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Flexible construction of hierarchical scale-free networks with general exponent.

Extensive studies have been done to understand the principles behind architectures of real networks. Recently, evidence for hierarchical organization in many real networks has also been reported. Here, we present a hierarchical model that reproduces the main experimental properties observed in real networks: scale-free of degree distribution P (k) [frequency of the nodes that are connected to k other nodes decays as a power law P (k) approximately k(-gamma) ] and power-law scaling of the clustering coefficient C (k) approximately k(-1) . The major points of our model can be summarized as follows. (a) The model generates networks with scale-free distribution for the degree of nodes with general exponent gamma>2 , and arbitrarily close to any specified value, being able to reproduce most of the observed hierarchical scale-free topologies. In contrast, previous models cannot obtain values of gamma>2.58 . (b) Our model has structural flexibility because (i) it can incorporate various types of basic building blocks (e.g., triangles, tetrahedrons, and, in general, fully connected clusters of n nodes) and (ii) it allows a large variety of configurations (i.e., the model can use more than n-1 copies of basic blocks of n nodes). The structural features of our proposed model might lead to a better understanding of architectures of biological and nonbiological networks.

Journal Article↗

The tmRNA database (tmRDB).

As of September, 1998, a total of 43 sequences are contained within the tmRNA database (tmRDB). The tmRNA sequences are arranged alphabetically and ordered phylogenetically. The alignment of the tmRNAs emphasizes the basepairs that are supported by comparative sequence analysis and establishes minimal secondary structures for the known tmRNAs. A corresponding alignment of the predicted tmRNA-encoded tag peptides is presented. The tmRDB also offers a small number of RNA secondary structure diagrams and PDB-formatted three-dimensional models generated with the program ERNA-3D. The data are available freely at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.++ +html

Bacteria↗

Accuracy and reproducibility of CFD predicted wall shear stress using 3D ultrasound images.

Computational fluid dynamics (CFD) flow simulation techniques have the potential to enhance our understanding of how haemodynamic factors are involved in atherosclerosis. Recently, 3D ultrasound has emerged as an alternative to other 3D imaging techniques, such as magnetic resonance angiography (MRA). The method can be used to generate realistic vascular geometry suitable for CFD simulations. In order to assess accuracy and reproducibility of the procedure from image acquisition to reconstruction to CFD simulation, a human carotid artery bifurcation phantom was scanned three times using 3D ultrasound. The geometry was reconstructed and flow simulations were carried out on the three sets as well as on a model generated using computer aided design (CAD) from the geometric information given by the manufacturer. It was found that the three reconstructed sets showed good reproducibility as well as satisfactory quantitative agreement with the CAD model. Analyzing two selected locations probably representing the 'worst cases,' accuracy comparing ultrasound and CAD reconstructed models was estimated to be between 7.2% and 7.7% of the maximum instantaneous WSS and reproducibility comparing the three scans to be between 8.2% and 10.7% of their average maximum.

Carotid Arteries↗

The program for phenotyping of genetically modified animals at AstraZeneca.

Genetically modified mice offer a wide range of possibilities in preclinical drug discovery, e.g. for use in target identification, target validation and disease model generation. However, genomic modification and alteration in gene expression may cause unpredicted phenotypic alterations in the organism other than the intended ones. The aim of this study was to determine the importance of establishing the phenotype of transgenic and knockout mice models for use in pharmaceutical research. A total number of 51 mouse models (transgenic and knockout) produced at AstraZeneca during a 4 year period were subjected to a thorough phenotyping package covering clinical as well as morphological aspects. Phenotype abnormalities were recorded in 36 (70.6%) of the mouse models. The majority of findings were considered to be minor in magnitude. Histopathological changes related to the genotype of the animals were observed in 33% of the mouse models, underlining the importance of pathology in the phenotyping program.

Animals↗

Solution of the structure of the cofactor-binding fragment of CysB: a struggle against non-isomorphism.

