Fast and accurate quantification using Genetic Algorithm optimized H-1-C-13 refocused constant-time INEPT

Using Genetic Algorithm, a global optimization method inspired by nature's evolutionary process, we have improved the quantitative refocused constant-time INEPT experiment (Q-INEPT-CT) of Makela et al. (JMR 204 (2010) 124-130) with various optimization constraints. The improved `average polarization transfer' and `min-max difference' of new delay sets effectively reduces the experimental time by a factor of two (compared with Q-INEPT-CT, Makela et al.) without compromising on accuracy. We also discuss a quantitative spectral editing technique based on average polarization transfer. (C) 2013 Elsevier Inc. All rights reserved.

Accurate point matching based on multi-objective Genetic Algorithm for multi-sensor satellite imagery

This paper investigates a novel approach for point matching of multi-sensor satellite imagery. The feature (corner) points extracted using an improved version of the Harris Corner Detector (HCD) is matched using multi-objective optimization based on a Genetic Algorithm (GA). An objective switching approach to optimization that incorporates an angle criterion, distance condition and point matching condition in the multi-objective fitness function is applied to match corresponding corner-points between the reference image and the sensed image. The matched points obtained in this way are used to align the sensed image with a reference image by applying an affine transformation. From the results obtained, the performance of the image registration is evaluated and compared with existing methods, namely Nearest Neighbor-Random SAmple Consensus (NN-Ran-SAC) and multi-objective Discrete Particle Swarm Optimization (DPSO). From the performed experiments it can be concluded that the proposed approach is an accurate method for registration of multi-sensor satellite imagery. (C) 2014 Elsevier Inc. All rights reserved.

A Genetic Analysis of the Functional Interactions within Mycobacterium tuberculosis Single-Stranded DNA Binding Protein

Single-stranded DNA binding proteins (SSBs) are vital in all organisms. SSBs of Escherichia coli (EcoSSB) and Mycobacterium tuberculosis (MtuSSB) are homotetrameric. The N-terminal domains (NTD) of these SSBs (responsible for their tetramerization and DNA binding) are structurally well defined. However, their C-terminal domains (CTD) possess undefined structures. EcoSSB NTD consists of beta 1-beta 1'-beta 2-beta 3-alpha-beta 4-beta 45(1)-beta 45(2)-beta 5 secondary structure elements. MtuSSB NTD includes an additional beta-strand (beta 6) forming a novel hook-like structure. Recently, we observed that MtuSSB complemented an E. coli Delta ssb strain. However, a chimeric SSB (m beta 4-beta 5), wherein only the terminal part of NTD (beta 4-beta 5 region possessing L-45 loop) of EcoSSB was substituted with that from MtuSSB, failed to function in E. coli in spite of its normal DNA binding and oligomerization properties. Here, we designed new chimeras by transplanting selected regions of MtuSSB into EcoSSB to understand the functional significance of the various secondary structure elements within SSB. All chimeric SSBs formed homotetramers and showed normal DNA binding. The m beta 4-beta 6 construct obtained by substitution of the region downstream of beta 5 in m beta 4-beta 5 SSB with the corresponding region (beta 6) of MtuSSB complemented the E. coli strain indicating a functional interaction between the L-45 loop and the beta 6 strand of MtuSSB.

Colored polydimethylsiloxane micropillar arrays for high throughput measurements of forces applied by genetic model organisms

Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semiautomated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of similar to 1 mu N on an individual pillar and a total average force of similar to 7.68 mu N. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4Hz applying an average force of similar to 1.58 mu N on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces applied by multiple model organisms that crawl or slither to travel through their environment. (C) 2015 AIP Publishing LLC.

