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  • Springer  (112)
  • Oxford University Press  (19)
  • Genetics Society of America (GSA)  (3)
  • 1
    Publication Date: 2015-02-18
    Description: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2013-11-27
    Description: Recent studies on microRNA (miRNA) evolution focused mainly on the comparison of miRNA complements between animal clades. However, evolution of miRNAs within such groups is poorly explored despite the availability of comparable data that in some cases lack only a few key taxa. For flatworms (Platyhelminthes), miRNA complements are available for some free-living flatworms and all major parasitic lineages, except for the Monogenea. We present the miRNA complement of the monogenean flatworm Gyrodactylus salaris that facilitates a comprehensive analysis of miRNA evolution in Platyhelminthes. Using the newly designed bioinformatics pipeline miRCandRef, the miRNA complement was disentangled from next-generation sequencing of small RNAs and genomic DNA without a priori genome assembly. It consists of 39 miRNA hairpin loci of conserved miRNA families, and 22 novel miRNAs. A comparison with the miRNA complements of Schmidtea mediterranea (Turbellaria), Schistosoma japonicum (Trematoda), and Echinococcus granulosus (Cestoda) reveals a substantial loss of conserved bilaterian, protostomian, and lophotrochozoan miRNAs. Eight of the 46 expected conserved miRNAs were lost in all flatworms, 16 in Neodermata and 24 conserved miRNAs could not be detected in the cestode and the trematode. Such a gradual loss of miRNAs has not been reported before for other animal phyla. Currently, little is known about miRNAs in Platyhelminthes, and for the majority of the lost miRNAs there is no prediction of function. As suggested earlier they might be related to morphological simplifications. The presence and absence of 153 conserved miRNAs was compared for platyhelminths and 32 other metazoan taxa. Phylogenetic analyses support the monophyly of Platyhelminthes (Turbellaria + Neodermata [Monogenea {Trematoda + Cestoda}]).
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 3
    Publication Date: 2013-12-18
    Description: We perform a suite of multimass cosmological zoom simulations of individual dark matter haloes and explore how to best select Lagrangian regions for resimulation without contaminating the halo of interest with low-resolution particles. Such contamination can lead to significant errors in the gas distribution of hydrodynamical simulations, as we show. For a fixed Lagrange volume, we find that the chance of contamination increases systematically with the level of zoom. In order to avoid contamination, the Lagrangian volume selected for resimulation must increase monotonically with the resolution difference between parent box and the zoom region. We provide a simple formula for selecting Lagrangian regions (in units of the halo virial volume) as a function of the level of zoom required. We also explore the degree to which a halo's Lagrangian volume correlates with other halo properties (concentration, spin, formation time, shape, etc.) and find no significant correlation. There is a mild correlation between Lagrange volume and environment, such that haloes living in the most clustered regions have larger Lagrangian volumes. Nevertheless, selecting haloes to be isolated is not the best way to ensure inexpensive zoom simulations. We explain how one can safely choose haloes with the smallest Lagrangian volumes, which are the least expensive to resimulate, without biasing one's sample.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Catalysis letters 4 (1990), S. 271-278 
    ISSN: 1572-879X
    Keywords: Transition metal clusters ; hydrogen chemisorption ; deuterium chemisorption ; platinum ; rhodium ; nickel ; palladium ; catalysts ; hydrogen(deuterium) saturation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Deuterium uptake experiments on gas phase transition metal cluster cations of Ni, Pt and Rh show that the small (〈 10 Å dia.) clusters can bind many (up to 8) deuterium atoms per metal atom in the cluster, in contast to (H(D)/M)max ratios near unity typically reported for single crystal metal surfaces and in previous uptake experiments on nickel and iron clusters [11]. Abnormally large (H(D)/M)max ratios appear to be the rule rather than the exception for small transition metal clusters, an effect which has strong implications in chemical and catalytic processes involving hydrogen chemisorption.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Naturwissenschaften 67 (1980), S. 511-512 
    ISSN: 1432-1904
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-1904
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Archives of environmental contamination and toxicology 38 (2000), S. 59-69 
    ISSN: 1432-0703
