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PubMedDate not supplied

Application of the wavelet method for the simultaneous quantitative determination of benazepril and hydrochlorothiazide in their mixtures.

The discrete and continuous wavelet transforms were applied to the overlapping signal analysis of the ratio data signal for simultaneous quantitative determination of the title subject compounds in samples. The ratio spectra data of the binary mixtures containing benazepril (BE) and hydrochlorothiazide (HCT) were transferred as data vectors into the wavelet domain. Signal compression, followed by a 1-dimension continuous wavelet transform (CWT), was used to obtain coincident transformed signals for pure BE and HCT and their mixtures. The coincident transformed amplitudes corresponding to both maximum and minimum points allowed construction of calibration graphs for each compound in the binary mixture. The validity of CWT calibrations was tested by analyzing synthetic mixtures of the investigated compounds, and successful results were obtained. All calculations were performed within EXCEL, C++, and MATLAB6.5 softwares. The obtained results indicated that our approach was flexible and applicable for the binary mixture analysis.

Algorithms↗
PubMed1991

A computer program for the deconvolution of mass spectral peak abundance data from experiments using stable isotopes.

A computer program is described for deconvoluting the overlap which is often found in mass spectral peak abundance data from stable isotope experiments. Peak intensity data from calibration standards are corrected using parameters calculated from the analysis of separate external standard solutions of analytes and internal standard. If the calibration data are satisfactory, the same parameters and the slope and intercept values from the least squares analysis of the calibration data are used to correct and quantitate the mass spectral peak intensity data from the quality assurance and experimental samples. Reports and graphs appropriate to the process are produced. Applications are given for the analysis of plasma samples from stable isotope experiments with carprofen, cifenline, and midazolam.

Carbazoles↗
PubMedDate not supplied

Edge-shrinking interpolation for medical images.

A new algorithm for interpolating the missing data between two adjacent medical images is presented. Our method is useful for solving the interpolation of any region-represented images of an object to be reconstructed, even when the object is stretched abruptly, branched or hollow, as often occurs in medical images, which cases can not be handled well by existing methods. When this algorithm is applied, the nonoverlapped regions of the same object in the two base images are first extracted and encoded by chamfer distance code on every pixel in these regions. Then, the outer edges of the nonoverlapping regions are shrunk inward simultaneously so that the stretched edges reach the edges of the overlapping regions at the same time. The distance codes in nonoverlapping regions are used to limit the shrinking of these edges in the interpolation process. The proposed method also provides object centralization and enlargement operations to obtain stable and reasonable results in complicated case. The experimental results show that the proposed method is more efficient in resolving general interpolation tasks than the existing methods (S.P. Raya and J. K. Udupa, IEEE Trans. Med. Image. 9, 32-42, 1990; G. T. Herman et al., IEEE Comput. Graph. Appl. 12, 69-79, 1992; J.F. Guo et al., Comput. Med. Imag. Graph. 19, 267-279, 1995.)

Algorithms↗
PubMed2006

Similarity measures based on Gaussian-type promolecular electron density models: alignment of small rigid molecules.

Various molecular similarity measures (overlap, Coulomb, kinetic, electrostatic energy) and similarity indices (Carbó, Hodgkin-Richards, Kulczynski, Shape Tanimoto) are applied to the superposition of 3D promolecular electron density (PED) distributions. The original aspect of the paper lies in the consideration of smoothed PEDs, which allow to decrease the number of local solutions to a superposition problem, together with the use of the less common kinetic and electrostatic energy similarity measures. Results are obtained for a family of five rigid endothiapepsin ligands that were already considered in previous applications, based on graph representations of their PED. In the present work, it is observed that the use of smoothed PED and the kinetic similarity measure, together with the Kulczynski or Shape Tanimoto index, performed the best to align molecules of different sizes.

Journal Article↗
PubMedDate not supplied

Comparison of mechanical deformation properties of metallic stents with use of stress-strain analysis.

