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Probability paper analysis of flow cytofluorometric measurements of cellular deoxyribonucleic acid content.

A graphic analysis of cellular deoxyribonucleic acid (DNA) histograms obtained by flow cytofluorometry is described. This technique utilizes probability paper that graphs data in cumulative percentile form. From this graphic representation, individual normal distributions contributing to the histogram may be isolated and statistically describe. G0G1 and G2M distributions are independently described and S phase is fit to 1--5 overlapping normal distributions as dictated by the analysis results. This technique offers several advantages, including relatively simple mathematical calculations and few assumptions or restraints placed on the analysis. It has proved to be useful in analyzing proliferating and nonproliferating populations as well as distributions with unusual findings such as debris or aberrant DNA contents.

Bone Marrow Cells↗

Simultaneous determination of fosinopril and hydrochlorothiazide in pharmaceutical formulations by spectrophotometric methods.

Three new spectrophotometric procedures for the simultaneous determination of fosinopril and hydrochlorothiazide are described. The first method, derivative-differential spectrophotometry, comprised of measurement of the difference absorptivities derivatized in the first-order (DeltaD(1)) of a tablet extract in 0.1 N NaOH relative to that of an equimolar solution in methanol at wavelengths of 227.6 and 276.4 nm, respectively. The second method, depends on the application ratio spectra derivative spectrophotometric method to resolve the interferance due to spectral overlapping. The analytical signals were measured at 237.9, 243.8 nm for fosinopril and 262.4, 269.3 and 278.6 nm for hydrochlorothiazide in the binary mixture, in the first derivative of the ratio spectra of the mixture solutions in methanol. Calibration graphs were established for 4.0-50.0 microg ml(-1) fosinopril and 2.0-14.0 microg ml(-1) hydrochlorothiazide in binary mixture. The third method, absorbance ratio method, the determination of fosinopril and hydrochlorothiazide was performed by using the absorbances read at 210.0, 219.5 and 271.7 nm in the zero-order spectra of their mixture. The developed methods were compared with absorbance ratio method. Application of the suggested procedures were successfully applied to the determination of this compound in synthetic mixtures and in pharmaceutical preparations, with high percentage of recovery, good accuracy and precision.

Angiotensin-Converting Enzyme Inhibitors↗

Robust error-minimization in the genetic code across physicochemical metrics and variant codes: A graph-theoretic analysis in GF(2)6.

The standard genetic code reduces the impact of point mutations, but the robustness of this property across physicochemical metrics, naturally occurring variant codes, and codon-reassignment mechanisms remains incompletely quantified. Embedding the 64 codons in GF(2)6 represents the hypercube Q6 as a coordinate-dependent subgraph of the encoding-independent single-nucleotide mutation graph H(3,4), and enables continuous &#x3c1;-interpolation between the two. Under a quartet-pattern shuffle null (n=10,000), the standard code is significantly low-cost across four established, code-independent physicochemical distance metrics with partially overlapping content (Grant ham p=0.0062; Miyata p<0.001; Woese polar requirement p=0.003; Kyte-Doolittle hydropathy p=0.001), and the signal strengthens monotonically as &#x3c1; moves Q6&#x2192;H(3,4). A structure-aware sensitivity analysis under the alignment-derived ProtSub matrix (Jia & Jernigan 2021) yields the most extreme percentile of any measure tested (p=0.0004; all five p-values pass Bonferroni at &#x3b1;=0.05). Across the 27 NCBI translation tables, near-optimality is preserved: 11 of 12 informative-distance variants retain top-5% placement after BH-FDR correction. Natural codon reassignments avoid disrupting codon-family connectivity: under the encoding-independent H(3,4) adjacency, observed events are topology-breaking at relative risk 0.32 versus the candidate landscape (permutation p&#x2264;10-4). The H(3,4) result is stable by construction; the Q6 decomposition is representation-specific and fails to show depletion under 8 of 24 base-to-bit encodings, so we report H(3,4) as the primary test and Q6 as a sensitivity. Event-level conditional-logit modelling shows that topology avoidance and local physicochemical cost provide complementary, only weakly correlated signal (rs=0.15), and that topology adds explanatory value beyond physicochemistry under both Q6 and encoding-independent H(3,4) adjacency. Retrospective reanalysis of nine genome-recoding datasets is consistent with codon-family topology operating as an evolutionary-trajectory constraint distinct from acute engineering fitness. The contribution is the second axis: code evolution is jointly constrained by physicochemical smoothness and codon-family topological integrity, and these two constraints are partly independent.

