An Assessment of Imaging Informatics for Precision Medicine in Cancer.

Objectives: Precision medicine requires the measurement, quantification, and cataloging of medical characteristics to identify the most effective medical intervention. However, the amount of available data exceeds our current capacity to extract meaningful information. We examine the informatics needs to achieve precision medicine from the perspective of quantitative imaging and oncology. Methods: The National Cancer Institute (NCI) organized several workshops on the topic of medical imaging and precision medicine. The observations and recommendations are summarized herein. Results: Recommendations include: use of standards in data collection and clinical correlates to promote interoperability; data sharing and validation of imaging tools; clinician's feedback in all phases of research and development; use of open-source architecture to encourage reproducibility and reusability; use of challenges which simulate real-world situations to incentivize innovation; partnership with industry to facilitate commercialization; and education in academic communities regarding the challenges involved with translation of technology from the research domain to clinical utility and the benefits of doing so. Conclusions: This article provides a survey of the role and priorities for imaging informatics to help advance quantitative imaging in the era of precision medicine. While these recommendations were drawn from oncology, they are relevant and applicable to other clinical domains where imaging aids precision medicine.

A fast, automatic segmentation algorithm for locating and delineating touching cell boundaries in imaged histopathology.

BACKGROUND: Automated analysis of imaged histopathology specimens could potentially provide support for improved reliability in detection and classification in a range of investigative and clinical cancer applications. Automated segmentation of cells in the digitized tissue microarray (TMA) is often the prerequisite for quantitative analysis. However overlapping cells usually bring significant challenges for traditional segmentation algorithms. OBJECTIVES: In this paper, we propose a novel, automatic algorithm to separate overlapping cells in stained histology specimens acquired using bright-field RGB imaging. METHODS: It starts by systematically identifying salient regions of interest throughout the image based upon their underlying visual content. The segmentation algorithm subsequently performs a quick, voting based seed detection. Finally, the contour of each cell is obtained using a repulsive level set deformable model using the seeds generated in the previous step. We compared the experimental results with the most current literature, and the pixel wise accuracy between human experts' annotation and those generated using the automatic segmentation algorithm. RESULTS: The method is tested with 100 image patches which contain more than 1000 overlapping cells. The overall precision and recall of the developed algorithm is 90% and 78%, respectively. We also implement the algorithm on GPU. The parallel implementation is 22 times faster than its C/C++ sequential implementation. CONCLUSION: The proposed segmentation algorithm can accurately detect and effectively separate each of the overlapping cells. GPU is proven to be an efficient parallel platform for overlapping cell segmentation.

Population and temperature effects on Lucilia sericata (Diptera: Calliphoridae) body size and minimum development time.

Understanding how ecological conditions influence physiological responses is fundamental to forensic entomology. When determining the minimum postmortem interval with blow fly evidence in forensic investigations, using a reliable and accurate model of development is integral. Many published studies vary in results, source populations, and experimental designs. Accordingly, disentangling genetic causes of developmental variation from environmental causes is difficult. This study determined the minimum time of development and pupal sizes of three populations of Lucilia sericata Meigen (Diptera: Calliphoridae; from California, Michigan, and West Virginia) at two temperatures (20 degrees C and 33.5 degrees C). Development times differed significantly between strain and temperature. In addition, California pupae were the largest and fastest developing at 20 degrees C, but at 33.5 degrees C, though they still maintained their rank in size among the three populations, they were the slowest to develop. These results indicate a need to account for genetic differences in development, and genetic variation in environmental responses, when estimating a postmortem interval with entomological data.

Viscoelasticity of the vessel wall: the role of collagen and elastic fibers.

The aortic wall contains collagen fibrils, smooth muscle cells, and elastic fibers as the primary load-bearing components. It is well known that the collagen fibrils bear loads in the circumferential direction, whereas elastic fibers provide longitudinal as well as circumferential support. Stiffening of the vessel wall is associated with loss of elastic tissue and increases in the collagen content: however, little is known about the mechanism of vessel wall stiffening with age. The purpose of this review is to attempt to relate structural changes that occur to the collagen and elastic fibers to changes in the viscoelastic behavior that are associated with aging. Analysis of the viscoelastic mechanical properties of collagen fibrils from tendon, skin, and aortic wall suggest that the collagen fibrils of aortic wall are different than those of other tissues. The elastic spring constant of the collacen fibrils in vessel walls is significantly less than that found in tendon, suggesting that the presence of type III collagen in aortic wall increases the flexibility of the collagen fibrils. Furthermore, it is hypothesized that changes in the interface between collagen fibrils, elastic fibers, and smooth muscle during aging and in connective tissue disorders leads to changes in the viscoelasticity of the vessel wall.