PURPOSE: Elastic and plastic deformation properties of the Wallstent, Palmaz stent, and Strecker stent were evaluated quantitatively with an in vitro model simulating forces exerted by an eccentric lesion. MATERIALS AND METHODS: A miniaturized compression testing device was constructed. Stress-strain graphs were obtained for each stent, and the elastic moduli and yield points were calculated. RESULTS: There is a 21-fold range in the elastic modulus among the Wallstent, Palmaz stent, and Strecker stents. The Palmaz stent was the only device to exhibit permanent plastic deformation. The 10-mm Palmaz stent will undergo 15% focal eccentric narrowing at 0.75 atm of pressure; the "standard braid" and "less shortening braid" 10-mm Wallstents at 0.55 and 0.25 atm, respectively; and the 10-mm tantalum Strecker stent at 0.08 atm. Overlapping of stents doubles the stiffness of the Wallstent and the Strecker stent and doubles the yield point of the Palmaz stent. The 4-9 mm Palmaz stent is 30% more resistant to deformation than the larger 8-12-mm version when expanded to identical 8-mm diameters. CONCLUSIONS: The "standard braid" version of the 10-mm Wallstent provides 2.3-fold additional strength for resistant stenoses compared with the "less shortening braid." Overlapping or nesting of stents may permit full expansion should there be incomplete expansion or recoil of a single stent. The 4-9-mm Palmaz stent is preferable from the standpoint of allowing the use of a smaller (7-F instead of 9-F) introducer sheath and also for providing superior resistance to deformation. A purely elastic stent such as the Wallstent is preferable in locations where permanent plastic deformation may occur, such as the thoracic outlet.

Alloys↗
PubMed2004

Evaluation of a simple carrier molecule to enhance drug penetration of dermal layers by utilizing multivariate methods, structure property correlations, and continuous system modeling.

Nicotinic acid is shown to be comparable to dihydropyridine in its capacity to facilitate penetration of an attached antibacterial drug through dermal layers. Antibacterial drugs examined with nicotinic acid or dihydropyridine carriers were beta-lactam antibiotics: methicillin, oxacillin, benzylpenicillin, penicillin F, penicillin dihydro F, propicillin, carbenicillin, penicillin K, penicillin X, and ampicillin. An oxymethyl (-O-CH2-) group is inserted as the linker between the antibiotic and the carrier group. Structure Property Correlations and multivariate methods such as regression analysis, cluster analysis, principal component analysis, discriminate analysis, self-organizing tree algorithm, and factor analysis clearly showed that nicotinic acid performs as an effective carrier drug and is comparable to dihydropyridine. The skin penetration constant Kp was calculated for all 10 antibiotics having either dihydropyridine or nicotinic acid as carrier, and was found to have a mean of 5.13E-05 cm/hour and 1.83E-05 cm/hour, respectively. The standard deviation for each group showed the numerical values overlap as did the 90% confidence interval for each group. A hierarchical tree organization of skin shows the overlapped dermal layers as they exist in normal skin and for the model utilized in this work. A Deming-Regression analysis also shows the nicotinic acid and dihydropyridine structures to have similar and correlated water solubility. Plotting Kp of the dihydropyridine structures as independent variable versus Kp of the nicotinic acid structures show good correlation (Pearson correlation r = 0.6606) and no significant departure from linearity. Connected box plots showed the majority of Kp values for each group of modified antibiotics to exist in a tight cluster. Polar graph of the Log Kow values showed the two groups of modified antibiotics to be correlated and numerically adjacent in trend. ChemSketch property calculations and modeling demonstrates the affects of structural oxygens, nitrogens, carbonyl groups, amide groups, and aromatic rings that are important in understanding the pervasiveness through dermal layers. Continuous model analysis by acslXtreme is utilized and demonstrates three models of the dispersion of drugs through dermal layers based on diffusivity constant (D), Log Kp from Log Kow and formula weight, and Kp as a function of time.

Administration, Topical↗
PubMed2003

The role of cardiac power and systemic vascular resistance in the pathophysiology and diagnosis of patients with acute congestive heart failure.

