WorldWideScience

Sample records for dna k-mer spectra

  1. K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

    Directory of Open Access Journals (Sweden)

    Aaron Sievers

    2017-04-01

    Full Text Available In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4 on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs, which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST and the

  2. Robust k-mer frequency estimation using gapped k-mers.

    Science.gov (United States)

    Ghandi, Mahmoud; Mohammad-Noori, Morteza; Beer, Michael A

    2014-08-01

    Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome.

  3. A k-mer-based barcode DNA classification methodology based on spectral representation and a neural gas network.

    Science.gov (United States)

    Fiannaca, Antonino; La Rosa, Massimo; Rizzo, Riccardo; Urso, Alfonso

    2015-07-01

    In this paper, an alignment-free method for DNA barcode classification that is based on both a spectral representation and a neural gas network for unsupervised clustering is proposed. In the proposed methodology, distinctive words are identified from a spectral representation of DNA sequences. A taxonomic classification of the DNA sequence is then performed using the sequence signature, i.e., the smallest set of k-mers that can assign a DNA sequence to its proper taxonomic category. Experiments were then performed to compare our method with other supervised machine learning classification algorithms, such as support vector machine, random forest, ripper, naïve Bayes, ridor, and classification tree, which also consider short DNA sequence fragments of 200 and 300 base pairs (bp). The experimental tests were conducted over 10 real barcode datasets belonging to different animal species, which were provided by the on-line resource "Barcode of Life Database". The experimental results showed that our k-mer-based approach is directly comparable, in terms of accuracy, recall and precision metrics, with the other classifiers when considering full-length sequences. In addition, we demonstrate the robustness of our method when a classification is performed task with a set of short DNA sequences that were randomly extracted from the original data. For example, the proposed method can reach the accuracy of 64.8% at the species level with 200-bp fragments. Under the same conditions, the best other classifier (random forest) reaches the accuracy of 20.9%. Our results indicate that we obtained a clear improvement over the other classifiers for the study of short DNA barcode sequence fragments. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier.

    Science.gov (United States)

    Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Rao, A R

    2016-11-05

    DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Enhanced regulatory sequence prediction using gapped k-mer features.

    Science.gov (United States)

    Ghandi, Mahmoud; Lee, Dongwon; Mohammad-Noori, Morteza; Beer, Michael A

    2014-07-01

    Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.

  6. Enhanced regulatory sequence prediction using gapped k-mer features.

    Directory of Open Access Journals (Sweden)

    Mahmoud Ghandi

    2014-07-01

    Full Text Available Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.

  7. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

    Directory of Open Access Journals (Sweden)

    Shairul Izan

    2017-08-01

    Full Text Available Whole Genome Shotgun (WGS sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb, Aegilops tauschii (4 Gb and Paphiopedilum henryanum (25 Gb. We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.

  8. Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.

    Science.gov (United States)

    Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

    2017-07-15

    Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning. We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k -mer embedding. We first split DNA sequences into k -mers and pre-train k -mer embedding vectors based on the co-occurrence matrix of k -mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k -mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm . tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn. Supplementary materials are available at

  9. Simrank: Rapid and sensitive general-purpose k-mer search tool

    Energy Technology Data Exchange (ETDEWEB)

    DeSantis, T.Z.; Keller, K.; Karaoz, U.; Alekseyenko, A.V; Singh, N.N.S.; Brodie, E.L; Pei, Z.; Andersen, G.L; Larsen, N.

    2011-04-01

    Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.

  10. Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction.

    Science.gov (United States)

    Allman, Elizabeth S; Rhodes, John A; Sullivant, Seth

    2017-02-01

    Frequencies of k-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared Euclidean distance between k-mer vectors to approximate a tree metric can be statistically inconsistent. To remedy this, we derive model-based distance corrections for orthologous sequences without gaps, which lead to consistent tree inference. The identifiability of model parameters from k-mer frequencies is also studied. Finally, we report simulations showing that the corrected distance outperforms many other k-mer methods, even when sequences are generated with an insertion and deletion process. These results have implications for multiple sequence alignment as well since k-mer methods are usually the first step in constructing a guide tree for such algorithms.

  11. Implementation of hierarchical clustering using k-mer sparse matrix to analyze MERS-CoV genetic relationship

    Science.gov (United States)

    Bustamam, A.; Ulul, E. D.; Hura, H. F. A.; Siswantining, T.

    2017-07-01

    Hierarchical clustering is one of effective methods in creating a phylogenetic tree based on the distance matrix between DNA (deoxyribonucleic acid) sequences. One of the well-known methods to calculate the distance matrix is k-mer method. Generally, k-mer is more efficient than some distance matrix calculation techniques. The steps of k-mer method are started from creating k-mer sparse matrix, and followed by creating k-mer singular value vectors. The last step is computing the distance amongst vectors. In this paper, we analyze the sequences of MERS-CoV (Middle East Respiratory Syndrome - Coronavirus) DNA by implementing hierarchical clustering using k-mer sparse matrix in order to perform the phylogenetic analysis. Our results show that the ancestor of our MERS-CoV is coming from Egypt. Moreover, we found that the MERS-CoV infection that occurs in one country may not necessarily come from the same country of origin. This suggests that the process of MERS-CoV mutation might not only be influenced by geographical factor.

  12. Multiple comparative metagenomics using multiset k-mer counting

    Directory of Open Access Journals (Sweden)

    Gaëtan Benoit

    2016-11-01

    Full Text Available Background Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today’s metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads. We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.

  13. Recapitulating phylogenies using k-mers: from trees to networks.

    Science.gov (United States)

    Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

    2016-01-01

    Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

  14. The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome.

    Science.gov (United States)

    Almutairy, Meznah; Torng, Eric

    2017-01-01

    One of the most common ways to search a sequence database for sequences that are similar to a query sequence is to use a k-mer index such as BLAST. A big problem with k-mer indexes is the space required to store the lists of all occurrences of all k-mers in the database. One method for reducing the space needed, and also query time, is sampling where only some k-mer occurrences are stored. Most previous work uses hard sampling, in which enough k-mer occurrences are retained so that all similar sequences are guaranteed to be found. In contrast, we study soft sampling, which further reduces the number of stored k-mer occurrences at a cost of decreasing query accuracy. We focus on finding highly similar local alignments (HSLA) over nucleotide sequences, an operation that is fundamental to biological applications such as cDNA sequence mapping. For our comparison, we use the NCBI BLAST tool with the human genome and human ESTs. When identifying HSLAs, we find that soft sampling significantly reduces both index size and query time with relatively small losses in query accuracy. For the human genome and HSLAs of length at least 100 bp, soft sampling reduces index size 4-10 times more than hard sampling and processes queries 2.3-6.8 times faster, while still achieving retention rates of at least 96.6%. When we apply soft sampling to the problem of mapping ESTs against the genome, we map more than 98% of ESTs perfectly while reducing the index size by a factor of 4 and query time by 23.3%. These results demonstrate that soft sampling is a simple but effective strategy for performing efficient searches for HSLAs. We also provide a new model for sampling with BLAST that predicts empirical retention rates with reasonable accuracy by modeling two key problem factors.

  15. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

    Science.gov (United States)

    Wang, Dapeng; Xu, Jiayue; Yu, Jun

    2015-09-16

    The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

  16. Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.

    Science.gov (United States)

    Almutairy, Meznah; Torng, Eric

    2018-01-01

    Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.

  17. Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.

    Directory of Open Access Journals (Sweden)

    Meznah Almutairy

    Full Text Available Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.

  18. Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches

    Science.gov (United States)

    Torng, Eric

    2018-01-01

    Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method. PMID:29389989

  19. Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

    Science.gov (United States)

    Pan, Tony; Flick, Patrick; Jain, Chirag; Liu, Yongchao; Aluru, Srinivas

    2017-10-09

    Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance parallel k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Kmerind's k-mer counter performs similarly or better than the best existing k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts k-mers in a 120 GB sequence read dataset in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1% of the k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. Kmerind is the first k-mer indexing library for distributed memory environments, and the first extensible library for general k-mer indexing and counting. Kmerind is available at https://github.com/ParBLiSS/kmerind.

  20. Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

    Directory of Open Access Journals (Sweden)

    Gruenheit Nicole

    2012-03-01

    Full Text Available Abstract Background Transcriptome analysis is increasingly being used to study the evolutionary origins and ecology of non-model plants. One issue for both transcriptome assembly and differential gene expression analyses is the common occurrence in plants of hybridisation and whole genome duplication (WGD and hybridization resulting in allopolyploidy. The divergence of duplicated genes following WGD creates near identical homeologues that can be problematic for de novo assembly and also reference based assembly protocols that use short reads (35 - 100 bp. Results Here we report a successful strategy for the assembly of two transcriptomes made using 75 bp Illumina reads from Pachycladon fastigiatum and Pachycladon cheesemanii. Both are allopolyploid plant species (2n = 20 that originated in the New Zealand Alps about 0.8 million years ago. In a systematic analysis of 19 different coverage cutoffs and 20 different k-mer sizes we showed that i none of the genes could be assembled across all of the parameter space ii assembly of each gene required an optimal set of parameter values and iii these parameter values could be explained in part by different gene expression levels and different degrees of similarity between genes. Conclusions To obtain optimal transcriptome assemblies for allopolyploid plants, k-mer size and k-mer coverage need to be considered simultaneously across a broad parameter space. This is important for assembling a maximum number of full length ESTs and for avoiding chimeric assemblies of homeologous and paralogous gene copies.

  1. A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

    Science.gov (United States)

    Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

    2014-03-12

    The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

  2. Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Yaron Orenstein

    2017-10-01

    Full Text Available With the rapidly increasing volume of deep sequencing data, more efficient algorithms and data structures are needed. Minimizers are a central recent paradigm that has improved various sequence analysis tasks, including hashing for faster read overlap detection, sparse suffix arrays for creating smaller indexes, and Bloom filters for speeding up sequence search. Here, we propose an alternative paradigm that can lead to substantial further improvement in these and other tasks. For integers k and L > k, we say that a set of k-mers is a universal hitting set (UHS if every possible L-long sequence must contain a k-mer from the set. We develop a heuristic called DOCKS to find a compact UHS, which works in two phases: The first phase is solved optimally, and for the second we propose several efficient heuristics, trading set size for speed and memory. The use of heuristics is motivated by showing the NP-hardness of a closely related problem. We show that DOCKS works well in practice and produces UHSs that are very close to a theoretical lower bound. We present results for various values of k and L and by applying them to real genomes show that UHSs indeed improve over minimizers. In particular, DOCKS uses less than 30% of the 10-mers needed to span the human genome compared to minimizers. The software and computed UHSs are freely available at github.com/Shamir-Lab/DOCKS/ and acgt.cs.tau.ac.il/docks/, respectively.

  3. A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction.

    Science.gov (United States)

    Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Guo, Xiaoyun; Gifford, David Kenneth

    2018-04-13

    The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k -mer set memory (KSM), which consists of a set of aligned k -mers that are overrepresented at TF binding sites, and a new method called KMAC for de novo discovery of KSMs. We find that KSMs more accurately predict in vivo binding sites than position weight matrix (PWM) models and other more complex motif models across a large set of ChIP-seq experiments. Furthermore, KSMs outperform PWMs and more complex motif models in predicting in vitro binding sites. KMAC also identifies correct motifs in more experiments than five state-of-the-art motif discovery methods. In addition, KSM-derived features outperform both PWM and deep learning model derived sequence features in predicting differential regulatory activities of expression quantitative trait loci (eQTL) alleles. Finally, we have applied KMAC to 1600 ENCODE TF ChIP-seq data sets and created a public resource of KSM and PWM motifs. We expect that the KSM representation and KMAC method will be valuable in characterizing TF binding specificities and in interpreting the effects of noncoding genetic variations. © 2018 Guo et al.; Published by Cold Spring Harbor Laboratory Press.

  4. MicroRNA categorization using sequence motifs and k-mers.

    Science.gov (United States)

    Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, Jens

    2017-03-14

    Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.

  5. Influence of defects on the effective electrical conductivity of a monolayer produced by random sequential adsorption of linear k-mers onto a square lattice

    Science.gov (United States)

    Tarasevich, Yuri Yu.; Laptev, Valeri V.; Goltseva, Valeria A.; Lebovka, Nikolai I.

    2017-07-01

    The effect of defects on the behaviour of electrical conductivity, σ, in a monolayer produced by the random sequential adsorption of linear k-mers (particles occupying k adjacent sites) onto a square lattice is studied by means of a Monte Carlo simulation. The k-mers are deposited on the substrate until a jamming state is reached. The presence of defects in the lattice (impurities) and of defects in the k-mers with concentrations of dl and dk, respectively, is assumed. The defects in the lattice are distributed randomly before deposition and these lattice sites are forbidden for the deposition of k-mers. The defects of the k-mers are distributed randomly on the deposited k-mers. The sites filled with k-mers have high electrical conductivity, σk, whereas the empty sites, and the sites filled by either types of defect have a low electrical conductivity, σl, i.e., a high-contrast, σk /σl ≫ 1, is assumed. We examined isotropic (both the possible x and y orientations of a particle are equiprobable) and anisotropic (all particles are aligned along one given direction, y) deposition. To calculate the effective electrical conductivity, the monolayer was presented as a random resistor network and the Frank-Lobb algorithm was used. The effects of the concentrations of defects dl and dk on the electrical conductivity for the values of k =2n, where n = 1 , 2 , … , 5, were studied. Increase of both the dl and dk parameters values resulted in decreases in the value of σ and the suppression of percolation. Moreover, for anisotropic deposition the electrical conductivity along the y direction was noticeably larger than in the perpendicular direction, x. Phase diagrams in the (dl ,dk)-plane for different values of k were obtained.

  6. kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

    Science.gov (United States)

    Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

    2017-09-01

    Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

  7. Geant4-DNA simulation of electron slowing-down spectra in liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Incerti, S., E-mail: sebastien.incerti@tdt.edu.vn [Division of Nuclear Physics, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Univ. Bordeaux, CENBG, UMR 5797, F-33170, Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Kyriakou, I. [Medical Physics Laboratory, University of Ioannina Medical School, 45110 Ioannina (Greece); Tran, H.N. [Division of Nuclear Physics, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam)

    2017-04-15

    This work presents the simulation of monoenergetic electron slowing-down spectra in liquid water by the Geant4-DNA extension of the Geant4 Monte Carlo toolkit (release 10.2p01). These spectra are simulated for several incident energies using the most recent Geant4-DNA physics models, and they are compared to literature data. The influence of Auger electron production is discussed. For the first time, a dedicated Geant4-DNA example allowing such simulations is described and is provided to Geant4 users, allowing further verification of Geant4-DNA track structure simulation capabilities.

  8. The role of DNA polymerase {iota} in UV mutational spectra

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jun-Hyuk [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Besaratinia, Ahmad [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Lee, Dong-Hyun [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Lee, Chong-Soon [Department of Biochemistry, College of Natural Sciences, Yeungnam University, Gyongsan 712-749 (Korea, Republic of); Pfeifer, Gerd P. [Division of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States)]. E-mail: gpfeifer@coh.org

    2006-07-25

    UVB (280-320 nm) and UVC (200-280 nm) irradiation generate predominantly cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts in DNA. CPDs are thought to be responsible for most of the UV-induced mutations. Thymine-thymine CPDs, and probably also CPDs containing cytosine, are replicated in vivo in a largely accurate manner by a DNA polymerase {eta} (Pol {eta}) dependent process. Pol {eta} is a DNA damage-tolerant and error-prone DNA polymerase encoded by the POLH (XPV) gene in humans. Another member of the Y family of error-prone DNA polymerases is POLI encoding DNA polymerase iota (Pol {iota}). In order to clarify the specific role of Pol {iota} in UV mutagenesis, we have used an siRNA knockdown approach in combination with a supF shuttle vector which replicates in mammalian cells, similar as we have previously done for Pol {eta}. Synthetic RNA duplexes were used to efficiently inhibit Pol {iota} expression in 293T cells. The supF shuttle vector was irradiated with 254 nm UVC and replicated in 293T cells in presence of anti-Pol {iota} siRNA. Surprisingly, there was a consistent reduction of recovered plasmid from cells with Pol {iota} knockdown and this was independent of UV irradiation of the plasmid. The supF mutant frequency was unchanged in the siRNA knockdown cells relative to control cells confirming that Pol {iota} does not play an important role in UV mutagenesis. UV-induced supF mutants were sequenced from siRNA-treated cells and controls. Neither the type of mutations nor their distribution along the supF gene were significantly different between controls and siRNA knockdown cells and were predominantly C to T and CC to TT transitions at dipyrimidine sites. These results show that Pol {iota} has no significant role in UV lesion bypass and mutagenesis in vivo and provides some initial data suggesting that this polymerase may be involved in replication of extrachromosomal DNA.

  9. Somatic mtDNA mutation spectra in the aging human putamen.

    Directory of Open Access Journals (Sweden)

    Siôn L Williams

    Full Text Available The accumulation of heteroplasmic mitochondrial DNA (mtDNA deletions and single nucleotide variants (SNVs is a well-accepted facet of the biology of aging, yet comprehensive mutation spectra have not been described. To address this, we have used next generation sequencing of mtDNA-enriched libraries (Mito-Seq to investigate mtDNA mutation spectra of putamen from young and aged donors. Frequencies of the "common" deletion and other "major arc" deletions were significantly increased in the aged cohort with the fold increase in the frequency of the common deletion exceeding that of major arc deletions. SNVs also increased with age with the highest rate of accumulation in the non-coding control region which contains elements necessary for translation and replication. Examination of predicted amino acid changes revealed a skew towards pathogenic SNVs in the coding region driven by mutation bias. Levels of the pathogenic m.3243A>G tRNA mutation were also found to increase with age. Novel multimeric tandem duplications that resemble murine control region multimers and yeast ρ(- mtDNAs, were identified in both young and aged specimens. Clonal ∼50 bp deletions in the control region were found at high frequencies in aged specimens. Our results reveal the complex manner in which the mitochondrial genome alters with age and provides a foundation for studies of other tissues and disease states.

  10. Action spectra and chromophores for lethal photosensitization of Candida albicans by DNA monoadducts formed by 8-methoxypsoralen and monofunctional furocoumarins

    International Nuclear Information System (INIS)

    Baydoun, S.; Gibbs, N.K.; Young, A.R.

    1992-01-01

    The red-shift furocoumarin action spectra, compared with their absorption spectra, has been investigated. An action spectrum for 8-methoxypsoralen (8-Mop) monoadduct formation in the yeast Candida albicans has been determined. The yeast cells were initially exposed to sublethal doses of monochromatic UV A at different wavelengths. Monoadduct formation was monitored by growth inhibition induced, after washing out any unbound 8-Mop, by re-irradiation with a constant second (non-lethal) dose of 330 nm radiation. A comparison between this action spectrum and the absorption spectrum of the dark complex of 8-Mop and DNA was made. In addition, the action spectra of monoadduct formation of five monofunctional compounds including a coumarin derivative have been determined. These action spectra were compared with their respective DNA dark complex absorption spectra. In general, the peaks of the furocoumarin DNA dark complexes show a red-shift when compared with the free furocoumarin molecule and the action spectra show peaks which correspond with the peaks of the dark complexes. Such data indicate that the DNA dark complex is the chromophore for growth inhibition in yeast rather than the free furocoumarin. The similarity of the 8-Mop monoadduct formation spectrum and 8-Mop action spectra suggests that spectral dependence for the photobiological effects (including the red-shift) is dependent on monoadduct formation rather than, as previously suggested by several authors, crosslink formation. The action spectrum for the coumarin derivative 4-methyl N-ethylpyrrolo (3,2-g) coumarin (PCNEt) correlated well with the free molecule absorption spectrum rather than DNA dark complex indicating that the free molecule is the chromophore. This was supported by studies which showed that PCNEt photosensitization is oxygen dependent. (author). 38 refs., 3 tabs., 7 figs

  11. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

    Directory of Open Access Journals (Sweden)

    James B Pettengill

    Full Text Available The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis. In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples and computational (petabytes of sequence data issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST scheme. When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates there are features (e.g., genomic, assembly, and contamination that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

  12. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

    Science.gov (United States)

    Pettengill, James B; Pightling, Arthur W; Baugher, Joseph D; Rand, Hugh; Strain, Errol

    2016-01-01

    The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

  13. Analysis of UV-induced mutation spectra in Escherichia coli by DNA polymerase {eta} from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Santiago, Maria Jesus [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain); Alejandre-Duran, Encarna [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain); Ruiz-Rubio, Manuel [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain)]. E-mail: ge1rurum@uco.es

    2006-10-10

    DNA polymerase {eta} belongs to the Y-family of DNA polymerases, enzymes that are able to synthesize past template lesions that block replication fork progression. This polymerase accurately bypasses UV-associated cis-syn cyclobutane thymine dimers in vitro and therefore may contributes to resistance against sunlight in vivo, both ameliorating survival and decreasing the level of mutagenesis. We cloned and sequenced a cDNA from Arabidopsis thaliana which encodes a protein containing several sequence motifs characteristics of Pol{eta} homologues, including a highly conserved sequence reported to be present in the active site of the Y-family DNA polymerases. The gene, named AtPOLH, contains 14 exons and 13 introns and is expressed in different plant tissues. A strain from Saccharomyces cerevisiae, deficient in Pol{eta} activity, was transformed with a yeast expression plasmid containing the AtPOLH cDNA. The rate of survival to UV irradiation in the transformed mutant increased to similar values of the wild type yeast strain, showing that AtPOLH encodes a functional protein. In addition, when AtPOLH is expressed in Escherichia coli, a change in the mutational spectra is detected when bacteria are irradiated with UV light. This observation might indicate that AtPOLH could compete with DNA polymerase V and then bypass cyclobutane pyrimidine dimers incorporating two adenylates.

  14. DNA oligonucleotide-cis-platin Binding: Ab initio interpretation of the vibrational spectra

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Wieser, H.; Bouř, Petr

    2007-01-01

    Roč. 111, č. 39 (2007), s. 9714-9723 ISSN 1089-5639 R&D Projects: GA AV ČR IAA400550702; GA ČR GA202/07/0732 Institutional research plan: CEZ:AV0Z40550506 Keywords : cis - platin * DNA * vibrational spektra * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.918, year: 2007

  15. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  16. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  17. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  18. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from total DNA Sequences.

    NARCIS (Netherlands)

    Izan, Shairul; Esselink, G.; Visser, R.G.F.; Smulders, M.J.M.; Borm, T.J.A.

    2017-01-01

    Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This

  19. Association between mutation spectra and stable and unstable DNA adduct profiles in Salmonella for benzo[a]pyrene and dibenzo[a,l]pyrene

    Energy Technology Data Exchange (ETDEWEB)

    DeMarini, David M., E-mail: demarini.david@epa.gov [Integrated Systems Toxicology Division, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711 (United States); Hanley, Nancy M.; Warren, Sarah H.; Adams, Linda D.; King, Leon C. [Integrated Systems Toxicology Division, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711 (United States)

    2011-09-01

    Highlights: {yields} Benzo[a]pyrene (BP) induces stable DNA adducts and mutations primarily at guanine. {yields} Dibenzo[a,l]pyrene (DBP) induces them primarily at adenine. {yields} BP induces abasic sites, but DBP does not in the Salmonella mutagenicity assay. {yields} Stable DNA adducts alone appear to account for the mutation spectrum of DBP. {yields} Stable DNA adducts and possibly abasic sites account for the mutation spectrum of BP. - Abstract: Benzo[a]pyrene (BP) and dibenzo[a,l]pyrene (DBP) are two polycyclic aromatic hydrocarbons (PAHs) that exhibit distinctly different mutagenicity and carcinogenicity profiles. Although some studies show that these PAHs produce unstable DNA adducts, conflicting data and arguments have been presented regarding the relative roles of these unstable adducts versus stable adducts, as well as oxidative damage, in the mutagenesis and tumor-mutation spectra of these PAHs. However, no study has determined the mutation spectra along with the stable and unstable DNA adducts in the same system with both PAHs. Thus, we determined the mutagenic potencies and mutation spectra of BP and DBP in strains TA98, TA100 and TA104 of Salmonella, and we also measured the levels of abasic sites (aldehydic-site assay) and characterized the stable DNA adducts ({sup 32}P-postlabeling/HPLC) induced by these PAHs in TA104. Our results for the mutation spectra and site specificity of stable adducts were consistent with those from other systems, showing that DBP was more mutagenic than BP in TA98 and TA100. The mutation spectra of DBP and BP were significantly different in TA98 and TA104, with 24% of the mutations induced by BP in TA98 being complex frameshifts, whereas DBP produced hardly any of these mutations. In TA104, BP produced primarily GC to TA transversions, whereas DBP produced primarily AT to TA transversions. The majority (96%) of stable adducts induced by BP were at guanine, whereas the majority (80%) induced by DBP were at adenine

  20. Effects of glycerol upon the biological actions of near-ultraviolet light: spectra and concentration dependence for transforming DNA and for Escherichia coli B/r

    International Nuclear Information System (INIS)

    Peak, J.G.; Peak, M.J.; Foote, C.S.

    1982-01-01

    The concentration dependence for the protection of isolated transforming DNA and Escherichia coli by glycerol against 365-nm monochromatic near-ultraviolet light (UV) was measured. Glycerol protection saturates at a concentration of about 0.1 M for DNA and 1.0 M for E. coli. Action spectra for glycerol protection of transforming DNA (tryptophan and histidine markers) are similar to those obtained previously for diazobicyclo[2.2.2.]octane (DABCO) protection, with protection reaching a maximum near 350-nm UV and decreasing rapidly at wavelengths above and below 350 nm. However, glycerol protects against near-UV about twice as efficiently as DABCO. The action spectrum for protection of E. coli by glycerol against the lethal effects of near-UV was not the same as the spectrum for DNA since glycerol sensitized the cells, but not the DNA, at wavelengths longer than about 380 nm. A possible role of hydroxyl or other radicals was supported by the observation that benzoate also protected DNA against inactivation by 334-nm UV. (author)

  1. High-Throughput Block Optical DNA Sequence Identification.

    Science.gov (United States)

    Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

    2018-01-01

    Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. DNA adducts, mutant frequencies and mutation spectra in λlacZ transgenic mice treated with N-nitrosodimethylamine

    NARCIS (Netherlands)

    Souliotis, V.L.; Delft, J.H.M. van; Steenwinkel, M.-J.S.T.; Baan, R.A.; Kyrtopoulos, S.A.

    1998-01-01

    Groups of λlacZ transgenic mice were treated i.p. with N-nitrosodimethylamine (NDMA) as single doses of 5 mg/kg or 10 mg/kg or as 10 daily doses of 1 mg/kg and changes in DNA N7- or O6-methylguanine or the repair enzyme O6-alkylguanine-DNA alkyltransferase (AGT) were followed for up to 14 days in

  3. Evaluation of the metabolic fate of munitions material (TNT & RDX) in plant systems. Initial assessment of plant DNA mutation spectra as a biomarker

    Energy Technology Data Exchange (ETDEWEB)

    Leung, F.; Cataldo, D.A.; Fellows, R.J.; Jarrell, A.E.; Harvey, S.D.

    1995-09-01

    Munitions material can enter the environment as a result of manufacturing activities and field usage. Predictor methodologies, or biomarkers would enhance evaluation of environmental impacts. The goal of this exploratory study deoxyribonucleic acid (DNA) mutation frequency as a biomarker for munitions exposure. The approach e resolution of an effective repetitive sequence probe for the identification of characteristic mutations, and (2) the development of a testing media [a clonal cell line of carrot (Daucus carota) spension cells]. Commercially available probes demonstrated marginal resolution therefore a low-C{sub o}t library was then constructed. Three colonies from the low-C{sub o}t DNA library were screened and the DNA isolates sequenced. A suspension culture of carrot (Daucus carota) was developed. A mutation spectra experiment was initiated at a 10-mg TNT/L exposure concentration with the attempt to clone over 1500 single TNT-exposed cells. Over the following six months greater than 98% of the initially isolated cells were unable to survive and produce micro calluses. The remaining calli were too few to be statistically significant and the experiment was terminated. The biomarker concept itself remains to be disproved, but the need for large numbers of uniform clones to differentiate true mutations suggest that more direct techniques using whole tissues need to be developed.

  4. Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity.

    Science.gov (United States)

    Traverse, Charles C; Ochman, Howard

    2017-08-29

    Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola , which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. IMPORTANCE The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions-errors that potentially have more dire effects on protein function-is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions

  5. Correlation of the UV-induced mutational spectra and the DNA damage distribution of the human HPRT gene: Automating the analysis

    International Nuclear Information System (INIS)

    Kotturi, G.; Erfle, H.; Koop, B.F.; Boer, J.G. de; Glickman, B.W.

    1994-01-01

    Automated DNA sequencers can be readily adapted for various types of sequence-based nucleic acid analysis: more recently it was determined the distribution of UV photoproducts in the E. coli laci gene using techniques developed for automated fluorescence-based analysis. We have been working to improve the automated approach of damage distribution. Our current method is more rigorous. We have new software that integrates the area under the individual peaks, rather than measuring the height of the curve. In addition, we now employ an internal standard. The analysis can also be partially automated. Detection limits for both major types of UV-photoproducts (cyclobutane dimers and pyrimidine (6-4) pyrimidone photoproducts) are reported. The UV-induced damage distribution in the hprt gene is compared to the mutational spectra in human and rodents cells

  6. Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.

    Science.gov (United States)

    Al-Nakeeb, Kosai; Petersen, Thomas Nordahl; Sicheritz-Pontén, Thomas

    2017-11-21

    Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal .

  7. DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

    Science.gov (United States)

    Ma, Wenxiu; Yang, Lin; Rohs, Remo; Noble, William Stafford

    2017-10-01

    Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites. We describe a sequence + shape kernel that leverages DNA sequence and shape information to better understand protein-DNA binding preference and affinity. This kernel extends an existing class of k-mer based sequence kernels, based on the recently described di-mismatch kernel. Using three in vitro benchmark datasets, derived from universal protein binding microarrays (uPBMs), genomic context PBMs (gcPBMs) and SELEX-seq data, we demonstrate that incorporating DNA shape information improves our ability to predict protein-DNA binding affinity. In particular, we observe that (i) the k-spectrum + shape model performs better than the classical k-spectrum kernel, particularly for small k values; (ii) the di-mismatch kernel performs better than the k-mer kernel, for larger k; and (iii) the di-mismatch + shape kernel performs better than the di-mismatch kernel for intermediate k values. The software is available at https://bitbucket.org/wenxiu/sequence-shape.git. rohs@usc.edu or william-noble@uw.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  8. MICA: desktop software for comprehensive searching of DNA databases

    Directory of Open Access Journals (Sweden)

    Glick Benjamin S

    2006-10-01

    Full Text Available Abstract Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software.

  9. BETA SPECTRA. I. Negatrons spectra

    International Nuclear Information System (INIS)

    Grau Malonda, A.; Garcia-Torano, E.

    1978-01-01

    Using the Fermi theory of beta decay, the beta spectra for 62 negatrons emitters have been computed introducing a correction factor for unique forbidden transitions. These spectra are plotted vs. energy, once normal i sed, and tabulated with the related Fermi functions. The average and median energies are calculated. (Author)

  10. DNA origami based Au–Ag-core–shell nanoparticle dimers with single-molecule SERS sensitivity† †Electronic supplementary information (ESI) available: Additional information about materials and methods, designs of DNA origami templates, height profiles, additional SERS spectra, assignment of DNA bands, SEM images, additional AFM images, FDTD simulations, additional reference spectra for Cy3 and detailed description of EF estimation, simulated absorption and scattering spectra. See DOI: 10.1039/c5nr08674d Click here for additional data file.

    Science.gov (United States)

    Prinz, J.; Heck, C.; Ellerik, L.; Merk, V.

    2016-01-01

    DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled. PMID:26892770

  11. Protection by DABCO against inactivation of transforming DNA by near-ultraviolet light: action spectra and implications for involvement of singlet oxygen

    International Nuclear Information System (INIS)

    Peak, J.G.; Peak, M.J.; Foote, C.S.

    1981-01-01

    Diazobicyclo (2.2.2) octane (DABCO) protects the genetic activity of purified transforming Bacillus subtilis DNA against inactivation by near-, but not far-, UV light. The maximum dose-modifying factor is 0.4, at 0.1 M DABCO. Maximal protection is at about 350 nm and no protection occurs below 313 nm. The spectrum for protection is similar to that described for 2-aminoethylisothiouronium bromide hydrobromide. The relevance of these observations with regard to the role of singlet oxygen in near-UV effects is discussed. (author)

  12. Beta spectra. II-Positron spectra

    International Nuclear Information System (INIS)

    Grau, A.; Garcia-Torano, E.

    1981-01-01

    Using the Fermi theory of beta decay, the beta spectra for 30 positron emitters have been computed, introducing a correction factor for unique forbidden transitions. The spectra are ploted vs. energy, once normalised, and tabulated with the related Fermi functions. The average and median energies are calculated. (author)

  13. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

    2015-01-01

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  14. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.

    Science.gov (United States)

    Novák, Petr; Ávila Robledillo, Laura; Koblížková, Andrea; Vrbová, Iva; Neumann, Pavel; Macas, Jirí

    2017-07-07

    Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun

    2015-06-11

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  16. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

    Science.gov (United States)

    Ozaki, Haruka; Iwasaki, Wataru

    2016-08-01

    As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Difference Raman spectroscopy of DNA molecules

    International Nuclear Information System (INIS)

    Anokhin, Andrey S; Yuzyuk, Yury I; Gorelik, Vladimir S; Dovbeshko, Galina I; Pyatyshev, Alexander Yu

    2015-01-01

    In this paper the micro-Raman spectra of calf DNA for different points of DNA sample have been recorded. The Raman spectra were made with help of difference Raman spectroscopy technique. Raman spectra were recorded with high spatial resolution from different points of the wet and dry samples in different spectral range (100÷4000cm −1 ) using two lasers: argon (514.5 nm) and helium -neon (632.8 nm). The significant differences in the Raman spectra for dry and wet DNA and for different points of DNA molecules were observed. The obtained data on difference Raman scattering spectra of DNA molecules may be used for identification of DNA types and for analysis of genetic information associated with the molecular structure of this molecule

  18. Spectra of Graphs

    NARCIS (Netherlands)

    Brouwer, A.E.; Haemers, W.H.

    2012-01-01

    This book gives an elementary treatment of the basic material about graph spectra, both for ordinary, and Laplace and Seidel spectra. The text progresses systematically, by covering standard topics before presenting some new material on trees, strongly regular graphs, two-graphs, association

  19. Spectra of alkali atoms

    International Nuclear Information System (INIS)

    Santoso, Budi; Arumbinang, Haryono.

    1981-01-01

    Emission spectra of alkali atoms has been determined by using spectrometer at the ultraviolet to infra red waves range. The spectra emission can be obtained by absorption spectrophotometric analysis. Comparative evaluations between experimental data and data handbook obtained by spark method were also presented. (author tr.)

  20. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  1. Vacuum ultraviolet (VUV) absorption spectra of chromatin and its components

    International Nuclear Information System (INIS)

    Dodonova, N.Y.; Kiseleva, M.N.; Petrov, M.Y.; Tsyganenko, N.M.; Bubyakina, V.V.; Chikhirzhina, G.I.

    1984-01-01

    The electron absorption spectra of thin films of chromatin and chromatin components in the ultraviolet region (140-280 nm) were investigated. The absorption coefficients μ(lambda) of chromatin, nucleosomes with and without histone H1, total histones (TH), and DNA were compared. The spectra of nucleosomes differ from the sum-spectrum of DNA plus TH. The chromatin and nucleosome spectra are not similar in the spectral region of 190-160 nm. The lack of additivity of absorption coefficients at different wavelengths may be explained by different conformational changes of DNA, TH in nucleosomes and chromatin during the process of drying aqueous solutions for the preparation of thin films. The μ(lambda) values are useful for an estimate of the DNA and TH absorption in chromatin and nucleosomes in discussing UV and VUV irradiation damages. (Auth.)

  2. Solar Energetic Particle Spectra

    Science.gov (United States)

    Ryan, J. M.; Boezio, M.; Bravar, U.; Bruno, A.; Christian, E. R.; de Nolfo, G. A.; Martucci, M.; Mergè, M.; Munini, R.; Ricci, M.; Sparvoli, R.; Stochaj, S.

    2017-12-01

    We report updated event-integrated spectra from several SEP events measured with PAMELA. The measurements were made from 2006 to 2014 in the energy range starting at 80 MeV and extending well above the neutron monitor threshold. The PAMELA instrument is in a high inclination, low Earth orbit and has access to SEPs when at high latitudes. Spectra have been assembled from these high-latitude measurements. The field of view of PAMELA is small and during the high-latitude passes it scans a wide range of asymptotic directions as the spacecraft orbits. Correcting for data gaps, solid angle effects and improved background corrections, we have compiled event-integrated intensity spectra for twenty-eight SEP events. Where statistics permit, the spectra exhibit power law shapes in energy with a high-energy exponential roll over. The events analyzed include two genuine ground level enhancements (GLE). In those cases the roll-over energy lies above the neutron monitor threshold ( 1 GV) while the others are lower. We see no qualitative difference between the spectra of GLE vs. non-GLE events, i.e., all roll over in an exponential fashion with rapidly decreasing intensity at high energies.

  3. Parameterization of rotational spectra

    International Nuclear Information System (INIS)

    Zhou Chunmei; Liu Tong

    1992-01-01

    The rotational spectra of the strongly deformed nuclei with low rotational frequencies and weak band mixture are analyzed. The strongly deformed nuclei are commonly encountered in the rare-earth region (e. g., 150 220). A lot of rotational band knowledge are presented

  4. Atomic Spectra Database (ASD)

    Science.gov (United States)

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  5. X-ray absorption spectra and emission spectra of plasmas

    International Nuclear Information System (INIS)

    Peng Yonglun; Yang Li; Wang Minsheng; Li Jiaming

    2002-01-01

    The author reports a theoretical method to calculate the resolved absorption spectra and emission spectra (optically thin) of hot dense plasmas. Due to its fully relativistic treatment incorporated with the quantum defect theory, it calculates the absorption spectra and emission spectra for single element or multi-element plasmas with little computational efforts. The calculated absorption spectra of LTE gold plasmas agree well with the experimental ones. It also calculates the optical thin emission spectra of LTE gold plasmas, which is helpful to diagnose the plasmas of relevant ICF plasmas. It can also provide the relevant parameters such as population density of various ionic stages, precise radiative properties for ICF studies

  6. Lattice vibration spectra. 16

    International Nuclear Information System (INIS)

    Lutz, H.D.; Willich, P.

    1977-01-01

    The FIR absorption spectra of pyrite type compounds RuS 2 , RuSsub(2-x)Sesub(x), RuSe 2 , RuTe 2 , OsS 2 , OsSe 2 , and PtP 2 as well as loellingite type phosphides FeP 2 , RuP 2 , and OsP 2 are reported. For RuS 2 , RuSe 2 , RuTe 2 , OsS 2 , and PtP 2 all of the five infrared allowed modes (k = 0) are observed. As a first result of a numerical normal coordinate treatment vibration forms of pyrite structure are communicated. The spectra show that lattice forces of corresponding sulfides, tellurides, and phosphides are about the same strength, but increase strongly by substitution of iron by ruthenium and especially of ruthenium by osmium. The lattice constants of the RuSsub(2-x)Sesub(x) solid solution obey Vegard's rule. (author)

  7. Deconvoluting double Doppler spectra

    International Nuclear Information System (INIS)

    Ho, K.F.; Beling, C.D.; Fung, S.; Chan, K.L.; Tang, H.W.

    2001-01-01

    The successful deconvolution of data from double Doppler broadening of annihilation radiation (D-DBAR) spectroscopy is a promising area of endeavour aimed at producing momentum distributions of a quality comparable to those of the angular correlation technique. The deconvolution procedure we test in the present study is the constrained generalized least square method. Trials with computer simulated DDBAR spectra are generated and deconvoluted in order to find the best form of regularizer and the regularization parameter. For these trials the Neumann (reflective) boundary condition is used to give a single matrix operation in Fourier space. Experimental D-DBAR spectra are also subject to the same type of deconvolution after having carried out a background subtraction and using a symmetrize resolution function obtained from an 85 Sr source with wide coincidence windows. (orig.)

  8. Spectra, Winter 2014

    Science.gov (United States)

    2014-01-01

    additional copies or more information, please email spectra@nrl.navy.mil. LEADINGEDGE 1 Contents 30 Navy Launches UAV from Submerged Submarine 31... multitasking have become mainstream concerns. For example, the New York Times in 2005 and Time magazine in 2006 both reported stories about...interruptions and multitasking , and how they affect performance by increasing human er- ror. In 2005, the information technol- ogy research firm Basex

  9. Thermoluminescence spectra of amethyst

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Q. [Suzhou Railway Teachers College (China). Dept. of Physics; Yang, B. [Beijing Normal University (China). Dept. of Physics; Wood, R.A.; White, D.R.R.; Townsend, P.D.; Luff, B.J. [Sussex Univ., Brighton (United Kingdom). School of Mathematical and Physical Sciences

    1994-04-01

    Thermoluminescence and cathodoluminescence data from natural and synthetic amethyst and synthetic quartz samples are compared. The spectra include features from the quartz host lattice and from impurity-generated recombination sites. Emission features exist throughout the wavelength range studied, 250-800 nm. The near infrared emission at 740-750 nm appears to be characteristic of the amethyst and is proposed to be due to Fe ion impurity. (Author).

  10. Auger spectra of alkanes

    International Nuclear Information System (INIS)

    Rye, R.R.; Jennison, D.R.; Houston, J.E.

    1980-01-01

    The gas-phase Auger line shapes of the linear alkanes C 1 through C 6 and of neopentane are presented and analyzed. The general shape of the spectra are characteristic of carbon in a tetrahedral environment with the major feature in all cases occurring at approx.249 eV. The relatively large spectral changes found between methane and ethane results from the direct interaction of the terminal methyl groups in ethane, and the spectra of the higher alkanes are shown to be a composite of contributions from terminal methyl and interior methylene group carbon atoms. Theoretical analysis based on a one-electron approximation is shown to be capable of making a molecular orbital assignment by comparing calculated vertical transitions to features in the Auger spectra of ethane and propane, and, in the case of ethane, of differentiating between the 2 E/sub g/ and 2 A/sub 1g/ assignment of the ground state of (C 2 H 6 ) + . A one-electron based molecular orbital treatment, however, is shown to partially break down in propane and neopentane. Analysis of neopentane and the observed absence of any noticeable major peak energy shift with increasing molecular size (as predicted by the one-electron treatment) suggests that some Auger final states occur in which both valence holes are localized on the same subunit of the molecule

  11. Pattern recognition in spectra

    International Nuclear Information System (INIS)

    Gebran, M; Paletou, F

    2017-01-01

    We present a new automated procedure that simultaneously derives the effective temperature T eff , surface gravity log g , metallicity [ Fe/H ], and equatorial projected rotational velocity v e sin i for stars. The procedure is inspired by the well-known PCA-based inversion of spectropolarimetric full-Stokes solar data, which was used both for Zeeman and Hanle effects. The efficiency and accuracy of this procedure have been proven for FGK, A, and late type dwarf stars of K and M spectral types. Learning databases are generated from the Elodie stellar spectra library using observed spectra for which fundamental parameters were already evaluated or with synthetic data. The synthetic spectra are calculated using ATLAS9 model atmospheres. This technique helped us to detect many peculiar stars such as Am, Ap, HgMn, SiEuCr and binaries. This fast and efficient technique could be used every time a pattern recognition is needed. One important application is the understanding of the physical properties of planetary surfaces by comparing aboard instrument data to synthetic ones. (paper)

  12. Interpreting peptide mass spectra by VEMS

    DEFF Research Database (Denmark)

    Mathiesen, Rune; Lundsgaard, M.; Welinder, Karen G.

    2003-01-01

    the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution......Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis...... of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares...

  13. Deconvolution of Positrons' Lifetime spectra

    International Nuclear Information System (INIS)

    Calderin Hidalgo, L.; Ortega Villafuerte, Y.

    1996-01-01

    In this paper, we explain the iterative method previously develop for the deconvolution of Doppler broadening spectra using the mathematical optimization theory. Also, we start the adaptation and application of this method to the deconvolution of positrons' lifetime annihilation spectra

  14. Vibrational spectra of aminoacetonitrile

    International Nuclear Information System (INIS)

    Bak, B.; Hansen, E.L.; Nicolaisen, F.M.; Nielsen, O.F.

    1975-01-01

    The preparation of pure, stable aminoacetonitrile(1-amino, 1'-cyanomethane)CH 2 NH 2 CN (1) is described. The Raman spectrum, now complete, and a novel infrared spectrum extending over the 50-3600 cm -1 region are reported. A tentative normal vibration analysis is presented and supported by Raman and infrared data from the spectra of CH 2 NHDCN (2) and CH 2 ND 2 CN (3). The predominance of the trans rotamer may be attributed to intramolecular hydrogen bonding but this is too unimportant to influence the vibrational frequencies of gaseous 1, 2, and 3. However, large gas/liquid frequency shifts occur. (author)

  15. Raman spectroscopic study of plasma-treated salmon DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Joon; Kim, Yong Hee; Choi, Eun Ha [Plasma Bioscience Research Center, Kwangwoon University, Seoul 139-701 (Korea, Republic of); Kwon, Young-Wan [Department of Chemistry, Korea University, Seoul 136-701 (Korea, Republic of)

    2013-01-14

    In this research, we studied the effect of plasma treatment on the optical/structural properties of the deoxyribonucleic acid (DNA) extracted from salmon sperm. DNA-cetyltrimethylammonium (CTMA) films were obtained by complexation of DNA with CTMA. Circular dichroism (CD) and Raman spectra indicated that DNA retained its double helical structure in the solid film. The Raman spectra exhibited several vibration modes corresponding to the nuclear bases and the deoxyribose-phosphate backbones of the DNA, as well as the alkylchains of CTMA. Dielectric-barrier-discharge (DBD) plasma treatment induced structural modification and damage to the DNA, as observed by changes in the ultraviolet-visible absorption, CD, and Raman spectra. The optical emission spectra of the DBD plasma confirmed that DNA modification was induced by plasma ions such as reactive oxygen species and reactive nitrogen species.

