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PubMed1978

Learning processes in multilayer threshold nets.

An algorithm of learning in multilayer threshold nets without feedbacks is proposed. The net is built of threshold elements with binary inputs. During a learning process each input vector chi is accompanied by a teacher's decision omega (omega epsilon(1,...,M)). The pairs (chi[n], omega[n]) appear in successive steps independently according to some unknown stationary distribution p(chi, omega). The problem of learning of a threshold net has been decomposed to a series of problems of learning of the threshold elements. The proposed learning algorithm of the threshold elements has a perceptron-like form. It was proven that a decision rule of the threshold net stabilizes after a finite number of steps. For definite classes (p(chi,omega))K of distributions p(chi, omega), an optimal decision rule stabilizes after a finite number of steps. These classes (p(chi, omega))K also contain distributions describing learning processes with perturbations.

Feedback↗
PubMed1990

Enhancer sequences from Arabidopsis thaliana obtained by library transformation of Nicotiana tabacum.

In this paper we report on the use of a bidirectional enhancer cloning vehicle to isolate and characterize new enhancer sequences from Arabidopsis thaliana. A library of A. thaliana genomic Sau3A segments was constructed in Escherichia coli in the binary plasmid enhancer cloning vehicle pROA97. The T-DNA based vector carries abbreviated TATA regions from the cauliflower mosaic virus 35S transcription unit upstream of two genes. The library was transferred via triparental mating into Agrobacterium tumefaciens. The neomycin phosphotransferase II gene was used for selection of kanamycin-resistant transformed tobacco callus cells. Approximately 1100 transgenic plants were regenerated and assayed for expression of the E. coli beta-glucuronidase (GUS) gene in leaves, stems, roots, or seeds. Plasmids carrying putative enhancer sequences were rescued from the genomes of transgenic plants and the cloned sequences were assayed for enhancer function in genetic selection experiments. Plants were regenerated from the kanamycin-resistant calli obtained in the secondary transformation experiments. Histochemical analysis of GUS activity in the leaf, stem, and root tissues of transgenic plants showed a variety of expression patterns. The DNA sequences are presented of five Arabidopsis segments which confer enhancer function.

Base Sequence↗
PubMed1989

A parallel implementation of the ALOPEX process.

Optimization techniques have found many applications in science, engineering, and industry. In all applications, the best value of a "cost function" is sought in a well-defined domain; this cost function in general depends on many parameters. An iterative optimization technique has been developed (ALOPEX) that uses feedback in order to optimize the response of a system. The cost function for this process is problem dependent and therefore quite flexible. The method has been applied successfully to different optimization problems such as pattern recognition, receptive field studies in the visual system of animals, curve fitting, etc. We present two special purpose hardware implementations for ALOPEX. The first method takes time O(logN + logm) and uses O(mN2) processing elements. The second method takes O(logN + m) time and uses O(N2) processing elements. Our basic architecture is a binary tree with N2 leaves (equal to the length of the vectors) and therefore had depth O(logN). Different implications of the two approaches will be discussed including similarities with the biological visual process.

Algorithms↗
PubMed1992

A new approach for three-dimensional reconstruction of arterial ultrasonography.

This report describes a computerized approach that allows the creation of realistic three-dimensional arterial images from two-dimensional contiguous slices derived from a conventional ultrasound scan. Furthermore, the study assesses the method's feasibility and accuracy by performing in vitro cadaver artery three-dimensional reconstructions. Images are digitized into a computer, with a resolution of 512 x 480 pixels, and a dynamic range of 8 bits/pixel (256 gray scale). After edge enhancement with convolution filters through the original binary data, the intraluminal and outer edges are traced and converted to a polygon vector within a defined three-dimensional space. Serial cuts, 2 mm apart, are then "stacked" into a three-dimensional model, with interpolation of polyhedra between slices. Sixteen normal and arteriosclerotic distal aortic and common iliac arteries were obtained from fresh cadavers. Three-dimensional reconstruction models were compared with gross examination of the original artery. Anatomically accurate reconstructions were obtained, all with detailed surface information. Data analyzed included diameter, area, residual lumen, and percent stenosis. Pearson's coefficients determined for the pairs of data indicated excellent correlation (greater than or equal to 0.90) between separate measurements. With use of the described technology it is feasible to perform arterial three-dimensional reconstructions on a personal computer, with detailed and accurate surface information. The three-dimensional reconstruction method used can reliably and consistently reproduce the anatomic specimens.

