John R. Gilbertson

Overview of telepathology, virtual microscopy, and whole slide imaging: prospects for the future ☆

Telepathology, the practice of pathology at a long distance, has advanced continuously since 1986. Today, fourth-generation telepathology systems, so-called virtual slide telepathology systems, are being used for education applications. Both conventional and innovative surgical pathology diagnostic services are being designed and implemented as well. The technology has been commercialized by more than 30 companies in Asia, the United States, and Europe. Early adopters of telepathology have been laboratories with special challenges in providing anatomic pathology services, ranging from the need to provide anatomic pathology services at great distances to the use of the technology to increase efficiency of services between hospitals less than a mile apart. As to what often happens in medicine, early adopters of new technologies are professionals who create model programs that are successful and then stimulate the creation of infrastructure (ie, reimbursement, telecommunications, information technologies, and so on) that forms the platforms for entry of later, mainstream, adopters. The trend at medical schools, in the United States, is to go entirely digital for their pathology courses, discarding their student light microscopes, and building virtual slide laboratories. This may create a generation of pathology trainees who prefer digital pathology imaging over the traditional hands-on light microscopy. The creation of standards for virtual slide telepathology is early in its development but accelerating. The field of telepathology has now reached a tipping point at which major corporations now investing in the technology will insist that standards be created for pathology digital imaging as a value added business proposition. A key to success in teleradiology, already a growth industry, has been the implementation of standards for digital radiology imaging. Telepathology is already the enabling technology for new, innovative laboratory services. Examples include STAT QA surgical pathology second opinions at a distance and a telehealth-enabled rapid breast care service. The innovative bundling of telemammography, telepathology, and teleoncology services may represent a new paradigm in breast care that helps address the serious issue of fragmentation of breast cancer care in the United States and elsewhere. Legal and regulatory issues in telepathology are being addressed and are regarded as a potential catalyst for the next wave of telepathology advances, applications, and implementations.

Design and analysis of a content-based pathology image retrieval system

A prototype, content-based image retrieval system has been built employing a client/server architecture to access supercomputing power from the physicians desktop. The system retrieves images and their associated annotations from a networked microscopic pathology image database based on content similarity to user supplied query images. Similarity is evaluated based on four image feature types: color histogram, image texture, Fourier coefficients, and wavelet coefficients, using the vector dot product as a distance metric. Current retrieval accuracy varies across pathological categories depending on the number of available training samples and the effectiveness of the feature set. The distance measure of the search algorithm was validated by agglomerative cluster analysis in light of the medical domain knowledge. Results show a correlation between pathological significance and the image document distance value generated by the computer algorithm. This correlation agrees with observed visual similarity. This validation method has an advantage over traditional statistical evaluation methods when sample size is small and where domain knowledge is important. A multi-dimensional scaling analysis shows a low dimensionality nature of the embedded space for the current test set.

Digital imaging in pathology: the case for standardization

The process of digital imaging in microscopy is a series of operations, each contributing to the quality of the final image that is displayed on the computer monitor. The operations include sample preparation and staining by histology, optical image formation by the microscope, digital image sampling by the camera sensor, postprocessing and compression, transmission across the network and display on the monitor. There is an extensive literature about digital imaging and each step of the process is fairly well understood. However, the complete process is very hard to standardize or even to understand fully. The important concepts for pathology imaging standards are: (1) systems should be able to share image files, (2) the standards should allow the transmission of information on baseline colours and recommended display parameters, (3) the images should be useful to the pathologist, not necessarily better or worse than direct examination of a slide under the microscope, (4) a mechanism to evaluate image quality objectively should be present, (5) a mechanism to adjust and correct the minor errors of tissue processing should be developed, (6) a public organization should support pathologists in the development of standards.

An informatics model for tissue banks – Lessons learned from the Cooperative Prostate Cancer Tissue Resource

BackgroundAdvances in molecular biology and growing requirements from biomarker validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control.MethodsData managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent.ResultsSince July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence.ConclusionBuilding a biorepository infrastructure that meets todays research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for biomarker validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems.

Partial purification of the NADPH-dependent aldehyde reductase from bovine cardiac muscl☆

Abstract An aldehyde reductase catalyzing the NADPH-dependent reduction of long-chain aldehydes has been purified 690-fold from bovine cardiac muscle. Based on the results obtained during gel filtration, this enzyme has an apparent molecular weight of 34,000. The pI of the aldehyde reductase was 6.1 and the enzymatic activity had a sharp pH optimum at 6.4. The enzyme catalyzed the reduction of aromatic aldehydes and aliphatic aldehydes having eight or more carbon atoms. Short-chain aldehydes, aldoses, or ketoses or long-chain methyl ketones were not utilized as substrates by this enzyme. However, the methyl ketone, pentadecan-2-one, was a competitive inhibitor of this enzyme with an apparent K i = 10 μ m when tetradecanal was the variable substrate. The reaction was not reversible when ethanol or hexadecanol was employed as substrate, utilizing either NAD + , or NADP + as a cofactor. The addition of 10 m m pyrazole to the incubation medium had no effect on the enzymatic activity.