  16. Action spectra in mammalian cells exposed to ultraviolet radiation

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    A review is given of the literature published since 1977 on action spectra in mammalian cells exposed to ultraviolet radiation in the wavelength region above 220 nm. Action spectra for lethal events are discussed for cell inactivation in normal cells, growth arrested cells and photosensitive cells. Action spectra for non-lethal events are also discussed in relation to pyrimidine dimer formation, photoreactivation and the use of photosensitisers. It was concluded from these studies that damage to the DNA, and the extent of the repair of this damage, seems to determine a cell's response to such parameters as inactivation, mutation, transformation, latent viral activation, cellular viral capacity and ultraviolet enhanced viral reactivation. In addition to the direct effects of UV on DNA, photosensitization of cellular responses with chemicals such as 8-MOP extend the wavelength range at which damage can be demonstrated. (U.K.)

  17. Catalogue of neutron spectra

    International Nuclear Information System (INIS)

    Buxerolle, M.; Massoutie, M.; Kurdjian, J.

    1987-09-01

    Neutron dosimetry problems have arisen as a result of developments in the applications of nuclear energy. The largest number of possible irradiation situations has been collected: they are presented in the form of a compilation of 44 neutron spectra. Diagrams show the variations of energy fluence and energy fluence weighted by the dose equivalent/fluence conversion factor, with the logarithm of the corresponding energy. The equivalent dose distributions are presented as percentages for the following energy bins: 0.01 eV/0.5 eV/50 keV/1 MeV/5 MeV/15 MeV. The dose equivalent, the mean energy and the effective energy for the dose equivalent for 1 neutron cm -2 are also given [fr

  18. Design energy spectra for Turkey

    OpenAIRE

    López Almansa, Francisco; Yazgan, Ahmet Utku; Benavent Climent, Amadeo

    2012-01-01

    This work proposes design energy spectra in terms of velocity, derived through linear dynamic analyses on Turkish registers and intended for regions with design peak acceleration 0.3 g or higher. In the long and mid period ranges the analyses are linear, taking profit of the rather insensitivity of the spectra to the structural parameters other than the fundamental period; in the short period range, the spectra are more sensitive to the structural parameters and nonlinear analyses would be re...

  19. Spectra of chemical trees

    International Nuclear Information System (INIS)

    Balasubramanian, K.

    1982-01-01

    A method is developed for obtaining the spectra of trees of NMR and chemical interests. The characteristic polynomials of branched trees can be obtained in terms of the characteristic polynomials of unbranched trees and branches by pruning the tree at the joints. The unbranched trees can also be broken down further until a tree containing just two vertices is obtained. The effectively reduces the order of the secular determinant of the tree used at the beginning to determinants of orders atmost equal to the number of vertices in the branch containing the largest number of vertices. An illustrative example of a NMR graph is given for which the 22 x 22 secular determinant is reduced to determinants of orders atmost 4 x 4 in just the second step of the algorithm. The tree pruning algorithm can be applied even to trees with no symmetry elements and such a factoring can be achieved. Methods developed here can be elegantly used to find if two trees are cospectral and to construct cospectral trees

  20. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  1. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  2. Raman spectra of lithium compounds

    Science.gov (United States)

    Gorelik, V. S.; Bi, Dongxue; Voinov, Y. P.; Vodchits, A. I.; Gorshunov, B. P.; Yurasov, N. I.; Yurasova, I. I.

    2017-11-01

    The paper is devoted to the results of investigating the spontaneous Raman scattering spectra in the lithium compounds crystals in a wide spectral range by the fibre-optic spectroscopy method. We also present the stimulated Raman scattering spectra in the lithium hydroxide and lithium deuteride crystals obtained with the use of powerful laser source. The symmetry properties of the lithium hydroxide, lithium hydroxide monohydrate and lithium deuteride crystals optical modes were analyzed by means of the irreducible representations of the point symmetry groups. We have established the selection rules in the Raman and infrared absorption spectra of LiOH, LiOH·H2O and LiD crystals.

  3. FSFE: Fake Spectra Flux Extractor

    Science.gov (United States)

    Bird, Simeon

    2017-10-01

    The fake spectra flux extractor generates simulated quasar absorption spectra from a particle or adaptive mesh-based hydrodynamic simulation. It is implemented as a python module. It can produce both hydrogen and metal line spectra, if the simulation includes metals. The cloudy table for metal ionization fractions is included. Unlike earlier spectral generation codes, it produces absorption from each particle close to the sight-line individually, rather than first producing an average density in each spectral pixel, thus substantially preserving more of the small-scale velocity structure of the gas. The code supports both Gadget (ascl:0003.001) and AREPO.

  4. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  5. Infrared spectra of mineral species

    CERN Document Server

    Chukanov, Nikita V

    2014-01-01

    This book details more than 3,000 IR spectra of more than 2,000 mineral species collected during last 30 years. It features full descriptions and analytical data of each sample for which IR spectrum was obtained.

  6. Correlation Functions and Power Spectra

    DEFF Research Database (Denmark)

    Larsen, Jan

    2006-01-01

    The present lecture note is a supplement to the textbook Digital Signal Processing by J. Proakis and D.G. Manolakis used in the IMM/DTU course 02451 Digital Signal Processing and provides an extended discussion of correlation functions and power spectra. The definitions of correlation functions...... and spectra for discrete-time and continuous-time (analog) signals are pretty similar. Consequently, we confine the discussion mainly to real discrete-time signals. The Appendix contains detailed definitions and properties of correlation functions and spectra for analog as well as discrete-time signals....... It is possible to define correlation functions and associated spectra for aperiodic, periodic and random signals although the interpretation is different. Moreover, we will discuss correlation functions when mixing these basic signal types. In addition, the note include several examples for the purpose...

  7. Multifractal spectra in shear flows

    Science.gov (United States)

    Keefe, L. R.; Deane, Anil E.

    1989-01-01

    Numerical simulations of three-dimensional homogeneous shear flow and fully developed channel flow, are used to calculate the associated multifractal spectra of the energy dissipation field. Only weak parameterization of the results with the nondimensional shear is found, and this only if the flow has reached its asymptotic development state. Multifractal spectra of these flows coincide with those from experiments only at the range alpha less than 1.

  8. Sequential Analysis of Gamma Spectra

    International Nuclear Information System (INIS)

    Fayez-Hassan, M.; Hella, Kh.M.

    2009-01-01

    This work shows how easy one can deal with a huge number of gamma spectra. The method can be used for radiation monitoring. It is based on the macro feature of the windows XP connected to QBASIC software. The routine was used usefully in generating accurate results free from human errors. One hundred measured gamma spectra were fully analyzed in 10 minutes using our fast and automated method controlling the Genie 2000 gamma acquisition analysis software.

  9. Response spectra in alluvial soils

    International Nuclear Information System (INIS)

    Chandrasekharan, A.R.; Paul, D.K.

    1975-01-01

    For aseismic design of structures, the ground motion data is assumed either in the form of ground acceleration as a function of time or indirectly in the form of response spectra. Though the response spectra approach has limitations like not being applicable for nonlinear problems, it is usually used for structures like nuclear power plants. Fifty accelerograms recorded at alluvial sites have been processed. Since different empirical formulas relating acceleration with magnitude and distance give a wide scatter of values, peak ground acceleration alone cannot be the parameter as is assumed by a number of authors. The spectra corresponding to 5% damping have been normalised with respect to three parameters, namely, peak ground acceleration, peak ground velocity and a nondimensional quantity ad/v 2 . Envelopee of maxima and minima as well as average response spectra has been obtained. A comparison with the USAEC spectra has been made. A relation between ground acceleration, ground velocity and ad/v 2 has been obtained which would nearly give the same magnification of the response. A design response spectra for alluvial soils has been recommended. (author)

  10. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  11. Norgal: Extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

    DEFF Research Database (Denmark)

    Al-Nakeeb, Kosai Ali Ahmed; Petersen, Thomas Nordahl; Sicheritz-Pontén, Thomas

    2017-01-01

    and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences...

  12. Biological Action Spectra (invited paper)

    International Nuclear Information System (INIS)

    Gruijl, F.R. de

    2000-01-01

    Ultraviolet (UV) radiation induces a wide variety of biological responses: ranging in humans from well-known short-term effects like sunburn to long-term effects like skin cancer. The wavelength dependencies ('action spectra') of the responses can differ significantly, depending on the UV-targeted molecules (their absorption spectra), their localisation (transmission to the target depth) and the photochemical reactions involved (e.g. quantum yields, competing reaction). An action spectrum (e.g. of sunburn) is usually determined in a wavelength by wavelength analysis of the response. This is not always possible (e.g. in case of skin cancer), and an action spectrum may then be extracted mathematically from differences in responses to broadband UV sources of various spectral compositions (yielding 'biological spectral weights'). However, relative spectral weights may shift with exposure levels and contributions from different wavelengths may not always add up. Under these circumstances conventional analyses will yield different action spectra for different experimental conditions. (author)

  13. Double photoionisation spectra of molecules

    CERN Document Server

    Eland, John

    2017-01-01

    This book contains spectra of the doubly charged positive ions (dications) of some 75 molecules, including the major constituents of terrestrial and planetary atmospheres and prototypes of major chemical groups. It is intended to be a new resource for research in all areas of molecular spectroscopy involving high energy environments, both terrestrial and extra-terrestrial. All the spectra have been produced by photoionisation using laboratory lamps or synchrotron radiation and have been measured using the magnetic bottle time-of-flight technique by coincidence detection of correlated electron pairs. Full references to published work on the same species are given, though for several molecules these are the first published spectra. Double ionisation energies are listed and discussed in relation to the molecular electronic structure of the molecules. A full introduction to the field of molecular double ionisation is included and the mechanisms by which double photoionisation can occur are examined in detail. A p...

  14. QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez Almeida, J.; Morales-Luis, A. B. [Instituto de Astrofisica de Canarias, E-38205 La Laguna, Tenerife (Spain); Terlevich, R.; Terlevich, E. [Instituto Nacional de Astrofisica, Optica y Electronica, Tonantzintla, Puebla (Mexico); Cid Fernandes, R., E-mail: jos@iac.es, E-mail: abml@iac.es, E-mail: rjt@ast.cam.ac.uk, E-mail: eterlevi@inaoep.mx, E-mail: cid@astro.ufsc.br [Departamento de Fisica-CFM, Universidade Federal de Santa Catarina, P.O. Box 476, 88040-900 Florianopolis, SC (Brazil)

    2012-09-10

    We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.

  15. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  16. The structure of BPS spectra

    Science.gov (United States)

    Longhi, Pietro

    In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for

  17. Automatic identification of mass spectra

    International Nuclear Information System (INIS)

    Drabloes, F.

    1992-01-01

    Several approaches to preprocessing and comparison of low resolution mass spectra have been evaluated by various test methods related to library search. It is shown that there is a clear correlation between the nature of any contamination of a spectrum, the basic principle of the transformation or distance measure, and the performance of the identification system. The identification of functionality from low resolution spectra has also been evaluated using several classification methods. It is shown that there is an upper limit to the success of this approach, but also that this can be improved significantly by using a very limited amount of additional information. 10 refs

  18. Investigation of gamma spectra analysis

    International Nuclear Information System (INIS)

    Wu Huailong; Liu Suping; Hao Fanhua; Gong Jian; Liu Xiaoya

    2006-01-01

    In the investigation of radiation fingerprint comparison, it is found out that some of the popular gamma spectra analysis software have shortcomings, which decrease the radiation fingerprint comparison precision. So a new analysis software is developed for solving the problems. In order to display the advantage of developed program, some typical simulative warhead gamma spectra are analyzed respectively by present software and GAMMAVISION and GENNIE2000. Present software can be applied not only in nuclear warheads deep-cuts verification, but also in any radiation measurement field. (authors)

  19. Ultraviolet spectra of planetary nebulae

    International Nuclear Information System (INIS)

    Adams, S.; Seaton, M.J.

    1982-01-01

    Features observed in infrared spectra suggest that certain very low excitation (VLE) nebulae have low C/O abundance ratios (Cohen and Barlow 1980; Aitken and Roche 1982). Fluxes in the multiplets [O II] lambda 2470 and C II] lambda 2326 have been measured for the VLE nebula He He 2-131 = HD 138403 using IUE high-dispersion spectra. An analysis similar to that of Harrington et al. (1980) for IC 418 gives C/O = 0.3 for He 2-131, compared with C/O = 1.3 for IC 418 and 0.6 for the Sun. (author)

  20. Investigation of gamma spectra analysis

    International Nuclear Information System (INIS)

    Wu Huailong; Liu Suping; Hao Fanhua

    2006-12-01

    During the investigation of radiation fingerprint comparison, it is found out that the popular gamma spectra analysis softwares are faultful, which decrease the precision of radiation fingerprint comparison. So a new analysis software is development for solving the problems. In order to display the advantage of new program, some typical simulative gamma spectra of radiation source are analyzed respectively by our software and GAMMAVISION and GENNIE2000. The software can be applied not only in nuclear warheads deep-cuts verification, but also in any radiation measurement field. (authors)

  1. Raman spectra studies of dipeptides

    International Nuclear Information System (INIS)

    Blanchard, Simone.

    1977-10-01

    This work deals with the homogenous and heterogeneous dipeptides derived from alanine and glycine, in the solid state or in aqueous solutions, in the zwitterions or chlorhydrates form. The Raman spectra comparative study of these various forms of hydrogenated or deuterated compounds allows to specify some of the attributions which are necessary in the conformational study of the like tripeptides. These compounds contain only one peptidic group; therefore there is no possibility of intramolecular hydrogen bond which caracterise vibrations of non bonded peptidic groups and end groups. Infrared spectra of solid dipeptides will be presented and discussed in the near future [fr

  2. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

    KAUST Repository

    Wang, Xiaolei

    2014-12-12

    Background: A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in Saccharomyces cerevisiae using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in S. cerevisiae demonstrated the generality of our method. Conclusion: We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify

  3. Classical Trajectories and Quantum Spectra

    Science.gov (United States)

    Mielnik, Bogdan; Reyes, Marco A.

    1996-01-01

    A classical model of the Schrodinger's wave packet is considered. The problem of finding the energy levels corresponds to a classical manipulation game. It leads to an approximate but non-perturbative method of finding the eigenvalues, exploring the bifurcations of classical trajectories. The role of squeezing turns out decisive in the generation of the discrete spectra.

  4. Vibrational spectra of ordered perovskites

    NARCIS (Netherlands)

    Corsmit, A.F.; Hoefdraad, H.E.; Blasse, G.

    1972-01-01

    The vibrational spectra of the molecular M6+O6 (M = Mo, Te, W) group in ordered perovskites of the type Ba2M2+M6+O6 are reported. These groups have symmetry Oh, whereas their site symmetry is also Oh. An assignment of the internal vibrations is presented.

  5. Raman spectra of graphene ribbons

    International Nuclear Information System (INIS)

    Saito, R; Furukawa, M; Dresselhaus, G; Dresselhaus, M S

    2010-01-01

    Raman spectra of graphene nanoribbons with zigzag and armchair edges are calculated within non-resonant Raman theory. Depending on the edge structure and polarization direction of the incident and scattered photon beam relative to the edge direction, a symmetry selection rule for the phonon type appears. These Raman selection rules will be useful for the identification of the edge structure of graphene nanoribbons.

  6. Explanation of earthquake response spectra

    OpenAIRE

    Douglas, John

    2017-01-01

    This is a set of five slides explaining how earthquake response spectra are derived from strong-motion records and simple models of structures and their purpose within seismic design and assessment. It dates from about 2002 and I have used it in various introductory lectures on engineering seismology.

  7. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  8. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  9. Skyshine spectra of gamma rays

    International Nuclear Information System (INIS)

    Swarup, Janardan

    1980-01-01

    A study of the spectra of gamma photons back-scattered in vertical direction by infinite air above ground (skyshine) is presented. The source for these measurements is a 650 Ci Cobalt-60 point-source and the skyshine spectra are reported for distances from 150 m to 325 m from the source, measured with a 5 cm x 5 cm NaI(Tl) detector collimated with collimators of 12 mm and 20 mm diameter and 5 cm length. These continuous spectra are unfolded with Gold's iterative technique. The photon-spectra so obtained have a distinct line at 72 keV due to multiply-scattered photons. This is an energy where photoelectric and Compton cross-sections for multiply-scattered photons balance each other. The intensity of the line(I) decreases exponentially with distance (d) from the source obeying a relation of the type I = Isub(o)esup(-μd) where μ is called as ''Multiply-Scatter Coefficient'', a constant of the medium which is air in these measurements. This relationship is explained in terms of a halo around the source comprising of multiply-scattered gamma photons, Isub(0) being the intensity of these scattered photons at the location of cobalt-source. A fraction called as ''Back-scattered Fraction'', the ratio of Isub(0) to the number of original photons from the cobalt-source entering the infinite air, is also calculated. It is shown that with a properly calibrated detector system, this fraction can be used to determine the strength of a large gamma source, viz. a nuclear explosion in air, and for mineral prospecting. These conclusions are general and can be applied to any other infinite medium. Some forward-scatter (transmission) spectra of cobalt-60 source through 10 cm of Pb and 2.5 cm of Al are also reported. (auth.)

  10. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  11. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  12. ACCELERATED FITTING OF STELLAR SPECTRA

    Energy Technology Data Exchange (ETDEWEB)

    Ting, Yuan-Sen; Conroy, Charlie [Harvard–Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Rix, Hans-Walter [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany)

    2016-07-20

    Stellar spectra are often modeled and fitted by interpolating within a rectilinear grid of synthetic spectra to derive the stars’ labels: stellar parameters and elemental abundances. However, the number of synthetic spectra needed for a rectilinear grid grows exponentially with the label space dimensions, precluding the simultaneous and self-consistent fitting of more than a few elemental abundances. Shortcuts such as fitting subsets of labels separately can introduce unknown systematics and do not produce correct error covariances in the derived labels. In this paper we present a new approach—Convex Hull Adaptive Tessellation (chat)—which includes several new ideas for inexpensively generating a sufficient stellar synthetic library, using linear algebra and the concept of an adaptive, data-driven grid. A convex hull approximates the region where the data lie in the label space. A variety of tests with mock data sets demonstrate that chat can reduce the number of required synthetic model calculations by three orders of magnitude in an eight-dimensional label space. The reduction will be even larger for higher dimensional label spaces. In chat the computational effort increases only linearly with the number of labels that are fit simultaneously. Around each of these grid points in the label space an approximate synthetic spectrum can be generated through linear expansion using a set of “gradient spectra” that represent flux derivatives at every wavelength point with respect to all labels. These techniques provide new opportunities to fit the full stellar spectra from large surveys with 15–30 labels simultaneously.

  13. Reconstruction of neutron spectra through neural networks

    International Nuclear Information System (INIS)

    Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E.

    2003-01-01

    A neural network has been used to reconstruct the neutron spectra starting from the counting rates of the detectors of the Bonner sphere spectrophotometric system. A group of 56 neutron spectra was selected to calculate the counting rates that would produce in a Bonner sphere system, with these data and the spectra it was trained the neural network. To prove the performance of the net, 12 spectra were used, 6 were taken of the group used for the training, 3 were obtained of mathematical functions and those other 3 correspond to real spectra. When comparing the original spectra of those reconstructed by the net we find that our net has a poor performance when reconstructing monoenergetic spectra, this attributes it to those characteristic of the spectra used for the training of the neural network, however for the other groups of spectra the results of the net are appropriate with the prospective ones. (Author)

  14. Biological Action Spectra (invited paper)

    Energy Technology Data Exchange (ETDEWEB)

    Gruijl, F.R. de

    2000-07-01

    Ultraviolet (UV) radiation induces a wide variety of biological responses: ranging in humans from well-known short-term effects like sunburn to long-term effects like skin cancer. The wavelength dependencies ('action spectra') of the responses can differ significantly, depending on the UV-targeted molecules (their absorption spectra), their localisation (transmission to the target depth) and the photochemical reactions involved (e.g. quantum yields, competing reaction). An action spectrum (e.g. of sunburn) is usually determined in a wavelength by wavelength analysis of the response. This is not always possible (e.g. in case of skin cancer), and an action spectrum may then be extracted mathematically from differences in responses to broadband UV sources of various spectral compositions (yielding 'biological spectral weights'). However, relative spectral weights may shift with exposure levels and contributions from different wavelengths may not always add up. Under these circumstances conventional analyses will yield different action spectra for different experimental conditions. (author)

  15. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  16. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  17. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  18. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  19. Comparative ultraviolet action spectra (254-320 nm) of five wild-type eukaryotic microorganisms and Escherichia coli

    International Nuclear Information System (INIS)

    Calkins, J.; Wheeler, J.S.; Keller, C.I.; Colley, E.; Hazle, J.D.

    1988-01-01

    The action spectra of five eukaryotic organisms and the prokaryote, Escherichia coli, were examined over the wavelength range, 254-320 nm. Both the repair competent and three repair defective strains (E. coli, Caenorhabditis elegans, Saccharomyces) were examined. Tetrahymena pyriformis action spectra were performed with and without the excision repair inhibitor caffeine present. Others have observed that lethality, mutation, and the production of pyrimidine dimers show much the same wavelength dependence as DNA absorption. The results presented here demonstrate several action spectra which deviate from the DNA absorption spectra. Ultraviolet sensitization ratios (repair competent/repair defective) were also examined and were shown to change over the wavelength range. These findings suggest that DNA may not be the only important chromophore leading to cell death in the uv wavelength range studied. Since uv-B is of major importance in solar uv damage, these findings may also yield important implications for solar uv studies

  20. Infrared spectra in monitoring biochemical parameters of human blood

    International Nuclear Information System (INIS)

    Prabhakar, S; Singh, R A; Jain, N

    2012-01-01

    Infrared spectroscopy is gaining recognition as a promising method. The infrared spectra of selected regions (2000-400cm -1 ) of blood tissue samples are reported. Present study related to the role of spectral peak fitting in the study of human blood and quantitative interpretations of infrared spectra based on chemometrics. The spectral variations are interpreted in terms of the biochemical and pathological processes involved. The mean RNA/DNA ratio of fitted intensities and analytical area as calculated from the transmittance peaks at 1121cm -1 /1020cm -1 is found to be 0.911A.U and 2.00A.U. respectively. The ratio of 1659cm -1 /1544cm -1 (amide-I/amide-II) bands is found to shed light on the change in the DNA content. The ratio of amide-I/amide-II is almost unity (≅1.054) for blood spectra. The deviation from unity is an indication of DNA absorption from the RBC cells. The total phosphate content has found to be 25.09A.U. The level for glycogen/phosphate ratio (areas under peaks 1030cm -1 /1082cm -1 ) is found to be 0.286A.U. The ratio of unsaturated and saturated carbonyl compounds (C=O) in blood samples is in form of esters and the analytical areas under the spectral peaks at 1740cm -1 and 1731cm -1 for unsaturated esters and saturated esters respectively found to be 0.618A.U.

  1. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  2. NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers

    International Nuclear Information System (INIS)

    Samuel, Newton T.; Lee, C.-Y.; Gamble, Lara J.; Fischer, Daniel A.; Castner, David G.

    2006-01-01

    Single stranded DNA oligomers (ssDNA) immobilized onto solid surfaces forms the basis for several biotechnological applications such as DNA microarrays, affinity separations, and biosensors. Surface structure of Surface-bound oligomers is expected to significantly influence their biological activity and interactions with the environment. In this study near-edge X-ray absorption fine structure spectroscopy (NEXAFS) is used to characterize the components of DNA (nucleobases, nucleotides and nucleosides) and the orientation information of surface-bound ssDNA. The K-edges of carbon, nitrogen and oxygen have spectra with features that are characteristic of the different chemical species present in the nucleobases of DNA. The effect of addition of the DNA sugar and phosphate components on the NEXAFS K-edge spectra was also investigated. The polarization-dependent nitrogen K-edge NEXAFS data show significant changes for different orientations of surface bound ssDNA. These results establish NEXAFS as a powerful technique for chemical and structural characterization of surface-bound DNA oligomers

  3. Design spectra development considering short time histories

    International Nuclear Information System (INIS)

    Weiner, E.O.

    1983-01-01

    The need for generation of seismic acceleration histories to prescribed response spectra arises several ways in structural dynamics. For example, one way of obtaining floor spectra is to generate a history from a foundation spectra and then solve for the floor motion from which a floor spectrum can be obtained. Two separate programs, MODQKE and MDOF, were written to provide a capability of obtaining equipment spectra from design spectra. MODQKE generates or modifies acceleration histories to conform with design spectra pertaining to, say, a foundation. MDOF is a simple linear modal superposition program that solves for equipment support histories using the design spectra conforming histories as input. Equipment spectra, then, are obtained from the support histories using MODQKE

  4. Gamma-ray burst spectra

    International Nuclear Information System (INIS)

    Teegarden, B.J.

    1982-01-01

    A review of recent results in gamma-ray burst spectroscopy is given. Particular attention is paid to the recent discovery of emission and absorption features in the burst spectra. These lines represent the strongest evidence to date that gamma-ray bursts originate on or near neutron stars. Line parameters give information on the temperature, magnetic field and possibly the gravitational potential of the neutron star. The behavior of the continuum spectrum is also discussed. A remarkably good fit to nearly all bursts is obtained with a thermal-bremsstrahlung-like continuum. Significant evolution is observed of both the continuum and line features within most events

  5. Wavelet spectra of JACEE events

    International Nuclear Information System (INIS)

    Suzuki, Naomichi; Biyajima, Minoru; Ohsawa, Akinori.

    1995-01-01

    Pseudo-rapidity distributions of two high multiplicity events Ca-C and Si-AgBr observed by the JACEE are analyzed by a wavelet transform. Wavelet spectra of those events are calculated and compared with the simulation calculations. The wavelet spectrum of the Ca-C event somewhat resembles that simulated with the uniform random numbers. That of Si-AgBr event, however, is not reproduced by simulation calculations with Poisson random numbers, uniform random numbers, or a p-model. (author)

  6. Uranium spectra in the ICP

    Energy Technology Data Exchange (ETDEWEB)

    Ghazi, A.A.; Qamar, S.; Atta, M.A. (Khan (A.Q.) Research Labs., Rawalpindi (Pakistan))

    1994-05-01

    Uranium spectra have been studied by inductively coupled plasma atomic emission spectroscopy (ICP-AES). In total, 8361 uranium lines were observed in the wavelength range of 235-500 nm. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hard copy text is accompanied by a disk with data files and test files for an IBM-compatible computer. The main article discusses the scientific aspects of the subject and explains the purpose of the data files. (Author).

  7. Identified hadron spectra from PHOBOS

    Science.gov (United States)

    Veres, Gábor I.; the PHOBOS Collaboration; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Becker, B.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Harrington, A. S.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Lee, J. W.; Lin, W. T.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Roland, C.; Roland, G.; Sagerer, J.; Sarin, P.; Sedykh, I.; Skulski, W.; Smith, C. E.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wolfs, F. L. H.; Wosiek, B.; Wozniak, K.; Wysłouch, B.; Zhang, J.

    2004-08-01

    Transverse momentum spectra of pions, kaons and protons, as well as antiparticle to particle ratios near mid-rapidity from d+Au collisions at \\sqrt{sNN} = 200 GeV have been measured by the PHOBOS experiment at RHIC. The transverse momentum range of particle identification was extended to beyond 3 GeV/c using the TOF detector and a new trigger system. The pseudorapidity dependence of the nuclear modification factor for charged hadrons in d+Au collisions is presented.

  8. Uranium spectra in the ICP

    International Nuclear Information System (INIS)

    Ghazi, A.A.; Qamar, S.; Atta, M.A.

    1994-01-01

    Uranium spectra have been studied by inductively coupled plasma atomic emission spectroscopy (ICP-AES). In total, 8361 uranium lines were observed in the wavelength range of 235-500 nm. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hard copy text is accompanied by a disk with data files and test files for an IBM-compatible computer. The main article discusses the scientific aspects of the subject and explains the purpose of the data files. (Author)

  9. Operator functions and localization of spectra

    CERN Document Server

    Gil’, Michael I

    2003-01-01

    "Operator Functions and Localization of Spectra" is the first book that presents a systematic exposition of bounds for the spectra of various linear nonself-adjoint operators in a Hilbert space, having discrete and continuous spectra. In particular bounds for the spectra of integral, differential and integro-differential operators, as well as finite and infinite matrices are established. The volume also presents a systematic exposition of estimates for norms of operator-valued functions and their applications.

  10. Comparison on the interaction of Al3+/nano-Al13 with calf thymus DNA /salmon sperm DNA

    Science.gov (United States)

    Ma, Fei; Ma, Yue; Du, Changwen; Yang, Xiaodi; Shen, Renfang

    2015-11-01

    The conformation change, binding mode and binding site between Al3+/nano-Al13 and calf thymus DNA/salmon sperm DNA were investigated by UV-vis absorption, FTIR spectra, Raman spectroscopy and CD spectra, as well as melting curves measurement. The UV-vis spectra and circular dichroism spectra results suggested that the phosphate group structure was changed when Al3+ interacted with DNA, while the double-helix was distorted when nano-Al13 interacted with DNA. The FTIR and Raman spectroscopy revealed that the binding sites were Al3+ … PO2, Al3+ … N7/guanine PO2 … Al13 … N7-C8/guanine with calf thymus DNA, and Al3+ … N3-O2/cytosine, Al3+ … N7-C8/guanine, PO2 … Al13 … N7-C8/guanine, PO2 … Al13 … N1/adenine with salmon sperm DNA, respectively. The electrostatic binding was existed between Al3+ and DNA, and the electrostatic binding and complexing were found between nano-Al13 and DNA.

  11. Raman spectra of SDW superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Rout, G.C. [Condensed Matter Physics Group, Department of Physics, Government Science College, Chatrapur, Orissa 761 020 (India)]. E-mail: gcr@iopb.res.in; Bishoyi, K.C. [P.G. Department of Physics, F.M. College (Autonomous), Balasore, Orissa 756 001 (India); Behera, S.N. [Institute of Physics, Bhubaneswar 751 005 (India)

    2005-03-15

    We report the calculation of the phonon response of the coexistent spin density wave (SDW) and superconducting (SC) state and predict the observation of SC gap in the Raman spectra of rare-earth nickel borocarbide superconductors. The SDW state normally does not couple to the lattice and hence, the phonons in the system are not expected to be affected by the SDW state. But there is a possibility of observing SC gap mode in the Raman spectra of a SDW superconductor due to the coupling of the SC gap excitation to the Raman active phonons in the system via the electron-phonon (e-p) interaction. A theoretical model is used for the coexistent phase and electron-phonon interaction. Phonon Green's function is calculated by Zubarev's technique and the phonon self-energy due to e-p interaction which is given by electron density response function in the coexistent state corresponding to the SDW wave vector q = Q is evaluated. The results so obtained exhibit agreement with the experimental observations.

  12. Raman spectra of SDW superconductors

    International Nuclear Information System (INIS)

    Rout, G.C.; Bishoyi, K.C.; Behera, S.N.

    2005-01-01

    We report the calculation of the phonon response of the coexistent spin density wave (SDW) and superconducting (SC) state and predict the observation of SC gap in the Raman spectra of rare-earth nickel borocarbide superconductors. The SDW state normally does not couple to the lattice and hence, the phonons in the system are not expected to be affected by the SDW state. But there is a possibility of observing SC gap mode in the Raman spectra of a SDW superconductor due to the coupling of the SC gap excitation to the Raman active phonons in the system via the electron-phonon (e-p) interaction. A theoretical model is used for the coexistent phase and electron-phonon interaction. Phonon Green's function is calculated by Zubarev's technique and the phonon self-energy due to e-p interaction which is given by electron density response function in the coexistent state corresponding to the SDW wave vector q = Q is evaluated. The results so obtained exhibit agreement with the experimental observations

  13. Multiscale climate emulator of multimodal wave spectra: MUSCLE-spectra

    Science.gov (United States)

    Rueda, Ana; Hegermiller, Christie A.; Antolinez, Jose A. A.; Camus, Paula; Vitousek, Sean; Ruggiero, Peter; Barnard, Patrick L.; Erikson, Li H.; Tomás, Antonio; Mendez, Fernando J.

    2017-02-01

    Characterization of multimodal directional wave spectra is important for many offshore and coastal applications, such as marine forecasting, coastal hazard assessment, and design of offshore wave energy farms and coastal structures. However, the multivariate and multiscale nature of wave climate variability makes this complex problem tractable using computationally expensive numerical models. So far, the skill of statistical-downscaling model-based parametric (unimodal) wave conditions is limited in large ocean basins such as the Pacific. The recent availability of long-term directional spectral data from buoys and wave hindcast models allows for development of stochastic models that include multimodal sea-state parameters. This work introduces a statistical downscaling framework based on weather types to predict multimodal wave spectra (e.g., significant wave height, mean wave period, and mean wave direction from different storm systems, including sea and swells) from large-scale atmospheric pressure fields. For each weather type, variables of interest are modeled using the categorical distribution for the sea-state type, the Generalized Extreme Value (GEV) distribution for wave height and wave period, a multivariate Gaussian copula for the interdependence between variables, and a Markov chain model for the chronology of daily weather types. We apply the model to the southern California coast, where local seas and swells from both the Northern and Southern Hemispheres contribute to the multimodal wave spectrum. This work allows attribution of particular extreme multimodal wave events to specific atmospheric conditions, expanding knowledge of time-dependent, climate-driven offshore and coastal sea-state conditions that have a significant influence on local nearshore processes, coastal morphology, and flood hazards.

  14. Scikit-spectra: Explorative Spectroscopy in Python

    Directory of Open Access Journals (Sweden)

    Adam Hughes

    2015-06-01

    Full Text Available Scikit-spectra is an intuitive framework for explorative spectroscopy in Python. Scikit-spectra leverages the Pandas library for powerful data processing to provide datastructures and an API designed for spectroscopy. Utilizing the new IPython Notebook widget system, scikit-spectra is headed towards a GUI when you want it, API when you need it approach to spectral analysis. As an application, analysis is presented of the surface-plasmon resonance shift in a solution of gold nanoparticles induced by proteins binding to the gold’s surface. Please refer to the scikit-spectra website for full documentation and support: http://hugadams.github.io/scikit-spectra/

  15. An RGB approach to extraordinary spectra

    Science.gov (United States)

    Grusche, Sascha; Theilmann, Florian

    2015-09-01

    After Newton had explained a series of ordinary spectra and Goethe had pointed out its complementary counterpart, Nussbaumer discovered a series of extraordinary spectra which are geometrically identical and colourwise analogous to Newton’s and Goethe’s spectra. To understand the geometry and colours of extraordinary spectra, the wavelength composition is explored with filters and spectroscopic setups. Visualized in a dispersion diagram, the wavelength composition is interpreted in terms of additive colour mixing. Finally, all spectra are simulated as the superposition of red, green, and blue images that are shifted apart. This RGB approach makes it easy to understand the complex relationship between wavelengths and colours.

  16. Different spectra with the same neutron source

    International Nuclear Information System (INIS)

    Vega C, H. R.; Ortiz R, J. M.; Hernandez D, V. M.; Martinez B, M. R.; Hernandez A, B.; Ortiz H, A. A.; Mercado, G. A.

    2010-01-01

    Using as source term the spectrum of a 239 Pu-Be source several neutron spectra have been calculated using Monte Carlo methods. The source term was located in the centre of spherical moderators made of light water, heavy water and polyethylene of different diameters. Also a 239 Pu-Be source was used to measure its neutron spectrum, bare and moderated by water. The neutron spectra were measured at 100 cm with a Bonner spheres spectrometer. Monte Carlo calculations were used to calculate the neutron spectra of bare and water-moderated spectra that were compared with those measured with the spectrometer. Resulting spectra are similar to those found in power plants with PWR, BWR and Candu nuclear reactors. Beside the spectra the dosimetric features were determined. Using moderators and a single neutron source can be produced neutron spectra alike those found in workplaces, this neutron fields can be utilized to calibrate neutron dosimeters and area monitors. (Author)

  17. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  18. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  19. Schottky spectra and crystalline beams

    International Nuclear Information System (INIS)

    Pestrikov, D.V.

    1996-01-01

    In this paper we revise the current dependence of the Schottky noise power of a cooled proton beam previously measured at NAP-M. More careful study of experimental data indicates a linear decrease in the inverse Schottky noise power with an increase in the beam intensity (N). The root of this function determines a threshold current which occurs at N = N th ≅1.2 x 10 8 particles. The inspection of measured Schottky spectra shows that this threshold does not correspond to some collective instability of the measured harmonic of the linear beam density. The found value of N th does not depend on the longitudinal beam temperature. For the case of NAP-M lattice, the study of the spectral properties of the Schottky noise in the crystalline string predicts the current dependence of the equilibrium momentum spread of the beam, which qualitatively agrees with that, recalculated from the NAP-M data. (orig.)

  20. Fractal analysis of power spectra

    International Nuclear Information System (INIS)

    Johnston, S.

    1982-01-01

    A general argument is presented concerning the Hausdorff dimension D of the power spectrum curve for a system of N weakly-coupled oscillators. Explicit upper and lower bounds for D are derived in terms of the number N of interacting modes. The mathematical reasoning relies upon the celebrated KAM theorem concerning the perturbation of Hamiltonian systems and the finite measure of the set of destroyed tori in phase space; this set can be related to Hausdorff dimension by certain mathematical theorems. An important consequence of these results is a simple empirical test for the applicability of Hamiltonian perturbation theory in the analysis of an experimentally observed spectrum. As an illustration, the theory is applied to the interpretation of a recent numerical analysis of both the power spectrum of the Sun and certain laboratory spectra of hydrodynamic turbulence. (Auth.)

  1. Spectra processing with computer graphics

    International Nuclear Information System (INIS)

    Kruse, H.

    1979-01-01

    A program of processng gamma-ray spectra in rock analysis is described. The peak search was performed by applying a cross-correlation function. The experimental data were approximated by an analytical function represented by the sum of a polynomial and a multiple peak function. The latter is Gaussian, joined with the low-energy side by an exponential. A modified Gauss-Newton algorithm is applied for the purpose of fitting the data to the function. The processing of the values derived from a lunar sample demonstrates the effect of different choices of polynomial orders for approximating the background for various fitting intervals. Observations on applications of interactive graphics are presented. 3 figures, 1 table

  2. Preliminary observations on differences in the Raman spectra of cancerous and noncancerous cells and connective tissue of human skin

    Science.gov (United States)

    Short, Michael A.; Lui, Harvey; McLean, David I.; Zeng, Haishan; Alajlan, Abdulmajeed; Chen, Michael X.

    2005-04-01

    A less invasive method of reliably detecting skin cancers is required. Raman spectroscopy is just one of several spectroscopic methods that look promising, but are not yet sufficiently reliable. More information is needed on how and why the Raman spectra of cancerous skin tissue is different from its normal counterpart. We have used confocal micro-Raman spectroscopy with a spatial resolution of about a micron to obtain spectra of unstained thin sections of human skin. We found that there were clear differences in the Raman spectra between cancerous and non-cancerous tissue both in cells and in the connective tissue. The DNA contribution to the spectra was generally stronger in malignant cells than normal ones. In regions of the dermis far away from the tumor one obtains the usual collagen spectra of normal skin, but adjacent to the tumor the spectra no longer appeared to be those of native collagen.

  3. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  4. Determination of the optical absorption spectra of thin layers from their photoacoustic spectra

    Science.gov (United States)

    Bychto, Leszek; Maliński, Mirosław; Patryn, Aleksy; Tivanov, Mikhail; Gremenok, Valery

    2018-05-01

    This paper presents a new method for computations of the optical absorption coefficient spectra from the normalized photoacoustic amplitude spectra of thin semiconductor samples deposited on the optically transparent and thermally thick substrates. This method was tested on CuIn(Te0.7Se0.3)2 thin films. From the normalized photoacoustic amplitude spectra, the optical absorption coefficient spectra were computed with the new formula as also with the numerical iterative method. From these spectra, the value of the energy gap of the thin film material and the type of the optical transitions were determined. From the experimental optical transmission spectra, the optical absorption coefficient spectra were computed too, and compared with the optical absorption coefficient spectra obtained from photoacoustic spectra.

  5. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL

    2012-01-01

    Structure of High-Resolution NMR Spectra provides the principles, theories, and mathematical and physical concepts of high-resolution nuclear magnetic resonance spectra.The book presents the elementary theory of magnetic resonance; the quantum mechanical theory of angular momentum; the general theory of steady state spectra; and multiple quantum transitions, double resonance and spin echo experiments.Physicists, chemists, and researchers will find the book a valuable reference text.

  6. Reflectance spectra of subarctic lichens

    International Nuclear Information System (INIS)

    Petzold, D.E.; Goward, S.N.

    1988-01-01

    Lichens constitute a major portion of the ground cover of high latitude environments, but little has been reported concerning their in situ solar spectral reflectance properties. Knowledge of these properties is important for the interpretation of remotely sensed observations from high latitude regions, as well as in studies of high latitude ecology and energy balance climatology. The spectral reflectance of common boreal vascular plants is similar to that of vascular plants of the mid latitudes. The dominant lichens, in contrast, display variable reflectance patterns in visible wavelengths. The relative reflectance peak at 0.55 μm, common to green vegetation, is absent or indistinct in spectra of pervasive boreal forest and tundra lichens, despite the presence of chlorophyll in the inner algal cells. Lichens of the dominant genus, Cladina, display strong absorption of ultraviolet energy and short-wavelength blue light relative to their absorption in other visible wavelengths. Since the Cladinae dominate both the surface vegetation in open woodlands of the boreal forest and the low arctic tundra, their unusual spectral reflectance patterns will enable accurate monitoring of the boreal forest-tundra ecotone and detection of its vigor and movement in the future. (author)

  7. Energy spectra of quantum rings.

    Science.gov (United States)

    Fuhrer, A; Lüscher, S; Ihn, T; Heinzel, T; Ensslin, K; Wegscheider, W; Bichler, M

    2001-10-25

    Quantum mechanical experiments in ring geometries have long fascinated physicists. Open rings connected to leads, for example, allow the observation of the Aharonov-Bohm effect, one of the best examples of quantum mechanical phase coherence. The phase coherence of electrons travelling through a quantum dot embedded in one arm of an open ring has also been demonstrated. The energy spectra of closed rings have only recently been studied by optical spectroscopy. The prediction that they allow persistent current has been explored in various experiments. Here we report magnetotransport experiments on closed rings in the Coulomb blockade regime. Our experiments show that a microscopic understanding of energy levels, so far limited to few-electron quantum dots, can be extended to a many-electron system. A semiclassical interpretation of our results indicates that electron motion in the rings is governed by regular rather than chaotic motion, an unexplored regime in many-electron quantum dots. This opens a way to experiments where even more complex structures can be investigated at a quantum mechanical level.

  8. Reflectance spectra of subarctic lichens

    Science.gov (United States)

    Petzold, Donald E.; Goward, Samuel N.

    1988-01-01

    Lichens constitute a major portion of the ground cover of high latitude environments, but little has been reported concerning their in situ solar spectral reflectance properties. Knowledge of these properties is important for the interpretation of remotely sensed observations from high latitude regions, as well as in studies of high latitude ecology and energy balance climatology. The spectral reflectance of common boreal vascular plants is similar to that of vascular plants of the midlatitudes. The dominant lichens, in contrast, display variable reflectance patterns in visible wavelengths. The relative reflectance peak at 0.55 microns, common to green vegetation, is absent or indistinct in spectra of pervasive boreal forest and tundra lichens, despite the presence of chlorophyll in the inner algal cells. Lichens of the dominant genus, Cladina, display strong absorption of ultraviolet energy and short-wavelength blue light relative to their absorption in other visible wavelengths. Since the Cladinae dominate both the surface vegetation in open woodlands of the boreal forest and the low arctic tundra, their unusual spectral reflectance patterns will enable accurate monitoring of the boreal forest-tundra ecotone and detection of its vigor and movement in the future.

  9. Ultraviolet spectra of planetary nebulae

    International Nuclear Information System (INIS)

    Harrington, J.P.; Seaton, M.J.; Adams, S.; Lutz, J.H.

    1982-01-01

    A detailed study of NGC 7662 is based on UV results obtained from 15 IUE spectra and on observations of other workers at optical, IR and radio wavelengths. Improved techniques are used to extract IUE data for an extended source. Relative fluxes in the different apertures which have been used are obtained using the brightness contours of Coleman, Reay and Worswick. There is close agreement between the reddening deduced from the ratios He II (lambda 1640)/(lambda 4686) and (radio)/(Hβ) and the nebular continuum emission observed with the IUE large slots agrees closely with that predicted using absolute radio and Hβ fluxes. The fluxes in nebular emission lines observed with the small slots are smaller than expected from brightness distributions; it is concluded that, for an extended source, the small slots have aperture transmission factors of 0.85 for SWP and 0.46 for LWR. The central star is fainter than has been previously supposed (by more than two magnitudes). The blackbody He II Zanstra temperature of 113 000 K is consistent with the UV colour temperature. Previous work on colour temperatures of central stars is discussed critically. Two models are discussed. (author)

  10. Methodology for analyzing weak spectra

    International Nuclear Information System (INIS)

    Yankovich, T.L.; Swainson, I.P.

    2000-02-01

    There is considerable interest in quantifying radionuclide transfer between environmental compartments. However, in many cases, it can be a challenge to detect concentrations of gamma-emitting radionuclides due to their low levels in environmental samples. As a result, it is valuable to develop analytical protocols to ensure consistent analysis of the areas under weak peaks. The current study has focused on testing how reproducibly peak areas and baselines can be determined using two analytical approaches. The first approach, which can be carried out using Maestro software, involves extracting net counts under a curve without fitting a functional form to the peak, whereas the second approach, which is used by most other peak fitting programs, determines net counts from spectra by fitting a Gaussian form to the data. It was found that the second approach produces more consistent peak area and baseline measurements, with the ability to de-convolute multiple, overlapping peaks. In addition, programs, such as Peak Fit, which can be used to fit a form to spectral data, often provide goodness of fit analyses, since the Gaussian form can be described using a characteristic equation against which peak data can be tested for their statistical significance. (author)

  11. Neutron and photon spectra in LINACs

    International Nuclear Information System (INIS)

    Vega-Carrillo, H.R.; Martínez-Ovalle, S.A.; Lallena, A.M.; Mercado, G.A.; Benites-Rengifo, J.L.

