Accurate genome-wide phasing from IBD data

As genotype databases increase in size, so too do the number of detectable segments of identity by descent (IBD): segments of the genome where two individuals share an identical copy of one of their two parental haplotypes, due to shared ancestry. We show that given a large enough genotype database, these segments of IBD collectively overlap entire chromosomes, including instances of IBD that span multiple chromosomes, and can be used to accurately separate the alleles inherited from each parent across the entire genome. The resulting phase is not an improvement over state-of-the-art local phasing methods, but provides accurate long-range phasing that indicates which of two haplotypes in different regions of the genome, including different chromosomes, was inherited from the same parent. We are able to separate the DNA inherited from each parent completely, across the entire genome, with 98% median accuracy in a test set of 30,000 individuals. We estimate the IBD data requirements for accurate genome-wide phasing, and we propose a method for estimating confidence in the resulting phase. We show that our methods do not require the genotypes of close family, and that they are robust to genotype errors and missing data. In fact, our method can impute missing data accurately and correct genotype errors.

Ancestry inference using reference labeled clusters of haplotypes

BACKGROUND

We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual's ancestry composition. Our approach works by modeling haplotype diversity from a large, admixed cohort of hundreds of thousands, then annotating those models with population information from reference panels of known ancestry.

RESULTS

The running time of ARCHes does not depend on the size of a reference panel because training and testing are separate processes, and the inferred population-annotated haplotype models can be written to disk and reused to label large test sets in parallel (in our experiments, it averages less than one minute to assign ancestry from 32 populations using 10 CPU). We test ARCHes on public data from the 1000 Genomes Project and the Human Genome Diversity Project (HGDP) as well as simulated examples of known admixture.

CONCLUSIONS

Our results demonstrate that ARCHes outperforms RFMix at correctly assigning both global and local ancestry at finer population scales regardless of the amount of population admixture.

Clustering of 770,000 genomes reveals post-colonial population structure of North America

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

CSAX: Characterizing Systematic Anomalies in eXpression Data

Methods for translating gene expression signatures into clinically relevant information have typically relied upon having many samples from patients with similar molecular phenotypes. Here, we address the question of what can be done when it is relatively easy to obtain healthy patient samples, but when abnormalities corresponding to disease states may be rare and one-of-a-kind. The associated computational challenge, anomaly detection, is a well-studied machine-learning problem. However, due to the dimensionality and variability of expression data, existing methods based on feature space analysis or individual anomalously expressed genes are insufficient. We present a novel approach, CSAX, that identifies pathways in an individual sample in which the normal expression relationships are disrupted. To evaluate our approach, we have compiled and released a compendium of public expression data sets, reformulated to create a test bed for anomaly detection. We demonstrate the accuracy of CSAX on the data sets in our compendium, compare it to other leading methods, and show that CSAX aids in both identifying anomalies and explaining their underlying biology. We describe an approach to characterizing the difficulty of specific expression anomaly detection tasks. We then illustrate CSAX's value in two developmental case studies. Confirming prior hypotheses, CSAX highlights disruption of platelet activation pathways in a neonate with retinopathy of prematurity and identifies, for the first time, dysregulated oxidative stress response in second trimester amniotic fluid of fetuses with obese mothers. Our approach provides an important step toward identification of individual disease patterns in the era of precision medicine.

