Cross-Modal Search and Exploration of Greek Painted Pottery

This paper focuses on digitally-supported research methods for an important group of cultural heritage objects, the Greek pottery, especially with figured decoration. The design, development and application of new digital methods for searching, comparing, and visually exploring these vases needs an interdisciplinary approach to effectively analyse the various features of the vases, like shape, decoration, and manufacturing techniques, and relationships between the vases. We motivate the need and opportunities by a multimodal representation of the objects, including 3D shape, material, and painting. We then illustrate a range of innovative methods for these representations, including quantified surface and capacity comparison, material analysis, image flattening from 3D objects, retrieval and comparison of shapes and paintings, and multidimensional data visualization. We also discuss challenges and future work in this area.Comment: 14 pages, 10 figures, preprint for a book chapter, supplementary video available at https://youtu.be/x_Xg0vy3nJ

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus

Structural analysis of the inhibitor Telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A shows that mutations at V36 and/or T54 result in impaired interaction with VX-950, explaining the development of viral breakthrough variants

Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease

It is a challenge to develop direct-acting antiviral agents (DAAs) that target the NS3/4A protease of hepatitis C virus (HCV) because resistant variants develop. Ketoamide compounds, designed to mimic the natural protease substrate, have been developed as inhibitors. However, clinical trials have revealed rapid selection of resistant mutants, most of which are considered to be pre-existing variants

Epigenetic dynamics of monocyte-to-macrophage differentiation

Background Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in vitro by addition of colony-stimulating factor 1 in serum-free medium. Results Numerous mRNAs and miRNAs were significantly up- or down-regulated. More than 100 discrete DNA regions, most often far away from transcription start sites, were rapidly demethylated by the ten eleven translocation enzymes, became nucleosome-free and gained histone marks indicative of active enhancers. These regions were unique for macrophages and associated with genes involved in the regulation of the actin cytoskeleton, phagocytosis and innate immune response. Conclusions In summary, we have discovered a phagocytic gene network that is repressed by DNA methylation in monocytes and rapidly de-repressed after the onset of macrophage differentiation

Customization options in consumer health information materials on type-2 diabetes mellitus—an analysis of modifiable features in different types of media

IntroductionThe understanding of health-related information is essential for making informed decisions. However, providing health information in an understandable format for everyone is challenging due to differences in consumers’ health status, disease knowledge, skills, and preferences. Tailoring health information to individual needs can improve comprehension and increase health literacy.ObjectiveThe aim of our research was to analyze the extent to which consumers can customize consumer health information materials (CHIMs) for type-2 diabetes mellitus through various media types.MethodsWe conducted a comprehensive search for various CHIMs across various media types, such as websites, apps, videos, and printed or printable forms. A representative sample of CHIMs was obtained for analysis through blocked randomization across the various media types. We conducted a quantitative content analysis to determine the frequency of user-centered customization options. Cross-comparisons were made to identify trends and variations in modifiable features among the media.ResultsIn our representative sample of 114 CHIMs, we identified a total of 24 modifiable features, which we grouped into five main categories: (i) language, (ii) text, (iii) audiovisual, (iv) presentation, and (v) medical content. Videos offered the most customization opportunities (95%), while 47% of websites and 26% of apps did not allow users to tailor health information. None of the printed or printable materials provided the option to customize the information. Overall, 65% of analyzed CHIMs did not allow users to tailor health information according to their needs.ConclusionOur results show that CHIMs for type-2 diabetes mellitus could be significantly improved by providing more customization options for users. Further research is needed to investigate the effectiveness and usability of these options to enhance the development and appropriate provision of modifiable features in health information

Limitations of Fe^(2+) and Mn^(2+) site occupancy in tourmaline: Evidence from Fe^(2+)- and Mn^(2+)-rich tourmaline

