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Dimension reduction for physiological variables using graphical modeling.

In intensive care, physiological variables of the critically ill are measured and recorded in short time intervals. The proper extraction and interpretation of the essential information contained in this flood of data can hardly be done by experience alone. Typically, decision making in intensive care is based on only a few selected variables. Alternatively, for a dimension reduction statistical latent variable techniques like principal component analysis or factor analysis can be applied. However, the interpretation of latent components extracted by these methods may be difficult. A more refined analysis is needed to provide suitable bedside decision support. Graphical models based on partial correlations provide information on the relationships among physiological variables that is helpful for variable selection and for identifying interpretable latent components. In a comparative study we investigate how much of the variability of the observed multivariate physiological time series can be explained by variable selection, by standard principal component analysis and by extracting latent compo-nents from groups of variables identified in a graphical model.

Aged↗

Proposal for reclassification of the TNM staging system in patients with locally advanced (pT3-4) renal cell carcinoma according to the cancer-related outcome.

OBJECTIVES: The optimal stratification of locally advanced renal cell carcinoma (RCC) is controversial, with the prognostic relevance of ipsilateral adrenal gland invasion and cranial extension of vena cava thrombosis being the most debatable issues. We evaluated the prognosis of patients with locally advanced RCC and identified a new model to stratify their outcome. MATERIALS AND METHODS: We analyzed the data of 227 patients who had undergone partial or radical nephrectomy for pT3-4 RCC at two academic centers between 1986 and 2002. The log-rank test and Cox proportional hazards model were used for univariate and multivariate analysis, respectively. RESULTS: At a median follow-up of 29 mo, we censored 108 (47.6%) cancer-related deaths. On univariate analysis, the 2002 T stage was not statistically significant. According to cancer-related outcome, we identified three subgroups of patients with different prognoses: pT3a(n): tumors with perirenal fat invasion or renal vein thrombosis or thrombosis within the vena cava below the diaphragm; pT3b(n): tumors with renal vein thrombosis or thrombosis within the vena cava below the diaphragm and concomitant perirenal fat invasion; pT4(n): adrenal gland or Gerota fascia invasion or thrombosis within the vena cava above the diaphragm. The three subgroups had significantly different prognoses. The new reclassification was an independent predictive variable on multivariate analysis, as well as the pathologic lymph node stage. CONCLUSIONS: The 2002 version of TNM of locally advanced RCC did not stratify patient outcome. The present study suggests the possibility of reclassifying pT3-4 RCC into three categories capable of predicting cancer-specific survival, regardless of all other prognostic factors.

Aged↗

A numerical model and spreadsheet interface for pumping test analysis.

Curve-matching techniques have been the standard method of aquifer test analysis for several decades. A variety of techniques provide the capability of evaluating test data from confined, unconfined, leaky aquitard, and other conditions. Each technique, however, is accompanied by a set of assumptions, and evaluation of a combination of conditions can be complicated or impossible due to intractable mathematics or nonuniqueness of the solution. Numerical modeling of pumping tests provides two major advantages: (1) the user can choose which properties to calibrate and what assumptions to make; and (2) in the calibration process the user is gaining insights into the conceptual model of the flow system and uncertainties in the analysis. Routine numerical modeling of pumping tests is now practical due to computer hardware and software advances of the last decade. The RADFLOW model and spreadsheet interface presented in this paper is an easy-to-use numerical model for estimation of aquifer properties from pumping test data. Layered conceptual models and their properties are evaluated in a trial-and-error estimation procedure. The RADFLOW model can treat most combinations of confined, unconfined, leaky aquitard, partial penetration, and borehole storage conditions. RADFLOW is especially useful in stratified aquifer systems with no identifiable lateral boundaries. It has been verified to several analytical solutions and has been applied in the Snake River Plain Aquifer to develop and test conceptual models and provide estimates of aquifer properties. Because the model assumes axially symmetrical flow, it is limited to representing multiple aquifer layers that are laterally continuous.

Environmental Monitoring↗

Acetylator phenotype-dependent and -independent expression of arylamine N-acetyltransferase isozymes in rapid and slow acetylator inbred rat liver.