    2012-01-01

    A Monte Carlo calculation, using the MCNPX code, was carried out in order to estimate the photon and neutron spectra in two locations of two linacs operating at 15 and 18 MV. Detailed models of both linac heads were used in the calculations. Spectra were estimated below the flattening filter and at the isocenter. Neutron spectra show two components due to evaporation and knock-on neutrons. Lethargy spectra under the filter were compared to the spectra calculated from the function quoted by Tosi et al. that describes reasonably well neutron spectra beyond 1 MeV, though tends to underestimate the energy region between 10 –6 and 1 MeV. Neutron and the Bremsstrahlung spectra show the same features regardless of the linac voltage. - Highlights: ► With MCNPX code realistic models of two LINACs were built. ► Photon and neutron spectra below the flattening filter and at the isocenter were calculated. ► Neutron spectrum at the flattening filter was compared against the Tosi et al. source-term model. ► Tosi et al. model underestimates the neutron contribution below 1 MeV. ► Photon spectra look alike to those published in literature.

  12. Optical absorption spectra of Ag-11 isomers

    DEFF Research Database (Denmark)

    Martinez, Jose Ignacio; Fernandez, E. M.

    2009-01-01

    The optical absorption spectra of the three most; stable structural isomers of the Ag-11 cluster were calculated using the time-dependent, density functional theory within the Casida formalism. The slightly different, spectra, of the isomers may permit the identification of the ground-stale confi......The optical absorption spectra of the three most; stable structural isomers of the Ag-11 cluster were calculated using the time-dependent, density functional theory within the Casida formalism. The slightly different, spectra, of the isomers may permit the identification of the ground...

  13. Fluctuation analysis of rotational spectra

    International Nuclear Information System (INIS)

    Doessing, T.; Bracco, A.; Broglia, R.A.; Matsuo, M.

    1996-01-01

    The compound state rotational degree of freedom is ''damped'' in the sense that the electric quadrupole decay of a single quantum state with angular momentum I exhibits a spectrum of final states all having spin I-2. In actual experiments, the cascade of γ-rays associated with each of the members of the ensemble of compound nuclei uses each of the ''discrete'' transitions many more times than the ''continuum'' transitions. Relatively large and small fluctuations in the recorded coincidence spectrum ensue, respectively. The analysis of the fluctuations will be shown to be instrumental to gain insight into the phenomenon of rotational damping. For this purpose, two- and higher-fold coincidence spectra emitted from rotating nuclei are analyzed with respect to the count fluctuations. The coincidences from consecutive γ-rays emitted from discrete rotational bands generate ridges in the E γ1 .E γ2 spectrum, and the fluctuation analysis of the ridges is based upon the ansatz of a random selection of transition energies from band to band. This ansatz is supported by a cranked mean-field calculation for the nucleus 168 Yb, as well as by analyzing resolved bands in 168 Yb and its neighbors. The fluctuation analysis of the central valley (E γ1 =E γ2 ) is based upon the ansatz of fluctuations in the intensity of the transitions of Porter-Thomas type superposed on a smooth spectrum of transition energies. This ansatz is again supported by a mixed-band calculation. The mathematical treatment of count fluctuations is formulated in general (orig.)

  14. DNA repair

    International Nuclear Information System (INIS)

    Van Zeeland, A.A.

    1984-01-01

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  15. Plasmid DNA damage induced by helium atmospheric pressure plasma jet

    Science.gov (United States)

    Han, Xu; Cantrell, William A.; Escobar, Erika E.; Ptasinska, Sylwia

    2014-03-01

    A helium atmospheric pressure plasma jet (APPJ) is applied to induce damage to aqueous plasmid DNA. The resulting fractions of the DNA conformers, which indicate intact molecules or DNA with single- or double-strand breaks, are determined using agarose gel electrophoresis. The DNA strand breaks increase with a decrease in the distance between the APPJ and DNA samples under two working conditions of the plasma source with different parameters of applied electric pulses. The damage level induced in the plasmid DNA is also enhanced with increased plasma irradiation time. The reactive species generated in the APPJ are characterized by optical emission spectra, and their roles in possible DNA damage processes occurring in an aqueous environment are also discussed.

  16. Area spectra of near extremal black holes

    International Nuclear Information System (INIS)

    Chen, Deyou; Yang, Haitang; Zu, Xiaotao

    2010-01-01

    Motivated by Maggiore's new interpretation of quasinormal modes, we investigate area spectra of a near extremal Schwarzschild-de Sitter black hole and a higher-dimensional near extremal Reissner-Nordstrom-de Sitter black hole. The result shows that the area spectra are equally spaced and irrelevant to the parameters of the black holes. (orig.)

  17. Composite Spectra Paper 1: HR 6902

    Indian Academy of Sciences (India)

    tribpo

    spectra; in many cases we have used the maximum width permitted by the optics of ... 10 mЕ, corresponding to 1 µm the plate, are the norm. ..... an inequality ..... on the spectra of HR 6902, we have thought it appropriate to weight the four ...

  18. Thermoluminescence spectra measured with a Michelson interferometer

    International Nuclear Information System (INIS)

    Haschberger, P.

    1991-01-01

    A Michelson interferometer was redesigned to prove its capabilities in the measurement of short-lived, low-intensity thermoluminescence spectra. Interferograms are collected during heating up the thermoluminescent probe in a heater plate. A personal computer controls the data acquisition and processes the Fourier transform. As the results show, even a comparatively simple and limited setup leads to relevant and reproducible spectra. (author)

  19. Near IR spectra of symbiotic stars

    International Nuclear Information System (INIS)

    Andrillat, Y.

    1982-01-01

    The author reports on recent observations from the near IR spectra of symbiotic stars. The helium and oxygen lines useful for the construction of theoretical models are identified. Observations for cool stars and novae (nebular phase) are outlined and the spectra of specific symbiotic stars between lambdalambda 8000-11000 are presented and discussed. (Auth./C.F.)

  20. Aircraft Measurements of Atmospheric Kinetic Energy Spectra

    DEFF Research Database (Denmark)

    Lundtang Petersen, Erik; Lilly, D. K.

    1983-01-01

    Wind velocity data obtained from a jet airliner are used to construct kinetic energy spectra over the range of wavelengths from 2.5 to 2500 km. The spectra exhibit an approximate -5/3 slope for wavelengths of less than about 150 km, steepening to about -2.2 at larger scales. These results support...

  1. PCA: Principal Component Analysis for spectra modeling

    Science.gov (United States)

    Hurley, Peter D.; Oliver, Seb; Farrah, Duncan; Wang, Lingyu; Efstathiou, Andreas

    2012-07-01

    The mid-infrared spectra of ultraluminous infrared galaxies (ULIRGs) contain a variety of spectral features that can be used as diagnostics to characterize the spectra. However, such diagnostics are biased by our prior prejudices on the origin of the features. Moreover, by using only part of the spectrum they do not utilize the full information content of the spectra. Blind statistical techniques such as principal component analysis (PCA) consider the whole spectrum, find correlated features and separate them out into distinct components. This code, written in IDL, classifies principal components of IRS spectra to define a new classification scheme using 5D Gaussian mixtures modelling. The five PCs and average spectra for the four classifications to classify objects are made available with the code.

  2. General Notes on Processes and Their Spectra

    Directory of Open Access Journals (Sweden)

    Gustav Cepciansky

    2012-01-01

    Full Text Available The frequency spectrum performs one of the main characteristics of a process. The aim of the paper is to show the coherence between the process and its own spectrum and how the behaviour and properties of a process itself can be deduced from its spectrum. Processes are categorized and general principles of their spectra calculation and recognition are given. The main stress is put on power spectra of electric and optic signals, as they also perform a kind of processes. These spectra can be directly measured, observed and examined by means of spectral analyzers and they are very important characteristics which can not be omitted at transmission techniques in telecommunication technologies. Further, the paper also deals with non electric processes, mainly with processes and spectra at mass servicing and how these spectra can be utilised in praxis.

  3. Design spectra development considering short time histories

    International Nuclear Information System (INIS)

    Weiner, E.O.

    1983-01-01

    Two separate programs, MODQKE and MDOF, were written to provide a capability of obtaining equipment spectra from design spectra. MODQKE generates or modifies acceleration histories to conform with design spectra pertaining to, say, a foundation. MDOF is a simple linear modal superposition program that solves for equipment support histories using the design spectra conforming histories as input. Equipment spectra, then, are obtained from the support histories using MODQKE. MODQKE was written to modify or provide new histories with special attention paid to short seismic records. A technique from the open literature was borrowed to generate an initial history that approximates a given response spectrum. Further refinement is done with smoothing cycles in which several correction signals are added to the history in a way that produces a least squares fit between actual and prescribed spectra. Provision is made for history shaping, a baseline correction, and final scaling. MODQKE performance has been demonstrated with seven examples having zero to ten percent damping ratios, and 2.5 seconds to 20 seconds durations and a variety of target spectra. The examples show the program is inexpensive to use. MDOF is a simple modal superposition program. It has no eigensolver, and the user supplies mode shapes, frequencies, and participation factors as input. Floor spectra can be generated from design spectra by using a history from MODQKE that conforms to the design spectrum as input to MDOF. Floor motions from MDOF can be fed back to MODQKE without modification to obtain the floor spectra. A simple example is given to show how equipment mass effects can be incorporated into the MDOF solution. Any transient solution capability can be used to replace MDOF. For example, a direct transient approach may be desirable if both the equipment and floor structures are to be included in the model with different damping fractions. (orig./HP)

  4. Studies on the arctiin and its interaction with DNA by spectral methods

    International Nuclear Information System (INIS)

    Sun Yantao; Zhang Hanqi; Bi Shuyun; Zhou Xiaofu; Wang Liang; Yan Yongsheng

    2011-01-01

    The emission spectra of arctiin were determined under various experimental conditions. In addition, a fluorescence method was developed to obtain the binding constants and sites of the interaction between arctiin and DNA. A competitive binding experiment and melting temperature mensuration were carried out to investigate the binding mechanism of arctiin and DNA. The experimental results showed that the interaction between arctiin and DNA belongs to a groove binding mode. - Highlights: → Determined the emission spectra of arctiin by fluorescence spectrometry. → Obtain the binding constants and sites of interaction between arctiin and DNA. → Calculate the binding parameters according an improved calculation method.

  5. Spectra of conformal sigma models

    International Nuclear Information System (INIS)

    Tlapak, Vaclav

    2015-04-01

    In this thesis the spectra of conformal sigma models defined on (generalized) symmetric spaces are analysed. The spaces where sigma models are conformal without the addition of a Wess-Zumino term are supermanifolds, in other words spaces that include fermionic directions. After a brief review of the general construction of vertex operators and the background field expansion, we compute the diagonal terms of the one-loop anomalous dimensions of sigma models on semi-symmetric spaces. We find that the results are formally identical to the symmetric case. However, unlike for sigma models on symmetric spaces, off diagonal terms that lead to operator mixing are also present. These are not computed here. We then present a detailed analysis of the one-loop spectrum of the supersphere S 3 vertical stroke 2 sigma model as one of the simplest examples. The analysis illustrates the power and simplicity of the construction. We use this data to revisit a duality with the OSP(4 vertical stroke 2) Gross-Neveu model that was proposed by Candu and Saleur. With the help of a recent all-loop result for the anomalous dimension of (1)/(2)BPS operators of Gross-Neveu models, we are able to recover the entire zero-mode spectrum of the supersphere model. We also argue that the sigma model constraints and its equations of motion are implemented correctly in the Gross-Neveu model, including the one-loop data. The duality is further supported by a new all-loop result for the anomalous dimension of the ground states of the sigma model. However, higher-gradient operators cannot be completely recovered. It is possible that this discrepancy is related to a known instability of the sigma model. The instability of sigma models is due to symmetry preserving high-gradient operators that become relevant at arbitrarily small values of the coupling. This feature has been observed long ago in one-loop calculations of the O(N)-vector model and soon been realized to be a generic property of sigma models

  6. Statistical properties of Fermi GBM GRBs' spectra

    Science.gov (United States)

    Rácz, István I.; Balázs, Lajos G.; Horvath, Istvan; Tóth, L. Viktor; Bagoly, Zsolt

    2018-03-01

    Statistical studies of gamma-ray burst (GRB) spectra may result in important information on the physics of GRBs. The Fermi GBM catalogue contains GRB parameters (peak energy, spectral indices, and intensity) estimated fitting the gamma-ray spectral energy distribution of the total emission (fluence, flnc), and during the time of the peak flux (pflx). Using contingency tables, we studied the relationship of the models best-fitting pflx and flnc time intervals. Our analysis revealed an ordering of the spectra into a power law - Comptonized - smoothly broken power law - Band series. This result was further supported by a correspondence analysis of the pflx and flnc spectra categorical variables. We performed a linear discriminant analysis (LDA) to find a relationship between categorical (spectral) and model independent physical data. LDA resulted in highly significant physical differences among the spectral types, that is more pronounced in the case of the pflx spectra, than for the flnc spectra. We interpreted this difference as caused by the temporal variation of the spectrum during the outburst. This spectral variability is confirmed by the differences in the low-energy spectral index and peak energy, between the pflx and flnc spectra. We found that the synchrotron radiation is significant in GBM spectra. The mean low-energy spectral index is close to the canonical value of α = -2/3 during the peak flux. However, α is ˜ -0.9 for the spectra of the fluences. We interpret this difference as showing that the effect of cooling is important only for the fluence spectra.

  7. Involvement of specialized DNA polymerases Pol II, Pol IV and DnaE2 in DNA replication in the absence of Pol I in Pseudomonas putida

    International Nuclear Information System (INIS)

    Sidorenko, Julia; Jatsenko, Tatjana; Saumaa, Signe; Teras, Riho; Tark-Dame, Mariliis; Horak, Rita; Kivisaar, Maia

    2011-01-01

    The majority of bacteria possess a different set of specialized DNA polymerases than those identified in the most common model organism Escherichia coli. Here, we have studied the ability of specialized DNA polymerases to substitute Pol I in DNA replication in Pseudomonas putida. Our results revealed that P. putida Pol I-deficient cells have severe growth defects in LB medium, which is accompanied by filamentous cell morphology. However, growth of Pol I-deficient bacteria on solid rich medium can be restored by reduction of reactive oxygen species in cells. Also, mutants with improved growth emerge rapidly. Similarly to the initial Pol I-deficient P. putida, its adapted derivatives express a moderate mutator phenotype, which indicates that DNA replication carried out in the absence of Pol I is erroneous both in the original Pol I-deficient bacteria and the adapted derivatives. Analysis of the spectra of spontaneous Rif r mutations in P. putida strains lacking different DNA polymerases revealed that the presence of specialized DNA polymerases Pol II and Pol IV influences the frequency of certain base substitutions in Pol I-proficient and Pol I-deficient backgrounds in opposite ways. Involvement of another specialized DNA polymerase DnaE2 in DNA replication in Pol I-deficient bacteria is stimulated by UV irradiation of bacteria, implying that DnaE2-provided translesion synthesis partially substitutes the absence of Pol I in cells containing heavily damaged DNA.

  8. Scaling properties of the transverse mass spectra

    International Nuclear Information System (INIS)

    Schaffner-Bielich, J.

    2002-01-01

    Motivated from the formation of an initial state of gluon-saturated matter, we discuss scaling relations for the transverse mass spectra at BNL's relativistic heavy-ion collider (RHIC). We show on linear plots, that the transverse mass spectra for various hadrons can be described by an universal function in m t . The transverse mass spectra for different centralities can be rescaled into each other. Finally, we demonstrate that m t -scaling is also present in proton-antiproton collider data and compare it to m t -scaling at RHIC. (orig.)

  9. IRAS low-resolution spectra of galaxies

    International Nuclear Information System (INIS)

    Cohen, M.; Volk, K.

    1989-01-01

    The spectra of external galaxies are selected and extracted from the IRAS LRS database. Twenty-one objects present viable spectra. One is a peculiar star-forming E-S0 galaxy. The remainder are all starburst or H II region galaxies. Their average spectrum demonstrates the importance of the PAH emission bands in the 8-23-micron region and reinforces the conclusion reached from ground-based spectra, that there is a strong correlation between the PAH bands and the starburst or H II region character of a galaxy. 32 refs

  10. Parametrization relating the fermionic mass spectra

    International Nuclear Information System (INIS)

    Kleppe, A.

    1993-01-01

    When parametrizing the fermionic mass spectra in terms of the unit matrix and a recursive matrix scrR 0 , which corresponds to an underlying scaling pattern in the mass spectra, each fermionic sector is characterized by three parameters: k, α, and R. Using the set of relations displayed by the parameters of the different sectors, it is possible to formulate a ''family Lagrangian'' which for each sector encompasses all the families. Relations between quark masses are furthermore deduced from these ''family Lagrangians.'' Using the relations between the parameters of the different charge sectors, it is also possible to ''derive'' the quark mass spectra from the (charged) leptonic mass spectrum

  11. DNA Repair Systems

    Indian Academy of Sciences (India)

    DNA molecule which makes it ideal for storage and propagation of genetic information. ... of these errors are broadly referred to as DNA repair. DNA can ... changes occur in the human genome per day. ..... nails, frequent physical and mental.

  12. Power spectra of currents off Bombay

    Digital Repository Service at National Institute of Oceanography (India)

    Varkey, M.J.

    Current measurements were carried out using a recording current meter across the continental shelf off Bombay, Maharashtra, India at 4 stations from an anchored ship. Power spectra were computed for selected lengths of records. Spectral energy...

  13. Contribution to the study of turbulence spectra

    Science.gov (United States)

    Dumas, R.

    1979-01-01

    An apparatus suitable for turbulence measurement between ranges of 1 to 5000 cps and from 6 to 16,000 cps was developed and is described. Turbulence spectra downstream of the grills were examined with reference to their general characteristics, their LF qualities, and the effects of periodic turbulence. Medium and HF are discussed. Turbulence spectra in the boundary layers are similarly examined, with reference to their fluctuations at right angles to the wall, and to lateral fluctuations. Turbulence spectra in a boundary layer with suction to the wall is discussed. Induced turbulence, and turbulence spectra at high Reynolds numbers. Calculations are presented relating to the effect of filtering on the value of the correlations in time and space.

  14. Experimental phase diagram for random laser spectra

    International Nuclear Information System (INIS)

    El-Dardiry, Ramy G S; Mooiweer, Ronald; Lagendijk, Ad

    2012-01-01

    We systematically study the presence of narrow spectral features in a wide variety of random laser samples. Less gain or stronger scattering are shown to lead to a crossover from spiky to smooth spectra. A decomposition of random laser spectra into a set of Lorentzians provides unprecedented detail in the analysis of random laser spectra. We suggest an interpretation in terms of mode competition that enables an understanding of the observed experimental trends. In this interpretation, smooth random laser spectra are a consequence of competing modes for which the loss and gain are proportional. Spectral spikes are associated with modes that are uncoupled from the mode competition in the bulk of the sample. (paper)

  15. On two-spectra inverse problems

    OpenAIRE

    Guliyev, Namig J.

    2018-01-01

    We consider a two-spectra inverse problem for the one-dimensional Schr\\"{o}dinger equation with boundary conditions containing rational Herglotz--Nevanlinna functions of the eigenvalue parameter and provide a complete solution of this problem.

  16. Angular Spectra of Polarized Galactic Foregrounds

    OpenAIRE

    Cho, Jung; Lazarian, A.

    2003-01-01

    It is believed that magnetic field lines are twisted and bend by turbulent motions in the Galaxy. Therefore, both Galactic synchrotron emission and thermal emission from dust reflects statistics of Galactic turbulence. Our simple model of Galactic turbulence, motivated by results of our simulations, predicts that Galactic disk and halo exhibit different angular power spectra. We show that observed angular spectra of synchrotron emission are compatible with our model. We also show that our mod...

  17. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  18. Generation of synthetic gamma spectra with MATLAB

    International Nuclear Information System (INIS)

    Palmerio, Julian J.; Coppo, Anibal D.

    2009-01-01

    Objectives: The aim of this work is the simulation of gamma spectra using the MATLAB program to generate the calibration curves in efficiency, which will be used to measure radioactive waste in drums. They are necessary for the proper characterization of these drums. A Monte Carlo simulation was basically developed with the random number generator Mersenne Twister and nuclear data obtained from NIST. This paper shows the results obtained and difficulties encountered until today. The physical correction of the simulated spectra has been the only aspect we have been working, up to this moment. Procedures: A simplified representation of the 'Laboratorio de Verificacion y Control de la Calidad' was chosen. Drums with cemented liquid waste are routinely measured in this laboratory. The commercial program MCNP was also used to get a valid reference in the field of simulation of spectra. We analyzed the spectra obtained by MATLAB in the light of classical literature photon detection and the spectrum obtained by MCNP. Conclusions: Currently the program developed seems adequate to simulate a measurement in the 'Laboratorio de Verificacion y Control de la Calidad'. The spectra obtained by MATLAB seem to physically represent what is observed in real spectra. However, it is a slow program. The current development efforts are directed to improve the speed of simulation. An alternative is to use the CUDA language for NVIDIA video cards to parallelized the simulation. An adequate simulation of the electronic measuring chain is also needed to obtain better representations of the shapes of the peaks. (author)

  19. Identifying Broadband Rotational Spectra with Neural Networks

    Science.gov (United States)

    Zaleski, Daniel P.; Prozument, Kirill

    2017-06-01

    A typical broadband rotational spectrum may contain several thousand observable transitions, spanning many species. Identifying the individual spectra, particularly when the dynamic range reaches 1,000:1 or even 10,000:1, can be challenging. One approach is to apply automated fitting routines. In this approach, combinations of 3 transitions can be created to form a "triple", which allows fitting of the A, B, and C rotational constants in a Watson-type Hamiltonian. On a standard desktop computer, with a target molecule of interest, a typical AUTOFIT routine takes 2-12 hours depending on the spectral density. A new approach is to utilize machine learning to train a computer to recognize the patterns (frequency spacing and relative intensities) inherit in rotational spectra and to identify the individual spectra in a raw broadband rotational spectrum. Here, recurrent neural networks have been trained to identify different types of rotational spectra and classify them accordingly. Furthermore, early results in applying convolutional neural networks for spectral object recognition in broadband rotational spectra appear promising. Perez et al. "Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer." Chem. Phys. Lett., 2013, 571, 1-15. Seifert et al. "AUTOFIT, an Automated Fitting Tool for Broadband Rotational Spectra, and Applications to 1-Hexanal." J. Mol. Spectrosc., 2015, 312, 13-21. Bishop. "Neural networks for pattern recognition." Oxford university press, 1995.

  20. Publicly Released Prompt Radiation Spectra Suitable for Nuclear Detonation Simulations, Revision 1

    Science.gov (United States)

    2017-12-01

    dominates the photon emission. During the Hiroshima and Nagasaki bombings , the prompt radiation contributed from 40% to 70% of the free-in-air dose...spectra for high-, intermediate- and low-yield thermonuclear weapons for initial radiation shielding calculations No Gritzner, et al. 1976 ( EM -1...Glasstone (Fission) Neutron Glasstone & Dolan 1977 7.760 x 1022 Terrell Neutron Glasstone & Dolan 1977 7.760 x 1022 DNA 4267F ( EM -1 Fission

  1. Good abundances from bad spectra - I. Techniques

    Science.gov (United States)

    Jones, J. Bryn; Gilmore, Gerard; Wyse, Rosemary F. G.

    1996-01-01

    Stellar spectra derived from multiple-object fibre-fed spectroscopic radial-velocity surveys, of the type feasible with, among other examples, AUTOFIB, 2dF, HYDRA, NESSIE, and the Sloan survey, differ significantly from those traditionally used for determination of stellar abundances. The spectra tend to be of moderate resolution (around 1A) and signal-to-noise ratio (around 10-20 per resolution element), and cannot usually have reliable continuum shapes determined over wavelength ranges in excess of a few tens of Angstroms. None the less, with care and a calibration of stellar effective temperature from photometry, independent of the spectroscopy, reliable iron abundances can be derived. We have developed techniques to extract true iron abundances and surface gravities from low-signal-to-noise ratio, intermediate-resolution spectra of G-type stars in the 4000-5000A wavelength region. Spectroscopic indices sensitive to iron abundance and gravity are defined from a set of narrow (few-several A wide) wavelength intervals. The indices are calibrated theoretically using synthetic spectra. Given adequate data and a photometrically determined effective temperature, one can derive estimates of the stellar iron abundance and surface gravity. We have also defined a single abundance indicator for the analysis of very low-signal-to-noise ratio spectra; with the further assumption of a value for the stellar surface gravity, this is able to provide useful iron abundance information from spectra having signal-to-noise ratios as low as 10 (1-A elements). The theoretical basis and calibration using synthetic spectra are described in this paper. The empirical calibration of these techniques by application to observational data is described in a separate paper (Jones, Wyse & Gilmore). The technique provides precise iron abundances, with zero-point correct to ~0.1 dex, and is reliable, with typical uncertainties being <~0.2 dex. A derivation of the in situ thick disc metallicity

  2. Differential dpa calculations with SPECTRA-PKA

    Science.gov (United States)

    Gilbert, M. R.; Sublet, J.-Ch.

    2018-06-01

    The processing code SPECTRA-PKA produces energy spectra of primary atomic recoil events (or primary knock-on atoms, PKAs) for any material composition exposed to an irradiation spectrum. Such evaluations are vital inputs for simulations aimed at understanding the evolution of damage in irradiated material, which is generated in cascade displacement events initiated by PKAs. These PKA spectra present the full complexity of the input (to SPECTRA-PKA) nuclear data-library evaluations of recoil events. However, the commonly used displacements per atom (dpa) measure, which is an integral measure over all possible recoil events of the displacement damage dose, is still widely used and has many useful applications - as both a comparative and correlative quantity. This paper describes the methodology employed that allows the SPECTRA-PKA code to evaluate dpa rates using the energy-dependent recoil (PKA) cross section data used for the PKA distributions. This avoids the need for integral displacement kerma cross sections and also provides new insight into the relative importance of different reaction channels (and associated different daughter residual and emitted particles) to the total integrated dpa damage dose. Results are presented for Fe, Ni, W, and SS316. Fusion dpa rates are compared to those in fission, highlighting the increased contribution to damage creation in the former from high-energy threshold reactions.

  3. Climatology of tropospheric vertical velocity spectra

    Science.gov (United States)

    Ecklund, W. L.; Gage, K. S.; Balsley, B. B.; Carter, D. A.

    1986-01-01

    Vertical velocity power spectra obtained from Poker Flat, Alaska; Platteville, Colorado; Rhone Delta, France; and Ponape, East Caroline Islands using 50-MHz clear-air radars with vertical beams are given. The spectra were obtained by analyzing the quietest periods from the one-minute-resolution time series for each site. The lengths of available vertical records ranged from as long as 6 months at Poker Flat to about 1 month at Platteville. The quiet-time vertical velocity spectra are shown. Spectral period ranging from 2 minutes to 4 hours is shown on the abscissa and power spectral density is given on the ordinate. The Brunt-Vaisala (B-V) periods (determined from nearby sounding balloons) are indicated. All spectra (except the one from Platteville) exhibit a peak at periods slightly longer than the B-V period, are flat at longer periods, and fall rapidly at periods less than the B-V period. This behavior is expected for a spectrum of internal waves and is very similar to what is observed in the ocean (Eriksen, 1978). The spectral amplitudes vary by only a factor of 2 or 3 about the mean, and show that under quiet conditions vertical velocity spectra from the troposphere are very similar at widely different locations.

  4. Artificial intelligence analysis of paraspinal power spectra.

    Science.gov (United States)

    Oliver, C W; Atsma, W J

    1996-10-01

    OBJECTIVE: As an aid to discrimination of sufferers with back pain an artificial intelligence neural network was constructed to differentiate paraspinal power spectra. DESIGN: Clinical investigation using surface electromyography. METHOD: The surface electromyogram power spectra from 60 subjects, 33 non-back-pain sufferers and 27 chronic back pain sufferers were used to construct a back propagation neural network that was then tested. Subjects were placed on a test frame in 30 degrees of lumbar forward flexion. An isometric load of two-thirds maximum voluntary contraction was held constant for 30 s whilst surface electromyograms were recorded at the level of the L(4-5). Paraspinal power spectra were calculated and loaded into the input layer of a three-layer back propagation network. The neural network classified the spectra into normal or back pain type. RESULTS: The back propagation neural was shown to have satisfactory convergence with a specificity of 79% and a sensitivity of 80%. CONCLUSIONS: Artificial intelligence neural networks appear to be a useful method of differentiating paraspinal power spectra in back-pain sufferers.

  5. Background noise spectra of global seismic stations

    Energy Technology Data Exchange (ETDEWEB)

    Wada, M.M.; Claassen, J.P.

    1996-08-01

    Over an extended period of time station noise spectra were collected from various sources for use in estimating the detection and location performance of global networks of seismic stations. As the database of noise spectra enlarged and duplicate entries became available, an effort was mounted to more carefully select station noise spectra while discarding others. This report discusses the methodology and criteria by which the noise spectra were selected. It also identifies and illustrates the station noise spectra which survived the selection process and which currently contribute to the modeling efforts. The resulting catalog of noise statistics not only benefits those who model network performance but also those who wish to select stations on the basis of their noise level as may occur in designing networks or in selecting seismological data for analysis on the basis of station noise level. In view of the various ways by which station noise were estimated by the different contributors, it is advisable that future efforts which predict network performance have available station noise data and spectral estimation methods which are compatible with the statistics underlying seismic noise. This appropriately requires (1) averaging noise over seasonal and/or diurnal cycles, (2) averaging noise over time intervals comparable to those employed by actual detectors, and (3) using logarithmic measures of the noise.

  6. Seismic spectra of events at regional distances

    International Nuclear Information System (INIS)

    Springer, D.L.; Denny, M.D.

    1976-01-01

    About 40 underground nuclear explosions detonated at the Nevada Test Site (NTS) were chosen for analysis of their spectra and any relationships they might have to source parameters such as yield, depth of burial, etc. The sample covered a large yield range (less than 20 kt to greater than 1 Mt). Broadband (0.05 to 20 Hz) data recorded by the four-station seismic network operated by Lawrence Livermore Laboratory were analyzed in a search for unusual explosion signatures in their spectra. Long time windows (total wave train) as well as shorter windows (for instance, P/sub n/) were used as input to calculate the spectra. Much variation in the spectra of the long windows is typical although some gross features are similar, such as a dominant peak in the microseismic window. The variation is such that selection of corner frequencies is impractical and yield scaling could not be determined. Spectra for one NTS earthquake showed more energy in the short periods (less than 1 sec) as well as in the long periods (greater than 8 sec) compared to those for NTS explosions

  7. MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.; Colby, Sean M.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

    2017-02-21

    MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

  8. Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers

    NARCIS (Netherlands)

    Yousef, Malik; Nigatu, Dawit; Levy, Dalit; Allmer, Jens; Henkel, Werner

    2017-01-01

    Background: Diseases like cancer can manifest themselves through changes in protein abundance, and microRNAs (miRNAs) play a key role in the modulation of protein quantity. MicroRNAs are used throughout all kingdoms and have been shown to be exploited by viruses to modulate their host

  9. FAST INVERSION OF SOLAR Ca II SPECTRA

    International Nuclear Information System (INIS)

    Beck, C.; Choudhary, D. P.; Rezaei, R.; Louis, R. E.

    2015-01-01

    We present a fast (<<1 s per profile) inversion code for solar Ca II lines. The code uses an archive of spectra that are synthesized prior to the inversion under the assumption of local thermodynamic equilibrium (LTE). We show that it can be successfully applied to spectrograph data or more sparsely sampled spectra from two-dimensional spectrometers. From a comparison to a non-LTE inversion of the same set of spectra, we derive a first-order non-LTE correction to the temperature stratifications derived in the LTE approach. The correction factor is close to unity up to log τ ∼ –3 and increases to values of 2.5 and 4 at log τ = –6 in the quiet Sun and the umbra, respectively

  10. Tunneling spectra of graphene on copper unraveled

    DEFF Research Database (Denmark)

    Zhang, Xin; Stradi, Daniele; Liu, Lei

    2016-01-01

    mechanisms, etc. The interpretation of the spectra can be complicated, however. Specifically for graphene grown on copper, there have been conflicting reports of tunneling spectra. A clear understanding of the mechanisms behind the variability is desired. In this work, we have revealed that the root cause...... of the variability in tunneling spectra is the variation in graphene-substrate coupling under various experimental conditions, providing a salutary perspective on the important role of 2D material-substrate interactions. The conclusions are drawn from measured data and theoretical calculations for monolayer, AB......-stacked bilayer, and twisted bilayer graphene coexisting on the same substrates in areas with and without intercalated oxygen, demonstrating a high degree of consistency. The Van Hove singularities of the twisted graphene unambiguously indicate the Dirac energy between them, lending strong evidence to our...

  11. Rotational structure in molecular infrared spectra

    CERN Document Server

    di Lauro, Carlo

    2013-01-01

    Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in many scientific disciplines, including applications in atmospheric and planetary research. Consequently, the basic principles of vibration-rotation absorption spectroscopy are addressed for contemporary applications. In addition to covering operational quantum mechanical methods, spherical tensor algebra, and group theoretical methods applied to molecular symmetry, attention is also given to phase conventions and their effe...

  12. Observed and theoretical spectra in the 10-100 A interval. [of solar spectra

    Science.gov (United States)

    Brown, W. A.; Bruner, M. E.; Acton, L. W.

    1988-01-01

    The soft X-ray spectra recorded in two sounding-rocket flights in 1982 and 1985 are compared with predicted spectra. The processed densitometer trace of the full spectrum is presented, together with the new spectrum from the 1985 experiment. The intensities of the lines are then compared with predictions.

  13. BETA SPECTRA. I. Negatrons spectra; ESPECTROS BETA. I. Espectros simples de negatrones

    Energy Technology Data Exchange (ETDEWEB)

    Grau Malonda, A; Garcia-Torano, E

    1978-07-01

    Using the Fermi theory of beta decay, the beta spectra for 62 negatrons emitters have been computed introducing a correction factor for unique forbidden transitions. These spectra are plotted vs. energy, once normal i sed, and tabulated with the related Fermi functions. The average and median energies are calculated. (Author)

  14. Algorithms for classification of astronomical object spectra

    Science.gov (United States)

    Wasiewicz, P.; Szuppe, J.; Hryniewicz, K.

    2015-09-01

    Obtaining interesting celestial objects from tens of thousands or even millions of recorded optical-ultraviolet spectra depends not only on the data quality but also on the accuracy of spectra decomposition. Additionally rapidly growing data volumes demands higher computing power and/or more efficient algorithms implementations. In this paper we speed up the process of substracting iron transitions and fitting Gaussian functions to emission peaks utilising C++ and OpenCL methods together with the NOSQL database. In this paper we implemented typical astronomical methods of detecting peaks in comparison to our previous hybrid methods implemented with CUDA.

  15. Nonlinear FMR spectra in yttrium iron garnet

    Directory of Open Access Journals (Sweden)

    Yu.M. Bunkov, P.M. Vetoshko, I.G. Motygullin, T.R. Safin, M.S. Tagirov, N.A. Tukmakova

    2015-12-01

    Full Text Available Results of demagnetizing effect studies in yttrium iron garnet Y3Fe5O12 thin films are reported. Experiments were performed on X-Band of electron paramagnetic resonance spectrometer at room temperature. The ferromagnetic resonance (FMR spectra were obtained for one-layer single crystal YIG films for different values of the applied microwave power. Nonlinear FMR spectra transformation by the microwave power increasing in various directions of magnetic field sweep was observed. It is explained by the influence of the demagnetization action of nonequilibrium magnons.

  16. Virtual photon spectra for finite nuclei

    International Nuclear Information System (INIS)

    Wolynec, E.; Martins, M.N.

    1988-01-01

    The experimental results of an isochromat of the virtual photon spectrum, obtained by measuring the number of ground-state protons emitted by the 16.28 MeV isobaric analogue state in 90 Zr as a function of electron incident energy in the range 17-105 MeV, are compared with the values predicted by a calculation of the E1 DWBA virtual photon spectra for finite nuclei. It is found that the calculations are in excellent agreement with the experimental results. The DWBA virtual photon spectra for finite nuclei for E2 and M1 multipoles are also assessed. (author) [pt

  17. IUE Archival Spectra of 31 Cygni

    Directory of Open Access Journals (Sweden)

    Young Woon Kang

    1991-06-01

    Full Text Available UV light curve of 31 Cygni has been made from the IUE high dispersion spectra. The depth of primary minimum of the light curve is 5.2 magnitudes because the B4 star's steep spectral gradient. The light curve has been analyzed by the method of Wilson and Devinney Differential Correction (WD. The radial velocities have been measured using the Mg II h lines. The spectroscopic elements have been determined by the method of WD. The change of the Mg II resonance doublet has been investigated based on the eight representative spectra taken at well distributed orbital phases.

  18. Approximation of Moessbauer spectra of metallic glasses

    International Nuclear Information System (INIS)

    Miglierini, M.; Sitek, J.

    1988-01-01

    Moessbauer spectra of iron-rich metallic glasses are approximated by means of six broadened lines which have line position relations similar to those of α-Fe. It is shown via the results of the DISPA (dispersion mode vs. absorption mode) line shape analysis that each spectral peak is broadened owing to a sum of Lorentzian lines weighted by a Gaussian distribution in the peak position. Moessbauer parameters of amorphous metallic Fe 83 B 17 and Fe 40 Ni 40 B 20 alloys are presented, derived from the fitted spectra. (author). 2 figs., 2 tabs., 21 refs

  19. What can we learn from inclusive spectra

    International Nuclear Information System (INIS)

    Nagamiya, S.

    1981-05-01

    The present experimental status on single particle inclusive measurements is described. Then, the geometrical aspect of the collision is discussed from the data of total integrated cross sections of nuclear charge or mass. The dynamical aspect of the collision, especially that for the participating region is discussed in connection with proton spectra, composite fragment spectra, pion production, ratios of π - /π + , n/p and t/ 3 He, and production of strange particles. The spectator physics is described from the data on projectile fragments

  20. Photoacoustic spectra of rare earth pentaphosphates

    International Nuclear Information System (INIS)

    Strek, W.; Lukowiak, E.; Marchewka, M.; Ratajczak, H.

    1987-01-01

    The photoacoustic (PA) spectra of raee earth pentaphosphates of the general formula REP 5 O 14 , where RE = Pr,Nd,Ho,Er,Tm, are reported. The photoacoustic bands were identified and compared with the absorption spectra. For quantitative analysis of PA bands of lanthanide (III) ions, the intensity ratio vector is introduced characterizing the intensity distribution of f-f transitions. It was found that the relative intensities of photoacoustic bands are comparable with the intensities of absorption bands. It is concluded that the nonradiative relaxation mechanism leading to the PA signal is independent of the manifold-to-manifold J-J' radiationless transitions

  1. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen; Gao, Xin; Liang, Faming

    2014-01-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic

  2. Sensitive Leptospira DNA detection using tapered optical fiber sensor.

    Science.gov (United States)

    Zainuddin, Nurul H; Chee, Hui Y; Ahmad, Muhammad Z; Mahdi, Mohd A; Abu Bakar, Muhammad H; Yaacob, Mohd H

    2018-03-23

    This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu-like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA-based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3-Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA-based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non-cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Mutagenesis and repair of DNA

    International Nuclear Information System (INIS)

    Janion, C.; Grzesiuk, E.; Fabisiewicz, A.; Tudek, B.; Ciesla, J.; Graziewicz, M.; Wojcik, A.; Speina, E.

    1998-01-01

    Full text. The discovery that the mfd gene codes for a transcription-coupling repair factor (TRCF) prompted us to re-investigate the MFD (mutation frequency decline) phenomenon in E.coli K-12 strain when mutations were induced by ultraviolet light, halogen light or MMS-treatment. These studies revealed that: (i) the process of MFD involves the proofreading activity of DNA pol III and the mismatch repair system, as well as, TRCF and the UvrABC-excinuclease (ii) a semi-rich plate test may be replaced by a rich liquid medium, (iii) the T-T pyrimidine dimers are the lesions excised with the highest activity, and (iv) overproduction of UmuD(D'C) proteins leads to a great increase in mutant frequency in irradiated and MMS-treated cells. The role of mismatch repair (MR) in MMS-induced mutagenesis is obscured by the fact that the spectra of mutational specificity are different in bacteria proficient and deficient in MR. It has been found that transposons Tn10 (and Tn5) when inserted into chromosomal DNA of E. coli influence the phenotype lowering the survival and frequency of mutations induced by UV or halogen light irradiation. This is connected with a deficiency of UmuD(D') and UmuC proteins. Transformation of bacteria with plasmids bearing the umuD(D')C genes, suppresses the effects of the transposon insertion, a phenomenon which has not been described before. Single-stranded DNA of M13mp18 phage was oxidized in vitro by a hydroxyl radical generating system including hypoxanthine/xanthine oxidase/Fe3+/EDTA, and it was found that Fapy-Ade, Fapy-Gua, 8-oxyAde and thymine glycol were the main products formed. Replication of the oxidized template by T7 phage DNA polymerase, Klenow fragment of polymerase I, or polymerase beta from bovine thymus has revealed that oxidized pyrimidines are stronger blockers than oxidized purines for T7 phage and Klenow fragment polymerases and the blocking potency depends on the neighboring bases and on the type of polymerase. Studies of

  4. Analysis of COSIMA spectra: Bayesian approach

    Directory of Open Access Journals (Sweden)

    H. J. Lehto

    2015-06-01

    secondary ion mass spectrometer (TOF-SIMS spectra. The method is applied to the COmetary Secondary Ion Mass Analyzer (COSIMA TOF-SIMS mass spectra where the analysis can be broken into subgroups of lines close to integer mass values. The effects of the instrumental dead time are discussed in a new way. The method finds the joint probability density functions of measured line parameters (number of lines, and their widths, peak amplitudes, integrated amplitudes and positions. In the case of two or more lines, these distributions can take complex forms. The derived line parameters can be used to further calibrate the mass scaling of TOF-SIMS and to feed the results into other analysis methods such as multivariate analyses of spectra. We intend to use the method, first as a comprehensive tool to perform quantitative analysis of spectra, and second as a fast tool for studying interesting targets for obtaining additional TOF-SIMS measurements of the sample, a property unique to COSIMA. Finally, we point out that the Bayesian method can be thought of as a means to solve inverse problems but with forward calculations, only with no iterative corrections or other manipulation of the observed data.

  5. Vibrational spectra for hydrogenated amorphous semiconductors

    International Nuclear Information System (INIS)

    Kamitakahara, W.A.; Bouchard, A.M.; Biswas, R.; Gompf, F.; Suck, J.B.

    1990-01-01

    Hydrogen vibration spectra have been measured by neutron scattering for several amorphous semiconductor materials, including a-Ge:H and a-SiC:H samples containing about 10 at. % H. The data for a-Ge:H are compared in detail with the results of realistic computer simulations

  6. RAMAN-SPECTRA OF HUMAN DENTAL CALCULUS

    NARCIS (Netherlands)

    TSUDA, H; ARENDS, J

    1993-01-01

    Raman spectra of human dental calculus have been observed for the first time by use of micro-Raman spectroscopy. The spectral features of calculus were influenced easily by heating caused by laser irradiation. Therefore, the measurements were carried out at relatively low power (5 mW, 1-mu m spot

  7. Automatic analysis of charged particle spectra

    International Nuclear Information System (INIS)

    Seres, Z.; Kiss, A.

    1975-11-01

    A computer program system is developed for off-line automatic analysis of a series of charged particle spectra measured by solid-state detectors and collected on magnetic tapes. The procedure results in complete angular distributions for the excited levels of the final nucleus up to about 15 MeV. (orig.) [de

  8. An adaptive method for γ spectra smoothing

    International Nuclear Information System (INIS)

    Xiao Gang; Zhou Chunlin; Li Tiantuo; Han Feng; Di Yuming

    2001-01-01

    Adaptive wavelet method and multinomial fitting gliding method are used for smoothing γ spectra, respectively, and then FWHM of 1332 keV peak of 60 Co and activities of 238 U standard specimen are calculated. Calculated results show that adaptive wavelet method is better than the other

  9. INTRAMOLECULAR ISOTOPE EFFECTS IN HYDROCARBON MASS SPECTRA

    Energy Technology Data Exchange (ETDEWEB)

    Stevenson, D. P.; Schachtschneider, J. H.

    1963-07-15

    Approximate calculations based on the quasi-equilibrium rate theory of the origin of mass spectra are shown to lead to an approximately correct magnitude for the intramolecular ( pi /sup -/) isotope effect on C--H bond dissociation probabilities of various deuterohydrocarbons. (auth)

  10. Library search with regular reflectance IR spectra

    International Nuclear Information System (INIS)

    Staat, H.; Korte, E.H.; Lampen, P.

    1989-01-01

    Characterisation in situ for coatings and other surface layers is generally favourable, but a prerequisite for precious items such as art objects. In infrared spectroscopy only reflection techniques are applicable here. However for attenuated total reflection (ATR) it is difficult to obtain the necessary optical contact of the crystal with the sample, when the latter is not perfectly plane or flexible. The measurement of diffuse reflectance demands a scattering sample and usually the reflectance is very poor. Therefore in most cases one is left with regular reflectance. Such spectra consist of dispersion-like feature instead of bands impeding their interpretation in the way the analyst is used to. Furthermore for computer search in common spectral libraries compiled from transmittance or absorbance spectra a transformation of the reflectance spectra is needed. The correct conversion is based on the Kramers-Kronig transformation. This somewhat time - consuming procedure can be speeded up by using appropriate approximations. A coarser conversion may be obtained from the first derivative of the reflectance spectrum which resembles the second derivative of a transmittance spectrum. The resulting distorted spectra can still be used successfully for the search in peak table libraries. Experiences with both transformations are presented. (author)

  11. Chaotic spectra: How to extract dynamic information

    International Nuclear Information System (INIS)

    Taylor, H.S.; Gomez Llorente, J.M.; Zakrzewski, J.; Kulander, K.C.

    1988-10-01

    Nonlinear dynamics is applied to chaotic unassignable atomic and molecular spectra with the aim of extracting detailed information about regular dynamic motions that exist over short intervals of time. It is shown how this motion can be extracted from high resolution spectra by doing low resolution studies or by Fourier transforming limited regions of the spectrum. These motions mimic those of periodic orbits (PO) and are inserts into the dominant chaotic motion. Considering these inserts and the PO as a dynamically decoupled region of space, resonant scattering theory and stabilization methods enable us to compute ladders of resonant states which interact with the chaotic quasi-continuum computed in principle from basis sets placed off the PO. The interaction of the resonances with the quasicontinuum explains the low resolution spectra seen in such experiments. It also allows one to associate low resolution features with a particular PO. The motion on the PO thereby supplies the molecular movements whose quantization causes the low resolution spectra. Characteristic properties of the periodic orbit based resonances are discussed. The method is illustrated on the photoabsorption spectrum of the hydrogen atom in a strong magnetic field and on the photodissociation spectrum of H 3 + . Other molecular systems which are currently under investigation using this formalism are also mentioned. 53 refs., 10 figs., 2 tabs

  12. Polarization Spectra of Extrasolar Giant Planets

    NARCIS (Netherlands)

    Stam, D.M.