Characterization and metabolism of free fatty alcohols fromEscherichia coli

Free fatty acohols have been established as lipid components ofE. coli K-12. Using combined gas liquid chromatography-mass spectrometry, the major alcohols in aerobically grown cells were identified as 1-tetradecanol (18%), 1-hexadecanol (28%), 1-octadecanol (14%), and 2-pentadecanol (27%). Small amounts of 1-hexadecenol (3%), 2-tridecanol (8%), and 2-tetradecanol (1.5%) were also detected. Analysis of anaerobically grown cells has shown a selective decrease of the secondary alcohols. 2-Pentadecanol was present as only 7% of the total alcohol fraction, and only traces of 2-tridecanol and 2-tetradecanol were found. The major alcohols in anaerobic cells were 1-tetradecanol, 1-pentadecanol, 1-hexadecenol and 1-hexadecanol. The above observations strongly suggest two pathways for the synthesis of fatty alcohols inE. coli. One pathway synthesizes the primary alcohols and does not require molecular oxygen, and a separate pathway synthesizes the secondary alcohols and has a requirement for molecular oxygen.

Computer aided diagnostic tools aim to empower rather than replace pathologists: Lessons learned from computational chess

Department of Pathology, University of Michigan, 4233A Medical Science I, 1301 Catherine, Ann Arbor, Michigan, 1Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, 2Department of Biomedical Engineering, Rutgers The State University of New Jersey, 599 Taylor Road, Piscataway, NJ, 3MGH Pathology Imaging and Communication, Technology (PICT) Center, 101 Merrimac Street, Boston, MA 02114-4719, 4National Institutes of Health, National Cancer Institute, Laboratory of Pathology, Advanced Technology Center, 8717 Grovemont Circle, Gaithersburg, MD 20877, 5Massachusetts General Hospital, Harvard Medical School, 16th Street Building 114, Charlestown, MA 02129, 6Department of Pathology, Massachusetts General Hospital, Harvard Medical School, 1 Longfellow Place, Suite 216, Boston, MA 02114, 7Esoterix Genetic Laboratories, LLC, Successor to Genzyme Genetics, Pathology Services, 5300 McConnell Ave, Los Angeles, CA 90066, USA

Histology, imaging and new diagnostic work-flows in pathology.

IntroductionSince their introduction in 1999, fully automated, high speed, high-resolution whole slide imaging devices have become increasing more reliable, fast and capable. While by no means perfect, these devices have evolved to a point where one can consider placing them in a pre-diagnostic role in a clinical histology lab.MethodsAt the Massachusetts General Hospital, we are running a pilot study placing high end WSI devices in our main clinical histology lab (after the cover slipper and before slides are sent to the pathologist) to examine the requirement for both the machine and the laboratory.ResultsPlacing WSI systems in the clinical lab stresses the system in terms of reliability and throughput. Significantly however, success requires significant modification to the lab workflow. It is likely laboratories need to move from manual, large batch processes to increasingly automated, continuous flow (or mini-batch) processes orchestrated by the LIS using bar coding to track and direct slides, and incorporating the decision to image into the specimen type and the histology orders. Furthermore, image quality, capture speed and reliability are functions of the quality of the histology presented to the WSI devices.ConclusionImaging in pathology does not begin in a WSI robot but in the grossing room and in the histology lab. As more and more imaging devices are placed in histology lab, the inter-relationships histology and pathology imaging will become increasing understood.

Effects of different culture media and oxygen upon lipids ofEscherichia coli K-12

The effects of altering the chemical composition of the culture media and the oxygen content of the environment upon the lipid metabolism ofEscherichia coli K-12 were investigated. WhenE. coli cells were grown on the same culture medium but under aerobic and anaerobic conditions, an increase in the free fatty acids of anaerobically grown cells was observed with a disproportionate increase in the unsaturated fatty acids. When glucose was the sole carbon source, both fatty alcohols and hydrocarbons were detected as component lipids of these cells, whether growth occurred under aerobic or anaerobic conditions. Based upon this observation, acetate is considered the initial precursor for fatty alcohol and hydrocarbon biosynthesis. A possible metabolic pathway involving fatty alcohols in hydrocarbon synthesis has been postulated.

In vivo and in vitro biosynthesis of free fatty alcohols inEscherichia Coli K-12

In vivo studies have indicated that exogenous free fatty acids may serve as precursors of the free fatty alcohols ofEscherichia coli K-12. Following disruption of the cells, the enzymatic activity capable of catalyzing the reduction of long chain fatty aldehydes to fatty alcohols was localized in the 100,000 x g supernatant fraction. Nicotinamide adenine dinucleotide phosphate, reduced form, was the required cofactor. The product of the reaction was characterized rigorously as 1-hexadecanol when hexadecanal was the substrate. Three independent, but complementary, assay methods were developed to assay the aldehyde reductase activity. By employing these methods, an equivalence between nicotinamide adenine dinucleotide phosphate, reduced form, oxidation and 1-hexadecanol synthesis was established. Two protein fractions catalyzing the reduction of fatty aldehydes to fatty alcohols were detected in the 100,000 x g supernatant fraction following ammonium sulfate fractionation and diethylaminoethyl-cellulose chromatography. Enzymatic activity (70%) applied to the diethylamino-ethyl-cellulose column was eluted at a phosphate concentration of 0.115 M. The remaining 30% was eluted at a concentration of 0.23 M. Following sephadex chromatography, it was observed that the enzyme eluting at 0.115 M phosphate had an apparent mol wt of 250,000 Daltons while that eluting at 0.23 M had an apparent mol wt of 62,000 Daltons. The enzymes were similar with respect to substrate specificity, pH optima, ionic strength optima, and stability with respect to thiol inhibitors, suggesting different sized aggregates of similar subunits.