanNuke: 0.99, TCGA: 0.92)

SmartWeb: Mobile Access to the Semantic Web

Ankolekar A, Cimiano P, Hitzler P, et al. SmartWeb: Mobile Access to the Semantic Web. In: Wache H, ed. Proceedings of the ESWC2006 poster and demo session. 2006: 3-4

Decatransin, a novel natural product inhibiting protein translocation at the Sec61/SecY translocon

A new cyclic decadepsipeptide was isolated from Chaetosphaeria tulasneorum with potent bioactivity on mammalian and yeast cells. Chemogenomic profiling in S. cerevisiae indicated that the Sec61 translocon, the machinery for protein translocation and membrane insertion at the endoplasmic reticulum, is the target. The profiles were similar to those of cyclic heptadepsipeptides of a distinct chemotype (HUN-7293/cotransin) that had previously been shown to inhibit cotranslational translocation at the mammalian Sec61 translocon. Unbiased, genome-wide mutagenesis followed by full-genome sequencing in both fungal and mammalian cells identified dominant mutations in Sec61p/Sec61α1 to confer resistance. Most, but not all, of these mutations affected inhibition by both chemotypes, despite an absence of structural similarity. Biochemical analysis confirmed inhibition of protein translocation into the endoplasmic reticulum of both co- and posttranslationally translocated substrates by both chemotypes, demonstrating a mechanism independent of a translating ribosome. Most interestingly, both chemotypes were found to also inhibit SecYEG, the bacterial Sec61 homolog. We suggest "decatransin" as the name for this novel decadepsipeptide translocation inhibitor

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Ontologies on Demand? - A Description of the State-of-the-Art, Applications, Challenges and Trends for Ontology Learning from Text

Cimiano P, Völker J, Studer R. Ontologies on Demand? - A Description of the State-of-the-Art, Applications, Challenges and Trends for Ontology Learning from Text. Information, Wissenschaft und Praxis. 2006;57(6-7):315-320