Finding novel molecular connections between developmental processes and disease

Identifying molecular connections between developmental processes and disease can lead to new hypotheses about health risks at all stages of life. Here we introduce a new approach to identifying significant connections between gene sets and disease genes, and apply it to several gene sets related to human development. To overcome the limits of incomplete and imperfect information linking genes to disease, we pool genes within disease subtrees in the MeSH taxonomy, and we demonstrate that such pooling improves the power and accuracy of our approach. Significance is assessed through permutation. We created a web-based visualization tool to facilitate multi-scale exploration of this large collection of significant connections (http://gda.cs.tufts.edu/development). High-level analysis of the results reveals expected connections between tissue-specific developmental processes and diseases linked to those tissues, and widespread connections to developmental disorders and cancers. Yet interesting new hypotheses may be derived from examining the unexpected connections. We highlight and discuss the implications of three such connections, linking dementia with bone development, polycystic ovary syndrome with cardiovascular development, and retinopathy of prematurity with lung development. Our results provide additional evidence that plays a key role in the early pathogenesis of polycystic ovary syndrome. Our evidence also suggests that the VEGF pathway and downstream NFKB signaling may explain the complex relationship between bronchopulmonary dysplasia and retinopathy of prematurity, and may form a bridge between two currently-competing hypotheses about the molecular origins of bronchopulmonary dysplasia. Further data exploration and similar queries about other gene sets may generate a variety of new information about the molecular relationships between additional diseases.

Understanding the roles that genes involved in normal human development can play in disease processes is an important part of predicting disease risk and designing novel treatment approaches. In this study, we have identified classes of disease that are associated with a surprisingly large number of genes involved in any of several tissue-specific developmental processes. To do so, we developed a novel approach whose strength comes from pooling genetic information across related diseases, overcoming problems ordinarily posed by limited information about individual gene-disease relationships. We demonstrate the method's efficacy both by examining its ability to highlight connections between gene sets and disease classes that are known to be related, and by demonstrating that the approach recovers expected broad classes of connections, such as those between heart development and cardiovascular disorders. However, by examining unexpected connections in this data set, we are able to develop new understanding of some surprising disease relationships, such as the one between dementia and osteoporosis. Such connections may lead to a better overall understanding of the role of development in lifelong health, as well as to the design of new methods to treat a range of diseases.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

BACKGROUND

Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them.

RESULTS

A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89% and the best AUC iP/R was 68%. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53%, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35%) the macro-averaged precision ranged between 50% and 80%, with a maximum F-Score of 55%.

CONCLUSIONS

The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows.

Identifying relevant data for a biological database: handcrafted rules versus machine learning

With well over 1,000 specialized biological databases in use today, the task of automatically identifying novel, relevant data for such databases is increasingly important. In this paper, we describe practical machine learning approaches for identifying MEDLINE documents and Swiss-Prot/TrEMBL protein records, for incorporation into a specialized biological database of transport proteins named TCDB. We show that both learning approaches outperform rules created by hand by a human expert. As one of the first case studies involving two different approaches to updating a deployed database, both the methods compared and the results will be of interest to curators of many specialized databases.

Anomaly Detection Using an Ensemble of Feature Models

We present a new approach to semi-supervised anomaly detection. Given a set of training examples believed to come from the same distribution or class, the task is to learn a model that will be able to distinguish examples in the future that do not belong to the same class. Traditional approaches typically compare the position of a new data point to the set of "normal" training data points in a chosen representation of the feature space. For some data sets, the normal data may not have discernible positions in feature space, but do have consistent relationships among some features that fail to appear in the anomalous examples. Our approach learns to predict the values of training set features from the values of other features. After we have formed an ensemble of predictors, we apply this ensemble to new data points. To combine the contribution of each predictor in our ensemble, we have developed a novel, information-theoretic anomaly measure that our experimental results show selects against noisy and irrelevant features. Our results on 47 data sets show that for most data sets, this approach significantly improves performance over current state-of-the-art feature space distance and density-based approaches.

The Transporter Classification Database: recent advances

The Transporter Classification Database (TCDB), freely accessible at http://www.tcdb.org, is a relational database containing sequence, structural, functional and evolutionary information about transport systems from a variety of living organisms, based on the International Union of Biochemistry and Molecular Biology-approved transporter classification (TC) system. It is a curated repository for factual information compiled largely from published references. It uses a functional/phylogenetic system of classification, and currently encompasses about 5000 representative transporters and putative transporters in more than 500 families. We here describe novel software designed to support and extend the usefulness of TCDB. Our recent efforts render it more user friendly, incorporate machine learning to input novel data in a semiautomatic fashion, and allow analyses that are more accurate and less time consuming. The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users.

