BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation.

We present BioGraph, a data integration and data mining platform for the exploration and discovery of biomedical information. The platform offers prioritizations of putative disease genes, supported by functional hypotheses. We show that BioGraph can retrospectively confirm recently discovered disease genes and identify potential susceptibility genes, outperforming existing technologies, without requiring prior domain knowledge. Additionally, BioGraph allows for generic biomedical applications beyond gene discovery. BioGraph is accessible at http://www.biograph.be.

Estimation of potential effects of improved community-based drug provision, to augment health-facility strengthening, on maternal mortality due to post-partum haemorrhage and sepsis in sub-Saharan Africa: an equity-effectiveness model.

BACKGROUND: Maternal mortality in Africa has changed little since 1990. We developed a mathematical model with the aim to assess whether improved community-based access to life-saving drugs, to augment a core programme of health-facility strengthening, could reduce maternal mortality due to post-partum haemorrhage or sepsis. METHODS: We developed a mathematical model by considering the key events leading to maternal death from post-partum haemorrhage or sepsis after delivery. With parameter estimates from published work of occurrence of post-partum haemorrhage and sepsis, case fatality, and the effectiveness of drugs, we used this model to estimate the effect of three potential packages of interventions: 1) health-facility strengthening; 2) health-facility strengthening combined with improved drug provision via antenatal-care appointments and community health workers; and 3) all interventions in package two combined with improved community-based drug provision via female volunteers in villages. The model was applied to Malawi and sub-Saharan Africa. FINDINGS: In the implementation of the model, the lowest risk deliveries were those in health facilities. With the model we estimated that of 2860 maternal deaths from post-partum haemorrhage or sepsis per year in Malawi, intervention package one could prevent 210 (7%) deaths, package two 720 (25%) deaths, and package three 1020 (36%) deaths. In sub-Saharan Africa, we estimated that of 182 000 of such maternal deaths per year, these three packages could prevent 21 300 (12%), 43 800 (24%), and 59 000 (32%) deaths, respectively. The estimated effect of community-based drug provision was greatest for the poorest women. INTERPRETATION: Community provision of misoprostol and antibiotics to reduce maternal deaths from post-partum haemorrhage and sepsis could be a highly effective addition to health-facility strengthening in Africa. Investigation of such interventions is urgently needed to establish the risks, benefits, and challenges of widespread implementation. FUNDING: Institute of Child Health and Faculty of Mathematical and Physical Sciences, University College London, and a donation from John and Ann-Margaret Walton.

Molecular circuits for associative learning in single-celled organisms.

We demonstrate how a single-celled organism could undertake associative learning. Although to date only one previous study has found experimental evidence for such learning, there is no reason in principle why it should not occur. We propose a gene regulatory network that is capable of associative learning between any pre-specified set of chemical signals, in a Hebbian manner, within a single cell. A mathematical model is developed, and simulations show a clear learned response. A preliminary design for implementing this model using plasmids within Escherichia coli is presented, along with an alternative approach, based on double-phosphorylated protein kinases.

Surgical treatment of nonmelanoma skin cancer.

Nonmelanoma skin cancer is the most common human malignancy. An estimated 2.75 million patients worldwide are diagnosed with skin cancer each year, with more than one million in the United States alone. Treatment for skin cancer includes methods such as cryosurgery, curettage and electrodessication, local excision, and Mohs micrographic surgery. Regardless of the method used, the goal is to provide the patient with the safest, most cost-effective and curative treatment.

Extracorporeal membrane oxygenation. Saving tiny lives.