Arteries↗
PubMed1992

A T-DNA transfer stimulator sequence in the vicinity of the right border of pRi8196.

An 8 bp sequence repeated 6 times is present to the right of the mannopine type pRi8196 T-DNA right-border sequence. Experiments were designed to test whether these repeats have a role in T-DNA transfer. Several constructs in which different lengths of pRi8196 right-border region were linked to the cucumopine synthesis gene on an Agrobacterium-Escherichia coli shuttle vector were made. The recombinant plasmids were tested for their efficiency to act as a source of T-DNA in a binary system in which a wild-type Ri plasmid provided virulence and root-inducing functions. The T-DNA transfer efficiency of the constructs was assessed by computing the relative frequency of roots containing cucumopine. Depending on the Ri plasmid used as source of virulence functions, a high level of T-DNA transfer was observed only if 6 (pRi8196) or 5 (pRiA4) repeats were present. These results were confirmed by looking for single-stranded T-DNA molecules (T-strands) in bacteria induced for virulence. The repetition of the 8 bp unit was named 'T-DNA transfer stimulator sequence' (TSS).

Base Sequence↗
PubMed1984

Construction of a gene bank of Rhodopseudomonas capsulata using a broad host range DNA cloning system.

A gene bank of the phototrophic bacterium Rhodopseudomonas capsulata was constructed using the binary plasmid system pRK290/pRK2013. Fragments of about 20 kb of chromosomal DNA of R. capsulata strain 37b4 were inserted into the cloning vector pRK290. The hybrid plasmids of the gene bank, maintained in Escherichia coli HB101 were transferred by conjugation to R. capsulata strains defective in the photosynthetic apparatus with frequencies of 5 X 10(-4) to 5 X 10(-2). Phototrophically growing transconjugants occurred with frequencies of 5 X 10(-7) to 5 X 10(-6). Recombination between the hybrid plasmids and the R. capsulata chromosome was shown. The hybrid plasmid pRCF1002, carrying a 25 kb insert of R. capsulata wild type DNA, was isolated from one E. coli clone of the gene bank. It reconstituted some bacteriochlorophyll- and photosynthetic negative mutants to phototrophic growth.

Cloning, Molecular↗
PubMed1990

Growth, morphology and division of flagellates of the genus Trypanoplasma (Protozoa, Kinetoplastida) in vitro.

Nine strains of trypanoplasms were grown in axenic culture. Cultures of Trypanoplasma borreli Laveran and Mesnil, 1901 from fish hosts Blicca bjoerkna, Cyprinus carpio, Scardinius erythrophthalmus and Tinca tinca and of T. guerneyorum Minchin, 1909 from Esox lucius and Trypanoplasma spp. from the leech Piscicola geometra were maintained in biphasic blood-agar medium SNB-9 supplemented with vitamins and antibiotics. In culture, the flagellates transformed into smaller, elongated stages with a little-developed undulating membrane and into short flagella that were morphologically similar to stages in the leech vector. The cultures were passaged weekly at 17-20 degrees C, but they also grew at 4 degrees C. The flagellates divided by binary fission, which was initiated by the formation of two new anterior flagella. The original anterior flagellum of the mother individual was gradually apposed to the cell surface and became the recurrent flagellum of one of the daughter individuals. In the meantime, nuclear division took place, followed by transverse cleavage of the kinetoplast. The division was completed by longitudinal fission of the mother individual into two offspring. Multiple fission that resulted in rosettes, which then cleaved into several daughter cells, was also observed, as well as some dyskinetoplastic and other anomalous forms. In cultures isolated from tenches with high parasitaemia, non-dividing, long filiform stages were observed. Culture stages were not infective for susceptible fishes.

Animals↗
PubMed1990

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. I. Generation of partition functions and mass balance equations.

