THE EFFECT OF ACIDS AND OTHER SUBSTANCES IN THE PRODUCTION OF ACUTE GASTRIC ULCERS

Although other investigators have attempted to demonstrate that histamine has the power of producing acute ulcers when injected locally into the stomach wall, our experiments show clearly that this is a very inconstant finding for, of six instances, we were only able to obtain a small healed mucosal ulcer in one. Even when dilute acid (0.3 per cent hydrochloric acid) was fed to these animals they did not develop ulcers or erosions. It has also been stated that histamine, given subcutaneously, may produce ulcers secondarily to oversecretion of acid, especially when at the same time histamine has been injected into the stomach wall. We have been unable to confirm this observation. In our series of experiments on dogs which were observed over a varying period of time ranging from 4 to 95 days we utilized other substances in addition to histamine. After establishing controls, sterile water, normal saline, 50 per cent glucose, skimmed milk, whole milk, omnadin, lipiodol, bismuth subcarbonate, pituitrin (S.), activin, histamine, adrenalin and insulin were injected into the muscular coat of the stomach and it was found that such procedures rarely produced any definite changes in the stomach mucosa even when supplemented by the feeding of dilute hydrochloric acid (0.3 per cent hydrochloric acid). We were able to demonstrate conclusively that the trauma involved in our operative procedure could not in itself account for any of the pathological findings. We were also able to show that the pressure due to the injected materials did not produce erosions or ulcerations. The injections of acids produced varying results. Diluted acid (0.3 per cent) injected into the stomach wall gave almost uniformly negative results but when combined with the feeding of acid of equal strength erosions were occasionally produced. Our results with 0.5 per cent hydrochloric add were also inconstant. The 1 per cent hydrochloric acid produced, in many instances, definite ulcerations even when not accompanied by the feeding of acid.

A boosted Bayesian multiresolution classifier for prostate cancer detection from digitized needle biopsies

Diagnosis of prostate cancer (CaP) currently involves examining tissue samples for CaP presence and extent via a microscope, a time-consuming and subjective process. With the advent of digital pathology, computer-aided algorithms can now be applied to disease detection on digitized glass slides. The size of these digitized histology images (hundreds of millions of pixels) presents a formidable challenge for any computerized image analysis program. In this paper, we present a boosted Bayesian multiresolution (BBMR) system to identify regions of CaP on digital biopsy slides. Such a system would serve as an important preceding step to a Gleason grading algorithm, where the objective would be to score the invasiveness and severity of the disease. In the first step, our algorithm decomposes the whole-slide image into an image pyramid comprising multiple resolution levels. Regions identified as cancer via a Bayesian classifier at lower resolution levels are subsequently examined in greater detail at higher resolution levels, thereby allowing for rapid and efficient analysis of large images. At each resolution level, ten image features are chosen from a pool of over 900 first-order statistical, second-order co-occurrence, and Gabor filter features using an AdaBoost ensemble method. The BBMR scheme, operating on 100 images obtained from 58 patients, yielded: 1) areas under the receiver operating characteristic curve (AUC) of 0.84, 0.83, and 0.76, respectively, at the lowest, intermediate, and highest resolution levels and 2) an eightfold savings in terms of computational time compared to running the algorithm directly at full (highest) resolution. The BBMR model outperformed (in terms of AUC): 1) individual features (no ensemble) and 2) a random forest classifier ensemble obtained by bagging multiple decision tree classifiers. The apparent drop-off in AUC at higher image resolutions is due to lack of fine detail in the expert annotation of CaP and is not an artifact of the classifier. The implicit feature selection done via the AdaBoost component of the BBMR classifier reveals that different classes and types of image features become more relevant for discriminating between CaP and benign areas at different image resolutions.

Cyclin D1b in human breast carcinoma and coexpression with cyclin D1a is associated with poor outcome

BACKGROUND/AIM

Cyclin D1 is a mediator of cell-cycle control that is frequently overexpressed in primary ductal breast carcinomas, but its role is controversial. A polymorphism in the CCND1 gene, G870A, results in an aberrantly spliced protein (cyclin D1b) lacking the Thr-286 phosphorylation site necessary for nuclear export. Studies of murine fibroblasts have shown that although overexpression of canonical cyclin D1 (cyclin D1a) alone is not sufficient to drive malignant transformation, expression of nuclear cyclin D1b is oncogenic. Our objectives were to determine whether cyclin D1b is expressed in human breast carcinomas and to characterize the relationship of this protein to both cyclin D1a and clinical outcome in breast cancer patients.

PATIENTS AND METHODS

We performed a prospective cohort study of women with early-stage breast cancer and analyzed cyclin D1a and D1b expression in primary breast tumor sections. Expression was tested for correlation with other breast cancer prognostic factors and clinical outcome, including recurrence or death.

RESULTS

A total of 118 patients were included in this analysis, with a median follow-up of 44 months. Cyclin D1b was expressed in 26% of tumors and cyclin D1a was overexpressed in 27%; co-expression occurred in 4%. Cyclin D1a and/or D1b expression were not significantly associated with estrogen or progesterone receptor negativity, Her2 overexpression, young age, lymph node positivity, high tumor grade, nor large tumor size. The risk of recurrence was higher in those co-expressing D1a and D1b compared to the expression of either alone (relative risk=5.3, 95% confidence interval 1.27 to 22.1, p=0.02). The hazard ratio for those with co-expression compared with those without was 6.05 (p=0.04).

CONCLUSION

Expression of cyclin D1b occurs in primary human breast carcinomas and its coexpression with cyclin D1a may be a marker for increased recurrence risk, independently of other factors.

Multiple oncogenic viruses identified in Ocular surface squamous neoplasia in HIV-1 patients

BACKGROUND

Ocular surface squamous neoplasia (OSSN) is a rare cancer that has increased in incidence with the HIV pandemic in Africa. The underlying cause of this cancer in HIV-infected patients from Botswana is not well defined.