Learning Hidden Markov Models for Regression using Path Aggregation

We consider the task of learning mappings from sequential data to real-valued responses. We present and evaluate an approach to learning a type of hidden Markov model (HMM) for regression. The learning process involves inferring the structure and parameters of a conventional HMM, while simultaneously learning a regression model that maps features that characterize paths through the model to continuous responses. Our results, in both synthetic and biological domains, demonstrate the value of jointly learning the two components of our approach.

Long pulse production of high current D(-) ion beams in the JT-60 negative ion source

The first long pulse production of high power D(-) ion beams has been demonstrated in the JT-60 U negative ion sources, each of which was designed to produce 22 A, 500 keV D(-) ion beams. Voltage holding capability and the grid power loading were examined for long pulse production of high power D(-) ion beams. From the correlation between voltage holding and the light intensity of cathodoluminescence from the Fiber Reinforced Plastic insulators, the acceleration voltage for stable voltage holding capability was found to be less than 320-340 kV where the light was sufficiently suppressed. By tuning the extraction voltage, the grid power loadings in the ion sources were decreased to the allowable levels for long pulse injection without a significant reduction of the beam power. After tuning the acceleration and extraction voltages, D(-) ion beams of 12.5 and 9.8 A were produced at 340 keV with cesium seeding at a rate of approximately 14 microg/s into the ion sources. The pulse duration of these D(-) ion beams was extended step by step, and then was successfully extended up to 18 s without degradation of the negative ion production. The D(-) ion beams were neutralized to yield 3.6 MW D(0) beams by a gas cell, and then injected into the JT-60 U plasma. Further, a slight reduction of D(-) ion beam power allowed the longer injection duration of 21 s at a D(0) beam power of 3.2 MW. The success in the long pulse production of a high power D(-) ion beam shows that negative ion beams can be produced during a few tens of seconds without degradations of negative ion production and the voltage holding in a large Cs-seeded negative ion source.

Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects

MOTIVATION

The process of transcription is controlled by systems of factors which bind in specific arrangements, called cis-regulatory modules (CRMs), in promoter regions. We present a discriminative learning algorithm which simultaneously learns the DNA binding site motifs as well as the logical structure and spatial aspects of CRMs.

RESULTS

Our results on yeast datasets show better predictive accuracy than a current state-of-the-art approach on the same datasets. Our results on yeast, fly and human datasets show that the inclusion of logical and spatial aspects improves the predictive accuracy of our learned models.

AVAILABILITY

Source code is available at http://www.cs.wisc.edu/~noto/crm

A specialized learner for inferring structured cis-regulatory modules

Background

The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis-regulatory modules (CRMs). We present an expressive and easily comprehensible CRM representation which is capable of capturing several aspects of a CRM's structure and distinguishing between DNA sequences which do or do not contain it. We also present a learning algorithm tailored for this domain, and a novel method to avoid overfitting by controlling the expressivity of the model.

Results

We are able to find statistically significant CRMs more often then a current state-of-the-art approach on the same data sets. We also show experimentally that each aspect of our expressive CRM model space makes a positive contribution to the learned models on yeast and fly data.

Conclusion

Structural aspects are an important part of CRMs, both in terms of interpreting them biologically and learning them accurately. Source code for our algorithm is available at:

Evaluation of MBR effluent characteristics for reuse purposes

One of the advantages of MBR is its excellent effluent quality, which is suitable for a wide range of reuse purposes. We investigated the characteristics of MBR effluent and evaluated them based on the Japanese guideline for the reuse of treated wastewater. As the result, MBR effluent showed qualitative coaracteristics that satisfy the requirement except chromaticity for recreational purpose. Further treatment, such as by oxone or activated carbon, will be required to remove the remaining color. MBR shows high removal efficiency of bacteria and other hazardous microorganisms such as Cryptosporidium. We investigated the removal efficiency of virus by MBR using coliphage as an alternative index. The results showed that high removal efficiency for coliphage could be obtained by MBR. The removal mechanism appears to be that coliphage are attached to the activated sludge and thus rejected by the membrane together with activated sludge particles. With regard to the endocrine disrupters, no significant differences were observed between MBR and CAS in the removal of main endocrine disrupters.

