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Sample records for alignment improves dna

  1. Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

    Institute of Scientific and Technical Information of China (English)

    Guang-Ming Tan; Lin Xu; Dong-Bo Bu; Sheng-Zhong Feng; Ning-Hui Sun

    2006-01-01

    MegaBlast is one of the most important programs in NCBI BLAST (Basic Local Alignment Search Tool)toolkits. However, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportional to the size of the query sequences set and subject (database) sequences set of product. This paper proposes a new strategy for optimizing MegaBlast. The new strategy exchanges the query and subject sequences sets, and builds a hash table based on new subject sequences. It overlaps I/O with computation, shortens the overall time and reduces the cost of memory,since the memory here is only proportional to the size of subject sequences set. The optimized algorithm is suitable to be parallelized in cluster systems. The parallel algorithm uses query segmentation method. As our experiments shown, the parallel program which is implemented with MPI has fine scalability.

  2. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily...... connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster...

  3. A DNA sequence alignment algorithm using quality information and a fuzzy inference method

    Institute of Scientific and Technical Information of China (English)

    Kwangbaek Kim; Minhwan Kim; Youngwoon Woo

    2008-01-01

    DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods.In this paper.We propose a DNA sequence alignment that Uses quality information and a fuzzy inference method developed based on the characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information.In conventional algorithms.DNA sequence alignment scores are calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch,which is established by using quality information of each DNA fragment.However,there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low.because only the overall DNA sequence quality information are used.In our proposed method.an exact DNA sequence alignment can be achieved in spite of the low quality of DNA fragment tips by improvement of conventional algorithms using quality information.Mapping score parameters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments.From the experiments by applying real genome data of National Center for Bioteclmology Information,we could see that the proposed method is more efficient than conventional algorithms.

  4. DNA Sequence Alignment during Homologous Recombination.

    Science.gov (United States)

    Greene, Eric C

    2016-05-27

    Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination.

  5. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...

  6. Choosing the best heuristic for seeded alignment of DNA sequences

    Directory of Open Access Journals (Sweden)

    Buhler Jeremy

    2006-03-01

    Full Text Available Abstract Background Seeded alignment is an important component of algorithms for fast, large-scale DNA similarity search. A good seed matching heuristic can reduce the execution time of genomic-scale sequence comparison without degrading sensitivity. Recently, many types of seed have been proposed to improve on the performance of traditional contiguous seeds as used in, e.g., NCBI BLASTN. Choosing among these seed types, particularly those that use information besides the presence or absence of matching residue pairs, requires practical guidance based on a rigorous comparison, including assessment of sensitivity, specificity, and computational efficiency. This work performs such a comparison, focusing on alignments in DNA outside widely studied coding regions. Results We compare seeds of several types, including those allowing transition mutations rather than matches at fixed positions, those allowing transitions at arbitrary positions ("BLASTZ" seeds, and those using a more general scoring matrix. For each seed type, we use an extended version of our Mandala seed design software to choose seeds with optimized sensitivity for various levels of specificity. Our results show that, on a test set biased toward alignments of noncoding DNA, transition information significantly improves seed performance, while finer distinctions between different types of mismatches do not. BLASTZ seeds perform especially well. These results depend on properties of our test set that are not shared by EST-based test sets with a strong bias toward coding DNA. Conclusion Practical seed design requires careful attention to the properties of the alignments being sought. For noncoding DNA sequences, seeds that use transition information, especially BLASTZ-style seeds, are particularly useful. The Mandala seed design software can be found at http://www.cse.wustl.edu/~yanni/mandala/.

  7. JavaScript DNA translator: DNA-aligned protein translations.

    Science.gov (United States)

    Perry, William L

    2002-12-01

    There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

  8. Can technology improve alignment during knee arthroplasty.

    Science.gov (United States)

    Thienpont, Emmanuel; Fennema, Peter; Price, Andrew

    2013-09-01

    Component malalignment remains a concern in total knee arthroplasty (TKA); therefore, a series of technologies have been developed to improve alignment. The authors conducted a systematic review to compare computer-assisted navigation with conventional instrumentation, and assess the current evidence for patient-matched instrumentation and robot-assisted implantation. An extensive search of the PubMed database for relevant meta-analyses, systematic reviews and original articles was performed, with each study scrutinised by two reviewers. Data on study characteristics and outcomes were extracted from each study and compared. In total 30 studies were included: 10 meta-analyses comparing computer-assisted navigation and conventional instrumentation, 13 studies examining patient-matched instrumentation, and seven investigating robot-assisted implantation. Computer-assisted navigation showed significant and reproducible improvements in mechanical alignment over conventional instrumentation. Patient-matched instrumentation appeared to achieve a high degree of mechanical alignment, although the majority of studies were of poor quality. The data for robot-assisted surgery was less indicative. Computer-assisted navigation improves alignment during TKA over conventional instrumentation. For patient-matched instrumentation and robot-assisted implantation, alignment benefits have not been reliably demonstrated. For all three technologies, clinical benefits cannot currently be assumed, and further studies are required. Although current technologies to improve alignment during TKA appear to result in intra-operative benefits, their clinical impact remains unclear, and surgeons should take this into account when considering their adoption.

  9. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    Science.gov (United States)

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  10. Interference Alignment via Improved Subspace Conditioning

    CERN Document Server

    Kim, Douglas

    2010-01-01

    For the K user, single input single output (SISO), frequency selective interference channel, a new low complexity transmit beamforming design that improves the achievable sum rate is presented. Jointly employing the interference alignment (IA) scheme presented by Cadambe and Jafar in [1] and linear minimum mean square error (MMSE) decoding at the transmitters and receivers, respectively, the new IA precoding design improves the average sum rate while preserving the achievable degrees of freedom of the Cadambe and Jafar scheme, K/2.

  11. Volume visualization of multiple alignment of genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Weber, Gunther H.; Dillard, Scott E.; Hamann, Bernd

    2004-05-01

    Genomes of hundreds of species have been sequenced to date and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We provide results for aligned DNA sequence data and compare it with traditional 1D line plots. Our technique, coupled with 1D line plots, results in effective multiresolution visualization of very large aligned sequence data sets.

  12. Aligned deposition and electrical measurements on single DNA molecules

    DEFF Research Database (Denmark)

    Eidelshtein, Gennady; Kotlyar, Alexander; Hashemi, Mohtadin;

    2015-01-01

    A reliable method of deposition of aligned individual dsDNA molecules on mica, silicon, and micro/nanofabricated circuits is presented. Complexes of biotinylated double stranded poly(dG)–poly(dC) DNA with avidin were prepared and deposited on mica and silicon surfaces in the absence of Mg2+ ions...... bound to the surface, while the DNA counterpart interacts with the substrates much more weakly and can be lifted from the surface and realigned in any direction. Using this technique, avidin–DNA complexes were deposited across platinum electrodes on a silicon substrate. Electrical measurements...

  13. Phylo: a citizen science approach for improving multiple sequence alignment.

    Directory of Open Access Journals (Sweden)

    Alexander Kawrykow

    Full Text Available BACKGROUND: Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. METHODOLOGY/PRINCIPAL FINDINGS: We introduce Phylo, a human-based computing framework applying "crowd sourcing" techniques to solve the Multiple Sequence Alignment (MSA problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. CONCLUSIONS/SIGNIFICANCE: We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of "human-brain peta-flops" of computation that are spent every day playing games

  14. Alignment and Sensitive Detection of DNA by a Moving Interface

    Science.gov (United States)

    Bensimon, A.; Simon, A.; Chiffaudel, A.; Croquette, V.; Heslot, F.; Bensimon, D.

    1994-09-01

    In a process called "molecular combing," DNA molecules attached at one end to a solid surface were extended and aligned by a receding air-water interface and left to dry on the surface. Molecular combing was observed to extend the length of the bacteriophage λ DNA molecule to 21.5 ± 0.5 micrometers (unextended length, 16.2 micrometers). With the combing process, it was possible to (i) extend a chromosomal Escherichia coli DNA fragment (10^6 base pairs) and (ii) detect a minute quantity of DNA (10^3 molecules). These results open the way for a faster physical mapping of the genome and for the detection of small quantities of target DNA from a population of molecules.

  15. Volume visualization of multiple alignment of large genomicDNA

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H.; Hamann, Bernd

    2005-07-25

    Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We demonstrate our technique using multi-millions-basepair-long aligned DNA sequence data and compare it with traditional 1D line plots. The results show that our technique is superior in providing an overview of entire data sets. Our technique, coupled with 1D line plots, results in effective multi-resolution visualization of very large aligned sequence data sets.

  16. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene; Fogel, Gary B.; Krink, Thimo

    2002-01-01

    Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this paper we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the wellknown Clustal V algorithm as a candidate solution seed of the initial EA population. Our results clearly show...

  17. Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

    Science.gov (United States)

    Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

    2013-01-01

    Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

  18. Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Shunichi Kosugi

    Full Text Available Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.

  19. Partial Alignment for Improvement of Beam Transmission at KOMAC

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Dong-Hyuk; Kim, Dae-Il; Ahn, Tae-Sung; Kim, Han-Sung; Kwon, Hyeok-Jung; Cho, Yong-Sub [KOMAC, Gyeongju (Korea, Republic of)

    2015-05-15

    The ion source and steering magnets were aligned for improving the beam transmission. It is expected that the re-alignment of accelerator components can reduce the beam loss which can occur for the dislocation among them. The center displacements of RFQ and 20MeV DTL are different to 100MeV DTL, so it is necessary to re-align in next maintenance period. 100MeV proton linac placed in KOMAC (Korea Multi-purpose Accelerator Complex) has been operated and provided to beam users. There are two maintenance periods every year, winter (Jan-Feb) and summer (Jul-Aug). In maintenance period, proton linac is re-aligned for the improvement of beam transmission. 4 newly steering magnet are installed in beam line. To align the steering magnet, network align in tunnel is measured using by laser tracker. In addition, the position of ion source is away from the position of RFQ in the result of the survey of network align. The alignment of steering magnet after installation is performed. At the same time, the position of accelerator component is checked and aligned partially.

  20. Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

    Science.gov (United States)

    Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T; Volk, David E

    2014-06-10

    Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.

  1. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

    DEFF Research Database (Denmark)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan;

    2009-01-01

    MOTIVATION: The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary...

  2. MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information.

    Science.gov (United States)

    Balech, Bachir; Vicario, Saverio; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-08-01

    Here we present the MSA-PAD application, a DNA multiple sequence alignment framework that uses PFAM protein domain information to align DNA sequences encoding either single or multiple protein domains. MSA-PAD has two alignment options: gene and genome mode.

  3. An Improved Model Facet Method to Support EA Alignment

    Directory of Open Access Journals (Sweden)

    Jonathan Pepin

    2016-12-01

    Full Text Available Information System evolution requires a well-structured Enterprise Architecture and its rigorous management. The alignment of the elements in the architecture according to various abstraction layers may contribute to the management but appropriate tools are needed. We propose improvements to the Facet technique and we develop accompanying tools to master the difficulties of the alignment of the models used to structure an Enterprise Architecture. This technique has been experimented on many real life cases to demonstrate the effectiveness of our EA alignment method. The tools are already integrated in the Eclipse EMF Facet project.

  4. SOAP2: an improved ultrafast tool for short read alignment

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Yu, Chang; Li, Yingrui

    2009-01-01

    SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy...... for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...... multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn....

  5. Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

    Directory of Open Access Journals (Sweden)

    Siddharthan Rahul

    2006-03-01

    Full Text Available Abstract Background Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch-like pairwise alignment methods. We introduce a new tool, Sigma, with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem acquires importance with the increasing number of published sequences of closely-related species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step. Much can also be learned about evolution from intergenic DNA, which tends to evolve faster than coding DNA. Sigma uses a strategy of seeking the best possible gapless local alignments (a strategy earlier used by DiAlign, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. Results Comparative tests of sigma with five earlier algorithms on synthetic data generated to mimic real data show excellent performance, with Sigma balancing high "sensitivity" (more bases aligned with effective filtering of "incorrect" alignments. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior. Conclusion By taking into account the peculiarities of non-coding DNA, Sigma fills a gap in the toolbox of bioinformatics.

  6. Navigation improves accuracy of rotational alignment in total knee arthroplasty.

    Science.gov (United States)

    Stöckl, Bernd; Nogler, Michael; Rosiek, Rafal; Fischer, Martin; Krismer, Martin; Kessler, Oliver

    2004-09-01

    Successful total knee arthroplasty is dependent on the correct alignment of implanted prostheses. Major clinical problems can be related to poor femoral component positioning, including sagittal plane and rotational malalignment. A prospective randomized study was designed to test whether an optical navigation system for total knee arthroplasty achieved greater implantation precision than a nonnavigated technique. The primary variable was rotation of the femoral component in the transverse plane, measured from postoperative radiographs and computed tomography images. Sixty-four patients were included in the study. All patients received the Duracon total knee prosthesis. The patients were randomly divided into two groups: Group C patients had conventional total knee arthroplasty without navigation; Group N patients had total knee arthroplasty using a computer-assisted knee navigation system. Analysis showed that patients in Group N had significantly better rotational alignment and flexion angle of the femoral component than patients in Group C. In addition, superior postoperative alignment of the mechanical axis, posterior tibial slope, and rotational alignment was achieved for patients in Group N. The use of a navigation system provides improved alignment accuracy, and can help to avoid femoral malrotation and errors in axial alignment.

  7. Aligned carbon nanotube thin films for DNA electrochemical sensing

    Energy Technology Data Exchange (ETDEWEB)

    Berti, F. [Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Firenze 50019 (Italy); Lozzi, L. [Department of Physics, University of L' Aquila, Coppito, L' Aquila 67100 (Italy); Palchetti, I. [Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Firenze 50019 (Italy); Santucci, S. [Department of Physics, University of L' Aquila, Coppito, L' Aquila 67100 (Italy); Marrazza, G. [Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Firenze 50019 (Italy)], E-mail: giovanna.marrazza@unifi.it

    2009-09-01

    Carbon nanotubes are interesting materials for DNA electrochemical sensing due to their unique electric properties: high surface area, fast heterogeneous electron transfer, and electrochemical stability. In this work aligned Carbon NanoTube (CNT) thin films were designed and tested as candidate platforms for DNA immobilization and for the development of an electrochemical genosensor. The films were prepared by Chemical Vapor Deposition (CVD) using acetylene and ammonia as precursor gases and nickel particles as catalyst. A preliminary electrochemical characterization was performed using cyclic voltammetry since, so far, these films have been used only for gas sensing. The surfaces were then covalently functionalized with a DNA oligonucleotide probe, complementary to the sequence of the most common inserts in the GMOs: the Promoter 35S. The genosensor format involved the immobilization of the probe onto the sensor surface, the hybridization with the target-sequence and the electrochemical detection of the duplex formation. Careful attention was paid to the probe immobilization conditions in order to minimize the signal due to non-specifically adsorbed sequences. For the detection of the hybridization event both label-free and enzyme-labelled methods were investigated. In case of the enzyme-labelled method a target concentration at nanomolar level can be easily detected, with a linear response from 50 nM to 200 nM, whereas the label-free method showed a linear response between 0.5 {mu}M and 10 {mu}M. The reproducibility was 11% and 20% with the enzyme-labelled method and the label-free method, respectively. The batch-to-batch reproducibility of the different sensors was also evaluated.