A distal upstream enhancer from the myelin basic protein gene regulates expression in myelin-forming schwann cells.

In peripheral nerves, large caliber axons are ensheathed by myelin-elaborating Schwann cells. Multiple lines of evidence demonstrate that expression of the genes encoding myelin structural proteins occurs in Schwann cells in response to axonal instructions. To gain further insight into the mechanisms controlling myelin gene expression, we used reporter constructs in transgenic mice to search for the DNA elements that regulate the myelin basic protein (MBP) gene. Through this in vivo investigation, we provide evidence for the participation of multiple, widely distributed, positive and negative elements in the overall control of MBP expression. Notably, all constructs bearing a 0.6 kb far-upstream sequence, designated Schwann cell enhancer 1 (SCE1), expressed at high levels in myelin-forming Schwann cells. In addition, robust targeting activity conferred by SCE1 was shown to be independent of other MBP 5' flanking sequence. These observations suggest that SCE1 will make available a powerful tool to drive transgene expression in myelinating Schwann cells and that a focused analysis of the SCE1 sequence will lead to the identification of transcription factor binding sites that positively regulate MBP expression.

Computer-assisted discrimination among malignant lymphomas and leukemia using immunophenotyping, intelligent image repositories, and telemicroscopy.

The process of discriminating among pathologies involving peripheral blood, bone marrow, and lymph node has traditionally begun with subjective morphological assessment of cellular materials viewed using light microscopy. The subtle visible differences exhibited by some malignant lymphomas and leukemia, however, give rise to a significant number of false negatives during microscopic evaluation by medical technologists. We have developed a distributed, clinical decision support prototype for distinguishing among hematologic malignancies. The system consists of two major components, a distributed telemicroscopy system and an intelligent image repository. The hybrid system enables individuals located at disparate clinical and research sites to engage in interactive consultation and to obtain computer-assisted decision support. Software, written in JAVA, allows primary users to control the specimen stage, objective lens, light levels, and focus of a robotic microscope remotely while a digital representation of the specimen is continuously broadcast to all session participants. Primary user status can be passed as a token. The system features shared graphical pointers, text messaging capability, and automated database management. Search engines for the database allow one to automatically identify and retrieve images, diagnoses, and correlated clinical data of cases from a "gold standard" database which exhibit spectral and spatial profiles which are most similar to a given query image. The system suggests the most likely diagnosis based on majority logic of the retrieved cases. The system was used to discriminate among three lymphoproliferative disorders and healthy cells. The system provided the correct classification in more than 83% of the cases studied. System performance was evaluated using rigorous statistical assessment and by comparison with human observers.

Compression guidelines for diagnostic telepathology.

As the healthcare community has begun to rely increasingly upon digital technologies for acquisition, storage, and transmission of pictorial data, image compression has become an indispensable tool. We have investigated the feasibility of lossy compression in a well-defined task domain, the clinical assessment of digitized images of chromatic microscopic pathology specimens. The effect of compression was measured under two distinct perceptual criteria, just noticeable difference (j.n.d.) and largest tolerable distortion (l.t.d.), differing in the involvement required from subjects, who were experts in pathology. For standard JPEG compressed images it was found that when the experiment is performed under the l.t.d. criterion, a significantly larger compression ratio is reported as satisfactory. It is concluded that lossy compression holds promise for diagnostic telepathology.

A network-based prototype for interactive telemedicine & automated management of distributed, clinical databases.

A network-based prototype has been developed to automate the process of generating and maintaining distributed databases of medical images and clinical reports, and for conducting interactive consultation among disparate clinical and research sites irrespective of the architecture of interacting computers. Pathologists routinely interpret gross and microscopic specimens to tender diagnoses and to engage in a broad spectrum of research. This assessment process leads to clinical decisions often limited by time constraints and by the availability of local expertise. Consultation with peers at other institutions is typically achieved by direct transfer of slides rather than images. A network of heterogeneous computer platforms, graphical user interfaces, and operating systems was established to test the performance of the software. Clinical diagnoses rendered by pathologists using the prototypical system and software were consistent with those reported two years earlier using conventional light microscopy in more than 97% of the cases studied.