RESULTS

Tissues were obtained from 28 OSSN and 8 pterygia patients. The tissues analyzed from OSSN patients were 83% positive for EBV, 75% were HPV positive, 70% were KSHV positive, 75% were HSV-1/2 positive, and 61% were CMV positive by PCR. Tissues from pterygium patients were 88% positive for EBV, 75% were HPV positive, 50% were KSHV positive, and 60% were CMV positive. None of the patients were JC or BK positive. In situ hybridization and immunohistochemistry analyses further identified HPV, EBV, and KSHV in a subset of the tissue samples.

CONCLUSION

We identified the known oncogenic viruses HPV, KSHV, and EBV in OSSN and pterygia tissues. The presence of these tumor viruses in OSSN suggests that they may contribute to the development of this malignancy in the HIV population. Further studies are necessary to characterize the molecular mechanisms associated with viral antigens and their potential role in the development of OSSN.

Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology

The presence of lymphocytic infiltration (LI) has been correlated with nodal metastasis and tumor recurrence in HER2+ breast cancer (BC). The ability to automatically detect and quantify extent of LI on histopathology imagery could potentially result in the development of an image based prognostic tool for human epidermal growth factor receptor-2 (HER2+) BC patients. Lymphocyte segmentation in hematoxylin and eosin (H&E) stained BC histopathology images is complicated by the similarity in appearance between lymphocyte nuclei and other structures (e.g., cancer nuclei) in the image. Additional challenges include biological variability, histological artifacts, and high prevalence of overlapping objects. Although active contours are widely employed in image segmentation, they are limited in their ability to segment overlapping objects and are sensitive to initialization. In this paper, we present a new segmentation scheme, expectation-maximization (EM) driven geodesic active contour with overlap resolution (EMaGACOR), which we apply to automatically detecting and segmenting lymphocytes on HER2+ BC histopathology images. EMaGACOR utilizes the expectation-maximization algorithm for automatically initializing a geodesic active contour (GAC) and includes a novel scheme based on heuristic splitting of contours via identification of high concavity points for resolving overlapping structures. EMaGACOR was evaluated on a total of 100 HER2+ breast biopsy histology images and was found to have a detection sensitivity of over 86% and a positive predictive value of over 64%. By comparison, the EMaGAC model (without overlap resolution) and GAC model yielded corresponding detection sensitivities of 42% and 19%, respectively. Furthermore, EMaGACOR was able to correctly resolve over 90% of overlaps between intersecting lymphocytes. Hausdorff distance (HD) and mean absolute distance (MAD) for EMaGACOR were found to be 2.1 and 0.9 pixels, respectively, and significantly better compared to the corresponding performance of the EMaGAC and GAC models. EMaGACOR is an efficient, robust, reproducible, and accurate segmentation technique that could potentially be applied to other biomedical image analysis problems.

Approximate Strong Equilibrium in Job Scheduling Games

A Nash Equilibrium (NE) is a strategy profile resilient to unilateral deviations, and is predominantly used in the analysis of multiagent systems. A downside of NE is that it is not necessarily stable against deviations by coalitions. Yet, as we show in this paper, in some cases, NE does exhibit stability against coalitional deviations, in that the benefits from a joint deviation are bounded. In this sense, NE approximates strong equilibrium. Coalition formation is a key issue in multiagent systems. We provide a framework for quantifying the stability and the performance of various assignment policies and solution concepts in the face of coalitional deviations. Within this framework we evaluate a given configuration according to three measures: (i) IR_min: the maximal number alpha, such that there exists a coalition in which the minimal improvement ratio among the coalition members is alpha, (ii) IR_max: the maximal number alpha, such that there exists a coalition in which the maximal improvement ratio among the coalition members is alpha, and (iii) DR_max: the maximal possible damage ratio of an agent outside the coalition. We analyze these measures in job scheduling games on identical machines. In particular, we provide upper and lower bounds for the above three measures for both NE and the well-known assignment rule Longest Processing Time (LPT). Our results indicate that LPT performs better than a general NE. However, LPT is not the best possible approximation. In particular, we present a polynomial time approximation scheme (PTAS) for the makespan minimization problem which provides a schedule with IR_min of 1+epsilon for any given epsilon. With respect to computational complexity, we show that given an NE on m >= 3 identical machines or m >= 2 unrelated machines, it is NP-hard to determine whether a given coalition can deviate such that every member decreases its cost.

Inhibition of KSHV-infected primary effusion lymphomas in NOD/SCID mice by gamma-secretase inhibitor

Primary effusion lymphoma (PEL) is a common cancer in AIDS patients closely associated with Kaposi's sarcoma-associated herpesvirus (KSHV). Previously, we showed that KSHV latency associated nuclear antigen (LANA) stabilizes intracellular activated Notch1 (ICN) involved in maintenance of the malignant phenotype of KSHV infected PEL cells in vitro. The gamma-secretase inhibitor (GSI) which specifically blocks the production of ICN slows down the proliferation of the KSHV infected PEL cell lines BCBL1, BC3 as well as JSC1 in vitro. In this study, we extended these studies to explore the possibility that manipulation of the Notch signaling by GSI would prevent the growth of the PEL tumors in vivo. We observed that the onset of tumorigenesis of KSHV infected PELs was significantly delayed in GSI treated SCID mice harboring the PEL cell lines. We also found that GSI treatment resulted in necrosis as well as apoptosis in tumors generated by the xenotransplanted KSHV positive PEL cell lines. In contrast, GSI had no effect on mice harboring BJAB cells, a KSHV negative Burkitt's lymphoma cell line where ICN levels were negligible. Our study provides further evidence to suggest that targeted downregulation of abnormal Notch signaling has therapeutic potential for KSHV related primary effusion lymphomas.