The thermodynamics of binding of a ligand A and/or proton H to a macromolecule M is treated by the partition function method. In complex systems, the representation of the equilibria by means of cumulative constants beta PQR used as coefficients in partition functions ZM, ZA, and ZH is ill-suited to least-squares refinement procedures because the cumulative constants are interrelated by common cooperativity functions gamma j(i) and common site affinity constants kappa j. There is therefore the need to express ZM, ZA, ZH as functions of site constants kappa j and cooperativity coefficients bj. This is done by developing an algebra of partition functions based on the following concepts: (i) factorability of partition functions; (ii) binary generating function Jj = (1 + kappa j[Y])i tau for each class j of sites, represented by column (Jj) and row (Jj) vectors; (iii) cooperativity between sites of one class described by functions gamma j(i), represented by diagonal matrices gamma j; (iv) probability of finding microspecies represented by elements of tensor product matrix Ll = (J1)[J2]; (v) statistical factors mij obtained from Newton polynomials, Jj; (vi) power operators Oi', O(i-l)', and O(i tau-l)', transforming vectors Jj; and (vii) operators Oi or O(i-l) indicating tensor products of i or (i-l) vectors Jj. Vectors Jj combined in tensors Ll give rise to both an affinity/cooperativity space and a parallel index space. The partition functions ZM, ZA, and ZH and the total amounts TM, TA, and TH can be obtained as an appropriate sum of elements of matrices Ll, each of which is represented in an index space by a combination p1, p2,...q1, q2,...r1, r2,... of indices ij. From these indices the contribution of that element to partition function ZM, ZA, or ZH and to total amount TM, TA, or TH is calculated in the affinity/cooperativity space as product of factors: [i tau !/i !(i tau-i)!]kappa ij(exp[bj (i-1)i])[X]i, i being any index p, q, r and X any component M, A, or H. Future applications of this algorithm to practical problems of macromolecule-ligand-proton equilibria are outlined.

Binding Sites↗
PubMed1977

Profiling of odor components and their mixtures.

Observers evaluated five odors and their 26 mixtures (two, three, four, and five components) by magnitude estimation. Estimates revealed that in mixtures there is moderate suppression of perceived intensity; a vector model proposed by Berglund (Annals of the New York Academy of Sciences, 1974, 237, 35-51) provides a good prediction of the intensity of binary mixtures, but overpredicts the intensity of three, four, and five component mixtures. Hedonic tones of mixtures were difficult to predict from hedonic tones of components. Qualities of mixtures were difficult to predict from quality of components. Intermediacy, of quality and hedonic values, was often observed.

Adult↗
PubMed1979

Electron microscopical studies on the development of Babesia canis (Sporozoa) in the salivary glands of the vector tick Dermacentor reticulatus.

The formation of sporozoites of Babesia canis was studied by light- and electron microscopy in the salivary gland cells of adult female ticks from the 2nd day after attachment until 1 day after detachment. It was found that this process was initiated by the binary division of kinetes that had already entered or entered during the period examined. During division the kinetes (15 X 2.5 microns) lost their typical organelles, reduced their three-layered pellicle to a single membrane and became spherical. After nuclear division and a further time-lag cell division occurred, giving rise to two cells in which this process was repeated. After numerous binary divisions the parasites acquired more and more closely the shape of the later infectious, pyriform sporozoite. These sporozoites measured about 2.5 X 1.5 microns and also had a three-layered pellicle, with rhoptries and a few micronemes, but never contained "spherical bodies". The formation process needed about 2--3 days so that the transmission to the dog could be carried out while the tick engorges and this is probably the stimulation for the development. Finally the cytological features of this sporozoite formation were compared to those in the Theileria species studied by our group.

Animals↗
PubMed1985

Automatic segmentation and quantification of electron micrographs: extracellular components.

Extracellular glycosaminoglycans when precipitated by tannic acid, appear in electron micrographs as amorphous reticulate masses or fragments sometimes finely beaded and often associated with collagen fibrils. An algorithm for automatic classification, segmentation, and quantification of the amount of tannic acid-precipitable material (TAPM) and collagen in electron microscopic images is presented. Small patches of a region are initially located and the patch boundaries are traced using a binary contour tracing algorithm. The patches are then grown out and merged together to form one large area. This area is classified using a two-dimensional feature vector into one of two classes: a region with TAPM and collagen, or one with cell bodies and/or processes. Once these areas are classified and segmented, the distribution of TAPM is measured. The algorithm was tested on several TAPM images displaying varying amounts and configurations of TAPM with good results. It may also be adapted to process other electron microscopic images containing elements of interest which have complex or amorphous form.

Animals↗
PubMed1984

Clinical classification of regional cerebral blood flow (RCBF) by partitioning.