Although mouse, hamster, and rabbit models of the human N-acetylation polymorphism have been identified and characterized, many investigations of arylamine toxicity and carcinogenicity are carried out in the rat, particularly the Fischer 344 (F-344) inbred rat. We partially characterized a new rat model of the N-acetylation polymorphism by determining expression of arylamine N-acetyltransferase activities in liver cytosols derived from adult male inbred F-344, WKY, and their F1 hybrid rat strains. Levels of N-acetyltransferase activity differed significantly between the strains for many arylamine substrates, with highest levels in F-344, lowest levels in WKY, and intermediate levels in F1 hybrids of these two parental strains. However, for some other arylamine substrates, levels of N-acetyltransferase activity did not differ significantly between the rat strains. Partial purification of rat liver cytosols from the three strains resulted in identification of two N-acetyltransferase isozymes. The levels of N-acetyltransferase activity of one isozyme differed significantly between strains analogous to the pattern observed in crude cytosol. In contrast, the levels of N-acetyltransferase activity of the second isozyme did not differ between the strains. Based upon these results, the F-344 inbred strain is designated a rapid acetylator phenotype, the WKY inbred strain is designated a slow acetylator phenotype, and F1 hybrids of the two parental strains are designated intermediate acetylator phenotype. The identification of acetylator phenotype-dependent and -independent hepatic N-acetyltransferase isozymes in the inbred rat mimics the biochemical basis for acetylator phenotype-dependent and -independent expressions of N-acetylation in humans and other mammalian species.

Acetylation↗

Evidence for the partial dominance of viability genes contributing to inbreeding depression in Mimulus guttatus.

The relative importance of different modes of gene expression of viability genes contributing to inbreeding depression was investigated in the wild plant, Mimulus guttatus. Viability genes were identified by self-fertilizing 31 outbred plants, each heterozygous for three to nine unlinked allozyme markers, and analyzing segregation ratios of selfed progeny at maturity for deviations from 1:2:1 ratios. In this study, 24 linkages of viability genes to marker loci were detected. To infer the nature of gene action for these viability genes, a "model-free" graphical method was developed that examines the "space" of segregation ratios allowed by each of seven selection models (i.e., overdominance, complete recessivity, partial recessivity, additivity, partial dominance, complete dominance and underdominance). Using this method, we found that, of 24 linkages detected, 18 were consistent with either partial dominance, complete dominance or underdominance. Six were consistent with either partial recessivity, complete recessivity or overdominance. This finding indicates that, in these chromosomal segments identified by allozyme markers, partial dominance plays the predominant role in inbreeding depression. This is inconsistent with either the dominance or overdominance hypotheses proposed to account for inbreeding depression.

Crosses, Genetic↗

Protein folds from pair interactions: a blind test in fold recognition.

We submitted nine predictions to CASP2 using our fold recognition program ProFIT. Two of these structures were still unsolved by the end of the experiment, six had a recognizable fold, and one fold was new. Four predictions of the six recognizable folds were correct. Two models were excellent in terms of alignment quality (T0031, T0004): in one the alignment was partially correct (T0014), and one fold was correctly identified (T0038). We discuss improvements of the program and analyze the prediction results.

Aldose-Ketose Isomerases↗

Age-related changes in D2 receptor binding with iodine-123-iodobenzofuran SPECT.

UNLABELLED: The purpose of this study was to evaluate the effects of age on D2 receptor binding with 123I-iodobenzofuran (IBF) SPECT. METHODS: Subjects were 40 healthy volunteers (age 19-83 yr), including 6 who had test/retest studies. Scans were acquired with a triple-head SPECT camera 3 hr postinjection of IBF (300 MBq). Striatal regions (caudate and putamen) were defined by two different region-of-interest (ROI) sets consisting of large volumes [(CLVs), 2.2 and 6.6 m] and small volumes [(SVs), 0.6 and 1.3 ml]. D2 binding (Rv=V3/V2) was quantified using our previously proposed multilinear regression technique. Effects of age on D2 binding were evaluated by fitting linear, exponential and logarithmic models. RESULTS: The mean Rvs were 26% lower than LV for both putamen and caudate than the corresponding values from the SV due to the partial-volume effect. Although the identifiability of Rv using SV deteriorated slightly, the test/retest reproducibility of Rv measurements was equally excellent for LV and SV. The mean Rvs were 11% higher for putamen compared with those for caudate. D2 binding declined significantly with age (p < 10(-5)) for all three models. The nonlinear models were slightly superior to the linear model in describing the relationship between Rv and age. In these models, D2 binding declined with age, equally for caudate and putamen at 7%-13% per decade; the decline was progressively smaller with age. CONCLUSION: IBF SPECT permitted reliable measurements of D2 binding in the caudate or putamen separately using small ROI volumes that significantly improved the quantitation loss from the partial-volume effect. Our results agreed with previous PET and postmortem findings of D2 binding losses with age. However, these age effects may be nonlinear. Age-related changes in D2 binding must be taken into consideration in clinical IBF SPECT investigations.