The role for regional autopsy centers in the evaluation of covered deaths. Survey of opinions of US and Canadian chairs of pathology and major health insurers in the United States.

OBJECTIVE: To evaluate the advantages and disadvantages of, as well as the attitudes of health care professionals and insurers toward, the development of regional autopsy services. DESIGN: Survey of 150 medical school departments of pathology in the United States and Canada and 12 representative major health insurers in the United States. RESULTS: Of the 25 respondents from the pathology departments, most were in favor of regionalization of autopsy services, if properly underwritten. Of the five respondents from the health insurers, most were disinterested in the autopsy as a measure of outcome and unwilling to provide support. CONCLUSIONS: Health care is being regionalized around networks of insurers rather than hospitals. The networks are defined by a mixture of hospitals, physician groups, and other health care professionals. Within networks, the goal is to subscribe groups of patients, covered lives, for all medical needs from primary to complex care. As the economic risk of caring for patients is shifted to physicians, the incentive to provide service at the lowest possible cost grows, as does the need to assure that medical mismanagement does not occur. To provide quality care at affordable costs, it is necessary that outcomes, including deaths, be professionally evaluated. The present system of death investigation involves hospital colleagues and is potentially biased. Regional autopsy centers that provide timely expert information should be part of the health care system. Medical schools are potential sites for regional autopsy programs because they have the personnel needed to conduct appropriate death-related studies. Most schools are affiliated programmatically and economically with surrounding hospitals and physicians in a manner in which outcomes, costs, and quality of clinical service are of common interest.

A method for quantitative image assessment based on redundant feature measurements and statistical reasoning.

Advances in computer graphics and electronics have contributed significantly to the increased utilization of digital imaging throughout the scientific community. Recently, as the volume of data being gathered for biomedical applications has begun to approach the human capacity for processing, emphasis has been placed on developing an automated approach to assist health scientists in assessing images. Methods that are currently used for analysis often lack sufficient sensitivity for discriminating among elements that exhibit subtle differences in feature measurements. In addition, most approaches are highly interactive. This paper presents an automated approach to segmentation and object recognition in which the spectral and spatial content of images is statistically exploited. Using this approach to assess noisy images resulted in correct classification of more than 97% of the pixels evaluated during segmentation and in recognition of geometric shapes irrespective of variations in size, orientation, and translation. The software was subsequently used to evaluate digitized stained blood smears.

Myelin acquisition in the central nervous system of the mouse revealed by an MBP-Lac Z transgene.

Myelin has pronounced effects upon the morphology, function, and growth of axons in the mammalian CNS. Consequently, oligodendrocyte development and myelination have been investigated using a wide variety of histological, immunocytochemical, ultrastructural, and biochemical techniques. While many of the spatial and temporal features of myelin appearance have been characterized, for any one species only limited regions of the CNS have been investigated. To address this limitation, we have derived transgenic mice in which the bacterial Lac Z gene is regulated by promoter elements of the myelin basic protein gene. When differentiating oligodendrocytes begin to elaborate recognizable myelin, they initiate expression of the MBP-Lac Z transgene and accumulate readily detectable levels of beta-galactosidase. Here, we exploit the sensitivity, resolution, and ease of beta-galactosidase histochemical assays to characterize the temporal and spatial patterns of CNS myelination in the mouse. Many features of the myelination program revealed by this approach were predicted by the immunocytochemical and ultrastructural data derived from other species. Nonetheless, previously undocumented patterns were also encountered. beta-Galactosidase was expressed first by oligodendrocytes in the ventral spinal cord, 1 d prior to birth. There, myelination proceeded in a strictly rostral-caudal direction, whereas in the dorsal cord, myelination initiated in the cervical enlargement and proceeded in both rostral and caudal directions. In the cerebellum, deep regions myelinated first, and in the optic nerve, myelination initiated at the retinal end. In contrast, the lateral olfactory tracts, pons, and optic chiasm initiated myelination along their entire course.(ABSTRACT TRUNCATED AT 250 WORDS)

Evidence of luminous bacterial symbionts in the light organs of myctophid and stomiiform fishes.