  8. Aligning DNA on Si surface and cutting off by tips of atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    DNA is a kind of promising molecule as nano-lead to build or connect nano-devices due to its stable linear structure and certain conductivity. Many methods have been applied to constructing nano-patterns by using DNA molecule. In this report it is presented that (-DNA was aligned on Si substrate by using the free-flowing method and then imaged by an atomic force microscope (AFM). After the second liquid flow, a catenary-like pattern and a crossed network of -DNA were formed. In addition, the aligned (-DNA was successfully cut off by tips of AFM.

  9. A pattern matching approach for the estimation of alignment between any two given DNA sequences.

    Science.gov (United States)

    Basu, K; Sriraam, N; Richard, R J A

    2007-08-01

    For a given DNA sequence, it is well known that pair wise alignment schemes are used to determine the similarity with the DNA sequences available in the databanks. The efficiency of the alignment decides the type of amino acids and its corresponding proteins. In order to evaluate the given DNA sequence for its proteomic identity, a pattern matching approach is proposed in this paper. A block based semi-global alignment scheme is introduced to determine the similarity between the DNA sequences (known and given). The two DNA sequences are divided into blocks of equal length and alignment is performed which minimizes the computational complexity. The efficiency of the alignment scheme is evaluated using the parameter, percentage of similarity (POS). Four essential DNA version of the amino acids that emphasize the importance of proteomic functionalities are chosen as patterns and matching is performed with the known and given DNA sequences to determine the similarity between them. The ratio of amino acid counts between the two sequences is estimated and the results are compared with that of the POS value. It is found from the experimental results that higher the POS value and the pattern matching higher are the similarity between the two DNA sequences. The optimal block is also identified based on the POS value and amino acids count.

  10. In-Plane Switching Mode for Liquid Crystal Displays Using a DNA Alignment Layer.

    Science.gov (United States)

    Cha, Yun Jeong; Gim, Min-Jun; Oh, Kyunghwan; Yoon, Dong Ki

    2015-06-24

    We successfully fabricated the in-plane switching mode (IPS) LC display (LCD) based on a double stranded DNA (dsDNA) alignment layer. As widely known, the DNA has the right-handed double helical structure that has naturally grown grooves with a very regular period, which can be used as an alignment layer to control the orientation of liquid crystal (LC) molecules. The LC molecules on this topographical layer of DNA material align obliquely at a specific angle with respect to the direction of DNA chains, providing an instant and convenient tool for the fabrication of the IPS display compared to the conventional ways such as rubbing and mechanical shearing methods. The electro-optical performance and response time of this device were also investigated. Our result will be of great use in further exploration of the electro-optical properties of the other biomaterials.

  11. Improving pan-genome annotation using whole genome multiple alignment

    Directory of Open Access Journals (Sweden)

    Salzberg Steven L

    2011-06-01

    Full Text Available Abstract Background Rapid annotation and comparisons of genomes from multiple isolates (pan-genomes is becoming commonplace due to advances in sequencing technology. Genome annotations can contain inconsistencies and errors that hinder comparative analysis even within a single species. Tools are needed to compare and improve annotation quality across sets of closely related genomes. Results We introduce a new tool, Mugsy-Annotator, that identifies orthologs and evaluates annotation quality in prokaryotic genomes using whole genome multiple alignment. Mugsy-Annotator identifies anomalies in annotated gene structures, including inconsistently located translation initiation sites and disrupted genes due to draft genome sequencing or pseudogenes. An evaluation of species pan-genomes using the tool indicates that such anomalies are common, especially at translation initiation sites. Mugsy-Annotator reports alternate annotations that improve consistency and are candidates for further review. Conclusions Whole genome multiple alignment can be used to efficiently identify orthologs and annotation problem areas in a bacterial pan-genome. Comparisons of annotated gene structures within a species may show more variation than is actually present in the genome, indicating errors in genome annotation. Our new tool Mugsy-Annotator assists re-annotation efforts by highlighting edits that improve annotation consistency.

  12. Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing.

    Science.gov (United States)

    Teschome, Bezu; Facsko, Stefan; Gothelf, Kurt V; Keller, Adrian

    2015-11-24

    DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.

  13. RNAalifold: improved consensus structure prediction for RNA alignments

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2008-11-01

    Full Text Available Abstract Background The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach. Results We show that the accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices. These improvements are achieved without compromising the computational efficiency of the algorithm. We show here that the new version of RNAalifold not only outperforms the old one, but also several other tools recently developed, on different datasets. Conclusion The new version of RNAalifold not only can replace the old one for almost any application but it is also competitive with other approaches including those based on SCFGs, maximum expected accuracy, or hierarchical nearest neighbor classifiers.

  14. Heterogeneity in DNA multiple alignments: modeling, inference, and applications in motif finding.

    Science.gov (United States)

    Chen, Gong; Zhou, Qing

    2010-09-01

    Transcription factors bind sequence-specific sites in DNA to regulate gene transcription. Identifying transcription factor binding sites (TFBSs) is an important step for understanding gene regulation. Although sophisticated in modeling TFBSs and their combinatorial patterns, computational methods for TFBS detection and motif finding often make oversimplified homogeneous model assumptions for background sequences. Since nucleotide base composition varies across genomic regions, it is expected to be helpful for motif finding to incorporate the heterogeneity into background modeling. When sequences from multiple species are utilized, variation in evolutionary conservation violates the common assumption of an identical conservation level in multiple alignments. To handle both types of heterogeneity, we propose a generative model in which a segmented Markov chain is used to partition a multiple alignment into regions of homogeneous nucleotide base composition and a hidden Markov model (HMM) is employed to account for different conservation levels. Bayesian inference on the model is developed via Gibbs sampling with dynamic programming recursions. Simulation studies and empirical evidence from biological data sets reveal the dramatic effect of background modeling on motif finding, and demonstrate that the proposed approach is able to achieve substantial improvements over commonly used background models.

  15. Improving Business-IT Alignment through Business Architecture

    Science.gov (United States)

    Li, Chingmei

    2010-01-01

    The business and Information Technology (IT) alignment issue has become one of the Top-10 IT management issues since 1980. IT has continually strived to achieve alignment with business goals and objectives. These IT efforts include ERP implementation to benefit from the best practices; data center consolidation and server virtualization to keep…

  16. Improving your target-template alignment with MODalign.

    KAUST Repository

    Barbato, Alessandro

    2012-02-04

    SUMMARY: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported. CONTACT: jan.kosinski@uniroma1.it.

  17. Improving polyphonic and poly-instrumental music to score alignment

    OpenAIRE

    Soulez, Ferréol; Rodet, Xavier; Schwarz, Diemo

    2003-01-01

    6pp; International audience; Music alignment links events in a score and points on the audio performance time axis. All the parts of a recording can be thus indexed according to score information. The automatic alignment presented in this paper is based on a dynamic time warping method. Local distances are computed using the signal's spectral features through an attack plus sustain note modeling. The method is applied to mixtures of harmonic sustained instruments, excluding percussion for the...

  18. A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors.

    Science.gov (United States)

    Kang, Seok Hee; Hwang, Wan Sik; Lin, Zhiqun; Kwon, Se Hun; Hong, Suck Won

    2015-12-01

    Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.

  19. PipMaker—A Web Server for Aligning Two Genomic DNA Sequences

    OpenAIRE

    Schwartz, Scott; Zheng ZHANG; Frazer, Kelly A; Smit, Arian; Riemer, Cathy; Bouck, John; Gibbs, Richard; Hardison, Ross; Miller, Webb

    2000-01-01

    PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. Positions along the horizontal axis can be labeled with features su...

  20. An optimized and low-cost FPGA-based DNA sequence alignment--a step towards personal genomics.

    Science.gov (United States)

    Shah, Hurmat Ali; Hasan, Laiq; Ahmad, Nasir

    2013-01-01

    DNA sequence alignment is a cardinal process in computational biology but also is much expensive computationally when performing through traditional computational platforms like CPU. Of many off the shelf platforms explored for speeding up the computation process, FPGA stands as the best candidate due to its performance per dollar spent and performance per watt. These two advantages make FPGA as the most appropriate choice for realizing the aim of personal genomics. The previous implementation of DNA sequence alignment did not take into consideration the price of the device on which optimization was performed. This paper presents optimization over previous FPGA implementation that increases the overall speed-up achieved as well as the price incurred by the platform that was optimized. The optimizations are (1) The array of processing elements is made to run on change in input value and not on clock, so eliminating the need for tight clock synchronization, (2) the implementation is unrestrained by the size of the sequences to be aligned, (3) the waiting time required for the sequences to load to FPGA is reduced to the minimum possible and (4) an efficient method is devised to store the output matrix that make possible to save the diagonal elements to be used in next pass, in parallel with the computation of output matrix. Implemented on Spartan3 FPGA, this implementation achieved 20 times performance improvement in terms of CUPS over GPP implementation.

  1. Statistical aspects of discerning indel-type structural variation via DNA sequence alignment

    Directory of Open Access Journals (Sweden)

    Wilson Richard K

    2009-08-01

    Full Text Available Abstract Background Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for. Results Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs. Conclusion The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.

  2. Measuring covariation in RNA alignments: Physical realism improves information measures

    DEFF Research Database (Denmark)

    Lindgreen, Stinus; Gardner, Paul Phillip; Krogh, Anders

    2006-01-01

    Motivation: The importance of non-coding RNAs is becoming increasingly evident, and often the function of these molecules depends on the structure. It is common to use alignments of related RNA sequences to deduce the consensus secondary structure by detecting patterns of co-evolution. A central ...

  3. Genomic Signal Processing Methods for Computation of Alignment-Free Distances from DNA Sequences

    Science.gov (United States)

    Borrayo, Ernesto; Mendizabal-Ruiz, E. Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P.; Morales, J. Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments. PMID:25393409

  4. Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

    Science.gov (United States)

    Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

  5. Self-assembled alignment of nanorod by using DNA brush (Conference Presentation)

    Science.gov (United States)

    Ijiro, Kuniharu; Nakamura, Satoshi; Mitomo, Hideyuki; Pike, Andrew; Matsuo, Yasutaka; Niikura, Kenichi

    2016-09-01

    Surface modification with polymer is widely applied to various kinds of applications. Recently, polymer brushes, which is a layer of polymers attached with one end to a surface, have attracted much attention as functionalized surfaces. In particular, ionic polymer brushes provide ultra-low friction or anti-fouling because they act as highly hydrated soft film. Almost ionic polymer brushes have been prepared from synthetic polymers. Few biopolymers have been investigated for polymer brush studies. DNA which is one of ionic biopolymers has unique functions and conformations which synthetic polymers don't have. We found that cationic gold nanorods (30 x 10 nm) were adsorbed to DNA bush (148 bp) prepared on a glass surface in an aqueous solution by observation using extinction spectra. When the cationic charge density of gold nanorods were decreased, nanorods were immobilized perpendicularly to the substrate by binding to DNA elongated. This indicates that self-assembled alignment of gold nanorods can be achieved by using DNA brush. Formed aligned gold nanorods can be used for plasmonic color analysis.

  6. EURRECA: development of tools to improve the alignment of micronutrient recommendations

    NARCIS (Netherlands)

    Matthys, C.; Bucchini, L.; Busstra, M.C.; Cavelaars, A.J.E.M.; Eleftheriou, P.; Garcia-Alvarez, A.; Fairweather-Tait, S.; Gurinovic, M.; Ommen, van B.; Contor, L.

    2010-01-01

    Approaches through which reference values for micronutrients are derived, as well as the reference values themselves, vary considerably across countries. Harmonisation is needed to improve nutrition policy and public health strategies. The EURRECA (EURopean micronutrient RECommendations Aligned, htt

  7. Improving DNA vaccine performance through vector design.

    Science.gov (United States)

    Williams, James A

    2014-01-01

    DNA vaccines are a rapidly deployed next generation vaccination platform for treatment of human and animal disease. DNA delivery devices, such as electroporation and needle free jet injectors, are used to increase gene transfer. This results in higher antigen expression which correlates with improved humoral and cellular immunity in humans and animals. This review highlights recent vector and transgene design innovations that improve DNA vaccine performance. These new vectors improve antigen expression, increase plasmid manufacturing yield and quality in bioreactors, and eliminate antibiotic selection and other potential safety issues. A flowchart for designing synthetic antigen transgenes, combining antigen targeting, codon-optimization and bioinformatics, is presented. Application of improved vectors, of antibiotic free plasmid production, and cost effective manufacturing technologies will be critical to ensure safety, efficacy, and economically viable manufacturing of DNA vaccines currently under development for infectious disease, cancer, autoimmunity, immunotolerance and allergy indications.

  8. Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.

    Science.gov (United States)

    Gouge, Jérôme; Rosario, Sandrine; Romain, Félix; Poitevin, Frédéric; Béguin, Pierre; Delarue, Marc

    2015-04-15

    Eukaryotic DNA polymerase mu of the PolX family can promote the association of the two 3'-protruding ends of a DNA double-strand break (DSB) being repaired (DNA synapsis) even in the absence of the core non-homologous end-joining (NHEJ) machinery. Here, we show that terminal deoxynucleotidyltransferase (TdT), a closely related PolX involved in V(D)J recombination, has the same property. We solved its crystal structure with an annealed DNA synapsis containing one micro-homology (MH) base pair and one nascent base pair. This structure reveals how the N-terminal domain and Loop 1 of Tdt cooperate for bridging the two DNA ends, providing a templating base in trans and limiting the MH search region to only two base pairs. A network of ordered water molecules is proposed to assist the incorporation of any nucleotide independently of the in trans templating base. These data are consistent with a recent model that explains the statistics of sequences synthesized in vivo by Tdt based solely on this dinucleotide step. Site-directed mutagenesis and functional tests suggest that this structural model is also valid for Pol mu during NHEJ.