Adult↗

Differential display and cloning of messenger RNAs from the late phase of rat liver regeneration.

Liver regeneration allows for recovery from hepatic injuries and regeneration after partial hepatectomy has been extensively used as a model system to study mitogenesis. Many genes have been identified that are induced in the early growing phase of liver regeneration but only a few genes have been identified that are induced in the later stages of regeneration before growth arrest. We used the newly discovered differential display method to identify several genes that were found to be induced at this later stage. Two of them were analyzed further. DNA sequencing of one of them revealed perfect homology to ribosomal protein S24. The sequence of the other gene did not have extensive homology to any sequence in the databases. These results may suggest a role of these two genes in the growth arrest phase of liver regeneration.

Aniline Compounds↗

Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 A resolution.

The X-ray crystal structure of the enzyme Streptomyces griseus aminopeptidase (SGAP) has been determined in its double zinc form to 1.75 A resolution, in its apo-enzyme from (zinc removed) to 2.1 A resolution, and as a mercury replaced derivative to 2.1 A resolution. The structure solution was achieved by single isomorphous replacement with phasing from anomalous scattering (SIRAS), followed by density modification with histogram matching. The protein consists of a central beta-sheet made up of eight parallel and antiparallel strands, surrounded by helices on either side. The active site is located at the carbonyl ends of two middle strands of the beta-sheet region. Two sections of the chain that could not be traced were Glu196 to Arg202, which borders the active site, and the final seven C-terminal residues starting with Gly278. The active site contains two zinc cations, each with similar ligands, at a distance of 3.6 A from each other. An unknown molecule appears to be bound to both zinc ions in the active site at partial occupancy and has been modelled as a phosphate ion. A calcium binding site has also been identified, consistent with the observations that calcium modulates the activity of the enzyme, and increases its heat stability. The mechanism by which the calcium cation modulates enzyme activity is not apparent, since the location of the calcium binding site is approximately 25 A distant from the active site zinc ions. Comparison of the structure of SGAP to other known aminopeptidases shows that the enzyme is most similar to Aeromonas proteolytica aminopeptidase (AAP). Both enzymes share a similar topology, although the overall sequence identity is very low (24% in aligned regions). The coordination of the two active site zinc cations in SGAP resembles that of AAP. These two microbial enzymes differ from bovine lens leucine aminopeptidase (LAP) in both overall structure and in coordination of the two zinc ions.

Aeromonas↗

Proximally delivered dilute heparin does not improve circuit life in continuous venovenous haemodiafiltration.