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

1. Host-parasite interactions have the potential to influence broadscale ecological and evolutionary processes, levels of endemism, divergence patterns and distributions in host populations. Understanding the mechanisms involved requires identification of the factors that shape parasite distribution and prevalence. 2. A lack of comparative information on community-level host-parasite associations limits our understanding of the role of parasites in host population divergence processes. Avian malaria (haemosporidian) parasites in bird communities offer a tractable model system to examine the potential for pathogens to influence evolutionary processes in natural host populations. 3. Using cytochrome b variation, we characterized phylogenetic diversity and prevalence of two genera of avian haemosporidian parasites, Plasmodium and Haemoproteus, and analysed biogeographic patterns of lineages across islands and avian hosts, in southern Melanesian bird communities to identify factors that explain patterns of infection. 4. Plasmodium spp. displayed isolation-by-distance effects, a significant amount of genetic variation distributed among islands but insignificant amounts among host species and families, and strong local island effects with respect to prevalence. Haemoproteus spp. did not display isolation-by-distance patterns, showed marked structuring of genetic variation among avian host species and families, and significant host species prevalence patterns. 5. These differences suggest that Plasmodium spp. infection patterns were shaped by geography and the abiotic environment, whereas Haemoproteus spp. infection patterns were shaped predominantly by host associations. Heterogeneity in the complement and prevalence of parasite lineages infecting local bird communities likely exposes host species to a mosaic of spatially divergent disease selection pressures across their naturally fragmented distributions in southern Melanesia. Host associations for Haemoproteus spp. indicate a capacity for the formation of locally co-adapted host-parasite relationships, a feature that may limit intraspecific gene flow or range expansions of closely related host species.

Genetic diversity and proviral DNA load in different neural compartments of HIV-1 subtype C infection

In India, the low prevalence of HIV-associated dementia (HAD) in the Human immunodeficiency virus type 1 (HIV-1) subtype C infection is quite paradoxical given the high-rate of macrophage infiltration into the brain. Whether the direct viral burden in individual brain compartments could be associated with the variability of the neurologic manifestations is controversial. To understand this paradox, we examined the proviral DNA load in nine different brain regions and three different peripheral tissues derived from ten human subjects at autopsy. Using a highly sensitive TaqMan probe-based real-time PCR, we determined the proviral load in multiple samples processed in parallel from each site. Unlike previously published reports, the present analysis identified uniform proviral distribution among the brain compartments examined without preferential accumulation of the DNA in any one of them. The overall viral DNA burden in the brain tissues was very low, approximately 1 viral integration per 1000 cells or less. In a subset of the tissue samples tested, the HIV DNA mostly existed in a free unintegrated form. The V3-V5 envelope sequences, demonstrated a brain-specific compartmentalization in four of the ten subjects and a phylogenetic overlap between the neural and non-neural compartments in three other subjects. The envelope sequences phylogenetically belonged to subtype C and the majority of them were R5 tropic. To the best of our knowledge, the present study represents the first analysis of the proviral burden in subtype C postmortem human brain tissues. Future studies should determine the presence of the viral antigens, the viral transcripts, and the proviral DNA, in parallel, in different brain compartments to shed more light on the significance of the viral burden on neurologic consequences of HIV infection.

Similarity of Matrices Over Local Rings of Length Two

Let R be a (commutative) local principal ideal ring of length two, for example, the ring R = Z/p(2)Z with p prime. In this paper, we develop a theory of normal forms for similarity classes in the matrix rings M-n (R) by interpreting them in terms of extensions of R t]-modules. Using this theory, we describe the similarity classes in M-n (R) for n <= 4, along with their centralizers. Among these, we characterize those classes which are similar to their transposes. Non-self-transpose classes are shown to exist for all n > 3. When R has finite residue field of order q, we enumerate the similarity classes and the cardinalities of their centralizers as polynomials in q. Surprisingly, the polynomials representing the number of similarity classes in M-n (R) turn out to have non-negative integer coefficients.

Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations

Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (F-ST = 0.154) and considerable inbreeding (F-IS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology.

