Genes Induced by Reovirus Infection Have a Distinct Modular Cis-Regulatory Architecture

The availability of complete genomes and global gene expression profiling has greatly facilitated analysis of complex genetic regulatory systems. We describe the use of a bioinformatics strategy for analyzing the cis-regulatory design of genes diferentially regulated during viral infection of a target cell. The large-scale transcriptional activity of human embryonic kidney (HEK293) cells to reovirus (serotype 3 Abney) infection was measured using the Affymetrix HU-95Av2 gene array. Comparing the 2000 base pairs of 5' upstream sequence for the most differentially expressed genes revealed highly preserved sequence regions, which we call "modules". Higher-order patterns of modules, called "super-modules", were significantly over-represented in the 5' upstream regions of transcriptionally responsive genes. These supermodules contain binding sites for multiple transcription factors and tend to define the role of genes in processes associated with reovirus infection. The supermodular design encodes a cis-regulatory logic for transducing upstream signaling for the control of expression of genes involved in similar biological processes. In the case of reovirus infection, these processes recapitulate the integrated response of cells including signal transduction, transcriptional regulation, cell cycle control, and apoptosis. The computational strategies described for analyzing gene expression data to discover cis-regulatory features and associating them with pathological processes represents a novel approach to studying the interaction of a pathogen with its target cells.

Symbolic inference of xenobiotic metabolism

We present a new symbolic computational approach to elucidate the biochemical networks of living systems de novo and we apply it to an important biomedical problem: xenobiotic metabolism. A crucial issue in analyzing and modeling a living organism is understanding its biochemical network beyond what is already known. Our objective is to use the available metabolic information in a representational framework that enables the inference of novel biochemical knowledge and whose results can be validated experimentally. We describe a symbolic computational approach consisting of two parts. First, biotransformation rules are inferred from the molecular graphs of compounds in enzyme-catalyzed reactions. Second, these rules are recursively applied to different compounds to generate novel metabolic networks, containing new biotransformations and new metabolites. Using data for 456 generic reactions and 825 generic compounds from KEGG we were able to extract 110 biotransformation rules, which generalize a subset of known biocatalytic functions. We tested our approach by applying these rules to ethanol, a common substance of abuse and to furfuryl alcohol, a xenobiotic organic solvent, which is absent in metabolic databases. In both cases our predictions on the fate of ethanol and furfuryl alcohol are consistent with the literature on the metabolism of these compounds.

PathMiner: predicting metabolic pathways by heuristic search

MOTIVATION

Automated methods for biochemical pathway inference are becoming increasingly important for understanding biological processes in living and synthetic systems. With the availability of data on complete genomes and increasing information about enzyme-catalyzed biochemistry it is becoming feasible to approach this problem computationally. In this paper we present PathMiner, a system for automatic metabolic pathway inference. PathMiner predicts metabolic routes by reasoning over transformations using chemical and biological information.

RESULTS

We build a biochemical state-space using data from known enzyme-catalyzed transformations in Ligand, including, 2917 unique transformations between 3890 different compounds. To predict metabolic pathways we explore this state-space by developing an informed search algorithm. For this purpose we develop a chemically motivated heuristic to guide the search. Since the algorithm does not depend on predefined pathways, it can efficiently identify plausible routes using known biochemical transformations.

Flexural strength of heat-polymerized polymethyl methacrylate denture resin reinforced with glass, aramid, or nylon fibers

STATEMENT OF PROBLEM

Despite the favorable properties of conventional PMMA used as a denture base material, its fracture resistance could be improved.

PURPOSE

This in vitro study was performed to determine whether the flexural strength of a commercially available, heat-polymerized acrylic denture base material could be improved through reinforcement with 3 types of fibers.

MATERIAL AND METHODS

Ten specimens of similar dimensions were prepared for each of the 4 experimental groups: conventional acrylic resin and the same resin reinforced with glass, aramid, or nylon fibers. Flexural strength was evaluated with a 3-point bending test. The results were analyzed with a 1-way analysis of variance.

RESULTS

All reinforced specimens showed better flexural strength than the conventional acrylic resin. Specimens reinforced with glass fibers showed the highest flexural strength, followed by aramid and nylon.

CONCLUSION

Within the limitations of this study, the flexural strength of heat-polymerized PMMA denture resin was improved after reinforcement with glass or aramid fibers. It may be possible to apply these results to distal extension partial denture bases and provisional fixed partial dentures.