The elucidation of the structure of CysB(88-324) by multiple isomorphous replacement (MIR) techniques was seriously delayed by problems encountered at every stage of the analysis. There was extensive non-isomorphism both between different native crystals and between native and heavy-atom-soaked crystals. The heavy-atom substitution was invariably weak and different soaking experiments frequently led to substitution at common sites. These correlated heavy-atom binding sites resulted in an overestimation of the phase information. Missing low-resolution reflections in the native data set, constituting only 2% of the total observations, reduced the power of density modification and phase refinement. Finally, the extensive dimer interface made it difficult to isolate a single molecule in the course of model building into the MIR maps. The power of maximum likelihood refinement (REFMAC) was exploited in solving the structure by means of iterative cycles of refinement of a partial model, initially comprising only 30% of the protein atoms in the final coordinate set. This technique, which uses experimental phases, can automatically discriminate the correct and incorrect parts of electron-density maps and give properly weighted combined phases which are better than the experimental or calculated ones. This allowed the model to be gradually extended by manual building into improved electron-density maps. A model generated in this way, containing just 50% of the protein atoms, proved good enough to find the transformations needed for multi-crystal averaging between different crystal forms. The averaging regime im-proved the phasing dramatically such that the complete model could be built. The problems, final solutions and some possible causes for the observed lack of isomorphism are discussed.

Bacterial Proteins↗

Intellectual development within transracial adoptive families: retesting the confluence model.

The confluence model of intellectual development was estimated for a within-family sample of 321 children from 101 transracial adoptive families. Mental ages of the children and their parents, as well as birth or adoption intervals, were used in a nonlinear least-squares estimation procedure to obtain children's predicted mental ages. Contrary to an earlier report using these data, the confluence model performed quite well, accounting for up to 50% of the variance in mental age. When the relationship between chronological and mental age was taken into account, the predictive power of the model was reduced but not eliminated. The confluence model was also fitted separately to various subsamples. The model generated a good fit to the data from both biological and adopted children and fit the data from early-adopted children much better than the data from later-adopted children. Both findings were taken as evidence that the confluence model provides an environmental account of intellectual development within the family.

Adolescent↗

Divergent evolution of a structural proteome: phenomenological models.

We develop models of the divergent evolution of genomes; the elementary object of sequence dynamics is the protein structural domain. To identify patterns of organization that reflect mechanisms of evolution, we consider the individual genomes of many procaryote species, studying the arrangement of protein structural domains in the space of all polypeptide structures. We view the network of structural similarities as a graph, called the organismal Protein Domain Universe Graph (oPDUG); vertices represent types of structural domains and edges represent strong structural similarity. As observed before, each oPDUG is a highly nonrandom graph, as evidenced in the vertex degree distribution, which resembles a Pareto law (which has a power-law asymptotic). To explain this and other peculiar properties of the oPDUGs, we construct an evolving-graph model for the long-timescale evolutionary dynamics of oPDUGs, containing only divergent mechanisms of domain discovery. The model generates degree distributions (resembling Pareto laws) and clustering-coefficient distributions that are characteristic of the oPDUGs. In the infinite-graph limit, we analytically compute the exponent for specific biological parameters, as well as the complete phase diagram of the model, finding two distinct regimes of domain innovation dynamics. Thus, divergent evolutionary dynamics quantitatively explains the nonrandom organization of oPDUGs.

Bacterial Proteins↗

Minimal model for membrane oscillations in the pancreatic beta-cell.

Following the experimental findings of Atwater et al. (In Biochemistry Biophysics of the Pancreatic-beta-Cell, George Thieme Verlag, New York, 100-107), we have formulated a mathematical model for ionic and electrical events that take place in pancreatic-beta-cells. Our formulation incorporates a Hodgkin-Huxley type gating mechanism for Ca2+ and K+ channels, in addition to Ca2+ gated K+-channels. Consistent with the experimental observations, our model generates spikes and bursts in beta-cell membrane potentials and gives the correct responses to additions of glucose, quinine, and tetraethylammonium ions. The response of the oscillations to ouabain and changing concentrations of external K+ can be incorporated into the present model, although a more complete treatment would require inclusion of the Na+/K+ pump.

Animals↗

General melting point prediction based on a diverse compound data set and artificial neural networks.

We report the development of a robust and general model for the prediction of melting points. It is based on a diverse data set of 4173 compounds and employs a large number of 2D and 3D descriptors to capture molecular physicochemical and other graph-based properties. Dimensionality reduction is performed by principal component analysis, while a fully connected feed-forward back-propagation artificial neural network is employed for model generation. The melting point is a fundamental physicochemical property of a molecule that is controlled by both single-molecule properties and intermolecular interactions due to packing in the solid state. Thus, it is difficult to predict, and previously only melting point models for clearly defined and smaller compound sets have been developed. Here we derive the first general model that covers a comparatively large and relevant part of organic chemical space. The final model is based on 2D descriptors, which are found to contain more relevant information than the 3D descriptors calculated. Internal random validation of the model achieves a correlation coefficient of R(2) = 0.661 with an average absolute error of 37.6 degrees C. The model is internally consistent with a correlation coefficient of the test set of Q(2) = 0.658 (average absolute error 38.2 degrees C) and a correlation coefficient of the internal validation set of Q(2) = 0.645 (average absolute error 39.8 degrees C). Additional validation was performed on an external drug data set consisting of 277 compounds. On this external data set a correlation coefficient of Q(2) = 0.662 (average absolute error 32.6 degrees C) was achieved, showing ability of the model to generalize. Compared to an earlier model for the prediction of melting points of druglike compounds our model exhibits slightly improved performance, despite the much larger chemical space covered. The remaining model error is due to molecular properties that are not captured using single-molecule based descriptors, namely both inter- and intramolecular interactions and crystal packing, for which examples of and reasons for outliers are given.