  9. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.

  10. An Improved Search Algorithm for Optimal Multiple-Sequence Alignment

    CERN Document Server

    Schroedl, S

    2011-01-01

    Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits of exact algorithms further. Since MSA can be cast as a classical path finding problem, it is attracting a growing number of AI researchers interested in heuristic search algorithms as a challenge with actual practical relevance. In this paper, we first review two previous, complementary lines of research. Based on Hirschbergs algorithm, Dynamic Programming needs O(kN^(k-1)) space to store both the search frontier and the nodes needed to reconstruct the solution path, for k sequences of length N. Best first search, on the other hand, has the advantage of bounding the search space that has to be explored using a heuristic. However, it is necessary to maintain all explored nodes up to the final solution in order to prevent the search from re-expanding them at hig...

  11. Engineered DNA Polymerase Improves PCR Results for Plastid DNA

    Directory of Open Access Journals (Sweden)

    Melanie Schori

    2013-02-01

    Full Text Available Premise of the study: Secondary metabolites often inhibit PCR and sequencing reactions in extractions from plant material, especially from silica-dried and herbarium material. A DNA polymerase that is tolerant to inhibitors improves PCR results. Methods and Results: A novel DNA amplification system, including a DNA polymerase engineered via directed evolution for improved tolerance to common plant-derived PCR inhibitors, was evaluated and PCR parameters optimized for three species. An additional 31 species were then tested with the engineered enzyme and optimized protocol, as well as with regular Taq polymerase. Conclusions: PCR products and high-quality sequence data were obtained for 96% of samples for rbcL and 79% for matK, compared to 29% and 21% with regular Taq polymerase.

  12. Highly improved homopolymer aware nucleotide-protein alignments with 454 data

    Directory of Open Access Journals (Sweden)

    Lysholm Fredrik

    2012-09-01

    Full Text Available Abstract Background Roche 454 sequencing is the leading sequencing technology for producing long read high throughput sequence data. Unlike most methods where sequencing errors translate to base uncertainties, 454 sequencing inaccuracies create nucleotide gaps. These gaps are particularly troublesome for translated search tools such as BLASTx where they introduce frame-shifts and result in regions of decreased identity and/or terminated alignments, which affect further analysis. Results To address this issue, the Homopolymer Aware Cross Alignment Tool (HAXAT was developed. HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values. The algorithm is an efficient minimal extension of the Smith-Waterman-Gotoh algorithm that easily fits in into other tools. Experiments using HAXAT demonstrate, through the introduction of 454 specific frame-shift penalties, significantly increased accuracy of alignments spanning homopolymer sequence errors. The full effect of the new parameters introduced with this novel alignment model is explored. Experimental results evaluating homopolymer inaccuracy through alignments show a two to five-fold increase in Matthews Correlation Coefficient over previous algorithms, for 454-derived data. Conclusions This increased accuracy provided by HAXAT does not only result in improved homologue estimations, but also provides un-interrupted reading-frames, which greatly facilitate further analysis of protein space, for example phylogenetic analysis. The alignment tool is available at http://bioinfo.ifm.liu.se/454tools/haxat.

  13. DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2005-03-01

    Full Text Available Abstract Background We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. Results In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. Conclusion On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.

  14. A new automatic alignment technology for single mode fiber-waveguide based on improved genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yu; CHEN Zhuang-zhuang; LI Ya-juan; DUAN Jian

    2009-01-01

    A novel automatic alignment algorithm of single mode fiber-waveguide based on improved genetic algorithm is proposed. The genetic searching is based on the dynamic crossover operator and the adaptive mutation operator to solve the premature convergence of simple genetic algorithm The improved genetic algorithm combines with hill-climbing method and pattern searching algorithm, to solve low precision of simple genetic algorithm in later searching. The simulation results indicate that the improved genetic algorithm can rise the alignment precision and reach the coupling loss of 0.01 dB when platform moves near 207 space points averagely.

  15. Re-grown aligned carbon nanotubes with improved field emission.

    Science.gov (United States)

    Lim, Xiaodai; Zhu, Yanwu; Varghese, Binni; Gao, Xingyu; Wee, Andrew Thye Shen; Sow, Chorng-Haur

    2012-01-01

    In this work, a simple technique to improve the field emission property of multi-walled carbon nanotubes is presented. Re-grown multi-walled carbon nanotubes are grown on the same substrates after the as-grown multi-walled carbon nanotubes are transferred to other substrates using polydimethylsiloxane as intermediation. For the duration of the synthesis of the re-grown multi-walled carbon nanotubes, similar synthesis parameters used in growing the as-grown multi-walled carbon nanotubes are utilized. As a form of possible application, field emission studies show -2.6 times improvement in field enhancement factor and more uniform emission for the re-grown multi-walled carbon nanotubes. In addition, the turn-on field is reduced from 2.85 V/microm to 1.40 V/microm. Such significant improvements are attributed to new emission sites comprising of sharp carbonaceous impurities encompassing both tip and upper portion of the multi-walled carbon nanotubes. As such, this technique presents a viable route for the production of multi-walled carbon nanotubes with better field emission quality.

  16. Improved calibration of IMU biases in analytic coarse alignment for AHRS

    Science.gov (United States)

    Lu, Jiazhen; Lei, Chaohua; Li, Baoguo; Wen, Ting

    2016-07-01

    An improved method for the inertial measurement unit (IMU) calibration of coarse alignment for the low-accuracy attitude heading reference system (AHRS) is proposed in this paper. The sensitivities of the Euler angles with respect to the inertial sensor biases are studied based on the analytic coarse alignment principle, and the errors of earth rotation rate and local gravity in the body frame caused by initial attitude error are analyzed. Then, an improved analytic coarse alignment algorithm with accelerometer and gyro bias calibration in an arbitrary three-position is proposed. Simulation and experiment results show that the novel method can calibrate accelerometer and gyro biases, reduce Euler angle attitude error, and improve navigation precision in practical applications. Moreover, this method can be applied to other low-accuracy inertial navigation systems.

  17. DNA hosted and aligned in aqueous interstitia of a lamellar liquid crystal – a membrane–biomacromolecule interaction model system

    KAUST Repository

    Carlsson, Nils

    2013-01-01

    We report that DNA molecules can be intercalated and macroscopically oriented in the aqueous interstitia of a lyotropic lamellar liquid crystal. Using UV-vis linear dichroism and fluorescence spectroscopy we show that double-stranded oligonucleotides (25 base pairs) in the water-octanoate-decanol system remain base-paired in the B conformation and are confined in two dimensions, with the helix axis preferentially parallel to the lipid bilayer surfaces but free to rotate within this plane. The degree of helix confinement and the corresponding 2-D orientation can be improved by decreasing the thickness of the water interstitia via the fraction of water in the ternary mixture. Not surprisingly, the corresponding single-stranded oligonucleotides are not aligned, with their persistence length being short in comparison to the lamellar interstitium thickness. We propose this as a model system for studying interactions of DNA-ligand complexes near a lipid bilayer membrane which we demonstrate by using dye probes that are either covalently attached to one end of the oligonucleotide or reversibly bound by intercalation between the base pairs. Three cationic dyes, all strongly bound by intercalation to DNA when free in solution, are found to not bind to DNA but to prefer the membrane surface. The covalently attached Cy5 also binds to the bilayer while Cy3 tends to end-stack to the oligonucleotide duplex. The orientation of Cy5 parallel to the membrane indicates that electrostatic surface binding predominates over insertion into the hydrophobic interior of the membrane. Anionic and zwitterionic dyes (FAM and ROX) are found to remain randomly oriented in the water between the lipid bilayer surfaces. © The Royal Society of Chemistry.

  18. Improved wafer-scale fabrication of aligned pdms-glass microchips with integrated electrodes

    NARCIS (Netherlands)

    Li, J.; Le Gac, S.; Berg, van den A.; Viovy, J.L.; Tabeling, P.; Descroix, S.; Malaquin, L.

    2007-01-01

    We report an improved fabrication process of PDMS-based hybrid chips at the scale of a whole wafer and including an alignment step. This implies a control of the dimension variations of this elastomer upon temperature changes and the production of a PDMS wafer compatible with the use of standard ali

  19. Design pattern mining using distributed learning automata and DNA sequence alignment.

    Directory of Open Access Journals (Sweden)

    Mansour Esmaeilpour

    Full Text Available CONTEXT: Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. OBJECTIVE: This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA and deoxyribonucleic acid (DNA sequences alignment. METHOD: The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. RESULTS: The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. CONCLUSION: The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

  20. Design Pattern Mining Using Distributed Learning Automata and DNA Sequence Alignment

    Science.gov (United States)

    Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

    2014-01-01

    Context Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. Objective This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. Method The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. Results The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. Conclusion The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns. PMID:25243670

  1. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

    Directory of Open Access Journals (Sweden)

    von Reumont Björn M

    2010-03-01

    Full Text Available Abstract Background Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Conclusions Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment

  2. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  3. Controlled growth of well-aligned ZnO nanowire arrays using the improved hydrothermal method

    Institute of Scientific and Technical Information of China (English)

    Han Zhitao; Li Sisi; Chu Jinkui; Chen Yong

    2013-01-01

    Well-aligned ZnO nanowires were hydrothermally synthesized based on a facile method for preparing the ZnO seed layer which was derived from the combination of a sol-gel process and the spin-coating technique.The effect of the contents of growth solution and the growth duration on the morphology ofZnO nanowires has been investigated.The results indicated that long and vertically aligned ZnO nanowires could be obtained by adjusting the contents of ammonia and polyethyleneimine (PEI) in the growth solution.Under the optimized condition,the length of ZnO nanowires increased fast and almost linearly with the growth duration.After 10 h incubation,ZnO nanowires more than 25μm in length were obtained.By combining the conventional photolithographic method with this hydrothermal approach,long and well-aligned ZnO nanowire arrays were selectively grown on the substrate.In addition,the bottom fusion at the foot of the nanowires has been obviously improved.The results demonstrated that the improved hydrothermal process is favorable to synthesize long and well-aligned ZnO nanowires,and possesses good process compatibility with the conventional photolithographic technique for preparing ZnO nanowire arrays.So it has great potential in applications such as display and field emission devices.

  4. Improved thermoplastic composite by alignment of vapor-grown carbon fiber

    Science.gov (United States)

    Kuriger, Rex Jerrald

    2000-10-01

    Vapor grown carbon fiber (VGCF) is a new and inexpensive carbon fiber produced by vapor deposition of hydrocarbons on metal catalysts. Unlike continuous conventional PAN or pitch-derived carbon fibers, VGCF is discontinuous with diameters of about 200 nanometers and lengths ranging from 10 to 200 micrometers. The microscopic size and random entanglement of the fibers create several problems when processing VGCF composites. It is particularly difficult to disperse the entangled fibers in the matrix and orient them along a preferred axis to provide directional reinforcement. This work introduces a technique to produce an improved polymeric composite by alignment of vapor grown carbon nano-fibers in a polypropylene matrix. A twin-screw extruder was used to shear mix and disperse the fibers in the polymer matrix. The composite mixtures were extruded through a converging-annular die that generates flow-induced fiber alignment along the extrusion direction. The effect that the various extrusion conditions have on the bulk properties of the extrudate was investigated. It was found that the extrusion process is strongly dependent on the fiber content of the composite. The extrusion pressure increased and the flow rate decreased with fiber volume fraction. The tensile strength and modulus for the composite samples varied with extrusion temperature and screw speed, and the void content increased with fiber volume fraction. It was shown that fiber alignment could be improved by increasing the residence time in the die channel and was verified using x-ray diffraction. The mechanical properties of the aligned samples increased with fiber content. Also, the tensile strength improved with greater fiber orientation; however, more fiber alignment had little affect on the modulus. To better predict the strength of these partially aligned fiber composites, an experimental and theoretical approach was introduced. The experimental data correspond reasonably well when compared with the

  5. String Match Algorithms and Applications in DNA Sequence Alignment%字符串匹配算法在 DNA 序列比对中的应用

    Institute of Scientific and Technical Information of China (English)

    陈建平

    2015-01-01

    The advancement of high-throughput sequencing technologies has led bioinformatics research into the big data era.New technologies generate huge amounts of biological genetic data,which pose significant challenges to data analysis. DNA sequence alignment is one critical step of the bioinformatics analysis flow,providing mapping information for the following variants calling processes.Question B of 201 5 “Shenzhen Cup ”Summer Camp of Mathematical Modeling discusses about DNA sequence alignment problem,requiring students to provide the best solution for fast sequence alignment.Here,we give a brief review on the students’work,then we introduce algorithms implemented in common DNA sequence alignment programs.%高通量测序技术的飞速发展让生物信息领域迎来了大数据时代。新技术在提供海量生物遗传信息的同时,也给分析这些数据带来了新的挑战。DNA 序列比对是信息分析流程中的关键步骤,为后续的变异检测提供序列比对信息。2015“深圳杯”数学建模夏令营 B 题以 DNA 序列比对为研究课题,希望参赛学生给出序列快速比对的最佳方案。本文简要点评了各参赛队伍的解答情况,然后介绍了现有 DNA 序列比对软件中用到的算法和数据结构。

  6. Computer navigation experience in hip resurfacing improves femoral component alignment using a conventional jig

    Directory of Open Access Journals (Sweden)

    Zachary Morison

    2013-01-01

    Full Text Available Background:The use of computer navigation has been shown to improve the accuracy of femoral component placement compared to conventional instrumentation in hip resurfacing. Whether exposure to computer navigation improves accuracy when the procedure is subsequently performed with conventional instrumentation without navigation has not been explored. We examined whether femoral component alignment utilizing a conventional jig improves following experience with the use of imageless computer navigation for hip resurfacing. Materials and Methods:Between December 2004 and December 2008, 213 consecutive hip resurfacings were performed by a single surgeon. The first 17 (Cohort 1 and the last 9 (Cohort 2 hip resurfacings were performed using a conventional guidewire alignment jig. In 187 cases, the femoral component was implanted using the imageless computer navigation. Cohorts 1 and 2 were compared for femoral component alignment accuracy. Results:All components in Cohort 2 achieved the position determined by the preoperative plan. The mean deviation of the stem-shaft angle (SSA from the preoperatively planned target position was 2.2° in Cohort 2 and 5.6° in Cohort 1 ( P = 0.01. Four implants in Cohort 1 were positioned at least 10° varus compared to the target SSA position and another four were retroverted. Conclusions: Femoral component placement utilizing conventional instrumentation may be more accurate following experience using imageless computer navigation.