[A senile case of acute necrotizing myopathy presenting prolonged severe muscle paralysis due to high dose glucocorticoid and muscle relaxant]

An 82-year old man was admitted with dyspnea, productive cough and wheezing. In addition to antibiotics (meropenem trihydrate 0.5 g/day), glucocorticoids (hydrocortisone 1.250 mg, methylpredonisolone 4.250 mg) were administered for the severe bronchospasms. Since his respiratory condition deteriorated, he underwent mechanical ventilation using a muscle relaxant (vecuronium bromide, total dose 776 mg) in combination with high dose glucocorticoid. As his pneumonia improved on the 10th hospital day, we started weaning him from the ventilator. However, we were unable to complete weaning from the ventilator because of prolonged quadriplegia and paralysis of the respiratory muscles. A few days later, myoglobinuria appeared. Electrophysiological examinations suggested the involvement of both neuromuscular junctions and muscles. Muscle biopsy showed rhabdomyolysis. Acute necrotizing myopathy was diagnosed due to high doses of glucocorticoid, muscle relaxant, or both. He required about 3 months to be weaned from the mechanical ventilation, and another 3 months to leave the hospital. Based on our experience, we should consider acute myopathy as an adverse effect of glucocorticoids, muscle relaxants or both in elderly patients who require mechanical ventilation.

[Microscopic polyangitis with pleuritis as the only pulmonary complication]

A 75-year-old woman was admitted to our hospital because of high fever and appetite loss. A chest roentgenogram and computed tomographic scans revealed pleural effusion without obvious infitrative or interstitial shadows in both lung fields. Laboratory data showed microhematuria, proteinuria, and telescoped sediment with a moderate increase in C-reactive protein, suggestive of acute glomerulonephritis. Because infectious pleuritis, was initially suspected, the patient was treated with antibiotics. However, her general condition deteriorated, and the right pleural effusion increased. Levels of myeloperoxidase-specific anti-neutrophil cytoplasmic antibody (MPO-ANCA) in serum and pleural effusion were markedly elevated, yielding a conclusive diagnosis of MPO-ANCA-related vasculitis, especially microscopic polyangitis (MPA). The Patient was immediately treated treated with prednisolone, cyclophosphamide, and plasma exchange. Several weeks later, her general condition dramatically improved, and the level of MPO-ANCA in serum markedly decreased. In addition, the pleural effusion completely disappeared. Unfortunately, the patient eventually died of opportunistic infections (MRSA-pneumonia and Aspergillus-pneumonia) 6 months after admission. This was a unique case of MPA associated with pleuritis without interstitial pneumonia or alveolar hemorrhage.

[Determination of urinary CA19-9 levels in urothelial cancer--assessment of its role in diagnosis]

BACKGROUND

Although Carbohydrate antigen19-9 (CA19-9) is known to be high of its positive rate in blood in pancreatic cancer, etc., recently there have been scattered of cases of urothelial carcinoma in which elevated CA19-9 levels have been detected in both serum and urine. In this study we determined both urine and serum levels of CA19-9 in order to evaluate their diagnostic role of urinary CA19-9.

MATERIALS

A total 82 patients, i.e., 32 with bladder cancer, 4 with renal pelvic/ureteral cancer, 5 with renal cancer, 13 with prostatic cancer, 5 with other malignancies, 10 with prostatic hyperplasia, 6 with urolithiasis, 7 with other benign diseases, served as the subjects of this study.

METHODS

CA19-9 was determined by EIA method in first-morning urine and serum using a CA19-9 measurement kit (Centocor). Urinary values corrected for the creatinine level in the same sample have been used and are shown as U/mg creatinine (Cr). Urinary CA19-9 and urinary cytology were evaluated in some cases. An immunohistochemical study of CA19-9 for surgical specimens was conducted by the ABC method, using a Histo 19-9 kit (COMPAGNIE ORIS INDUSTRIES S.A.).