Journal Article↗

A computational approach to botanical drug design by modeling quantitative composition-activity relationship.

Herbal medicine has been successfully applied in clinical therapeutics throughout the world. Following the concept of quantitative composition-activity relationship, the presented study proposes a computational strategy to predict bioactivity of herbal medicine and design new botanical drug. As a case, the quantitative relationship between chemical composition and decreasing cholesterol effect of Qi-Xue-Bing-Zhi-Fang, a widely used herbal medicine in China, was investigated. Quantitative composition-activity relationship models generated by multiple linear regression, artificial neural networks, and support vector regression exhibited different capabilities of predictive accuracy. Moreover, the proportion of two active components of Qi-Xue-Bing-Zhi-Fang was optimized based on the quantitative composition-activity relationship model to obtain new formulation. Validation experiments showed that the optimized herbal medicine has greater activity. The results indicate that the presented method is an efficient approach to botanical drug design.

Algorithms↗

Review of insulin and insulin-like growth factor expression, signaling, and malfunction in the central nervous system: relevance to Alzheimer's disease.

Interest in characterizing the role of impaired insulin actions in Alzheimer's disease (AD) and vascular dementia is growing exponentially. This review details what is currently known about insulin, insulin-like growth factor type I (IGF-I) and IGF-II proteins and their corresponding receptors in the brain, and delineates the major controversies pertaining to alterations in the expression and function of these molecules in AD. The various experimental animal models generated by over-expression, mutation, or depletion of genes that are critical to the insulin or IGF signaling cascades are summarized, noting the degrees to which they reproduce the histopathological, biochemical, molecular, or behavioral abnormalities associated with AD. Although no single model was determined to be truly representative of AD, depletion of the neuronal insulin receptor and intracerebroventricular injection of Streptozotocin reproduce a number of important aspects of AD-type neurodegeneration, and therefore provide supportive evidence that AD may be caused in part by neuronal insulin resistance, i.e. brain diabetes. The extant literature did not resolve whether the CNS insulin resistance in AD represents a local disease process, or complication/extension of peripheral insulin resistance, i.e. chronic hyperglycemia, hyperinsulinemia, and Type 2 diabetes mellitus. The available epidemiological data are largely inconclusive with regard to the contribution of Type 2 diabetes mellitus to cognitive impairment and AD-type neurodegeneration. A major conclusion drawn from this review is that there is a genuine need for thorough and comprehensive study of the neuropathological changes associated with diabetes mellitus, in the presence or absence of superimposed AD or vascular dementia. Strategies for intervention may depend entirely upon whether the CNS disease processes are mediated by peripheral, central, or both types of insulin resistance.

Alzheimer Disease↗

Fluorescence imaging of multiple myeloma cells in a clinically relevant SCID/NOD in vivo model: biologic and clinical implications.

The in vivo preclinical testing of investigational therapies for multiple myeloma (MM) is hampered by the fact that models generated to recapitulate the development of diffuse skeletal lesions after i.v. injections of tumor cells do not allow for ready detection of the exact site(s) of lesions or for comprehensive monitoring of their progression. We therefore developed an in vivo MM model in severe combined immunodeficient/nonobese diabetic mice in which diffuse MM lesions developed after tail vein i.v. injection of human RPMI-8226/S MM cells stably transfected with a construct for green fluorescent protein (GFP). Using whole-body real-time fluorescence imaging to detect autofluorescent GFP(+) MM cells (and confirming the sensitivity and specificity of these findings both histologically and by flow cytometric detection of GFP(+) cells), we serially monitored, in a cohort of 75 mice, the development and progression of MM tumors. Their anatomical distribution and pathophysiological manifestations were consistent with the clinical course of MM in human patients, i.e., hallmarked by major involvement of the axial skeleton (e.g., spine, skull, and pelvis) and frequent development of paralysis secondary to spinal lesions without significant tumor spread to lungs, liver, spleen, or kidney. This model both recapitulates the diffuse bone disease of human MM and allows for serial whole-body visualization of its spatiotemporal progression. It therefore provides a valuable in vivo system to elucidate the molecular mechanisms underlying the marked osteotropism of MM, particularly for the axial skeleton, and for assessment of in vivo activity of novel anti-MM therapeutics.