Query Click and Text Similarity Graph for Query Suggestions

Query suggestion is an important feature of the search engine with the explosive and diverse growth of web contents. Different kind of suggestions like query, image, movies, music and book etc. are used every day. Various types of data sources are used for the suggestions. If we model the data into various kinds of graphs then we can build a general method for any suggestions. In this paper, we have proposed a general method for query suggestion by combining two graphs: (1) query click graph which captures the relationship between queries frequently clicked on common URLs and (2) query text similarity graph which finds the similarity between two queries using Jaccard similarity. The proposed method provides literally as well as semantically relevant queries for users' need. Simulation results show that the proposed algorithm outperforms heat diffusion method by providing more number of relevant queries. It can be used for recommendation tasks like query, image, and product suggestion.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Application of Similarity Theory to the Characterization of Non-Transferred Laminar Plasma Jet Generation

Laminar-flow non-transferred DC plasma jets were generated by a torch with an inter-electrode insert by which the arc column was limited to a length of about 20 mm. Current–voltage characteristics, thermal efficiency and jet length, a parameter which changes greatly with the generating parameters in contrast with the almost unchangeable jet length of the turbulent plasma, were investigated systematically, by using the similarity theory combined with the corresponding experimental examination. Formulae in non-dimensional forms were derived for predicting the characteristics of the laminar plasma jet generation, within the parameter ranges where no transfer to turbulent flow occurs. Mean arc temperature in the torch channel and mean jet-flow temperature at the torch exit were obtained, and the results indicate that the thermal conductivity feature of the working gas seems to be an important factor affecting thermal efficiency of laminar plasma generation.

Novel Investigation on Principle of Similarity for Microgravity Two-Phase Flow

根据两流体同心环状流线性稳定性分析的结果 ,对微重力气 /液两相流地面模拟实验所应遵循的相似准则进行了探讨 ,得到了一个新的重力无关性准则 ,即Bond数和环形区流体相的毛细数之比的绝对值不大于 1 .此外 ,微重力气 /液两相流模拟实验还必须满足两个条件 ,即流量比和气相表观Weber数应与所模拟的流动中对应数值相等 . In the present paper, the principle of similarity for two phase flows at microgravity is studied based on the results of the linear stability analysis of the two fluid concentric annular flow configuration. A new criterion of gravity independence, namely the absolute value of the ratio between the Bond number and the capillary number of the phase flowing in the annulus is no more than one, is achieved. It is also pointed out that the flowrate ratio and the gas superficial Weber number must have the same ...

The role of androgens in fetal growth: observational study in two genetic models of disordered androgen signalling.

OBJECTIVE: To examine the role of androgens on birth weight in genetic models of altered androgen signalling. SETTING: Cambridge Disorders of Sex Development (DSD) database and the Swedish national screening programme for congenital adrenal hyperplasia (CAH). PATIENTS: (1) 29 girls with XY karyotype and mutation positive complete androgen insensitivity syndrome (CAIS); (2) 43 girls and 30 boys with genotype confirmed CAH. MAIN OUTCOME MEASURES: Birth weight, birth weight-for-gestational-age (birth weight standard deviation score (SDS)) calculated by comparison with national references. RESULTS: Mean birth weight SDS in CAIS XY infants was higher than the reference for girls (mean, 95% CI: 0.4, 0.1 to 0.7; p=0.02) and was similar to the national reference for boys (0.1, -0.2 to 0.4). Birth weight SDS in CAH girls was similar to the national reference for girls (0.0, -0.2 to 0.2) and did not vary by severity of gene mutation. Birth weight SDS in CAH boys was also similar to the national reference for boys (0.2, -0.2 to 0.6). CONCLUSION: CAIS XY infants have a birth weight distribution similar to normal male infants and birth weight is not increased in infants with CAH. Alterations in androgen signalling have little impact on birth weight. Sex dimorphism in birth size is unrelated to prenatal androgen exposure.

Similarity consideration of structural bifurcation buckling

Many structural bifurcation buckling problems exhibit a scaling or power law property. Dimensional analysis is used to analyze the general scaling property. The concept of a new dimensionless number, the response number-Rn, suggested by the present author for the dynamic plastic response and failure of beams, plates and so on, subjected to large dynamic loading, is generalized in this paper to study the elastic, plastic, dynamic elastic as well as dynamic plastic buckling problems of columns, plates as well as shells. Structural bifurcation buckling can be considered when Rn(n) reaches a critical value.