OBJECTIVE: To assess the effect on circuit life in continuous venovenous haemodiafiltration (CVVHD) by manipulating heparin dilution and point of administration. DESIGN: Repeated crossover design. Cases were randomised for first circuit and heparin dilution, after which crossovers occurred until treatment was stopped. SETTING: A 24-bed combined general and surgical intensive care unit admitting 1900 patients a year. On average, 54 cases a year receive CVVHD. PATIENTS: 26 critically ill adult patients requiring CVVHD were enrolled, 18 of whom used at least one standard circuit and one modified circuit. INTERVENTIONS: Two circuit configurations and heparin dilutions were compared. In combination A, standard CVVHD blood lines and heparin concentration (100 units/ml) were used. In combination B, heparin was delivered in a more dilute volume (10 units/ml) via a modified circuit design with an administration port immediately adjacent to the venous access. MEASUREMENTS AND RESULTS: 18 randomised crossovers of circuits A and B occurred. Mean/median circuit life for the standard heparin/circuit combination A was 20.1/17.5 (SD 14.6) and for the modified combination B 21.4/15.4 (SD 19.2). There was no significant difference between circuits (paired t-test, p = 0.8175). To identify other factors which could have influenced circuit life (platelet count, heparin dose and pre- and post-filter activated partial thromboplastin time, APTT) all circuits terminated for the reasons identified (n = 105) were analysed using linear modelling. Survival analysis was used to determine the survival function of the circuit. Pre-heparin APTT was the only factor associated with an increase in filter life (p = 0.035). The hazard rate for filter failure was 0.049/h (95% confidence interval 0.04 to 0.06), the range of time until filters failed was 1.8 to 78.5 h. CONCLUSIONS: Proximally administered dilute heparin is not associated with a significant increase in circuit life.

Acute Kidney Injury↗

Parallel hybrid modeling methods for a full-scale cokes wastewater treatment plant.

Parallel hybrid modeling methods are applied to a full-scale cokes wastewater treatment plant. Within the hybrid model structure, a mechanistic model specifies the basic dynamics of the relevant process and a non-parametric model compensates for the inaccuracy of the mechanistic model. First, a simplified mechanistic model is developed based on Activated Sludge Model No. 1 and the specific process knowledge of the cokes wastewater treatment process. Then, the mechanistic model is combined with five different non-parametric models--feedforward back-propagation neural network, radial basis function network, linear partial least squares (PLS), quadratic PLS and neural network PLS (NNPLS)--in parallel configuration. These models are identified with the same data obtained from the plant operation to predict dynamic behavior of the process. The performance of each parallel hybrid model is compared based on their ease of model building, prediction accuracy and interpretability. For this application, the parallel hybrid model with NNPLS as non-parametric model gives better performance than other parallel hybrid models. In addition, the NNPLS model is used to analyze the behavior of the operation data in the reduced space and allows for fault detection and isolation.

Bioreactors↗

Reliability and validity of a new Medication Adherence Rating Scale (MARS) for the psychoses.

Medication compliance is one of the foremost problems affecting neuroleptic efficacy in psychiatric patients. To date, compliancy has most commonly been assessed with the Drug Attitude Inventory (DAI) developed by Hogan et al. (Hogan, T.P., Awad, A.G., Eastwood, R., 1983. A self-report scale predictive of drug compliance in schizophrenics: reliability and discriminative validity. Psychol. Med. 13, 177-183). The present study identified several deficiencies in the DAI. Using the partial credit version of the Item Response Theory measurement model, the DAI was refined with the aim of greater validity and clinical utility. The new inventory was administered to 66 patients, the majority of whom were diagnosed with schizophrenia. When available, lithium levels and carer ratings of compliance were also recorded and used to verify compliancy. The new inventory appears to be a valid and reliable measure of compliancy for psychoactive medications.

Adult↗

Mining the NCI anticancer drug discovery databases: genetic function approximation for the QSAR study of anticancer ellipticine analogues.

The U.S. National Cancer Institute (NCI) conducts a drug discovery program in which approximately 10,000 compounds are screened every year in vitro against a panel of 60 human cancer cell lines from different organs of origin. Since 1990, approximately 63,000 compounds have been tested, and their patterns of activity profiled. Recently, we analyzed the antitumor activity patterns of 112 ellipticine analogues using a hierarchical clustering algorithm. Dramatic coherence between molecular structures and activity patterns was observed qualitatively from the cluster tree. In the present study, we further investigate the quantitative structure-activity relationships (QSAR) of these compounds, in particular with respect to the influence of p53-status and the CNS cell selectivity of the activity patterns. Independent variables (i.e., chemical structural descriptors of the ellipticine analogues) were calculated from the Cerius2 molecular modeling package. Important structural descriptors, including partial atomic charges on the ellipticine ring-forming atoms, were identified by the recently developed genetic function approximation (GFA) method. For our data set, the GFA method gave better correlation and cross-validation results (R2 and CVR2 were usually approximately 0.3 higher) than did classical stepwise linear regression. A procedure for improving the performance of GFA is proposed, and the relative advantages and disadvantages of using GFA for QSAR studies are discussed.