OBJECTIVE: Conventional hemodynamic indexes (cardiac index (CI), and pulmonary capillary wedge pressure) are of limited value in the diagnosis and treatment of patients with acute congestive heart failure (CHF). PATIENTS AND METHODS: We measured CI, wedge pressure, right atrial pressure (RAP) and mean arterial blood pressure (MAP) in 89 consecutive patients admitted due to acute CHF (exacerbated systolic CHF, n=56; hypertensive crisis, n=5; pulmonary edema, n=11; and cardiogenic shock, n=17) and in two control groups. The two control groups were 11 patients with septic shock and 20 healthy volunteers. Systemic vascular resistance index (SVRi) was calculated as SVRi=(MAP-RAP)/CI. Cardiac contractility was estimated by the cardiac power index (Cpi), calculated as CIxMAP. RESULTS AND DISCUSSION: We found that CI<2.7 l/min/m(2) and wedge pressure >12 mmHg are found consistently in patients with acute CHF. However, these measures often overlapped in patients with different acute CHF syndromes, while Cpi and SVRi permitted more accurate differentiation. Cpi was low in patients with exacerbated systolic CHF and extremely low in patients with cardiogenic shock, while SVRi was increased in patients with exacerbated systolic CHF and extremely high in patients with pulmonary edema. By using a two-dimensional presentation of Cpi vs. SVRi we found that these clinical syndromes can be accurately characterized hemodynamically. The paired measurements of each clinical group segregated into a specific region on the Cpi/SVRi diagnostic graph, that could be mathematically defined by a statistically significant line (Lambda=0.95). Therefore, measurement of SVRi and Cpi and their two-dimensional graphic representation enables accurate hemodynamic diagnosis and follow-up of individual patients with acute CHF.

Aged↗
PubMed2005

Quality evaluation of solid organ transplant in Italy for the period 2000 to 2002 data from the national transplant center.

BACKGROUND: As part of the increased need for transparency and disclosure of information in health care, the Italian Minister of Health has commissioned the Superior Institute of Health to study health outcomes for several procedures, among which is solid organ transplants. We herein report the results of a quality evaluation of solid organ transplants and on the relationship between hospital volume of activity and outcomes, using the data routinely collected by the National Transplant Center during the period 2000 to 2002. METHODS: We collected and analyzed all the information on solid organ transplants between 2000 and 2002, along with clinical information before and after transplant. Multivariate survival analysis was performed to adjust the follow-up data for the complexity of the cases. Correlation graphs are presented that assess the association between the number of transplants and the adjusted 1-year survival of both the organ and the patient. RESULTS: One-year survival was 92.4% for kidney, 77.8% for liver, and 83.9% for heart. Patient survival was 97.0%, 84.1%, and 83.9%, respectively. A negative correlation was observed between the number of transplants performed by each center and 1-year survival of the organ. CONCLUSIONS: Our study indicated that survival after organ transplants in Italy is good and that hospital quality, indirectly measured through survival, overlaps that observed in other Western countries.

Humans↗
PubMed2002

Pattern recognition technique in immunological antigenic tests to identify Mycobacterium tuberculosis infection.

UNLABELLED: The importance of a diagnostic test that is simple and quick to identify Mycobacterium tuberculosis infection needs no emphasis. The tuberculin skin test (TST - 1 TU RT23) is the diagnostic tool for identifying M. tuberculosis infection at present. The test reaction on the skin is measured after 48-72 h. It is observed that often multi-modes are seen, when the reactions are drawn as a graph and the bimodality is seen very feebly. Because of the difficulties in the administration of TST, several serological tests were developed over three decades, but none of the studies showed the desired results. One study to evaluate purified protein derivative (PPD) antigen resulted in a claim of 80% sensitivity and 4% false-positivity rate (14), while other researchers were not able to obtain similar results. In addition, several problems were encountered due to the non-availability of antigens, and data analyses from an ELISA-based diagnostic test showed considerable overlap of distributions of optical density (OD) values among patients and healthy individuals (10). Classical statistical techniques cannot explain the cause of these overlaps. Hence, an attempt is made in this article to resolve these difficulties by the pattern recognition technique (PRT). The technique lies in splitting the data into clusters using a supervised algorithm. The data set is normally split into a training set, a test set and a validation set. The PRT gets "trained" through the training data set until the infected and uninfected groups of individuals are correctly classified. The training occurs based on an algorithm on the training set. On successful completion of the training, this technique is further tested and validated in the respective data sets. SETTING: A total of 273 finger-prick specimens were collected from five categories (Al, A2, B, C, D, E) of subjects not vaccinated with (bacille Calmette Guerin) (BCG) from Trivellore BCG Trial area adopted by the Tuberculosis Research Center, Chennai, India. OBJECTIVE: The study was conducted with the primary aim of evaluating purified antigens--r38 kDa, PPD and 30 kDa--for their usefulness as diagnostic tools and to test the applicability of the PRT in the evaluation of diagnostic tests. Individuals in two main categories (definitely not infected categories Al, A2 and D, and definitely infected categories B, E and C based on reaction to TST) were assembled for the purpose. RESULTS: The overall PRT performance of 30 kDa was 72.3% sensitivity and 90.9% specificity for identifying M. tuberculosis infection, while the r38 kDa antigen recorded a sensitivity of 73.8% and a specificity of 84.6%. In the case of PPD, the results were not promising. CONCLUSION: This paper on ELISA-based diagnostic tests attempts to implement an optimal decision support system through PRT that would identify the outcome (as infected or non-infected) based on the OD values. The PRT was able to predict the outcome for individual suspects. Further, Kullback-Leibler distance measurement has validated the PRT in distinguishing infected individuals from healthy subjects (based on the OD values).