Codon reassignment↗

An efficient peak assignment algorithm for two-dimensional NMR correlation spectra of framework structures.

An algorithm is described for efficiently assigning the resonances in NMR spectra to the inequivalent atoms in the structure under study based on the information in two-dimensional NMR correlation experiments and the 'connectivities' known from the structure. The algorithm, which is based on basic graph theory concepts, finds all possible assignments sets which are consistent with the experimentally observed correlations and known connectivities in a very efficient manner. It is designed to deal with less than ideal experimental data in which there may be overlapping peaks and uncertainty about the presence or absence of correlation peaks. The algorithm was primarily developed for assigning the peaks in the high-resolution solid-state 29Si MAS NMR spectra of highly siliceous zeolites based on two-dimensional 29Si INADEQUATE spectra and is described using the zeolites ZSM-12 and ZSM-5 as working examples. Peak assignment for zeolite frameworks is particularly challenging since there is often little or no information to distinguish peaks from one another such as characteristic chemical shifts, relative intensities, or different relaxation times. The algorithm may be a useful tool for easily, reliably, and efficiently working out peak assignments from other types of correlation experiments on other types of systems and further examples are provided in the Supplementary material.

Algorithms↗

A graphical judgmental aid which summarizes obtained and chance reliability data and helps assess the believability of experimental effects.

Interval by interval reliability has been criticized for "inflating" observer agreement when target behavior rates are very low or very high. Scored interval reliability and its converse, unscored interval reliability, however, vary as target behavior rates vary when observer disagreement rates are constant. These problems, along with the existence of "chance" values of each reliability which also vary as a function of response rate, may cause researchers and consumers difficulty in interpreting observer agreement measures. Because each of these reliabilities essentially compares observer disagreements to a different base, it is suggested that the disagreement rate itself be the first measure of agreement examined, and its magnitude relative to occurrence and to nonoccurrence agreements then be considered. This is easily done via a graphic presentation of the disagreement range as a bandwidth around reported rates of target behavior. Such a graphic presentation summarizes all the information collected during reliability assessments and permits visual determination of each of the three reliabilities. In addition, graphing the "chance" disagreement range around the bandwidth permits easy determination of whether or not true observer agreement has likely been demonstrated. Finally, the limits of the disagreement bandwidth help assess the believability of claimed experimental effects: those leaving no overlap between disagreement ranges are probably believable, others are not.

Journal Article↗

Colorectal cancer "methylator phenotype": fact or artifact?

It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP)," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI). We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF) in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.

Adaptor Proteins, Signal Transducing↗

GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D.

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

Algorithms↗

Simultaneous stopped-flow determination of butylated hydroxyanisole and propyl gallate using a T-format luminescence spectrometer.

A simple and fast luminescent method is used for the first time to resolve a mixture of two synthetic antioxidants, propyl gallate (PG) and butylated hydroxyanisole (BHA), by the joint use of the stopped-flow mixing technique and a T-format luminescence spectrometer. The determination of these compounds involves two different and independent reactions. On the one hand, PG determination is based on an energy transfer process that involves the formation of a lanthanide chelate with terbium in the presence of Triton X-100 and tri-n-octylphosphine oxide. On the other hand, BHA is determined using a reaction between the oxidized form of Nile Blue and the antioxidant. Both systems are excited at the same excitation wavelength (310 nm), and the emission wavelengths are 545 and 665 nm for PG and BHA, respectively. The absence of overlap in the emission spectra makes it possible to measure separately the analytes in each channel of the instrument. Initial rate and equilibrium signal are used as analytical parameters and measured in 0.1 and 1 s for PG and BHA, respectively. Calibration graphs are linear over the range 0.09-3.5 microg mL(-)(1) for PG and 0.3-15 microg mL(-)(1) for BHA. The relative standard deviations of both systems are close to 2%. The proposed method is applied to the determination of these two antioxidants in several commercial food samples with recoveries ranging between 94.8 and 102.9% for PG and between 94.1 and 102.1% for BHA.

Butylated Hydroxyanisole↗

The complexity of the overlap method for sequencing biopolymers.