Novel ubiquitin-dependent quality control in the endoplasmic reticulum

Proteins of the endomembrane system undergo assisted folding in the endoplasmic reticulum (ER), then quality-control and, if misfolded, ER-associated degradation (ERAD). Recent findings on the biogenesis of a type-I membrane protein (an LRP6 mutant) lead us to hypothesize the existence of a novel mechanism promoting folding of membrane proteins from the cytosolic side of the ER. The proposed folding mechanism involves cycles of chaperone binding through mono-ubiquitylation and de-ubiquitylation, followed eventually by poly-ubiquitylation and ERAD. This suggests a novel dual role for ubiquitylation in the ER - dependent on the type of ubiquitin chains involved - in folding and in degradation, and highlights the potential importance of de-ubiquitylating enzymes.

Genome size in natural and synthetic autopolyploids and in a natural segmental allopolyploid of several Triticeae species

Nuclear DNA amount (1C) was determined by flow cytometry in the autotetraploid cytotype of Hordeum bulbosum, in the cytologically diploidized autotetraploid cytotypes of Elymus elongatus, Hordeum murinum subsp. murinum and Hordeum murinum subsp. leporinum, in Hordeum marinum subsp. gussoneanum, in their progenitor diploid cytotypes, and in a newly synthesized autotetraploid line of E. elongatus. Several lines collected from different regions of the distribution area of every taxon, each represented by a number of plants, were analyzed in each taxon. The intracytotype variation in nuclear DNA amount of every diploid and autotetraploid cytotype was very small, indicating that no significant changes have occurred in DNA amount either after speciation or after autopolyploid formation. The autotetraploid cytotypes of H. bulbosum and the cytologically diploidized H. marinum subsp. gussoneanum had the expected additive amount of their diploid cytotypes. On the other hand, the cytologically diploidized autotetraploid cytotypes of E. elongatus and H. murinum subsp. murinum and H. murinum subsp. leporinum had considerably less nuclear DNA (10%-23%) than the expected additive value. Also, the newly synthesized autotetraploid line of E. elongatus showed similar reduction in DNA as its natural counterpart, indicating that the reduction in genome size occurred in the natural cytotype during autopolyploidization. It is suggested that the diploid-like meiotic behavior of these cytologically dipolidized autotetraploids is caused by the instantaneous elimination of a large number of DNA sequences, different sequences from different homologous pairs, leading to differentiation of the constituent genomes. The eliminated sequences are likely to include those that participate in homologous recognition and initiation of meiotic pairing. A gene system determining exclusive bivalent pairing by utilizing the differentiation between the two groups of homologues has been presumably superimposed on the DNA reduction process.

Genetic structure of a wide-spectrum chicken gene pool

The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as 'Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool.

MicroRNA expression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues

microRNAs (miRNAs) are approximately 22nt RNAs that regulate target gene expression. Altered expression of miRNAs has been demonstrated in many different human cancers. Many studies using microarray technologies to characterize miRNA expression profiles have relied on fresh tissue to determine the miRNA signatures. In this study, we prepared total RNA from paired samples of formalin-fixed paraffin-embedded (FFPE) and fresh frozen malignant melanoma, and used that in microarray experiments to compare miRNA expression profiles between FFPE and fresh tissue with corresponding mRNA expression profiles from the same tissue sources. We demonstrate that miRNA expression profile from FFPE tissues closely resembles that from fresh tissues, and the correlation is significantly better than that for mRNA profiles from FFPE and fresh tissues. These results underscore the suitability of FFPE tissues as appropriate resources for molecular expression analyses and support the notion that miRNAs are more vigorous analytes for this purpose than mRNAs.

Genome size and genome evolution in diploid Triticeae species

One of the intriguing issues concerning the dynamics of plant genomes is the occurrence of intraspecific variation in nuclear DNA amount. The aim of this work was to assess the ranges of intraspecific, interspecific, and intergeneric variation in nuclear DNA content of diploid species of the tribe Triticeae (Poaceae) and to examine the relation between life form or habitat and genome size. Altogether, 438 plants representing 272 lines that belong to 22 species were analyzed. Nuclear DNA content was estimated by flow cytometry. Very small intraspecific variation in DNA amount was found between lines of Triticeae diploid species collected from different habitats or between different morphs. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various diploid species. Within the genus Aegilops, the 1C DNA amount ranged from 4.84 pg in A. caudata to 7.52 pg in A. sharonensis; among genera, the 1C DNA amount ranged from 4.18 pg in Heteranthelium piliferum to 9.45 pg in Secale montanum. No evidence was found for a smaller genome size in annual, self-pollinating species relative to perennial, cross-pollinating ones. Diploids that grow in the southern part of the group's distribution have larger genomes than those growing in other parts of the distribution. The contrast between the low variation at the intraspecific level and the high variation at the interspecific one suggests that changes in genome size originated in close temporal proximity to the speciation event, i.e., before, during, or immediately after it. The possible effects of sudden changes in genome size on speciation processes are discussed.

National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research

BACKGROUND

Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need.

METHODS

The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid (caBIG, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software.

RESULT

The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews.

CONCLUSION

The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers.

Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the generaAegilopsandTriticum

Recent molecular studies in the genera Aegilops and Triticum showed that allopolyploidization (interspecific or intergeneric hybridization followed by chromosome doubling) generated rapid elimination of low-copy or high-copy, non-coding and coding DNA sequences. The aims of this work were to determine the amount of nuclear DNA in allopolyploid species of the group and to see to what extent elimination of DNA sequences affected genome size. Nuclear DNA amount was determined by the flow cytometry method in 27 natural allopolyploid species (most of which were represented by several lines and each line by several plants) as well as 14 newly synthesized allopolyploids (each represented by several plants) and their parental plants. Very small intraspecific variation in DNA amount was found between lines of allopolyploid species collected from different habitats or between wild and domesticated forms of allopolyploid wheat. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various allopolyploid species, at both the tetraploid and hexaploid levels. In most allopolyploids nuclear DNA amount was significantly less than the sum of DNA amounts of the parental species. Newly synthesized allopolyploids exhibited a similar decrease in nuclear DNA amount in the first generation, indicating that genome downsizing occurs during and (or) immediately after the formation of the allopolyploids and that there are no further changes in genome size during the life of the allopolyploids. Phylogenetic considerations of the origin of the B genome of allopolyploid wheat, based on nuclear DNA amount, are discussed.