  7. A new method for improving functional-to-structural MRI alignment using local Pearson correlation.

    Science.gov (United States)

    Saad, Ziad S; Glen, Daniel R; Chen, Gang; Beauchamp, Michael S; Desai, Rutvik; Cox, Robert W

    2009-02-01

    Accurate registration of Functional Magnetic Resonance Imaging (FMRI) T2-weighted volumes to same-subject high-resolution T1-weighted structural volumes is important for Blood Oxygenation Level Dependent (BOLD) FMRI and crucial for applications such as cortical surface-based analyses and pre-surgical planning. Such registration is generally implemented by minimizing a cost functional, which measures the mismatch between two image volumes over the group of proper affine transformations. Widely used cost functionals, such as mutual information (MI) and correlation ratio (CR), appear to yield decent alignments when visually judged by matching outer brain contours. However, close inspection reveals that internal brain structures are often significantly misaligned. Poor registration is most evident in the ventricles and sulcal folds, where CSF is concentrated. This observation motivated our development of an improved modality-specific cost functional which uses a weighted local Pearson coefficient (LPC) to align T2- and T1-weighted images. In the absence of an alignment gold standard, we used three human observers blinded to registration method to provide an independent assessment of the quality of the registration for each cost functional. We found that LPC performed significantly better (p<0.001) than generic cost functionals including MI and CR. Generic cost functionals were very often not minimal near the best alignment, thereby suggesting that optimization is not the cause of their failure. Lastly, we emphasize the importance of precise visual inspection of alignment quality and present an automated method for generating composite images that help capture errors of misalignment.

  8. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2008-04-01

    Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

  9. Beyond clinical engagement: a pragmatic model for quality improvement interventions, aligning clinical and managerial priorities.

    Science.gov (United States)

    Pannick, Samuel; Sevdalis, Nick; Athanasiou, Thanos

    2016-09-01

    Despite taking advantage of established learning from other industries, quality improvement initiatives in healthcare may struggle to outperform secular trends. The reasons for this are rarely explored in detail, and are often attributed merely to difficulties in engaging clinicians in quality improvement work. In a narrative review of the literature, we argue that this focus on clinicians, at the relative expense of managerial staff, has proven counterproductive. Clinical engagement is not a universal challenge; moreover, there is evidence that managers-particularly middle managers-also have a role to play in quality improvement. Yet managerial participation in quality improvement interventions is often assumed, rather than proven. We identify specific factors that influence the coordination of front-line staff and managers in quality improvement, and integrate these factors into a novel model: the model of alignment. We use this model to explore the implementation of an interdisciplinary intervention in a recent trial, describing different participation incentives and barriers for different staff groups. The extent to which clinical and managerial interests align may be an important determinant of the ultimate success of quality improvement interventions.

  10. Membranes having aligned 1-D nanoparticles in a matrix layer for improved fluid separation

    Energy Technology Data Exchange (ETDEWEB)

    Revanur, Ravindra; Lulevich, Valentin; Roh, Il Juhn; Klare, Jennifer E.; Kim, Sangil; Noy, Aleksandr; Bakajin, Olgica

    2015-12-22

    Membranes for fluid separation are disclosed. These membranes have a matrix layer sandwiched between an active layer and a porous support layer. The matrix layer includes 1-D nanoparticles that are vertically aligned in a porous polymer matrix, and which substantially extend through the matrix layer. The active layer provides species-specific transport, while the support layer provides mechanical support. A matrix layer of this type has favorable surface morphology for forming the active layer. Furthermore, the pores that form in the matrix layer tend to be smaller and more evenly distributed as a result of the presence of aligned 1-D nanoparticles. Improved performance of separation membranes of this type is attributed to these effects.

  11. Patient-specific instrumentation does not improve radiographic alignment or clinical outcomes after total knee arthroplasty.

    Science.gov (United States)

    Huijbregts, Henricus J T A M; Khan, Riaz J K; Sorensen, Emma; Fick, Daniel P; Haebich, Samantha

    2016-08-01

    Background and purpose - Patient-specific instrumentation (PSI) for total knee arthroplasty (TKA) has been introduced to improve alignment and reduce outliers, increase efficiency, and reduce operation time. In order to improve our understanding of the outcomes of patient-specific instrumentation, we conducted a meta-analysis. Patients and methods - We identified randomized and quasi-randomized controlled trials (RCTs) comparing patient-specific and conventional instrumentation in TKA. Weighted mean differences and risk ratios were determined for radiographic accuracy, operation time, hospital stay, blood loss, number of surgical trays required, and patient-reported outcome measures. Results - 21 RCTs involving 1,587 TKAs were included. Patient-specific instrumentation resulted in slightly more accurate hip-knee-ankle axis (0.3°), coronal femoral alignment (0.3°, femoral flexion (0.9°), tibial slope (0.7°), and femoral component rotation (0.5°). The risk ratio of a coronal plane outlier (> 3° deviation of chosen target) for the tibial component was statistically significantly increased in the PSI group (RR =1.64). No significance was found for other radiographic measures. Operation time, blood loss, and transfusion rate were similar. Hospital stay was significantly shortened, by approximately 8 h, and the number of surgical trays used decreased by 4 in the PSI group. Knee Society scores and Oxford knee scores were similar. Interpretation - Patient-specific instrumentation does not result in clinically meaningful improvement in alignment, fewer outliers, or better early patient-reported outcome measures. Efficiency is improved by reducing the number of trays used, but PSI does not reduce operation time.

  12. A scheme for multiple sequence alignment optimization--an improvement based on family representative mechanics features.

    Science.gov (United States)

    Liu, Xin; Zhao, Ya-Pu

    2009-12-21

    As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue-residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue-residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (approximately 50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

  13. Improvement of the CMS Muon Reconstruction Performance due to Precise Track-based Alignment

    Science.gov (United States)

    Brown, Malachi

    2017-01-01

    The performance of the CMS muon system depends on a precise knowledge of the positions and orientations of all its elements. The muon tracks reconstructed in proton-proton collision data at the LHC are used to align the individual muon detectors with respect to the inner silicon tracker. The alignment procedure measures these positions and provides geometries of the muon system that must be validated to ensure the performance of the detectors. In this report we present a set of sophisticated validation tools, developed to test the accuracy of a given muon system geometry with data from collisions. The validation procedure uses events with pairs of muons from Z-boson decays and events with very high pT muons, in order to quantify the reconstruction performance of the muon system for a given geometry. Kinematic properties of muons reconstructed using information from the muon system are compared to the properties of muons built using information from the tracker. We demonstrate improvements of the muon reconstruction performance after track-based alignment procedures are performed with 2016 data.

  14. HIV DNA Vaccine: Stepwise Improvements Make a Difference

    Directory of Open Access Journals (Sweden)

    Barbara K. Felber

    2014-05-01

    Full Text Available Inefficient DNA delivery methods and low expression of plasmid DNA have been major obstacles for the use of plasmid DNA as vaccine for HIV/AIDS. This review describes successful efforts to improve DNA vaccine methodology over the past ~30 years. DNA vaccination, either alone or in combination with other methods, has the potential to be a rapid, safe, and effective vaccine platform against AIDS. Recent clinical trials suggest the feasibility of its translation to the clinic.

  15. Measurement of word frequencies in genomic DNA sequences based on partial alignment and fuzzy set.

    Science.gov (United States)

    Shida, Fumiya; Mizuta, Satoshi

    2014-08-01

    Accompanied with the rapid increase of the amount of data registered in the databases of biological sequences, the need for a fast method of sequence comparison applicable to sequences of large size is also increasing. In general, alignment is used for sequence comparison. However, the alignment may not be appropriate for comparison of sequences of large size such as whole genome sequences due to its large time complexity. In this article, we propose a semi alignment-free method of sequence comparison based on word frequency distributions, in which we partially use the alignment to measure word frequencies along with the idea of fuzzy set theory. Experiments with ten bacterial genome sequences demonstrated that the fuzzy measurements has the effect that facilitates discrimination between close relatives and distant relatives.

  16. DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment

    Science.gov (United States)

    Li, Yushuang; Liu, Qian; Zheng, Xiaoqi

    2016-08-01

    A highly compact and simple 2D graphical representation of DNA sequences, named DUC-Curve, is constructed through mapping four nucleotides to a unit circle with a cyclic order. DUC-Curve could directly detect nucleotide, di-nucleotide compositions and microsatellite structure from DNA sequences. Moreover, it also could be used for DNA sequence alignment. Taking geometric center vectors of DUC-Curves as sequence descriptor, we perform similarity analysis on the first exons of β-globin genes of 11 species, oncogene TP53 of 27 species and twenty-four Influenza A viruses, respectively. The obtained reasonable results illustrate that the proposed method is very effective in sequence comparison problems, and will at least play a complementary role in classification and clustering problems.

  17. Quality improvement education to improve performance on ulcerative colitis quality measures and care processes aligned with National Quality Strategy priorities.

    Science.gov (United States)

    Greene, Laurence; Moreo, Kathleen

    2015-01-01

    Studies on inflammatory bowel disease (IBD) have reported suboptimal approaches to patient care. In the United States, the findings have motivated leading gastroenterology organizations to call for initiatives that support clinicians in aligning their practices with quality measures for IBD and priorities of the National Quality Strategy (NQS). We designed and implemented a quality improvement (QI) education program on ulcerative colitis in which patient charts were audited for 30 gastroenterologists before (n = 300 charts) and after (n = 290 charts) they participated in QI-focused educational activities. Charts were audited for nine measures, selected for their alignment with four NQS priorities: making care safer, ensuring patient engagement, promoting communication, and promoting effective treatment practices. Four of the measures, including guideline-directed vaccinations and assessments of disease type and activity, were part of the CMS Physician Quality Reporting System (PQRS). The other five measures involved counseling patients on various topics in ulcerative colitis management, documentation of side effects, assessment of adherence status, and simplification of dosing. The gastroenterologists also completed baseline and post-education surveys designed to assess qualitative outcomes. One of the educational interventions was a private audit feedback session conducted for each gastroenterologist. The sessions were designed to support participants in identifying measures reflecting suboptimal care quality and developing action plans for improvement. In continuous improvement cycles, follow-up interventions included QI tools and educational monographs. Across the nine chart variables, post-education improvements ranged from 0% to 48%, with a mean improvement of 15.9%. Survey findings revealed improvements in self-reported understanding of quality measures and intentions to apply them to practice, and lower rates of perceived significant barriers to high

  18. Improved taboo search algorithm for designing DNA sequences

    Institute of Scientific and Technical Information of China (English)

    Kai Zhang; Jin Xu; Xiutang Geng; Jianhua Xiao; Linqiang Pan

    2008-01-01

    The design of DNA sequences is one of the most practical and important research topics in DNA computing.We adopt taboo search algorithm and improve the method for the systematic design of equal-length DNA sequences,which can satisfy certain combinatorial and thermodynamic constraints.Using taboo search algorithm,our method can avoid trapping into local optimization and can find a set of good DNA sequences satisfying required constraints.

  19. Cellulose nanowhiskers and fiber alignment greatly improve mechanical properties of electrospun prolamin protein fibers.

    Science.gov (United States)

    Wang, Yixiang; Chen, Lingyun

    2014-02-12

    Electrospun fibers from natural polymers must possess appropriate mechanical properties if they are to be functional in numerous applications. In this research, two convenient physical approaches were applied to reinforce the assembled hordein/zein electrospun nanofabrics: incorporation of surface-modified cellulose nanowhiskers (SCN) and fiber alignment. The mechanical properties and stability of the modified fibers were tested in relation to fiber morphology and structure as characterized by scanning electron microscopy, transmission electron microscopy, Fourier-transform infrared spectroscopy, and Raman spectroscopy. SCN modified by quaternary ammonium salt were well-dispersed in hordein/zein networks, leading to fibers with significantly improved mechanical properties and water resistance. With the addition of 3 wt % SCN, the tensile strength and Young's modulus of hordein/zein fibers increased from 4.36 ± 0.29 to 7.79 ± 0.36 MPa and from 195.80 ± 13.02 to 396.64 ± 18.33 MPa, respectively, and the elongation at break was retained because of the formation of a percolating network of SCN. The alignment of electrospun fibers strengthened the hordein/zein nanofabrics in both tangential and normal directions to 17.26 ± 1.41 and 14.02 ± 0.74 MPa, respectively, by not only altering the piling up pattern, but also by promoting phase separation and improved interactions. When applying both of the reinforcing methods, the tensile strength of hordein/zein fibers was further enhanced to 21.99 ± 1.19 MPa, stronger than that of cancellous bones (5-10 MPa). All the reinforced fibers exhibited a reduced burst effect in phosphate-buffered saline (PBS) while releasing the incorporated bioactive molecule in a controlled manner. These physically reinforced prolamin protein fibers possessed significantly improved mechanical properties and may have potential to be used as tissue engineering scaffold materials or natural delivery systems for biomedical applications.

  20. Improved toluidine blue-DNA agar for detection of DNA hydrolysis by campylobacters.

    OpenAIRE

    Lior, H.; Patel, A.

    1987-01-01

    Our improved toluidine blue-DNA agar was compared with methyl green DNase test agar for the detection of DNA hydrolysis by campylobacters. The toluidine blue-DNA agar gave clear-cut positive and negative reactions with campylobacter strains belonging to several species.