The problem of trying to reconstruct the sequence of a biopolymer by using overlapping fragments obtained from cleaving agents is shown to be computationally intractable. This strongly suggests that any computer program for overlap sequencing, even though it may work well for a limited number of inputs, will not work sufficiently for all inputs. However, if the problem is restricted so that certain crucial fragments are known, called prime strings, a sequence can be found efficiently in all cases. Graph theory techniques for doing so can also be used to count the number of sequences consistent with the fragment data to determine whether a unique sequence has been obtained.

Amino Acid Sequence↗

Building and analysing genome-wide gene disruption networks.

MOTIVATION: Microarray experiments comparing expression levels of all genes in yeast for hundreds of mutants allow us to examine properties of gene regulatory networks on a genomic scale. We can investigate questions such as network modularity, connectivity, and look for genes with particular roles in the network structure. RESULTS: We have built genome-wide disruption networks for yeast, using a representation of gene expression data as directed labelled graphs. Nodes represent genes and arcs connect nodes if the disruption of the source gene significantly alters the expression of the target gene. We are interested in features of the resulting disruption networks that are robust over a range of significance cutoffs. The networks show a significant overlap with analogous networks constructed from scientific literature. In disruption networks the number of arcs adjacent to different nodes are distributed roughly according to a power-law, like in many complex systems where the robustness against perturbations is important. The networks are dominated by a single large component and do not have an obvious modular structure. Genes with the highest outdegrees often encode proteins with regulatory functions, whereas genes with the highest indegrees are predominantly involved in metabolism. The local structure of the networks is meaningful, genes involved in the same cellular processes are close together in the network. AVAILABILITY: http://www.ebi.ac.uk/microarray/networks

Chromosome Mapping↗

Interaction graph mining for protein complexes using local clique merging.

While recent technological advances have made available large datasets of experimentally-detected pairwise protein-protein interactions, there is still a lack of experimentally-determined protein complex data. To make up for this lack of protein complex data, we explore the mining of existing protein interaction graphs for protein complexes. This paper proposes a novel graph mining algorithm to detect the dense neighborhoods (highly connected regions) in an interaction graph which may correspond to protein complexes. Our algorithm first locates local cliques for each graph vertex (protein) and then merge the detected local cliques according to their affinity to form maximal dense regions. We present experimental results with yeast protein interaction data to demonstrate the effectiveness of our proposed method. Compared with other existing techniques, our predicted complexes can match or overlap significantly better with the known protein complexes in the MIPS benchmark database. Novel protein complexes were also predicted to help biologists in their search for new protein complexes.

Algorithms↗

Generating protein interaction maps from incomplete data: application to fold assignment.

MOTIVATION: We present a framework to generate comprehensive overviews of protein-protein interactions. In the post-genomic view of cellular function, each biological entity is seen in the context of a complex network of interactions. Accordingly, we model functional space by representing protein-protein-interaction data as undirected graphs. We suggest a general approach to generate interaction maps of cellular networks in the presence of huge amounts of fragmented and incomplete data, and to derive representations of large networks which hide clutter while keeping the essential architecture of the interaction space. This is achieved by contracting the graphs according to domain-specific hierarchical classifications. The key concept here is the notion of induced interaction, which allows the integration, comparison and analysis of interaction data from different sources and different organisms at a given level of abstraction. RESULTS: We apply this approach to compute the overlap between the DIP compendium of interaction data and a dataset of yeast two-hybrid experiments. The architecture of this network is scale-free, as frequently seen in biological networks, and this property persists through many levels of abstraction. Connections in the network can be projected downwards from higher levels of abstraction down to the level of individual proteins. As an example, we describe an algorithm for fold assignment by network context. This method currently predicts protein folds at 30% accuracy without any requirement of detectable sequence similarity of the query protein to a protein of known structure. We used this algorithm to compile a list of structural assignments for previously unassigned genes from yeast. Finally we discuss ways forward to use interaction networks for the prediction of novel protein-protein interactions. AVAILABILITY: http://www.ebi.ac.uk/~lappe/FoldPred/.

Algorithms↗

Smashing peacocks further: drawing quasi-trees from biconnected components.