Infants with CDH require a dedicated nursing team that often comes from three different critical care areas: neonatal ICU, the ECMO unit, and the operating room. The team works together to directly affect the outcome of these infants through their preoperative, intraoperative, and postoperative care. The physiologic status of the patient and the psychosocial aspects of the family unit are of prime concern to the nursing team involved. Controversy still surrounds the use of ECMO because long-term effects on its survivors are unknown. It will be important for members of the team that manages the infant diagnosed with CDH to understand the benefits and limitations of ECMO. Even with its controversial aspects, ECMO offers the infant with CDH an alternative when conventional therapy fails. The collaborative efforts of the multidisciplinary team that manages these neonates must continue to evaluate treatment modalities and update techniques to maintain quality of care for this challenging population.

Inhibition of phosphatidylcholine biosynthesis following induction of apoptosis in HL-60 cells.

Induction of apoptosis in HL-60 cells, using a variety of cytotoxic drugs, resulted, in all cases, in inhibition of CDP-choline:1, 2-diacylglycerol choline phosphotransferase, leading to an accumulation of its substrate, CDP-choline, and inhibition of phosphatidylcholine biosynthesis. Incubation of the cells with phosphatidylcholine reduced the number displaying an apoptotic morphology following drug treatment, and this was inversely related to the degree to which the drugs inhibited phosphatidylcholine biosynthesis. Inhibition of choline phosphotransferase by two of the drugs, farnesol and chelerythrine, was shown to be due to direct inhibition of the enzyme, while inhibition by the other drugs, etoposide and camptothecin, could be explained by the intracellular acidification that followed induction of apoptosis.

Laparoscopic splenectomy in children with sickle cell disease.

Sickle cell disease is a group of genetic disorders that are characterized by the production of hemoglobin S, anemia, and acute and chronic tissue damage secondary to blockages caused by abnormally shaped (i.e., sickle-shaped) red blood cells. In children, complications of sickle cell disease (e.g., splenic sequestration and splenomegaly) increase the risks for postoperative complications due to the physical stress of the large incisions previously require for splenectomy. An intracorporeal splenic fragmentation technique is now being used to avoid these complications and will be discussed in this article.

Induction of apoptosis in two mammalian cell lines results in increased levels of fructose-1,6-bisphosphate and CDP-choline as determined by 31P MRS.

Programmed cell death or apoptosis was induced in human promyelocytic leukemia (HL-60) and Chinese hamster ovary (CHO-K1) cells using several cytotoxic drugs that have different modes of action, including camptothecin, ceramide, chelerythrine, etoposide, farnesol, geranyl geraniol, and hexadecylphosphocholine. The consequent changes in cellular metabolism were monitored using 31P MRS measurements on intact cells and cell extracts. Cells undergoing programmed cell death exhibited characteristic changes in the levels of glycolytic and phospholipid metabolites. The most significant changes were increases in the concentration of the glycolytic intermediate, fructose-1,6-bisphosphate and in the concentration of CDP-choline, which is an intermediate in phosphatidylcholine biosynthesis. In HL-60 cells, the increase in fructose-1,6-bisphosphate levels could be explained by depletion of cellular NAD(H) levels. All of the agents used to induce apoptosis caused the accumulation of CDP-choline. Since the resonances of this compound occur in a relatively well resolved region of tissue spectra, it could provide a marker for apoptosis that would allow the noninvasive detection of the process in vivo using 31P MRS measurements.

Nursing students and Haiku.

The emphasis in nursing education is frequently on facts, details, and linear issues. Students need more encouragement to use the creative abilities which exist in each of them. The use of haiku, a simple unrhymed Japanese verse, is one method which stimulates nursing students to use their creativity. A haiku exercise worked well in encouraging a group of nursing students to express their feelings.

A cultural values assessment tool.

Faculty members at a small liberal arts college teaching in a course entitled "Contemporary Cultures: China, Guatemala and Nigeria" found that using a cultural values assessment tool strengthened the course. This assessment tool was developed by a faculty member teaching in the course when no standardized tool of this type could be found. Students and faculty involved with this senior core course found the cultural values assessment tool to be effective in introducing the course, in stimulating some critical thinking throughout the course and in concluding the course.