  1. Improved recovery of DNA from polyacrylamide gels after in situ DNA footprinting

    NARCIS (Netherlands)

    van Keulen, G; Meijer, WG

    2003-01-01

    Methods used to date for the isolation of DNA from polyacrylamide gels are elution based, time-consuming and with low yield in DNA. This paper describes an improved system employing polyacrylamide gels made of a meltable matrix. The new system was successfully applied to in situ DNA footprinting fol

  2. Employing Ontology-Alignment and Locality-Sensitive Hashing to Improve Attribute Interoperability in Federated eID Systems

    Directory of Open Access Journals (Sweden)

    Walter Priesnitz Filho

    2016-10-01

    Full Text Available Achieving interoperability, i.e. creating identity federations between different Electronic identities (eID systems, has gained relevance throughout the past years. A serious problem of identity federations is the missing harmonization between various attribute providers (APs. In closed eID systems, ontologies allow a higher degree of automation in the process of aligning and aggregating attributes from different APs. This approach does not work for identity federations, as each eID system uses its own ontology to represent its attributes. Furthermore, providing attributes to intermediate entities required to align and aggregate attributes potentially violates privacy rules. To tackle these problems, we propose the use of combined ontology-alignment (OA approaches and locality-sensitive hashing (LSH functions. We assess existing implementations of these concepts defining and using criteria that are special for identity federations. Obtained results confirm that proper implementations of these concepts exist and that they can be used to achieve interoperability between eID systems on attribute level. A prototype is implemented showing that combining the two assessment winners (AlignAPI for ontology-alignment and Nilsimsa for LSH functions achieves interoperability between eID systems. In addition, the improvement obtained in the alignment process by combining the two assessment winners does not impact negatively the privacy of the user’s data, since no clear-text data is exchanged in the alignment process.

  3. A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion.

    Science.gov (United States)

    Kedzierska, Anna; Husmeier, Dirk

    2006-01-01

    We propose a heuristic approach to the detection of evidence for recombination and gene conversion in multiple DNA sequence alignments. The proposed method consists of two stages. In the first stage, a sliding window is moved along the DNA sequence alignment, and phylogenetic trees are sampled from the conditional posterior distribution with MCMC. To reduce the noise intrinsic to inference from the limited amount of data available in the typically short sliding window, a clustering algorithm based on the Robinson-Foulds distance is applied to the trees thus sampled, and the posterior distribution over tree clusters is obtained for each window position. While changes in this posterior distribution are indicative of recombination or gene conversion events, it is difficult to decide when such a change is statistically significant. This problem is addressed in the second stage of the proposed algorithm, where the distributions obtained in the first stage are post-processed with a Bayesian hidden Markov model (HMM). The emission states of the HMM are associated with posterior distributions over phylogenetic tree topology clusters. The hidden states of the HMM indicate putative recombinant segments. Inference is done in a Bayesian sense, sampling parameters from the posterior distribution with MCMC. Of particular interest is the determination of the number of hidden states as an indication of the number of putative recombinant regions. To this end, we apply reversible jump MCMC, and sample the number of hidden states from the respective posterior distribution.

  4. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing.

    Directory of Open Access Journals (Sweden)

    Chao Shi

    Full Text Available BACKGROUND: Chloroplast genomes supply valuable genetic information for evolutionary and functional studies in plants. The past five years have witnessed a dramatic increase in the number of completely sequenced chloroplast genomes with the application of second-generation sequencing technology in plastid genome sequencing projects. However, cost-effective high-throughput chloroplast DNA (cpDNA extraction becomes a major bottleneck restricting the application, as conventional methods are difficult to make a balance between the quality and yield of cpDNAs. METHODOLOGY/PRINCIPAL FINDINGS: We first tested two traditional methods to isolate cpDNA from the three species, Oryza brachyantha, Leersia japonica and Prinsepia utihis. Both of them failed to obtain properly defined cpDNA bands. However, we developed a simple but efficient method based on sucrose gradients and found that the modified protocol worked efficiently to isolate the cpDNA from the same three plant species. We sequenced the isolated DNA samples with Illumina (Solexa sequencing technology to test cpDNA purity according to aligning sequence reads to the reference chloroplast genomes, showing that the reference genome was properly covered. We show that 40-50% cpDNA purity is achieved with our method. CONCLUSION: Here we provide an improved method used to isolate cpDNA from angiosperms. The Illumina sequencing results suggest that the isolated cpDNA has reached enough yield and sufficient purity to perform subsequent genome assembly. The cpDNA isolation protocol thus will be widely applicable to the plant chloroplast genome sequencing projects.

  5. ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding.

    Science.gov (United States)

    Zhang, Wei; Yuan, Yuan; Yang, Shuo; Huang, Jianjun; Huang, Luqi

    2015-01-01

    DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb "Mu tong" were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species.

  6. ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    Full Text Available DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb "Mu tong" were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species.

  7. Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment

    CERN Document Server

    Lee, Dominic J; Albrecht, Tim; Kornyshev, Alexei A

    2014-01-01

    Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignmen...

  8. Improving Atm Security Check Using DNA Biometrics

    Directory of Open Access Journals (Sweden)

    Igwe, Agu Felix

    2015-06-01

    Full Text Available This paper exposes how DNA can be used to identify account owner of a particular bank.DNA samples were obtained from body fluid. Buccal swab was used for sample collection .Buccal cell collection involves wiping a small piece of filter paper or a cotton swab against the inside of armpit in order to collect shed epithelial cells. The swab was then air dried or could be pressed against a treated collection card in order to transfer epithelial cells for storage purposes. The stored samples were later amplified and separated .The data generated from the samples were stored and saved in the database so that if a customer comes to claim money, the system checks whether it matches with what is stored in the database ,if it matches with the one in the database, access is granted to the customer,.if it does not match with what is stored in the database ,access is denied from the customer

  9. Stability Improvements of DNA Photonic Devices

    Science.gov (United States)

    2008-12-20

    concentration as 1g to 100ml TEMOS. The TEMO solution was spin- coated onto Teflon- coated glass plate to obtain films by irradiating UV light to cause...optical characteristics, such as refractive indices, absorbance and fluorescence intensity, and photochromic properties, of spiropyran-doped DNA...mixed solution of EtOH:CHCl3=1:4, together with optical dye compounds. Finally, the solution was poured onto a Teflon- coated dish, followed by

  10. Improving cancer immunotherapy with DNA methyltransferase inhibitors.

    Science.gov (United States)

    Saleh, Mohammad H; Wang, Lei; Goldberg, Michael S

    2016-07-01

    Immunotherapy confers durable clinical benefit to melanoma, lung, and kidney cancer patients. Challengingly, most other solid tumors, including ovarian carcinoma, are not particularly responsive to immunotherapy, so combination with a complementary therapy may be beneficial. Recent findings suggest that epigenetic modifying drugs can prime antitumor immunity by increasing expression of tumor-associated antigens, chemokines, and activating ligands by cancer cells as well as cytokines by immune cells. This review, drawing from both preclinical and clinical data, describes some of the mechanisms of action that enable DNA methyltransferase inhibitors to facilitate the establishment of antitumor immunity.

  11. Alignment in organisations : does an interpretative perspective lead to a better understanding of the subject? A suggestion for participative self-organisation as a way to improve alignment

    NARCIS (Netherlands)

    Blomme, R.J.; Beasley-Suffolk, A.-M.

    2010-01-01

    This article discusses the concept of alignment and the different domains in which it is used. The standard functionalist perspective on alignment hampers our understanding of this concept. We therefore put forward a social constructionist approach to conducting research into alignment. Using this a

  12. Improvements in spinal alignment after high tibial osteotomy in patients with medial compartment knee osteoarthritis.

    Science.gov (United States)

    Kim, Yoon Hyuk; Dorj, Ariunzaya; Han, Ahreum; Kim, Kyungsoo; Nha, Kyung Wook

    2016-07-01

    Since the correlation between spinal and lower extremity alignments is high, high tibial osteotomy (HTO) surgery may also affect spinal alignment, where the spinal alignment parameters are the most important parameters for the evaluation of spinal disorders. In this study, the effect of HTO surgery on spinal alignment during gait was investigated by comparing spinal alignment parameters between patients with knee osteoarthritis (OA) and healthy young controls. Eight patients (age, 55.0±5.1years; height, 160.3±7.0cm; weight, 71.3±14.1kg) with a medial compartment knee OA participated in the gait experiment two times approximately one week before and one year after HTO surgery and eight healthy young controls (age, 26.7±1.7years; height, 163.4±6.5cm; weight, 58.4±11.3kg) participated only once. Cervical curvature angle, thoracic curvature angle, lumbar curvature angle, coronal vertical axis, and coronal pelvic tilt in the coronal plane and cervical lordosis, thoracic kyphosis, lumbar lordosis, sagittal vertical axis, and sagittal pelvic tilt in the sagittal plane were estimated using motion analysis system with skin markers. All spinal alignment parameters after HTO surgery were significantly closer to those of healthy young subjects than those before HTO, especially in the coronal plane. These findings suggest that the HTO had a positive effect on spinal alignment, as well as lower extremity alignment, and moreover, reduced the abnormality that may result in spinal problems such as degeneration or pain.

  13. Improvement of Synthetic Biology Tools for DNA Editing

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda

    with the development and improvement of DNA editing strategies,compatible with other DNA assembly methodologies, genome engineering and,eventually, automation processes. Expanding and optimizing the synbio toolkit has important applications in pathway optimization for metabolic engineering, design and characterization...... of gene circuits, synthesis of whole genomes and natural product discovery. In line with this, it is also described in this thesis how discovery of new cytochromes P450 (CYPs) from marine bacteria could benefit industrial processes....

  14. Using MathML to Represent Units of Measurement for Improved Ontology Alignment

    NARCIS (Netherlands)

    Do, C.; Pauwels, E.J.

    2013-01-01

    Ontologies provide a formal description of concepts and their relationships in a knowledge domain. The goal of ontology alignment is to identify semantically matching concepts and relationships across independently developed ontologies that purport to describe the same knowledge. In order to handle

  15. Automated invariant alignment to improve canonical variates in image fusion of satellite and weather radar data

    DEFF Research Database (Denmark)

    Vestergaard, Jacob Schack; Nielsen, Allan Aasbjerg

    2013-01-01

    data sets, was observed, corrupting the subspace. A method for aligning the two data sets is proposed, in order to overcome this issue and render a useful subspace projection. The observed corruption of the subspace gives rise to the hypothesis that the optimal correspondence, between a heavily...

  16. Improving head and body pose estimation through semi-supervised manifold alignment

    KAUST Repository

    Heili, Alexandre

    2014-10-27

    In this paper, we explore the use of a semi-supervised manifold alignment method for domain adaptation in the context of human body and head pose estimation in videos. We build upon an existing state-of-the-art system that leverages on external labelled datasets for the body and head features, and on the unlabelled test data with weak velocity labels to do a coupled estimation of the body and head pose. While this previous approach showed promising results, the learning of the underlying manifold structure of the features in the train and target data and the need to align them were not explored despite the fact that the pose features between two datasets may vary according to the scene, e.g. due to different camera point of view or perspective. In this paper, we propose to use a semi-supervised manifold alignment method to bring the train and target samples closer within the resulting embedded space. To this end, we consider an adaptation set from the target data and rely on (weak) labels, given for example by the velocity direction whenever they are reliable. These labels, along with the training labels are used to bias the manifold distance within each manifold and to establish correspondences for alignment.

  17. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons.

    Science.gov (United States)

    Hunter, Margaret E; Oyler-McCance, Sara J; Dorazio, Robert M; Fike, Jennifer A; Smith, Brian J; Hunter, Charles T; Reed, Robert N; Hart, Kristen M

    2015-01-01

    Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors

  18. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons

    Science.gov (United States)

    Hunter, Margaret E.; Oyler-McCance, Sara J.; Dorazio, Robert M.; Fike, Jennifer A.; Smith, Brian J.; Hunter, Charles T.; Reed, Robert N.; Hart, Kristen M.

    2015-01-01

    Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors

  19. Environmental DNA (eDNA sampling improves occurrence and detection estimates of invasive burmese pythons.

    Directory of Open Access Journals (Sweden)

    Margaret E Hunter

    Full Text Available Environmental DNA (eDNA methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR for the Burmese python (Python molurus bivittatus, Northern African python (P. sebae, boa constrictor (Boa constrictor, and the green (Eunectes murinus and yellow anaconda (E. notaeus. Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive

  20. Vector Design for Improved DNA Vaccine Efficacy, Safety and Production

    Directory of Open Access Journals (Sweden)

    James A. Williams

    2013-06-01

    Full Text Available DNA vaccination is a disruptive technology that offers the promise of a new rapidly deployed vaccination platform to treat human and animal disease with gene-based materials. Innovations such as electroporation, needle free jet delivery and lipid-based carriers increase transgene expression and immunogenicity through more effective gene delivery. This review summarizes complementary vector design innovations that, when combined with leading delivery platforms, further enhance DNA vaccine performance. These next generation vectors also address potential safety issues such as antibiotic selection, and increase plasmid manufacturing quality and yield in exemplary fermentation production processes. Application of optimized constructs in combination with improved delivery platforms tangibly improves the prospect of successful application of DNA vaccination as prophylactic vaccines for diverse human infectious disease targets or as therapeutic vaccines for cancer and allergy.

  1. An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts.

    Science.gov (United States)

    Kallmeyer, Jens; Smith, David C

    2009-07-01

    We present a method for the rapid and simple extraction of DNA from marine sediments using electroelution. It effectively separates DNA from compounds, including humic substances, that interfere with subsequent DNA quantification and amplification. After extraction of the DNA from the sediment into an aqueous solution, the crude sample is encased in 2% agarose gel and exposed to an electrical current, which draws the DNA out of the gel into a centrifugal filter vial. After electroelution, the sample is centrifuged to remove contaminants method is quantitative and does not discriminate on the basis of size, as determined using DNA standards and DNA extracts from environmental samples. Amplification of DNA is considerably improved due to removal of PCR inhibitors. For Archaea, only these purified extracts yielded PCR products. This method allows for the use of relatively large volumes of sediment and is particularly useful for sediments containing low biomass such as deeply buried marine sediments. It works with both organic-rich and -poor sediment, as well as with sediment where calcium carbonate is abundant and sediment where it is limited; consequently, adjustment of protocols is unnecessary for samples with very different organic and mineral contents.

  2. Does improved instrumentation result in better component alignment in total knee arthroplasty?

    Directory of Open Access Journals (Sweden)

    Mo Hassaballa

    2011-03-01

    Full Text Available Accurate component alignment and joint line reproduction in total knee replacement (TKR is crucial for successful clinical outcome. Advances in instrumentation and better understanding of the biomechanics can help to achieve better three dimensional alignments of TKR components and joint line restoration. We compared the accuracy of component alignment and joint line restoration with the use of 2 different TKR instrumentation kits (an older Gobot and a newer Xcelerate. Retrospective study of 150 consecutive patients undergoing primary TKR had their pre and post-operative x-rays reviewed. Seventy-five patients (group A had their TKR using the older instrumentation kit (Gobot and 75 (group B had the newer version (Xcelerate. The positioning of the prosthesis components were assessed using the American Knee society radiographic evaluation method and the joint line position using the Figgie’s method. The results from the two groups were statistically compared. There was a significantly greater elevation of the joint line position in TKRs done with the Gobot instrumentation (mean 4.49 mm vs. 2.71 mm in group B, P=0.03, and significant differences in the mean tibial component angle cTCA (group A 88.6º, group B 90.1º, P=0.04 and the mean Q angle (group A 6.28º valgus, group B 8.45º valgus, P=0.04. Use of the newer Xcelerate instrumentation was associated with better restoration of joint line position, however the femoral component flexion and posterior slope of the tibial component ere found to be above the desired level. Hence the overall differences between the two groups were found to be small.