Immunohistochemical method identifies lymphovascular invasion in a majority of oral squamous cell carcinomas and discriminates between blood and lymphatic vessel invasion

Tumor invasion into blood and/or lymphatic channels is an important component of cancer staging and prognosis. Standard pathological methods do not provide sufficient contrast to discriminate between invasion into each type of vessel and are complicated by tissue retraction artifacts. We evaluated the ability of a triple-stain immunohistochemical method, combining cytokeratin, CD34, and podoplanin stains in a single section, to distinguish blood from lymphatic vascular invasion in oral squamous cell carcinoma and confirmed its results using multispectral analysis. The triple-stain method was significantly more sensitive in detecting invasive events than the standard hematoxylin and eosin staining method and easily discriminated between blood and lymphatic vessel invasion. Invasive events were present in blood and/or lymphatic vessels in the majority of patients with and without presentation of lymph node metastasis, indicating that vessel invasion in this cancer model is common and is not a rate-limiting step for lymph node metastasis.

Lymphatic invasion revealed by multispectral imaging is common in primary melanomas and associates with prognosis

Lymphatic invasion by tumor cells has been noted infrequently in primary melanomas. Our primary hypotheses were that using immunohistochemical markers of lymphatic vessels and of tumor cells would improve detection of lymphatic invasion and that lymphatic invasion would correlate with regional nodal metastatic disease. This study included 106 patients who were diagnosed between 1972 and 1991 and who had 10 years or more of follow-up. We performed dual immunohistochemical stains for podoplanin (for lymphatic vessels) and S-100 (for melanoma cells). Lymphatic invasion was identified by light microscopy and confirmed by multispectral imaging analysis. Lymphatic invasion was detected by morphology alone in 5 cases (4.7%) in contrast to immunohistochemical staining augmented by multispectral imaging analysis where 35 cases (33%) were identified (P < .0001). Lymphatic invasion was significantly associated with time to regional nodal metastatic disease, as well as first metastasis and melanoma-specific death. "Local metastasis," defined by immunohistochemistry-detected lymphatic invasion, satellites, or neural invasion, identified 64% of those who had regional nodal metastatic disease within 5 years of diagnosis. Lymphatic invasion is an underobserved phenomenon in primary melanomas that can be better detected by immunohistochemical staining. The presence of lymphatic invasion may be a clinically useful predictor of regionally metastatic disease.

Detecting prostatic adenocarcinoma from digitized histology using a multi-scale hierarchical classification approach

In this paper we present a computer-aided diagnosis (CAD) system to automatically detect prostatic adenocarcinoma from high resolution digital histopathological slides. This is especially desirable considering the large number of tissue slides that are currently analyzed manually - a laborious and time-consuming task. Our methodology is novel in that texture-based classification is performed using a hierarchical classifier within a multi-scale framework. Pyramidal decomposition is used to reduce an image into its constituent scales. The cascaded image analysis across multiple scales is similar to the manner in which pathologists analyze histopathology. Nearly 600 different image texture features at multiple orientations are extracted at every pixel at each image scale. At each image scale the classifier only analyzes those image pixels that have been determined to be tumor at the preceding lower scale. Results of quantitative evaluation on 20 patient studies indicate (1) an overall accuracy of over 90% and (2) an approximate 8-fold savings in terms of computational time. Both the AdaBoost and Decision Tree classifiers were considered and in both cases tumor detection sensitivity was found to be relatively constant across different scales. Detection specificity was however found to increase at higher scales reflecting the availability of additional discriminatory information.

Primary sinonasal undifferentiated carcinoma presenting with bilateral retrobulbar optic neuropathy

A 43-year-old man presented with acute bilateral visual loss. Ophthalmologic examination revealed no light perception in the right eye and a visual acuity of 20/50 in the left eye with a right afferent pupillary defect. Ophthalmoscopic examination was normal. Brain MRI showed an intracranial but extra-axial mass in the floor of the anterior cranial fossa extending along the olfactory groove and into the sinonasal vault. Endoscopic biopsy showed a high-grade neoplasm consistent with sinonasal undifferentiated carcinoma. This case report highlights an unusual clinical presentation for this rare and aggressive neoplasm.

Registering histologic and MR images of prostate for image-based cancer detection

RATIONALE AND OBJECTIVES

Needle biopsy is currently the only way to confirm prostate cancer. To increase prostate cancer diagnostic rate, needles are expected to be deployed at suspicious cancer locations. High-contrast magnetic resonance (MR) imaging provides a powerful tool for detecting suspicious cancerous tissues. To do this, MR appearances of cancerous tissue should be characterized and learned from a sufficient number of prostate MR images with known cancer information. However, ground-truth cancer information is only available in histologic images. Therefore it is necessary to warp ground-truth cancerous regions in histological images to MR images by a registration procedure. The objective of this article is to develop a registration technique for aligning histological and MR images of the same prostate.

MATERIAL AND METHODS

Five pairs of histological and T2-weighted MR images of radical prostatectomy specimens are collected. For each pair, registration is guided by two sets of correspondences that can be reliably established on prostate boundaries and internal salient bloblike structures of histologic and MR images.

RESULTS

Our developed registration method can accurately register histologic and MR images. It yields results comparable to manual registration, in terms of landmark distance and volume overlap. It also outperforms both affine registration and boundary-guided registration methods.

CONCLUSIONS

We have developed a novel method for deformable registration of histologic and MR images of the same prostate. Besides the collection of ground-truth cancer information in MR images, the method has other potential applications. An automatic, accurate registration of histologic and MR images actually builds a bridge between in vivo anatomical information and ex vivo pathologic information, which is valuable for various clinical studies.