The myctophids and stomiiforms represent two common groups of luminous fishes, but the source of luminescence in these animals has remained undetermined. In this study, labeled luciferase gene fragments from luminous marine bacteria were used to probe DNA isolated from specific fish tissues. A positive signal was obtained from skin DNA in all luminous fishes examined, whereas muscle DNA gave a weaker signal and brain DNA was negative. This observation is consistent with luminous bacteria acting as the light source in myctophids and stomiiforms and argues against the genes necessary for luminescence residing on the fish chromosomes. To confirm the location of this signal, a bacterial probe was hybridized in situ to sections of a stomiiform. A strong signal was generated directly over specific regions of the fish light organs, whereas no signal was found over other internal or epidermal tissues of the fish. Taken together, these data provide the first indication that luminous bacterial symbionts exist in myctophids and stomiiforms and that these symbionts account for luminescence in these fishes.

Assessment of cell proliferation on porous microcarriers by means of image analysis.

Spherical porous microcarriers (PMCs) made from collagen-glycosaminoglycan crosslinked copolymers have exhibited considerable promise as growth surfaces for the proliferation of anchorage-dependent mammalian cell lines and have demonstrated the ability to entrap anchorage-independent cells. However, quantification of cell growth on PMCs has proved difficult. A method of measuring the proliferation of PMCs, based on image analysis, is presented. Using CV1 and CHO cell lines, samples of PMCs were removed from culture at various times, fixed, embedded and sectioned. The 2 microns sections were stained, photographed and digitized in three colors. A computer program was developed to evaluate digitized PMC cross-sections and to classify pixels as conforming to either background, cytoplasmic, matrix or nuclear parameters, based on a set of classification rules determined by statistical analysis. Growth curves were generated by relating the number of pixels occupied by cellular material to the total number of pixels in the PMC cross-section. The PMCs were found to foster cell proliferation, with cell densities approaching 100% occupancy.

Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis.

The mitochondrial DNA (mtDNA) control regions for common chimpanzee, pygmy chimpanzee and gorilla were sequenced and the lengths and termini of their D-loop DNA's characterized. In these and all other species for which there are data, 5' termini map to sequences that contain the trinucleotide YAY. 3' termini are 25-51 nucleotides downstream from a sequence that is moderately conserved among vertebrates. Substitutions were greater than 1.5 times more frequent in the control region than in regions encoding structural genes. Additions and deletions were also frequent, especially in gorilla. Sequences of promoters and of two of four transcription factor binding sites were highly conserved. Comparisons of sequence similarity and transition/transversion ratios suggest that human and chimpanzees may be more closely related to each other than either is to gorilla, if substitution rates are approximately equal among these species.

Evolution of two actin genes in the sea urchin Strongylocentrotus franciscanus.

The complete nucleotide sequences of two chromosomally linked actin genes from the sea urchin Strongylocentrotus franciscanus are presented. The genes are separated by 5.7 kilobases, occur in the same transcriptional orientation, and contain introns in identical positions. The structures and nucleotide sequences of the two genes are extremely similar, suggesting that they arose through a recent duplication. Comparison of the nucleotide sequences of the genes allows inferences to be made about mutational mechanisms active since the duplication event. Whereas point mutations predominate in the coding regions, the introns and flanking DNA are more heavily influenced by a variety of events that cause simultaneous changes in short regions of DNA.

Organization and evolution of the actin gene family in sea urchins.

Genomic libraries of the sea urchins Strongylocentrotus franciscanus and Lytechinus pictus were screened with an actin cDNA clone from Strongylocentrotus purpuratus. Four nonoverlapping clones were isolated and characterized from the S. franciscanus library; three were isolated and characterized from the L. pictus library. Linked genes having the same transcriptional orientation were found on all S. franciscanus clones. Three clones contained two actin genes each; the other clone contained three. In contrast, the L. pictus clones contained only one actin gene. Comparison of actin genomic clones from these three species indicated a difference in the genomic organization of sea urchin actin genes in that the genes appear to be more highly clustered in S. franciscanus than in S. purpuratus and L. pictus. Genomic dot blots and reassociation kinetics demonstrated that the copy number of actin genes in all three species is 15 to 20. Nucleotide sequence homology of actin genes within and among the species was measured by thermal elution. These experiments indicated that there is a high degree of interspecies actin gene sequence homology but that, within each species, actin gene sequences may differ by as much as 30%. Sequencing of two S. franciscanus actin genes revealed introns at the same amino acid positions, 121 and 204, reported for S. purpuratus actin genes. These data demonstrated that the genomic copy number, the transcriptional orientation of linked genes, and, to the extent studied, the intron position of actin genes have evolved similarly in these three species. In contrast, significant change has occurred in the chromosomal arrangement of sea urchin actin genes.