An algorithm is proposed to classify the regional cerebral blood flow (RCBF) of two groups of subjects. A 32-tuple training vector is defined corresponding to 32 detectors used to measure 133Xe washout following inhalation. For any index of 133Xe washout, each detector is associated with two cumulative distributions (cds) each corresponding to a population. The 32 index values at which the differences between cds are maximum are defined as partition values. All index values are then compared to their partitions and are designated binary values of 1 or 0 for being above or below the partitions. A representative sum of the binary numbers (0 to 16) indicates the number of detectors in each hemisphere which exceed their respective threshold. In the example, a normal group of subjects (n = 40) is compared to an abnormal group (n = 82). The abnormal group was identified independently of RCBF by clinical testing as having Alzheimer's disease, a subcategory of dementing diseases. The classification algorithm defined a training vector to which the two populations were compared. The normal subjects had higher representative scores than the abnormals with a tight clustering of these scores. Although some abnormals scored well, the great majority had representative scores well below 12 for each cerebral hemisphere. The training vector can be used to classify new studies or can be updated by new studies until no significant changes result. At this point, the new tracing vector is used as a reference set of partition values.

Alzheimer Disease↗
PubMed1988

Estimators and tests in the analysis of multiple nonindependent 2 x 2 tables with partially missing observations.

We present methods for the analysis of a K-variate binary measure for two independent groups where some observations may be incomplete, as in the case of K repeated measures in a comparative trial. For the K 2 X 2 tables, let theta = (theta 1,..., theta K) be a vector of association parameters where theta k is a measure of association that is a continuous function of the probabilities pi ik in each group (i = 1, 2; k = 1,..., K), such as the log odds ratio or log relative risk. The asymptotic distribution of the estimates theta = (theta 1,..., theta K) is derived. Under the assumption that theta k = theta for all k, we describe the maximally efficient linear estimator theta of the common parameter theta. Tests of contrasts on the theta are presented which provide a test of homogeneity Ha: theta k = theta l for all k not equal to l. We then present maximally efficient tests of aggregate association Hb: theta = theta 0, where theta 0 is a given value. It is shown that the test of aggregate association Hb is asymptotically independent of the preliminary test of homogeneity Ha. These methods generalize the efficient estimators of Gart (1962, Biometrics 18, 601-610), and the Cochran (1954, Biometrics 10, 417-451), Mantel-Haenszel (1959, Journal of the National Cancer Institute 22, 719-748), and Radhakrishna (1965, Biometrics 21, 86-98) tests to nonindependent tables. The methods are illustrated with an analysis of repeated morphologic evaluations of liver biopsies obtained in the National Cooperative Gallstone Study.

Analysis of Variance↗
PubMed1977

Polydisperse particulate solids mixing and segregation: nonstationary Markov chains.

The feasibility of analyzing interparticulate translocations within agitated beds of polydisperse particulate solids in terms of Markov chains was investigated. A binary mixture of spherical particles subjected to vertical sine wave vibration is shown to behave in accordance with a nonstationary. Markov chain having singly stochastic transition matrixes. The transition probability elements of such matrixes, calculated from a knowledge of the initial and final occupancy vectors, agree with those estimated using tracer particles. With appropriate restrictions, the former method, based on the solution of simultaneous equations, permits a quantitative evaluation of particle mobilities throughout the bed.

Chemistry, Pharmaceutical↗
PubMedDate not supplied

[The susceptibility of mosquitoes for Plasmodium gallinaceum in the joint use of biologically active substances].

Making use of a model pair Aedes aegypti--Plasmodium gallinaceum, the authors assess the susceptibility of mosquito female survivors to malaria agent after treatment of larvae with various bioactive substances. Eight binary combinations of 6 preparations have been tried: dimilin and uvemon, insect development regulators; fundosol and copper sulfate, fungicides; phytobacteriomicin (PBM), a larvicidal antibiotic; bactoculicide, a bacterial agent. Combinations of PBM with compounds differing by their mechanisms of action were found to inhibit the specific effect of PBM on the vector, PBM specific effect consisting in depression of mosquito susceptibility to P. gallinaceum. PBM combinations with some agents may alter other parameters of the vector potential: combinations of copper sulfate or uvemon with low concentrations of PBM potentiated the larvicidal effect, and PBM mixtures with fungicides reduces the activity of female attacks.

Aedes↗
PubMed1986

Polyamine depletion following exposure to DL-alpha-difluoromethylornithine both in vivo and in vitro initiates morphological alterations and mitochondrial activation in a monomorphic strain of Trypanosoma brucei brucei.

