Automatic image annotation using visual content and folksonomies

Automatic image annotation is an important and challenging task, and becomes increasingly necessary when managing large image collections. This paper describes techniques for automatic image annotation that take advantage of collaboratively annotated image databases, so called visual folksonomies. Our approach applies two techniques based on image analysis: First, classification annotates images with a controlled vocabulary and second tag propagation along visually similar images. The latter propagates user generated, folksonomic annotations and is therefore capable of dealing with an unlimited vocabulary. Experiments with a pool of Flickr images demonstrate the high accuracy and efficiency of the proposed methods in the task of automatic image annotation. Both techniques were applied in the prototypical tag recommender “tagr”.     

Partial Reduction in BRCA1 Gene Dose Modulates DNA Replication Stress Level and Thereby Contributes to Sensitivity or Resistance

BRCA1 is a well-known breast cancer risk gene, involved in DNA damage repair via homologous recombination (HR) and replication fork protection. Therapy resistance was linked to loss and amplification of the BRCA1 gene causing inferior survival of breast cancer patients. Most studies have focused on the analysis of complete loss or mutations in functional domains of BRCA1. How mutations in non-functional domains contribute to resistance mechanisms remains elusive and was the focus of this study. Therefore, clones of the breast cancer cell line MCF7 with indels in BRCA1 exon 9 and 14 were generated using CRISPR/Cas9. Clones with successful introduced BRCA1 mutations were evaluated regarding their capacity to perform HR, how they handle DNA replication stress (RS), and the consequences on the sensitivity to MMC, PARP1 inhibition, and ionizing radiation. Unexpectedly, BRCA1 mutations resulted in both increased sensitivity and resistance to exogenous DNA damage, despite a reduction of HR capacity in all clones. Resistance was associated with improved DNA double-strand break repair and reduction in replication stress (RS). Lower RS was accompanied by increased activation and interaction of proteins essential for the S phase-specific DNA damage response consisting of HR proteins, FANCD2, and CHK1.     

Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization,Multiplex RNA Hybridization,Sequencing and Subtyping

Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.     

Synthesis and Metabolic Fate of 4-Methylthiouridine in Bacterial tRNA

Ribonucleic acid (RNA) is central to many life processes and, to fulfill its function, it has a substantial chemical variety in its building blocks. Enzymatic thiolation of uridine introduces 4-thiouridine (s⁴U) into many bacterial transfer RNAs (tRNAs), which is used as a sensor for UV radiation. A similar modified nucleoside, 2-thiocytidine, was recently found to be sulfur-methylated especially in bacteria exposed to antibiotics and simple methylating reagents. Herein, we report the synthesis of 4-methylthiouridine (ms⁴U) and confirm its presence and additional formation under stress in Escherichia coli. We used the synthetic ms⁴U for isotope dilution mass spectrometry and compared its abundance to other reported tRNA damage products. In addition, we applied sophisticated stable-isotope pulse chase studies (NAIL-MS) and showed its AlkB-independent removal in vivo. Our findings reveal the complex nature of bacterial RNA damage repair.     

Microstructure and fracture mechanical response of wood

Investigations on the fracture properties of wood in relation to its microstructure are reported. The inhomogeneous and hierarchical structure of wood is addressed. Wood species, the influence of orientation, the role of structural features, like rays are considered and discussed. Likewise the mode of loading, which determines the mode of fracturing, and the influence of humidity have been studied by using new fracture mechanical techniques and ways of evaluation. The specific fracture energy has been determined under crack opening conditions. In-situ loading in an environmental scanning electron microscope (ESEM), which allows observation in moistured condition, has been performed in order to investigate the mechanisms of fracturing of wood on a sub-microscopic scale. In the nanometer range, especially the influence of the microfibril angle on deformation and fracture behaviour has been studied.     

Phase relations and homogeneity region of the hightemperature superconducting phase (Bi,Pb)2Sr2Ca2Cu3O10+d

For the nominal composition of Bi_2.27−xPb_xSr₂Ca₂Cu₃O_10+d, the lead content was varied from x < 0.05 to 0.45. The compositions were examined between 800 and 890‡C which is supposed to be the temperatue range over which the so-called 2223 phase (Bi₂Sr₂Ca₂Cu₃O_10+d) is stable. Only compositions between x < 0.18 to 0.36 could be synthezised in a single phase state. For x <0.36, a lead-containing phase with a stoichiometry of Pb₄(Sr,Ca)₅CuO_d with a small solubiliy of Bi is formed, for x > 0.18 mainly Bi₂Sr₂CaCu₂O_8+d and cuprates are the equilibrium phases. The temperature range for the 2223 phase was found to be 800 to 890‡C but the 2223 phase has extremely varying cation ratios over this temperaure range. Former single phase 2223 samples turn to multiphase samples when annealed at slightly higher or lower temperaures. A decrease in the Pb solubility with increasing as well as decreasing temperature with a maximum at about 850‡C was found for the 2223 phase.     

Colloidal Stability and Surface Chemistry Are Key Factors for the Composition of the Protein Corona of Inorganic Gold Nanoparticles

To study the influence of colloidal stability on protein corona formation, gold nanoparticles are synthesized with five distinct surface modifications: coating with citric acid, bis(p‐sulfonatophenyl)phenylphosphine dihydrate dipotassium salt, thiol‐terminated methoxy‐polyethylene glycol, dodecylamine‐grafted poly(isobutylene‐alt‐maleic anhydride), and dodecylamine‐grafted poly(isobutylene‐alt‐maleic anhydride) conjugated with polyethylene glycol. The nanoparticles are incubated with serum or bronchoalveolar lavage fluid from C57BL/6 mice (15 min or 24 h) to assess the effect of differential nanoparticle surface presentation on protein corona formation in the air–blood barrier exposure pathway. Proteomic quantification and nanoparticle size measurements are used to assess protein corona formation. We show that surface modification has a clear effect on the size and the composition of the protein corona that is related to the colloidal stability of the studied nanoparticles. Additionally, differences in the composition and size of the protein corona are shown between biological media and duration of exposure, indicating evolution of the corona through this exposure pathway. Consequently, a major determinant of protein corona formation is the colloidal stability of nanoparticles in biological media and chemical or environmental modification of the nanoparticles alters the surface presentation of the functional epitope in vivo. Therefore, the colloidal stability of nanoparticles has a decisive influence on nano–bio interactions.