RESULTS

The cut-off value for serum levels was 37 U/ml, and urine levels were determined in U/mg Cr with a cut-off value of 100 U/mg Cr. The urinary CA19-9 levels was significantly higher (390.9 +/- 934.1 U/mg Cr) in urothelial cancer than in the control group (91.48 +/- 20.0 U/ mg Cr). In urothelial cancer, grade 1 and grade 2 cases were more sensitive than grade 3 cases and they also tended to be high level, although only 27.8% of urothelial cancer patients showed an elevation of serum CA19-9. CA19-9 was detected in all urothelial cancers which could be studied immunohistochemically. In 8 out of 16 superficial cancers CA19-9 was detected in more than 90% of cancer cells, though there were few CA19-9 positive cells in infiltrating cancers. Urinary CA19-9 was more sensitive than urinary cytology, especially in low grade cancers.

CONCLUSION

The determination of urinary CA19-9 may be a useful tumor marker of urothelial cancer, and especially in low grade cancer it may be useful in diagnosing of them because its urinary level is high and it is more sensitive than urinary cytology.

[Cardiac sarcoidosis with myopathy and advanced A-V nodal block in a woman with a previous diagnosis of sarcoidosis]

In 1992, a 49-year-old woman was admitted to the hospital because of exertional dyspnea. Three years earlier sarcoidosis had been diagnosed, and the patient was found to have bilateral hilar lymphadenopathy. The eye, skin, and knee joint were also involved. During the second hospital stay, atrial flutter with advanced A-V nodal block, scattered defects on a 201T1 scintigram, and marked cardiomegaly on chest roentgenogram led to the diagnosis of cardiac sarcoidosis. Signs and symptoms of cardiac failure subsided after placement of an artificial cardiac pacemaker, but the patient still complained of mild muscle weakness in the lower extremities on exertion. 67Ga scintigraphy revealed marked accumulation in the lower extremities, and muscle biopsy of the left gastrocnemius revealed numerous epithelioid cell granulomas with muscle fiber degeneration. Oral corticosteroid therapy was effective. A review of the 24 cases of sarcoid myopathy reported in Japan indicated that the male-to-female ratio is 1:3.8. As compared to patients in whom myopathy led to the diagnosis of sarcoidosis, those in whom myopathy developed after sarcoidosis was diagnosed were (1) relatively older, (2) more likely to have multiple organ involvement, and (3) more likely to have cardiac sarcoidosis. Corticosteroids were beneficial in about three quarters of these 16 cases, who received corticosteroid therapy.

Identification and functional characterization of mouse CD29 with a mAb

The beta 1 integrin subfamily, alternatively called very late activation antigen (VLA), has been implicated in various cellular functions. In this study, we generated a mAb against the mouse beta 1 subunit (CD29) to examine the functional property of mouse VLA proteins. After immunization with affinity-purified mouse VLA-4 (alpha 4 beta 1), a hamster mAb, HM beta 1-1, was established by screening mAb that reacted with alpha 4-negative neuroblastoma C1300. The antigen defined by HM beta 1-1 was widely distributed in various mouse cell lines and HM beta 1-1 immunoprecipitated a 110-120 kDa protein common to VLA-1 and VLA-6, indicating that HM beta 1-1 recognizes the beta 1 subunit of mouse integrins. We then examined the inhibitory effect of HM beta 1-1 on VLA-dependent cell adhesion and activation. HM beta 1-1 blocked the adhesion of mouse tumor cell lines to extracellular matrix proteins including collagen, laminin and fibronectin. Moreover, splenic T cell proliferation induced by anti-CD3 mAb and allogeneic mixed lymphocyte response were strongly inhibited by HM beta 1-1 in combination with an anti-LFA-1 mAb. We conclude that HM beta 1-1 reactive with mouse CD29 can inhibit VLA-dependent cellular functions and, thus, would be useful for studying the physiological role of beta 1 integrins in vivo.