    2004-01-01

    We present simulated spectra of the flux and degree of polarization of starlight that is reflected by extrasolar giant planets (EGPs). In particular the polarization depends strongly on the structure of the planetary atmosphere, and appears to be a valuable tool for the characterization of EGPs.

  13. Temperatures of fragment kinetic energy spectra

    International Nuclear Information System (INIS)

    Bauer, W.

    1995-01-01

    Multifragmentation reactions without large compression in the initial state (proton-induced reactions, reverse kinematics, projectile fragmentation) are examined, and it is verified quantitatively that the high temperatures obtained from fragment kinetic energy spectra and lower temperatures obtained from observables such as level population or isotope ratios can be understood in a common framework

  14. A comparison of floor response spectra techniques

    International Nuclear Information System (INIS)

    Yan, M.J.; Galford, J.E.

    1983-01-01

    Floor response spectra (FRS) conventionally have been generated using a time-history method. Babcock and Wilcox has developed a new technique, the Fast Floor Response Spectra (FFRS) method, in which dynamic analyses are done entirely in the frequency domain. This paper compares the two techniques and demonstrates that the FFRS method complies with the 'equivalency' and 'conservatism' requirements of the US NRC's Standard Review Plan. The upper end of a once-through steam generator in the B and W 205 nuclear steam supply system (NSSS) was used to demonstrate that the FFRS method is equivalent to the time-history technique. The two techniques were compared with respect to frequency content and magnitude of response for a given point on the structure. First, the specified forcing function was described in terms of an acceleration time history and an acceleration spectra enveloping that time history. The time-history forcing function was then used in a direct transient analysis to determine the response at the specified point on the NSSS. The resultant response was subsequently converted to a floor response spectra for that point. To show that the FFRS method gave equivalent and conservative results, the FFRS technique was used to determine the modal response directly from the spectral description of the forcing function. The FFRS- and time-history-generated data agreed to within 13 (worst case on conservative side) of each other with the former cutting analytical costs by 99%. (orig./HP)

  15. Microdosimetric spectra measurements of JANUS neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, I.R.; Williamson, F.S.

    1985-01-01

    Neutron radiation from the JANUS reactor at Argonne National Laboratory is being used with increasing frequency for major biological experiments. The fast neutron spectrum has a Kerma-weighted mean energy of 0.8 MeV and low gamma-ray contamination. In 1984 the JANUS fission converter plate of highly enriched uranium was replaced by one made of low-enriched uranium. We recorded microdosimetric spectra at several different positions in the high-flux irradiation room of JANUS before the change of the converter plate. Each set of measurements consisted of spectra taken at three different site diameters (0.5, 1.0, and 5.0 ..mu..m) and in both ''attenuator up'' and ''attenuator down'' configurations. At two conventional dosimetry reference positions, two sets of measurements were recorded. At three biological reference positions, measurements simulating several biological irradiation conditions, were taken. The dose rate at each position was estimated and compared with dose rates obtained previously by conventional dosimetry. Comparison of the different measurements showed no major change in spectra as a function of position or irradiation condition. First results from similar sets of measurements recorded after the installment of the new converter plate indicate no major change in the spectra. 11 refs., 4 figs., 5 tabs.

  16. Mass Spectra of Tetraselenafulvalenes, Diselenadithiafulvalenes and Tetrathiafulvalenes

    DEFF Research Database (Denmark)

    Andersen, Jan Rud; Egsgaard, Helge; Larsen, Elfinn

    1978-01-01

    fragmentation of the molecular ion, as the selenium fulvalenes lose an alkyne molecule, whereas the sulphur fulvalenes first lose an (SĊR) radical. An important feature of the spectra of the simple heterofulvalenes is the formation of a rearrangement ion by migration of a heteroatom. The mechanism...

  17. Analysis of low-intensity scintillation spectra

    International Nuclear Information System (INIS)

    Muravsky, V.; Tolstov, S.A.

    2002-01-01

    The maximum likelihood algorithms for nuclides activities estimation from low intensity scintillation γ-ray spectra have been created. The algorithms treat full energy peaks and Compton parts of spectra, and they are more effective than least squares estimators. The factors that could lead to the bias of activity estimates are taken into account. Theoretical analysis of the problem of choosing the optimal set of initial spectra for the spectrum model to minimize errors of the activities estimation has been carried out for the general case of the N-components with Gaussian or Poisson statistics. The obtained criterion allows to exclude superfluous initial spectra of nuclides from the model. A special calibration procedure for scintillation γ-spectrometers has been developed. This procedure is required for application of the maximum likelihood activity estimators processing all the channels of the scintillation γ-spectrum, including the Compton part. It allows one to take into account the influence of the sample mass density variation. The algorithm for testing the spectrum model adequacy to the processed scintillation spectrum has been developed. The algorithms are realized in Borland Pascal 7 as a library of procedures and functions. The developed library is compatible with Delphi 1.0 and higher versions. It can be used as the algorithmic basis for analysis of highly sensitive scintillation γ- and β-spectrometric devices. (author)

  18. Ultraviolet spectra of Mg in liquid helium

    International Nuclear Information System (INIS)

    Moriwaki, Y.; Morita, N.

    1999-01-01

    Emission and absorption spectra of Mg atoms implanted in liquid helium have been observed in the ultraviolet region. We have presented a model of exciplex formation of Mg-He 10 and found that this model is more suitable for understanding the dynamics in the 3s3p 1 P→3s 21 S transition than the bubble model. (orig.)

  19. Raman spectra of lignin model compounds

    Science.gov (United States)

    Umesh P. Agarwal; Richard S. Reiner; Ashok K. Pandey; Sally A. Ralph; Kolby C. Hirth; Rajai H. Atalla

    2005-01-01

    To fully exploit the value of Raman spectroscopy for analyzing lignins and lignin containing materials, a detailed understanding of lignins’ Raman spectra needs to be achieved. Although advances made thus far have led to significant growth in application of Raman techniques, further developments are needed to improve upon the existing knowledge. Considering that lignin...

  20. Microdosimetric spectra measurements of JANUS neutrons

    International Nuclear Information System (INIS)

    Marshall, I.R.; Williamson, F.S.

    1985-01-01

    Neutron radiation from the JANUS reactor at Argonne National Laboratory is being used with increasing frequency for major biological experiments. The fast neutron spectrum has a Kerma-weighted mean energy of 0.8 MeV and low gamma-ray contamination. In 1984 the JANUS fission converter plate of highly enriched uranium was replaced by one made of low-enriched uranium. We recorded microdosimetric spectra at several different positions in the high-flux irradiation room of JANUS before the change of the converter plate. Each set of measurements consisted of spectra taken at three different site diameters (0.5, 1.0, and 5.0 μm) and in both ''attenuator up'' and ''attenuator down'' configurations. At two conventional dosimetry reference positions, two sets of measurements were recorded. At three biological reference positions, measurements simulating several biological irradiation conditions, were taken. The dose rate at each position was estimated and compared with dose rates obtained previously by conventional dosimetry. Comparison of the different measurements showed no major change in spectra as a function of position or irradiation condition. First results from similar sets of measurements recorded after the installment of the new converter plate indicate no major change in the spectra. 11 refs., 4 figs., 5 tabs

  1. Nuclear Neutrino Spectra in Late Stellar Evolution

    Science.gov (United States)

    Misch, G. Wendell; Sun, Yang; Fuller, George

    2018-05-01

    Neutrinos are the principle carriers of energy in massive stars, beginning from core carbon burning and continuing through core collapse and after the core bounce. In fact, it may be possible to detect neutrinos from nearby pre-supernova stars. Therefore, it is of great interest to understand the neutrino energy spectra from these stars. Leading up to core collapse, beginning around core silicon burning, nuclei become dominant producers of neutrinos, particularly at high neutrino energy, so a systematic study of nuclear neutrino spectra is desirable. We have done such a study, and we present our sd-shell model calculations of nuclear neutrino energy spectra for nuclei in the mass number range A = 21 - 35. Our study includes neutrinos produced by charged lepton capture, charged lepton emission, and neutral current nuclear deexcitation. Previous authors have tabulated the rates of charged current nuclear weak interactions in astrophysical conditions, but the present work expands on this not only by providing neutrino energy spectra, but also by including the heretofore untabulated neutral current de-excitation neutrino pairs.

  2. Variations on supersymmetry breaking and neutrino spectra

    International Nuclear Information System (INIS)

    Borzumati, F.; Hamaguchi, K.; Nomura, Y.; Yanagida, T.

    2000-01-01

    The problem of generating light neutrinos within supersymmetric models is discussed. It is shown that the hierarchy of scales induced by supersymmetry breaking can give rise to suppression factors of the correct order of magnitude to produce experimentally allowed neutrino spectra

  3. Autonomous System Design for Moessbauer Spectra Acquisition

    International Nuclear Information System (INIS)

    Morales, A. L.; Zuluaga, J.; Cely, A.; Tobon, J.

    2001-01-01

    An autonomous system for Moessbauer spectroscopy based in a microcontroller has been designed. A timer of the microcontroller was used to generate the control signal for the Moessbauer linear motor, and a counter for the spectra acquisition. Additionally, the system has its own memory for data storage and a serial port to transmit the data to a computer for its later processing and display

  4. Fitting PAC spectra with a hybrid algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Alves, M. A., E-mail: mauro@sepn.org [Instituto de Aeronautica e Espaco (Brazil); Carbonari, A. W., E-mail: carbonar@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (Brazil)

    2008-01-15

    A hybrid algorithm (HA) that blends features of genetic algorithms (GA) and simulated annealing (SA) was implemented for simultaneous fits of perturbed angular correlation (PAC) spectra. The main characteristic of the HA is the incorporation of a selection criterion based on SA into the basic structure of GA. The results obtained with the HA compare favorably with fits performed with conventional methods.

  5. Savannah River Site disaggregated seismic spectra

    International Nuclear Information System (INIS)

    Stephenson, D.E.

    1993-02-01

    The objective of this technical note is to characterize seismic ground motion at the Savannah River Site (SRS) by postulated earthquakes that may impact facilities at the site. This task is accomplished by reviewing the deterministic and probabilistic assessments of the seismic hazard to establish the earthquakes that control the hazard to establish the earthquakes that control the hazard at the site and then evaluate the associated seismic ground motions in terms of response spectra. For engineering design criteria of earthquake-resistant structures, response spectra serve the function of characterizing ground motions as a function of period or frequency. These motions then provide the input parameters that are used in the analysis of structural response. Because they use the maximum response, the response spectra are an inherently conservative design tool. Response spectra are described in terms of amplitude, duration, and frequency content, and these are related to source parameters, travel path, and site conditions. Studies by a number of investigators have shown by statistical analysis that for different magnitudes the response spectrum values are different for differing periods. These facts support Jennings' position that using different shapes of design spectra for earthquakes of different magnitudes and travel paths is a better practice than employing a single, general-purpose shape. All seismic ground motion characterization results indicate that the PGA is controlled by a local event with M w < 6 and R < 30km. The results also show that lower frequencies are controlled by a larger, more distant event, typically the Charleston source. The PGA of 0.2 g, based originally on the Blume study, is consistent with LLNL report UCRL-15910 (1990) and with the DOE position on LLNL/EPRI

  6. Improving interpretation of infrared spectra for OM characterization by subtraction of spectra from incinerated samples

    Science.gov (United States)

    Ellerbrock, Ruth H.; Gerke, Horst H.; Leue, Martin

    2017-04-01

    Non-destructive methods such as diffuse reflectance infrared Fourier transform spectroscopy (DRIFT) have been applied to characterize organic matter (OM) at intact structural surfaces among others. However, it is often difficult to distinguish effects of organic components on DRIFT signal intensities from those of mineral components. The objective of this study was to re-evaluate DRIFT spectra from intact earthworm burrow walls and coated cracks to improve the interpretation of C-H and C=O bands. We compared DRIFT and transmission Fourier transform infrared (FTIR) spectra of entire samples that were from the same pedogenetic soil horizon, but different in mineral composition and texture (i.e., glacial till versus loess). Spectra of incinerated samples were subtracted from the original spectra. Transmission FTIR and DRIFT spectra were almost identical for entire soil samples. However, the DRIFT spectra were affected by the bulk mode bands (i.e., wavenumbers 2000 to 1700 cm-1) that affected spectral resolution and reproducibility. The ratios between C-H and C=O band intensities as indicator for OM quality obtained with DRIFT were smaller than those obtained from transmission FTIR. A spectral subtraction procedure was found to reduce effects of mineral absorption bands on DRIFT spectra allowing an improved interpretation. DRIFT spectroscopy as a non-destructive method for analyzing OM composition at intact surfaces in structured soils could be calibrated with information obtained with the more detailed transmission FTIR and complementary methods.

  7. DNA preservation in silk.

    Science.gov (United States)

    Liu, Yawen; Zheng, Zhaozhu; Gong, He; Liu, Meng; Guo, Shaozhe; Li, Gang; Wang, Xiaoqin; Kaplan, David L

    2017-06-27

    The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility. After air-drying and water extraction, 50-70% of the DNA and silk could be retrieved and showed a single band on electrophoretic gels. 6% silk/DNA + PT-filter samples provided improved stability in comparison with 3% silk/DNA + filter samples and DNA + filter samples for DNA preservation, with ∼40% of the band intensity remaining at 37 °C after 40 days and ∼10% after exposure to UV light for 10 hours. Quantitative analysis using the PicoGreen assay confirmed the results. The use of Tris/borate/EDTA (TBE) buffer enhanced the preservation and/or extraction of the DNA. The DNA extracted after storage maintained integrity and function based on serving as a functional template for PCR amplification of the gene for zinc finger protein 750 (ZNF750) and for transgene expression of red fluorescence protein (dsRed) in HEK293 cells. The high molecular weight and high content of a crystalline beta-sheet structure formed on the coated surfaces likely accounted for the preservation effects observed for the silk/DNA + PT-filter samples. Although similar preservation effects were also obtained for lyophilized silk/DNA samples, the rapid and simple processing available with the silk-DNA-filter membrane system makes it appealing for future applications.

  8. Force induced DNA melting

    International Nuclear Information System (INIS)

    Santosh, Mogurampelly; Maiti, Prabal K

    2009-01-01

    When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates by roughly twice its initial contour length at a pulling force of about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying a force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA, this being a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double-strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA starts melting abruptly/smoothly above a critical force depending on the pulling direction. The critical force f m , at which DNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base pairs. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.

  9. DNA damage and autophagy

    International Nuclear Information System (INIS)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  10. DNA Open states and DNA hydratation

    International Nuclear Information System (INIS)

    Lema-Larre, B. de; Martin-Landrove, M

    1995-01-01

    It is a very well-known fact that an protonic exchange exists among natural DNA filaments and synthetic polynucleotides with the solvent (1--2). The existence of DNA open states, that is to say states for which the interior of the DNA molecule is exposed to the external environment, it has been demonstrated by means of proton-deuterium exchange (3). This work has carried out experiments measuring the dispersion of the traverse relaxation rate (4), as a pulsation rate function in a Carr-Purcell-Meiboom-Gill (CPMG) pulses sequence rate, to determine changes in the moist layer of the DNA molecule. The experiments were carried out under different experimental conditions in order to vary the probability that open states occurs, such as temperature or the exposure to electromagnetic fields. Some theoretical models were supposed to adjust the experimental results including those related to DNA non linear dynamic [es

  11. Immunoassay of DNA damage

    International Nuclear Information System (INIS)

    Gasparro, F.P.; Santella, R.M.

    1988-01-01

    The direct photomodification of DNA by ultraviolet light or the photo-induced addition of exogenous compounds to DNA components results in alterations of DNA structure ranging from subtle to profound. There are two consequences of these conformational changes. First, cells in which the DNA has been damaged are capable of executing repair steps. Second, the DNA which is usually of very low immunogenicity now becomes highly antigenic. This latter property has allowed the production of a series of monoclonal antibodies that recognize photo-induced DNA damage. Monoclonal antibodies have been generated that recognize the 4',5'-monoadduct and the crosslink of 8-methoxypsoralen in DNA. In addition, another antibody has been prepared which recognizes the furan-side monoadduct of 6,4,4'-trimethylangelicin in DNA. These monoclonal antibodies have been characterized as to sensitivity and specificity using non-competitive and competitive enzyme-linked-immunosorbent assays (ELISA). (author)

  12. Immunoassay of DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Gasparro, F P; Santella, R M

    1988-09-01

    The direct photomodification of DNA by ultraviolet light or the photo-induced addition of exogenous compounds to DNA components results in alterations of DNA structure ranging from subtle to profound. There are two consequences of these conformational changes. First, cells in which the DNA has been damaged are capable of executing repair steps. Second, the DNA which is usually of very low immunogenicity now becomes highly antigenic. This latter property has allowed the production of a series of monoclonal antibodies that recognize photo-induced DNA damage. Monoclonal antibodies have been generated that recognize the 4',5'-monoadduct and the crosslink of 8-methoxypsoralen in DNA. In addition, another antibody has been prepared which recognizes the furan-side monoadduct of 6,4,4'-trimethylangelicin in DNA. These monoclonal antibodies have been characterized as to sensitivity and specificity using non-competitive and competitive enzyme-linked-immunosorbent assays (ELISA).

  13. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  14. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  15. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  16. Observational and theoretical spectra of supernovae

    Science.gov (United States)

    Wheeler, J. Craig; Swartz, Douglas A.; Harkness, Robert P.

    1993-05-01

    Progress in nuclear astrophysics by means of quantitative supernova spectroscopy is discussed with special concentration on type Ia, Ib and Ic and on SN 1987A. Spectral calculations continue to support an exploding C/O white dwarf as the best model of a SN Ia. Deflagration model W7 produces good maximum light spectra of SN Ia and seems to have a better composition distribution compared to delayed detonation models, but proper treatment of opacity remains a problem and the physical basis of SN Ia explosions is still not completely understood. All models for SN Ia predict large quantities of 56Co in the ejecta, but it is not clear that observations confirm this. Although the evolutionary origin of SN Ia remains uncertain, there is recent evidence that transfer of hydrogen in a binary system may be involved, as long suspected. There has been progress in comparing dynamical models with the optical/IR spectra of SN 1987A. The evolution of the [OI] λλ6300, 6364 feature and the presence of strong persistent HeI λ10 830 indicate that both the envelope and core material contribute substantially to the formation of emission lines in the nebular phase and that neither the core nor the envelope can be neglected. Blending with nearby hydrogen lines may affect both of these spectral features, thereby complicating the analysis of the lines. The effects of continuum transfer and photoionization have been included and are under study. The discrepancies between theoretical and observed spectra are due primarily to the one-dimensional hydrodynamic models. The spectral data are not consistent with the high density ``spike'' (in radial coordinate) of the core material that is predicted by all such models. Analysis of the light curves of SN Ib and SN Ic supernovae implies that there are significant differences in their physical properties. Some SN Ib have considerably more ejecta mass than SN Ic events. SN Ib require He-rich atmospheres to produce the observed strong optical lines of

  17. Synthesis and characterization of a lamellar hydroxyapatite/DNA nanohybrid

    Energy Technology Data Exchange (ETDEWEB)

    Zuo Guifu; Wan Yizao; Meng Xianguang [School of Materials Science and Engineering, Tianjin University, Tianjin 300072 (China); Zhao Qing [School of Agriculture and Bioengineering, Tianjin University, Tianjin 300072 (China); Ren Kaijing [Department of Joint Surgery, Tianjin Hospital, Tianjin 300211 (China); Jia Shiru [Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, 29, 13th Street, TEDA, Tianjin 300457 (China); Wang Jiehua, E-mail: gfzuo@tju.edu.cn [School of Agriculture and Bioengineering, Tianjin University, Tianjin 300072 (China)

    2011-04-15

    Research highlights: {yields} A lamellar hydroxyapatite (HAp)/DNA nanohybrid was prepared as a novel gene delivering vector. {yields} Gel electrophoresis analysis confirmed that the lamellar HAp could protect DNA from degradation of DNase I. {yields} The protected DNA in the HAp/DNA nanohybrid could be recovered readily under acid conditions. - Abstract: Two-dimensional layered materials exhibit desired functionalities when being used as gene delivery materials. In this study, a novel gene delivering vector, lamellar hydroxyapatite (HAp)/DNA nanohybrid was prepared. The structure of HAp/DNA nanohybrid was investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Fourier transform infrared (FT-IR) spectroscopy analysis revealed that ion-exchange occurred during the process. Gel electrophoresis analysis confirmed that the lamellar HAp could protect DNA from degradation of DNase I and the protected DNA could be recovered readily under acid conditions. Furthermore, the integrity of released DNA was confirmed by UV-vis spectra.

  18. Synthesis and characterization of a lamellar hydroxyapatite/DNA nanohybrid

    International Nuclear Information System (INIS)

    Zuo Guifu; Wan Yizao; Meng Xianguang; Zhao Qing; Ren Kaijing; Jia Shiru; Wang Jiehua

    2011-01-01

    Research highlights: → A lamellar hydroxyapatite (HAp)/DNA nanohybrid was prepared as a novel gene delivering vector. → Gel electrophoresis analysis confirmed that the lamellar HAp could protect DNA from degradation of DNase I. → The protected DNA in the HAp/DNA nanohybrid could be recovered readily under acid conditions. - Abstract: Two-dimensional layered materials exhibit desired functionalities when being used as gene delivery materials. In this study, a novel gene delivering vector, lamellar hydroxyapatite (HAp)/DNA nanohybrid was prepared. The structure of HAp/DNA nanohybrid was investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Fourier transform infrared (FT-IR) spectroscopy analysis revealed that ion-exchange occurred during the process. Gel electrophoresis analysis confirmed that the lamellar HAp could protect DNA from degradation of DNase I and the protected DNA could be recovered readily under acid conditions. Furthermore, the integrity of released DNA was confirmed by UV-vis spectra.

  19. Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures

    Directory of Open Access Journals (Sweden)

    Yogini P. Bhavsar

    2011-01-01

    Full Text Available Topological variants of single-strand DNA (ssDNA structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC and 1,3-diaza-2-oxophenoxazine (tC∘, can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC∘ is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.

  20. Cyclic perylene diimide: Selective ligand for tetraplex DNA binding over double stranded DNA.

    Science.gov (United States)

    Vasimalla, Suresh; Sato, Shinobu; Takenaka, Fuminori; Kurose, Yui; Takenaka, Shigeori

    2017-12-15

    Synthesized cyclic perylene diimide, cPDI, showed the binding constant of 6.3 × 10 6  M -1 with binding number of n = 2 with TA-core as a tetraplex DNA in 50 mM Tris-HCl buffer (pH = 7.4) containing 100 mM KCl using Schatchard analysis and showed a higher preference for tetraplex DNA than for double stranded DNA with over 10 3 times. CD spectra showed that TA-core induced its antiparallel conformation upon addition of cPDI in the absence or presence of K + or Na + ions. The cPDI inhibits the telomerase activity with IC 50 of 0.3 µM using TRAP assay which is potential anti-cancer drug with low side effect. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. The interaction of taurine-salicylaldehyde Schiff base copper(II) complex with DNA and the determination of DNA using the complex as a fluorescence probe

    Science.gov (United States)

    Zhang, Xiaoyan; Wang, Yong; Zhang, Qianru; Yang, Zhousheng

    2010-09-01

    The interaction of taurine-salicylaldehyde Schiff base copper(II) (Cu(TSSB) 22+) complex with DNA was explored by using UV-vis, fluorescence spectrophotometry, and voltammetry. In pH 7.4 Tris-HCl buffer solution, the binding constant of the Cu(TSSB) 22+ complex interaction with DNA was 3.49 × 10 4 L mol -1. Moreover, due to the fluorescence enhancing of Cu(TSSB) 22+ complex in the presence of DNA, a method for determination of DNA with Cu(TSSB) 22+ complex as a fluorescence probe was developed. The fluorescence spectra indicated that the maximum excitation and emission wavelength were 389 nm and 512 nm, respectively. Under optimal conditions, the calibration graphs are linear over the range of 0.03-9.03 μg mL -1 for calf thymus DNA (CT-DNA), 0.10-36 μg mL -1 for yeast DNA and 0.01-10.01 μg mL -1 for salmon DNA (SM-DNA), respectively. The corresponding detection limits are 7 ng mL -1 for CT-DNA, 3 ng mL -1 for yeast DNA and 3 ng mL -1 for SM-DNA. Using this method, DNA in synthetic samples was determined with satisfactory results.

  2. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...

  3. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  4. Remarks about the displaced spectra techniques

    International Nuclear Information System (INIS)

    Behringer, K.; Pineyro, J.

    1989-01-01

    In a recent paper a new method, called displaced spectra techniques, was presented for distinguishing between sinusoidal components and narrowband random noise contributions in otherwise random noise data. It is based on Fourier transform techniques, and uses the power spectral density (PSD) and a newly-introduced second-order displaced power spectra density (SDPSD) function. In order to distinguish between the two peak types, a validation criterion has been established. In this note, three topics are covered: a) improved numerical data for the validation criterion are given by using the refined estimation procedure of the PSD and SDPSD functions by the Welch method; b) the validation criterion requires the subtraction of the background below the peaks. A semiautomatic procedure is described; c) it was observed that peaks in the real part of the SDPSD function can be accompanied by fine structure phenomena which are unresolved in the PSD function. A few remarks are made about this problem. (author)

  5. EPR spectra of some irradiated polycrystalline perrhenate

    International Nuclear Information System (INIS)

    Zaitseva, N.G.; Constantinescu, M.; Georgescu, R.; Constantinescu, O.

    1978-10-01

    An EPR study of the paramagnetic centers formed by γ, electron and neutron irradiation of the NaReO 4 and KReO 4 was made. In the EPR spectra of the powder samples irradiated γ, with electrons and neutrons, the presence of three types of paramagnetic centers was observed. From the EPR parameters, the centers were attributed to the ReOsub(4)sup(.), ReOsub(3)sup(.) and ReOsub(2)sup(.) radicals respectively. The lower intensity of the spectra observed by KReO 4 samples irradiation showed a higher radioresistance of the KReO 4 than that of NaReO 4 . A radiolitical scheme taking into account the paramagnetic centers formation was proposed. (author)

  6. Raman spectra of filled carbon nanotubes

    International Nuclear Information System (INIS)

    Bose, S.M.; Behera, S.N.; Sarangi, S.N.; Entel, P.

    2004-01-01

    The Raman spectra of a metallic carbon nanotube filled with atoms or molecules have been investigated theoretically. It is found that there will be a three way splitting of the main Raman lines due to the interaction of the nanotube phonon with the collective excitations (plasmons) of the conduction electrons of the nanotube as well as its coupling with the phonon of the filling material. The positions and relative strengths of these Raman peaks depend on the strength of the electron-phonon interaction, phonon frequency of the filling atom and the strength of interaction of the nanotube phonon and the phonon of the filling atoms. Careful experimental studies of the Raman spectra of filled nanotubes should show these three peaks. It is also shown that in a semiconducting nanotube the Raman line will split into two and should be observed experimentally

  7. Benchmarking statistical averaging of spectra with HULLAC

    Science.gov (United States)

    Klapisch, Marcel; Busquet, Michel

    2008-11-01

    Knowledge of radiative properties of hot plasmas is important for ICF, astrophysics, etc When mid-Z or high-Z elements are present, the spectra are so complex that one commonly uses statistically averaged description of atomic systems [1]. In a recent experiment on Fe[2], performed under controlled conditions, high resolution transmission spectra were obtained. The new version of HULLAC [3] allows the use of the same model with different levels of details/averaging. We will take advantage of this feature to check the effect of averaging with comparison with experiment. [1] A Bar-Shalom, J Oreg, and M Klapisch, J. Quant. Spectros. Rad. Transf. 65, 43 (2000). [2] J. E. Bailey, G. A. Rochau, C. A. Iglesias et al., Phys. Rev. Lett. 99, 265002-4 (2007). [3]. M. Klapisch, M. Busquet, and A. Bar-Shalom, AIP Conference Proceedings 926, 206-15 (2007).

  8. The new NIST atomic spectra database

    International Nuclear Information System (INIS)

    Kelleher, D.E.; Martin, W.C.; Wiese, W.L.; Sugar, J.; Fuhr, J.R.; Olsen, K.; Musgrove, A.; Mohr, P.J.; Reader, J.; Dalton, G.R.

    1999-01-01

    The new atomic spectra database (ASD), Version 2.0, of the National Institute of Standards and Technology (NIST) contains significantly more data and covers a wider range of atomic and ionic transitions and energy levels than earlier versions. All data are integrated. It also has a new user interface and search engine. ASD contains spectral reference data which have been critically evaluated and compiled by NIST. Version 2.0 contains data on 900 spectra, with about 70000 energy levels and 91000 lines ranging from about 1 Aangstroem to 200 micrometers, roughly half of which have transition probabilities with estimated uncertainties. References to the NIST compilations and original data sources are listed in the ASD bibliography. A detailed ''Help'' file serves as a user's manual, and full search and filter capabilities are provided. (orig.)

  9. Graphics based PC analysis of alpha spectra

    International Nuclear Information System (INIS)

    Chapman, T.C.

    1991-01-01

    New personal computer (PC) software performs interactive analysis of alpha spectra using EGA graphics. Spectra are collected with a commercial MCA board and analyzed using the software described here. The operator is required to approve each peak integration area before analysis proceeds. Sample analysis can use detector efficiencies or spike yields or both. Background corrections are made and upper limit values are calculated when specified. Nuclide identification uses a library of up to 64 nuclides with up to 8 alpha lines for each nuclide. Any one of 32 subset libraries can be used in an analysis. Analysis time is short and is limited by interaction with the operator, not by calculation time. Utilities include nuclide library editing, library subset editing, energy calibration, efficiency calibration, and background update

  10. Predicting transmittance spectra of electrophotographic color prints

    Science.gov (United States)

    Mourad, Safer; Emmel, Patrick; Hersch, Roger D.

    2000-12-01

    For dry toner electrophotographic color printers, we present a numerical simulation model describing the color printer responses based on a physical characterization of the different electrophotographic process steps. The proposed model introduces a Cross Transfer Efficiency designed to predict the color transmittance spectra of multi-color prints by taking into account the transfer influence of each deposited color toner layer upon the other layers. The simulation model leads to a better understanding of the factors that have an impact on printing quality. In order to avoid the additional optical non-linearities produced by light reflection on paper, we have limited the present investigation to transparency prints. The proposed model succeeded to predict the transmittance spectra of printed wedges combining two color toner layers with a mean deviation less than CIE-LAB (Delta) E equals 2.5.

  11. Measurement and interpretation of plutonium spectra

    International Nuclear Information System (INIS)

    Blaise, J.; Fred, M.S.; Carnall, W.T.; Crosswhite, H.M.; Crosswhite, H.

    1982-01-01

    The atomic spectroscopic data available for plutonium are among the rickest of any in the periodic system. They include high-resolution grating and Fourier-transform spectra as well as extensive Zeeman and isotope-shift studies. We summarize the present status of the term analysis and cite the configurations that have been identified. A least-squares adjustment of a parametric Hamiltonian for configurations of both Pu I and Pu II has shown that almost all of the expected low levels are now known. The use of a model Hamiltonian applicable to both lanthanide and actinide atomic species has been applied to the low configurations of Pu I and Pu II making use of trends predicted by ab initio calculations. This same model has been used to describe the energy levels of Pu 3+ in LaCl 3 , and an extension has permitted preliminary calculations of the spectra of other valence states

  12. The XUV spectra of highly ionised molybdenum

    International Nuclear Information System (INIS)

    Mansfield, M.W.D.; Peacock, N.J.; Smith, C.C.; Hobby, M.G.; Cowan, R.D.

    1978-01-01

    The spectra of molybdenum ions produced in Tokamaks in the wavelength range 10-200 A have been reproduced in a plasma formed by laser beam irradiation of solid molybdenum targets. Lines from highly ionised stages of molybdenum (Mo XXX to Mo XXXII) have been distinguished by varying the laser beam intensity. Detailed analyses of the simpler ions, Mo XV (Ni-like), Mo XVI (Co-like), Mo XXXII (Na-like), and to a lesser extent Mo XXXI (Mg-like) and Mo XVII (Fe-like), have been achieved by comparison with ab initio calculations. A general interpretation of intermediate ion stages is also given but it is shown that most of these spectra are so complex, as a result of inner-subshell excitation, that detailed term-scheme analyses are nearly impossible. (author)

  13. Graphics of diffraction spectra for PC

    International Nuclear Information System (INIS)

    Macias B, L.R.

    1991-09-01

    The materials can be studied by means of diffraction if these are crystalline; of the type of study will depend the technique to apply, the first step is the obtaining of a digital register that allows to build the corresponding spectra. The digital register should have well-known the initial and final angular data. The main objective of this work, is starting of a digital register of data or an arrangement CPSi type (counts per second measured by the detection system) generated by means of the diffractometer, to create the graph of the corresponding spectra in visual form in the screen of a microcomputer and if is required, to obtain the graph in printed form by means of the same computer program for microcomputer. (Author)

  14. Hadronic spectra from collisions of heavy nuclei

    International Nuclear Information System (INIS)

    Jacobs, P.

    1997-03-01

    Hadronic spectra from collisions of heavy ions at ultrarelativistic energies are discussed, concentrating on recent measurements at the SPS of central Pb+Pb collisions at 158 GeV/nucleon, which are compared to collisions of lighter ions and at lower beam energies. Baryon stopping is seen to be larger for heavier systems and lower energies. Total yields of pions and kaons scale with the number of participants in central collisions at the SPS; in particular, the K/π ratio is constant between central S+S and Pb+Pb at the SPS. Transverse mass spectra indicate significantly larger radial flow for the heavier systems. At midrapidity, an enhancement of - >/ + > and - >/ + > at low P T are best explained by final state Coulomb interaction with the residual charge of the fireball

  15. Absorption spectra of AA-stacked graphite

    International Nuclear Information System (INIS)

    Chiu, C W; Lee, S H; Chen, S C; Lin, M F; Shyu, F L

    2010-01-01

    AA-stacked graphite shows strong anisotropy in geometric structures and velocity matrix elements. However, the absorption spectra are isotropic for the polarization vector on the graphene plane. The spectra exhibit one prominent plateau at middle energy and one shoulder structure at lower energy. These structures directly reflect the unique geometric and band structures and provide sufficient information for experimental fitting of the intralayer and interlayer atomic interactions. On the other hand, monolayer graphene shows a sharp absorption peak but no shoulder structure; AA-stacked bilayer graphene has two absorption peaks at middle energy and abruptly vanishes at lower energy. Furthermore, the isotropic features are expected to exist in other graphene-related systems. The calculated results and the predicted atomic interactions could be verified by optical measurements.

  16. XUV spectra of highly ionised molybdenum

    Energy Technology Data Exchange (ETDEWEB)

    Mansfield, M W.D.; Peacock, N J; Smith, C C; Hobby, M G [UKAEA, Abingdon. Culham Lab.; Cowan, R D

    1978-05-14

    The spectra of molybdenum ions produced in Tokamaks in the wavelength range 10-200 A have been reproduced in a plasma formed by laser beam irradiation of solid molybdenum targets. Lines from highly ionised stages of molybdenum (Mo XXX to Mo XXXII) have been distinguished by varying the laser beam intensity. Detailed analyses of the simpler ions, Mo XV (Ni-like), Mo XVI (Co-like), Mo XXXII (Na-like), and to a lesser extent Mo XXXI (Mg-like) and Mo XVII (Fe-like), have been achieved by comparison with ab initio calculations. A general interpretation of intermediate ion stages is also given but it is shown that most of these spectra are so complex, as a result of inner-subshell excitation, that detailed term-scheme analyses are nearly impossible.

  17. Digital dynamic amplitude-frequency spectra analyzer

    International Nuclear Information System (INIS)

    Kalinnikov, V.A.; )

    2006-01-01

    The spectra analyzer is intended for the dynamic spectral analysis of signals physical installations and noise filtering. The recurrence Fourier transformation algorithm is used in the digital dynamic analyzer. It is realized on the basis of the fast logic FPGA matrix and the special signal ADSP microprocessor. The discretization frequency is 2 kHz-10 MHz. The number of calculated spectral coefficients is not less 512. The functional fast-action is 20 ns [ru

  18. Fourier evaluation of broad Moessbauer spectra

    International Nuclear Information System (INIS)

    Vincze, I.

    1981-01-01

    It is shown by the Fourier analysis of broad Moessbauer spectra that the even part of the distribution of the dominant hyperfine interaction (hyperfine field or quadrupole splitting) can be obtained directly without using least-square fitting procedures. Also the odd part of this distribution correlated with other hyperfine parameters (e.g. isomer shift) can be directly determined. Examples for amorphous magnetic and paramagnetic iron-based alloys are presented. (author)

  19. Fourier evaluation of broad Moessbauer spectra

    International Nuclear Information System (INIS)

    Vincze, I.

    1981-09-01

    It is shown by the Fourier analysis of broad Moessbauer spectra that the even part of the distribution of the dominant hyperfine interaction (hyperfine field or quadrupole splitting) can be obtained directly without using least-square fitting procedures. Also the odd part of this distribution correlated with other hyperfine parameters (e.g. isomer shift) can be directly determined. Examples covering the case of amorphous magnetic and paramagnetic iron-based alloys are presented. (author)

  20. Ghost lines in Moessbauer relaxation spectra

    International Nuclear Information System (INIS)

    Price, D.C.

    1985-01-01

    The appearance in Moessbauer relaxation spectra of 'ghost' lines, which are narrow lines that do not correspond to transitions between real hyperfine energy levels of the resonant system, is examined. It is shown that in many cases of interest, the appearance of these 'ghost' lines can be interpreted in terms of the relaxational averaging of one or more of the static interactions of the ion. (orig.)

  1. Automation of the Analysis of Moessbauer Spectra

    International Nuclear Information System (INIS)

    Souza, Paulo A. de Jr.; Garg, R.; Garg, V. K.

    1998-01-01

    In the present report we propose the automation of least square fitting of Moessbauer spectra, the identification of the substance, its crystal structure and the access to the references with the help of a genetic algorith, Fuzzy logic, and the artificial neural network associated with a databank of Moessbauer parameters and references. This system could be useful for specialists and non-specialists, in industry as well as in research laboratories

  2. GRETEL, Ge(Li) Gamma Spectra Unfolding

    International Nuclear Information System (INIS)

    1975-01-01

    1 - Nature of physical problem solved: The program performs the quantitative analysis of gamma-ray spectra obtained by Ge(Li) detectors, using special libraries which are prepared for each particular problem. 2 - Method of solution: The computer routines which detect and evaluate peak areas perform the following operations: - local smoothing of the spectrum; - first derivative of the smoothed spectrum, - peak location according to the change of sign of the first derivative; - computation of the net area of each peak found

  3. Electronic spectra of astrophysically interesting cations

    Energy Technology Data Exchange (ETDEWEB)

    Maier, John P., E-mail: j.p.maier@unibas.ch; Rice, Corey A., E-mail: j.p.maier@unibas.ch; Mazzotti, Fabio J., E-mail: j.p.maier@unibas.ch; Johnson, Anatoly, E-mail: j.p.maier@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstr. 80, CH-4056 Basel (Switzerland)

    2015-01-22

    The electronic spectra of polyacetylene cations were recorded at 20K in the laboratory in an ion trap instrument. These can then be compared with diffuse interstellar band (DIB) absorptions. Examination of recently published data shows that the attribution of a weak DIB at ∼506.9 nm to diacetylene cation is not justified. Study of the higher excited electronic states of polyacetylene cations shows that their widths can still be sufficiently narrow for consideration as DIB carriers.

  4. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  5. The Rovibronic Spectra of the Cyclopentadienyl Radical

    Science.gov (United States)

    Sharma, Ketan; Miller, Terry A.; Stanton, John F.; Nesbitt, David

    2017-06-01

    Cyclopentadienyl (Cp) radical has been subject to numerous studies for the greater part of half a century. Experimental work has involved photo-electron spectroscopy, laser induced fluorescence excitation and emission, infrared absorption spectroscopy, and recently rotationally resolved spectra in the CH stretch region taken at JILA. Even more theoretical works appear in the literature, but substantial advances in computation have occurred since their completion. Cp's highly symmetric (D_{5h}) structure and doubly degenerate electronic ground (˜{X}^2E_1^{''}), which is subject to linear Jahn-Teller distortion, have been a great motivation for work on it. We have commenced new computational work to obtain a broad understanding of the electronic, vibrational, and rotational, i.e. rovibronic, structure of the Cp radical as revealed by its spectra, with particular emphasis on the new infrared spectra. The goal is to guide experiments and their analyses and reconcile results from spectroscopy and quantum chemistry calculations. T. Ichino, et al. J. Chem. Phys. 129, 084310 (2008) L. Yu, S. C. Foster, J. M. Williamson, M. C. Heaven and T. A. Miller J. Phys. Chem. 92, 4263 (1988) B. E. Applegate, A. J. Bezant and T. A. Miller J. Chem. Phys 114, 4869 (2001) D. Leicht, M. Kaufmann, G. Schwaab, and M. Havenith J. Chem. Phys. 145, 7 (2016), 074304.

  6. MAGNETIC ENERGY SPECTRA IN SOLAR ACTIVE REGIONS

    International Nuclear Information System (INIS)

    Abramenko, Valentyna; Yurchyshyn, Vasyl

    2010-01-01

    Line-of-sight magnetograms for 217 active regions (ARs) with different flare rates observed at the solar disk center from 1997 January until 2006 December are utilized to study the turbulence regime and its relationship to flare productivity. Data from the SOHO/MDI instrument recorded in the high-resolution mode and data from the BBSO magnetograph were used. The turbulence regime was probed via magnetic energy spectra and magnetic dissipation spectra. We found steeper energy spectra for ARs with higher flare productivity. We also report that both the power index, α, of the energy spectrum, E(k) ∼ k -α , and the total spectral energy, W = ∫E(k)dk, are comparably correlated with the flare index, A, of an AR. The correlations are found to be stronger than those found between the flare index and the total unsigned flux. The flare index for an AR can be estimated based on measurements of α and W as A = 10 b (αW) c , with b = -7.92 ± 0.58 and c = 1.85 ± 0.13. We found that the regime of the fully developed turbulence occurs in decaying ARs and in emerging ARs (at the very early stage of emergence). Well-developed ARs display underdeveloped turbulence with strong magnetic dissipation at all scales.

  7. VARIABILITY IN OPTICAL SPECTRA OF ε ORIONIS

    International Nuclear Information System (INIS)

    Thompson, Gregory B.; Morrison, Nancy D.

    2013-01-01

    We present the results of a time series analysis of 130 échelle spectra of ε Ori (B0 Ia), acquired over seven observing seasons between 1998 and 2006 at Ritter Observatory. The equivalent widths of Hα (net) and He I λ5876 were measured and radial velocities were obtained from the central absorption of He I λ5876. Temporal variance spectra (TVS) revealed significant wind variability in both Hα and He I λ5876. The He I TVS have a double-peaked profile consistent with radial velocity oscillations. A periodicity search was carried out on the equivalent width and radial velocity data, as well as on wavelength-binned spectra. This analysis has revealed several periods in the variability with timescales of two to seven days. Many of these periods exhibit sinusoidal modulation in the associated phase diagrams. Several of these periods were present in both Hα and He I, indicating a possible connection between the wind and the photosphere. Due to the harmonic nature of these periods, stellar pulsations may be the origin of some of the observed variability. Periods on the order of the rotational period were also detected in the He I line in the 1998-1999 season and in both lines during the 2004-2005 season. These periods may indicate rotational modulation due to structure in the wind.

  8. Secondary charged particle spectra and kerma calculations

    International Nuclear Information System (INIS)

    Coyne, J.J.; Gerstenberg, H.M.; Hennen, L.A.

    1985-01-01

    The calculation of kerma factors from known cross sections is not as simple as is often implied. The kerma factors are strongly influenced by the reaction mechanism assumed. An important example of this dependence on the reaction mechanism is the contribution of the 12 C(n,n')3α reaction to the total kerma in carbon. First, a short review will be given of the ENDF/B-V carbon cross sections which were used in the calculation of carbon kerma factors. Using the reaction channels implied in the ENDF/B-V evaluation, the contribution of various reactions to the total kerma factors in carbon will be given. A detailed analysis of the reaction mechanisms which could contribute to the (n,n')3α reaction in carbon has been carried out. First their contribution to kerma, independent of cross section, will be calculated and then the initial spectra of alpha particles produced by the various reaction mechanisms will be given. A discussion of possible ways of experimentally distinguishing the reaction mechanisms will be made by comparing their different initial spectra and their variation in kerma with neutron energy. Finally, the event-size spectra for tissue-equivalent proportional counters will be presented, giving only the contributions from the (n,n')3α reaction and its various possible reaction channels. 3 refs., 11 figs., 4 tabs

  9. Optical spectra analysis for breast cancer diagnostics

    Science.gov (United States)

    Belkov, S. A.; Kochemasov, G. G.; Lyubynskaya, T. E.; Maslov, N. V.; Nuzhny, A. S.; da Silva, L. B.; Rubenchik, A.

    2011-11-01

    Minimally invasive probe and optical biopsy system based on optical spectra recording and analysis seem to be a promising tool for early diagnostics of breast cancer. Light scattering and absorption spectra are generated continuously as far as the needle-like probe with one emitting and several collecting optical fibers penetrates through the tissues toward to the suspicious area. That allows analyzing not only the state of local site, but also the structure of tissues along the needle trace. The suggested method has the advantages of automated on-line diagnosing and minimal tissue destruction and in parallel with the conventional diagnostic procedures provides the ground for decision-making. 165 medical trials were completed in Nizhny Novgorod Regional Oncology Centre, Russia. Independent diagnoses were the results of fine biopsy and histology. Application of wavelet expansion and clasterization techniques for spectra analysis revealed several main spectral types for malignant and benign tumors. Automatic classification algorithm demonstrated specificity ˜90% and sensitivity ˜91%. Large amount of information, fuzziness in criteria and data noisiness make neural networks to be an attractive analytic tool. The model based on three-layer perceptron was tested over the sample of 29 `cancer' and 29 `non-cancer' cases and demonstrated total separation.