(1)H NMR spectroscopic studies on the characterization of renal cell lines and identification of novel potential markers of in vitro nephrotoxicity.

Abstract Cell cultures are increasingly used in the evaluation of chemically-induced nephrotoxicity. The utili of renal cell culture systems in toxicology would be improved, however, if better characterized and more specific markers of toxicity were available. High resolution proton nuclear magnetic resonance ((1)H NMR) spectroscopy is well suited to the study of toxicological events and has identified many novel markers of nephrotoxicity in vivo. In this study, (1)H NMR spectroscopy has been used to characterize the biochemical composition of two renal cell lines of different nephronal origin, LLC-PK1 (pig proximal tubule) and Madin-Darby canine kidney (MDCK, distal tubule). The early biochemical responses of these cell lines to the model proximal tubular toxin S-(1,2dichlorovinyl)i-L-cysteine (DCVC) and the renal medullary toxin 2-chloroethanamine (CEA) have also been investigated. For each line, 500 MHz (1)H NMR spectra of protein-free acetone extracts of cells and culture medium gave characteristic and reproducible profiles of low MW constituents, including amino and organic acids, glucose and soluble membrane precursors, such as choline and myo-inositol. Treatment-related changes in several low MW compounds not routinely measured in toxicological studies were revealed by NMR specboscopy before marked cytotoxicity was observed by phase contrast microscopy. For example, LLC-PK1 cells treated with 60 µM DCVC showed a marked decrease in intracellular choline levels within 3 h which suggests an effect on the balance of choline synthesis and utilization. Wrthin 9 h of treatment with DCVC there were decreases in intracellular acetate and alanine concentrations which may be indicative of a decrease in fatty acid oxidation and biglyceride metabolism accompanied by an increase in gluconeogenesis. In MDCK cells, 1 h post treatment with 5 mM CEA, intracellular glycine was decreased. This study indicates the potential power and applicability of (1)H NMR spectroscopy for evaluating the biochemical and metabolic effects of toxins in cell culture systems and provides a novel approach to identifying new markers of tissue damage.

1H NMR spectroscopic studies on the reactions of haloalkylamines with bicarbonate ions: formation of N-carbamates and 2-oxazolidones in cell culture media and blood plasma.

1H NMR spectroscopic methods have been applied to compare the in vitro reactivity of the renal papillary nephrotoxin 2-bromoethanamine (BEA) with those of selected halide-substituted nephrotoxic analogues, 2-chloroethanamine (CEA), 2-fluoroethanamine (FEA), and 1-phenyl-2-iodoethanamine (PIEA). The primary 1H NMR-detectable transformation during a 24 h incubation of confluent Madin Darby canine kidney (MDCK) cells with BEA, CEA, and FEA (at concentrations up to the IC50 determined by neutral red uptake) was the appearance in cell culture media of 2-oxazolidone (OX). Additional novel signals assigned as FEA carbamate (N-carbamoyl-2-fluoroethanamine) were observed in media collected following incubation of cells with FEA. We propose that N-carbamate intermediates are formed from the spontaneous reaction of these haloalkylamines with HCO(3-)-buffered growth media and that OX is formed from the carbamate via elimination of the hydrogen halide. Further 1H NMR experiments, conducted for up to 8 h at 25 degrees C on 5 mM solutions of BEA, CEA, and FEA in 2H2O containing a 20-fold excess of HCO3- at pH 7.6, demonstrated a time-dependent decrease in the concentration of the free haloalkylamines accompanied by the production of N-carbamate intermediates and OX. Under these pseudo-first-order reaction conditions, the formation of OX from BEA was complete within approximately 6 h. In similar reaction conditions OX formation from CEA (24 h after initiation) had reached 54% of its final equilibrium concentration. Equivalent experiments demonstrated that PIEA was almost completely converted to 4-phenyl-2-oxazolidinone (PHOX) within 2 h. These observations reveal the strong disposition of this series of haloalkylamines toward reaction with HCO3- and indicate that the compounds in this family may exist only transiently as free amines in vivo, where there will virtually always be excess HCO3-. The physiological relevance of the in vitro findings is further indicated by the NMR-detectable conversion of BEA to OX and also an alkylating aziridine (AZ) moiety in rat plasma containing BEA. The ability to form carbamoylated species and OX (or PHOX) may mediate the toxicity of this series of haloalkylamines and hence is potentially of considerable significance.