Adolescent↗
PubMed2001

Clinical significance of neurobiochemical profiles in the lumbar cerebrospinal fluid of Alzheimer's disease patients.

Immunoreactivities of total apolipoprotein E (ApoE-IR), amyloid beta peptide(1-42) (Abeta42-IR), interleukin-6 (IL-6-IR), substance P (SPIR) and total tau protein (TTIR) were measured in lumbar cerebrospinal fluid samples of patients with Alzheimer's disease (AD), non-Alzheimer's dementias (NAD), neurological disorders without cognitive impairment (OND) and controls without central nervous system disease using sensitive and specific enzyme immunoassay methods. TTIR was highly significantly increased (P < 0,001) and Abeta42-IR was significantly decreased (P < 0,001 vs. OND/CO, P < 0,03 vs. NAD) in the AD cohort compared with the other diagnostic groups. Significant increases in AD were also found for ApoE-IR (P < 0,001) and IL-6 (P < 0,03), but there was a considerable overlap between groups. In the total AD cohort, SPIR was not significantly changed, but AD patients with late disease onset (>65 years) showed significantly higher values than both early onset patients (<65 years) and controls (P < 0,05). Discriminant function analysis showed that Abeta42-IR (cut-off value 375pg/ml) and TTIR (cut-off value 440 pg/ml) levels contributed most to the group classification of patients. At 85% sensitivity for AD and 100% specificity for controls, the combined evaluation of Abeta42-IR and TTIR in this cross-sectional study resulted in a graph separating AD from non-AD patients with increased specificity of 91% and 75% for AD versus OND and NAD, respectively.

Aged↗
PubMed2005

Simultaneous determination of carvedilol and ampicillin sodium by synchronous fluorimetry.

The carvedilol and ampicillin sodium were simultaneously determined by the synchronous fluorimetry. With excitation wavelength at 254 nm, the maximum emission wavelengths of carvedilol and ampicillin sodium were at 357 and 426 nm, respectively. Because the emission spectra of carvedilol and ampicillin sodium were overlapped partially, carvedilol and ampicillin sodium cannot be determined directly by normal fluorimetric method. However, the synchronous fluorimetry can be used for determining both drugs simultaneously without separation procedure. The (Delta)(lambda) = 80 nm was used. Iso-propanol was selected as sensing reagent. Effects of pH, organic solvents and foreign ions on the determination of both drugs were studied. The linear relationship was obtained between the relative fluorescence intensity and concentration of carvedilol and ampicillin sodium in the range of 0.005-0.1 and 5.0-70.0 microg ml(-1), respectively. The linear regression equation of calibration graph for carvedilol is C = 0.000151F - 0.00210, and for ampicillin sodium is C = 0.0770F - 2.62. The correlation coefficient of linear regression equation is 0.9995 for carvedilol and 0.9998 for ampicillin sodium, respectively. The detection limit is 1 ng ml(-1) for carvedilol and 1 microg ml(-1) for ampicillin sodium. The relative standard deviations of carvidelol and ampicillin sodium are 2.47 and 1.61%, respectively. The recovery is from 96.0 to 103.0% for carcvedilol and from 98.0 to 105.0% for ampicillin sodium. This method was rapid, simple and highly sensitive for the determination of carvedilol and ampicillin sodium without pre-separation. The results obtained by this method agreed with those by the official methods. This method can be used for the determination of carvedilol and ampicillin sodium in the medicine dosage.

2-Propanol↗
PubMed2003

Three new spectrophotometric methods applied to the simultaneous determination of hydrochlorothiazide and irbesartan.