Detection of agriculturally important QTLs in chickens and analysis of the factors affecting genotyping strategy

Three single cross populations were generated in order to analyze factors affecting the ability to detect true linkage with minimum false positive or false negative associations, and to detect associations between markers and quantitative traits. The three populations are: (1) a broiler x broiler cross of a single sire and 34 dams, resulting in 266 progeny; (2) a broiler x broiler cross of a single sire and 41 dams resulting in 360 progeny; and (3) a broiler x layer cross of a single sire with 56 dams resulting in 1180 progeny. Based on these three resource populations we show that: a) gradient selective genotyping was more effective than the random selective genotyping; b) selective genotyping was significant at a selected proportion less than 62% of the cumulative truncation point; c) as few as 10% of selected individuals (5% of each of the two tails) were sufficient to show significant association between markers and phenotypes; d) a gradient slices approach was more powerful than using replicates of the extreme groups; and e) in resource populations resulting from crosses between lines of different backgrounds, most of the microsatellite markers used are polymorphic. We also used simulation to test factors affecting power to detect true associations between markers and traits that are hard to detect in experimental resource populations. Using defined populations in the simulation, we concluded that the following guidelines provide reliable detection of linked QTLs: 1) the resource population size should be larger than 100; 2) a QTL effect larger than 0.4 SD is detectable with a reasonable number of markers (>100) and resource population size (>200 subjects); 3) the DNA pool from each tail of the trait distribution should contain at least 10% of the resource family; 4) each of the two DNA pools should include more than 35 individuals. Some of these guidelines that were deduced from the simulation analysis have been confirmed in the experimental part of this study.

Predictors of depressive symptoms in primary caregivers of young children with or at risk for developmental delay

BACKGROUND

Despite extensive research with families raising children with or at risk for developmental delay (DD), it is not clear whether primary caregivers of these children are at increased risk for depressive symptoms. Discrepant findings in the literature may be owing to heterogeneity of child problems. More research is needed on child, parent and family variables that may increase risk for, or resilience to, caregiver depressive symptoms. Some studies have found that parental resources (e.g. social support and coping strategies) may buffer the effects of parental distress, while other studies have highlighted the role of parental self-efficacy.

METHODS

We examined Beck Depression Inventory (BDI) scores in 178 primary caregivers (mainly biological mothers) who had 2-year-old children with or at risk for DD owing to: (a) low birthweight, prematurity or multiple birth (n = 58), (b) other known reasons (e.g. Down syndrome, spina bifida) (n = 67), or (c) unknown reasons (n = 69).

RESULTS

We found that 20% (n = 35) of the caregivers scored above the BDI clinical cut-off for depression. Analysis of variance revealed that caregivers with elevated BDI scores had higher child behaviour problem and escape-avoidance coping scores, and lower social support and parent self-efficacy, compared with caregivers without depressive symptoms. Caregivers with children who had DD for unknown reasons had higher BDI scores than caregivers of the other two groups of children. Regression analyses showed that child behaviour problems, escape-avoidance coping strategies and social support predicted caregiver BDI scores, but caregiver self-efficacy only did so when entered independently of social support. Only social support mediated and (marginally) moderated the relationship between child behaviour problems and caregiver depressive symptoms.

CONCLUSIONS

These findings suggest that early intervention programmes should carefully consider the interaction of child characteristics (e.g. Diagnosis and behaviour problems), caregiver resources (e.g. coping strategies and social support), and parental mental health and mood when planning and tailoring services for families of children with or at risk for DD.

Clinical validation of breast cancer biomarkers using tissue microarray technology

The results of previous studies done in our laboratory on breast cancer gene expression profile, using DNA microarrays, led to the discovery of several genes associated with breast cancer progression. Further evaluation of these genes and their involvement at various stages of cancer progression required performance of immunohistochemistry on thousands of different tissue blocks. Tissue microarray (TMA) technology facilitates rapid translation of DNA microarrays results to clinical specimens by using immunohistochemical analysis of protein expression. DNA microarray analysis done in our laboratory showed a significantly higher expression of prostatic-specific antigen (PSA) in invasive ductal carcinomas as compared to ductal carcinoma in situ, a finding contrary to the previously published data for PSA immunoreactivity in breast carcinomas. To find out whether TMA strategy could be used to explore the expression of the candidate genes involved in the breast cancer progression, we constructed a breast cancer progression TMA. It consisted of 2 normal ductal epithelium, 8 ductal carcinoma in situ, 19 invasive ductal carcinomas, and 3 metastatic ductal carcinomas of breast in triplets. Two prostatic adenocarcinomas and 2 normal colons were used as positive and negative controls, respectively. We first used well-documented and well-tested markers, such as antibodies to estrogen receptor, progesterone receptor, and p53. Results of these 3 antibodies were according to the previously published data. To validate our result, we then used antibody to PSA and looked for the expression of this protein on breast cancer progression TMA. Except for the 2 positive controls all 98 cores were found to be negative for PSA expression highlighting the importance of validation studies for DNA microarray results.

A case of respiratory epithelial adenomatoid hamartoma

We report a case of a 70-year-old man diagnosed with a respiratory epithelial adenomatoid hamartoma (REAH) of the nasal cavity after a past sinus surgery and associated with nasal polyposis. REAH is a recently described pathologic entity that can present with nasal obstruction, congestion, rhinorrhea, epistaxis, hyposmia, and headaches. It is a rare lesion of nasal and paranasal sinuses, but should be considered in the differential diagnosis because it is a benign lesion and complete surgical resection is curative.

Distribution of dendritic cell subtypes in primary oral squamous cell carcinoma is inconsistent with a functional response

Dendritic cell (DC) function will likely be important for immunological cancer therapies, but our knowledge of the roles of DCs in tumors is limited, in part because most studies were performed before DC subtypes were defined. We studied the distributions of immature epidermal, immature dermal, mature, and plasmacytoid DCs in 63 primary tumors and eight lymph node metastases from oral squamous cell carcinoma patients without evidence of distant metastasis. Immature CD207/Langerin+ and CD209/DC-SIGN+ DCs were present in the primary tumor region, but CD209/DC-SIGN+ cells rarely infiltrated the tumor. Mature DCs were rare, and presence of CD123+ plasmacytoid DCs was associated with poorer outcome. Unexpectedly, migration and maturation of DCs was associated with a worse outcome. Overall, the distribution of DC subtypes indicated that ineffective DC response to tumor is a failure of DC function rather than recruitment, suggesting that a strategy of shifting the balance of secreted factors in the tumor milieu may be more effective in restoring anti-tumor immune function than current methods restoring only one population of DCs to the immunosuppressive tumor region.