  10. Application of capillary gas chromatography-mass spectrometry to chemical characterization of radiation-induced base damage of DNA: implications for assessing DNA repair processes

    International Nuclear Information System (INIS)

    Dizdaroglu, M.

    1985-01-01

    The application of capillary gas chromatography-mass spectrometry (GC-MS) to the chemical characterization of radiation-induced base products of calf thymus DNA is presented. Samples of calf thymus DNA irradiated in N 2 O-saturated aqueous solution were hydrolyzed with HCOOH, trimethylsilylated, and subjected to GC-MS analysis using a fused-silica capillary column. Hydrolysis conditions suitable for the simultaneous analysis of the radiation-induced products of all four DNA bases in a single run were determined. The trimethylsilyl derivatives of these products had excellent GC properties and easily interpretable mass spectra; an intense molecular ion (M+.) and a characteristic (M-CH 3 )+ ion were observed. The complementary use of t-butyldimethylsilyl derivatives was also demonstrated. These derivatives provided an intense characteristic (M-57)+ ion, which appeared as either the base peak or the second most intense ion in the spectra. All mass spectra obtained are discussed

  11. The study of genomic DNA adsorption and subsequent interactions using total internal reflection ellipsometry.

    Science.gov (United States)

    Nabok, Alexei; Tsargorodskaya, Anna; Davis, Frank; Higson, Séamus P J

    2007-10-31

    The adsorption of genomic DNA and subsequent interactions between adsorbed and solvated DNA was studied using a novel sensitive optical method of total internal reflection ellipsometry (TIRE), which combines spectroscopic ellipsometry with surface plasmon resonance (SPR). Single strands of DNA of two species of fish (herring and salmon) were electrostatically adsorbed on top of polyethylenimine films deposited upon gold coated glass slides. The ellipsometric spectra were recorded and data fitting utilized to extract optical parameters (thickness and refractive index) of adsorbed DNA layers. The further adsorption of single stranded DNA from an identical source, i.e. herring ss-DNA on herring ss-DNA or salmon ss-DNA on salmon ss-DNA, on the surface was observed to give rise to substantial film thickness increases at the surface of about 20-21 nm. Conversely adsorption of DNA from alternate species, i.e. salmon ss-DNA on herring ss-DNA or herring ss-DNA on salmon ss-DNA, yielded much smaller changes in thickness of 3-5 nm. AFM studies of the surface roughness of adsorbed layers were in line with the TIRE data.

  12. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  13. Radiation and DNA

    Energy Technology Data Exchange (ETDEWEB)

    Riabchenko, N I

    1979-01-01

    Consideration is given to the effects of ionizing radiation on the structure of DNA. Physical and chemical methods of determining radiation damage to the primary (polynucleotide chain and nitrogenous base) and secondary (helical) structure of DNA are discussed, and the effects of ionizing radiation on deoxyribonucleoprotein complexes are considered. The radiolysis of DNA in vitro and in bacterial and mammalian cells is examined and cellular mechanisms for the repair of radiation-damaged DNA are considered, taking into account single-strand and double-strand breaks, gamma-radiation damage and deoxyribonucleoprotein-membrane complex damage. Postradiation DNA degradation in bacteria and lymphatic cells is also discussed.

  14. DNA-Mediated Electrochemistry

    Science.gov (United States)

    Gorodetsky, Alon A.; Buzzeo, Marisa C.

    2009-01-01

    The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

  15. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  16. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  17. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

    Science.gov (United States)

    Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

    2017-08-30

    A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

  18. Spectroscopic study on the interaction of eugenol with salmon sperm DNA in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun, E-mail: sy_bi@sina.com [College of Chemistry, Changchun Normal University, Changchun 130032 (China); Yan Lili; Wang Yu; Pang Bong; Wang Tianjiao [College of Chemistry, Changchun Normal University, Changchun 130032 (China)

    2012-09-15

    Fluorescence spectra, absorption spectra, melting temperature, ionic strength effect, and viscosity experiments were described that characterize the interaction of eugenol with salmon sperm DNA in vitro. Eugenol was found to bind but weakly to DNA, with binding constants of 4.23 Multiplication-Sign 10{sup 3}, 3.62 Multiplication-Sign 10{sup 3} and 2.47 Multiplication-Sign 10{sup 3} L mol{sup -1} at 18, 28 and 38 Degree-Sign C respectively. The Stern-Volmer plots at different temperatures suggested that the quenching type of fluorescence of eugenol by DNA was a static quenching. Both the relative viscosity and the melting temperature of DNA were increased by the addition of eugenol. The changes of ionic strength had no affect on the binding. In addition, the binding constant of eugenol with single stranded DNA (ssDNA) was larger than that of eugenol with double stranded DNA (dsDNA). These results revealed that the binding mode of eugenol to DNA was intercalative binding. The thermodynamic parameters {Delta}H, {Delta}G and {Delta}S were also obtained according to the Van't Hoff equations, which suggested that hydrogen bond or van der Waals force might play an important role in a binding of eugenol to DNA. Based on the theory of the Foerster energy transference, the binding distance between DNA and eugenol was determined as 4.40 nm, indicating that the static fluorescence quenching of eugenol by DNA was also a non-radiation energy transfer process. - Highlights: Black-Right-Pointing-Pointer DNA quenched the fluorescence of eugenol. Black-Right-Pointing-Pointer Binding constant, binding site and binding force were determined. Black-Right-Pointing-Pointer Binding mode of eugenol to DNA was intercalative. Black-Right-Pointing-Pointer Energy transfer occurred between eugenol and DNA.

  19. Mutagenesis and cytotoxicity in human epithelial cells by far- and near-ultraviolet radiations: action spectra

    International Nuclear Information System (INIS)

    Jones, C.A.; Huberman, E.; Cunningham, M.L.; Peak, M.J.

    1987-01-01

    Action spectra were determined for cell killing and mutation by monochromatic ultraviolet and visible radiations (254-434 nm) in cultured human epithelial P3 cells. Cell killing was more efficient following radiation at the shorter wavelengths (254-434 nm) than at longer wavelengths (365-434 nm). At 254 nm, for example, a fluence of 11 Jm-2 gave 37% cell survival, while at 365 nm, 17 X 10(5) Jm-2 gave equivalent survival. At 434 nm little killing was observed with fluences up to 3 X 10(6) Jm-2. Mutant induction, determined at the hypoxanthine-guanine phosphoribosyltransferase locus, was caused by radiation at 254, 313, and 365 nm. There was no mutant induction at 334 nm although this wavelength was highly cytotoxic. Mutagenesis was not induced by 434 nm radiation, either. There was a weak response at 405 nm; the mutant frequencies were only slightly increased above background levels. For the mutagenic wavelengths, log-log plots of the mutation frequency against fluence showed linear regressions with positive slopes of 2.5, consistent with data from a previous study using Escherichia coli. The data points of the action spectra for lethality and mutagenesis were similar to the spectrum for DNA damage at wavelengths shorter than 313 nm, whereas at longer wavelengths the lethality spectrum had a shoulder, and the mutagenesis spectrum had a secondary peak at 365 nm. No correlation was observed for the P3 cells between the spectra for cell killing and mutagenesis caused by wavelengths longer than 313 nm and the induction of DNA breakage or the formation of DNA-to-protein covalent bonds in these cells

  20. Core nucleosomes by digestion of reconstructed histone-DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bryan, P N; Wright, E B; Olins, D E

    1979-04-01

    Reconstructed complexes of the inner histones (H2A, H2B, H3, H4) and a variety of DNAs were digested with micrococcal nuclease to yield very homogeneous populations of core nucleosomes (..nu../sub 1/). Nucleosomes containing Micrococcus luteus DNA (72% G+C); chicken DNA (43% G+C), Clostridium perfringens DNA (29% G+C); or poly(dA-dT).poly(dA-dT) have been examined by circular dichroism, thermal denaturation, electron microscopy, and DNAse I digestion. Circular dichroism spectra of all particles show a typically suppressed ellipticity at 260 to 280 nm and a prominent ..cap alpha..-helix signal at 222 nm. All particles show biphasic melting except ..nu../sub 1/(dA-dT), which show three prominent melting transitions at ionic strength less than or equal to 1 mM. DNAse I digestion of ..nu../sub 1/ (dA-dT) produces a ladder of DNA fragments differing in length by one base residue. ..nu../sub 1/ (dA-dT) contain 146 base pairs of DNA and exhibit an average DNA helix pitch of 10.4 to 10.5 bases per turn. There appear to be two regions of different DNA pitch within ..nu../sub 1/ (dA-dT). It is suggested that the two regions of DNA pitch might correspond to the two regions of the melting profiles.

  1. Photon and photoneutron spectra produced in radiotherapy Linacs

    International Nuclear Information System (INIS)

    Vega C, H. R.; Martinez O, S. A.; Benites R, J. L.; Lallena, A. M.

    2011-10-01

    A Monte Carlo calculation, using the MCNPX code, was carried out in order to estimate the photon and neutron spectra in two locations of two linacs operating at 15 and 18 MV. Detailed models of both linac heads were used in the calculations. Spectra were estimated below the flattening filter and at the isocenter. Neutron spectra show two components due to evaporation and knock-on neutrons. Lethargy spectra under the filter were compared to the spectra calculated from the function quoted by Tosi et al. that describes reasonably well neutron spectra beyond 1 MeV, though tends to underestimate the energy region between 10 -6 and 1 MeV. Neutron and Bremsstrahlung spectra show the same features regardless of the linac voltage. The amount of photons and neutrons produced by the 15 MV linac is smaller than that found for the 18 MV linac. As expected, Bremsstrahlung spectra ends according to the voltage used to accelerate the electrons. (Author)

  2. Time-of-flight neutron spectra measurements in Zenith

    Energy Technology Data Exchange (ETDEWEB)

    Barclay, F R; Coates, M S; Diment, K M; Durrani, S A; Gayther, D B; Poole, M J; Reed, D L

    1962-01-15

    Neutron spectra in the second core loading of ZENITH have been measured using a neutron chopper. Spectra at two positions in the reactore core were obtained over a range of temperatures extending to 650 deg C.

  3. Quantum synchrotron spectra from semirelativistic electrons in teragauss magnetic fields

    International Nuclear Information System (INIS)

    Brainerd, J.J.

    1987-01-01

    Synchrotron spectra are calculated from quantum electrodynamic transition rates for thermal and power-law electron distributions. It is shown that quantum effects appear in thermal spectra when the photon energy is greater than the electron temperature, and in power-law spectra when the electron energy in units of the electron rest mass times the magnetic field strength in units of the critical field strength is of order unity. These spectra are compared with spectra calculated from the ultrarelativistic approximation for synchrotron emission. It is found that the approximation for the power-law spectra is good, and the approximation for thermal spectra produces the shape of the spectrum accurately but fails to give the correct normalization. Single photon pair creation masks the quantum effects for power-law distributions, so only modifications to thermal spectra are important for gamma-ray bursts. 13 references

  4. Evaluation of secondary and prompt fission neutron spectra

    Energy Technology Data Exchange (ETDEWEB)

    Porodzinskij, Yu.V.; Sukhovitskij, E.Sh. [Radiation Physics and Chemistry Problems Inst., Minsk-Sosny (Belarus)

    1997-03-01

    A simple model allowing to split neutron emission spectra into reaction partials is suggested. Predicted spectra of (n,n`{gamma}), (n,n`f), etc appear to be much harder than usually evaluated. (author)

  5. Study on Moessbauer spectra of hemoglobin in thalassemia

    International Nuclear Information System (INIS)

    Guo Xuanhui; Zhao Nanming; Zhang Xiufang

    1988-01-01

    The 57 Fe Moessbauer spectra of erythrocytes in normal subjects and nine patients of different thalassemias were studied. Together with clinical analysis, the correlation between the components in the spectra and different types of anemias was discussed. (orig.)

  6. Study on Mössbauer spectra of hemoglobin in thalassemia

    Science.gov (United States)

    Xuanhui, Guo; Nanming, Zhao; Xiufang, Zhang; Naifei, Gao; Youwen, Huang; Rongxin, Wang

    1988-02-01

    The57Fe Mössbauer spectra of erythrocytes in normal subjects and nine patients of different thalassemias were studied. Together with clinical analysis, the correlation between the components in the spectra and different types of anemias was discussed.

  7. Photon and photoneutron spectra produced in radiotherapy Linacs

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H. R. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico); Martinez O, S. A. [Universidad Pedagogica y Tecnologica de Colombia, Grupo de Fisica Nuclear Aplicada y Simulacion, Av. Central del Norte Km. 1, Via Paipa Tunja, Boyaca (Colombia); Benites R, J. L. [Universidad Autonoma de Nayarit, Postgrado CBAP, Carretera Tepic Compostela Km. 9, Xalisco, Nayarit (Mexico); Lallena, A. M., E-mail: fermineutron@yahoo.com [Universida de Granada, Departamento de Fisica Atomica, Molecular y Nuclear, E-18071 Granada (Spain)

    2011-10-15

    A Monte Carlo calculation, using the MCNPX code, was carried out in order to estimate the photon and neutron spectra in two locations of two linacs operating at 15 and 18 MV. Detailed models of both linac heads were used in the calculations. Spectra were estimated below the flattening filter and at the isocenter. Neutron spectra show two components due to evaporation and knock-on neutrons. Lethargy spectra under the filter were compared to the spectra calculated from the function quoted by Tosi et al. that describes reasonably well neutron spectra beyond 1 MeV, though tends to underestimate the energy region between 10{sup -6} and 1 MeV. Neutron and Bremsstrahlung spectra show the same features regardless of the linac voltage. The amount of photons and neutrons produced by the 15 MV linac is smaller than that found for the 18 MV linac. As expected, Bremsstrahlung spectra ends according to the voltage used to accelerate the electrons. (Author)

  8. Theoretical microcontact spectra of metal electron-phonon coupling

    International Nuclear Information System (INIS)

    Kulagina, T.N.; Zhernov, A.P.

    1987-01-01

    Theoretical and experimental microcontact spectra of simple and certain transition metals are discussed. The Eliashberg thermodynamic functions for the metals are considered, as well as correlations between spectra peculiarities and parameters of metals and microbridge models

  9. Development of site specific response spectra

    International Nuclear Information System (INIS)

    Bernreuter, D.L.; Chen, J.C.; Savy, J.B.

    1987-03-01

    For a number of years the US Nuclear Regulatory Commission (NRC) has employed site specific spectra (SSSP) in their evaluation of the adequacy of the Safe Shutdown Earthquake (SSE). These spectra were developed only from the spectra of the horizontal components of the ground motion and from a very limited data set. As the data set has considerably increased for Eastern North America (ENA) and as more relevant data has become available from earthquakes occurring in other parts of the world (e.g., Italy), together with the fact that recent data indicated the importance of the vertical component, it became clear that an update of the SSSP's for ENA was desirable. The methodology used in this study is similar to the previous ones in that it used actual earthquake ground motion data with magnitudes within a certain range and recorded at distances and at sites similar to those that would be chosen for the definition of an SSE. An extensive analysis of the origin and size of the uncertainty is an important part of this study. The results of this analysis of the uncertainties is used to develop criteria for selecting the earthquake records to be used in the derivation of the SSSP's. We concluded that the SSSPs were not very sensitive to the distribution of the source to site distance of the earthquake records used in the analysis. That is, the variability (uncertainty) introduced by the range of distances was relatively small compared to the variability introduced by other factors. We also concluded that the SSSP are somewhat sensitive to the distribution of the magnitudes of these earthquakes, particularly at rock sites and, by inference, at shallow soil sites. We found that one important criterion in selecting records to generate SSSP is the depth of soil at the site

  10. Characterizing Sky Spectra Using SDSS BOSS Data

    Science.gov (United States)

    Florez, Lina Maria; Strauss, Michael A.

    2018-01-01

    In the optical/near-infrared spectra gathered by a ground-based telescope observing very faint sources, the strengths of the emission lines due to the Earth’s atmosphere can be many times larger than the fluxes of the sources we are interested in. Thus the limiting factor in faint-object spectroscopy is the degree to which systematics in the sky subtraction can be minimized. Longwards of 6000 Angstroms, the night-sky spectrum is dominated by multiple vibrational/rotational transitions of the OH radical from our upper atmosphere. While the wavelengths of these lines are the same in each sky spectrum, their relative strengths vary considerably as a function of time and position on the sky. The better we can model their strengths, the better we can hope to subtract them off. We expect that the strength of lines from common upper energy levels will be correlated with one another. We used flux-calibrated sky spectra from the Sloan Digital Sky Survey Baryon Oscillation Spectroscopic Survey (SDSS BOSS) to explore these correlations. Our aim is to use these correlations for creating improved sky subtraction algorithms for the Prime Focus Spectrograph (PFS) on the 8.2-meter Subaru Telescope. When PFS starts gathering data in 2019, it will be the most powerful multi-object spectrograph in the world. Since PFS will be gathering data on sources as faint as 24th magnitude and fainter, it's of upmost importance to be able to accurately measure and subtract sky spectra from the data that we receive.

  11. Prediction of peak overlap in NMR spectra

    International Nuclear Information System (INIS)

    Hefke, Frederik; Schmucki, Roland; Güntert, Peter

    2013-01-01

    Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

  12. Authentication of Fish Products by Large-Scale Comparison of Tandem Mass Spectra

    DEFF Research Database (Denmark)

    Wulff, Tune; Nielsen, Michael Engelbrecht; Deelder, André M.

    2013-01-01

    Authentication of food is a major concern worldwide to ensure that food products are correctly labeled in terms of which animals are actually processed for consumption. Normally authentication is based on species recognition by comparison of selected sequences of DNA or protein. We here present...... a new robust, proteome-wide tandem mass spectrometry method for species recognition and food product authentication. The method does not use or require any genome sequences or selection of tandem mass spectra but uses all acquired data. The experimental steps were performed in a simple, standardized...

  13. Molecular geometry in the ultraviolet absorption spectra

    International Nuclear Information System (INIS)

    Albuquerque, S.F. de; Monteiro, L.S.; Adamis, L.M.B.; Baltar, M.C.P.; Silva, R.M. da

    1977-01-01

    The ultraviolet absorption spectra may be sensibly affected by steric effects. These effects can cause a lot of difficulties and unexpected changes in spectrum. The most general source of such difficulties is steric inhibition of resonance. In addition to this, ultraviolet epectra may be markedly changed by steric factors which change the positions of dipoles in the molecule with respect to each other and by the interaction of nonconjugated chromophores suitably located in space. We have studied in detail each of these effects presenting a lot of usual and importants examples in Organic Chemistry. Others relevants subjects were not considerated in this present work [pt

  14. Maximum entropy decomposition of quadrupole mass spectra

    International Nuclear Information System (INIS)

    Toussaint, U. von; Dose, V.; Golan, A.

    2004-01-01

    We present an information-theoretic method called generalized maximum entropy (GME) for decomposing mass spectra of gas mixtures from noisy measurements. In this GME approach to the noisy, underdetermined inverse problem, the joint entropies of concentration, cracking, and noise probabilities are maximized subject to the measured data. This provides a robust estimation for the unknown cracking patterns and the concentrations of the contributing molecules. The method is applied to mass spectroscopic data of hydrocarbons, and the estimates are compared with those received from a Bayesian approach. We show that the GME method is efficient and is computationally fast

  15. Spectra from foil-excited molybdenum ions

    International Nuclear Information System (INIS)

    Johnson, B.M.; Jones, K.W.; Cecchi, J.L.; Kruse, T.H.

    1978-01-01

    The extreme-ultraviolet spectra (5 to 55 nm) for foil-excited molybdenum ions have been measured using 22 to 200 MeV beams from the Brookhaven National Laboratory MP tandem Van de Graaff accelerator facility, 20 μg/cm 2 C stripping foils, and a grazing incidence spectrometer. The mean ion charge states (13 to 28) and the narrow distribution widths (about 2 charge states) were accurately predictable from experimental parameters. Where possible, comparisons are given with Mo radiation from tokamaks, vacuum sparks, and laser-excited plasmas

  16. Perturbative description of inclusive energy spectra

    Energy Technology Data Exchange (ETDEWEB)

    Lupia, S. [Max-Planck-Institut fuer Physik, Muenchen (Germany). Werner-Heisenberg-Institut

    1996-03-01

    The recent LEP-1.5 data of charged particle inclusive energy spectra are analyzed within the analytical QCD approach based on modified leading log approximation plus local parton hadron duality. The shape, the position of the maximum and the cumulant moments of the inclusive energy spectrum are well described within this model. The sensitivity of the results to the running of the coupling is pointed out. A scaling law for the one-particle invariant density E dn/d{sup 3}p at small momenta is observed, consistently with the predictions of colour coherence in soft gluon bremsstrahlung. (orig.).

  17. Perturbative description of inclusive energy spectra

    International Nuclear Information System (INIS)

    Lupia, S.

    1996-01-01

    The recent LEP-1.5 data of charged particle inclusive energy spectra are analyzed within the analytical QCD approach based on modified leading log approximation plus local parton hadron duality. The shape, the position of the maximum and the cumulant moments of the inclusive energy spectrum are well described within this model. The sensitivity of the results to the running of the coupling is pointed out. A scaling law for the one-particle invariant density E dn/d 3 p at small momenta is observed, consistently with the predictions of colour coherence in soft gluon bremsstrahlung. (orig.)

  18. Process and apparatus for determining molecular spectra

    International Nuclear Information System (INIS)

    Boesl, U.; Neusser, H.J.; Schlag, E.W.

    1984-01-01

    A process for determining molecular spectra in unseparated mixtures, in particular unseparated isotopic mixtures, which comprises allowing said mixture to successively flow through a photoreactor which is irradiated by an adjustable-wavelength laser and then through a mass spectrometer wherein the concentration of particles of specified mass is determined by variation of the wavelength of the laser or variation of the mass setting of the mass spectrometer in such a manner that a two-dimensional spectrum results having the parameters of wavelength and mass

  19. Multifractal spectra in homogeneous shear flow

    Science.gov (United States)

    Deane, A. E.; Keefe, L. R.

    1988-01-01

    Employing numerical simulations of 3-D homogeneous shear flow, the associated multifractal spectra of the energy dissipation, scalar dissipation and vorticity fields were calculated. The results for (128) cubed simulations of this flow, and those obtained in recent experiments that analyzed 1- and 2-D intersections of atmospheric and laboratory flows, are in some agreement. A two-scale Cantor set model of the energy cascade process which describes the experimental results from 1-D intersections quite well, describes the 3-D results only marginally.

  20. Inelastic response spectra of simple degrading systems

    International Nuclear Information System (INIS)

    Andreaus, U.; Ceradini, G.; D'Asdia, P.; Gaudenzi, P.

    1985-01-01

    Ductility was first stated, for single-degree-of-freedom elastic-perfectly plastic systems as the ratio of maximum to yield displacements. An alternative approach, aimed to reduce design forces for ductile structures and based on the energy dissipated during earthquake allows to obtain more reliable ductility factors even when system restoring characteristics are affected by deterioration during loading history. Inelastic response of SDOF systems has been investigated under seimic excitation, assuming stable and degrading constitutive laws to model their structural behaviour. Energy spectra and ductility requirent diagrams are generated and compared with those of the corresponding elastic-perfectly plastic systems. (orig.)

  1. Beamstrahlung spectra in next generation linear colliders

    Energy Technology Data Exchange (ETDEWEB)

    Barklow, T.; Chen, P. (Stanford Linear Accelerator Center, Menlo Park, CA (United States)); Kozanecki, W. (DAPNIA-SPP, CEN-Saclay (France))

    1992-04-01

    For the next generation of linear colliders, the energy loss due to beamstrahlung during the collision of the e{sup +}e{sup {minus}} beams is expected to substantially influence the effective center-of-mass energy distribution of the colliding particles. In this paper, we first derive analytical formulae for the electron and photon energy spectra under multiple beamstrahlung processes, and for the e{sup +}e{sup {minus}} and {gamma}{gamma} differential luminosities. We then apply our formulation to various classes of 500 GeV e{sup +}e{sup {minus}} linear collider designs currently under study.

  2. Exclusion Statistics in Conformal Field Theory Spectra

    International Nuclear Information System (INIS)

    Schoutens, K.

    1997-01-01

    We propose a new method for investigating the exclusion statistics of quasiparticles in conformal field theory (CFT) spectra. The method leads to one-particle distribution functions, which generalize the Fermi-Dirac distribution. For the simplest SU(n) invariant CFTs we find a generalization of Gentile parafermions, and we obtain new distributions for the simplest Z N -invariant CFTs. In special examples, our approach reproduces distributions based on 'fractional exclusion statistics' in the sense of Haldane. We comment on applications to fractional quantum Hall effect edge theories. copyright 1997 The American Physical Society

  3. Far-infrared spectra of acetanilide revisited

    Science.gov (United States)

    Spire, A.; Barthes, M.; Kellouai, H.; De Nunzio, G.

    2000-03-01

    A new investigation of the temperature dependence of the far-infrared spectra of acetanilide and some isotopomers is presented. Four absorption bands are considered at 31, 42, 64, and 80 cm-1, and no significant change of their integrated intensity is observed when reducing the temperature. The temperature induced frequency shift values and other properties of these bands are consistent with an assignment as anharmonic lattice phonons. These results rule out the assignment of the 64, 80, and 106 cm-1 bands as normal modes of the polaronic excitation, as previously suggested.

  4. SIMULATION OF PARTICLE SPECTRA AT RHIC

    International Nuclear Information System (INIS)

    KAHANA, D.E.; KAHANA, S.H.

    2001-01-01

    A purely hadronic simulation is performed of the recently reported data from PHOBOS at energies of √s = 56, 130 GeV using the relativistic heavy ion cascade LUCIFER which had previously given a good description of the NA49 inclusive spectra at √s = 17.2 GeV/A. The results compare well with these early measurements at RHIC and indeed successfully predict the increase in multiplicity now seen by PHOBOS and the other RHIC detectors at the nominal maximum energy of √s = 200 GeV/A, suggesting that evidence for quark-gluon matter remains elusive

  5. Boundary layer heights derived from velocity spectra

    Energy Technology Data Exchange (ETDEWEB)

    Hoejstrup, J.; Barthelmie, R.J. [Risoe National Lab., Roskilde (Denmark); Kaellstrand, B. [Univ. of Uppsala, Uppsala (Sweden)

    1997-10-01

    It is a well-known fact that the height of the mixed layer determines the size of the largest and most energetic eddies that can be observed in the unstable boundary layer, and consequently a peak can be observed in the power spectra of the along-wind velocity component at scales comparable to the mixed layer depth. We will now show how the mixed layer depth can be derived from the u-specta and the results will be compared with direct measurements using pibal and tethersonde measurements. (au)

  6. Photographic infrared spectra of symbiotic stars

    International Nuclear Information System (INIS)

    Andrillat, Y.; Houziaux, L.

    1982-01-01

    The authors have observed six symbiotic stars during the period 1962-1977 with a grating spectrograph attached to the newtonian focus of the 120-cm telescope at Observatoire de Haute Provence. The reciprocal dispersion is 230 A.mm -1 and the region 5800 to 8800 A has been covered using hypersensitized IN plates. The minimum equivalent width for an emission line to be seen is about 0.5 A. The spectra are displayed and the main spectral characteristics are reviewed briefly. (Auth.)

  7. Beyond DNA repair: DNA-PK function in cancer

    OpenAIRE

    Goodwin, Jonathan F.; Knudsen, Karen E.

    2014-01-01

    The DNA-dependent protein kinase (DNA-PK) is a pivotal component of the DNA repair machinery that governs the response to DNA damage, serving to maintain genome integrity. However, the DNA-PK kinase component was initially isolated with transcriptional complexes, and recent findings have illuminated the impact of DNA-PK-mediated transcriptional regulation on tumor progression and therapeutic response. DNA-PK expression has also been correlated with poor outcome in selected tumor types, furthe...

  8. Non-B DNA-forming sequences and WRN deficiency independently increase the frequency of base substitution in human cells

    DEFF Research Database (Denmark)

    Bacolla, Albino; Wang, Guliang; Jain, Aklank

    2011-01-01

    Although alternative DNA secondary structures (non-B DNA) can induce genomic rearrangements, their associated mutational spectra remain largely unknown. The helicase activity of WRN, which is absent in the human progeroid Werner syndrome, is thought to counteract this genomic instability. We dete...

  9. Raman microspectroscopic study on low-pH-induced DNA structural transitions in the presence of magnesium ions

    NARCIS (Netherlands)

    Muntean, C.M.; Puppels, G.J.; Greve, Jan; Segers-Nolten, Gezina M.J.; Cinta-Pinzaru, S.

    2002-01-01

    Low-pH-induced DNA structural changes were investigated in the pH range 6.8-2.10 by Raman microspectroscopy. Measurements were carried out on calf thymus DNA in the presence of low concentrations of Mg2+ ions. Vibrational spectra are presented in the wavenumber region 500-1650 cm-1. Large changes in

  10. Photorepair of UV damage to DNA: purification and properties of DNA photolyase (the DNA-photoreactivating enzyme). Progress report, August 1, 1975--July 31, 1976

    International Nuclear Information System (INIS)

    Werbin, H.

    1976-01-01

    Progress is reported on the following research projects: separation of photolyase subunits by sucrose gradient sedimentation; determination of whether fluorescent material is the chromophore for photolyase; studies on tryptophane and lysine residues to determine whether these are involved in the binding and photolytic steps; nmr spectrum of activator of photolyase; damage to pea chromatin by solar near uv and repair of damage; tryptophan residues in yeast DNA photolyase; photolyase in pea seedlings; and nuclear magnetic resonance spectra of purified activator

  11. The use of synthetic spectra to test the preparedness to evaluate and analyze complex gamma spectra

    International Nuclear Information System (INIS)

    Nikkinen, M

    2001-10-01

    This is the report of two exercises that were run under the NKS BOK-1.1 sub-project. In these exercises synthetic gamma spectra were developed to exercise the analysis of difficult spectra typically seen after a severe nuclear accident. The spectra were analyzed twice; first, participants were given short time to give results to resemble an actual emergency preparedness situation, then a longer period of time was allowed to tune the laboratory analysis results for quality assurance purposes. The exercise did prove that it is possible to move measurement data from one laboratory to another if second opinion of the analysis is needed. It was also felt that this kind of exercise would enhance the experience the laboratories have in analyzing accident data. Participants expressed the need for additional exercises of this type, this is inexpensive and an easy way to exercise quick emergency response situations not normally seen in daily laboratory routines. (au)

  12. Vibronic spectra of Gd3+ in metaphosphate glasses: Comparison with Raman and infrared spectra

    International Nuclear Information System (INIS)

    Hall, D.W.; Brawer, S.A.; Weber, M.J.

    1982-01-01

    Vibronic sidebands associated with the 6 P/sub 7/2/→ 8 S/sub 7/2/ transition of Gd 3+ -doped metaphosphate glasses are observed using line-narrowed fluorescence techniques. Glasses having metal cations of different mass and charge (La,Al,Mg,Ba) are examined. Vibronic spectra, which probe vibrations about the rare-earth element site, are compared with polarized Raman scattering data and the infrared dielectric constant obtained from near-normal reflectance measurements. Results indicate that in metaphosphate glasses vibronic selection rules are similar to HV (vertical height) Raman selection rules. The wavelengths and relative intensities of peaks in the high-frequency portion of the vibronic spectra change with respect to corresponding peaks in the Raman spectra when the mass and/or charge of Gd 3+ differs significantly from that of the metal cation

  13. Hole transfer in DNA studied by pulse radiolysis

    International Nuclear Information System (INIS)

    Majima, T.; Kawai, K.; Takada, T.

    2003-01-01

    Attention has been paid to charge transfer in DNA with respect to oxidation damage of DNA and nano bio-devices such as DNA molecular wire. We report hole transfer in DNA during pulse radiolysis of molecule-conjugated DNA (M-DNA). Direct measurement of the charge transfer in DNA has never been reported due to the low extinction coefficient of nucleobase radical ions and to difficult definition of nucleobases. We have used M-DNA in which M radical cation has enough extinction coefficient and distinct absorption. Radical cation was generated in M-DNA during pulse radiolysis in water, and hole transfer through DNA was monitored by time-resolved transient absorption spectra of the radical cations. Hole was generated in Py-DNA by pulse radiolysis in water. Hole transfer to Py through DNA was monitored by transient absorption of Py'+ at 465 nm. The hole hopping rate (k) from G-region to Py was determined to be 104 s-1 which decreased with intervening A-T base-pairs between Py and G-region. We suppose that G(-H+)-radical and C(+H+) basepair can alive in DNA more than 100 us and that this long lifetime is responsible to the long-distance hole transfer. The dependence of k against the distance between the G-region and Py led to the slope of 0.3 Angstroms-1 which is due to multi-step k with the smaller distance dependence. On the other hand, beta = 0.6 Angstroms-1 was found for the single-step k in DNA. On the basis of pulse radiolytic studied on various molecule-conjugated DNA, we found that hole transfer between two chromophores (A and B)-conjugated DNA increased with decreasing the distance between A and B and was accelerated slightly with increasing the number of Gs of the bridge between A and B, and that k was modulated by the bridged base sequences. We also found that weak distance dependent hole transfer in DNA by adenine hopping mechanism

  14. Generate floor response spectra, Part 2: Response spectra for equipment-structure resonance

    International Nuclear Information System (INIS)

    Li, Bo; Jiang, Wei; Xie, Wei-Chau; Pandey, Mahesh D.

    2015-01-01

    Highlights: • The concept of tRS is proposed to deal with tuning of equipment and structures. • Established statistical approaches for estimating tRS corresponding to given GRS. • Derived a new modal combination rule from the theory of random vibration. • Developed efficient and accurate direct method for generating floor response spectra. - Abstract: When generating floor response spectra (FRS) using the direct spectra-to-spectra method developed in the companion paper, probability distribution of t-response spectrum (tRS), which deals with equipment-structure resonance or tuning, corresponding to a specified ground response spectrum (GRS) is required. In this paper, simulation results using a large number of horizontal and vertical ground motions are employed to establish statistical relationships between tRS and GRS. It is observed that the influence of site conditions on horizontal statistical relationships is negligible, whereas the effect of site conditions on vertical statistical relationships cannot be ignored. Considering the influence of site conditions, horizontal statistical relationship suitable for all site conditions and vertical statistical relationships suitable for hard sites and soft sites, respectively, are established. The horizontal and vertical statistical relationships are suitable to estimate tRS for design spectra in USNRC R.G. 1.60 and NUREG/CR-0098, Uniform Hazard Spectra (UHS) in Western North America (WNA), or any GRS falling inside the valid coverage of the statistical relationship. For UHS with significant high frequency spectral accelerations, such as UHS in Central and Eastern North America (CENA), an amplification ratio method is proposed to estimate tRS. Numerical examples demonstrate that the statistical relationships and the amplification ratio method are acceptable to estimate tRS for given GRS and to generate FRS using the direct method in different practical situations.

  15. Generate floor response spectra, Part 2: Response spectra for equipment-structure resonance

    Energy Technology Data Exchange (ETDEWEB)

    Li, Bo, E-mail: b68li@uwaterloo.ca; Jiang, Wei, E-mail: w46jiang@uwaterloo.ca; Xie, Wei-Chau, E-mail: xie@uwaterloo.ca; Pandey, Mahesh D., E-mail: mdpandey@uwaterloo.ca

    2015-11-15

    Highlights: • The concept of tRS is proposed to deal with tuning of equipment and structures. • Established statistical approaches for estimating tRS corresponding to given GRS. • Derived a new modal combination rule from the theory of random vibration. • Developed efficient and accurate direct method for generating floor response spectra. - Abstract: When generating floor response spectra (FRS) using the direct spectra-to-spectra method developed in the companion paper, probability distribution of t-response spectrum (tRS), which deals with equipment-structure resonance or tuning, corresponding to a specified ground response spectrum (GRS) is required. In this paper, simulation results using a large number of horizontal and vertical ground motions are employed to establish statistical relationships between tRS and GRS. It is observed that the influence of site conditions on horizontal statistical relationships is negligible, whereas the effect of site conditions on vertical statistical relationships cannot be ignored. Considering the influence of site conditions, horizontal statistical relationship suitable for all site conditions and vertical statistical relationships suitable for hard sites and soft sites, respectively, are established. The horizontal and vertical statistical relationships are suitable to estimate tRS for design spectra in USNRC R.G. 1.60 and NUREG/CR-0098, Uniform Hazard Spectra (UHS) in Western North America (WNA), or any GRS falling inside the valid coverage of the statistical relationship. For UHS with significant high frequency spectral accelerations, such as UHS in Central and Eastern North America (CENA), an amplification ratio method is proposed to estimate tRS. Numerical examples demonstrate that the statistical relationships and the amplification ratio method are acceptable to estimate tRS for given GRS and to generate FRS using the direct method in different practical situations.

  16. Comparison of fish-community size spectra based on length ...

    African Journals Online (AJOL)

    Estimates of fish-community size spectra are promising indicators of the impact of fishing on fish assemblages. Size spectra consist of logarithmic graphs of abundance plotted against fish body size. Size spectra may either be constructed from length frequency data or estimated from the mean sizes and abundances of the ...

  17. Radiation-induced luminescence from dry and hydrated DNA and related macromolecules

    International Nuclear Information System (INIS)

    Al-Kazwini, A.T.; O'Neill, P.; Fielden, E.M.; Adams, G.E.

    1988-01-01

    The radiation-induced luminescence from three types of fibrous DNA and a series of polydeoxynucleotides was measured under vacuum or in the presence of oxygen at 77 and 293K. The in-pulse emission spectra, generated by electrons with energies 50% water by wt (1.2:1 w/w, H 2 O/DNA), the in-pulse luminescence spectrum is similar to that of dry DNA. These findings are discussed in terms of energy or charge migration induced in DNA upon irradiation and the possible effects of conformational changes, caused by hydration, on charge migration. (author)

  18. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  19. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  20. Automated element identification for EDS spectra evaluation using quantification and integrated spectra simulation approaches

    International Nuclear Information System (INIS)

    Eggert, F

    2010-01-01

    This work describes first real automated solution for qualitative evaluation of EDS spectra in X-ray microanalysis. It uses a combination of integrated standardless quantitative evaluation, computation of analytical errors to a final uncertainty, and parts of recently developed simulation approaches. Multiple spectra reconstruction assessments and peak searches of the residual spectrum are powerful enough to solve the qualitative analytical question automatically for totally unknown specimens. The integrated quantitative assessment is useful to improve the confidence of the qualitative analysis. Therefore, the qualitative element analysis becomes a part of integrated quantitative spectrum evaluation, where the quantitative results are used to iteratively refine element decisions, spectrum deconvolution, and simulation steps.

  1. Mapping SOC in a river catchment by integrating laboratory spectra wavelength with remote sensing spectra

    DEFF Research Database (Denmark)

    Peng, Yi; Xiong, Xiong; Knadel, Maria

    There is potential to use soil ·-proximal and remote sensing derived spectra concomitantly to develop soil organic carbon (SOC) models. Yet mixing spectral data from different sources and technologies to improve soil models is still in its infancy. The objective of this study was to incorporate...... soil spectral features indicative of SOC from laboratory visible near-infrared reflectance (vis-NlR) spectra and incorporate them with remote sensing (RS) images to improve predictions of top SOC in the Skjem river catchment, Denmark. The secondary objective was to improve prediction results...

  2. DNA-based machines.

    Science.gov (United States)

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

  3. DNA repair and cancer

    International Nuclear Information System (INIS)

    Rathore, Shakuntla; Joshi, Pankaj Kumar; Gaur, Sudha

    2012-01-01

    DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecule that encode it's genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many one million individual molecular lesions per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions include potentially harmful mutation in cell's genome which affect the survival of it's daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. Inherited mutation that affect DNA repair genes are strongly associated with high cancer risks in humans. Hereditary non polyposis colorectal cancer (HNPCC) is strongly associated with specific mutation in the DNA mismatch repair pathway. BRCA1, BRCA2 two famous mutation conferring a hugely increased risk of breast cancer on carrier, are both associated with a large number of DNA repair pathway, especially NHEJ and homologous recombination. Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the capacity of the cell to repair DNA damage, resulting in cell death. Cells that are most rapidly dividing most typically cancer cells are preferentially affected. The side effect is that other non-cancerous but rapidly dividing cells such as stem cells in the bone marrow are also affected. Modern cancer treatment attempt to localize the DNA damage to cells and tissue only associated with cancer, either by physical means (concentrating the therapeutic agent in the region of the tumor) or by biochemical means (exploiting a feature unique to cancer cells in the body). (author)

  4. On statistical fluctuations in the dibaryon spectra

    International Nuclear Information System (INIS)

    Bazhanskij, I.I.; Luk'yanov, V.K.; Reznik, B.L.; Titov, A.I.

    1988-01-01

    The aim of this report is to show, that idea about statistical nature of dibaryon resonances corresponds to the present experimental data. Condition for cross section fluctuation occurrence is linked with value of decay width for isolated dibaryon in nucleon channel. Γ in terms of dibaryon potential quark model and q 6 → NN dibaryon decay for q 6 state with S 6 orbital symmetry and (S=I, I=0) deuteron quantum numbers are calculated as an example. np → ppπ - , dp → ppn and elastic pp-scattering are considered and distributions of cross sections and correlation functions obtained from these reactions are presented to investigate cross section fluctuations in spectra of effective masses of two-nucleon systems. Supposition about fluctuation pattern does not contradict the experiment. Curves, calculated with x l α < or approx. 0.05 partial amplitude parameter and full width of Γ < or approx. 20 MeV dibaryon resonances comply to the present experiment best. Fluctuation peculiarities -peaks in cross sections have approximately the same energy width (Γ ∼ 15-20 MeV) as the observed narrow peak in effective mass spectra of some reactions. 16 refs.; 3 figs

  5. [Fluorescence spectra analysis of the scrophularia soup].

    Science.gov (United States)

    Yan, Li-hua; Song, Feng; Han, Juan; Su, Jing; Qu, Fei-fei; Song, Yi-zhan; Hu, Bo-lin; Tian, Jian-guo

    2008-08-01

    The cold-water and boiled-water soaked scrophularia soups have been prepared. The emission and excitation spectra of each scrophularia soup under different conditions have been measured at room temperature. The pH values of the different scrophularia soups have been also detected. There are obvious differences between the cold-water soaked scrophularia soup and the boiled-water soaked scrophularia. For both soups the emission wavelength increases with the wavelength of the excitation, but the peaks of the emission spectra for cold-water and boiled-water soaked scrophularia soup are different, which are 441 and 532 nm, respectively. Excitation spectrum has double peaks in the cold-water soaked scrophularia soup while only one peak with longer wavelength in the boiled-water soaked one. The pH value changes from 5.5 to 4.1. According to the organic admixture fluorescence mechanism we analyzed the reasons of the experimental results. Through heating, the interaction in different fluorescence molecular and the energy transfer process in the same fluorescence molecular become more active, and the conjugate structures and the generation of hydrogen bonds, increase. The fluorescence measurement is of value for the scrophularia pharmacology analysis and provides an analytical method for the quality identification of scrophularia soup.

  6. Primordial spectra from sudden turning trajectory

    Science.gov (United States)

    Noumi, Toshifumi; Yamaguchi, Masahide

    2013-12-01

    Effects of heavy fields on primordial spectra of curvature perturbations are discussed in inflationary models with a sudden turning trajectory. When heavy fields are excited after the sudden turn and oscillate around the bottom of the potential, the following two effects are generically induced: deformation of the inflationary background spacetime and conversion interactions between adiabatic and isocurvature perturbations, both of which can affect the primordial density perturbations. In this paper, we calculate primordial spectra in inflationary models with sudden turning potentials taking into account both of the two effects appropriately. We find that there are some non-trivial correlations between the two effects in the power spectrum and, as a consequence, the primordial scalar power spectrum has a peak around the scale exiting the horizon at the turn. Though both effects can induce parametric resonance amplifications, they are shown to be canceled out for the case with the canonical kinetic terms. The peak feature and the scale dependence of bispectra are also discussed.

  7. Interstellar dehydrogenated PAH anions: vibrational spectra

    Science.gov (United States)

    Buragohain, Mridusmita; Pathak, Amit; Sarre, Peter; Gour, Nand Kishor

    2018-03-01

    Interstellar polycyclic aromatic hydrocarbon (PAH) molecules exist in diverse forms depending on the local physical environment. Formation of ionized PAHs (anions and cations) is favourable in the extreme conditions of the interstellar medium (ISM). Besides in their pure form, PAHs are also likely to exist in substituted forms; for example, PAHs with functional groups, dehydrogenated PAHs etc. A dehydrogenated PAH molecule might subsequently form fullerenes in the ISM as a result of ongoing chemical processes. This work presents a density functional theory (DFT) calculation on dehydrogenated PAH anions to explore the infrared emission spectra of these molecules and discuss any possible contribution towards observed IR features in the ISM. The results suggest that dehydrogenated PAH anions might be significantly contributing to the 3.3 μm region. Spectroscopic features unique to dehydrogenated PAH anions are highlighted that may be used for their possible identification in the ISM. A comparison has also been made to see the size effect on spectra of these PAHs.

  8. Blind Source Separation For Ion Mobility Spectra

    International Nuclear Information System (INIS)

    Marco, S.; Pomareda, V.; Pardo, A.; Kessler, M.; Goebel, J.; Mueller, G.

    2009-01-01

    Miniaturization is a powerful trend for smart chemical instrumentation in a diversity of applications. It is know that miniaturization in IMS leads to a degradation of the system characteristics. For the present work, we are interested in signal processing solutions to mitigate limitations introduced by limited drift tube length that basically involve a loss of chemical selectivity. While blind source separation techniques (BSS) are popular in other domains, their application for smart chemical instrumentation is limited. However, in some conditions, basically linearity, BSS may fully recover the concentration time evolution and the pure spectra with few underlying hypothesis. This is extremely helpful in conditions where non-expected chemical interferents may appear, or unwanted perturbations may pollute the spectra. SIMPLISMA has been advocated by Harrington et al. in several papers. However, more modern methods of BSS for bilinear decomposition with the restriction of positiveness have appeared in the last decade. In order to explore and compare the performances of those methods a series of experiments were performed.

  9. Beta-energy averaging and beta spectra

    International Nuclear Information System (INIS)

    Stamatelatos, M.G.; England, T.R.