Quasi-trees, namely graphs with tree-like structure, appear in many application domains, including bioinformatics and computer networks. Our new SPF approach exploits the structure of these graphs with a two-level approach to drawing, where the graph is decomposed into a tree of biconnected components. The low-level biconnected components are drawn with a force-directed approach that uses a spanning tree skeleton as a starting point for the layout. The higher-level structure of the graph is a true tree with meta-nodes of variable size that contain each biconnected component. That tree is drawn with a new area-aware variant of a tree drawing algorithm that handles high-degree nodes gracefully, at the cost of allowing edge-node overlaps. SPF performs an order of magnitude faster than the best previous approaches, while producing drawings of commensurate or improved quality.

Journal Article↗

Simultaneous determination of the binary mixtures of cefsulodin and clavulanic acid by using first-derivative spectrophotometry.

Two-component mixtures of cefsulodin and clavulanic acid were analysed by a first-derivative spectrophotometric method using a zero-crossing technique of measurement. The relative ease offered by this derivative technique for the quantification of these drugs, with closely overlapping spectral bands, was clearly demonstrated. As the absorption band of clavulanic acid closely overlaps with that of cefsulodin, both direct and derivative spectrophotometric methods have been investigated and evaluated by an exhaustive statistical analysis of the experimental data. The first-derivative spectrophotometric method was found to be more rapid, accurate and reproducible. The procedure does not require any separation step. The calibration graphs were linear in the range 2.0-56.0 micrograms ml-1 for cefsulodin and 2.0-28.0 micrograms ml-1 for clavulanic acid. The lower detection limits of cefsulodin and clavulinic acid (P 0.05 level) were calculated to be 0.16 and 0.24 microgram ml-1, respectively. Mixtures of cefsulodin and clavulanic acid in ratios of 1:4-7:2 were satisfactorily resolved. Both components were also determined in physiological solutions used to prepare intravenous infusions of these antibiotics.

Anti-Bacterial Agents↗

Spectrophotometric determination of sulphamethoxazole and trimethoprim (co-trimoxazole) in binary mixtures and in tablets.

BACKGROUND: The formulation of sulphamethoxazole (S) and trimethoprin (T) (CO-TRIMOXAZOLE) in a combination mixture is very good pharmacologically since it enhances the efficacy of the individual drugs. However in this combination, difficulties in analysis on ordinary UV spectrophotometry are introduced because the two components give overlapping spectral bands on zero-order. The United States Pharmacopoea (USP)-recommended HPLC analytical method is quite expensive. OBJECTIVE: The objective of the present work was to assess whether derivative spectrophotometry could be used to circumvent the overlapping spectral bands of the components and hence use it for routine analysis of the drug. STUDY DESIGN: Experimental. METHODS: The aqueous solution of the individual drugs and their binary mixtures were scanned on zero order and on first derivative at the wave length between 200- 300 nm and at the pH of 4.5. RESULTS: The zero-order spectra of the compounds were completely overlapping. However the first-derivative scan offered better separation and hence T was determined from the absorbance at 237.6 nm with negligible contribution from S (since at this point it was reading zero). Likewise S was determined at a wavelength of 259 nm when T was reading zero. The linear calibration graphs were obtained for 4-25 microg x ml(-1) of S and for 4-20 microg x ml(-1) of T. CONCLUSION: The method is rapid, simple and can be applied successfully to assay a mixture of the two drugs in pharmaceutical preparations.

Reproducibility of Results↗

Classification of diagnostic tests.

A method is described for classifying diagnostic tests. It is valid for the large subgroup of tests for which the measured diagnostic variable has a normal distribution for the affected and non-affected individuals. It is based on placing each diagnostic test as a point on a two-dimensional graph, called a separation-asymmetry (SA) diagram, whose x-axis is the separation between the two normal distributions and whose y-axis is the logarithm of the ratio of their standard deviations. The SA diagram is partitioned into functional regions by curves of constant performance, as measured by the percent overlap between the two normal distributions. The concept of 'eccentricity' in a diagnostic test is defined, and the relationship between eccentricity and test validity is discussed. This quantity is also incorporated into SA diagrams, thus allowing a clinician to determine, by inspection, if a given diagnostic test positioned on an SA diagram is valid for clinical use. The logic engine used for calculating iso-performance curves is given, as well as the computer programs which utilize it. Possible ways of using this classification scheme are suggested.

Algorithms↗

Topology and graph theory applied to cortical anatomy may help explain working memory capacity for three or four simultaneous items.