Primary pancreatic lymphoma: a case report, literature review, and proposal for nomenclature

Primary neoplasms of the pancreas are most often adenocarcinoma. Non-Hodgkin's lymphoma (NHL) involving the pancreas is less common but well documented; the pancreas as the primary site of NHL is rare. The majority of patients with pancreatic cancer, whether it is adenocarcinoma or lymphoma, present with a mass in the head of the gland. Pancreatic lymphoma is often described as a large homogeneous mass with extra-pancreatic extension, with or without associated lymphadenopathy. Less common presentations are masses in the body or tail, or more rarely diffuse involvement of the pancreas. We present a case of diffuse pancreatic lymphoma with extra-pancreatic dissemination to the spleen and lymph nodes, and review the literature on pancreatic lymphoma. Because the definition of pancreatic lymphoma and primary pancreatic lymphoma varies, we also propose a nomenclature system to make future studies of pancreatic lymphoma more comparable.

Visual management of large scale data mining projects

This paper describes a unified framework for visualizing the preparations for, and results of, hundreds of machine learning experiments. These experiments were designed to improve the accuracy of enzyme functional predictions from sequence, and in many cases were successful. Our system provides graphical user interfaces for defining and exploring training datasets and various representational alternatives, for inspecting the hypotheses induced by various types of learning algorithms, for visualizing the global results, and for inspecting in detail results for specific training sets (functions) and examples (proteins). The visualization tools serve as a navigational aid through a large amount of sequence data and induced knowledge. They provided significant help in understanding both the significance and the underlying biological explanations of our successes and failures. Using these visualizations it was possible to efficiently identify weaknesses of the modular sequence representations and induction algorithms which suggest better learning strategies. The context in which our data mining visualization toolkit was developed was the problem of accurately predicting enzyme function from protein sequence data. Previous work demonstrated that approximately 6% of enzyme protein sequences are likely to be assigned incorrect functions on the basis of sequence similarity alone. In order to test the hypothesis that more detailed sequence analysis using machine learning techniques and modular domain representations could address many of these failures, we designed a series of more than 250 experiments using information-theoretic decision tree induction and naive Bayesian learning on local sequence domain representations of problematic enzyme function classes. In more than half of these cases, our methods were able to perfectly discriminate among various possible functions of similar sequences. We developed and tested our visualization techniques on this application.

Leptospirosis - an under-diagnosed clinical condition

Leptospirosis is a zoonotic disease caused by leptospiral spirochaete. Two cases in children are described presenting with hepatorenal dysfunction.

Identification of divergent functions in homologous proteins by induction over conserved modules

Homologous proteins do not necessarily exhibit identical biochemical function. Despite this fact, local or global sequence similarity is widely used as an indication of functional identity. Of the 1327 Enzyme Commission defined functional classes with more than one annotated example in the sequence databases, similarity scores alone are inadequate in 251 (19%) of the cases. We test the hypothesis that conserved domains, as defined in the ProDom database, can be used to discriminate between alternative functions for homologous proteins in these cases. Using machine learning methods, we were able to induce correct discriminators for more than half of these 251 challenging functional classes. These results show that the combination of modular representations of proteins with sequence similarity improves the ability to infer function from sequence over similarity scores alone.

Visualization based on the Enzyme Commission nomenclature

We developed a tool for visualizing data related to protein function, based on the nomenclature defined by the International Enzyme Commission. The method represents the 1327 specific reaction types and three additional levels of abstract classifications in the nomenclature as an interactive graph. Each node and link in the graph can have associated with it stored or computed data values of various types, each of which can be assigned to any of a set of visualization methods, including color, size, various chart types and text. Visualizations can then be interactively created for single nodes, groups of nodes or the entire graph. This visualization tool is particularly useful for exploring the distribution of quantitative attributes across protein function classes. As a test of this tool, we developed a visualization of data measuring the effectiveness of sequence similarity for prediction of EC class. Using this tool, it was possible to rapidly scan hundreds of functional classes, and to correlate predictability from sequence with other attributes, facilitating the generation of hypotheses about the causes of predictive failure.