Algorithms↗

Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection.

Pseudomonas aeruginosa, an opportunistic human pathogen, is a major causative agent of mortality and morbidity in immunocompromised patients and those with cystic fibrosis genetic disease. To identify new virulence genes of P. aeruginosa, a selection system was developed based on the in vivo expression technology (IVET) that was first reported in Salmonella system. An adenine-requiring auxotrophic mutant strain of P. aeruginosa was isolated and found avirulent on neutropenic mice. A DNA fragment that can complement the mutant strain, containing purEK operon that is required for de novo biosynthesis of purine, was sequenced and used in the IVET vector construction. By applying the IVET selection system to a neutropenic mouse infection model, genetic loci that are specifically induced in vivo were identified. Twenty-two such loci were partially sequenced and analyzed. One of them was a well-studied virulence factor, pyochelin receptor (FptA), that is involved in iron acquisition. Fifteen showed significant homology to reported sequences in GenBank, while the remaining six did not. One locus, designated np20, encodes an open reading frame that shares amino acid sequence homology to transcriptional regulators, especially to the ferric uptake regulator (Fur) proteins of other bacteria. An insertional np20 null mutant strain of P. aeruginosa did not show a growth defect on laboratory media; however, its virulence on neutropenic mice was significantly reduced compared with that of a wild-type parent strain, demonstrating the importance of the np20 locus in the bacterial virulence. The successful isolation of genetic loci that affect bacterial virulence demonstrates the utility of the IVET system in identification of new virulence genes of P. aeruginosa.

Amino Acid Sequence↗

Cooperative regulation of the invasive and metastatic phenotypes by different domains of the type I insulin-like growth factor receptor beta subunit.

The receptor for the type 1 insulin-like growth factor (IGF-I) regulates multiple cellular functions impacting on the metastatic phenotype of tumor cells, including cellular proliferation, anchorage-independent growth, survival, migration, synthesis of the 72-kDa type IV collagenase and invasion. We have used site-directed mutagenesis to generate domain-specific mutants of the receptor beta subunit to analyze the role of specific tyrosines in the regulation of the invasive/metastatic phenotype. Poorly invasive M-27 carcinoma cells expressing low receptor numbers were transfected with a plasmid vector expressing IGF-I receptor cDNA in which single or multiple tyrosine codons in the kinase domain, namely Tyr-1131, Tyr-1135, and Tyr-1136 or the C-terminal tyrosines 1250 and 1251 were substituted with phenylalanine. Changes in the invasive and metastatic properties were analyzed relative to M-27 cells expressing the wild type receptor. We found that cells expressing the Y1131F,Y1135F,Y1136F or Y1135F receptor mutants lost all IGF-IR-dependent functions and their phenotypes were indistinguishable from, or suppressed relative to, the parent line. The Y1250F,Y1251F substitution abolished anchorage-independent growth, cell spreading, and the anti-apoptotic effect of IGF-I whereas all other IGF-IR-dependent phenotypes were either unperturbed (i.e. mitogenicity) or only partially reduced (migration and invasion). The results identify three types of receptor-dependent functions in this model: those dependent only on an intact kinase domain (DNA synthesis), those dependent equally on kinase domain and Tyr-1250/1251 signaling (e.g. apoptosis, soft agar cloning) and those dependent on kinase domain and enhanced through Tyr-1250/1251 signaling (migration, invasion). They suggest that signals derived from both regions of the receptor cooperate to enhance tumor metastasis.

Cell Movement↗

Integrated Metabolomic and Transcriptomic Analysis Reveals Tissue-Specific Secondary Metabolic Differentiation and Indole Alkaloid Accumulation in Evodia rutaecarpa.