This work involves the simultaneous determination of hydrochlorothiazide and irbesartan in a binary mixture without previous separation by three new analytical methods. The first method, based on compensation technique, is presented for the derivative spectrophotometric determination of binary mixtures with overlapping spectra. By using ratios of the derivative maxima or the derivative minimum, the exact contribution of either component in the binary mixture can be measured and the amounts quantified. The second method uses of the first derivative of the ratio spectra. The ratio spectra were obtained by dividing the absorption spectra of the binary mixture by that of one of the components. The amplitudes in the first derivative of the ratio spectra at 231, 266, 279, 238 and 248 nm were selected to determine hydrochlorothiazide and irbesartan in binary mixtures. The concentration of the other components are then determined from their respective calibration graphs treated similarly. With the third method, the absorbance ratio method, the determination of hydrochlorothiazide and irbesartan was performed using the absorbances read at 272 nm, 241 nm and 263 nm in the zero-order spectra of their mixture. The absorbance ratio was also developed as a comparison method. The three methods are simple, accurate, rapid and require no preliminary separation steps and can, therefore, be used for routine analysis of both drugs in quality control laboratories.

Antihypertensive Agents↗
PubMed2003

Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as edges. On the basis of the concept of functional groups, 68 atom types (node types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding and to detect optimal local matches (simply connected common subgraphs). Our procedure was applied to the comparison and clustering of 9383 compounds, mostly metabolic compounds, in the KEGG/LIGAND database. The largest clusters of similar compounds were related to carbohydrates, and the clusters corresponded well to the categorization of pathways as represented by the KEGG pathway map numbers. When each pathway map was examined in more detail, finer clusters could be identified corresponding to subpathways or pathway modules containing continuous sets of reaction steps. Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes.

Algorithms↗
PubMed2000

Development of an indirect Tams1 enzyme-linked immunosorbent assay for diagnosis of Theileria annulata infection in cattle.

An enzyme-linked immunosorbent assay (ELISA) was developed based on a recombinant major Theileria annulata merozoite surface antigen, Tams1. Four different recombinant proteins derived from two different Tams1 alleles, both in two different truncated forms, were tested for their performance in the ELISA. Furthermore, antigen concentration, various buffers, washing protocol, and the choice of anti-total-immunoglobulin G (IgG), anti-IgG1, or anti-IgG2 as second antibody were evaluated. The performance of the resulting ELISA was analyzed by measuring the coefficient of variation (CV). A total of 22 sera were analyzed over the measurement range, resulting in a CV of ca. 10%, whereas 30% variation is the maximum acceptable. The cutoff value was determined by the two-graph receiver operating characteristic (TG-ROC), using the indirect fluorescent antibody test (IFAT) as a reference. It was shown that up to 3 months postinfection (p.i.) IFAT is more sensitive and specific, whereas beyond 3 months p.i. ELISA performed as well as IFAT. The cutoff was determined at maximal sensitivity, based on the TG-ROC after 3 months p.i. Nine calves experimentally infected with four different T. annulata stocks remained positive in the ELISA for at least 1 year p.i. Finally, limited cross-reaction was found only with T. parva antisera, but not with any other Theileria or Babesia species. Since the T. parva endemic area hardly overlaps with T. annulata, the Tams1 ELISA has the potential to become a useful tool in the epidemiology of tropical theileriosis.

Animals↗
PubMedDate not supplied

Fuzzy attributes of a DNA complex: development of a fuzzy inference engine for codon-"junk" codon delineation.

OBJECTIVE: The present study is concerned with the need that exists in bioinformatics to identify and delineate overlapping codon and noncodon structures in a deoxyribonucleic acid (DNA) complex so as to ascertain the boundary of separation between them. Codons refer to those parts in a DNA complex encoded towards forming a desired set of proteins. Also coexist in the DNA structure noncodons (or "junk" codons), whose functions are not so well defined. Such codon and noncodon parts (at least over some sections of a DNA chain) may conform to diffused (overlapping) states exhibiting sharpless boundaries with indistinctive statistics of occurrence of their constituents. Such overlapping mix of codon and noncodon entities constitutes a (fuzzy) universe with information constituent having a fuzzy structure, which can only be identified in descriptive norms with characteristic membership of belonging to certain attributes. Hence, this work is directed to develop a fuzzy inference engine (FIE), which delineates the fuzzy codon-noncodon parts. METHODS AND MATERIAL: Relevant algorithms developed for the fuzzy inference in question are based on information-theoretic (IT) considerations applied to symbolic as well as binary sequence data representing the DNA. Pseudocodes, as needed are furnished. RESULTS: Simulated studies using human and other bacterial codon statistics are presented to illustrate the efficacy of the approach pursued. The outcome of the study is illustrated via tabulated results and graphs depicting the delineation sought. CONCLUSION: The results signify the success of IT-approach pursued in delineating imprecise codon/noncodon boundaries. The FIE applies both for human and bacterial codon statistics.