Chloroquine resistance in Pakistan and the upsurge of falciparum malaria in Pakistani and Afghan refugee populations

Surveys conducted in Pakistan during the last decade show that falciparum malaria has become resistant to chloroquine in Pakistani and Afghan refugee populations throughout the country. Although RI resistance is common everywhere (with a frequency of 30%-84%), RII is rarer (2%-36%), and RIII resistance has yet to be detected. The national policy is to prescribe chloroquine as first-line treatment of malaria. A repeated in-vivo survey in a sentinel village indicated that prescription of chloroquine can lead to a 15% increase in the frequency of resistance in a single year, and similar trends were observed in other districts. Coinciding with the spread of resistance is a 6-fold increase in the number of falciparum cases recorded nationally between 1982 and 1992 and a parallel, 5-fold increase in the number of cases recorded in the Afghan refugee population. Resistance contributes to this trend in various ways. Firstly, patients with resistant malaria make repeated visits to health centres. In the sentinel village, for example, where resistance was measured at 71%, recrudescent infections inflated by 66% the genuine incidence of new infections recorded at the health centre. Secondly, owing to ineffective treatment, resistant infections are often still patent during the post-transmission season. This may enlarge the 'overwintering' parasite reservoir, leading to a surge of new cases when transmission resumes. Other factors potentially contributing to the upsurge in falciparum include the decrease availability of insecticide for indoor spraying. Despite the problems posed by resistance for case management, the evidence from the vector-control programme among the refugees is that malaria control through well-targeted campaigns of insecticide spraying is still able to reduce the incidence of falciparum malaria to a level that existed before the advent of resistance.

Fertility and contraception in Europe: the case of low fertility in southern Europe

Demographic trends in Europe can be summarized in terms of a declining proportion of its population in the world total, low fertility, and a slow population growth. Fertility in Western Europe was already below the replacement level in 1970-75 and has remained low. Fertility has substantially declined in Eastern and Southern Europe, with Italy and Spain recording one of the lowest levels (1.2 children per woman) in 1994. Some explanations of the dramatic fertility decline in Southern Europe are: (1) The emancipation of women and their increased participation in the labor force; (2) Economic aspects such as costs for child care and education; and (3) The couple's motivation for low fertility because of the expanded choices for travel and leisure and their concerns for improving their standard of living. Social pressures on childbearing outside marriage remain quite strong; cohabitation and extramarital births is Southern Europe are not as prevalent as in other European regions and there is a trend toward delaying the birth of the first child rather than foregoing childbearing.

Knowledge and perceptions about AIDS among married women in Bangkok

People's knowledge and perceptions about AIDS are critical in efforts to combat the further spread of this disease. Using data from a study on "Determinants and Consequences of Contraceptive Use Patterns in Thailand", this paper investigates the knowledge and perceptions about AIDS among ever-married women in Bangkok Metropolis. Differentials in knowledge and perceptions are investigated by socio-economic subgroups. The results indicate the need to inform and educate people about AIDS, especially those in low-income groups or with lower levels of education.

Thermogravimetric analysis of urinary stones

Routine thermogravimetric (TG) analysis of 501 upper urinary calculi from the State of Jammu and Kashmir is described. The technique is simple, rapid and quantitative, and the equipment is easily maintained. The technique was found to be helpful in 95.4% of urinary stones and it is suggested that TG analysis may be employed as a technique of first choice in the routine quantitative analysis of all urinary calculi.

The AI/RHEUM knowledge-based computer consultant system in rheumatology. Performance in the diagnosis of 59 connective tissue disease patients from Japan

AI/RHEUM is a knowledge-based computer consultant system for the diagnosis of rheumatic diseases. Its diagnostic accuracy was evaluated using information that was supplied by Japanese rheumatologists on 59 patients with connective tissue diseases. The diagnoses of the AI/RHEUM model were in full or partial agreement with those of the Japanese rheumatologists in 54 of 59 cases (92%). Preliminary evaluation of the criteria tissue disease showed a sensitivity of 90% and a specificity of 96%.

Pharmacokinetics and tolerance of intravenous and intramuscular recombinant alpha 2 interferon in patients with malignancies

Fifteen patients with advanced hematopoietic and other malignancies were treated with recombinant DNA produced Alpha 2 Interferon (IFN) (Schering) by intravenous (IV) and intramuscular (IM) routes at weekly intervals in escalating doses from 1 X 10(6) IU to 100 X 10(6) IU in order to determine the tolerance and pharmacokinetics. The most common side effects included fever, chills, myalgia, and arthralgia. At doses of 60 X 10(6) or above, severe but reversible hypotension was observed in five patients receiving interferon by intravenous route. Patients receiving interferon by intramuscular route had fever, chills, and myalgias but did not develop hypotension at the same dosage. Two patients with non-Hodgkin lymphoma showed objective evidence of regression. Our data suggest a biphasic pattern of elimination with terminal half-life ranging from 1.9 to 2.9 hours and peak titer of 16,000 units and under for IV interferon, and terminal half-life of 6 hours with peak titers of 600 units for intramuscular interferon. However, interpatient variability precludes a definite conclusion. Although the areas under the serum concentration vs time curves were similar, the intravenous route provided higher but unsustained levels of interferon than the intramuscular route.