A case of arterial priapism treated by embolization

An 18-year-old unmarried man, who had shown arterial priapism caused by mild perineal trauma sustained during skate-boarding, has been successfully treated by autologous clot embolization at the common penile artery. He was able to have a normal erection and ejaculate 5 d after embolization.

[Gene transfer to airway epithelial cells: current status and future direction]

Advances in recombinant DNA technology and molecular and cellular biology have made it feasible to introduce genes into living cells. The most sophisticated gene transduction methods have bee applied to gene therapy strategies for the potential treatment of genetic diseases. In regard to lung diseases, alpha 1-antitrypsin deficiency and cystic fibrosis, the most common hereditary lung disorders in Caucasians, have been targeted for gene therapy. To date, gene therapy studies have been confined to ex vivo strategies for treatment of ADA deficiency with retroviral vectors. However, there are two major obstacles to gene transfer to the bronchial epithelium. First, bronchial epithelium, such as that with ciliated cells, is terminally differentiated, and does not divide rapidly. Second, the complex architecture of the lung precludes replacing the existing bronchial epithelium with cells modified by gene transfer. In the context of these properties of bronchial epithelium, adenovirus vectors have been evaluated for direct introduction of therapeutic genes to bronchial epithelium via the airway in vivo. An in vivo experiment revealed that gene transfer with a replication-deficient adenovirus containing the E. coli lacZ (beta-galactosidase) gene driven by cytomegalovirus promoter (AdCMVlacZ) was 10(4) times more efficient than gene transfer with a plasmid containing the same expression cassette (pCMVlacZ). An experiment based on in vitro data was done to evaluate the distribution of the expression of the exogenous genes transferred by adenovirus vectors. Intratracheal administration of AdCMVlacZ into lungs of experimental animals resulted in a high number of beta-gal-positive epithelial cells in bronchiols, rather than in proximal bronchi. Thus, a replication-deficient adenovirus can be used to transfer exogenous genes to airway epithelial cells in vivo. This technique may be useful in gene therapy for cystic fibrosis. Gene transfer can be thought of as the use of genetic information to modity the milieu of the target organ. In addition, gene transfer may allow the introduction of new genes, or the alteration tion of existing genes in intact animals. Gene transfer could them be used to produce animal models of human lung diseases that are particularly difficult to study.

[Structures and functions of adhesion molecules--involvement of adhesion molecules in the pathogenesis]

Previous studies have revealed that adhesion molecules are involved in immune responses, such as the interaction between T cells and antigen presenting cells. Recent investigations demonstrated that one of these molecules, integrins, which was concerned with cell-cell adhesion and cell-extracellular matrix proteins, was prominently expressed on lymphocytes and neutrophils in inflammatory diseases. In addition, administration of monoclonal antibodies against integrins in vivo abrogated the inflammatory responses completely in rats. These findings suggest that adhesion molecules are involved in not only immune responses but also in the pathogenesis of inflammatory diseases. As shown here, integrins also play an important role in the metastasis of small cell lung cancers.

[A case report: occurrence of bladder carcinoma in the defunctionalised bladder in a patient after operation of left ureteral carcinoma]

An eighty year-old woman was diagnosed as left ureteral carcinoma and right dysfunctional kidney in 1984. Left partial ureterectomy, partial cystectomy, and left ureterocutaneostomy were performed and her bladder was left behind after the operation. In 1990 (72 months after the operation), she was aware of bleeding from the urethra. A bladder wash was performed, demonstrating malignant cells on cytological examination, and cystoscopy revealed a papillary tumor in the defunctionalized bladder. Total cystectomy was performed and the histological findings of the surgical specimen showed transitional cell carcinoma, grade 2, pTaNoMo. This case shows the need for periodic examinations of the defunctionalized bladder, because renal pelvic and ureteral carcinoma tends to recur in the bladder within two years after operation and because tumors rarely developed in the defunctionalized bladder.