    1976-07-01

    A simple yet highly accurate method for approximately calculating spectrum-averaged beta energies and beta spectra for radioactive nuclei is presented. This method should prove useful for users who wish to obtain accurate answers without complicated calculations of Fermi functions, complex gamma functions, and time-consuming numerical integrations as required by the more exact theoretical expressions. Therefore, this method should be a good time-saving alternative for investigators who need to make calculations involving large numbers of nuclei (e.g., fission products) as well as for occasional users interested in restricted number of nuclides. The average beta-energy values calculated by this method differ from those calculated by ''exact'' methods by no more than 1 percent for nuclides with atomic numbers in the 20 to 100 range and which emit betas of energies up to approximately 8 MeV. These include all fission products and the actinides. The beta-energy spectra calculated by the present method are also of the same quality

  10. Spectra of γ rays feeding superdeformed bands

    International Nuclear Information System (INIS)

    Lauritsen, T.; Khoo, T.L.; Henry, R.G.

    1995-01-01

    The spectrum of γrays coincident with SD transitions contains the transitions which populate the SD band. This spectrum can provide information on the feeding mechanism and on the properties (moment of inertia, collectivity) of excited SD states. We used a model we developed to explain the feeding of SD bands, to calculate the spectrum of feeding γrays. The Monte Carlo simulations take into account the trigger conditions present in our Eurogam experiment. Both experimental and theoretical spectra contain a statistical component and a broad E2 peak (from transitions occurring between excited states in the SD well). There is good resemblance between the measured and calculated spectra although the calculated multiplicity of an E2 bump is low by ∼30%. Work is continuing to improve the quality of the fits, which will result in a better understanding of excited SD states. In addition, a model for the last steps, which cool the γ cascade into the SD yrast line, needs to be developed. A strong M1/E2 low-energy component, which we believe is responsible for this cooling, was observed

  11. Low resolution infrared spectra of quasars

    International Nuclear Information System (INIS)

    Soifer, B.T.; Neugebauer, G.; Oke, J.B.; Matthews, K.

    1980-01-01

    Low resolution spectra of a significant sample of quasars show that the Paschen α and Balmer line ratios do not agree with the radiative recombination case B result and vary widely within the quasars sampled. The range in Pα:Hβ ratios is a factor of approximately 6, while the range in Lyα:Hα ratios is a factor of approximately 5. For the Pα:Balmer series, the deviations from case B recombination are not consistent with reddening, but appear, within large dispersions, to be consistent with optical depth effects in the Balmer lines affecting the line ratios. The Lyα:Hα ratio is, however, correlated with the continuum spectral index, and can be explained as due to reddening affecting both the lines and continuum. Recent observational results based on a joint infrared/optical survey of the hydrogen line spectra of a significant number of the brightest low and high redshift quasars are summarised. This survey includes 12 quasars in the redshift range 0.07 1.5, where Hα and/or Hβ is redshifted into the 1.65μm or 2.2μm atmospheric windows. (Auth.)

  12. Continuous particle spectra and their angular distributions

    International Nuclear Information System (INIS)

    Sastry, Ch.V.; Jain, R.K.; Rama Rao, J.; Ernst, J.; Machner, H.

    1996-01-01

    The angular distribution of continuous particle spectra in pre-equilibrium reactions is still an unsolved problem, particularly so at forward angles. In the present work, the angular distributions of alpha particles emitted in (α, α',x) reactions in the target elements gold and rhodium have been studied in detail. Alpha particle beams of energy 60 MeV from the Variable Energy Cyclotron of Calcutta were used in these experiments. The theoretical calculations were done using an extended exciton model of Kalbach incorporated into the Computer Code PRECO-D2. The formalism used in the exciton model was modified to include division of pre equilibrium cross section into multi-step direct (MSD) and multi-step compound (MSC) components. These MSD and MSC cross sections were used to calculate the angular distributions in terms of Legendre polynomials whose coefficients are given by simple phenomenological relations. Even with a reasonable set of parameters, the agreement between theory and experiment was far from satisfactory at forward angles. Similar conclusion was also drawn in the case of continuous particle spectra of deuterons in (d, d'x) reactions at 25 MeV in various targets. (author). 10 refs., 2 figs

  13. Fourier transform spectra of quantum dots

    Science.gov (United States)

    Damian, V.; Ardelean, I.; Armăşelu, Anca; Apostol, D.

    2010-05-01

    Semiconductor quantum dots are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. These nanocrystals absorb light over a very broad spectral range as compared to molecular fluorophores which have very narrow excitation spectra. High-quality QDs are proper to be use in different biological and medical applications (as fluorescent labels, the cancer treatment and the drug delivery). In this article, we discuss Fourier transform visible spectroscopy of commercial quantum dots. We reveal that QDs produced by Evident Technologies when are enlightened by laser or luminescent diode light provides a spectral shift of their fluorescence spectra correlated to exciting emission wavelengths, as shown by the ARCspectroNIR Fourier Transform Spectrometer. In the final part of this paper we show an important biological application of CdSe/ZnS core-shell ODs as microbial labeling both for pure cultures of cyanobacteria (Synechocystis PCC 6803) and for mixed cultures of phototrophic and heterotrophic microorganisms.

  14. Spectra of {gamma} rays feeding superdeformed bands

    Energy Technology Data Exchange (ETDEWEB)

    Lauritsen, T.; Khoo, T.L.; Henry, R.G. [and others

    1995-08-01

    The spectrum of {gamma}rays coincident with SD transitions contains the transitions which populate the SD band. This spectrum can provide information on the feeding mechanism and on the properties (moment of inertia, collectivity) of excited SD states. We used a model we developed to explain the feeding of SD bands, to calculate the spectrum of feeding {gamma}rays. The Monte Carlo simulations take into account the trigger conditions present in our Eurogam experiment. Both experimental and theoretical spectra contain a statistical component and a broad E2 peak (from transitions occurring between excited states in the SD well). There is good resemblance between the measured and calculated spectra although the calculated multiplicity of an E2 bump is low by {approximately}30%. Work is continuing to improve the quality of the fits, which will result in a better understanding of excited SD states. In addition, a model for the last steps, which cool the {gamma} cascade into the SD yrast line, needs to be developed. A strong M1/E2 low-energy component, which we believe is responsible for this cooling, was observed.

  15. Radio spectra of pulsars. Pt. 1

    International Nuclear Information System (INIS)

    Izekova, V.A.; Kuzmin, A.D.; Malofeev, V.M.; Shitov, Yu.P.

    1981-01-01

    The results of flux pulsar radioemission measurements at meter wavelength, made at Pushchino Radio Astronomical Observatory of the Lebedev Physical Institute, are presented. Flux densities at 102, 85, 61 and 39 MHz have been measured for 85, 29, 37 and 23 pulsars correspondingly. Some of them were performed at all frequencies simultaneously. On the basis of these data and high frequencies data obtained by other authors, spectra of 52 pulsars were plotted. In practically all investigated pulsars we have detected a turn-over frequency at which the flux density of pulsar radioemission attained its maximum. Its mean value is vsub(m) = 130 +- 80 MHz. Averaged on many pulsars, the spectral index is negative in the 39-61 MHz frequency range (anti ALPHA 39 sub(-) 61 = -1.4 +- 0.4) and passes through zero at frequencies of about 100 MHz, becoming positive in the 100-400 MHz frequency range. It was noticed that the spectral index in the 100-400 MHz interval depends upon such pulsar periods as α 100 sub(-) 400 = 0.7 log p + 0.9. Using the spectra, more precise radio luminosities of pulsars have been computed. (orig.)

  16. Vibration spectra of single atomic nanocontacts

    International Nuclear Information System (INIS)

    Bourahla, B; Khater, A; Rafil, O; Tigrine, R

    2006-01-01

    This paper introduces a simple model for an atomic nanocontact, where its mechanical properties are analysed by calculating numerically the local spectral properties at the contact atom and the nearby atoms. The standard methodology for calculating phonon spectral densities is extended to enable the calculation of localized contact modes and local density of states (DOS). The model system considered for the nanocontact consists of two sets of triple parallel semi-infinite atomic chains joined by a single atom in between. The matching method is used, in the harmonic approximation, to calculate the local Green's functions for the irreducible set of sites that constitute the inhomogeneous nanocontact domain. The Green's functions yield the vibration spectra and the DOS for the atomic sites. These are numerically calculated for different cases of elastic hardening and softening of the nanocontact domain. The purpose is to investigate how the local dynamics respond to local changes in the elastic environment. The analysis of the spectra and of the DOS identifies characteristic features and demonstrates the central role of a core subset of these sites for the dynamics of the nanocontact. The system models a situation which may be appropriate for contact atomic force microscopy

  17. Analysis of the FF Aqr spectra

    Science.gov (United States)

    Shimanskaya, N. N.; Bikmaev, I. F.; Shimansky, V. V.

    2011-07-01

    We determine the atmospheric parameters of the secondary in the close binary system FF Aqr and analyze its chemical composition. A series of high-resolution spectra are taken at different orbital phases using the coude echelle spectrometer of the 1.5-m Russian-Turkish Telescope (RTT150). We show that the absorption line intensity of heavy elements varies with phase due to the spotty nature of the cool component. We determine the abundances of heavy elements in the star's atmosphere by modelling the synthetic spectra and performing a differential analysis of the chemical composition of FF Aqr relative to the solar composition. Our analysis of the averaged spectrum of FF Aqr yielded 539 abundance estimates for 21 chemical elements. We found the metallicity of the star ([ Fe/H] = -0.11 ± 0.08) to be close solar, in agreement with the hypothesis that FF Aqr should belong to the Galactic disk. The inferred chemical composition of the objects exhibits no anomalous abundances of the α-, r-, and s-process elements like those earlier found in other systems (IN Com, LW Hya, V471 Tau). The lack of such anomalies in FF Aqr must be due to the fact that the elements heavier than 16 O cannot be synthesized in the core of the primary during the last stages of its evolution.

  18. Stellar parametrization from Gaia RVS spectra

    Science.gov (United States)

    Recio-Blanco, A.; de Laverny, P.; Allende Prieto, C.; Fustes, D.; Manteiga, M.; Arcay, B.; Bijaoui, A.; Dafonte, C.; Ordenovic, C.; Ordoñez Blanco, D.

    2016-01-01

    Context. Among the myriad of data collected by the ESA Gaia satellite, about 150 million spectra will be delivered by the Radial Velocity Spectrometer (RVS) for stars as faint as GRVS~ 16. A specific stellar parametrization will be performed on most of these RVS spectra, I.e. those with enough high signal-to-noise ratio (S/N), which should correspond to single stars that have a magnitude in the RVS band brighter than ~14.5. Some individual chemical abundances will also be estimated for the brightest targets. Aims: We describe the different parametrization codes that have been specifically developed or adapted for RVS spectra within the GSP-Spec working group of the analysis consortium. The tested codes are based on optimisation (FERRE and GAUGUIN), projection (MATISSE), or pattern-recognition methods (Artificial Neural Networks). We present and discuss each of their expected performances in the recovered stellar atmospheric parameters (effective temperature, surface gravity, overall metallicity) for B- to K-type stars. The performances for determining of [α/Fe] ratios are also presented for cool stars. Methods: Each code has been homogeneously tested with a large grid of RVS simulated synthetic spectra of BAFGK-spectral types (dwarfs and giants), with metallicities varying from 10-2.5 to 10+ 0.5 the solar metallicity, and taking variations of ±0.4 dex in the composition of the α-elements into consideration. The tests were performed for S/N ranging from ten to 350. Results: For all the stellar types we considered, stars brighter than GRVS~ 12.5 are very efficiently parametrized by the GSP-Spec pipeline, including reliable estimations of [α/Fe]. Typical internal errors for FGK metal-rich and metal-intermediate stars are around 40 K in Teff, 0.10 dex in log(g), 0.04 dex in [M/H], and 0.03 dex in [α/Fe] at GRVS = 10.3. They degrade to 155 K in Teff, 0.15 dex in log(g), 0.10 dex in [M/H], and 0.1 dex in [α/Fe] at GRVS~ 12. Similar accuracies in Teff and [M/H] are

  19. Interaction of water with oriented DNA in the A- and B-form conformations

    International Nuclear Information System (INIS)

    Brandes, R.; Rupprecht, A.; Kearns, D.R.

    1989-01-01

    High resolution 2 H nuclear magnetic resonance (NMR) was used to investigate the interaction of D 2 O with solid samples of uniaxially oriented Li-DNA (B-form DNA) and Na-DNA (A- and B-form DNA). At low levels of hydration, 0 approximately 4 D 2 O/nucleotide, the 2 H spectra shows a very weak (due to short T2) broad single resonance, suggestive of unrestricted rotational diffusion of the water. At approximately 5 or more D 2 O/nucleotide, the Li-DNA (B-form) spectra suddenly exhibit a large doublet splitting, characteristic of partially ordered water. With increasing hydration, the general trend is a decrease of this splitting. From our analysis we show that the DNA water structure reorganizes as the DNA is progressively hydrated. The D 2 O interaction with Na-DNA is rather different than with Li-DNA. Below 10 D 2 O/nucleotide Na-DNA is normally expected to be in the A-form, and a small, or negligible splitting is observed. In the range 9-19 D 2 O/nucleotide, the splitting increases with increasing hydration. Above approximately 20 D 2 O/nucleotide Na-DNA converts entirely to the B-form and the D 2 O splittings are then similar to those found in Li-DNA. We show that the complex Na-DNA results obtained in the range 0-20 D 2 O/nucleotide are caused by a mixture of A- and B-DNA in those samples

  20. Nonisotopic DNA probe techniques

    National Research Council Canada - National Science Library

    Kricka, Larry J

    1992-01-01

    The objective of this book is to bring together descriptions of the principal nonisotopic methods for DNA hybridization assays, together with experimental details of the methods, including labelling...

  1. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  2. Forensic DNA testing.

    Science.gov (United States)

    Butler, John M

    2011-12-01

    Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.

  3. Structure of DNA toroids and electrostatic attraction of DNA duplexes

    International Nuclear Information System (INIS)

    Cherstvy, A G

    2005-01-01

    DNA-DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter is in agreement with recent cryo-electron microscopy studies on DNA condensed with cobalt hexammine. We treat the DNA-DNA interactions within the modern theory of electrostatic interaction between helical macromolecules. The size and thickness of the toroids is calculated within a simple model; other models of stability of DNA toroids are discussed and compared

  4. An experiment on multibubble sonoluminescence spectra in sodium chloride solution

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhan; XU JunFeng; HUANG Wei; CHEN WeiZhong; MIAO GuoQing

    2008-01-01

    We investigated experimentally the spectra of MBSL in sodium chloride water solution with krypton as dissolved gas. We observed and compared the spectra of hydroxyl ion at 310 nm and that of sodium atom at 589 nm. It has been found that under the same experimental condition, the intensity of sodium atom spectra is obviously higher than that of the hydroxyl ion spectra, and is more sensitive to the experimental condition. The krypton content, the concentration of sodium chloride solution, and the driving sound pressure obviously affect the spectra intensity in certain range.

  5. Raman Spectra from Pesticides on the Surface of Fruits

    International Nuclear Information System (INIS)

    Zhang, P X; Zhou Xiaofang; Cheng, Andrew Y S; Fang Yan

    2006-01-01

    Raman spectra of several vegetables and fruits were studied by micro-Raman spectrometer (514.5 nm) and Near-infrared Fourier Transform Raman spectrometer (FTRaman). It is shown that at 514.5 nm excitation, most of the spectra are from that of carotene with some very strong fluorescence in some cases. While at 1064 nm wavelength excitation, the spectra from the different samples demonstrate different characteristic Raman spectra without fluorescence. We discuss the spectroscopic difference by the two excitation wavelengths, and the application of Raman spectra for detection of pesticides left on the surface of vegetables and fruits. Raman spectra of fruits and pesticides were successfully recorded, and using the FT-Raman spectra the pesticides left on the surface of the fruits can be detected conveniently

  6. Energetic Proton Spectra Measured by the Van Allen Probes

    Science.gov (United States)

    Summers, Danny; Shi, Run; Engebretson, Mark J.; Oksavik, Kjellmar; Manweiler, Jerry W.; Mitchell, Donald G.

    2017-10-01

    We test the hypothesis that pitch angle scattering by electromagnetic ion cyclotron (EMIC) waves can limit ring current proton fluxes. For two chosen magnetic storms, during 17-20 March 2013 and 17-20 March 2015, we measure proton energy spectra in the region 3 ≤ L ≤ 6 using the RBSPICE-B instrument on the Van Allen Probes. The most intense proton spectra are observed to occur during the recovery periods of the respective storms. Using proton precipitation data from the POES (NOAA and MetOp) spacecraft, we deduce that EMIC wave action was prevalent at the times and L-shell locations of the most intense proton spectra. We calculate limiting ring current proton energy spectra from recently developed theory. Comparisons between the observed proton energy spectra and the theoretical limiting spectra show reasonable agreement. We conclude that the measurements of the most intense proton spectra are consistent with self-limiting by EMIC wave scattering.

  7. Spectroscopic studies of the interaction between pirimicarb and calf thymus DNA

    Science.gov (United States)

    Zhang, Guowen; Hu, Xing; Pan, Junhui

    2011-02-01

    The interaction between pirimicarb and calf thymus DNA in physiological buffer (pH 7.4) was investigated with the use of Neutral Red (NR) dye as a spectral probe by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, as well as viscosity measurements and DNA melting techniques. The results revealed that an intercalation binding should be the interaction mode of pirimicarb to DNA. CD spectra indicated that pirimicarb induced conformational changes of DNA. The binding constants of pirimicarb with DNA were obtained by the fluorescence quenching method. The thermodynamic parameters, enthalpy change (Δ Hθ) and entropy change (Δ Sθ) were calculated to be -52.13 ± 2.04 kJ mol -1 and -108.8 ± 6.72 J mol -1 K -1 according to the van't Hoff equation, which suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of pirimicarb to DNA. Further, the alternative least squares (ALS) method was applied to resolve a complex two-way array of the absorption spectra data, which provided simultaneously the concentration information for the three reaction components, pirimicarb, NR and DNA-NR. This ALS analysis indicated that the intercalation of pirimicarb into the DNA by substituting for NR in the DNA-NR complex.

  8. Spectroscopic studies of the interaction between pirimicarb and calf thymus DNA.

    Science.gov (United States)

    Zhang, Guowen; Hu, Xing; Pan, Junhui

    2011-02-01

    The interaction between pirimicarb and calf thymus DNA in physiological buffer (pH 7.4) was investigated with the use of Neutral Red (NR) dye as a spectral probe by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, as well as viscosity measurements and DNA melting techniques. The results revealed that an intercalation binding should be the interaction mode of pirimicarb to DNA. CD spectra indicated that pirimicarb induced conformational changes of DNA. The binding constants of pirimicarb with DNA were obtained by the fluorescence quenching method. The thermodynamic parameters, enthalpy change (ΔHθ) and entropy change (ΔSθ) were calculated to be -52.13±2.04 kJ mol(-1) and -108.8±6.72 J mol(-1) K(-1) according to the van't Hoff equation, which suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of pirimicarb to DNA. Further, the alternative least squares (ALS) method was applied to resolve a complex two-way array of the absorption spectra data, which provided simultaneously the concentration information for the three reaction components, pirimicarb, NR and DNA-NR. This ALS analysis indicated that the intercalation of pirimicarb into the DNA by substituting for NR in the DNA-NR complex. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Running of featureful primordial power spectra

    Science.gov (United States)

    Gariazzo, Stefano; Mena, Olga; Miralles, Victor; Ramírez, Héctor; Boubekeur, Lotfi

    2017-06-01

    Current measurements of the temperature and polarization anisotropy power spectra of the cosmic microwave background (CMB) seem to indicate that the naive expectation for the slow-roll hierarchy within the most simple inflationary paradigm may not be respected in nature. We show that a primordial power spectrum with localized features could in principle give rise to the observed slow-roll anarchy when fitted to a featureless power spectrum. From a model comparison perspective, and assuming that nature has chosen a featureless primordial power spectrum, we find that, while with mock Planck data there is only weak evidence against a model with localized features, upcoming CMB missions may provide compelling evidence against such a nonstandard primordial power spectrum. This evidence could be reinforced if a featureless primordial power spectrum is independently confirmed from bispectrum and/or galaxy clustering measurements.

  10. Boundary spectra in superspace σ-models

    International Nuclear Information System (INIS)

    Quella, T.; Schomerus, V.; Creutzig, T.

    2007-12-01

    In this note we compute exact boundary spectra for D-instantons in σ-models on the supergroup PSL(22). Our results are obtained through an explicit summation of the perturbative expansion for conformal dimensions to all orders in the curvature radius. The analysis exploits several remarkable properties of the perturbation series that arises from rescalings of the metric on PSL(22) relative to a fixed Wess- Zumino term. According to Berkovits, Vafa and Witten, the models are relevant in the context of string theory on AdS 3 with non-vanishing RR-flux. The note concludes with a number of comments on various possible generalizations to other supergroups and higher dimensional supercoset theories. (orig.)

  11. Automated analysis of slitless spectra. II. Quasars

    International Nuclear Information System (INIS)

    Edwards, G.; Beauchemin, M.; Borra, F.

    1988-01-01

    Automated software have been developed to process slitless spectra. The software, described in a previous paper, automatically separates stars from extended objects and quasars from stars. This paper describes the quasar search techniques and discusses the results. The performance of the software is compared and calibrated with a plate taken in a region of SA 57 that has been extensively surveyed by others using a variety of techniques: the proposed automated software performs very well. It is found that an eye search of the same plate is less complete than the automated search: surveys that rely on eye searches suffer from incompleteness at least from a magnitude brighter than the plate limit. It is shown how the complete automated analysis of a plate and computer simulations are used to calibrate and understand the characteristics of the present data. 20 references

  12. Assessment of smoothed spectra using autocorrelation function

    International Nuclear Information System (INIS)

    Urbanski, P.; Kowalska, E.

    2006-01-01

    Recently, data and signal smoothing became almost standard procedures in the spectrometric and chromatographic methods. In radiometry, the main purpose to apply smoothing is minimisation of the statistical fluctuation and avoid distortion. The aim of the work was to find a qualitative parameter, which could be used, as a figure of merit for detecting distortion of the smoothed spectra, based on the linear model. It is assumed that as long as the part of the raw spectrum removed by the smoothing procedure (v s ) will be of random nature, the smoothed spectrum can be considered as undistorted. Thanks to this feature of the autocorrelation function, drifts of the mean value in the removed noise vs as well as its periodicity can be more easily detected from the autocorrelogram than from the original data

  13. Closed N-shell alkali spectra

    International Nuclear Information System (INIS)

    Ellis, D.G.; Curtis, L.J.

    1982-01-01

    Term values and ionization potentials have been calculated for several ions in the promethium (N = 61) isoelectronic sequence. As the nuclear charge is increased, the ground configuration changes from 4f 13 5s 2 to 4f 14 5s giving the upper portion of the sequence an alkali-like character. According to our most recent Hartree-Fock calculations with first-order relativistic corrections, the ground term is 5s 2 S for Z > 77 (Ir XVII) and the first excited term is 5p 2 P 0 for Z > 84 (P 0 XXIV). Comparisons are made with calculations of Cowan in W XIV. The prospects for observation of these spectra in fast ion beams are discussed. (orig.)

  14. Dielectric spectra of proteins in conducting media

    International Nuclear Information System (INIS)

    Ruderman, G.; Xammar Oro, J.R. de

    1990-10-01

    Dielectric measurements of serum albumin and myoglobin in solutions of varying conductivities were performed. The results presented confirm that also for protein solutions, the Maxwell predictions of a threshold frequency in conducting materials holds. The threshold frequency of a serum albumin solution was experimentally determined. Attention should be recalled that, if the dielectric spectra of proteins solutions want to be measured, three distinct frequency regions are to be observed: a low frequency region, where the sample behaves like a conductor; an intermediate region centered around the threshold frequency, where the free charges partially screen the fixed ones; and a high frequency region where the sample behaves like a good dielectric. (author). 8 refs, 5 figs

  15. Conformal Symmetry Patterns in Baryon Spectra

    International Nuclear Information System (INIS)

    Kirchbach, Mariana; Compean, Cliffor B

    2011-01-01

    Attention is drawn to the fact that the spectra of the baryons of the lightest flavors, the nucleon and the Δ, carry quantum numbers characteristic for an unitary representation of the conformal group. We show that the above phenomenon is well explained for baryons whose internal structure is dominated by a quark-diquark configuration that resides in a conformally compactified Minkowski space time, R 1 x S 3 , and is described by means of the conformal scale equation there. The R 1 x S 3 space-time represents the boundary of the conformally compactified AdS 5 , on which one expects to encounter a conformal theory in accord with the gauge-gravity duality. Within this context, our model is congruent with AdS 5 /CFT 4 .

  16. Automated analysis of objective-prism spectra

    International Nuclear Information System (INIS)

    Hewett, P.C.; Irwin, M.J.; Bunclark, P.; Bridgeland, M.T.; Kibblewhite, E.J.; Smith, M.G.

    1985-01-01

    A fully automated system for the location, measurement and analysis of large numbers of low-resolution objective-prism spectra is described. The system is based on the APM facility at the University of Cambridge, and allows processing of objective-prism, grens or grism data. Particular emphasis is placed on techniques to obtain the maximum signal-to-noise ratio from the data, both in the initial spectral estimation procedure and for subsequent feature identification. Comparison of a high-quality visual catalogue of faint quasar candidates with an equivalent automated sample demonstrates the ability of the APM system to identify all the visually selected quasar candidates. In addition, a large population of new, faint (msub(J)approx. 20) candidates is identified. (author)

  17. Modeling degradation in SOEC impedance spectra

    DEFF Research Database (Denmark)

    Jensen, Søren Højgaard; Hauch, Anne; Knibbe, Ruth

    2013-01-01

    Solid oxide cell (SOC) performance is limited by various processes. One way to investigate these processes is by electrochemical impedance spectroscopy. In order to quantify and characterize the processes, an equivalent circuit can be used to model the SOC impedance spectra (IS). Unfortunately......, the optimal equivalent circuit is often unknown and to complicate matters further, several processes contribute to the SOC impedance - making detailed process characterization difficult. In this work we analyze and model a series of IS measured during steam electrolysis operation of an SOC. During testing......, degradation is only observed in the Ni/YSZ electrode and not in the electrolyte or the LSM/YSZ electrode. A batch fit of the differences between the IS shows that a modified Gerischer element provides a better fit to the Ni/YSZ electrode impedance than the frequently used RQ element - albeit neither...

  18. Infrared Model Spectra for Evolving Red Supergiants

    Directory of Open Access Journals (Sweden)

    Kyung-Won Suh

    1993-06-01

    Full Text Available The space and ground based infrared spectra of red supergiants are modeled and arranged in order of their evolutionary status with their theoretical model parameters. The chemical compositions of the dust shells around red supergiants are affected by the nuclear reaction and dredge-up processes of the cental stars. The processes are sensitively dependent on the initial mass, the initial chemical composition, and the evolutionary status. Miras, infrared carbon stars, and OH/IR stars have close link in their evolution in manu aspects, i,e., the chemical composition, the optical depths and the mass loss rates. The evolutionary tracks for the three classes of red supergiants on infrared two-color diagrams have been made from model calculations and IRAS observational data.

  19. Increased Elemental Specificity of Positron Annihilation Spectra

    International Nuclear Information System (INIS)

    Asoka-Kumar, P.; Alatalo, M.; Ghosh, V.J.; Kruseman, A.C.; Nielsen, B.; Lynn, K.G.

    1996-01-01

    Positron annihilation spectroscopy (PAS) is a sensitive probe for studying the electronic structure of defects in solids. We show that the high-momentum part of the Doppler-broadened annihilation spectra can be used to distinguish different elements. This is achieved by using a new two-detector coincidence system to examine the line shape variations originating from high-momentum core electrons. Because the core electrons retain their atomic character even when atoms form a solid, these results can be directly compared to simple theoretical predictions. The new approach adds increased elemental specificity to the PAS technique, and is useful in studying the elemental variations around a defect site. copyright 1996 The American Physical Society

  20. Molecular mechanisms of the direct radiation effects on the DNA: ESR spectroscopy for examining oriented fibres after X-ray exposure

    International Nuclear Information System (INIS)

    Voit, K.

    1986-01-01

    This thesis contains experiments, investigating molecular interactions between X radiation and DNA. ESR-spectra of the primary radicals are simulated. The types of secondary radicals are described. (AJ) [de

  1. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao

    2012-01-01

    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  2. Dna fingerprinting - review paper

    OpenAIRE

    Blundell, Renald

    2006-01-01

    Before the Polymerase Chain Reaction (PCR) was established, DNA fingerprinting technology has relied for years on Restriction Fragment Length Polymorphism (RFLP) and Variable Number of Tandom Repeats (VNTR) analysis, a very efficient technique but quite laborious and not suitable for high throughput mapping. Since its, development, PCR has provided a new and powerful tool for DNA fingerprinting.

  3. DNA Repair Systems

    Indian Academy of Sciences (India)

    Thanks to the pioneering research work of Lindahl, Sancar, Modrich and their colleagues, we now have an holistic awareness of how DNA damage occurs and how the damage is rectified in bacteria as well as in higher organisms including human beings. A comprehensive understanding of DNA repair has proven crucial ...

  4. DNA repair genes

    International Nuclear Information System (INIS)

    Morimyo, Mitsuoki

    1995-01-01

    Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

  5. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2018-05-15

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  6. Characterization of muntjac DNA

    International Nuclear Information System (INIS)

    Davis, R.C.

    1981-01-01

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange

  7. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  8. Characterization of muntjac DNA

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  9. Parameterization of MARVELS Spectra Using Deep Learning

    Science.gov (United States)

    Gilda, Sankalp; Ge, Jian; MARVELS

    2018-01-01

    Like many large-scale surveys, the Multi-Object APO Radial Velocity Exoplanet Large-area Survey (MARVELS) was designed to operate at a moderate spectral resolution ($\\sim$12,000) for efficiency in observing large samples, which makes the stellar parameterization difficult due to the high degree of blending of spectral features. Two extant solutions to deal with this issue are to utilize spectral synthesis, and to utilize spectral indices [Ghezzi et al. 2014]. While the former is a powerful and tested technique, it can often yield strongly coupled atmospheric parameters, and often requires high spectral resolution (Valenti & Piskunov 1996). The latter, though a promising technique utilizing measurements of equivalent widths of spectral indices, has only been employed with respect to FKG dwarfs and sub-giants and not red-giant branch stars, which constitute ~30% of MARVELS targets. In this work, we tackle this problem using a convolution neural network (CNN). In particular, we train a one-dimensional CNN on appropriately processed PHOENIX synthetic spectra using supervised training to automatically distinguish the features relevant for the determination of each of the three atmospheric parameters – T_eff, log(g), [Fe/H] – and use the knowledge thus gained by the network to parameterize 849 MARVELS giants. When tested on the synthetic spectra themselves, our estimates of the parameters were consistent to within 11 K, .02 dex, and .02 dex (in terms of mean absolute errors), respectively. For MARVELS dwarfs, the accuracies are 80K, .16 dex and .10 dex, respectively.

  10. A climatology of visible surface reflectance spectra

    International Nuclear Information System (INIS)

    Zoogman, Peter; Liu, Xiong; Chance, Kelly; Sun, Qingsong; Schaaf, Crystal; Mahr, Tobias; Wagner, Thomas

    2016-01-01

    We present a high spectral resolution climatology of visible surface reflectance as a function of wavelength for use in satellite measurements of ozone and other atmospheric species. The Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument is planned to measure backscattered solar radiation in the 290–740 nm range, including the ultraviolet and visible Chappuis ozone bands. Observation in the weak Chappuis band takes advantage of the relative transparency of the atmosphere in the visible to achieve sensitivity to near-surface ozone. However, due to the weakness of the ozone absorption features this measurement is more sensitive to errors in visible surface reflectance, which is highly variable. We utilize reflectance measurements of individual plant, man-made, and other surface types to calculate the primary modes of variability of visible surface reflectance at a high spectral resolution, comparable to that of TEMPO (0.6 nm). Using the Moderate-resolution Imaging Spectroradiometer (MODIS) Bidirection Reflectance Distribution Function (BRDF)/albedo product and our derived primary modes we construct a high spatial resolution climatology of wavelength-dependent surface reflectance over all viewing scenes and geometries. The Global Ozone Monitoring Experiment–2 (GOME-2) Lambertian Equivalent Reflectance (LER) product provides complementary information over water and snow scenes. Preliminary results using this approach in multispectral ultraviolet+visible ozone retrievals from the GOME-2 instrument show significant improvement to the fitting residuals over vegetated scenes. - Highlights: • Our goals was visible surface reflectance for satellite trace gas measurements. • Captured the range of surface reflectance spectra through EOF analysis. • Used satellite surface reflectance products for each given scene to anchor EOFs. • Generated a climatology of time/geometry dependent surface reflectance spectra. • Demonstrated potential to

  11. Spectra of small Koronis family members

    Science.gov (United States)

    Thomas, C.; Rivkin, A.; Trilling, D.; Moskovitz, N.

    2014-07-01

    The space-weathering process and its implications for the relationships between S- and Q-type asteroids and ordinary chondrite meteorites are long-standing problems in asteroid science. Although the visible and near-infrared spectra of S- and Q-type objects qualitatively show the same absorption features and quantitatively show evidence of the same minerals, the S types display increased spectral slopes and muted absorption features compared to the Q types. This spectral mismatch is consistent with the effects of the space weathering process. Binzel et al. provided the missing link between Q- and S-type bodies in near-Earth space by showing a reddening of spectral slope in objects from 0.1 to 5 km that corresponded to the transition from Q- to S-type spectra. This result implied that size, and therefore age, is related to the relationship between Q- and S-type. The existence of Q-type objects in the main belt was not confirmed until Mothe-Diniz and Nesvorny (2008) found them in young S-type clusters. To investigate the trend from Q to S in the main belt, we examined space weathering within the old main-belt Koronis family using a spectrophotometric survey (Rivkin et al. 2011, Thomas et al. 2011). Rivkin et al. (2011) identified several potential Q-type objects within the Koronis family. Our Q-type candidates were identified using broad-band spectrophotometry and could not be taxonomically classified on that basis alone. We obtained follow-up visible and near-infrared spectral observations of our potential Q-type objects, (26970) Elias, (45610) 2000 DJ_{48}, and (37411) 2001 XF_{152}, using Gemini and Magellan. We will present the results of these spectral follow-up observations. Observations of (26970) Elias demonstrate that the object is more consistent with the average Q-type spectrum than the average S-type spectrum.

  12. Strong ground motion spectra for layered media

    International Nuclear Information System (INIS)

    Askar, A.; Cakmak, A.S.; Engin, H.

    1977-01-01

    This article presents an analytic method and calculations of strong motion spectra for the energy, displacement, velocity and acceleration based on the physical and geometric ground properties at a site. Although earthquakes occur with large deformations and high stress intensities which necessarily lead to nonlinear phenomena, most analytical efforts to date have been based on linear analyses in engineering seismology and soil dynamics. There are, however, a wealth of problems such as the shifts in frequency, dispersion due to the amplitude, the generation of harmonics, removal of resonance infinities, which cannot be accounted for by a linear theory. In the study, the stress-strain law for soil is taken as tau=G 0 γ+G 1 γ 3 +etaγ where tau is the stress, γ is the strain, G 0 and G 1 are the elasticity coefficients and eta is the damping and are different in each layer. The above stress-strain law describes soils with hysterisis where the hysterisis loops for various amplitudes of the strain are no longer concentric ellipses as for linear relations but are oval shapes rotated with respect to each other similar to the materials with the Osgood-Ramberg law. It is observed that even slight nonlinearities may drastically alter the various response spectra from that given by linear analysis. In fact, primary waves cause resonance conditions such that secondary waves are generated. As a result, a weak energy transfer from the primary to the secondary waves takes place, thus altering the wave spectrum. The mathematical technique that is utilized for the solution of the nonlinear equation is a special perturbation method as an extension of Poincare's procedure. The method considers shifts in the frequencies which are determined by the boundedness of the energy

  13. Spectroscopic modeling for tungsten EUV spectra

    International Nuclear Information System (INIS)

    Murakami, Izumi; Kato, Daiji; Sakaue, Hiroyuki A.; Suzuki, Chihiro; Morita, Shigeru; Goto, Motoshi; Sasaki, Akira; Nakamura, Nobuyuki; Yamamoto, Norimasa; Koike, Fumihiro

    2014-01-01

    We have constructed an atomic model for tungsten extreme ultraviolet (EUV) spectra to reconstruct characteristic spectral feature of unresolved transition array (UTA) observed at 4-7 nm for tungsten ions. In the tungsten atomic modeling, we considered fine-structure levels with the quantum principal number n up to 6 as the atomic structure and calculated the electron-impact collision cross sections by relativistic distorted-wave method, using HULLAC atomic code. We measured tungsten EUV spectra in Large Helical Device (LHD) and Compact Electron Beam Ion Trap device (CoBIT) and compared them with the model calculation. The model successfully explain series of emission peaks at 1.5-3.5 nm as n=5-4 and 6-4 transitions of W"2"4"+ - W"3"2"+ measured in CoBIT and LHD and the charge state distributions were estimated for LHD plasma. The UTA feature observed at 4-7 nm was also successfully reconstructed with our model. The peak at ∼5 nm is produced mainly by many 4f-4d transition of W"2"2"+ - W"3"5"+ ions, and the second peak at ∼6 nm is produced by 4f-4d transition of W"2"5"+ - W"2"8"+ ions, and 4d-4p inner-shell transitions, 4p"54d"n"+"1 - 4p"64d"n, of W"2"9"+ - W"3"5"+ ions. These 4d-4p inner-shell transitions become strong since we included higher excited states such as 4p"54d"n4f state, which ADAS atomic data set does not include for spectroscopic modeling with fine structure levels. (author)

  14. Curved Radio Spectra of Weak Cluster Shocks

    Science.gov (United States)

    Kang, Hyesung; Ryu, Dongsu

    2015-08-01

    In order to understand certain observed features of arc-like giant radio relics such as the rareness, uniform surface brightness, and curved integrated spectra, we explore a diffusive shock acceleration (DSA) model for radio relics in which a spherical shock impinges on a magnetized cloud containing fossil relativistic electrons. Toward this end, we perform DSA simulations of spherical shocks with the parameters relevant for the Sausage radio relic in cluster CIZA J2242.8+5301, and calculate the ensuing radio synchrotron emission from re-accelerated electrons. Three types of fossil electron populations are considered: a delta-function like population with the shock injection momentum, a power-law distribution, and a power law with an exponential cutoff. The surface brightness profile of the radio-emitting postshock region and the volume-integrated radio spectrum are calculated and compared with observations. We find that the observed width of the Sausage relic can be explained reasonably well by shocks with speed {u}{{s}}˜ 3× {10}3 {km} {{{s}}}-1 and sonic Mach number {M}{{s}}˜ 3. These shocks produce curved radio spectra that steepen gradually over (0.1-10){ν }{br} with a break frequency {ν }{br}˜ 1 GHz if the duration of electron acceleration is ˜60-80 Myr. However, the abrupt increase in the spectral index above ˜1.5 GHz observed in the Sausage relic seems to indicate that additional physical processes, other than radiative losses, operate for electrons with {γ }{{e}}≳ {10}4.

  15. [Raman spectra of monkey cerebral cortex tissue].

    Science.gov (United States)

    Zhu, Ji-chun; Guo, Jian-yu; Cai, Wei-ying; Wang, Zu-geng; Sun, Zhen-rong

    2010-01-01

    Monkey cerebral cortex, an important part in the brain to control action and thought activities, is mainly composed of grey matter and nerve cell. In the present paper, the in situ Raman spectra of the cerebral cortex of the birth, teenage and aged monkeys were achieved for the first time. The results show that the Raman spectra for the different age monkey cerebral cortex exhibit most obvious changes in the regions of 1000-1400 and 2800-3000 cm(-1). With monkey growing up, the relative intensities of the Raman bands at 1313 and 2885 cm(-1) mainly assigned to CH2 chain vibrational mode of lipid become stronger and stronger whereas the relative intensities of the Raman bands at 1338 and 2932 cm(-1) mainly assigned to CH3 chain vibrational mode of protein become weaker and weaker. In addition, the two new Raman bands at 1296 and 2850 cm(-1) are only observed in the aged monkey cerebral cortex, therefore, the two bands can be considered as a character or "marker" to differentiate the caducity degree with monkey growth In order to further explore the changes, the relative intensity ratios of the Raman band at 1313 cm(-1) to that at 1338 cm(-1) and the Raman band at 2885 cm(-1) to that at 2 932 cm(-1), I1313/I1338 and I2885/I2932, which are the lipid-to-protein ratios, are introduced to denote the degree of the lipid content. The results show that the relative intensity ratios increase significantly with monkey growth, namely, the lipid content in the cerebral cortex increases greatly with monkey growth. So, the authors can deduce that the overmuch lipid is an important cause to induce the caducity. Therefore, the results will be a powerful assistance and valuable parameter to study the order of life growth and diagnose diseases.

  16. Spectra and physical properties of Taurid meteoroids

    Science.gov (United States)

    Matlovič, Pavol; Tóth, Juraj; Rudawska, Regina; Kornoš, Leonard

    2017-09-01

    Taurids are an extensive stream of particles produced by comet 2P/Encke, which can be observed mainly in October and November as a series of meteor showers rich in bright fireballs. Several near-Earth asteroids have also been linked with the meteoroid complex, and recently the orbits of two carbonaceous meteorites were proposed to be related to the stream, raising interesting questions about the origin of the complex and the composition of 2P/Encke. Our aim is to investigate the nature and diversity of Taurid meteoroids by studying their spectral, orbital, and physical properties determined from video meteor observations. Here we analyze 33 Taurid meteor spectra captured during the predicted outburst in November 2015 by stations in Slovakia and Chile, including 14 multi-station observations for which the orbital elements, material strength parameters, dynamic pressures, and mineralogical densities were determined. It was found that while orbits of the 2015 Taurids show similarities with several associated asteroids, the obtained spectral and physical characteristics point towards cometary origin with highly heterogeneous content. Observed spectra exhibited large dispersion of iron content and significant Na intensity in all cases. The determined material strengths are typically cometary in the KB classification, while PE criterion is on average close to values characteristic for carbonaceous bodies. The studied meteoroids were found to break up under low dynamic pressures of 0.02-0.10 MPa, and were characterized by low mineralogical densities of 1.3-2.5 g cm-3. The widest spectral classification of Taurid meteors to date is presented.

  17. PCR performance of a thermostable heterodimeric archaeal DNA polymerase

    Science.gov (United States)

    Killelea, Tom; Ralec, Céline; Bossé, Audrey; Henneke, Ghislaine

    2014-01-01

    DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3' primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications. PMID:24847315

  18. PCR performance of a thermostable heterodimeric archaeal DNA polymerase

    Directory of Open Access Journals (Sweden)

    Tom eKillelea

    2014-05-01

    Full Text Available DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR, cDNA cloning, genome sequencing and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3’ primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.

  19. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle

    2013-01-01

    This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly...... talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases...

  20. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  1. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Action spectra for inactivation of normal and xeroderma pigmentosum human skin fibroblasts by ultraviolet radiations

    International Nuclear Information System (INIS)

    Keyse, S.M.; Moss, S.H.; Davies, D.J.G.

    1983-01-01

    Action spectra for UV-induced lethality as measured by colony forming ability were determined both for a normal human skin fibroblast strain (1BR) and for an excision deficient xeroderma pigmentosum strain (XP4LO) assigned to complementation group A using 7 monochromatic wavelengths in the range 254-365 nm. The relative sensitivity of the XP strain compared to the normal skin fibroblasts shows a marked decrease at wavelengths longer than 313 nm, changing from a ratio of about 20 at the shorter wavelengths to just greater than 1.0 at the longer wavelengths. The action spectra thus indicate that the influence on cell inactivation of the DNA repair defect associated with XP cells is decreased and almost reaches zero at longer UV wavelengths. This would occur, for example, if the importance of pyrimidine dimers as the lethal lesion decreased with increasing wavelength. These results are consistent with pyrimidine dimers induced in DNA being the major lethal lesion in both cell strains over the wavelength range 254-313 nm. However, it is indicated that different mechanisms of inactivation operate at wavelengths longer than 313 nm. (author)

  3. Path spectra derived from inversion of source and site spectra for earthquakes in Southern California

    Science.gov (United States)

    Klimasewski, A.; Sahakian, V. J.; Baltay, A.; Boatwright, J.; Fletcher, J. B.; Baker, L. M.

    2017-12-01

    A large source of epistemic uncertainty in Ground Motion Prediction Equations (GMPEs) is derived from the path term, currently represented as a simple geometric spreading and intrinsic attenuation term. Including additional physical relationships between the path properties and predicted ground motions would produce more accurate and precise, region-specific GMPEs by reclassifying some of the random, aleatory uncertainty as epistemic. This study focuses on regions of Southern California, using data from the Anza network and Southern California Seismic network to create a catalog of events magnitude 2.5 and larger from 1998 to 2016. The catalog encompasses regions of varying geology and therefore varying path and site attenuation. Within this catalog of events, we investigate several collections of event region-to-station pairs, each of which share similar origin locations and stations so that all events have similar paths. Compared with a simple regional GMPE, these paths consistently have high or low residuals. By working with events that have the same path, we can isolate source and site effects, and focus on the remaining residual as path effects. We decompose the recordings into source and site spectra for each unique event and site in our greater Southern California regional database using the inversion method of Andrews (1986). This model represents each natural log record spectra as the sum of its natural log event and site spectra, while constraining each record to a reference site or Brune source spectrum. We estimate a regional, path-specific anelastic attenuation (Q) and site attenuation (t*) from the inversion site spectra and corner frequency from the inversion event spectra. We then compute the residuals between the observed record data, and the inversion model prediction (event*site spectra). This residual is representative of path effects, likely anelastic attenuation along the path that varies from the regional median attenuation. We examine the

  4. Nanostructures via DNA scaffold metallization

    OpenAIRE

    Ning, C.; Zinchenko, A.; Baigl, D.; Pyshkina, O.; Sergeyev, V.; Endo, Kazunaka; Yoshikawa, K.

    2005-01-01

    The critical role of polymers in process of noble metals nanostructures formation is well known, however, the use of DNA chain template in this process is yet largely unknown. In this study we demonstrate different ways of silver deposition on DNA template and report the influence of silver nanostructures formation on DNA conformational state. Metallization of DNA chain proceeds by two different scenarios depending on DNA conformation. If DNA chain is unfolded (elongated) chain, silver reduct...