Diagnostic morphometry of the adult respiratory distress syndrome (shock lung)

In the pathogenesis of "shock lung", the morphometric analysis allows us to determine the "point of no return" when the exudative alveolitis turns into the life-threatening sclerosing form. In addition, we found that this "point of no return" is reached much earlier in septic than in traumatic shock. Our studies confirm that the term "shock lung" should not be simply substituted for "respiratory lung". Based on our morphometric methods, we conclude that shock-induced pulmonary fibrosis differs with regard to its functional pathogenesis from the non-shock-induced type of fibrosis.

Acute basophilic leukemia

Acute basophilic leukemia was diagnosed in a 61-year-old black woman on the basis of 85 to 90 percent basophils in the peripheral blood as well as bone marrow and very high serum histamine level (more than 10,000 ng/ml). These complications occurred as a transformation from essential thrombocythemia. Accompanying this transformation, there was also cytogenetic change from 46XX karyotype to 46XX 2p+ in 66 to 90 percent of cells in the bone marrow. This may be the first reported occurrence of transformation of essential thrombocythemia into acute basophilic leukemia.

Sickle cell anemia and epidural extramedullary hematopoiesis

Acute flaccid paralysis due to epidural extramedullary hematopoiesis developed in a 43-year-old man with sickle cell anemia. The patient showed no response to emergency decompressive laminectomy, radiotherapy, or exchange transfusion, and his neurologic deficit persisted unimproved. This is the first reported case of acute or irreversible spinal cord compression due to epidural extramedullary hematopoiesis in a patient with sickle cell anemia.

Role of sialyltransferase in hypercupraemia of non-Hodgkin's lymphoma

Copper, ceruloplasmin and sialyltransferase activity were measured in serum of 25 patients with lymphoreticular malignancies, in an attempt to study the sialyltransferase activity and correlation if any with the activity of the disease and ceruloplasmin. All 3 parameters were elevated in active disease but no definite correlation between sialyltransferase activity and copper or ceruloplasmin could be found. We conclude that plasma sialyltransferase activity is increased in lymphomas.

True histiocytic lymphoma. A report of four cases

Clinical, morphologic, cytochemical, immunologic, and ultrastructural features of four cases of true histiocytic lymphoma are described. The neoplastic cells were large, ranging from 20 to 45 mu in diameter with round, folded, or convoluted nuclei, and abundant eosinophilic cytoplasm. They exhibited diffuse nonspecific esterase activity. Diffuse acid phosphatase activity was present in two cases so tested. Muramidase activity was present in half of the cases. Finely granular PAS-positive material was seen in the cytoplasm. Methyl green-pyronin positivity was variable. An occasional neoplastic cell showed erythropagocytosis in one case. Malignant cells either contained no cytoplasmic immunoglobulins (three cases) or had immunoglobulins of multiple classes (one case). Surface markers were studied in two cases; they were absent in one case, and were of multiple classes in another case. Ultrastructurally the neoplastic cells had lysosomal granules in three cases so examined, and phagolysosomes, phagocytized material and residual bodies in one of three cases so studied. Patients ranged in age from 28 to 60 years. Two patients had extralymphatic tumors. Survival of more than 5 years was seen in one patient.

Renal oncocytoma associated with diffuse lymphoma

We report on a sixty-six-year-old man with a poorly differentiated, diffuse lymphoma in whom bilateral multiple renal masses developed six months after starting chemotherapy. Computerized tomography and selective renal arteriograms were suggestive of either recurrence of lymphoma or renal cell carcinoma. Kidney biopsy revealed renal oncocytomas, benign renal tumors. The patient was spared further courses of cytotoxic therapy.

Correlation of hypercupremia with other acute phase reactants in malignant lymphoma

Levels of copper, haptoglobin, fibrinogen and Factor VIII were measured in 30 patients with non-Hodgkin's lymphoma on 90 occasions in an attempt to demonstrate a possible correlation between hypercupremia and other acute phase reactants. The four parameters were measured simultaneously in active disease and in remission. The serum copper, along with other parameters, was significantly elevated in the active disease (P less than 0.001) and there was a high correlation between the levels of serum copper, fibrinogen and haptoglobin (P less than 0.001).