[Electron microscopic observations of the porcine middle ear--normal cases]

Pigs are frequently used in basic studies of the middle ear because they have a middle ear air cell system which resembles the human mastoid air cell system. However, the morphology of epithelial cells of the middle ear of pigs has not been thoroughly studied. In this study, the morphological features of the mucosal epithelium of the normal porcine middle ear from juveniles to adults were investigated by scanning and transmission electron microscopy. The features were compared with the mucosal epithelium of the human middle ear. Macroscopic observation of the resected middle ears showed all normal. The mucoepithelial cells of the normal porcine middle ear consisted of ciliated cells, non-ciliated cells, secretory cells and basal cells. Ciliated cells were distributed most densely in the Eustachian tube and tube orifice of the middle ear cleft, decreasing in number towards the air cell system, where no ciliated cells were found. The distribution of secretory cells was similar to that of ciliated cells, while non-ciliated cells distributed conversely. Ciliated cells of juvenile pigs had 40 to 100 cilia 5 to 6 mu in length and 0.2 to 0.3 mu in thickness and microvilli on the cell surface. On the other hand, pigs 4 weeks old or older, had ciliated cells with 80 to 100 cilia 5 to 8 mu in length and 0.3 to 0.4 mu in thickness. Younger pigs had a smaller range of ciliated cell distribution. The range increased with growth, and rapidly expanded by 2 weeks after birth; then the expansion slowed down to 4 weeks, when the distribution was similar that in maturity.(ABSTRACT TRUNCATED AT 250 WORDS)

[Electron microscopic observations of the porcine middle ear--inflammatory changes]

In previous studies, the morphology of the mucoepithelial cells of the middle ear of normal pigs has been found to be similar to that of humans. In this study, otitis media was induced in 18 ears by transcanal injection of glycerin into the middle ear cleft and morphological changes were investigated by scanning and transmission electron microscopy. The mucoepithelial cells of the inflamed porcine middle ear consisted of ciliated cells, non-ciliated cells, secretory cells and basal cells, and the distribution of these cells was similar to that of normal cases. In the inflamed Eustachian tube and middle ear cleft, the epithelial cells were detached, the intracellular junctions ruptured and there was subepithelial thickening in some places. In addition, the cilia were detached or deformed irregularly. On the other hand, ciliated cells, bulging non-ciliated cells, secretory cells and columnar cells were increased in numbers. These features suggested that the muco-ciliary system of the inflamed ears had been stimulated. In the air cell system, however, there were signs of mucoepithelial cell injury, but no evidence suggesting that the muco-ciliary system had been stimulated as in the Eustachian tube or middle ear cleft. The inflammatory changes in the mucoepithelial cells in the Eustachian tube and middle ear cleft gradually returned to normal but in the air cell system, the changes were persistent. Moreover, the signs of mucoepithelial cell injury remained longer when inflammation occurred at a younger age.(ABSTRACT TRUNCATED AT 250 WORDS)

[Rapid etiologic diagnosis of epidemic keratoconjunctivitis]

We evaluated enzyme-linked immunosorbent assay (Adenoclone) in 253 cases of epidemic keratoconjunctivitis (EKC), pharyngeal conjunctival fever (PCF) and acute conjunctivitis. The clinical diagnosis due to adenoviral ocular infection was 86/114 (75%) in EKC, 26/50 (52%) in PCF and 25/89 (28%) in acute conjunctivitis, Adenoclone was positive only within 7 days after the disease onset. The specificity (87%) and sensitivity (74%) of Adenoclone were confirmed by isolate cell culture. Cases with corneal complication due to adenoviral infection show higher a value than the OD value in Adenoclone and the bulbar conjunctiva is a suitable site to detect adenoviral antigen. In this survey, isolated adnovirus type 4 was recognized in 53%, Ad8 in 14%, Ad3 in 13%, Ad37 in 5%, Ad19 in 2% and non typed Ad in 12%. Clinical findings due to Ad4 showed EKC in 50%, PCF in 30% and acute conjunctivitis in 20% respectively.