Spatio-temporal genetic variation in populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, as revealed by AFLP analysis

Genetic structure of natural populations of wild crop relatives has been the subject of many studies. Yet, most of them focused on the assessment of spatial genetic diversity, while information on long-term variation, affected by yearly changes, has been considered only in few cases. The present study aimed therefore, to estimate the spatio-temporal genetic variation in populations of wild emmer wheat, the progenitor of domesticated wheat, and to assess the contribution of spatial versus temporal factors to the maintenance of genetic variation in a population. Single spikes were collected in the years 1988 and 2002 from plants that grew in the same sampling points, from six different habitats in the Ammiad conservation site, Eastern Galilee, Israel. Seeds were planted in a nursery and DNA was extracted from each plant and analyzed by the AFLP method. Fourteen primer combinations yielded 1,545 bands of which 50.0 and 48.8% were polymorphic in the years 1988 and 2002, respectively. Genetic diversity was much larger within populations than between populations and the temporal genetic diversity was considerably smaller than the spatial one. Nevertheless, population genetic structure may vary to some degree in different years, mainly due to fluctuations in population size because of yearly rainfall variations. This may lead to predominance of different genotypes in different years. Clustering the plants by their genetic distances grouped them according to their habitats, indicating the existence of genotype-environment affinities. The significance of the results in relation to factors affecting the maintenance of polymorphism in natural populations is discussed.

Registering histological and MR images of prostate for image-based cancer detection

This paper presents a deformable registration method to co-register histological images with MR images of the same prostate. By considering various distortion and cutting artifacts in histological images and also fundamentally different nature of histological and MR images, our registration method is thus guided by two types of landmark points that can be reliably detected in both histological and MR images, i.e., prostate boundary points, and internal salient points that can be identified by a scale-space analysis method. The similarity between these automatically detected landmarks in histological and MR images are defined by geometric features and normalized mutual information, respectively. By optimizing a function, which integrates the similarities between landmarks with spatial constraints, the correspondences between the landmarks as well as the deformable transformation between histological and MR images can be simultaneously obtained. The performance of our proposed registration algorithm has been evaluated by various designed experiments. This work is part of a larger effort to develop statistical atlases of prostate cancer using both imaging and histological information, and to use these atlases for optimal biopsy and therapy planning.

An animal model for the study of topical medications in sinusitis

BACKGROUND

Rhinosinusitis after functional endoscopic sinus surgery often is recalcitrant to conventional medical management. Topical therapies have been popularized as a method to deliver powerful medications to diseased mucosa while limiting systemic toxicity. The aim of this study was to develop an animal model that will provide objective data in studying the efficacy of topical medications and establish a platform for translation to human clinical trials.

METHODS

The maxillary sinus ostium of white rabbits was obstructed with a pledget through an antrostomy created in the anterior face of the maxilla. The sinus was inoculated with Pseudomonas aeruginosa (PAO1) and 7 days later the antrostomy was reopened, the ostial obstruction was removed, and a single lumen catheter was placed. Normal saline was irrigated through the catheter for 7 days in one group of rabbits while a control group received no irrigation. At the end of 7 days, the rabbits were euthanized, analyzed under light microscopy, and bacterial counts of the nasal lavage were determined.

RESULTS

Sinusitis was confirmed in all rabbits 7 days after inoculation. Purulence, mucosal, and underlying bony inflammation persisted in both the control and the saline irrigation groups at study end. Nasal lavage bacterial counts were persistently elevated throughout the study period, indicative of bacterial viability.

CONCLUSION

An animal model has been created for the study of topical medications in sinusitis. A novel catheter delivery system within an unoccluded maxillary sinus is described that will aid in efficacy studies of topical medications in the management of recalcitrant rhinosinusitis.

Detection of THCA in oral fluid by GC-MS-MS

A major marijuana metabolite, 11-nor-9-carboxy-tetrahydrocannabinol (THCA), has been identified in oral fluids from donors that previously tested positive for Delta(9)-tetrahydrocannabinol (THC). The method consisted of solid-phase extraction of the oral fluid samples followed by gas chromatography-tandem mass spectrometry analysis of the extracts. Testing for THCA was performed on 223 oral fluid samples previously analyzed for THC. The THCA assay was linear from 10 to 240 pg/mL. The mean recovery of spiked THCA in oral fluid was 104%, and precision was 4% at 20 pg/mL using fortified negative samples. This method was rugged and robust, providing detection and quantification of THCA in oral fluids at levels not previously reported. Results of this study showed that THCA was detectable in 21 of 26 oral fluid samples previously reported positive for THC. The range of concentrations from these samples was from 10 pg/mL up to 142 pg/mL THCA.

Tumor necrosis factor-alpha damages tumor blood vessel integrity by targeting VE-cadherin

BACKGROUND

Isolated limb perfusion using high-dose human tumor necrosis factor-alpha with melphalan is effective therapy for bulky extremity in-transit melanoma and sarcoma.

OBJECTIVE

While it is widely accepted that melphalan is a DNA alkylating agent, the mechanism of selective antitumor effect of tumor necrosis factor-alpha is unclear.