Algorithms↗
PubMed2004

Functional topology in a network of protein interactions.

MOTIVATION: The building blocks of biological networks are individual protein-protein interactions (PPIs). The cumulative PPI data set in Saccharomyces cerevisiae now exceeds 78 000. Studying the network of these interactions will provide valuable insight into the inner workings of cells. RESULTS: We performed a systematic graph theory-based analysis of this PPI network to construct computational models for describing and predicting the properties of lethal mutations and proteins participating in genetic interactions, functional groups, protein complexes and signaling pathways. Our analysis suggests that lethal mutations are not only highly connected within the network, but they also satisfy an additional property: their removal causes a disruption in network structure. We also provide evidence for the existence of alternate paths that bypass viable proteins in PPI networks, while such paths do not exist for lethal mutations. In addition, we show that distinct functional classes of proteins have differing network properties. We also demonstrate a way to extract and iteratively predict protein complexes and signaling pathways. We evaluate the power of predictions by comparing them with a random model, and assess accuracy of predictions by analyzing their overlap with MIPS database. CONCLUSIONS: Our models provide a means for understanding the complex wiring underlying cellular function, and enable us to predict essentiality, genetic interaction, function, protein complexes and cellular pathways. This analysis uncovers structure-function relationships observable in a large PPI network.

Algorithms↗
PubMedDate not supplied

Using max cut to enhance rooted trees consistency.

Supertree methods are used to construct a large tree over a large set of taxa from a set of small trees over overlapping subsets of the complete taxa set. Since accurate reconstruction methods are currently limited to a maximum of a few dozen taxa, the use of a supertree method in order to construct the tree of life is inevitable. Supertree methods are broadly divided according to the input trees: When the input trees are unrooted, the basic reconstruction unit is a quartet tree. In this case, the basic decision problem of whether there exists a tree that agrees with all quartets is NP-complete. On the other hand, when the input trees are rooted, the basic reconstruction unit is a rooted triplet and the above decision problem has a polynomial time algorithm. However, when there is no tree which agrees with all triplets, it would be desirable to find the tree that agrees with the maximum number of triplets. However, this optimization problem was shown to be NP-hard. Current heuristic approaches perform min cut on a graph representing the triplets inconsistency and return a tree that is guaranteed to satisfy some required properties. In this work, we present a different heuristic approach that guarantees the properties provided by the current methods and give experimental evidence that it significantly outperforms currently used methods. This method is based on a divide and conquer approach, where the min cut in the divide step is replaced by a max cut in a variant of the same graph. The latter is achieved by a lightweight semidefinite programming-like heuristic that leads to very fast running times.

Algorithms↗
PubMed2004

Proteomic traces of speciation.

Recent work has shown that the network of structural similarity between protein domains exhibits a power-law distribution of edges per node. The scale-free nature of this graph, termed the protein domain universe graph or PDUG, may be reproduced via a divergent model of structural evolution. The performance of this model, however, does not preclude the existence of a successful convergent model. To further resolve the issue of protein structural evolution, we explore the predictions of both convergent and divergent models directly. We show that when nodes from the PDUG are partitioned into subgraphs on the basis of their occurrence in the proteomes of particular organisms, these subgraphs exhibit a scale-free nature as well. We explore a simple convergent model of structural evolution and find that the implications of this model are inconsistent with features of these organismal subgraphs. Importantly, we find that biased convergent models are inconsistent with our data. We find that when speciation mechanisms are added to a simple divergent model, subgraphs similar to the organismal subgraphs are produced, demonstrating that dynamic models can easily explain the distributions of structural similarity that exist within proteomes. We show that speciation events must be included in a divergent model of structural evolution to account for the non-random overlap of structural proteomes. These findings have implications for the long-standing debate over convergent and divergent models of protein structural evolution, and for the study of the evolution of organisms as a whole.

Bacterial Proteins↗