Comparison of circulating colony-forming cells in chronic granulocytic leukemia and leukemoid reaction

In vitro culture studies of peripheral blood leukocytes using semi-solid media from 8 patients with chronic granulocytic leukemia (CGL) and 5 patients with granulocytic leukemoid reaction were performed. A markedly increased number of circulating colony-forming units were present in patients with CGL (mean 343 +/- 47) as opposed to those having granulocytic leukemoid reaction (mean 7.0 +/- 4). The colony size was larger in CGL than in granulocytic leukemoid reaction or in normal peripheral blood.

Karyotypic polymorphism in acute myelofibrosis

Acute myelofibrosis (AMF) was diagnosed in a 59-yr-old black male in September 1978, on the basis of pancytopenia, lack of hepatosplenomegaly, fibrosis of the marrow, and paucity of teardrop red blood cells in the peripheral blood. Since then the patient has demonstrated an unusually long survival of 36 mo with a changing cytogenetic course. His initial 46, XY normal karyotype changed in 20 mo to trisomy 8, followed 1 yr later by 1:4 translocation in peripheral blood. Simultaneously with these changes, the fibrosis in the bone marrow progressively decreased, ultimately terminating in chronic granulocytic leukemia-like presentation with reversal to 46, XY karyotype. Fibroblast culture failed to show any evidence of cytogenetic abnormalities. The disappearance of fibrosis confirmed by trichrome and reticulin stains and lack of cytogenetic abnormalities in fibroblasts confirms the secondary role of fibrosis.

Granulocyte yields using the Haemonetics 30. Effects of variations in corticosteroid regimen and donor selection

The factors of donor selection, corticosteroid drug choice, dose, timing and route of administration were studied to optimize granulocyte yield employing the Haemonetics Model 30 Blood Processor. Our data suggest that donors giving one excellent yield do not necessarily do so again. Donors with high initial granulocyte counts had only marginal increases in counts after taking corticosteroids. Selecting donors on the basis of high previous yield or granulocyte count is not a feasible strategy for improving granulocyte yields. Highest yields of granulocytes (16 X 10(9) total; 4 X 10(9)/liter processed) were obtained with any of four split-dose corticosteroid regimen. This increment is almost twice as large as the previously reported improvement using continuous-flow centrifugation. The choice of steroid, the route of administration and the timing of the split doses are not critical.

Agranulocytosis associated with chronic oral administration of cloxacillin for suppression of staphylococcal osteomyelitis

Oral cloxacillin was used for chronic suppression of a 59-year-old woman with staphylococcal osteomyelitis. She received 380.5 gm of cloxacillin over 263 consecutive days. Severe agranulocytosis followed, reverting rapidly to normal with cessation of drug. The absence of signs of an allergic reactions such as rash, fever, or eosinophilia suggests that cloxacillin, like other semisynthetic penicillins, may exert a direct bone marrow toxicity.

Evaluation of individuals deferred from blood donation for medical reasons

Modern techniques of blood collection require health screening of donors by non-physicians using general guidelines. Health problems of concern to the donor and possible loss to future donation of actually individuals are inherent in this acceptance and deferral process. Of the 108,908 donors presenting at the bloodmobiles of regional blood center from September 1978 to February 1979, 9,542 were deferred. Of these, 1,203 with possible medical problems other than hepatitis, hypertension, or infectious disease were referred to their physician for further information concerning their suitability as donors. Over 80% had irregular pulses or histories suggestive of potential cardiovascular problems. The purpose of this study was to review the evaluation mechanism. Responses for evaluation were received from only 222 out of 1,203 (18%), and of these all but 29 (13%) were granted full permission to donate. Since only one evaluated individual with pulse or cardiovascular findings of possible significance was under the age of 35 years, this age is a reasonable cutoff for such deferrals. The minimum increase in collections with this change in deferral screening would be over 1,000 units per year in Connecticut, and perhaps 60,000 nationwide.

DNA in Lennert's lymphoma. Report of a case with cytophotometric studies

We present the first case of Lennert's Lymphoma in which cytophotometric determinations for DNA contents are undertaken. DNA Histograms of lymphoid cells, Immunoblasts, and epitheloid cells are evaluated for their euploid or aneuploid DNA contents. The aneuploid DNA stem line pattern found in the case under discussion testifies to the malignant nature of Lennert's Lyphoma.