  3. Assembly Test of Elastic Averaging Technique to Improve Mechanical Alignment for Accelerating Structure Assemblies in CLIC

    CERN Document Server

    Huopana, J

    2010-01-01

    The CLIC (Compact LInear Collider) is being studied at CERN as a potential multi-TeV e+e- collider [1]. The manufacturing and assembly tolerances for the required RF-components are important for the final efficiency and for the operation of CLIC. The proper function of an accelerating structure is very sensitive to errors in shape and location of the accelerating cavity. This causes considerable issues in the field of mechanical design and manufacturing. Currently the design of the accelerating structures is a disk design. Alternatively it is possible to create the accelerating assembly from quadrants, which favour the mass manufacturing. The functional shape inside of the accelerating structure remains the same and a single assembly uses less parts. The alignment of these quadrants has been previously made kinematic by using steel pins or spheres to align the pieces together. This method proved to be a quite tedious and time consuming method of assembly. To limit the number of different error sources, a meth...

  4. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  5. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  6. Interference alignment for degrees of freedom improvement in 3-relay half-duplex systems

    KAUST Repository

    Park, Seongho

    2011-12-01

    In a half-duplex relaying, the capacity pre-log factor is a major drawback in spectral efficiency. This paper proposes a linear precoding scheme and an alternate relaying protocol in a dual-hop half-duplex system where three relays help the communication between the source and the destination. In our proposed scheme, we consider a phase incoherent method in relays in which the source alternately transmits message signals to the different relays. In addition, we propose a linear interference alignment scheme which can eliminate the inter-relay interference resulted from the phase incoherence of relaying. Based on our analysis of degrees of freedom and our simulation results, we show that our proposed scheme achieves additional degrees of freedom compared to the conventional half-duplex relaying. © 2011 IEEE.

  7. Assessing fit, interplay, and scale: Aligning governance and information for improved water management in a changing climate

    Science.gov (United States)

    Kirchhoff, C.; Dilling, L.

    2011-12-01

    Water managers have long experienced the challenges of managing water resources in a variable climate. However, climate change has the potential to reshape the experiential landscape by, for example, increasing the intensity and duration of droughts, shifting precipitation timing and amounts, and changing sea levels. Given the uncertainty in evaluating potential climate risks as well as future water availability and water demands, scholars suggest water managers employ more flexible and adaptive science-based management to manage uncertainty (NRC 2009). While such an approach is appropriate, for adaptive science-based management to be effective both governance and information must be concordant across three measures: fit, interplay and scale (Young 2002)(Note 1). Our research relies on interviews of state water managers and related experts (n=50) and documentary analysis in five U.S. states to understand the drivers and constraints to improving water resource planning and decision-making in a changing climate using an assessment of fit, interplay and scale as an evaluative framework. We apply this framework to assess and compare how water managers plan and respond to current or anticipated water resource challenges within each state. We hypothesize that better alignment between the data and management framework and the water resource problem improves water managers' facility to understand (via available, relevant, timely information) and respond appropriately (through institutional response mechanisms). In addition, better alignment between governance mechanisms (between the scope of the problem and identified appropriate responses) improves water management. Moreover, because many of the management challenges analyzed in this study concern present day issues with scarcity brought on by a combination of growth and drought, better alignment of fit, interplay, and scale today will enable and prepare water managers to be more successful in adapting to climate change

  8. Directional plasticity rapidly improves 3D vestibulo-ocular reflex alignment in monkeys using a multichannel vestibular prosthesis.

    Science.gov (United States)

    Dai, Chenkai; Fridman, Gene Y; Chiang, Bryce; Rahman, Mehdi A; Ahn, Joong Ho; Davidovics, Natan S; Della Santina, Charles C

    2013-12-01

    Bilateral loss of vestibular sensation can be disabling. We have shown that a multichannel vestibular prosthesis (MVP) can partly restore vestibular sensation as evidenced by improvements in the 3-dimensional angular vestibulo-ocular reflex (3D VOR). However, a key challenge is to minimize misalignment between the axes of eye and head rotation, which is apparently caused by current spread beyond each electrode's targeted nerve branch. We recently reported that rodents wearing a MVP markedly improve 3D VOR alignment during the first week after MVP activation, probably through the same central nervous system adaptive mechanisms that mediate cross-axis adaptation over time in normal individuals wearing prisms that cause visual scene movement about an axis different than the axis of head rotation. We hypothesized that rhesus monkeys would exhibit similar improvements with continuous prosthetic stimulation over time. We created bilateral vestibular deficiency in four rhesus monkeys via intratympanic injection of gentamicin. A MVP was mounted to the cranium, and eye movements in response to whole-body passive rotation in darkness were measured repeatedly over 1 week of continuous head motion-modulated prosthetic electrical stimulation. 3D VOR responses to whole-body rotations about each semicircular canal axis were measured on days 1, 3, and 7 of chronic stimulation. Horizontal VOR gain during 1 Hz, 50 °/s peak whole-body rotations before the prosthesis was turned on was <0.1, which is profoundly below normal (0.94 ± 0.12). On stimulation day 1, VOR gain was 0.4-0.8, but the axis of observed eye movements aligned poorly with head rotation (misalignment range ∼30-40 °). Substantial improvement of axis misalignment was observed after 7 days of continuous motion-modulated prosthetic stimulation under normal diurnal lighting. Similar improvements were noted for all animals, all three axes of rotation tested, for all sinusoidal frequencies tested (0.05-5 Hz), and for

  9. Role of Recombinant DNA Technology to Improve Life

    Directory of Open Access Journals (Sweden)

    Suliman Khan

    2016-01-01

    Full Text Available In the past century, the recombinant DNA technology was just an imagination that desirable characteristics can be improved in the living bodies by controlling the expressions of target genes. However, in recent era, this field has demonstrated unique impacts in bringing advancement in human life. By virtue of this technology, crucial proteins required for health problems and dietary purposes can be produced safely, affordably, and sufficiently. This technology has multidisciplinary applications and potential to deal with important aspects of life, for instance, improving health, enhancing food resources, and resistance to divergent adverse environmental effects. Particularly in agriculture, the genetically modified plants have augmented resistance to harmful agents, enhanced product yield, and shown increased adaptability for better survival. Moreover, recombinant pharmaceuticals are now being used confidently and rapidly attaining commercial approvals. Techniques of recombinant DNA technology, gene therapy, and genetic modifications are also widely used for the purpose of bioremediation and treating serious diseases. Due to tremendous advancement and broad range of application in the field of recombinant DNA technology, this review article mainly focuses on its importance and the possible applications in daily life.

  10. Role of Recombinant DNA Technology to Improve Life.

    Science.gov (United States)

    Khan, Suliman; Ullah, Muhammad Wajid; Siddique, Rabeea; Nabi, Ghulam; Manan, Sehrish; Yousaf, Muhammad; Hou, Hongwei

    2016-01-01

    In the past century, the recombinant DNA technology was just an imagination that desirable characteristics can be improved in the living bodies by controlling the expressions of target genes. However, in recent era, this field has demonstrated unique impacts in bringing advancement in human life. By virtue of this technology, crucial proteins required for health problems and dietary purposes can be produced safely, affordably, and sufficiently. This technology has multidisciplinary applications and potential to deal with important aspects of life, for instance, improving health, enhancing food resources, and resistance to divergent adverse environmental effects. Particularly in agriculture, the genetically modified plants have augmented resistance to harmful agents, enhanced product yield, and shown increased adaptability for better survival. Moreover, recombinant pharmaceuticals are now being used confidently and rapidly attaining commercial approvals. Techniques of recombinant DNA technology, gene therapy, and genetic modifications are also widely used for the purpose of bioremediation and treating serious diseases. Due to tremendous advancement and broad range of application in the field of recombinant DNA technology, this review article mainly focuses on its importance and the possible applications in daily life.

  11. Role of Recombinant DNA Technology to Improve Life

    Science.gov (United States)

    Khan, Suliman; Ullah, Muhammad Wajid; Siddique, Rabeea; Nabi, Ghulam; Manan, Sehrish; Yousaf, Muhammad

    2016-01-01

    In the past century, the recombinant DNA technology was just an imagination that desirable characteristics can be improved in the living bodies by controlling the expressions of target genes. However, in recent era, this field has demonstrated unique impacts in bringing advancement in human life. By virtue of this technology, crucial proteins required for health problems and dietary purposes can be produced safely, affordably, and sufficiently. This technology has multidisciplinary applications and potential to deal with important aspects of life, for instance, improving health, enhancing food resources, and resistance to divergent adverse environmental effects. Particularly in agriculture, the genetically modified plants have augmented resistance to harmful agents, enhanced product yield, and shown increased adaptability for better survival. Moreover, recombinant pharmaceuticals are now being used confidently and rapidly attaining commercial approvals. Techniques of recombinant DNA technology, gene therapy, and genetic modifications are also widely used for the purpose of bioremediation and treating serious diseases. Due to tremendous advancement and broad range of application in the field of recombinant DNA technology, this review article mainly focuses on its importance and the possible applications in daily life. PMID:28053975

  12. 改进的自适应汉维句子对齐%Improved adaptive algorithm for Chinese-Uyghur sentence alignment

    Institute of Scientific and Technical Information of China (English)

    田生伟; 禹龙; 杨飞宇

    2011-01-01

    This paper proposes an improved adaptive algorithm for Chinese-Uyghur sentence alignment.Traditional alignment methods can not well adapt to change in types of corpus,the algorithm makes ues of current Chinese-Uyghur text length ratio of bytes and historical matching model, modifies the alignment model parameters dynamically to meet the changes in types of corpus and improves sentence alignment algorithm performance.Compared with alignment algorithm based on length, alignment improves alignment accuarcy 3.5 percentage and recall 2.7 percentage, compared with mixed-aligned model .alignment improves 1.9 percentage and 1.8 percentage.Experimental results show that the algorithm can adapt to change in types of corpus well.%提出了改进的自适应汉维句子对齐算法对齐汉维语句子.针对传统对齐方法不能较好地适应语料类型的变化,算法利用当前待对齐汉维文本的字节长度比和历史匹配模式数据,动态修正对齐模型的参数,使其适应语料类型的变化,提高了汉维句子对齐算法的性能,对齐的正确率和召回率较长度对齐模型分别提高了3.5个百分点和2.7个百分点,较混合对齐提高了1.9个百分点和1.8个百分点.实验结果验证了该算法能够有效地适应语料类型的变化.

  13. Improved Lower Bounds for Constant GC-Content DNA Codes

    CERN Document Server

    Chee, Yeow Meng

    2008-01-01

    The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA computing, DNA microarray technologies, and molecular bar coding. Various techniques have been studied for the construction of such oligonucleotide libraries, ranging from algorithmic constructions via stochastic local search to theoretical constructions via coding theory. We introduce a new stochastic local search method which yields improvements up to more than one third of the benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide libraries when n <= 14. We also found several optimal libraries by computing maximum cliques on certain graphs.

  14. Improved performance and stability in quantum dot solar cells through band alignment engineering

    Science.gov (United States)

    Chuang, Chia-Hao M.; Brown, Patrick R.; Bulović, Vladimir; Bawendi, Moungi G.

    2014-08-01

    Solution processing is a promising route for the realization of low-cost, large-area, flexible and lightweight photovoltaic devices with short energy payback time and high specific power. However, solar cells based on solution-processed organic, inorganic and hybrid materials reported thus far generally suffer from poor air stability, require an inert-atmosphere processing environment or necessitate high-temperature processing, all of which increase manufacturing complexities and costs. Simultaneously fulfilling the goals of high efficiency, low-temperature fabrication conditions and good atmospheric stability remains a major technical challenge, which may be addressed, as we demonstrate here, with the development of room-temperature solution-processed ZnO/PbS quantum dot solar cells. By engineering the band alignment of the quantum dot layers through the use of different ligand treatments, a certified efficiency of 8.55% has been reached. Furthermore, the performance of unencapsulated devices remains unchanged for over 150 days of storage in air. This material system introduces a new approach towards the goal of high-performance air-stable solar cells compatible with simple solution processes and deposition on flexible substrates.

  15. An improved procedure for subcellular spatial alignment during live-cell CLEM.

    Directory of Open Access Journals (Sweden)

    Benjamin S Padman

    Full Text Available Live-cell correlative light and electron microscopy (CLEM offers unique insights into the ultrastructure of dynamic cellular processes. A critical and technically challenging part of CLEM is the 3-dimensional relocation of the intracellular region of interest during sample processing. We have developed a simple CLEM procedure that uses toner particles from a laser printer as orientation marks. This facilitates easy tracking of a region of interest even by eye throughout the whole procedure. Combined with subcellular fluorescence markers for the plasma membrane and nucleus, the toner particles allow for precise subcellular spatial alignment of the optical and electron microscopy data sets. The toner-based reference grid is printed and transferred onto a polymer film using a standard office printer and laminator. We have also designed a polymer film holder that is compatible with most inverted microscopes, and have validated our strategy by following the ultrastructure of mitochondria that were selectively photo-irradiated during live-cell microscopy. In summary, our inexpensive and robust CLEM procedure simplifies optical imaging, without limiting the choice of optical microscope.

  16. Trapping of defect point to improve response time via controlled azimuthal anchoring in a vertically aligned liquid crystal cell with polymer wall

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Gyun; Kim, Sung Min; Kim, Youn Sik; Lee, Hee Kyu; Lee, Seung Hee [Polymer BIN Fusion Research Center, School of Advanced Materials Engineering, Chonbuk National University, Chonju, Chonbuk 561-756 (Korea, Republic of); Lyu, Jae-Jin; Kim, Kyeong Hyeon [AMLCD Division, Samsung Electronics, Kiheung, Kyunggi-Do 449-711 (Korea, Republic of); Lu, Ruibo; Wu, Shin-Tson [College of Optics and Photonics, University of Central Florida, Orlando FL 32816 (United States)], E-mail: lsh1@chonbuk.ac.kr

    2008-03-07

    Conventional multi-domain vertically aligned liquid crystal (LC) cells have defect points due to the collision of LC directors during the formation of multiple domains. In addition, the location of defects changes with time resulting in a slow response time. This paper proposes a robust vertically aligned LC cell, where the LCs are locked by polymer walls, and the azimuthal anchoring on the surface of the alignment layer is controlled by the polymerization of a UV curable reactive mesogen monomer. As a result, the defect points are trapped at a single position, resulting in a greatly improved response time.