Classification of toxin-induced changes in 1H NMR spectra of urine using an artificial neural network.

NMR spectra of urine from rats treated with a range of liver, kidney and testicular toxins at various doses were measured and classified using neural network methods. Toxin-induced changes in the levels of 18 low molecular weight endogenous urinary metabolites were assessed using a simple semi-quantitative scoring system. These scores were used as input to an artificial neural network, the use of which has been explored as a means of predicting the class of toxin. With this limited data set, based only the level of the maximal changes of these 18 metabolites, the network was able to predict the class and hence target organ of the toxins. Renal cortical toxicity was well predicted as was liver toxicity. The few examples of renal medullary toxins in the data set resulted in relatively poor training of the network although correct classification was still possible.

Pattern recognition classification of the site of nephrotoxicity based on metabolic data derived from proton nuclear magnetic resonance spectra of urine.

The computer-based pattern recognition procedures of nonlinear mapping and principal-component analysis have been applied to analyze 1H NMR-generated metabolic data on the biochemical effects of 15 acute nephrotoxin treatments affecting the renal cortex and/or renal medulla in rats. The 1H NMR signal intensities for 16 urinary metabolites representative of several major intermediary biochemical pathways were estimated using either a simple semiquantitative scoring system or complete peak intensity quantitation. NMR-derived data were treated as input coordinates in a multidimensional metabolic space and were analyzed by pattern recognition methods through which the dimensionality was reduced for display and categorization purposes. Different nephrotoxin treatments were initially classified using semiquantitative metabolite scores on the basis of their 1H NMR-detectable biochemical effects, and a good separation of renal cortical toxin treatments from renal medullary toxin treatments was achieved. The refinement of using exact peak heights rather than metabolic data scores utilized the available metabolic information more fully and provided a unique classification of each type of toxin according to its pattern of biochemical effects and site of toxic action. Principal-component analysis provided consistently better results than did nonlinear mapping in terms of discrimination between different sites of toxicity, and maps generated from correlation matrices gave improved discrimination, compared with those based directly on the original metabolic data. A comparison between the use of an added internal quantitation standard (3-trimethylsilyl-[2,2,3,3-2H4]-1-propionate) and independently determined glucose excretion rates for scaling to the NMR-detected urinary glucose levels demonstrated that the consistent classification of site-specific nephrotoxicity was independent of the quantitation standard used. This study has provided a rigorous assessment of data processing, relative quantitation, and pattern recognition methods, and the utility of applying these methods to the classification of NMR-derived toxicological data. The considerable potential of the NMR-pattern recognition approach in the assessment of nephrotoxicity has also been confirmed with the discovery of new combinations of molecular markers of renal cellular damage.

Studies on the comparative toxicity of S-(1,2-dichlorovinyl)-L-cysteine, S-(1,2-dichlorovinyl)-L-homocysteine and 1,1,2-trichloro-3,3,3-trifluoro-1-propene in the Fischer 344 rat.