Evodia rutaecarpa is a valuable medicinal plant, yet its non-medicinal tissues remain largely underexplored. Here, we integrated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics and RNA sequencing (RNA-seq) transcriptomics to systematically profile the metabolic and transcriptional landscapes of roots, stems, leaves, and flowers of Evodia rutaecarpa (Juss.) Benth. Our aim was to characterize tissue-specific metabolic differentiation and its underlying transcriptional regulatory mechanisms. Metabolomic analysis, employing principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) with robust model parameters (R2Y > 0.9, Q2 > 0.5), identified 3090 differential metabolite features (variable importance in projection, VIP > 1.0; p < 0.05) across the four tissues, which exhibited distinct tissue-specific clustering patterns. Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and weighted gene co-expression network analysis (WGCNA) revealed that roots specifically accumulated quinolone alkaloids and flavonoid glycosides, accompanied by the coordinated upregulation of genes involved in flavonoid and phenylpropanoid biosynthetic pathways. In contrast, stems, leaves, and flowers were enriched in indole alkaloids (evodiamine and rutaecarpine) and volatile oil precursors, with concurrent upregulation of genes involved in tryptophan metabolism and indole alkaloid biosynthesis (e.g., tryptophan decarboxylase, TDC; s N-methyltransferase, NMT). Notably, leaves and flowers displayed particularly high accumulation levels of these bioactive alkaloids, suggesting their potential as alternative sources for industrial and pharmaceutical applications. WGCNA further identified multiple transcription factors and structural gene modules tightly correlated with evodiamine accumulation, offering promising candidate regulators for future biosynthetic pathway engineering. Collectively, this multi-omics integration study systematically elucidates the tissue-partitioned secondary metabolism of Evodia rutaecarpa (Juss.) Benth. and provides a solid scientific foundation for full-plant resource utilization, targeted development of non-medicinal tissues, and future metabolic engineering of indole alkaloid production.

Evodia rutaecarpa↗

VR1 protein expression increases in undamaged DRG neurons after partial nerve injury.

Changes in phenotype or connectivity of primary afferent neurons following peripheral nerve injury may contribute to the hyperalgesia and allodynia associated with neuropathic pain conditions. Although earlier studies using partial nerve injury models have focused on the role of damaged fibres in the generation of ectopic discharges and pain, it is now thought that remaining undamaged fibres may be equally important. We have examined the expression of the sensory neuron-specific cation channel Vanilloid Receptor 1 (VR1), an important transducer of noxious stimuli, in three models of nerve injury in the rat, using anatomical separation or fluorescent retrograde tracers to identify damaged or undamaged sensory neurons. After total or partial sciatic nerve transection, or spinal nerve ligation, VR1-immunoreactivity (IR) was significantly reduced in the somata of all damaged dorsal root ganglion (DRG) neuronal profiles, compared to controls. However, after partial transection or spinal nerve ligation, VR1 expression was greater in the undamaged DRG somata than in controls. Unexpectedly, after L5 spinal nerve ligation, VR1-IR of the A-fibre somata increased approximately 3-fold in the uninjured L4 DRG compared to controls; a much greater increase than seen in the somata with C-fibres. Furthermore, we found that VR1-IR persisted in the transected sciatic nerve proximal to the lesion, despite its down-regulation in the damaged neuronal somata. This persistence in the nerve proximal to the lesion after nerve section, together with increased VR1 in DRG neurons left undamaged after partial nerve injury, may be crucial to the development or maintenance of neuropathic pain.

Animals↗

A molecular modeling and QSAR study of suppressors of the growth of Trypanosoma cruzi epimastigotes.

In this work, we have used molecular modeling and QSAR tools to study 18 dithiocarbamate suppressors of the growth of Trypanosoma cruzi epimastigotes, which have been reported in the literature as superoxide dismutase (SOD) inhibitors. The principal component analysis (PCA) showed that the descriptors superficial area, heat of formation, logarithm of the partition coefficient, charge of the nitrogen atom from the dithiocarbamate group and Charges of the two carbon atoms adjacent to that nitrogen are responsible for the classification between the higher and lower trypanomicid activity. Using multiple linear regression (MLR) and docking methods it was possible to identify the probable bioactive isomers that suppress of the growth of T. cruzi epimastigotes. Our best partial least square (PLS) model obtained with these six descriptors yields a good correlation between experimental and predicted biological activities and compares two different SODs as possible target for interaction with the dithiocarbamates.

Amino Acid Sequence↗