  5. DNA damage and polyploidization.

    Science.gov (United States)

    Chow, Jeremy; Poon, Randy Y C

    2010-01-01

    A growing body of evidence indicates that polyploidization triggers chromosomal instability and contributes to tumorigenesis. DNA damage is increasingly being recognized for its roles in promoting polyploidization. Although elegant mechanisms known as the DNA damage checkpoints are responsible for halting the cell cycle after DNA damage, agents that uncouple the checkpoints can induce unscheduled entry into mitosis. Likewise, defects of the checkpoints in several disorders permit mitotic entry even in the presence of DNA damage. Forcing cells with damaged DNA into mitosis causes severe chromosome segregation defects, including lagging chromosomes, chromosomal fragments and chromosomal bridges. The presence of these lesions in the cleavage plane is believed to abort cytokinesis. It is postulated that if cytokinesis failure is coupled with defects of the p53-dependent postmitotic checkpoint pathway, cells can enter S phase and become polyploids. Progress in the past several years has unraveled some of the underlying principles of these pathways and underscored the important role of DNA damage in polyploidization. Furthermore, polyploidization per se may also be an important determinant of sensitivity to DNA damage, thereby may offer an opportunity for novel therapies.

  6. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  7. Regulating DNA Self-assembly by DNA-Surface Interactions.

    Science.gov (United States)

    Liu, Longfei; Li, Yulin; Wang, Yong; Zheng, Jianwei; Mao, Chengde

    2017-12-14

    DNA self-assembly provides a powerful approach for preparation of nanostructures. It is often studied in bulk solution and involves only DNA-DNA interactions. When confined to surfaces, DNA-surface interactions become an additional, important factor to DNA self-assembly. However, the way in which DNA-surface interactions influence DNA self-assembly is not well studied. In this study, we showed that weak DNA-DNA interactions could be stabilized by DNA-surface interactions to allow large DNA nanostructures to form. In addition, the assembly can be conducted isothermally at room temperature in as little as 5 seconds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    Science.gov (United States)

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  9. DNA electronic circular dichroism on the inter-base pair scale

    DEFF Research Database (Denmark)

    Di Meo, Florent; Nørby, Morten Steen; Rubio-Magnieto, Jenifer

    2015-01-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens...... the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. (Chemical Equation Presented)....

  10. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen

    2014-02-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  11. Peakr: simulating solid-state NMR spectra of proteins

    International Nuclear Information System (INIS)

    Schneider, Robert; Odronitz, Florian; Hammesfahr, Bjorn; Hellkamp, Marcel; Kollmar, Martin

    2013-01-01

    When analyzing solid-state nuclear magnetic resonance (NMR) spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, for example, chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings. Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra and produces lists and visualizations useful for analyzing measured spectra. Compared with other solutions, it is fast, versatile and user friendly. (authors)

  12. Principal spectra describing magnetooptic permittivity tensor in cubic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Hamrlová, Jana [Nanotechnology Centre, VSB – Technical University of Ostrava, listopadu 15, Ostrava, 708 33 Czech Republic (Czech Republic); IT4Innovations Centre, VSB – Technical University of Ostrava, listopadu 15, Ostrava, 708 33 Czech Republic (Czech Republic); Legut, Dominik [IT4Innovations Centre, VSB – Technical University of Ostrava, listopadu 15, Ostrava, 708 33 Czech Republic (Czech Republic); Veis, Martin [Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 121 16 Czech Republic (Czech Republic); Pištora, Jaromír [Nanotechnology Centre, VSB – Technical University of Ostrava, listopadu 15, Ostrava, 708 33 Czech Republic (Czech Republic); Hamrle, Jaroslav, E-mail: jaroslav.hamrle@vsb.cz [IT4Innovations Centre, VSB – Technical University of Ostrava, listopadu 15, Ostrava, 708 33 Czech Republic (Czech Republic); Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 121 16 Czech Republic (Czech Republic); Department of Physics, VSB – Technical University of Ostrava, 17. listopadu 15, Ostrava, 708 33 Czech Republic (Czech Republic)

    2016-12-15

    We provide unified phenomenological description of magnetooptic effects being linear and quadratic in magnetization. The description is based on few principal spectra, describing elements of permittivity tensor up to the second order in magnetization. Each permittivity tensor element for any magnetization direction and any sample surface orientation is simply determined by weighted summation of the principal spectra, where weights are given by crystallographic and magnetization orientations. The number of principal spectra depends on the symmetry of the crystal. In cubic crystals owning point symmetry we need only four principal spectra. Here, the principal spectra are expressed by ab initio calculations for bcc Fe, fcc Co and fcc Ni in optical range as well as in hard and soft x-ray energy range, i.e. at the 2p- and 3p-edges. We also express principal spectra analytically using modified Kubo formula.

  13. "Artifactual" arsenate DNA

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2012-01-01

    The recent claim by Wolfe-Simon et al. that the Halomonas bacterial strain GFAJ-1 when grown in arsenate-containing medium with limiting phosphate is able to substitute phosphate with arsenate in biomolecules including nucleic acids and in particular DNA(1) arose much skepticism, primarily due...... to the very limited chemical stability of arsenate esters (see ref. 2 and references therein). A major part of the criticisms was concerned with the insufficient (bio)chemical evidence in the Wolfe-Simon study for the actual chemical incorporation of arsenate in DNA (and/or RNA). Redfield et al. now present...... evidence that the identification of arsenate DNA was artifactual....

  14. Fidelity and mutational spectrum of Pfu DNA polymerase on a human mitochondrial DNA sequence.

    Science.gov (United States)

    André, P; Kim, A; Khrapko, K; Thilly, W G

    1997-08-01

    The study of rare genetic changes in human tissues requires specialized techniques. Point mutations at fractions at or below 10(-6) must be observed to discover even the most prominent features of the point mutational spectrum. PCR permits the increase in number of mutant copies but does so at the expense of creating many additional mutations or "PCR noise". Thus, each DNA sequence studied must be characterized with regard to the DNA polymerase and conditions used to avoid interpreting a PCR-generated mutation as one arising in human tissue. The thermostable DNA polymerase derived from Pyrococcus furiosus designated Pfu has the highest fidelity of any DNA thermostable polymerase studied to date, and this property recommends it for analyses of tissue mutational spectra. Here, we apply constant denaturant capillary electrophoresis (CDCE) to separate and isolate the products of DNA amplification. This new strategy permitted direct enumeration and identification of point mutations created by Pfu DNA polymerase in a 96-bp low melting domain of a human mitochondrial sequence despite the very low mutant fractions generated in the PCR process. This sequence, containing part of the tRNA glycine and NADH dehydrogenase subunit 3 genes, is the target of our studies of mitochondrial mutagenesis in human cells and tissues. Incorrectly synthesized sequences were separated from the wild type as mutant/wild-type heteroduplexes by sequential enrichment on CDCE. An artificially constructed mutant was used as an internal standard to permit calculation of the mutant fraction. Our study found that the average error rate (mutations per base pair duplication) of Pfu was 6.5 x 10(-7), and five of its more frequent mutations (hot spots) consisted of three transversions (GC-->TA, AT-->TA, and AT-->CG), one transition (AT-->GC), and one 1-bp deletion (in an AAAAAA sequence). To achieve an even higher sensitivity, the amount of Pfu-induced mutants must be reduced.

  15. Inclusive sum rules and spectra of neutrons at the ISR

    International Nuclear Information System (INIS)

    Grigoryan, A.A.

    1975-01-01

    Neutron spectra in pp collisions at ISR energies are studied in the framework of sum rules for inclusive processes. The contributions of protons, π- and E- mesons to the energy sum rule are calculated at √5 = 53 GeV. It is shown by means of this sum rule that the spectra of neutrons at the ISR are in contradiction with the spectra of other particles also measured at the ISR

  16. A method to enhance the resolution of broadened spectra

    Energy Technology Data Exchange (ETDEWEB)

    Cabral P, A.; Jimenez D, H.; Torres V, M.; Azorin N, J.; Gutierrez C, A.; Gonzalez M, P.R.; Lopez E, J. [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico); Fuentes Z, G.A.; Cordoba, A. [UAM-I, 09340 Mexico D.F. (Mexico)

    1992-02-15

    A deconvolution method to analyze line overlapping broadened spectra is presented. Two approximation expressions from which the user can remove, either a Lorentzian or a Gaussian line from observed spectra are utilized. Moessbauer spectra, EPR and Thermoluminescence spectroscopies are analyzed. It is shown that in each case, the de convolved spectrum may provide valuable data to get a much closer characterization of a substance. (Author)

  17. A method to enhance the resolution of broadened spectra

    International Nuclear Information System (INIS)

    Cabral P, A.; Jimenez D, H.; Torres V, M.; Azorin N, J.; Gutierrez C, A.; Gonzalez M, P.R.; Lopez E, J.; Fuentes Z, G.A.; Cordoba, A.

    1992-02-01

    A deconvolution method to analyze line overlapping broadened spectra is presented. Two approximation expressions from which the user can remove, either a Lorentzian or a Gaussian line from observed spectra are utilized. Moessbauer spectra, EPR and Thermoluminescence spectroscopies are analyzed. It is shown that in each case, the de convolved spectrum may provide valuable data to get a much closer characterization of a substance. (Author)

  18. Geal: A general program for the analysis of alpha spectra

    International Nuclear Information System (INIS)

    Garcia-Torano, E.; Acena Barrenechea, M.L.

    1978-01-01

    A computing program for analysis and representation of alpha spectra obtained with surface barrier detectors is described. Several methods for fitting spectra are studied. A monoenergetic line or a doublet previously fitted has been used as a standard for the analyses of all kind of spectra. Some examples of application as well as a list of the program are shown. The program has been written in Fortran V language. (author)

  19. Incorporating Nuisance Parameters in Likelihoods for Multisource Spectra

    CERN Document Server

    Conway, J.S.

    2011-01-01

    We describe here the general mathematical approach to constructing likelihoods for fitting observed spectra in one or more dimensions with multiple sources, including the effects of systematic uncertainties represented as nuisance parameters, when the likelihood is to be maximized with respect to these parameters. We consider three types of nuisance parameters: simple multiplicative factors, source spectra "morphing" parameters, and parameters representing statistical uncertainties in the predicted source spectra.

  20. Atomic and molecular effects in the VUV spectra of solids

    International Nuclear Information System (INIS)

    Sonntag, B.

    1977-10-01

    The VUV spectra of solids are often dominated by atomic or molecular effects, which clearly manifest themselves in the gross features of the spectra and the fine structure at inner shell excitation thresholds. Evidence for the influence of atomic and molecular matrix elements, multiplet-splitting and correlation is presented. Special emphasis is given to the direct experimental verification based on the comparison of atomic and solid state spectra. (orig.) [de

  1. Theory of optical spectra of solvated electrons

    International Nuclear Information System (INIS)

    Kestner, N.R.

    1975-01-01

    During the last few years better theoretical models of solvated electron have been developed. These models allow one to calculate a priori the observable properties of the trapped electron. One of the most important and most widely determined properties is the optical spectrum. In this paper we consider the predictions of the theories not only as to the band maximum but line shape and width. In addition we will review how the theories predict these will depend on the solvent, pressure, temperature, and solvent density. In all cases extensive comparisons will be made with experimental work. In addition four new areas will be explored and recent results will be presented. These concern electrons in dense polar gases, the time development of the solvated electron spectrum, solvated electrons in mixed solvents, and photoelectron emission spectra (PEE) as it relates to higher excited states. This paper will review all recent theoretical calculations and present a critical review of the present status and future developments which are anticipated. The best theories are quite successful in predicting trends, and qualitative agreement concerning band maximum. The theory is still weak in predicting line shape and line width

  2. Mass spectra of alicylic compounds Pt. 8

    International Nuclear Information System (INIS)

    Remane, H.; Haufe, G.

    1980-01-01

    Mass spectrometric fragmentation of C 5 -C 8 as well as C 12 ring systems of tBHC and tBMC is discussed and compared to the fragmentation of Br-, hydroxy- and methoxy cycloalkanes of similar ring sizes. The dominant processes are the splitting of the functional groups yielding M-H 2 O 1+ , M-HOCH 3 1+ and M-Br 1+ fragments, and the disintegration of the rings producing C 3 H 4 X 1+ fragments (X=Br, OH, OCH 3 ). Intensities of the more important fragments correspond to the size of the ring. The isomers can be distinguished by their mass spectra due to the inequality of the intensities of the trans- and cis-forms of BHC and BMC. Functional groups influence mass spectrometric fragmentation as it is indicated by the correlation of the fragments of the bis-functional tBHC and tBMC and the fragments of monofractional compounds. (Sz.J.)

  3. On temperature spectra in grid turbulence

    International Nuclear Information System (INIS)

    Jayesh; Tong, C.; Warhaft, Z.

    1994-01-01

    This paper reports wind tunnel measurements of passive temperature spectra in decaying grid generated turbulence both with and without a mean transverse temperature gradient. The measurements cover a turbulence Reynolds number range 60 l 3/4 l . The remarkably low Reynolds number onset (Re l ∼70) of Kolmogorov--Obukhov--Corrsin scaling in isotropic grid turbulence is contrasted to the case of scalars in (anisotropic) shear flows where KOC scaling only appears at very high-Reynolds numbers (Re l ∼10 5 ). It is also shown that when the temperature fluctuations are inserted very close to the grid in the absence of a gradient (by means of a mandoline), the temperature spectrum behaves in a similar way to the linear gradient case, i.e., a spectrum with a scaling exponent close to -5/3 is observed, a result noted earlier in heated grid experiments. However, when the scalar is inserted farther downstream of the grid (in the fully developed turbulence), the spectrum has a scaling region of -1.3 and its dilation with Re is less well defined than for the other cases. The velocity spectrum is also shown to have a scaling region, of slope -1.3, and its onset occurs at higher Reynolds number than for the case of the scalar experiments that exhibit the KOC scaling

  4. System of pattern analysis of PIXE spectra

    Energy Technology Data Exchange (ETDEWEB)

    Murozono, K; Iwasaki, S; Inoue, J; Ishii, K; Kitamura, M [Tohoku Univ., Sendai (Japan). Faculty of Engineering; Sera, K; Futatsugawa, S

    1996-07-01

    We have developed an analysis system based on the pattern analysis method. By testing the system, several difficulties of the present method have been identified. We found the following solutions for them: pre-selection of candidate elements in a sample and the use of a proper absorber. The pre-selection of the candidate elements will not be a serious drawback in the industrial PIXE, because it will be easy to pre-process the spectra for a few samples in the beginning of the mass processing of samples of the same kind. On the other hand, reduction of the efficiency due to the use of funny filter is significant only in the lower energy region, where we usually do not suffer from insufficient yields of lighter elements in common samples. The selection of the most suitable filter requires PIXE user to be deeply experienced. In particular, it is not easy to choose the best filter to suppress the yield of peak of an abundant element as the absorption edge filter. It will be important task to find a set of suitable combination of representative samples and corresponding filters. Furthermore, the peak profile model should be improved from the simple Gaussian approximation to more realistic ones with exponential tail, flat component below the peak and escape peaks, etc. It is also necessary to develop a theoretical approach for the background shape of the bremsstrahlung. (J.P.N.)

  5. Evaluating Lyapunov exponent spectra with neural networks

    International Nuclear Information System (INIS)

    Maus, A.; Sprott, J.C.

    2013-01-01

    Highlights: • Cross-correlation is employed to remove spurious Lyapunov exponents from a spectrum. • Neural networks are shown to accurately model Lyapunov exponent spectra. • Neural networks compare favorably to local linear fits in modeling Lyapunov exponents. • Numerical experiments are performed with time series of varying length and noise. • Methods perform reasonably well on discrete time series. -- Abstract: A method using discrete cross-correlation for identifying and removing spurious Lyapunov exponents when embedding experimental data in a dimension greater than the original system is introduced. The method uses a distribution of calculated exponent values produced by modeling a single time series many times or multiple instances of a time series. For this task, global models are shown to compare favorably to local models traditionally used for time series taken from the Hénon map and delayed Hénon map, especially when the time series are short or contaminated by noise. An additional merit of global modeling is its ability to estimate the dynamical and geometrical properties of the original system such as the attractor dimension, entropy, and lag space, although consideration must be taken for the time it takes to train the global models

  6. Estimating Eulerian spectra from pairs of drifters

    Science.gov (United States)

    LaCasce, Joe

    2017-04-01

    GPS-tracked surface drifters offer the possibility of sampling energetic variations at the ocean surface on scales of only 10s of meters, much less than that resolved by satellite. Here we investigate whether velocity differences between pairs of drifters can be used to estimate kinetic energy spectra. Theoretical relations between the spectrum and the second-order longitudinal structure function for 2D non-divergent flow are derived. The structure function is a natural statistic for particle pairs and is easily calculated. However it integrates contributions across wavenumber, and this tends to obscure the spectral dependencies when turbulent inertial ranges are of finite extent. Nevertheless, the transform from spectrum to structure function is robust, as illustrated with Eulerian data collected from aircraft. The inverse transform, from structure function to spectrum, is much less robust, yielding poor results in particular at large wavenumbers. This occurs because the transform involves a filter function which magnifies contributions from large pair separations, which tend to be noisy. Fitting the structure function to a polynomial improves the spectral estimate, but not sufficiently to distinguish correct inertial range dependencies. Thus with Lagrangian data, it is appears preferable to focus on structure functions, despite their shortcomings.

  7. Absorption Spectra of Gold Nanoparticle Suspensions

    Science.gov (United States)

    Anan'eva, M. V.; Nurmukhametov, D. R.; Zverev, A. S.; Nelyubina, N. V.; Zvekov, A. A.; Russakov, D. M.; Kalenskii, A. V.; Eremenko, A. N.

    2018-02-01

    Three gold nanoparticle suspensions are obtained, and mean radii in distributions - (6.1 ± 0.2), (11.9 ± 0.3), and (17.3 ± 0.7) nm - are determined by the transmission electron microscopy method. The optical absorption spectra of suspensions are obtained and studied. Calculation of spectral dependences of the absorption index of suspensions at values of the gold complex refractive index taken from the literature showed a significant deviation of experimental and calculated data in the region of 450-800 nm. Spectral dependences of the absorption of suspensions are simulated within the framework of the Mie-Drude theory taking into account the interband absorption in the form of an additional term in the imaginary part of the dielectric permittivity of the Gaussian type. It is shown that to quantify the spectral dependences in the region of the plasmon absorption band of nanoparticles, correction of the parameters of the interband absorption is necessary in addition to the increase of the relaxation parameter of the Drude theory. Spectral dependences of the dielectric permittivity of gold in nanodimensional state are refined from the solution of the inverse problem. The results of the present work are important for predicting the special features of operation of photonic devices and optical detonators based on gold nanoparticles.

  8. Program for the surface muon spectra calculation

    International Nuclear Information System (INIS)

    Arkatov, Yu.M.; Voloshchuk, V.I.; Zolenko, V.A.; Prokhorets, I.M.; Soldatov, S.A.

    1987-01-01

    Program for the ''surface'' muon spectrum calculation is described. The algorithm is based on simulation of coordinates of π-meson birth point and direction of its escape from meson-forming target (MFT) according to angular distribution with the use of Monte Carlo method. Ionization losses of π-(μ)-mesons in the target are taken into account in the program. Calculation of ''surface'' muon spectrum is performed in the range of electron energies from 150 MeV up to 1000 MeV. Spectra of π-mesons are calculated with account of ionization losses in the target and without it. Distributions over lengths of π-meson paths in MFT and contribution of separate sections of the target to pion flux at the outlet of meson channel are calculated as well. Meson-forming target for calculation can be made of any material. The program provides for the use of the MFT itself in the form of photon converter or photon converter is located in front of the target. The program is composed of 13 subprograms; 2 of them represent generators of pseudorandom numbers, distributed uniformly in the range from 0 up to 1, and numbers with Gauss distribution. Example of calculation for copper target of 3 cm length, electron beam current-1 μA, energy-300 MeV is presented

  9. Inflationary power spectra with quantum holonomy corrections

    Energy Technology Data Exchange (ETDEWEB)

    Mielczarek, Jakub, E-mail: jakub.mielczarek@uj.edu.pl [Institute of Physics, Jagiellonian University, Reymonta 4, Cracow, 30-059 Poland (Poland)

    2014-03-01

    In this paper we study slow-roll inflation with holonomy corrections from loop quantum cosmology. It was previously shown that, in the Planck epoch, these corrections lead to such effects as singularity avoidance, metric signature change and a state of silence. Here, we consider holonomy corrections affecting the phase of cosmic inflation, which takes place away from the Planck epoch. Both tensor and scalar power spectra of primordial inflationary perturbations are computed up to the first order in slow-roll parameters and V/ρ{sub c}, where V is a potential of the scalar field and ρ{sub c} is a critical energy density (expected to be of the order of the Planck energy density). Possible normalizations of modes at short scales are discussed. In case the normalization is performed with use of the Wronskian condition applied to adiabatic vacuum, the tensor and scalar spectral indices are not quantum corrected in the leading order. However, by choosing an alternative method of normalization one can obtain quantum corrections in the leading order. Furthermore, we show that the holonomy-corrected equations of motion for tensor and scalar modes can be derived based on effective background metrics. This allows us to show that the classical Wronskian normalization condition is well defined for the cosmological perturbations with holonomy corrections.

  10. Collapse postulate for observables with continuous spectra

    International Nuclear Information System (INIS)

    Srinivas, M.D.; Madras Univ.

    1980-01-01

    In order to provide a mathematical framework for discussing the statistical correlations between the outcomes, when an arbitrary sequence of observables are measured, it is necessary to generalize the conventional von Neumann-Lueders collapse postulate to observables with a continuous spectrum. It is shown that the standard prescription in conventional quantum theory for the joint probabilities of compatible observables is sufficient to characterize, more or less completely, the appropriate 'generalized collapse postulate' which associates with each observable a unique 'finitely additive expectation valued measure'. An interesting feature of the collapse associated with observables with continuous spectra, which again follows from the basic principles of conventional quantum theory, is that it must be formulated in terms of the so-called non-normal conditional expectations, which implies that the joint probabilities associated with successive observations of such observables are not in general sigma-additive. The implications of this non-sigma-additivity on the determination of expectation values, correlation functions etc., are also investigated. It is demonstrated that the basic prescriptions introduced in this paper constitute a natural completion of the framework of conventional quantum theory for discussing the statistics of an arbitrary sequence of observations. (orig.) 891 HJ/orig. 892 CKA

  11. Efficiency and yield spectra of inorganic scintillates

    International Nuclear Information System (INIS)

    Rodnyi, P.A.

    1998-01-01

    Recent developments in the field of energy loss in inorganic scintillators are reviewed. The main parameters, which control the fundamental limit of the scintillator energy efficiency, are determined. It is shown that together with simple cascade processes one should take into account the production of plasmons to estimate the energy efficiency of scintillators or other phosphors excited by an ionizing radiation. Core-to-valence luminescence related to 5pCs→3pCl transitions is investigated in some chlorides: CsCl, KCl, RbCl, NaCl, KCaCl 3 , RbCaCl 3 . The yield spectra of the crystals in the VUV and X-ray regions are also studied. It is shown that the 4pRb-core states are involved in the process of creation of holes in the 5pCs-core band in Rb-based crystals. The formation of holes in the potassium core band acts as a competing process and suppresses the radiative core-to-valence transitions

  12. The Global Signature of Ocean Wave Spectra

    Science.gov (United States)

    Portilla-Yandún, Jesús

    2018-01-01

    A global atlas of ocean wave spectra is developed and presented. The development is based on a new technique for deriving wave spectral statistics, which is applied to the extensive ERA-Interim database from European Centre of Medium-Range Weather Forecasts. Spectral statistics is based on the idea of long-term wave systems, which are unique and distinct at every geographical point. The identification of those wave systems allows their separation from the overall spectrum using the partition technique. Their further characterization is made using standard integrated parameters, which turn out much more meaningful when applied to the individual components than to the total spectrum. The parameters developed include the density distribution of spectral partitions, which is the main descriptor; the identified wave systems; the individual distribution of the characteristic frequencies, directions, wave height, wave age, seasonal variability of wind and waves; return periods derived from extreme value analysis; and crossing-sea probabilities. This information is made available in web format for public use at http://www.modemat.epn.edu.ec/#/nereo. It is found that wave spectral statistics offers the possibility to synthesize data while providing a direct and comprehensive view of the local and regional wave conditions.

  13. Emissive spectra of shock-heated argon

    International Nuclear Information System (INIS)

    Tang Jingyou; Gu Yan; Peng Qixian; Bai Yulin; Li Ping

    2003-01-01

    To study the radiant properties of argon under weak shock compression, an aluminum target filled with gaseous argon at ambient states was impacted by a tungsten alloy projectile which was launched from a two-stage light gun to 2.00 km/s. The radiant signals of single shock-compressed argon were recorded by a six-channel pyrometer and oscilloscopes, which varied with time linearly for the five channels from 405 nm to 700 nm and exponentially for the channel 800 nm, and the corresponding velocity of shock wave was determined to be 4.10 ± 0.09 km/s. By the present experiment, it has been shown that the absorbability of the shock-heated argon is low for visual light and the optical depths of argon gas turn from thin to thick as wavelengths gradually increase. The time-resolved spectra in the rising-front of the radiant signal in the re-shocked argon were recorded by means of an OMA, and strong emissive spectrum bands near 450 nm light-wave length but no linear spectrum were found. The emissive spectrum properties of shock-compression argon were qualitatively explained by the state parameters and ionization degree

  14. FT-Raman and QM/MM study of the interaction between histamine and DNA

    International Nuclear Information System (INIS)

    Ruiz-Chica, A.J.; Soriano, A.; Tunon, I.; Sanchez-Jimenez, F.M.; Silla, E.; Ramirez, F.J.

    2006-01-01

    The interaction between histamine and highly polymerized calf-thymus DNA has been investigated using FT-Raman spectroscopy and the hybrid QM/MM (quantum mechanics/molecular mechanics) methodology. Raman spectra of solutions containing histamine and calf-thymus DNA, at different molar ratios, were recorded. Solutions were prepared at physiological settings of pH and ionic strength, using both natural and heavy water as the solvent. The analysis of the spectral changes on the DNA Raman spectra when adding different concentrations of histamine allowed us to identify the reactive sites of DNA and histamine, which were used to built two minor groove and one intercalated binding models. They were further used as starting points of the QM/MM theoretical study. However, minimal energy points were only reached for the two minor groove models. For each optimized structure, we calculated analytical force constants of histamine molecule in order to perform the vibrational dynamics. Normal mode descriptions allowed us to compare calculated wavenumbers for DNA-interacting histamine to those measured in the Raman spectra of DNA-histamine solutions

  15. A pulse radiolysis study of the electron reaction with DNA in aqueous solution and ice

    International Nuclear Information System (INIS)

    Verberne, J.B.

    1981-01-01

    Research is described into some aspects of the interaction of ionizing radiation with DNA, the main emphasis being on the indirect effect where the radiation causes the formation of intermediates in the surrounding medium which then interact with the DNA. Experiments are described which have been carried out to examine the dependence of the reaction rate constant on ionic strength and counterion charge. They show that for double stranded DNA (dsDNA) the reaction rate constant increases with ionic strength. To see whether quantitative agreement can be obtained between the observations and a physical interpretation the author combines a model for reaction kinetics and a refined model for the electrostatic potential into one to obtain a theoretical rate constant for reaction with a cylindrical polyelectrolyte. Optical absorption spectra of the electron adducts of ss- and dsDNA are shown to exist and they differ significantly from the spectra of the H and OH adducts. The spectra of the electron adducts of the nucleotides have been measured. Experiments are also described devoted to the precursor of the hydrated electron: the thermalized, dry electron. Although from a radiation chemical point of view the experiments yielded a lot of information (a direct observation of the dry electron, the kinetics of electron localization, the role of ice defects in the solvation process, etc.), they proved also that the dry electron does not react with DNA in an ice matrix. (Auth.)

  16. [Experimental study on spectra of compressed air microwave plasma].

    Science.gov (United States)

    Liu, Yong-Xi; Zhang, Gui-Xin; Wang, Qiang; Hou, Ling-Yun

    2013-03-01

    Using a microwave plasma generator, compressed air microwave plasma was excited under 1 - 5 atm pressures. Under different pressures and different incident microwave power, the emission spectra of compressed air microwave plasma were studied with a spectra measuring system. The results show that continuum is significant at atmospheric pressure and the characteristic will be weakened as the pressure increases. The band spectra intensity will be reduced with the falling of the incident microwave power and the band spectra were still significant. The experimental results are valuable to studying the characteristics of compressed air microwave plasma and the generating conditions of NO active groups.

  17. [Study of the interaction mechanism between brodifacoum and DNA by spectroscopy].

    Science.gov (United States)

    Duan, Yun-qing; Min, Shun-geng

    2009-04-01

    The interaction between brodifacoum (3-[3-(4'-bromophenyl-4) 1,2,3,4-tetralin-10]-4-hydroxyl-coumarin) (BDF), an anticoagulant rodenticide, and calf thymus DNA (ct-DNA) was studied by UV spectrum and fluorescence spectrum. The results were summarized as follows: There was a hypochromic effect of low concentration ct-DNA on the UV spectra. The fluorescence quenching studies showed a regular decrease in the fluorescence intensity after addition of ct-DNA by the static quenching mode with a quenching constant (Ksv) of 1.21 x 10(4) L x mol(-1) at 27 degrees C. The BDF possibly bonded to ct-DNA mainly via Van der Waals forces by the corresponding thermodynamics parameter. KI quenching experiment found that there was not obvious protection of ct-DNA to BDF. The fluorescence intensity of BDF/ct-DNA system changed with the variation in ionic strength Quenching of ct-DNA on the fluorescence of BDF/beta-CD inclusion complex was reduced in contrast with the free BDF, which showed that beta-CD could provide BDF with protection. So the comprehensive interaction mode of BDF with ct-DNA may be the groove binding by the above results. It was indicated that there had been static-electro interaction between BDF and ct-DNA at the same time. The conjunct action of Van der Waals forces and electrostatic attraction favorably provide BDF bonding interaction in the groove of ct-DNA.

  18. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted

    2011-01-01

    Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient...... genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little...... systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear...

  19. DNA fusion gene vaccines

    DEFF Research Database (Denmark)

    Holst, Peter Johannes; Bassi, Maria Rosaria; Thomsen, Allan Randrup

    2010-01-01

    DNA vaccines are versatile and safe, but limited immunogenicity has prevented their use in the clinical setting. Experimentally, immunogenicity may be enhanced by the use of new delivery technologies, by coadministration of cytokines and pathogen-associated molecular patterns, or by fusion...... of antigens into molecular domains that enhance antigen presentation. More specifically, the immunogenicity of DNA vaccines may benefit from increased protein synthesis, increased T-cell help and MHC class I presentation, and the addition of a range of specific cytokines and pathogen-associated molecular...... with viral-vectored vaccines, various synergistic components may need to be incorporated into DNA vaccines. From the perspective of the future clinical use of DNA vaccines, it has been suggested that antigen presentation should be improved and cytokine coadministration attempted. However, even...

  20. DNA Sampling Hook

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

  1. Retroviral DNA Integration

    Science.gov (United States)

    2016-01-01

    The integration of a DNA copy of the viral RNA genome into host chromatin is the defining step of retroviral replication. This enzymatic process is catalyzed by the virus-encoded integrase protein, which is conserved among retroviruses and LTR-retrotransposons. Retroviral integration proceeds via two integrase activities: 3′-processing of the viral DNA ends, followed by the strand transfer of the processed ends into host cell chromosomal DNA. Herein we review the molecular mechanism of retroviral DNA integration, with an emphasis on reaction chemistries and architectures of the nucleoprotein complexes involved. We additionally discuss the latest advances on anti-integrase drug development for the treatment of AIDS and the utility of integrating retroviral vectors in gene therapy applications. PMID:27198982

  2. DNA damage and carcinogenesis

    International Nuclear Information System (INIS)

    Stelow, R.B.

    1980-01-01

    Although cancer may arise as a result of many different types of molecular changes, there is little reason to doubt that changes to DNA are one of the more important ones in cancer initiation. Although DNA repair mechanisms seem able to eliminate a very large fraction of deleterious changes to DNA, we not only have little insight into the molecular mechanisms involved in such repair, but have a negligible amount of information to permit us to estimate the shape of dose response relations at low doses. The case of skin cancer is a special one, in that the average population is exposed to sufficient solar uv so that the effects of small increments in uv dose may be estimated. An approximate 85% reduction in DNA repair increases skin cancer incidence 10 4 fold

  3. DNA-Origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Gothelf, Kurt Vesterager

    2010-01-01

    DNA-nanostrukturer giver nye muligheder for studier af individuelle molekyler. Ved at udnytte DNAs unikke selvsamlende egenskaber kan man designe systemer, hvorpå der kan studeres kemiske reaktioner, fluoroforer og biiomolekyler på enkeltmolekyle-niveau....

  4. DNA Microarray Technology

    Science.gov (United States)

    Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

  5. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  6. Close encounters with DNA

    Science.gov (United States)

    Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

    2014-01-01

    Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

  7. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  8. HPV DNA test

    Science.gov (United States)

    ... test; Cancer of cervix - HPV DNA test References Hacker NF. Cervical dysplasia and cancer. In: Hacker NF, Gambone JC, Hobel CJ, eds. Hacker and Moore's Essentials of Obstetrics and Gynecology . 6th ...

  9. Close encounters with DNA.

    Science.gov (United States)

    Maffeo, C; Yoo, J; Comer, J; Wells, D B; Luan, B; Aksimentiev, A

    2014-10-15

    Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

  10. FBI's DNA analysis program

    Science.gov (United States)

    Brown, John R.

    1994-03-01

    Forensic DNA profiling technology is a significant law enforcement tool due to its superior discriminating power. Applying the principles of population genetics to the DNA profile obtained in violent crime investigations results in low frequency of occurrence estimates for the DNA profile. These estimates often range from a frequency of occurrence of 1 in 50 unrelated individuals to 1 in a million unrelated individuals or even smaller. It is this power to discriminate among individuals in the population that has propelled forensic DNA technology to the forefront of forensic testing in violent crime cases. Not only is the technology extremely powerful in including or excluding a criminal suspect as the perpetrator, but it also gives rise to the potential of identifying criminal suspects in cases where the investigators of unknown suspect cases have exhausted all other available leads.

  11. Making DNA Fingerprints.

    Science.gov (United States)

    Nunley, Kathie F.

    1996-01-01

    Presents an activity to simulate electrophoresis using everyday items. Uses adding machine paper to construct a set of DNA fingerprints that can be used to solve crime cases designed by students in any biology class. (JRH)

  12. Radiation damage in DNA

    International Nuclear Information System (INIS)

    Lafleur, V.

    1978-01-01

    A number of experiments are described with the purpose to obtain a better insight in the chemical nature and the biological significance of radiation-induced damage in DNA, with some emphasis on the significance of alkali-labile sites. It is shown that not only reactions of OH radicals but also of H radicals introduce breaks and other inactivating damage in single-standed phiX174 DNA. It is found that phosphate buffer is very suitable for the study of the reactions of H radicals with DNA, as the H 2 PO 4 - ions convert the hydrated electrons into H radicals. The hydrated electron, which does react with DNA, does not cause a detectable inactivation. (Auth.)

  13. DNA to DNA transcription might exist in eukaryotic cells

    OpenAIRE

    Li, Gao-De

    2016-01-01

    Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the functions of certain noncoding DNA in the human and other eukaryotic genomes.

  14. Patterning nanocrystals using DNA

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Shara Carol [Univ. of California, Berkeley, CA (United States)

    2003-01-01

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices

  15. Das DNA-Puzzle

    Science.gov (United States)

    Kirchner, Stefan

    Im Jahre 1953 wurde von James Watson und Francis Crick erstmalig der strukturelle Aufbau der sogenannten DNA (Desoxyribonukleinsäure) beschrieben, welche das Erbgut jedes Lebewesens enthält. Der wesentliche Teil des Erbguts wird dabei durch eine sehr lange Folge der vier Basen Adenin (A), Cytosin (C), Guanin (G) und Thymin (T) codiert. Seit einigen Jahren ist es möglich, die Folge der vier Basen zu einer gegebenen DNA zu bestimmen. Biologen bezeichnen diesen Vorgang als Sequenzierung.

  16. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  17. Racemic DNA Crystallography

    OpenAIRE

    Mandal , Pradeep K.; Collie , Gavin W.; Kauffmann , Brice; Huc , Ivan

    2014-01-01

    International audience; Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of Land D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propens...

  18. Celebrating DNA's Repair Crew.

    Science.gov (United States)

    Kunkel, Thomas A

    2015-12-03

    This year, the Nobel Prize in Chemistry has been awarded to Tomas Lindahl, Aziz Sancar, and Paul Modrich for their seminal studies of the mechanisms by which cells from bacteria to man repair DNA damage that is generated by normal cellular metabolism and stress from the environment. These studies beautifully illustrate the remarkable power of DNA repair to influence life from evolution through disease susceptibility. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Introduction to DNA methods

    International Nuclear Information System (INIS)

    Delincee, H.

    1991-01-01

    The purpose of this session is to discuss the various possibilities for detecting modifications in DNA after irradiation and whether these changes can be utilized as an indicator for the irradiation treatment of foods. The requirement to be fulfilled is that the method be able to distinguish irradiated food without the presence of a control sample, thus the measured response after irradiation must be large enough to supersede background levels from other treatments. Much work has been performed on the effects of radiation on DNA, particularly due to its importance in radiation biology. The main lesions of DNA as a result of irradiation are base damage, damage of the sugar moiety, single strand and double strand breaks. Crosslinking between bases also occurs, e.g. production of thymine dimers, or between DNA and protein. A valuable review on how to utilize these DNA changes for detection purposes has already appeared. Tables 1, 2 and 3 list the proposed methods of detecting changes in irradiated DNA, some identified products as examples for a possible irradiation indicator, in the case of immunoassay the substance used as antigen, and some selected literature references. In this short review, it is not intended to provide a complete literature survey

  20. Variations in brain DNA

    Directory of Open Access Journals (Sweden)

    Jesus eAvila

    2014-11-01

    Full Text Available It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.

  1. Order and correlations in genomic DNA sequences. The spectral approach

    International Nuclear Information System (INIS)

    Lobzin, Vasilii V; Chechetkin, Vladimir R

    2000-01-01

    The structural analysis of genomic DNA sequences is discussed in the framework of the spectral approach, which is sufficiently universal due to the reciprocal correspondence and mutual complementarity of Fourier transform length scales. The spectral characteristics of random sequences of the same nucleotide composition possess the property of self-averaging for relatively short sequences of length M≥100-300. Comparison with the characteristics of random sequences determines the statistical significance of the structural features observed. Apart from traditional applications to the search for hidden periodicities, spectral methods are also efficient in studying mutual correlations in DNA sequences. By combining spectra for structure factors and correlation functions, not only integral correlations can be estimated but also their origin identified. Using the structural spectral entropy approach, the regularity of a sequence can be quantitatively assessed. A brief introduction to the problem is also presented and other major methods of DNA sequence analysis described. (reviews of topical problems)

  2. The re-entrant cholesteric phase of DNA

    Science.gov (United States)

    Yevdokimov, Yu. M.; Skuridin, S. G.; Salyanov, V. I.; Semenov, S. V.; Shtykova, E. V.; Dadinova, L. A.; Kompanets, O. N.; Kats, E. I.

    2017-07-01

    The character of packing of double-stranded DNA molecules in particles of liquid-crystal dispersions formed as a result of the phase exclusion of DNA molecules from aqueous salt polyethylene glycol solutions has been estimated by comparing the circular dichroism (CD) spectra of these dispersions recorded at different osmotic pressures and temperatures. It is shown that the first cycle of heating of dispersion particles with hexagonally packed double-stranded DNA molecules leads to the occurrence of abnormal optical activity of these particles, which manifests itself in the form of a strong negative CD band, characteristic of DNA cholesterics. Moreover, subsequent cooling is accompanied by a further increase in the abnormal optical activity, which indicates the existence of the "hexagonal → cholesteric packing" phase transition, controlled by both the osmotic pressure of the solution and its temperature. The result obtained can be described in terms of "quasi-nematic" layers composed of orientationally ordered DNA molecules in the structure of dispersion particles. There are two possible ways of packing for these layers, which determine their hexagonal or cholesteric spatial structure. The second heating → cooling cycle confirms these results and is indicative of possible differences in the packing of double-stranded DNA molecules in the hexagonal phase, which depend on the osmotic pressure of the solution.

  3. Optical Detection of Non-amplified Genomic DNA

    Science.gov (United States)

    Li, Di; Fan, Chunhai

    Nucleic acid sequences are unique to every living organisms including animals, plants and even bacteria and virus, which provide a practical molecular target for the identification and diagnosis of various diseases. DNA contains heterocyclic rings that has inherent optical absorbance at 260 nm, which is widely used to quantify single and double stranded DNA in biology. However, this simple quantification method could not differentiate sequences; therefore it is not suitable for sequence-specific analyte detection. In addition to a few exceptions such as chiral-related circular dichroism spectra, DNA hybridization does not produce significant changes in optical signals, thus an optical label is generally needed for sequence-specific DNA detection with optical means. During the last two decades, we have witnessed explosive progress in the area of optical DNA detection, especially with the help of simultaneously rapidly developed nanomaterials. In this chapter, we will summarize recent advances in optical DNA detection including colorimetric, fluorescent, luminescent, surface plasmon resonance (SPR) and Raman scattering assays. Challenges and problems remained to be addressed are also discussed.

  4. Indirect measurements of X-ray spectra

    International Nuclear Information System (INIS)

    Mainardi, R.T.

    2006-01-01

    To the effects of measuring the spectral distribution of the radiation emitted by the x-ray tubes and electron accelerators, numerous procedures that are grouped in two big categories exist at the present time: direct and indirect methods. The first ones use high resolution detectors that should be positioned, together with the appropriate collimator, in the direction of the x ray beam. The user should be an expert in the use and correction of the obtained data by the different effects that affect the detector operation such as efficiency and resolution in terms of the energy of the detected radiation. The indirect procedures, although its are more simple to use, its also require a considerable space along the beam to position the ionization chamber and the necessary absorbents to construct by this way the denominated attenuation curve. We will analyze the operation principle of the indirect methods and a new proposal in which such important novelties are introduced as the beam dispersion to avoid to measure along the main beam and that of determination of the attenuation curve in simultaneous form. By this way, with a single shot of the tube, the attenuation curve is measured, being necessary at most a shot of additional calibration to know the relative response of the detectors used in the experimental array. The physical processes involved in the obtaining of an attenuation curve are very well well-known and this it finishes it can be theoretically calculated if the analytic form of the spectrum is supposed well-known. Finally, we will see a spectra reconstruction example with the Kramers parametric form and comparisons with numeric simulations carried out with broadly validated programs as well as the possibility of the use of solid state dosemeters in the obtention of the attenuation curve. (Author)

  5. Use and generation of floor response spectra

    International Nuclear Information System (INIS)

    Ordonez Villalobos, A.

    1983-01-01

    One of the main objectives of the dynamic analysis of the structures of a nuclear power plant is the determination of the dynamic input that these structures transmit to the equipment and substructures they support, usually given as Floor Response Spectra (FRS). A close collaboration and feedback between the different groups that use and develop the FRS, is considered to be a very important factor in order to adapt the scope and content of the FRS to the precision required for a proper analysis or testing of the equipment; not only for the action of simple events but also for multiple combined actions. These aspects should be evaluated not only in the final stages of qualification of the equipment users schedules do not coincide with the schedules of the analysis group that develops the FRS. Different mechanisms of interchange of information and colaboration are suggested in order to optimize the availability, use and production of FRS. In the aspect of FRS generation, different procedures are reviewed including the direct procedures, not only for FRS but also for secondary FRS that are needed for the evaluation of equipment supported on other equipment or subsystems. It is concluded that in many cases, the direct procedures can be developed economically with the advantage that is easy to take into account the variability not only of the transfer function (including damping, stiffness and modal mass ratio). Different probabilities of excedence levels can be stabilized in order to obtain a more realistic dynamic response of the equipment. These last aspects can contribute to a more flexible procedure for the availability and generation of the FRS. (orig./HP)

  6. Specdata: Automated Analysis Software for Broadband Spectra

    Science.gov (United States)

    Oliveira, Jasmine N.; Martin-Drumel, Marie-Aline; McCarthy, Michael C.

    2017-06-01

    With the advancement of chirped-pulse techniques, broadband rotational spectra with a few tens to several hundred GHz of spectral coverage are now routinely recorded. When studying multi-component mixtures that might result, for example, with the use of an electrical discharge, lines of new chemical species are often obscured by those of known compounds, and analysis can be laborious. To address this issue, we have developed SPECdata, an open source, interactive tool which is designed to simplify and greatly accelerate the spectral analysis and discovery. Our software tool combines both automated and manual components that free the user from computation, while giving him/her considerable flexibility to assign, manipulate, interpret and export their analysis. The automated - and key - component of the new software is a database query system that rapidly assigns transitions of known species in an experimental spectrum. For each experiment, the software identifies spectral features, and subsequently assigns them to known molecules within an in-house database (Pickett .cat files, list of frequencies...), or those catalogued in Splatalogue (using automatic on-line queries). With suggested assignments, the control is then handed over to the user who can choose to accept, decline or add additional species. Data visualization, statistical information, and interactive widgets assist the user in making decisions about their data. SPECdata has several other useful features intended to improve the user experience. Exporting a full report of the analysis, or a peak file in which assigned lines are removed are among several options. A user may also save their progress to continue at another time. Additional features of SPECdata help the user to maintain and expand their database for future use. A user-friendly interface allows one to search, upload, edit or update catalog or experiment entries.