Animals↗

BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.

Genome-scale metabolic models are widely used to investigate cellular metabolism, but their interpretation and comparison are limited by the lack of reproducible pathway-level visualizations with a common spatial organization. This study presents BioEMMA, a Python-based tool for the automated generation of model-specific metabolic pathway maps in the Escher JSON format using coordinate information from curated KEGG pathway maps. BioEMMA parses KGML files, map reaction and metabolite identifiers to model database namespaces, filters pathway elements according to an input SBML model, adds non-primary metabolites, reconstructs Escher-compatible layouts, and supports flux visualization. The tool was integrated into a reproducible BioUML workflow for metabolic model reconstruction. BioEMMA was evaluated using the e_coli_core model and the KEGG glycolysis/gluconeogenesis pathway while generating a model-specific map with overlaid FBA fluxes. It was then applied to compare E. coli reconstructions generated by gapseq, ModelSEEDpy, and Reconstructor across three central carbon metabolism pathways. To broaden the evaluation, BioEMMA was applied using 87 prokaryotic BiGG models and three eukaryotic models. The analysis revealed pathway-specific differences in reaction coverage, shared and model-specific reactions, and predicted flux activity. BioEMMA therefore provides a reproducible framework for pathway-level visualization and comparison of genome-scale metabolic reconstructions within a common spatial coordinate system.

Escher maps↗

Early coagulopathy predicts mortality in trauma.

BACKGROUND: Coagulopathy and hemorrhage are known contributors to trauma mortality; however, the actual relationship of prothrombin time (PT) and partial thromboplastin time (PTT) to mortality is unknown. Our objective was to measure the predictive value of the initial coagulopathy profile for trauma-related mortality. METHODS: We reviewed prospectively collected data on trauma patients presenting to a Level I trauma center. A logistic regression analysis was performed of PT, PTT, platelet count, and confounders to determine whether coagulopathy is a predictor of all-cause mortality. RESULTS: From a trauma registry cohort of 20103 patients, 14397 had complete disposition data for initial analysis and 7638 had complete data for all variables in the final analysis. The total cohort was 76.2% male, the mean age was 38 years (range, 1-108 years), and the median Injury Severity Score was 9. There were 1276 deaths (all-cause mortality, 8.9%). The prevalence of coagulopathy early in the postinjury period was substantial, with 28% of patients having an abnormal PT (2994 of 10790) and 8% of patients having an abnormal PTT (826 of 10453) on arrival at the trauma bay. In patients with disposition data and a normal PT, 489 of 7796 died, as compared with 579 of 2994 with an abnormal PT (6.3% vs. 19.3%; chi2 = 414.1, p < 0.001). Univariate analysis generated an odds ratio of 3.6 (95% confidence interval [CI], 3.15-4.08; p < 0.0001) for death with abnormal PT and 7.81 (95% CI, 6.65-9.17; p < 0.001) for deaths with an abnormal PTT. The PT and PTT remained independent predictors of mortality in a multiple regression model, whereas platelet count did not. The model also included the independent risk factors age, Injury Severity Score, scene and trauma-bay blood pressure, hematocrit, base deficit, and head injury. The model generated an adjusted odds ratio of 1.35 for PT (95% CI, 1.11-1.68; p < 0.001) and 4.26 for PTT (95% CI, 3.23-5.63; p < 0.001). CONCLUSION: The incidence of coagulation abnormalities, early after trauma, is high and they are independent predictors of mortality even in the presence of other risk factors. An initial abnormal PT increases the adjusted odds of dying by 35% and an initial abnormal PTT increases the adjusted odds of dying by 326%.

Adult↗

Comparison of isotropic and orthotropic material property assignments on femoral finite element models under two loading conditions.

CT data has been widely used in the finite element modeling of bone. It can provide useful information on the geometrical topology and material properties of bone. Based on CT data, the assignment of bone material properties to finite element meshes is a fundamental step in the model generation. Most work done in this area has adopted isotropic assignment strategy due to its simplicity. However, bone material has been recognized as an orthotropic material. This work is aimed to investigate the effects of orthotropic material property assignment on femoral finite element model by comparing with isotropic material property assignment on the same model. There were 72 finite element models obtained from the frozen CT male dataset of visible human project. Based on the analysis results of the maximum equivalent Von Mises stress and the maximum nodal displacement, three parameters were defined to achieve this comparison. The results have shown that the differences between the two material property assignments are small under two loading conditions (double-leg standing and single-leg standing) investigated in this work.