DL-alpha-difluoromethylornithine (DFMO), a specific irreversible inhibitor of ornithine decarboxylase (ODC), rapidly depletes cells of intracellular putrescine. When administered to animals and humans, DFMO cures acute infections of trypanosomiasis. In order to determine if the mechanism of drug action is related to initiation of transformation and biochemical alterations subsequent to polyamine depletion, trypanosome morphology and mitochondrial activation were studied in a monomorphic strain of Trypanosoma brucei brucei. Exposure of trypanosomes to DFMO in vivo in infected rodents or in vitro in culture resulted in a depletion of intracellular putrescine and a cessation of cell division without specific cytotoxicity. These events were followed by a transformation of the long slender bloodstream form to a short stumpy form via an intermediate morphology. Putrescine, the product of the ODC reaction, abrogates this effect. When introduced into SDM-79 medium, the intermediate form is capable of further transformation to an "insect" procyclic trypomastigote whereas the long slender form and short stumpy form are not. Short stumpy forms are incapable of binary fission and have lost their infectivity for the vertebrate host. In addition, the mitochondrial marker enzyme, NAD diaphorase, was found only in the short stumpy and intermediate forms. We hypothesize that the short stumpy phenotype may not be a viable stage in the natural transformation of the trypanosome from its mammalian host to the insect vector.

Animals↗
PubMed1990

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. II. Relationships between chemical model and partition function algorithm.

The relationships between the chemical properties of a system and the partition function algorithm as applied to the description of multiple equilibria in solution are explained. The partition functions ZM, ZA, and ZH are obtained from powers of the binary generating functions Jj = (1 + kappa j gamma j,i[Y])i tau j, where i tau j = p tau j, q tau j, or r tau j represent the maximum number of sites in sites in class j, for Y = M, A, or H, respectively. Each term of the generating function can be considered an element (ij) of a vector Jj and each power of the cooperativity factor gamma ij,i can be considered an element of a diagonal cooperativity matrix gamma j. The vectors Jj are combined in tensor product matrices L tau = (J1) [J2]...[Jj]..., thus representing different receptor-ligand combinations. The partition functions are obtained by summing elements of the tensor matrices. The relationship of the partition functions with the total chemical amounts TM, TA, and TH has been found. The aim is to describe the total chemical amounts TM, TA, and TH as functions of the site affinity constants kappa j and cooperativity coefficients bj. The total amounts are calculated from the sum of elements of tensor matrices Ll. Each set of indices (pj..., qj..., rj...) represents one element of a tensor matrix L tau and defines each term of the summation. Each term corresponds to the concentration of a chemical microspecies. The distinction between microspecies MpjAqjHrj with ligands bound on specific sites and macrospecies MpAqHR corresponding to a chemical stoichiometric composition is shown. The translation of the properties of chemical model schemes into the algorithms for the generation of partition functions is illustrated with reference to a series of examples of gradually increasing complexity. The equilibria examined concern: (1) a unique class of sites; (2) the protonation of a base with two classes of sites; (3) the simultaneous binding of ligand A and proton H to a macromolecule or receptor M with four classes of sites; and (4) the binding to a macromolecule M of ligand A which is in turn a receptor for proton H. With reference to a specific example, it is shown how a computer program for least-squares refinement of variables kappa j and bj can be organized. The chemical model from the free components M, A, and H to the saturated macrospecies MpAQHR, with possible complex macrospecies MpAq and AHR, is defined first.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1985

Differentiation in Trypanosoma brucei: host-parasite cell junctions and their persistence during acquisition of the variable antigen coat.

Acquisition of the variable antigen-containing surface coat of Trypanosoma brucei occurs at the metacyclic stage in the salivary glands of the tsetse fly vector. The differentiation of the metacyclic trypanosome in the gland has been studied by scanning electron microscopy and by transmission electron microscopy of thin sections and freeze-fracture replicas. The uncoated epimastigote trypanosomes (with a prenuclear kinetoplast) divide while attached to the salivary gland epithelium brush border by elaborate branched flagellar outgrowths, which ramify between the host cell microvilli and form punctate hemidesmosome-like attachment plaques where they are indented by the microvilli. These outgrowths become reduced as the epimastigotes transform to uncoated trypomastigotes (with postnuclear kinetoplast), which remain attached and capable of binary fission. The flagellar outgrowths disappear but the attachment plaques persist as the uncoated trypomastigotes (premetacyclics) stop dividing and acquire the surface coat to become 'nascent metacyclics'. Coat acquisition therefore occurs in the attached trypanosome and not, as previously believed, after detachment. Coating is accompanied by morphological changes in the glycosomes and mitochondrion of the parasite. Freeze-fracture replicas of the host-parasite junctional complexes show membrane particle aggregates on the host membrane but not on the parasite membrane. It is suggested that disruption of the complex occurs when maximum packing of the glycoprotein molecules has been achieved in the trypanosome surface coat, releasing the metacyclic trypanosome into the lumen of the gland.

Animals↗