  7. Lyman Limit Absorbers in GALEX Spectra

    Science.gov (United States)

    Williger, Gerard M.; Haberzettl, Lutz G.; Ribaudo, Joseph; Kuchner, Marc J.; Burchett, Joseph; Clowes, Roger G.; Lauroesch, James T.; Mills, Brianna; Borden, Jeremy

    2018-01-01

    We describe the method and early results for crowdsourcing a search for low-redshift partial and complete Lyman Limit Systems (pLLSs and LLSs) in the GALEX spectral archive. LLSs have been found in large numbers at z>3 and traced to lower redshift through a relatively small number of QSO spectra from spaced-based telescopes. From a sample of 44 pLLSs and 11 LLSs at 0.1 = -0.32 +/- 0.07 and the low-metallicity portion centered at = -1.87 +/- 0.11.The GALEX spectral archive offers a vast dataset potentially containing hundreds of LLSs, which may be leveraged to search for such a bimodality and track its evolution within the unconstrained near-UV gap at 1data coverage and signal-to-noise ratio are highly variable, which hampers an automated search. We have therefore begun crowdsourcing a subset of the GALEX archive for LLSs and pLLSs via a Zooniverse project. Initially, undergraduate physics majors are performing a pilot project before releasing to citizen scientists in the public at large. We will then vet candidate systems and estimate column densities in a follow-up analysis. Upon assessing the accuracy of the physics majors’ identifications, the results will be used to devise a larger program with the help of the general public. The resulting data set would then provide the best available link between the HST-selected far-UV and ground-based pLLS+LLS samples and provide an ideal sample for consequent metallicity determinations.

  8. BASACF, Integral Neutron Spectra Adjustment and Dosimetry

    International Nuclear Information System (INIS)

    Tichy, Milos

    1996-01-01

    1 - Description of program or function: Adjustment of a neutron spectrum based on integral detector measurements and calculation of an integral dosimetric quantity (integral flux, d.p.a., dose equivalent) and its variance. The program requires measured data (activities and their covariance matrix) and a priori information (spectrum, dosimetry cross sections, integral quantity conversion factor and their covariance matrices). All a priori covariance matrices can be read in from a file prepared by some other code or can be generated by means of three different methods (by subroutines included in the program). A subroutine which can normalize the a priori flux to measured data is also included. The program provides also adjusted dosimetry cross sections (with covariance matrix) so that it can be used for an adjustment of cross sections (or response functions of e.g. Bonner balls) by measurements in well-known neutron spectra. 2 - Method of solution: Bayesian theorem on conditional probability applied to linearized relation between activities, dosimetry cross sections and flux. All probability distributions are supposed to be normal and this supposition leads to minimizing of the same functional as least squares method (STAY'SL). This task is solved by a covariance filter method which avoids any matrix inversion and is numerically robust and stable. 3 - Restrictions on the complexity of the problem: This version can use 45 energy groups and 5 detectors and occupies 310 kB of main memory. This restriction can be modified according to available memory. The covariance matrix of activities is supposed diagonal. A solution is produced for any set of input data but in the case of non-consistent data, when measured activities do not match the a priori flux, the solution is not very meaningful

  9. Measuring Transmission Spectra from the Ground

    Science.gov (United States)

    Jordan, Andres; Espinoza, Nestor; Eyheramendy, Susana

    2015-08-01

    Transmission spectroscopy allows study of the atmospheres of exoplanets without the need of spatially resolving them from their parent stars and is one of the most valuable follow-up possibilities offered by transiting systems. The measurement of a transmission spectrum, i.e. the apparent planetary size in units in the stellar radius as a function of wavelength, is conceptually simple, but the expected features that need to be discerned are on the order of one part in a thousand or less, and need to be extracted against a background of (potentially correlated) noise and systematic effects with amplitudes greatly exceeding that of the sought signal. In this talk I will describe how we have tackled the estimation of transmission spectra in a ground based survey we are carrying out with IMACS at Las Campanas Observatory, the Arizona-CfA-Catolica Exoplanet Spectroscopy Survey. Our treatment assumes an additive model consisting of the signal, common systematics and one of a set of stochastic processes with different memory characteristics for the noise. Common systematics are estimated from comparison stars using principal component analysis and the model parameter posterior distributions are estimated using MCMC. Model comparison is used to let the data select the model with the most appropriate noise component. I will illustrate the performance of our approach, and discuss possible avenues of improvement. I will also illustrate the importance of potential biases arising from our incomplete knowledge of stellar properties. In particular, I will show that limb darkening assumptions can limit the accuracy of our estimates of planetary radii above the achievable precisions in regimes currently being probed.

  10. Theoretical modelling of actinide spectra in solution

    International Nuclear Information System (INIS)

    Danilo, Cecile

    2009-01-01

    The framework of this PhD is the interpretation of Nuclear Magnetic Relaxation Dispersion experiments performed on solvated U"4"+, NpO_2"+ and PuO_2"2"+, which all have a f"2 configuration. Unexpectedly the two actinyl ions have a much higher relaxivity than U"4"+,. One possible explanation is that the electronic relaxation rate is faster for Uranium(IV) than for the actinyl ions. We address this problem by exploring the electronic spectrum of the three compounds in gas phase and in solution with a two-step SOCI (Spin-Orbit Configuration-Interaction) method. The influence of electron correlation (treated in the first step) and spin-orbit relaxation effects (considered in the second step) has been discussed thoroughly. Solvent effects have been investigated as well. Another issue that has been questioned is the accuracy of Density Functional Theory for the study of actinide species. This matter has been discussed by comparing its performance to wave-function based correlated methods. The chemical problem chosen was the water exchange in [UO_2"2"+ (H_2O)_5]. We looked at the associative and at the dissociative mechanisms using a model with one additional water in the second hydration sphere. The last part of the thesis dealt with the spectroscopy of coordinated Uranyl(V). Absorption spectrum of Uranyl(V) with various ligands has been recorded. The first sharp absorption bands in the Near-Infrared region were assigned to the Uranium centered 5f-5f transitions, but uncertainties remained for the assignment of transitions observed in the Visible region. We computed the spectra of naked UO_2"+ and [UO_2(CO_3)_3]"5"- to elucidate the spectral changes induced by the carbonate ligands. (author) [fr

  11. Database-Driven Analyses of Astronomical Spectra

    Science.gov (United States)

    Cami, Jan

    2012-03-01

    species to the fullerene species C60 and C70 [4]. Given the large number and variety of molecules detected in space, molecular infrared spectroscopy can be used to study pretty much any astrophysical environment that is not too energetic to dissociate the molecules. At the lowest energies, it is interesting to note that molecules such as CN have been used to measure the temperature of the Cosmic Microwave Background (see e.g., Ref. 15). The great diagnostic potential of infrared molecular spectroscopy comes at a price though. Extracting the physical parameters from the observations requires expertise in knowing how various physical processes and instrumental characteristics play together in producing the observed spectra. In addition to the astronomical aspects, this often includes interpreting and understanding the limitations of laboratory data and quantum-chemical calculations; the study of the interaction of matter with radiation at microscopic scales (called radiative transfer, akin to ray tracing) and the effects of observing (e.g., smoothing and resampling) on the resulting spectra and possible instrumental effects (e.g., fringes). All this is not trivial. To make matters worse, observational spectra often contain many components, and might include spectral contributions stemming from very different physical conditions. Fully analyzing such observations is thus a time-consuming task that requires mastery of several techniques. And with ever-increasing rates of observational data acquisition, it seems clear that in the near future, some form of automation is required to handle the data stream. It is thus appealing to consider what part of such analyses could be done without too much human intervention. Two different aspects can be separated: the first step involves simply identifying the molecular species present in the observations. Once the molecular inventory is known, we can try to extract the physical parameters from the observed spectral properties. For both

  12. Geometry-dependent DNA-TiO2 immobilization mechanism: A spectroscopic approach

    Science.gov (United States)

    Silva-Moraes, M. O.; Garcia-Basabe, Y.; de Souza, R. F. B.; Mota, A. J.; Passos, R. R.; Galante, D.; Fonseca Filho, H. D.; Romaguera-Barcelay, Y.; Rocco, M. L. M.; Brito, W. R.

    2018-06-01

    DNA nucleotides are used as a molecular recognition system on electrodes modified to be applied in the detection of various diseases, but immobilization mechanisms, as well as, charge transfers are not satisfactorily described in the literature. An electrochemical and spectroscopic study was carried out to characterize the molecular groups involved in the direct immobilization of DNA structures on the surface of nanostructured TiO2 with the aim of evaluating the influence of the geometrical aspects. X-ray photoelectron spectroscopy at O1s and P2p core levels indicate that immobilization of DNA samples occurs through covalent (Psbnd Osbnd Ti) bonds. X-ray absorption spectra at the Ti2p edge reinforce this conclusion. A new species at 138.5 eV was reported from P2p XPS spectra analysis which plays an important role in DNA-TiO2 immobilization. The Psbnd Osbnd Ti/Osbnd Ti ratio showed that quantitatively the DNA immobilization mechanism is dependent on their geometry, becoming more efficient for plasmid ds-DNA structures than for PCR ds-DNA structures. The analysis of photoabsorption spectra at C1s edge revealed that the molecular groups that participate in the C1s → LUMO electronic transitions have different pathways in the charge transfer processes at the DNA-TiO2 interface. Our results may contribute to additional studies of immobilization mechanisms understanding the influence of the geometry of different DNA molecules on nanostructured semiconductor and possible impact to the charge transfer processes with application in biosensors or aptamers.

  13. Blood extracellular DNA after irradiation

    International Nuclear Information System (INIS)

    Vladimirov, V.G.; Tishchenko, L.I.; Surkova, E.A.; Vasil'eva, I.N.

    1993-01-01

    It has been shown that blood extracellular DNA of irradiated rats largely consists of the low-molecular DNA and its oligomers. Molecular masses of oligomers are multiple to molecular mass of monomer fragment with nucleosome size. The low-molecular DNA has linear form. The average content of GC-pairs in low-molecular DNA is higher than in total rat's DNA (48.5% against 41.5%). The low-molecular DNA is a part of complex containing RNA, acidic proteins and lipids. It is assumed that the formation of low-molecular DNA is a result of Ca/Mg - dependent nuclear endonuclease action

  14. DNA Knots: Theory and Experiments

    Science.gov (United States)

    Sumners, D. W.

    Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

  15. Modeling photoionization of aqueous DNA and its components.

    Science.gov (United States)

    Pluhařová, Eva; Slavíček, Petr; Jungwirth, Pavel

    2015-05-19

    Radiation damage to DNA is usually considered in terms of UVA and UVB radiation. These ultraviolet rays, which are part of the solar spectrum, can indeed cause chemical lesions in DNA, triggered by photoexcitation particularly in the UVB range. Damage can, however, be also caused by higher energy radiation, which can ionize directly the DNA or its immediate surroundings, leading to indirect damage. Thanks to absorption in the atmosphere, the intensity of such ionizing radiation is negligible in the solar spectrum at the surface of Earth. Nevertheless, such an ionizing scenario can become dangerously plausible for astronauts or flight personnel, as well as for persons present at nuclear power plant accidents. On the beneficial side, ionizing radiation is employed as means for destroying the DNA of cancer cells during radiation therapy. Quantitative information about ionization of DNA and its components is important not only for DNA radiation damage, but also for understanding redox properties of DNA in redox sensing or labeling, as well as charge migration along the double helix in nanoelectronics applications. Until recently, the vast majority of experimental and computational data on DNA ionization was pertinent to its components in the gas phase, which is far from its native aqueous environment. The situation has, however, changed for the better due to the advent of photoelectron spectroscopy in liquid microjets and its most recent application to photoionization of aqueous nucleosides, nucleotides, and larger DNA fragments. Here, we present a consistent and efficient computational methodology, which allows to accurately evaluate ionization energies and model photoelectron spectra of aqueous DNA and its individual components. After careful benchmarking, the method based on density functional theory and its time-dependent variant with properly chosen hybrid functionals and polarizable continuum solvent model provides ionization energies with accuracy of 0.2-0.3 e

  16. Vibrational spectra of double oxides of calcium and indium

    International Nuclear Information System (INIS)

    Porotnikov, N.V.; Kondratov, O.I.; Petrov, K.I.; Olikov, I.I.

    1980-01-01

    Vibrational spectra of Ca 40 In 2 O 4 and Ca 44 In 2 O 4 dioxides have been studied. Calculations of a theoretical vibrational spectrum of isotope-substituted compounds have been carried out in the approximation of polymer chains of the valence-force field method. The assignment of experimental spectra is proposed. The force field of crystals is evaluated [ru

  17. Distortions in power spectra of digitized signals - II: Suggested solution

    International Nuclear Information System (INIS)

    Njau, E.C.

    1982-04-01

    In Part I of this report we developed analytical expressions which represent exactly the energy density spectra of ''digitization processes'' that are essentially involved in spectral analysis of continuous signals. Besides, we related the spectral energy density of each digitization process to the parameters of the exact spectral energy density of the corresponding signal. On this basis, we briefly discussed the forms of distortions (or false structures) which are present in normally computed power spectra when the corresponding spectra of the digitization processes are not sufficiently decoupled from or nullified in the computed spectra. The biggest worry with regard to these distortions is not only that they may mask the actual information contained in the original signal, but also they may tempt the researcher to establish false characteristics about the signal involved. It is, in this context, that any reasonable method that could be used (even conditionally) to pinpoint false structures in computed power spectra would be both timely and useful. A simple, handy guidance through which some portions of computed energy density spectra which are dominated by the false structures mentioned above, can be located is presented herein. Equations are presented which give the various frequencies at which false peaks may be located in such ''contaminated'' portions of computed energy density spectra. The occurrence of frequency shifts in computed power spectra is also briefly discussed. (author)

  18. Gamma-ray spectra deconvolution by maximum-entropy methods

    International Nuclear Information System (INIS)

    Los Arcos, J.M.

    1996-01-01

    A maximum-entropy method which includes the response of detectors and the statistical fluctuations of spectra is described and applied to the deconvolution of γ-ray spectra. Resolution enhancement of 25% can be reached for experimental peaks and up to 50% for simulated ones, while the intensities are conserved within 1-2%. (orig.)

  19. Monte Carlo simulation of x-ray spectra in mammography

    Energy Technology Data Exchange (ETDEWEB)

    Ng, K.P. [Department of Optometry and Radiography, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China). E-mail: benngkp at netvigator.com; Kwok, C.S.; Ng, K.P.; Tang, F.H. [Department of Optometry and Radiography, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (China)

    2000-05-01

    A model for generating x-ray spectra in mammography is presented. This model used the ITS version 3 Monte Carlo code for simulating the radiation transport. Various target/filter combinations such as tungsten/aluminium, molybdenum/molybdenum, molybdenum/rhodium and rhodium/rhodium were used in the simulation. Both bremsstrahlung and characteristic x-ray production were included in the model. The simulated x-ray emission spectra were compared with two sets of spectra, those of Boone et al (1997 Med. Phys. 24 1863-74) and IPEM report 78. The {chi}{sup 2} test was used for the overall goodness of fit of the spectral data. There is good agreement between the simulated x-ray spectra and the comparison spectra as the test yielded a probability value of nearly 1. When the transmitted x-ray spectra for specific target/filter combinations were generated and compared with a measured molybdenum/rhodium spectrum and spectra generated in IPEM report 78, close agreement is also observed. This was demonstrated by the probability value for the {chi}{sup 2} test being almost 1 for all the cases. However, minor differences between the simulated spectra and the 'standard' ones are observed. (author)

  20. Monte Carlo simulation of x-ray spectra in mammography

    International Nuclear Information System (INIS)

    Ng, K.P.

    2000-01-01

    A model for generating x-ray spectra in mammography is presented. This model used the ITS version 3 Monte Carlo code for simulating the radiation transport. Various target/filter combinations such as tungsten/aluminium, molybdenum/molybdenum, molybdenum/rhodium and rhodium/rhodium were used in the simulation. Both bremsstrahlung and characteristic x-ray production were included in the model. The simulated x-ray emission spectra were compared with two sets of spectra, those of Boone et al (1997 Med. Phys. 24 1863-74) and IPEM report 78. The χ 2 test was used for the overall goodness of fit of the spectral data. There is good agreement between the simulated x-ray spectra and the comparison spectra as the test yielded a probability value of nearly 1. When the transmitted x-ray spectra for specific target/filter combinations were generated and compared with a measured molybdenum/rhodium spectrum and spectra generated in IPEM report 78, close agreement is also observed. This was demonstrated by the probability value for the χ 2 test being almost 1 for all the cases. However, minor differences between the simulated spectra and the 'standard' ones are observed. (author)

  1. Velocity Spectra in the Unstable Planetary Boundary Layer

    DEFF Research Database (Denmark)

    Højstrup, Jørgen

    1982-01-01

    Models for velocity spectra of all three components in the lower half of the unstable PBL are presented. The model spectra are written as a sum of two parts, nS(n) = A(fi, z/zi)w*2 + B(f, z/zi)u*02, a mixed layer part with a stability dependence, and a surface layer part without stability...

  2. Combination spectra in long-period variable stars

    International Nuclear Information System (INIS)

    Bruce, C.E.R.

    1975-01-01

    The electrical discharge theory of the variation in excitation observed in the atmosphere of the long period variable stars offers an explanation for the combination spectra exhibited by many of these stars, which is shown to be in accord with several of the most outstanding changes in their spectra and magnitude. (author)

  3. Soil carbon estimation from eucalyptus grandis using canopy spectra

    African Journals Online (AJOL)

    Mapping soil fertility parameters, such as soil carbon (C), is fundamentally important for forest management and research related to forest growth and climate change. This study seeks to establish the link between Eucalyptus grandis canopy spectra and soil carbon using raw and continuum-removed spectra. Canopy-level ...

  4. Vibrational spectra and thermodynamics of biomolecule: 5-chlorocytosine

    Czech Academy of Sciences Publication Activity Database

    Rastori, V. K.; Palafox, M. A.; Lang, Kamil; Singhal, S.K.; Soni, R.K.; Sharma, R.

    2006-01-01

    Roč. 44, č. 9 (2006), s. 653-660 ISSN 0019-5596 Institutional research plan: CEZ:AV0Z40320502 Keywords : vibrational spectra * 5-chlorocytosine * laser Raman spectra Subject RIV: CA - Inorganic Chemistry Impact factor: 0.380, year: 2006

  5. Synthesis and infrared spectra of alkaline earth metal carbonates ...

    Indian Academy of Sciences (India)

    Unknown

    Abstract. The metal carbonate, MCO3 (M = Ca, Sr and Ba), was synthesized by a novel method of reacting aqueous solution of each of Ca2+, Sr2+ and Ba2+ salts with urea at high temperature, ~ 80°C. The reaction products were characterized through elemental analysis and infrared spectra. The infrared spectra of the.

  6. Synthesis and infrared spectra of alkaline earth metal carbonates

    Indian Academy of Sciences (India)

    The metal carbonate, MCO3 (M = Ca, Sr and Ba), was synthesized by a novel method of reacting aqueous solution of each of Ca2+, Sr2+ and Ba2+ salts with urea at high temperature, ∼ 80°C. The reaction products were characterized through elemental analysis and infrared spectra. The infrared spectra of the products are ...

  7. Tips for deciphering and quick calculation of radiation spectra

    Science.gov (United States)

    Bondarenco, M. V.

    2018-04-01

    Radiation spectra from ultra-relativistic electrons in thin [Tll lf(ω)] and thick [Tgg lf(ω)] targets are discussed. The method of simplified averaging is described by examples of Landau-Pomeranchuk-Migdal effect and radiation at doughnut scattering. General infrared and ultraviolet asymptotic properties of radiation spectra are discussed.

  8. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

    Science.gov (United States)

    Prior, C; Danilāne, L; Oganesyan, V S

    2018-05-16

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

  9. Crystallographically-based analysis of the NMR spectra of maghemite

    International Nuclear Information System (INIS)

    Spiers, K.M.; Cashion, J.D.

    2012-01-01

    All possible iron environments with respect to nearest neighbour vacancies in vacancy-ordered and vacancy-disordered maghemite have been evaluated and used as the foundation for a crystallographically-based analysis of the published NMR spectra of maghemite. The spectral components have been assigned to particular configurations and excellent agreement obtained in comparing predicted spectra with published spectra taken in applied magnetic fields. The broadness of the published NMR lines has been explained by calculations of the magnetic dipole fields at the various iron sites and consideration of the supertransferred hyperfine fields. - Highlights: ► Analysis of 57 Fe NMR of maghemite based on vacancy ordering and nearest neighbour vacancies. ► Assignment of NMR spectral components based on crystallographic analysis of unique iron sites. ► Strong agreement between predicted spectra and published spectra taken in applied magnetic fields. ► Maghemite NMR spectral broadening due to various iron sites and supertransferred hyperfine field.

  10. Preservation of information in Fourier theory based deconvolved nuclear spectra

    International Nuclear Information System (INIS)

    Madan, V.K.; Gopalakrishnan, K.R.; Sharma, R.C.; Rattan, S.S.

    1995-01-01

    Nuclear spectroscopy is extremely useful to the internal radiation dosimetry for the estimation of body burden due to gamma emitters. Analysis of nuclear spectra is concerned with the extraction of qualitative and quantitative information embedded in the spectra. A spectral deconvolution method based on Fourier theory is probably the simplest method of deconvolving nuclear spectra. It is proved mathematically that the deconvolution method preserves the qualitative information. It is shown by using simulated spectra and an observed gamma ray spectrum that the method preserves the quantitative information. This may provide a novel approach of information extraction from a deconvolved spectrum. The paper discusses the methodology, mathematical analysis, and the results obtained by deconvolving spectra. (author). 6 refs., 2 tabs

  11. Soft x-ray absorption spectra of ilmenite family.

    Science.gov (United States)

    Agui, A; Mizumaki, M; Saitoh, Y; Matsushita, T; Nakatani, T; Fukaya, A; Torikai, E

    2001-03-01

    We have carried out soft x-ray absorption spectroscopy to study the electronic structure of ilmenite family, such as MnTiO3, FeTiO3, and CoTiO3 at the soft x-ray beamline, BL23SU, at the SPring-8. The Ti and M L2,3 absorption spectra of MTiO3 (M=Mn, Fe, and Co) show spectra of Ti4+ and M2+ electron configurations, respectively. Except the Fe L2,3 spectrum, those spectra were understood within the O(h) symmetry around the transition metal ions. The Fe L3-edge spectrum clearly shows a doublet peak at the L3 edge, which is attributed to Fe2+ state, moreover the very high-resolution the L-edge spectra of transition metals show fine structures. The spectra of those ilmenites are compared.

  12. Adjusted neutron spectra of STEK cores for reactivity calculations

    International Nuclear Information System (INIS)

    Dekker, J.W.M.; Dragt, J.B.; Janssen, A.J.; Heijboer, R.J.; Klippel, H.Th.

    1978-02-01

    Neutron flux and adjoint flux spectra form a pre-requisite in the analysis of reactivity worth data measured in the STEK facility. First, a survey of all available information about these spectra is given. Next a special application of a general adjustment method is described. This method has been used to obtain adjusted STEK group flux and adjoint flux spectra, starting from calculated spectra. These theoretical spectra were adjusted to reactivity worths of natural boron (nat. B) and 235 U as well as a number of fission reaction rates. As a by-product in this adjustment calculation adjusted fission group cross sections of 235 U were obtained. The results, viz. group fluxes and adjoint fluxes and adjusted fission cross sections of 235 U are given. They have been used for the interpretation of fission product reactivity worth measurements made in STEK

  13. Spectra of turbulent static pressure fluctuations in jet mixing layers

    Science.gov (United States)

    Jones, B. G.; Adrian, R. J.; Nithianandan, C. K.; Planchon, H. P., Jr.

    1977-01-01

    Spectral similarity laws are derived for the power spectra of turbulent static pressure fluctuations by application of dimensional analysis in the limit of large turbulent Reynolds number. The theory predicts that pressure spectra are generated by three distinct types of interaction in the velocity fields: a fourth order interaction between fluctuating velocities, an interaction between the first order mean shear and the third order velocity fluctuations, and an interaction between the second order mean shear rate and the second order fluctuating velocity. Measurements of one-dimensional power spectra of the turbulent static pressure fluctuations in the driven mixing layer of a subsonic, circular jet are presented, and the spectra are examined for evidence of spectral similarity. Spectral similarity is found for the low wavenumber range when the large scale flow on the centerline of the mixing layer is self-preserving. The data are also consistent with the existence of universal inertial subranges for the spectra of each interaction mode.

  14. Photoreactivation and other ultraviolet/visible light effects on DNA in human skin

    International Nuclear Information System (INIS)

    Sutherland, B.M.; Blackett, A.D.; Feng, N.I.; Freeman, S.E.; Ogut, E.S.; Gange, R.W.; Sutherland, J.C.

    1985-01-01

    Wavelengths of light present in sunlight, sunlamps, and fluorescent and incandescent lamps induce changes in human skin DNA in a multiplicity of reactions. UVB and UVA exposures can induce damage in DNA as well as can the inducement of tanning to protect against such damage. Longer wavelength ultraviolet radiation can mediate enzymatic (or perhaps nonenzymatic) reversal of dimers. None of the action spectra, kinetics, or other characteristics of such reactions are known. Elucidation of their properties will provide essential information to allow evaluation of the interaction of light with human skin DNA

  15. Study on the Electric Conductivity of Ag-Doped DNA in Transverse Direction

    Directory of Open Access Journals (Sweden)

    Ban Ge

    2009-01-01

    Full Text Available Abstract In this article, we reported a novel experiment results on Ag-doped DNA conductor in transverse direction.I–Vcharacteristics were measured and the relative conductances were calculated for different silver ions concentrations. With the increase of the concentration of silver ions, the conductive ability of DNA risen rapidly, the relative conductance of DNA enhanced about three magnitudes and reached a stable value when Ag+concentration was up to 0.005 mM. In addition, Raman spectra were carried out to analyse and confirm conduction mechanism.

  16. DNA damage in oral cancer cells induced by nitrogen atmospheric pressure plasma jets

    Energy Technology Data Exchange (ETDEWEB)

    Han, Xu; Ptasinska, Sylwia [Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Klas, Matej [Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Liu, Yueying [Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Sharon Stack, M. [Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (United States)

    2013-06-10

    The nitrogen atmospheric pressure plasma jet (APPJ) was applied to induce DNA damage of SCC-25 oral cancer cells. Optical emission spectra were taken to characterize the reactive species produced in APPJ. In order to explore the spatial distribution of plasma effects, cells were placed onto photo-etched grid slides and the antibody H2A.X was used to locate double strand breaks of DNA inside nuclei using an immunofluorescence assay. The number of cells with double strand breaks in DNA was observed to be varied due to the distance from the irradiation center and duration of plasma treatment.

  17. DNA damage in oral cancer cells induced by nitrogen atmospheric pressure plasma jets

    International Nuclear Information System (INIS)

    Han, Xu; Ptasinska, Sylwia; Klas, Matej; Liu, Yueying; Sharon Stack, M.

    2013-01-01

    The nitrogen atmospheric pressure plasma jet (APPJ) was applied to induce DNA damage of SCC-25 oral cancer cells. Optical emission spectra were taken to characterize the reactive species produced in APPJ. In order to explore the spatial distribution of plasma effects, cells were placed onto photo-etched grid slides and the antibody H2A.X was used to locate double strand breaks of DNA inside nuclei using an immunofluorescence assay. The number of cells with double strand breaks in DNA was observed to be varied due to the distance from the irradiation center and duration of plasma treatment.

  18. Structural Analysis of DNA Interactions with Magnesium Ion Studied by Raman Spectroscopy

    OpenAIRE

    S. Ponkumar; P. Duraisamy; N. Iyandurai

    2011-01-01

    Problem statement: In the present study, FT Raman spectroscopy had been used to extend our knowledge about Magnesium ion - DNA interactions at various volume ratios (1:50, 1:20, 1:10 and 1:5). Approach: The analysis of FT Raman data supported the existence of structural specificities in the interaction and also the stability of DNA secondary structure. Results: Results from the Raman spectra clearly indicate that the interaction of Magnesium ion with DNA is mainly through the phosphate groups...

  19. Raman Spectroscopy of DNA Packaging in Individual Human Sperm Cells distinguishes Normal from Abnormal Cells

    Energy Technology Data Exchange (ETDEWEB)

    Huser, T; Orme, C; Hollars, C; Corzett, M; Balhorn, R

    2009-03-09

    Healthy human males produce sperm cells of which about 25-40% have abnormal head shapes. Increases in the percentage of sperm exhibiting aberrant sperm head morphologies have been correlated with male infertility, and biochemical studies of pooled sperm have suggested that sperm with abnormal shape may contain DNA that has not been properly repackaged by protamine during spermatid development. We have used micro-Raman spectroscopy to obtain Raman spectra from individual human sperm cells and examined how differences in the Raman spectra of sperm chromatin correlate with cell shape. We show that Raman spectra of individual sperm cells contain vibrational marker modes that can be used to assess the efficiency of DNA-packaging for each cell. Raman spectra obtained from sperm cells with normal shape provide evidence that DNA in these sperm is very efficiently packaged. We find, however, that the relative protein content per cell and DNA packaging efficiencies are distributed over a relatively wide range for sperm cells with both normal and abnormal shape. These findings indicate that single cell Raman spectroscopy should be a valuable tool in assessing the quality of sperm cells for in-vitro fertilization.

  20. Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

    Science.gov (United States)

    Gerasimova, N S; Pestov, N A; Kulaeva, O I; Clark, D J; Studitsky, V M

    2016-05-26

    RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

  1. EFFECTS OF FORSTERITE GRAIN SHAPE ON INFRARED SPECTRA

    International Nuclear Information System (INIS)

    Koike, C.; Imai, Y.; Chihara, H.; Murata, K.; Tsuchiyama, A.; Suto, H.; Tachibana, S.; Ohara, S.

    2010-01-01

    The Infrared Space Observatory (ISO) detected several sharp infrared features around young stars, comets, and evolved stars. These sharp features were identified as Mg-rich crystalline silicates of forsterite and enstatite by comparison with spectra from laboratory data. However, certain infrared emission bands in the observed spectra cannot be identified because they appear at slightly shorter wavelengths than the peaks in forsterite laboratory spectra, where the shapes of forsterite particles are irregular. To solve this problem, we measured infrared spectra of forsterite grains of various shapes (irregular, plate-like with no sharp edges, elliptical, cauliflower, and spherical) in the infrared spectral region between 5 and 100 μm. The spectra depend on particle shape. The spectra of the 11, 19, 23, and 33 μm bands, in particular, are extremely sensitive to particle shape, whereas some peaks such as the 11.9, 49, and 69 μm bands remained almost unchanged despite different particle shapes. This becomes most evident from the spectra of near-spherical particles produced by annealing an originally amorphous silicate sample at temperature from 600 to 1150 deg. C. The spectra of these samples differ strongly from those of other ones, showing peaks at much shorter wavelengths. At a higher annealing temperature of 1200 deg. C, the particle shapes changed drastically from spherical to irregular and the spectra became similar to those of forsterite particles with irregular shapes. Based on ISO data and other observational data, the spectra of outflow sources and disk sources may correspond to differences in forsterite shape, and further some unidentified peaks, such as those at 32.8 or 32.5 μm, may be due to spherical or spherical-like forsterite.

  2. Infrared spectra of interstellar deuteronated PAHs

    Science.gov (United States)

    Buragohain, Mridusmita; Pathak, Amit; Sarre, Peter

    2015-08-01

    Polycyclic Aromatic Hydrocarbon (PAH) molecules have emerged as a potential constituent of the ISM that emit strong features at 3.3, 6.2, 7.7, 8.6, 11.2 and 12.7 μm with weaker and blended features in the 3-20μm region. These features are proposed to arise from the vibrational relaxation of PAH molecules on absorption of background UV photons (Tielens 2008). These IR features have been observed towards almost all types of astronomical objects; say H II regions, photodissociation regions, reflection nebulae, planetary nebulae, young star forming regions, external galaxies, etc. A recent observation has proposed that interstellar PAHs are major reservoir for interstellar deuterium (D) (Peeters et al. 2004). According to the `deuterium depletion model' as suggested by Draine (2006), some of the Ds formed in the big bang are depleted in PAHs, which can account for the present value of D/H in the ISM. Hence, study of deuterated PAHs (PADs) is essential in order to measure D/H in the ISM.In this work, we consider another probable category of the large PAH family, i.e. Deuteronated PAHs (DPAH+). Onaka et al. have proposed a D/H ratio which is an order of magnitude smaller than the proposed value of D/H by Draine suggesting that if Ds are depleted in PAHs, they might be accommodated in large PAHs (Onaka et al. 2014). This work reports a `Density Functional Theory' calculation of large deuteronated PAHs (coronene, ovalene, circumcoronene and circumcircumcoronene) to determine the expected region of emission features and to find a D/H ratio that is comparable to the observational results. We present a detailed analysis of the IR spectra of these molecules and discuss the possible astrophysical implications.ReferencesDraine B. T. 2006, in ASP Conf. Ser. 348, Proc. Astrophysics in the Far Ultraviolet: Five Years of Discovery with FUSE, ed. G. Sonneborn, H. Moos, B-G Andersson (San Francisco, CA:ASP) 58Onaka T., Mori T. I., Sakon I., Ohsawa R., Kaneda H., Okada Y., Tanaka M

  3. Uranyl oxalate hydrates: structures and IR spectra

    International Nuclear Information System (INIS)

    Giesting, P.A.; Porter, N.J.; Burns, P.C.

    2006-01-01

    The novel compound (UO 2 ) 2 C 2 O 4 (OH) 2 (H 2 O) 2 (UrOx2A) and the previously studied compound UO 2 C 2 O 4 (H 2 O) 3 (UrOx3) have been synthesized by mild hydrothermal methods. Single crystal diffraction data collected at 125 K using MoK α radiation and a CCD-based area detector were used to solve and refine the crystal structures by full-matrix least-squares techniques to agreement indices (UrOx2A, UrOx3) wR 2 = 0.037, 0.049 for all data, and R1 0.015, 0.024 calculated for 1285, 2194 unique reflections respectively. The compound UrOx2A is triclinic, space group P1, Z = 1, a = 5.5353(4), b 6.0866(4), c = 7.7686(6) Aa, α = 85.6410(10) , β = 89.7740(10) , γ = 82.5090(10) , V = 258.74(3) Aa 3 . The compound UrOx3 is monoclinic, space group P2 1 /c, Z = 4, a = 5.5921(4), b = 16.9931(13), c = 9.3594(7) Aa, β = 99.5330(10) , V = 877.11(11) Aa 3 . The structures consist of chains of uranyl pentagonal bipyramids connected by oxalate groups and, in UrOx2A, hydroxyl groups; UrOx2A is also notable for its high (2:1) ratio of uranyl to oxalate groups, higher than any observed in other published structures of uranyl oxalates. The structure determined for UrOx3, previously studied by Jayadevan and Chackraburtty (1972); Mikhailov et al. (1999) is in agreement with the previous results; however, the increased precision of the present low-temperature structure refinement allows for the assignment of H atom positions based on the difference Fourier map of electron density. The infrared spectra of these two materials collected at room temperature are also presented and compared with previous work on uranyl oxalate systems. (orig.)

  4. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.; Oke, Muse; Hamdan, Samir

    2014-01-01

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  5. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.

    2014-11-21

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  6. DNA replication stress restricts ribosomal DNA copy number

    Science.gov (United States)

    Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

    2017-01-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

  7. DNA replication stress restricts ribosomal DNA copy number.

    Science.gov (United States)

    Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

    2017-09-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  8. DNA replication stress restricts ribosomal DNA copy number.

    Directory of Open Access Journals (Sweden)

    Devika Salim

    2017-09-01

    Full Text Available Ribosomal RNAs (rRNAs in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  9. DNA repair synthesis in human fibroblasts requires DNA polymerase delta

    International Nuclear Information System (INIS)

    Nishida, C.; Reinhard, P.; Linn, S.

    1988-01-01

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernatant of similarly treated HeLa cells. Extensive purification of this factor yielded a 10.2 S, 220,000-dalton polypeptide with the DNA polymerase and 3'- to 5'-exonuclease activities reported for DNA polymerase delta II. Monoclonal antibody to KB cell DNA polymerase alpha, while binding to HeLa DNA polymerase alpha, did not bind to the HeLa DNA polymerase delta. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGTP) and 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase alpha, but did not inhibit the DNA polymerase delta. Neither purified DNA polymerase alpha nor beta could promote repair DNA synthesis in the permeabilized cells. Furthermore, under conditions which inhibited purified DNA polymerase alpha by greater than 90%, neither monoclonal antibodies to DNA polymerase alpha, BuPdGTP, nor BuAdATP was able to inhibit significantly the DNA repair synthesis mediated by the DNA polymerase delta. Thus, it appears that a major portion of DNA repair synthesis induced by UV irradiation might be catalyzed by DNA polymerase delta. When xeroderma pigmentosum human diploid fibroblasts were utilized, DNA repair synthesis dependent upon ultraviolet light could be restored by addition of both T4 endonuclease V and DNA polymerase delta, but not by addition of either one alone

  10. Comparison between simplified load spectra in accordance with Germanische Lloyd guidelines, and load spectra derived from time domain simulations

    Energy Technology Data Exchange (ETDEWEB)

    Rees, M [Aerodyn Energiesysteme gmbH, Rendsburg (Germany)

    1996-09-01

    The Germanische Lloyd guideline allows calculations of load spectra in two fundamentally different ways. In the case of the so-called `simplified load spectra` the maximum amplitude of fluctuation of a load component is formed as {+-}75% of the average value of the purely aerodynamic loads of this component at rated wind conditions, together with an overlay of mass-related loads. The second method allowed in the GL guideline is the calculation of load spectra from simulation results in the time domain. For a number of average wind speeds the time-dependent characteristics of the load components are calculated taking account of the natural spatial turbulence of the wind. These are converted into load spectra using the rainflow method. In a parametric study the load spectra are calculated according to both methods and compared. The calculations are performed for turbines with rated powers of 100 kW to 2000 kW, with two and three blades, and also for stall-controlled and pitch-controlled turbines. The calculated load spectra are compared with each by means of 1 P fatigue equivalent load spectra. The influence of individual parameters is presented, as is the validity of the simplified load spectra. (au)

  11. Clusters of DNA induced by ionizing radiation: formation of short DNA fragments. I. Theoretical modeling

    Science.gov (United States)

    Holley, W. R.; Chatterjee, A.

    1996-01-01

    We have developed a general theoretical model for the interaction of ionizing radiation with chromatin. Chromatin is modeled as a 30-nm-diameter solenoidal fiber comprised of 20 turns of nucleosomes, 6 nucleosomes per turn. Charged-particle tracks are modeled by partitioning the energy deposition between primary track core, resulting from glancing collisions with 100 eV or less per event, and delta rays due to knock-on collisions involving energy transfers >100 eV. A Monte Carlo simulation incorporates damages due to the following molecular mechanisms: (1) ionization of water molecules leading to the formation of OH, H, eaq, etc.; (2) OH attack on sugar molecules leading to strand breaks: (3) OH attack on bases; (4) direct ionization of the sugar molecules leading to strand breaks; (5) direct ionization of the bases. Our calculations predict significant clustering of damage both locally, over regions up to 40 bp and over regions extending to several kilobase pairs. A characteristic feature of the regional damage predicted by our model is the production of short fragments of DNA associated with multiple nearby strand breaks. The shapes of the spectra of DNA fragment lengths depend on the symmetries or approximate symmetries of the chromatin structure. Such fragments have subsequently been detected experimentally and are reported in an accompanying paper (B. Rydberg, Radiat, Res. 145, 200-209, 1996) after exposure to both high- and low-LET radiation. The overall measured yields agree well quantitatively with the theoretical predictions. Our theoretical results predict the existence of a strong peak at about 85 bp, which represents the revolution period about the nucleosome. Other peaks at multiples of about 1,000 bp correspond to the periodicity of the particular solenoid model of chromatin used in these calculations. Theoretical results in combination with experimental data on fragmentation spectra may help determine the consensus or average structure of the

  12. Principles of DNA architectonics: design of DNA-based nanoobjects

    International Nuclear Information System (INIS)

    Vinogradova, O A; Pyshnyi, D V

    2012-01-01

    The methods of preparation of monomeric DNA blocks that serve as key building units for the construction of complex DNA objects are described. Examples are given of the formation of DNA blocks based on native and modified oligonucleotide components using hydrogen bonding and nucleic acid-specific types of bonding and also some affinity interactions with RNA, proteins, ligands. The static discrete and periodic two- and three-dimensional DNA objects reported to date are described systematically. Methods used to prove the structures of DNA objects and the prospects for practical application of nanostructures based on DNA and its analogues in biology, medicine and biophysics are considered. The bibliography includes 195 references.

  13. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  14. Duplication in DNA Sequences

    Science.gov (United States)

    Ito, Masami; Kari, Lila; Kincaid, Zachary; Seki, Shinnosuke

    The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.

  15. DNA methylation in obesity

    Directory of Open Access Journals (Sweden)

    Małgorzata Pokrywka

    2014-11-01

    Full Text Available The number of overweight and obese people is increasing at an alarming rate, especially in the developed and developing countries. Obesity is a major risk factor for diabetes, cardiovascular disease, and cancer, and in consequence for premature death. The development of obesity results from the interplay of both genetic and environmental factors, which include sedentary life style and abnormal eating habits. In the past few years a number of events accompanying obesity, affecting expression of genes which are not directly connected with the DNA base sequence (e.g. epigenetic changes, have been described. Epigenetic processes include DNA methylation, histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation, as well as non-coding micro-RNA (miRNA synthesis. In this review, the known changes in the profile of DNA methylation as a factor affecting obesity and its complications are described.

  16. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  17. Sequence- and structure-dependent DNA base dynamics: Synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA

    International Nuclear Information System (INIS)

    Spaltenstein, A.; Robinson, B.H.; Hopkins, P.B.

    1989-01-01

    A nitroxide spin-labeled analogue of thymidine (1a), in which the methyl group is replaced by an acetylene-tethered nitroxide, was evaluated as a probe for structural and dynamics studies of sequence specifically spin-labeled DNA. Residue 1a was incorporated into synthetic deoxyoligonucleotides by using automated phosphite triester methods. 1 H NMR, CD, and thermal denaturation studies indicate that 1a (T) does not significantly alter the structure of 5'-d(CGCGAATT*CGCG) from that of the native dodecamer. EPR studies on monomer, single-stranded, and duplexed DNA show that 1a readily distinguishes environments of different rigidity. Comparison of the general line-shape features of the observed EPR spectra of several small duplexes (12-mer, 24-mer) with simulated EPR spectra assuming isotropic motion suggests that probe 1a monitors global tumbling of small duplexes. Increasing the length of the DNA oligomers results in significant deviation from isotropic motion, with line-shape features similar to those of calculated spectra of objects with isotropic rotational correlation times of 20-100 ns. EPR spectra of a spin-labeled GT mismatch and a T bulge in long DNAs are distinct from those of spin-labeled Watson-Crick paired DNAs, further demonstrating the value of EPR as a tool in the evaluation of local dynamic and structural features in macromolecules

  18. Proposal and Evaluation of Subordinate Standard Solar Irradiance Spectra: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Habte, Aron M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Wilbert, Stefan [German Aerospace Center (DLR); Jessen, Wilko [German Aerospace Center (DLR); Gueymard, Chris [Solar Consulting Services; Polo, Jesus [CIEMAT; Bian, Zeqiang [China Meteorological Administration; Driesse, Anton [Photovoltaic Performance Labs; Marzo, Aitor [University of Antofagasta; Armstrong, Peter [Masdar Institute of Science & Technology; Vignola, Frank [University of Oregon; Ramirez, Lourdes [CIEMAT

    2018-04-12

    This paper introduces a concept for global tilted irradiance (GTI) subordinate standard spectra to supplement the current standard spectra used in solar photovoltaic applications as defined in ASTM G173 and IEC60904. The proposed subordinate standard spectra correspond to atmospheric conditions and tilt angles that depart significantly from the main standard spectrum, and they can be used to more accurately represent various local conditions. For the definition of subordinate standard spectra cases with an elevation 1.5 km above sea level, the question arises whether the air mass should be calculated including a pressure correction or not. This study focuses on the impact of air mass used in standard spectra, and it uses data from 29 locations to examine which air mass is most appropriate for GTI and direct normal irradiance (DNI) spectra. Overall, it is found that the pressure-corrected air mass of 1.5 is most appropriate for DNI spectra. For GTI, a non-pressure-corrected air mass of 1.5 was found to be more appropriate.

  19. Analysis of the experimental positron lifetime spectra by neural networks

    International Nuclear Information System (INIS)

    Avdic, S.; Chakarova, R.; Pazsit, I.

    2003-01-01

    This paper deals with the analysis of experimental positron lifetime spectra in polymer materials by using various algorithms of neural networks. A method based on the use of artificial neural networks for unfolding the mean lifetime and intensity of the spectral components of simulated positron lifetime spectra was previously suggested and tested on simulated data [Pazsit et al., Applied Surface Science, 149 (1998), 97]. In this work, the applicability of the method to the analysis of experimental positron spectra has been verified in the case of spectra from polymer materials with three components. It has been demonstrated that the backpropagation neural network can determine the spectral parameters with a high accuracy and perform the decomposition of lifetimes which differ by 10% or more. The backpropagation network has not been suitable for the identification of both the parameters and the number of spectral components. Therefore, a separate artificial neural network module has been designed to solve the classification problem. Module types based on self-organizing map and learning vector quantization algorithms have been tested. The learning vector quantization algorithm was found to have better performance and reliability. A complete artificial neural network analysis tool of positron lifetime spectra has been constructed to include a spectra classification module and parameter evaluation modules for spectra with a different number of components. In this way, both flexibility and high resolution can be achieved. (author)

  20. THE Be STAR SPECTRA (BeSS) DATABASE

    International Nuclear Information System (INIS)

    Neiner, C.; De Batz, B.; Cochard, F.; Floquet, M.; Mekkas, A.; Desnoux, V.

    2011-01-01

    Be stars vary on many timescales, from hours to decades. A long time base of observations to analyze certain phenomena in these stars is therefore necessary. Collecting all existing and future Be star spectra into one database has thus emerged as an important tool for the Be star community. Moreover, for statistical studies, it is useful to have centralized information on all known Be stars via an up-to-date catalog. These two goals are what the Be Star Spectra (BeSS, http://basebe.obspm.fr) database proposes to achieve. The database contains an as-complete-as-possible catalog of known Be stars with stellar parameters, as well as spectra of Be stars from all origins (any wavelength, any epoch, any resolution, etc.). It currently contains over 54,000 spectra of more than 600 different Be stars among the ∼2000 Be stars in the catalog. A user can access and query this database to retrieve information on Be stars or spectra. Registered members can also upload spectra to enrich the database. Spectra obtained by professional as well as amateur astronomers are individually validated in terms of format and science before being included in BeSS. In this paper, we present the database itself as well as examples of the use of BeSS data in terms of statistics and the study of individual stars.