Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study

Background: Tissue MicroArray technology aims to perform immunohistochemical staining on hundreds of different tissue samples simultaneously. It allows faster analysis, considerably reducing costs incurred in staining. A time consuming phase of the methodology is the selection of tissue areas within paraffin blocks: no utilities have been developed for the identification of areas to be punched from the donor block and assembled in the recipient block.Results: The presented work supports, in the specific case of a primary subtype of breast cancer (tubular breast cancer), the semi-automatic discrimination and localization between normal and pathological regions within the tissues. The diagnosis is performed by analysing specific morphological features of the sample such as the absence of a double layer of cells around the lumen and the decay of a regular glands-and-lobules structure. These features are analysed using an algorithm which performs the extraction of morphological parameters from images and compares them to experimentally validated threshold values. Results are satisfactory since in most of the cases the automatic diagnosis matches the response of the pathologists. In particular, on a total of 1296 sub-images showing normal and pathological areas of breast specimens, algorithm accuracy, sensitivity and specificity are respectively 89%, 84% and 94%.Conclusions: The proposed work is a first attempt to demonstrate that automation in the Tissue MicroArray field is feasible and it can represent an important tool for scientists to cope with this high-throughput technique

Automatic Tumor-Stroma Separation in Fluorescence TMAs Enables the Quantitative High-Throughput Analysis of Multiple Cancer Biomarkers

The upcoming quantification and automation in biomarker based histological tumor evaluation will require computational methods capable of automatically identifying tumor areas and differentiating them from the stroma. As no single generally applicable tumor biomarker is available, pathology routinely uses morphological criteria as a spatial reference system. We here present and evaluate a method capable of performing the classification in immunofluorescence histological slides solely using a DAPI background stain. Due to the restriction to a single color channel this is inherently challenging. We formed cell graphs based on the topological distribution of the tissue cell nuclei and extracted the corresponding graph features. By using topological, morphological and intensity based features we could systematically quantify and compare the discrimination capability individual features contribute to the overall algorithm. We here show that when classifying fluorescence tissue slides in the DAPI channel, morphological and intensity based features clearly outpace topological ones which have been used exclusively in related previous approaches. We assembled the 15 best features to train a support vector machine based on Keratin stained tumor areas. On a test set of TMAs with 210 cores of triple negative breast cancers our classifier was able to distinguish between tumor and stroma tissue with a total overall accuracy of 88%. Our method yields first results on the discrimination capability of features groups which is essential for an automated tumor diagnostics. Also, it provides an objective spatial reference system for the multiplex analysis of biomarkers in fluorescence immunohistochemistry

Extremely Electron-Rich, Boron-Functionalized, Icosahedral Carborane-Based Phosphinoboranes

We have prepared the first examples of B9-connected trivalent aryl and alkyl phosphinoborane species via Pd-catalyzed phosphination of 9-iodo-meta-carborane. Our studies highlight the unique electronic features of the B9-connected meta-carboranyl moiety as compared to its C1-based analogue. This work suggests that the B9-functionalized meta-carboranyl substituent in these ligands exhibits more electron-releasing character than any other known carbon-based substituent, ultimately laying the foundation for a new class of phosphine ligands with extremely electron-rich character.National Institutes of Health (U.S.) (GM46059)National Institutes of Health (U.S.) (Fellowship 1F32GM101762

Extremely Electron-Rich, Boron-Functionalized, Icosahedral Carborane-Based Phosphinoboranes

We have prepared the first examples of B9-connected trivalent aryl and alkyl phosphinoborane species via Pd-catalyzed phosphination of 9-iodo-<i>meta</i>-carborane. Our studies highlight the unique electronic features of the B9-connected <i>meta</i>-carboranyl moiety as compared to its C1-based analogue. This work suggests that the B9-functionalized <i>meta</i>-carboranyl substituent in these ligands exhibits more electron-releasing character than any other known carbon-based substituent, ultimately laying the foundation for a new class of phosphine ligands with extremely electron-rich character

Extremely Electron-Rich, Boron-Functionalized, Icosahedral Carborane-Based Phosphinoboranes

We have prepared the first examples of B9-connected trivalent aryl and alkyl phosphinoborane species via Pd-catalyzed phosphination of 9-iodo-<i>meta</i>-carborane. Our studies highlight the unique electronic features of the B9-connected <i>meta</i>-carboranyl moiety as compared to its C1-based analogue. This work suggests that the B9-functionalized <i>meta</i>-carboranyl substituent in these ligands exhibits more electron-releasing character than any other known carbon-based substituent, ultimately laying the foundation for a new class of phosphine ligands with extremely electron-rich character

Formation of ArF from LPdAr(F): Catalytic Conversion of Aryl Triflates to Aryl Fluorides

Despite increasing pharmaceutical importance, fluorinated aromatic organic molecules remain difficult to synthesize. Present methods require either harsh reaction conditions or highly specialized reagents, making the preparation of complex fluoroarenes challenging. Thus, the development of general methods for their preparation that overcome the limitations of those techniques currently in use is of great interest. We have prepared [LPd(II)Ar(F)] complexes, where L is a biaryl monophosphine ligand and Ar is an aryl group, and identified conditions under which reductive elimination occurs to form an Ar-F bond. On the basis of these results, we have developed a catalytic process that converts aryl bromides and aryl triflates into the corresponding fluorinated arenes by using simple fluoride salts. We expect this method to allow the introduction of fluorine atoms into advanced, highly functionalized intermediates.National Institutes of Health (U.S.) (Grant GM46059)Merck & Co., Inc.Boehringer Ingelheim PharmaceuticalsBASFNational Science Foundation (U.S.) (Grant CHE 9808061)National Institutes of Health (U.S.) (Grant DBI 9729592