  17. Enhancing Crystallinity and Orientation by Hot-Stretching to Improve the Mechanical Properties of Electrospun Partially Aligned Polyacrylonitrile (PAN Nanocomposites

    Directory of Open Access Journals (Sweden)

    Xiaoxiao Hou

    2011-04-01

    Full Text Available Partially aligned polyacrylonitrile (PAN-based nanofibers were electrospun from PAN and PAN/single-walled carbon nanotubes (SWNTs in a solution of dimethylformamide (DMF to make the nanofiber composites. The as-spun nanofibers were then hot-stretched in the oven to enhance its orientation and crystallinity. With the introduction of SWNTs and by the hot-stretched process, the mechanical properties will be enhanced correspondingly. Scanning electron microscopy (SEM, transmission electron microscopy (TEM, X-ray scattering (XRD, differential scanning calorimetry (DSC, and the tensile test were used to characterize the microstructure and performances of the nanofibers. The orientation and crystallinity of the as-spun and hot-stretched nanofibers confirmed by X-ray have increased. Differential scanning calorimetry showed that the glass transition temperature of PAN increased about 3 °C by an addition of 0.75 wt% SWNTs indicating a strong interfacial interaction between PAN and SWNTs. The tensile strength and the modulus of the nanofibers increased revealing significant load transfer across the nanotube-matrix interface. For PAN nanofibers, the improved fiber alignment, orientation and crystallinity resulted in enhanced mechanical properties, such as the tensile strength and modulus of the nanofibers. It was concluded that the hot-stretched nanofiber and the PAN/SWNTs nanofibers can be used as a potential precursor to produce high-performance nanocomposites.

  18. Large scale multiplex PCR improves pathogen detection by DNA microarrays

    Directory of Open Access Journals (Sweden)

    Krönke Martin

    2009-01-01

    Full Text Available Abstract Background Medium density DNA microchips that carry a collection of probes for a broad spectrum of pathogens, have the potential to be powerful tools for simultaneous species identification, detection of virulence factors and antimicrobial resistance determinants. However, their widespread use in microbiological diagnostics is limited by the problem of low pathogen numbers in clinical specimens revealing relatively low amounts of pathogen DNA. Results To increase the detection power of a fluorescence-based prototype-microarray designed to identify pathogenic microorganisms involved in sepsis, we propose a large scale multiplex PCR (LSplex PCR for amplification of several dozens of gene-segments of 9 pathogenic species. This protocol employs a large set of primer pairs, potentially able to amplify 800 different gene segments that correspond to the capture probes spotted on the microarray. The LSplex protocol is shown to selectively amplify only the gene segments corresponding to the specific pathogen present in the analyte. Application of LSplex increases the microarray detection of target templates by a factor of 100 to 1000. Conclusion Our data provide a proof of principle for the improvement of detection of pathogen DNA by microarray hybridization by using LSplex PCR.

  19. Breaking the DNA damage response to improve cervical cancer treatment.

    Science.gov (United States)

    Wieringa, Hylke W; van der Zee, Ate G J; de Vries, Elisabeth G E; van Vugt, Marcel A T M

    2016-01-01

    Every year, cervical cancer affects ∼500,000 women worldwide, and ∼275,000 patients die of this disease. The addition of platin-based chemotherapy to primary radiotherapy has increased 5-year survival of advanced-stage cervical cancer patients, which is, however, still only 66%. One of the factors thought to contribute to treatment failure is the ability of tumor cells to repair chemoradiotherapy-induced DNA damage. Therefore, sensitization of tumor cells for chemoradiotherapy via inhibition of the DNA damage response (DDR) as a novel strategy to improve therapy effect, is currently studied pre-clinically as well as in the clinic. Almost invariably, cervical carcinogenesis involves infection with the human papillomavirus (HPV), which inactivates part of the DNA damage response. This HPV-mediated partial inactivation of the DDR presents therapeutic targeting of the residual DDR as an interesting approach to achieve chemoradio-sensitization for cervical cancer. How the DDR can be most efficiently targeted, however, remains unclear. The fact that cisplatin and radiotherapy activate multiple signaling axes within the DDR further complicates a rational choice of therapeutic targets within the DDR. In this review, we provide an overview of the current preclinical and clinical knowledge about targeting the DDR in cervical cancer.

  20. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  1. Chain alignment for improved properties - Optimization of PLA and PHB-V by crystallization and reinforcement

    Science.gov (United States)

    Moser, K.; Bergmann, B.; Diemert, J.; Elsner, P.

    2014-05-01

    In this paper two promising ways to improve the material characteristics of PLA and PHB-V are presented by showing their positive effects on mechanical, optical, and thermal properties. The optimization is achieved by increasing the crystallization from the melt of the polymer chains and the other by means of a reinforcement of the matrices by bio-based materials. In the case of crystallization specific nucleating agents and optimized process parameters promote optimized crystallization conditions and lead particularly in toughness to significant improvements. In addition to crystallization the introduction of cellulose-based reinforcing materials is also a good alternative to improve the ductility of a biopolymer matrix considerably. Due to their polar surface structure cellulose fibres are favouring a very good interaction to the also polar biopolymers. In addition, the polar surfaces of both materials results in very homogeneous dispersion within the compound.

  2. Aligning health information technologies with effective service delivery models to improve chronic disease care

    Science.gov (United States)

    Bauer, Amy M.; Thielke, Stephen M.; Katon, Wayne; Unützer, Jürgen; Areán, Patricia

    2014-01-01

    Objective Healthcare reforms in the United States, including the Affordable Care and HITECH Acts, and the NCQA criteria for the Patient Centered Medical Home have promoted health information technology (HIT) and the integration of general medical and mental health services. These developments, which aim to improve chronic disease care have largely occurred in parallel, with little attention to the need for coordination. In this article, the fundamental connections between HIT and improvements in chronic disease management are explored. We use the evidence-based collaborative care model as an example, with attention to health literacy improvement for supporting patient engagement in care. Method A review of the literature was conducted to identify how HIT and collaborative care, an evidence-based model of chronic disease care, support each other. Results Five key principles of effective collaborative care are outlined: care is patient-centered, evidence-based, measurement-based, population-based, and accountable. The potential role of HIT in implementing each principle is discussed. Key features of the mobile health paradigm are described, including how they can extend evidence-based treatment beyond traditional clinical settings. Conclusion HIT, and particularly mobile health, can enhance collaborative care interventions, and thus improve the health of individuals and populations when deployed in integrated delivery systems. PMID:24963895

  3. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  4. Novel hybrid genetic algorithm for progressive multiple sequence alignment.

    Science.gov (United States)

    Afridi, Muhammad Ishaq

    2013-01-01

    The family of evolutionary or genetic algorithms is used in various fields of bioinformatics. Genetic algorithms (GAs) can be used for simultaneous comparison of a large pool of DNA or protein sequences. This article explains how the GA is used in combination with other methods like the progressive multiple sequence alignment strategy to get an optimal multiple sequence alignment (MSA). Optimal MSA get much importance in the field of bioinformatics and some other related disciplines. Evolutionary algorithms evolve and improve their performance. In this optimisation, the initial pair-wise alignment is achieved through a progressive method and then a good objective function is used to select and align more alignments and profiles. Child and subpopulation initialisation is based upon changes in the probability of similarity or the distance matrix of the alignment population. In this genetic algorithm, optimisation of mutation, crossover and migration in the population of candidate solution reflect events of natural organic evolution.

  5. DNA Nanoparticles for Improved Protein Synthesis In Vitro.

    Science.gov (United States)

    Galinis, Robertas; Stonyte, Greta; Kiseliovas, Vaidotas; Zilionis, Rapolas; Studer, Sabine; Hilvert, Donald; Janulaitis, Arvydas; Mazutis, Linas

    2016-02-24

    The amplification and digital quantification of single DNA molecules are important in biomedicine and diagnostics. Beyond quantifying DNA molecules in a sample, the ability to express proteins from the amplified DNA would open even broader applications in synthetic biology, directed evolution, and proteomics. Herein, a microfluidic approach is reported for the production of condensed DNA nanoparticles that can serve as efficient templates for in vitro protein synthesis. Using phi29 DNA polymerase and a multiple displacement amplification reaction, single DNA molecules were converted into DNA nanoparticles containing up to about 10(4)  clonal gene copies of the starting template. DNA nanoparticle formation was triggered by accumulation of inorganic pyrophosphate (produced during DNA synthesis) and magnesium ions from the buffer. Transcription-translation reactions performed in vitro showed that individual DNA nanoparticles can serve as efficient templates for protein synthesis in vitro.

  6. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Z. Szillasi and G. Gomez.

    2013-01-01

    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

  7. Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene.

    Science.gov (United States)

    Prasongkit, Jariyanee; Feliciano, Gustavo T; Rocha, Alexandre R; He, Yuhui; Osotchan, Tanakorn; Ahuja, Rajeev; Scheicher, Ralph H

    2015-12-04

    Fast, cost effective, single-shot DNA sequencing could be the prelude of a new era in genetics. As DNA encodes the information for the production of proteins in all known living beings on Earth, determining the nucleobase sequences is the first and necessary step in that direction. Graphene-based nanopore devices hold great promise for next-generation DNA sequencing. In this work, we develop a novel approach for sequencing DNA using bilayer graphene to read the interlayer conductance through the layers in the presence of target nucleobases. Classical molecular dynamics simulations of DNA translocation through the pore were performed to trace the nucleobase trajectories and evaluate the interaction between the nucleobases and the nanopore. This interaction stabilizes the bases in different orientations, resulting in smaller fluctuations of the nucleobases inside the pore. We assessed the performance of a bilayer graphene nanopore setup for the purpose of DNA sequencing by employing density functional theory and non-equilibrium Green's function method to investigate the interlayer conductance of nucleobases coupling simultaneously to the top and bottom graphene layers. The obtained conductance is significantly affected by the presence of DNA in the bilayer graphene nanopore, allowing us to analyze DNA sequences.

  8. Improved concentration and separation of particles in a 3D dielectrophoretic chip integrating focusing, aligning and trapping

    KAUST Repository

    Li, Ming

    2012-10-18

    This article presents a dielectrophoresis (DEP)-based microfluidic device with the three-dimensional (3D) microelectrode configuration for concentrating and separating particles in a continuous throughflow. The 3D electrode structure, where microelectrode array are patterned on both the top and bottom surfaces of the microchannel, is composed of three units: focusing, aligning and trapping. As particles flowing through the microfluidic channel, they are firstly focused and aligned by the funnel-shaped and parallel electrode array, respectively, before being captured at the trapping unit due to negative DEP force. For a mixture of two particle populations of different sizes or dielectric properties, with a careful selection of suspending medium and applied field, the population exhibits stronger negative DEP manipulated by the microelectrode array and, therefore, separated from the other population which is easily carried away toward the outlet due to hydrodynamic force. The functionality of the proposed microdevice was verified by concentrating different-sized polystyrene (PS) microparticles and yeast cells dynamically flowing in the microchannel. Moreover, separation based on size and dielectric properties was achieved by sorting PS microparticles, and isolating 5 μm PS particles from yeast cells, respectively. The performance of the proposed micro-concentrator and separator was also studied, including the threshold voltage at which particles begin to be trapped, variation of cell-trapping efficiency with respect to the applied voltage and flow rate, and the efficiency of separation experiments. The proposed microdevice has various advantages, including multi-functionality, improved manipulation efficiency and throughput, easy fabrication and operation, etc., which shows a great potential for biological, chemical and medical applications. © 2012 Springer-Verlag Berlin Heidelberg.

  9. An improved method of mitochondrial DNA isolation for XL-PCR

    Institute of Scientific and Technical Information of China (English)

    SHI Duo; ZHU Ke-jun; WANG Xue-min; WANG Zhen-cheng; ZHENG Jian-ming; MIAO Ming-yong; JIAO Bing-hua

    2006-01-01

    Objective: To obtain high quality of mitochondrial DNA (mtDNA) and carry out extra-long PCR (XL-PCR). Methods: Mitochondria were isolated by differential centrifugation, and membranes were disrupted using 10%SDS (pH 7.0). mtDNA was then extracted using phenol and chloroform. Results: The mtDNA obtained by using our improved method can be used as effective template for XL-PCR,and total mtDNA (16 kb) can be amplified easily. Conclusion: Our improved method is effective in preparing high quality of mtDNA, which can be used as template for XL-PCR.

  10. Genetic Approaches to Appearance and Ancestry : Improving Forensic DNA Analysis

    NARCIS (Netherlands)

    L.C. Chaitanya (Lakshmi)

    2016-01-01

    textabstractTraditionally, routine forensic casework is based on comparative grounds. DNA profiles obtained from crime-scenes are compared with those of potential suspects or DNA profiles deposited in forensic DNA databases. The principal limitation of such comparative approach is that trace donors

  11. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

    2007-01-01

    BACKGROUND: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. RESULTS: MaxAlign is a program that optimizes...... the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical...... analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign...

  12. Multiple sequence alignment with user-defined anchor points

    Directory of Open Access Journals (Sweden)

    Pöhler Dirk

    2006-04-01

    Full Text Available Abstract Background Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system.

  13. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

  14. Exogenous DNA internalisation by sperm cells is improved by combining lipofection and restriction enzyme mediated integration.

    Science.gov (United States)

    Churchil, R R; Gupta, J; Singh, A; Sharma, D

    2011-06-01

    1. Three types of exogenous DNA inserts, i.e. complete linearised pVIVO2-GFP/LacZ vector (9620 bp), the LacZ gene (5317 bp) and the GFP gene (2152 bp) were used to transfect chicken spermatozoa through simple incubation of sperm cells with insert. 2. PCR assay, Dot Blot hybridisation and Southern hybridisation showed the successful internalisation of exogenous DNA by chicken sperm cells. 3. Lipofection and Restriction Enzyme Mediated Integration (REMI) were used to improve the rate of internalisation of exogenous DNA by sperm cells. 4. Results from dot blot as well as Southern hybridisation were semi-quantified and improved exogenous DNA uptake by sperm cells through lipofection and REMI. Stronger signals were observed from hybridisation of LacZ as well as GFP specific probe with the DNA from lipofected exogenous DNA transfected sperm DNA in comparison with those transfected with nude exogenous DNA.