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Notes: Abstract. The present study describes the use of a fish hepatoma cell line (PLHC-1) in monitoring the biological effects of sediments collected from recipient waters of the oil shale industry. Sampling sites were located in River Purtse and River Kohtla in northeast Estonia. The effects of pure oil shale on the PLHC-1 cells were also studied. The cells were exposed to n-hexane–extracted samples in 48-well plates for 24 h, and 7-ethoxyresorufin O-deethylase (EROD) activity, total protein, and porphyrin content were measured in the exposed cells. Polycyclic aromatic hydrocarbon (PAH) contents in the samples were measured by high-performance liquid chromatography (HPLC). All the sediment and oil shale samples induced CYP1A activity and led to porphyrin accumulation in the cells. The most potent inducers were the sediments collected near the oil shale processing plants (site Lüganuse in River Purtse and Kohtla in River Kohtla), as well as those at the most downstream site in River Purtse (Purtse). These samples possessed high total PAH contents, ranging from 4,270 to nearly 150,000 μg/kg dry sediment. The presence of other lipophilic organic contaminants in the samples was not determined in this study. Both EROD activity and porphyrin content exhibited biphasic induction curves, and the ED50 1 values for EROD activity were lower than the ED50s for porphyrin content. 2,3,7,8-Tetrachlorodibenzo-p-dioxin induction equivalents (TCDD-EQs) calculated from EROD induction potencies correlated well with total PAHs (r 2 = 0.827 and p = 0.003 for log-transformed data) and also with individual PAHs. TCDD-EQs for porphyrin content did not correlate significantly with total PAHs (log-log r2 = 0.785, p = 0.116). The biological potency and PAH contamination of the samples showed the same rank order, except at Lüganuse, where sediment extracts induced CYP1A and porphyrins more than could have been expected based on PAH contents. Bioassay-derived induction EQs (normalized to dibenz(a,h)anthracene) were 20- to 3,200-fold greater than EQs calculated from the concentrations of five PAHs, suggesting important contributions from other compounds or nonadditive effects. The PLHC-1 cells proved to be a sensitive bioanalytical tool for sediments contaminated with PAH-type pollutants in the oil shale processing area. We suggest further use of this bioassay in screening and monitoring waters with similar background of pollution as in northeast Estonia.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Cellular and molecular life sciences 42 (1986), S. 104-104 
    ISSN: 1420-9071
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-1041
    Keywords: Cholestyramine ; interaction with absorption ; phenprocoumon ; acetylosalicylic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary The effect of cholestyramine on the absorption of phenprocoumon and acetylosalicylic acid has been studied in volunteers by comparing their serum concentrations after a single oral dose either of the drug alone or simultaneously with the resin in a crossover repetition arrangement. In four volunteers cholestyramine 8 g significantly reduced the absorption of a simultaneous 15 mg dose of phenprocoumon. The effect of the latter on coagulation, as measured by the thrombotest method was also diminished. The absorption of acetylosalicylic acid 500 mg was delayed by cholestyramine but there was no appreciable effect on the total amount absorbed. These results are in accordance with the stronger binding of phenprocoumon to cholestyramine inin vitro experiments.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-072X
    Keywords: Bradyrhizobium ; Electron microscopy ; Mutants ; Nitrogen fixation ; Nodulation ; Soybean ; Symbiosis ; Transposon Tn5
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genome of the slow-growing Bradyrhizobium japonicum (strain 110) was mutagenized with transposon Tn5. A total of 1623 kanamycin/streptomycin resistant derivatives were screened in soybean infection tests for nodulation (Nod) and symbiotic nitrogen fixation (Fix). In this report we describe 14 strains possessing a stable, reproducible Nod+Fix- phenotype. These strains were also grown under microaerobic culture conditions to test them for free-living nitrogen fixation activity (Nif). In addition to strains having reduced Fix and Nif activities, there were also strains that had reduced symbiotic Fix activity but were Nif+ ex planta. Analysis of the genomic structure revealed that the majority of the strains had a single Tn5 insertion without any further apparent physical alteration. A few strains had additional insertions (by Tn5 or IS50), or a deletion, or had cointegrated part of the vector used for Tn5 mutagenesis. One of the insertions was found in a known nif gene (nifD) whereas all other mutations seem to affect different, hitherto unknown genes or operons. Several mutant strains had an altered nodulation phenotype, inducing numerous, small, widely distributed nodules. Light and electron microscopy revealed that most of these mutants were defective in different stages of bacteroid development and/or bacteroid persistence. The protein patterns of the mutants were inspected by two-dimensional gel electrophoresis after labelling microaerobic cultures with l-(35S)methionine. Of particular interest were mutants lacking a group of proteins the synthesis of which was known to be under oxygen control. Such strains can be regarded as potential regulatory mutants.
    Type of Medium: Electronic Resource
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