Fe^(2+)- and Mn^(2+)-rich tourmalines were used to test whether Fe^(2+) and Mn^(2+) substitute on the Z site of tourmaline to a detectable degree. Fe-rich tourmaline from a pegmatite from Lower Austria was characterized by crystal-structure refinement, chemical analyses, and Mössbauer and optical spectroscopy. The sample has large amounts of Fe^(2+) (~2.3 apfu), and substantial amounts of Fe^(3+) (~1.0 apfu). On basis of the collected data, the structural refinement and the spectroscopic data, an initial formula was determined by assigning the entire amount of Fe^(3+) (no delocalized electrons) and Ti^(4+) to the Z site and the amount of Fe^(2+) and Fe^(3+) from delocalized electrons to the Y-Z ED doublet (delocalized electrons between Y-Z and Y-Y): X(Na_(0.9)Ca_(0.1)) ^Y(Fe^(2+)_(2.0)Al_(0.4)Mn^(2+)_(0.3)Fe^(3+)_(0.2)) ^Z(Al_(4.8)Fe^(3+)_(0.8)Fe^(2+)_(0.2)Ti^(4+)_(0.1)) ^T(Si_(5.9)Al_(0.1))O_(18) (BO_3)_3^V(OH)_3 ^W[O_(0.5)F_(0.3)(OH)_(0.2)] with α = 16.039(1) and c = 7.254(1) Å. This formula is consistent with lack of Fe^(2+) at the Z site, apart from that occupancy connected with delocalization of a hopping electron. The formula was further modified by considering two ED doublets to yield: ^X(Na_(0.9)Ca_(0.1)) ^Y(Fe^(2+)_(1.8)Al_(0.5)Mn^(2+)_(0.3)Fe^(3+)_(0.3)) ^Z(Al_(4.8)Fe^(3+)_(0.7)Fe^(2+)_(0.4)Ti^(4+)_(0.1)) ^T(Si_(5.9_Al_(0.1))O_(18) (BO_3)_3 ^V(OH)_3 ^W[O_(0.5)F_(0.3)(OH)_(0.2)]. This formula requires some Fe^(2+) (~0.3 apfu) at the Z site, apart from that connected with delocalization of a hopping electron. Optical spectra were recorded from this sample as well as from two other Fe^(2+)-rich tourmalines to determine if there is any evidence for Fe^(2+) at Y and Z sites. If Fe^(2+) were to occupy two different 6-coordinated sites in significant amounts and if these polyhedra have different geometries or metal-oxygen distances, bands from each site should be observed. However, even in high-quality spectra we see no evidence for such a doubling of the bands. We conclude that there is no ultimate proof for Fe^(2+) at the Z site, apart from that occupancy connected with delocalization of hopping electrons involving Fe cations at the Y and Z sites. A very Mn-rich tourmaline from a pegmatite on Elba Island, Italy, was characterized by crystal-structure determination, chemical analyses, and optical spectroscopy. The optimized structural formula is ^X(Na_(0.6)□_(0.4)) ^Y(Mn^(2+)_(1.3)Al_(1.2)Li_(0.5)) ^ZAl_6 ^TSi_6O_(18) (BO_3)_3 ^V(OH)_3 ^W[F_(0.5)O_(0.5)], with α = 15.951(2) and c = 7.138(1) Å. Within a 3σ error there is no evidence for Mn occupancy at the Z site by refinement of Al ↔ Mn, and, thus, no final proof for Mn^(2+) at the Z site, either. Oxidation of these tourmalines at 700–750 °C and 1 bar for 10–72 h converted Fe^(2+) to Fe^(3+) and Mn^(2+) to Mn^(3+) with concomitant exchange with Al of the Z site. The refined ^ZFe content in the Fe-rich tourmaline increased by ~40% relative to its initial occupancy. The refined YFe content was smaller and the distance was significantly reduced relative to the unoxidized sample. A similar effect was observed for the oxidized Mn^(2+)-rich tourmaline. Simultaneously, H and F were expelled from both samples as indicated by structural refinements, and H expulsion was indicated by infrared spectroscopy. The final species after oxidizing the Fe^(2+)-rich tourmaline is buergerite. Its color had changed from blackish to brown-red. After oxidizing the Mn^(2+)-rich tourmaline, the previously dark yellow sample was very dark brown-red, as expected for the oxidation of Mn^(2+) to Mn^(3+). The unit-cell parameter α decreased during oxidation whereas the c parameter showed a slight increase

Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays

BACKGROUND: The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially understood. cDNA microarrays can be used to decipher gene regulation events at a genome-wide level and to identify novel unknown genes that might be involved in perpetuating inflammatory disease progression. METHODS AND FINDINGS: High-density cDNA microarrays representing 33,792 UniGene clusters were prepared. Biopsies were taken from the sigmoid colon of normal controls (n = 11), CD patients (n = 10) and UC patients (n = 10). (33)P-radiolabeled cDNA from purified poly(A)(+) RNA extracted from biopsies (unpooled) was hybridized to the arrays. We identified 500 and 272 transcripts differentially regulated in CD and UC, respectively. Interesting hits were independently verified by real-time PCR in a second sample of 100 individuals, and immunohistochemistry was used for exemplary localization. The main findings point to novel molecules important in abnormal immune regulation and the highly disturbed cell biology of colonic epithelial cells in IBD pathogenesis, e.g., CYLD (cylindromatosis, turban tumor syndrome) and CDH11 (cadherin 11, type 2). By the nature of the array setup, many of the genes identified were to our knowledge previously uncharacterized, and prediction of the putative function of a subsection of these genes indicate that some could be involved in early events in disease pathophysiology. CONCLUSION: A comprehensive set of candidate genes not previously associated with IBD was revealed, which underlines the polygenic and complex nature of the disease. It points out substantial differences in pathophysiology between CD and UC. The multiple unknown genes identified may stimulate new research in the fields of barrier mechanisms and cell signalling in the context of IBD, and ultimately new therapeutic approaches

Mutations in the MutSα interaction interface of MLH1 can abolish DNA mismatch repair

MutLα, a heterodimer of MLH1 and PMS2, plays a central role in human DNA mismatch repair. It interacts ATP-dependently with the mismatch detector MutSα and assembles and controls further repair enzymes. We tested if the interaction of MutLα with DNA-bound MutSα is impaired by cancer-associated mutations in MLH1, and identified one mutation (Ala128Pro) which abolished interaction as well as mismatch repair activity. Further examinations revealed three more residues whose mutation interfered with interaction. Homology modelling of MLH1 showed that all residues clustered in a small accessible surface patch, suggesting that the major interaction interface of MutLα for MutSα is located on the edge of an extensive β-sheet that backs the MLH1 ATP binding pocket. Bioinformatic analysis confirmed that this patch corresponds to a conserved potential protein–protein interaction interface which is present in both human MLH1 and its E.coli homologue MutL. MutL could be site-specifically crosslinked to MutS from this patch, confirming that the bacterial MutL–MutS complex is established by the corresponding interface in MutL. This is the first study that identifies the conserved major MutLα–MutSα interaction interface in MLH1 and demonstrates that mutations in this interface can affect interaction and mismatch repair, and thereby can also contribute to cancer development

Preserving Charge and Oxidation State of Au(III) Ions in an Agent-Functionalized Nanocrystal Model System

Supporting functional molecules on crystal facets is an established technique in nanotechnology. To preserve the original activity of ionic metallorganic agents on a supporting template, conservation of the charge and oxidation state of, the active center is indispensable. We. present a model system of a metallorganic agent that, indeed, fulfills this design criterion on a technologically relevant metal support With potential Impact on Au(III)-porphyrin-functionalized nanoparticles for an improved anticancer-drug delivery. Employing scanning tunneling microscopy and -spectroscopy in combination with photoemission spectroscopy,we clarify at the single-molecule level the underlying mechanisms of this exceptional adsorption mode. It is based on the balance between a high-energy oxidation state and an electrostatic screening-response of the surface (image charge). Modeling with first principles methods reveals submolecular details of the metal-ligand bonding interaction and completes the study by providing an Illustrative electrostatic.. model relevant for ionic metalorganic agent molecules, in general