METHODS AND RESULTS

Electron microscopic analyses of human melanoma biopsies, pre- and post-melphalan perfusion, showed that the addition of tumor necrosis factor-alpha caused gapping between endothelial cells by 3 to 6 hours post-treatment followed by vascular erythrostasis in treated tumors. In human melanoma xenografts raised in mice, tumor necrosis factor-alpha selectively increased tumor vascular permeability by 3 hours and decreased tumor blood flow by 6 hours post-treatment relative to treated normal tissue. In an in vitro tumor endothelial cell model, tumor necrosis factor-alpha caused vascular endothelial adherens junction protein, VE-cadherin, to relocalize within the cell membrane away from cell-cell junctions leading to gapping between endothelial cells by 3 to 6 hours post-treatment. Phosphotyrosinylation was a prerequisite for movement of VE-cadherin away from endothelial cell junctions and for gapping between endothelial cells. Clinical isolated limb perfusion tumor specimens, at 3 hours postperfusion, showed a discontinuous and irregular pattern of VE-cadherin expression at endothelial cell junctions when compared with normal (skin) or pretreatment tumor tissue.

CONCLUSIONS

Together, the data suggest that tumor necrosis factor-alpha selectively damages the integrity of tumor vasculature by disrupting VE-cadherin complexes at vascular endothelial cell junctions leading to gapping between endothelial cells, causing increased vascular leak and erythrostasis in tumors. VE-cadherin appears to be a potentially good target for selective antitumor therapy.

The incidence of concurrent osteitis in patients with chronic rhinosinusitis: a clinicopathological study

BACKGROUND

The pathogenesis of chronic rhinosinusitis (CRS) has been found to be multifactorial, with environmental, general host, and local anatomic factors all contributing to its development. Recent studies have indicated that local osteitis of the underlying bone also may play a critical role in the elaboration of CRS by inducing persistent inflammatory changes in the surrounding mucosa. The purpose of this study was to determine the clinical incidence rate of osteitis in patients with CRS undergoing functional endoscopic sinus surgery.

METHODS

From January to July 2003, a prospective study was performed on 121 patients undergoing functional endoscopic sinus surgery for CRS. Age, number of previous surgeries, radiographic bony characteristics, and pathological findings were all documented. The presence of concurrent osteitis was assessed using both radiographic (neoosteogenesis) and pathological (bony remodeling) criteria.

RESULTS

The mean age of the patients was 44.3 years. Fifty-eight percent of the cases were revision surgeries, with each patient having an average of 2.2 operative procedures in the past. Computed tomography (CT) showed neoosteogenesis in 36% of patients, and 53% showed pathological evidence of osteitis on histological analysis of surgical specimens.

CONCLUSION

Concurrent osteitis can be found in 36-53% of patients with CRS, using both radiographic and pathological criteria, respectively. Although a causal relationship between osteitis and CRS can not be inferred from this data, these clinical findings correlate well with previous evidence of bone involvement in CRS found in animal models, further reaffirming the association between underlying osteitis and the pathogenesis of CRS.

Disposition of Hydrocodone in Hair

The use of prescription drugs, including synthetic opiates, is increasing in the U.S., with emergency room reports showing a dramatic rise in prescription opiate abuse. As part of an ongoing study, the hair of admitted opiate users was analyzed for hydrocodone and hydromorphone, as well as codeine, morphine, and 6-acetylmorphine in order to determine if there was any correlation between self-reported frequency of opiate intake and the concentration of drug detected in hair. The hairs were confirmed using gas chromatography-mass spectrometry following screening by enzyme linked immunosorbent assay (ELISA). Twenty-four hair specimens collected from volunteers showed the presence of hydrocodone (130-15,933 pg/mg); four of those also contained hydromorphone (59-504 pg/mg). The specimens were also analyzed for morphine, codeine, and 6-acetylmorphine. Hair specimens from five self-reported codeine users showed concentrations of hydrocodone between 592 and 15,933 pg/mg. In addition, codeine was present at concentrations of 575-20,543 pg/mg, but neither morphine nor hydromorphone were present in any of those hair specimens. Though the analysis of some opiates in hair has been previously published, this is the first study where the hydrocodone and hydromorphone concentrations have been measured following self-reported opiate intake.

Genome-Wide Profiling of Oral Squamous Cell Carcinoma by Array-Based Comparative Genomic Hybridization

OBJECTIVES

Array-based comparative genomic hybridization (aCGH) was used to develop a genome-wide molecular profile of oral squamous cell carcinoma (OSCC). Copy number alterations (CNAs) were identified by chromosomal region, mapped to specific genes, and compared with several previously documented CNAs associated with head and neck squamous cell carcinoma (HNSCC). The status of 512 commonly altered cancer genes was assessed and evaluated as potential correlates of tumor behavior.

METHODS

Tumor tissue DNA was isolated for aCGH from 21 prospectively collected fresh-frozen OSCC specimens. aCGH was performed at 0.9-Mb resolution to identify distinct regions of genomic alteration and their associated genes. Cancer genes commonly altered were then correlated with clinicopathologic tumor data.

RESULTS

Genomic regions most frequently amplified (>35%) were located on 3q, 5p, 8q, 9q, and 20q, although regions most frequently deleted (>40%) involved chromosomes 3p, 8p, 13q, and 18q. Minimal regions of CNA identified, by aCGH narrowed larger, previously documented CNAs associated with HNSCC to significantly smaller regions, yielding shorter lists of candidate genes. Cancer-related genes altered in greater than 25% OSCC samples were identified (22 amplified, 17 deleted). Several genes associated with the Fanconi anemia DNA-damage response pathway were frequently altered, including BRCA1, BRCA2, FANCD2, and FANCG. Other cancer-related genes linked to hereditary cancer syndromes include VHL, MLH1, XPC, and RB1.

CONCLUSIONS

Genome-wide aCGH can be used to detect and map CNAs in OSCC tissue specimens with high resolution. These data implicate several candidate genes and gene pathways in the tumorigenesis of sporadic OSCC.