The renal tubular toxicity of various halogenated xenobiotics has been attributed to their enzymatic bioactivation to reactive intermediates by S-conjugation. A combination of high resolution proton nuclear magnetic resonance (1H NMR) spectroscopy of urine, renal histopathology and more routinely used clinical chemistry methods has been used to explore the acute toxic and biochemical effects of S-(1,2-dichlorovinyl)-L-cysteine (DCVC), S-(1,2-dichlorovinyl)-L-homocysteine (DCVHC) and 1,1,2-trichloro-3,3,3-trifluoro-1-propene (TCTFP) up to 48 h following their administration to male Fischer 344 (F344) rats. In the absence of gross renal pathology, 1H NMR urinalysis revealed increased excretion of the tricarboxylic acid cycle intermediates citrate and succinate following DCVC administration. In contrast, both DCVHC and TCTFP produced functional defects in the S2 and S3 segments of the proximal tubule that were confirmed histologically. In these cases, 1H NMR urinalysis revealed increased excretion of glucose, L-lactate, acetate and 3-D-hydroxybutyrate (HB) as well as selective amino aciduria (alanine, valine, glutamate and glutamine). The significance of the proximal nephropathies induced by DCVHC and TCTFP is discussed in relation to biochemical observations on other xenobiotics that are toxic by similar mechanisms.

Studies of the biochemical toxicology of uranyl nitrate in the rat.

High resolution 1H NMR spectroscopy of urine and plasma, conventional clinical chemical methods and histopathology have been applied to investigate the effects of uranyl nitrate (UN) on renal function and biochemistry in the Fischer 344 (F344) rat. Administration of UN (5-20 mg/kg) to male F344 rats resulted in a dose-related proximal nephropathy assessed conventionally by histopathology and urinary excretion of N-acetyl-beta-D-glucosaminidase (NAG), and related to changes in the patterns of low MW metabolites observed in 400 MHz 1H NMR spectra of urine. The changes in urinary metabolite profiles included elevations in glucose accompanied by minor elevations in certain amino acids (alanine, valine and glutamate). 1H NMR urinalysis also revealed altered excretion of low MW metabolites which are not routinely measured, such as L-lactate, acetate, citrate, succinate and 2-oxoglutarate (2-OG). In addition, the striking appearance of high concentrations of 3-D-hydroxybutyrate (HB) in the urine was noted, in the absence of acetoacetate or acetone, and it is suggested that this may provide a new marker of proximal tubular damage for certain types of nephrotoxic mechanism. Broadening of the 1H NMR signals of citrate following 10 mg/kg UN was shown to be due to a dynamic exchange process involving chelation with urinary Ca2+ and Mg2+ ions. Conventional biochemical analysis of plasma from UN-treated rats revealed dose-related increases in creatinine, urea and HB concentrations. 1H NMR-detected evidence of raised alanine amino-transferase (ALT) levels in rats administered the highest dose of UN was indicated by the partial deuteration of alanine in lyophilised plasma reconstituted in 2H2O. The degree of 1H NMR-detected abnormalities agreed well with histopathological observations and conventional biochemical indices of nephrotoxicity and more fully characterised the renal changes produced by UN. The significance of HB-uria in UN-induced proximal nephropathy is discussed in relation to biochemical observations on other proximal nephrotoxins.

Raised transaminase activity of blood plasma from rats with experimentally-induced kidney damage detected by spin-echo 1H-NMR spectroscopy.

We report the application of spin-echo 1H-NMR spectroscopy to the detection of raised plasma transaminase activity in rats treated with the nephrotoxic cephalosporin antibiotic cephaloridine (CPH). Spin-echo 1H-NMR analysis of lyophilized plasma, reconstituted in H2O reveals a doublet at delta 1.48 for alanine. However when samples were reconstituted with 2H2O we noted that in samples from CPH-treated rats (but not in control samples) there was a variable degree of appearance of a singlet at delta 1.47 together with a reduction in the doublet at delta 1.48. We suggest that this is due to the release of transaminases from damaged tissue which, via a reversible conversion of alanine to pyruvate, causes selective deuteration of alanine at the alpha-hydrogen (alpha-CH) position. This observation suggests that these 1H-NMR spectral patterns are dependent on the level of plasma transaminases and this may provide a novel indicator of tissue damage.