Cognitive experimentation suggests that at any single instant only three or four items ("chunks") are simultaneously prominent as a working memory (WM) trace, if we disregard the rehearsal component of WM. The reason for small WM capacity may concern combinatorial manageability. How might the neural representations of these few coactive chunks occupy a spatially distributed set of areas of the sheet-like cortex, while providing both order and flexibility to associate items in WM? Each attribute of each simultaneously active WM item must have broad access to the representational facilities of the cortical sheet, comprising tens of thousands of modular "cortical columns." The two hypothesized neural levels of WM during any moment of cognition comprise (a) "binding" together of many distributed attribute representations within each respective WM chunk, and (b) combinatorial play among three or four WM chunk-representations. Anatomical and functional evidence of cortical unity through its depth suggests that cortex may be viewed as essentially planar in its distribution of activations. Thus, a moment's WM is hypothesized here to reside in myriad activated cortical planar "patches," each subdivided into up to four amoeboid "subpatches." Two different lines of topological reasoning suggest orderly associations of such representations. (1) The four-color principle of map topology, and the related K(4) is planar theorem of graph theory, imply that if a small cortical area is dynamically subdivided into no more than four, discretely bounded planar subareas, then each such segment has ample free access to each of the others. (2) A hypothetical alternative to such associative adjacency of simultaneously active cortical representations of chunk-attributes is associative overlap, whereby, in dense cortical neuropil, activated subpatches behave like Venn diagrams of intersecting sets. As the number of Venn-like coactive subpatches within a patch increases, maintaining ad hoc associativity among all combinations requires exponentially proliferating intersections. Beyond four, serpentine subpatch shapes are required, which could easily lead to pathologies of omission or commission. As hypothesized by many researchers, the binding of the widely distributed cortical modules that represent a given chunk may involve synchrony or coherence of a single EEG frequency. Elsewhere, I have conjectured that such a binding frequency for a single chunk may bear a harmonic relationship with the additional EEG frequencies that are simultaneously binding the other WM chunks. Other possible mechanisms of binding have also been hypothesized. Whatever the mechanism, the many attributes of a moment's complement of three or four WM chunks must generally have an accidental relationship with the spatial distribution of the cortical feature analyzers that must be activated to represent those attributes. Therefore, the cortex may need, and have, comprehensive anatomical connections of each of its modules for representing an attribute (or of small redundant module groupings) with every other. If such whole-part cortico-cortical connections are somehow exploited not only to fully represent each cognitive chunk in its bound-together attributes, but also to bring the major business of intensive WM information processing down to the level of local circuits, in the sorts of topological patterning hypothesized here, there may be two adaptive results: (1) Time and other economies would be achieved in the reduction of activity in distant cortico-cortical connections to lower-energy global orchestration, or binding processes. (2) The piecemeal local topological limit to four subpatches would be writ large, across the entire cortex, preventing an unconstrained combinatorial explosion of associations among all attributes of all three or four simultaneously active chunks. Such hypothetical convergence to foci in local subpatch interactions might take place primarily in association cortex, and/or it might involve temporary shifts in response properties in some cortical subpat might involve temporary shifts in response properties in some cortical subpatches. Quantitative studies of the densely packed cortical fine structure, by Braitenberg and Schüz, and others, seem potentially consistent with this vision of cortical function in cognition.

Animals↗

Toward simplifying and accurately formulating fragment assembly.

The fragment assembly problem is that of reconstructing a DNA sequence from a collection of randomly sampled fragments. Traditionally, the objective of this problem has been to produce the shortest string that contains all the fragments as substrings, but in the case of repetitive target sequences this objective produces answers that are overcompressed. In this paper, the problem is reformulated as one of finding a maximum-likelihood reconstruction with respect to the two-sided Kolmogorov-Smirnov statistic, and it is argued that this is a better formulation of the problem. Next the fragment assembly problem is recast in graph-theoretic terms as one of finding a noncyclic subgraph with certain properties and the objectives of being shortest or maximally likely are also recast in this framework. Finally, a series of graph reduction transformations are given that dramatically reduce the size of the graph to be explored in practical instances of the problem. This reduction is very important as the underlying problems are NP-hard. In practice, the transformed problems are so small that simple branch-and-bound algorithms successfully solve them, thus permitting auxiliary experimental information to be taken into account in the form of overlap, orientation, and distance constraints.

Base Sequence↗