Adult↗

Unexpected ICD pulse generator failure due to electronic circuit damage caused by electrical overstress.

Because it is a lifesaving device, the unexpected failure of an ICD can be catastrophic. We report ICD electronic circuit failure due to electrical overstress damage (EOS) to the high voltage hybird circuit and other electronic components in a series of ICD pulse generator models. Data were obtained from the Multicenter Registry of Pacemaker and ICD Pacemaker and Lead Failures, and from the manufactures' adverse event reports, that were in the FDA's Manufacturer and User Facility Device Experience (MAUDE) database. Of 16 nonbattery Guidant/CPI ICD pulse generator failures reported to the registry, 6 (38%) have been confirmed by the manufacturer to be EOS related, and Guidant/CPI has reported 273 such failures to the FDA as of 12/29/00. The signs of failure included loss of telemetry and inability to deliver therapy, and some patients have experienced serious adverse events. Hybrid circuit damage may have occurred during capacitor charging or reform, and the majority appears to have happened during normal ICD function. While the incidence of this problem is unknown, a management strategy should be adopted that includes routine follow-up every 3 months and device evaluation after a shock or exposure to external defibrillation or electrosurgical devices. This study suggests that additional data are needed to determine the incidence of this problem, and that our present methods for monitoring the performance of ICD's following market release are inadequate.

Defibrillators, Implantable↗

Low resolution structural study of two human HSP40 chaperones in solution. DJA1 from subfamily A and DJB4 from subfamily B have different quaternary structures.

Proteins that belong to the heat shock protein (Hsp) 40 family assist Hsp70 in many cellular functions and are important for maintaining cell viability. A knowledge of the structural and functional characteristics of the Hsp40 family is therefore essential for understanding the role of the Hsp70 chaperone system in cells. In this work, we used small angle x-ray scattering and analytical ultracentrifugation to study two representatives of human Hsp40, namely, DjA1 (Hdj2/dj2/HSDJ/Rdj1) from subfamily A and DjB4 (Hlj1/DnaJW) from subfamily B, and to determine their quaternary structure. We also constructed low resolution models for the structure of DjA1-(1-332), a C-terminal-deleted mutant of DjA1 in which dimer formation is prevented. Our results, together with the current structural information of the Hsp40 C-terminal and J-domains, were used to generate models of the internal structural organization of DjA1 and DjB4. The characteristics of these models indicated that DjA1 and DjB4 were both dimers, but with substantial differences in their quaternary structures: whereas DjA1 consisted of a compact dimer in which the N and C termini of the two monomers faced each other, DjB4 formed a dimer in which only the C termini of the two monomers were in contact. The two proteins also differed in their ability to bind unfolded luciferase. Overall, our results indicate that these representatives of subfamilies A and B of human Hsp40 have different quaternary structures and chaperone functions.

Amino Acid Sequence↗

Helical structure determined by NMR of the HIV-1 (345-392)Gag sequence, surrounding p2: implications for particle assembly and RNA packaging.

Gag protein oligomerization, an essential step during virus assembly, results in budding of spherical virus particles. This process is critically dependent on the spacer p2, located between the capsid and the nucleocapsid proteins. P2 contributes also, in association with NCp7, to specific recognition of the HIV-1 packaging signal resulting in viral genome encapsidation. There is no structural information about the 20 last amino acids of the C-terminal part of capsid (CA[CTD]) and p2, in the molecular mechanism of Gag assembly. In this study the structure of a peptide encompassing the 14 residues of p2 with the upstream 21 residues and the downstream 13 residues was determined by (1)H NMR in 30% trifluoroethanol (TFE). The main structural motif is a well-defined amphipathic alpha-helix including p2, the seven last residues of the CA(CTD), and the two first residues of NCp7. Peptides containing the p2 domain have a strong tendency to aggregate in solution, as shown by gel filtration analyses in pure H(2)O. To take into account the aggregation phenomena, models of dimer and trimer formed through hydrophobic or hydrophilic interfaces were constructed by molecular dynamic simulations. Gel shift experiments demonstrate that the presence of at least p2 and the 13 first residues of NCp7 is required for RNA binding. A computer-generated model of the Gag polyprotein segment (282-434)Gag interacting with the packaging element SL3 is proposed, illustrating the importance of p2 and NCp7 in genomic encapsidation.

Amino Acid Motifs↗