Molecular investigation and long-term clinical progress in Greek Cypriot families with recessive distal renal tubular acidosis and sensorineural deafness due to mutations in the ATP6V1B1 gene

The spectrum of distal renal tubular acidosis (dRTA) includes a genetically heterogeneous group of inherited conditions of both autosomal-dominant and recessive mode of inheritance. The basic defect is linked to the renal part of acid-base homeostasis, which is partly achieved by the regulated luminal secretion of H+ at the apical surface of the alpha-intercalated cells of renal collecting ducts. This is coupled to bicarbonate reabsorption with chloride counter transport across the basolateral membranes. Here, we describe the molecular findings of the first two Greek Cypriot families with recessive dRTA and the long-term clinical findings in four of five affected members. DNA linkage analysis with four polymorphic markers flanking the ATP6V1B1 gene on chromosome 2 gave evidence for positive linkage; direct DNA analysis by automated DNA sequencing revealed that patients in one family were homozygous for mutation 229+1G>T (IVS7+1G>T) and that patients in the second family were compound heterozygous for 229+1G>T and R157C. The mutations were found on four different haplotypes. Both the mutations were previously reported in patients of Turkish origin. Three known polymorphic variants were also identified. The five patients demonstrated the whole clinical spectrum of the disease including death in infancy, failure to thrive, rickets, nephrocalcinosis, nephrolithiasis, and episodes of hypokalemic paralysis. Some of the family members are now in their mid 30s and late 20s, and nephrolithiasis with recurrent renal colics is their main problem. Renal function has remained normal. In conclusion, early diagnosis in infancy and prompt treatment with alkali and potassium supplements is of great benefit to the patient with dRTA and ensures normal growth. The identification of responsible mutations facilitates antenatal or postnatal diagnosis in concerned families and improves the prognosis.

A boosting cascade for automated detection of prostate cancer from digitized histology

Current diagnosis of prostatic adenocarcinoma is done by manual analysis of biopsy tissue samples for tumor presence. However, the recent advent of whole slide digital scanners has made histopathological tissue specimens amenable to computer-aided diagnosis (CAD). In this paper, we present a CAD system to assist pathologists by automatically detecting prostate cancer from digitized images of prostate histological specimens. Automated diagnosis on very large high resolution images is done via a multi-resolution scheme similar to the manner in which a pathologist isolates regions of interest on a glass slide. Nearly 600 image texture features are extracted and used to perform pixel-wise Bayesian classification at each image scale to obtain corresponding likelihood scenes. Starting at the lowest scale, we apply the AdaBoost algorithm to combine the most discriminating features, and we analyze only pixels with a high combined probability of malignancy at subsequent higher scales. The system was evaluated on 22 studies by comparing the CAD result to a pathologist's manual segmentation of cancer (which served as ground truth) and found to have an overall accuracy of 88%. Our results show that (1) CAD detection sensitivity remains consistently high across image scales while CAD specificity increases with higher scales, (2) the method is robust to choice of training samples, and (3) the multi-scale cascaded approach results in significant savings in computational time.

Allopolyploidy--a shaping force in the evolution of wheat genomes

Recent studies have shown that allopolyploidy accelerates genome evolution in wheat in two ways: (1) allopolyploidization triggers rapid genome changes (revolutionary changes) through the instantaneous generation of a variety of cardinal genetic and epigenetic alterations, and (2) the allopolyploid condition facilitates sporadic genomic changes during the life of the species (evolutionary changes) that are not attainable at the diploid level. The revolutionary changes comprise (1) non-random elimination of coding and non-coding DNA sequences, (2) epigenetic changes such as DNA methylation of coding and non-coding DNA leading, among others, to gene silencing, (3) activation of genes and retroelements which in turn alters the expression of adjacent genes. These highly reproducible changes occur in the F1 hybrids or in the first generation(s) of the nascent allopolyploids and were similar to those that occurred twice in nature: first in the formation of allotetraploid wheat (approximately 0.5 million years ago) and second in the formation of hexaploid wheat (approximately 10,000 years ago). Elimination of non-coding sequences from one of the two homoeologous pairs in tetraploids and from two homoeologous pairs in hexaploids, augments the differentiation of homoeologous chromosomes at the polyploid level, thus providing the physical basis for the diploid-like meiotic behavior of allopolyploid wheat. Regulation of gene expression may lead to improved inter-genomic interactions. Gene inactivation brings about rapid diploidization while activation of genes through demethylation or through transcriptional activation of retroelements altering the expression of adjacent genes, leads to novel expression patterns. The evolutionary changes comprise (1) horizontal inter-genomic transfer of chromosome segments between the constituent genomes, (2) production of recombinant genomes through hybridization and introgression between different allopolyploid species or, more seldom, between allopolyploids and diploids, and (3) mutations. These phenomena, emphasizing the plasticity of the genome with regards to both structure and function, might improve the adaptability of the newly formed allopolyploids and facilitate their rapid and successful establishment in nature.

Analysis of outcome of laparoscopic splenectomy for idiopathic thrombocytopenic purpura by platelet count

Laparoscopic splenectomy (LS) is now performed routinely in patients with idiopathic thrombocytopenic purpura (ITP) refractory to the medical treatment. Low preoperative platelet count was deemed to be a contraindication for a laparoscopic approach; however, there is no data reporting the outcome in those patients. We aimed to evaluate the influence of the preoperative platelet count on the operative and postoperative course and complication rate. Retrospective cohort study that was conducted in tertiary care university-affiliated medical center and included 110 consecutive patients who underwent LS. All patients were divided into three groups by their preoperative platelet counts: <or=20 x 10(9)/L (n = 12), (20-50) x 10(9)/L (n = 18), and >50 x 10(9)/L (n = 80). The outcome and the influence of preoperative factors predictive of complications, blood transfusion, and length of stay were compared between the groups. Patients with a platelet count of <or=20 x 10(9)/L had a much longer hospital stay, received more blood transfusions, and suffered more complications than patients with platelet counts of (20-50) x 10(9)/L or higher (P < 0.05). Transfused patients had a longer hospital stay than non-transfused patients (2.08 vs. 6.4 days, P = 0.029). The strongest predictor for transfusion was the platelet count (odds ratio = 23, P = 0.008). LS in patients with very low platelet counts is feasible and reasonably safe, but the platelet count is a major determinant of morbidity. Every effort should be made to elevate platelet levels to >20 x 10(9)/L before surgery. Patients with counts >20 x 10(9)/L can safely undergo LS.