  15. Click-iT assay with improved DNA distribution histograms.

    Science.gov (United States)

    Hamelik, Ronald M; Krishan, Awtar

    2009-10-01

    The Click-iT Assay developed and commercialized by Invitrogen is based on incorporation of a new 5-bromo-2'-deoxyuridine analog, 5-ethynyl-2'-deoxyuridine (EdU) into newly synthesized DNA and its recognition by azide dyes via a copper mediated "click" reaction. This relatively convenient and useful procedure depends on fixation of cells with paraformaldehyde and staining of the DNA with 7-aminoactinomycin-D (7-AAD). Both of these procedures result in DNA histograms with broad coefficients of variation (CV's). In this report, we have shown that after EdU incorporation, nuclei isolated by lysis can be incubated with the Click-iT Assay and stained with propidium iodide for generation of DNA histograms with low CV's. This modified procedure results in better DNA histograms by replacing 7-AAD with propidium iodide and also saves processing time by eliminating the fixation and permeabilization steps.

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

  17. DNA-free genome editing methods for targeted crop improvement.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala

    2016-07-01

    Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted.

  18. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair.

    Science.gov (United States)

    Akbari, Mansour; Keijzers, Guido; Maynard, Scott; Scheibye-Knudsen, Morten; Desler, Claus; Hickson, Ian D; Bohr, Vilhelm A

    2014-04-01

    Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial DNA replication and transcription and generate mutations. We carried out BER analysis in highly purified mitochondrial extracts from human cell lines U2OS and HeLa, and mouse brain using a circular DNA substrate containing a lesion at a specific position. We found that DNA ligation is significantly slower than the preceding mitochondrial BER steps. Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress and reduced autophagy following the inhibition of the mitochondrial electron transport chain complex I by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional mitochondria by autophagy.

  19. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  20. Paramagnetic Cellulose DNA Isolation Improves DNA Yield and Quality Among Diverse Plant Taxa

    Directory of Open Access Journals (Sweden)

    Jackson R. Moeller

    2014-10-01

    Full Text Available Premise of the study: The chemical diversity of land plants ensures that no single DNA isolation method results in high yield and purity with little effort for all species. Here we evaluate a new technique originally developed for forensic science, based on MagnaCel paramagnetic cellulose particles (PMC, to determine its efficacy in extracting DNA from 25 plant species representing 21 families and 15 orders. Methods and Results: Yield and purity of DNA isolated by PMC, DNeasy Plant Mini Kit (silica column, and cetyltrimethylammonium bromide (CTAB methods were compared among four individuals for each of 25 plant species. PMC gave a two-fold advantage in average yield, and the relative advantage of the PMC method was greatest for samples with the lowest DNA yields. PMC also produced more consistent sample purity based on absorbance ratios at 260 : 280 and 260 : 230 nm. Conclusions: PMC technology is a promising alternative for plant DNA isolation.

  1. A systematic review and meta-analysis of patient-specific instrumentation for improving alignment of the components in total knee replacement.

    Science.gov (United States)

    Thienpont, E; Schwab, P E; Fennema, P

    2014-08-01

    We conducted a meta-analysis, including randomised controlled trials (RCTs) and cohort studies, to examine the effect of patient-specific instruments (PSI) on radiological outcomes after total knee replacement (TKR) including: mechanical axis alignment and malalignment of the femoral and tibial components in the coronal, sagittal and axial planes, at a threshold of > 3º from neutral. Relative risks (RR) for malalignment were determined for all studies and for RCTs and cohort studies separately. Of 325 studies initially identified, 16 met the eligibility criteria, including eight RCTs and eight cohort studies. There was no significant difference in the likelihood of mechanical axis malalignment with PSI versus conventional TKR across all studies (RR = 0.84, p = 0.304), in the RCTs (RR = 1.14, p = 0.445) or in the cohort studies (RR = 0.70, p = 0.289). The results for the alignment of the tibial component were significantly worse using PSI TKR than conventional TKR in the coronal and sagittal planes (RR = 1.75, p = 0.028; and RR = 1.34, p = 0.019, respectively, on pooled analysis). PSI TKR showed a significant advantage over conventional TKR for alignment of the femoral component in the coronal plane (RR = 0.65, p = 0.028 on pooled analysis), but not in the sagittal plane (RR = 1.12, p = 0.437). Axial alignment of the tibial (p = 0.460) and femoral components (p = 0.127) was not significantly different. We conclude that PSI does not improve the accuracy of alignment of the components in TKR compared with conventional instrumentation.

  2. Alignment validation

    Energy Technology Data Exchange (ETDEWEB)

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  3. An anisotropically and heterogeneously aligned patterned electrospun scaffold with tailored mechanical property and improved bioactivity for vascular tissue engineering.

    Science.gov (United States)

    Xu, He; Li, Haiyan; Ke, Qinfei; Chang, Jiang

    2015-04-29

    The development of vascular scaffolds with controlled mechanical properties and stimulatory effects on biological activities of endothelial cells still remains a significant challenge to vascular tissue engineering. In this work, we reported an innovative approach to prepare a new type of vascular scaffolds with anisotropically and heterogeneously aligned patterns using electrospinning technique with unique wire spring templates, and further investigated the structural effects of the patterned electrospun scaffolds on mechanical properties and angiogenic differentiation of human umbilical vein endothelial cells (HUVECs). Results showed that anisotropically aligned patterned nanofibrous structure was obtained by depositing nanofibers on template in a structurally different manner, one part of nanofibers densely deposited on the embossments of wire spring and formed cylindrical-like structures in the transverse direction, while others loosely suspended and aligned along the longitudinal direction, forming a three-dimensional porous microstructure. We further found that such structures could efficiently control the mechanical properties of electrospun vascular scaffolds in both longitudinal and transverse directions by altering the interval distances between the embossments of patterned scaffolds. When HUVECs were cultured on scaffolds with different microstructures, the patterned scaffolds distinctively promoted adhesion of HUVECs at early stage and proliferation during the culture period. Most importantly, cells experienced a large shape change associated with cell cytoskeleton and nuclei remodeling, leading to a stimulatory effect on angiogenesis differentiation of HUVECs by the patterned microstructures of electrospun scaffolds, and the scaffolds with larger distances of intervals showed a higher stimulatory effect. These results suggest that electrospun scaffolds with the anisotropically and heterogeneously aligned patterns, which could efficiently control the

  4. Fabrication Process Changes for Performance Improvement of a RF MEMS Resonator: Conformable Contact Lithography, Moire Alignment, and Chlorine Dry Etching

    Science.gov (United States)

    2007-11-02

    trigonometry . x = cos(c)* a (2.3.6) y = sin(c)* a (2.3.7) 2.3.2 Centroid Location A source of error that was to be expected was finding the location of...in relation to their standard deviation radius. 2.5.5 Commanded versus Actual Movement A major obstacle to achieving an automated alignment system is

  5. Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type

    Science.gov (United States)

    Gregg, Jacob; Thompson, Rachel L.; Purcell, Maureen; Friedman, Carolyn S.; Hershberger, Paul

    2016-01-01

    Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1–5.8S–ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species.

  6. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  7. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  8. Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

    Science.gov (United States)

    Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

    2016-03-01

    Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

  9. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng

    2015-06-13

    Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

      A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

  11. An improved protocol for DNA extraction from alkaline soil and sediment samples for constructing metagenomic libraries.

    Science.gov (United States)

    Verma, Digvijay; Satyanarayana, T

    2011-09-01

    An improved single-step protocol has been developed for extracting pure community humic substance-free DNA from alkaline soils and sediments. The method is based on direct cell lysis in the presence of powdered activated charcoal and polyvinylpolypyrrolidone followed by precipitation with polyethyleneglycol and isopropanol. The strategy allows simultaneous isolation and purification of DNA while minimizing the loss of DNA with respect to other available protocols for metagenomic DNA extraction. Moreover, the purity levels are significant, which are difficult to attain with any of the methods reported in the literature for DNA extraction from soils. The DNA thus extracted was free from humic substances and, therefore, could be processed for restriction digestion, PCR amplification as well as for the construction of metagenomic libraries.

  12. An improved protocol for the isolation of total genomic DNA from Labyrinthulomycetes.

    Science.gov (United States)

    Ranasinghe, Chaminda Padmashantha; Harding, Rob; Hargreaves, Megan

    2015-03-01

    Many protocols have been used for extraction of DNA from Thraustochytrids. These generally involve the use of CTAB, phenol/chloroform and ethanol. They also feature mechanical grinding, sonication, N2 freezing or bead beating. However, the resulting chemical and physical damage to extracted DNA reduces its quality. The methods are also unsuitable for large numbers of samples. Commercially-available DNA extraction kits give better quality and yields but are expensive. Therefore, an optimized DNA extraction protocol was developed which is suitable for Thraustochytrids to both minimise expensive and time-consuming steps prior to DNA extraction and also to improve the yield. The most effective method is a combination of single bead in TissueLyser (Qiagen) and Proteinase K. Results were conclusive: both the quality and the yield of extracted DNA were higher than with any other method giving an average yield of 8.5 µg/100 mg biomass.

  13. DNA extraction of birch leaves by improved CTAB method and optimization of its ISSR system

    Institute of Scientific and Technical Information of China (English)

    PAN hua; YANG Chuan-ping; WEI Zhi-gang; JIANG Jing

    2006-01-01

    The basic method of DNA extraction (CTAB) was improved as the multi-times STE-CTAB extraction method and used to extract the DNA of birch leaved in this experiment. Results showed that the improved method is suitable not only for genomic DNA extraction of birch but also for that of other plants. The purity of genomic DNA extracted by the multi-times STE-CTAB extraction method is higher than that by one time STE-CTAB method, and it does not need the process of RNase. The factors of influencing ISSR system were explored based on the genomic DNA of birch extracted by the two methods. The optimal conditions for ISSR system were determined as follows: cycles of denaturation for 30 s at 94℃, annealing for 30 s at 51 ℃, extension for 30 s at 72℃, and a final 7 min extension at 72 ℃.

  14. A designer bleomycin with significantly improved DNA cleavage activity.

    Science.gov (United States)

    Huang, Sheng-Xiong; Feng, Zhiyang; Wang, Liyan; Galm, Ute; Wendt-Pienkowski, Evelyn; Yang, Dong; Tao, Meifeng; Coughlin, Jane M; Duan, Yanwen; Shen, Ben

    2012-08-15

    The bleomycins (BLMs) are used clinically in combination with a number of other agents for the treatment of several types of tumors, and the BLM, etoposide, and cisplatin treatment regimen cures 90-95% of metastatic testicular cancer patients. BLM-induced pneumonitis is the most feared, dose-limiting side effect of BLM in chemotherapy, which can progress into lung fibrosis and affect up to 46% of the total patient population. There have been continued efforts to develop new BLM analogues in the search for anticancer drugs with better clinical efficacy and lower lung toxicity. We have previously cloned and characterized the biosynthetic gene clusters for BLMs from Streptomyces verticillus ATCC15003, tallysomycins from Streptoalloteichus hindustanus E465-94 ATCC31158, and zorbamycin (ZBM) from Streptomyces flavoviridis SB9001. Comparative analysis of the three biosynthetic machineries provided the molecular basis for the formulation of hypotheses to engineer novel analogues. We now report engineered production of three new analogues, 6'-hydroxy-ZBM, BLM Z, and 6'-deoxy-BLM Z and the evaluation of their DNA cleavage activities as a measurement for their potential anticancer activity. Our findings unveiled: (i) the disaccharide moiety plays an important role in the DNA cleavage activity of BLMs and ZBMs, (ii) the ZBM disaccharide significantly enhances the potency of BLM, and (iii) 6'-deoxy-BLM Z represents the most potent BLM analogue known to date. The fact that 6'-deoxy-BLM Z can be produced in reasonable quantities by microbial fermentation should greatly facilitate follow-up mechanistic and preclinical studies to potentially advance this analogue into a clinical drug.

  15. DNA extraction methods and multiple sampling to improve molecular diagnosis of Sarcocystis spp. in cattle hearts.

    Science.gov (United States)

    Bräunig, Patrícia; Portella, Luiza Pires; Cezar, Alfredo Skrebsky; Libardoni, Felipe; Sangioni, Luis Antonio; Vogel, Fernanda Silveira Flores; Gonçalves, Paulo Bayard Dias

    2016-10-01

    Molecular detection of Sarcocystis spp. in tissue samples can be useful for experimental and diagnostic purposes. However, the parasite spreads unevenly through tissues, forming tissue cysts, and the cystic wall is an obstacle in DNA extraction protocols. Therefore, adequate sampling and effective disruption of the cysts are essential to improve the accuracy of DNA detection by PCR. The aims of this study were to evaluate the suitability of four protocols for DNA extraction from cysts of Sarcocystis spp. present in bovine myocardium samples or after their harvest in phosphate-buffered saline (PBS) solution as well as determine the effects of single or multiple sampling on the accuracy of molecular diagnosis of sarcocystosis in cattle hearts. Cysts and myocardium samples from nine bovine hearts were randomly distributed to four DNA extraction protocols: kit, kit with modification, DNAzol, and cetyl-trimethyl ammonium bromide (CTAB). Samples were submitted to DNA extraction and PCR as replicates of each heart (simplicate, duplicate, and triplicate), and the probability of a true positive diagnostic was calculated. Among the protocols tested, the kit with modification was determined to be the most suitable for DNA extraction from cysts in PBS solution (92.6 % of DNA detection by PCR); DNAzol resulted in higher DNA detection frequency from bovine myocardium samples (48.1 %). Multiple sampling improved the molecular diagnosis of Sarcocystis spp. infection in cattle hearts, increasing at 22.2 % the rate of true positive diagnostic.

  16. Beyond Alignment

    DEFF Research Database (Denmark)

    Beyond Alignment: Applying Systems Thinking to Architecting Enterprises is a comprehensive reader about how enterprises can apply systems thinking in their enterprise architecture practice, for business transformation and for strategic execution. The book's contributors find that systems thinking...... is a valuable way of thinking about the viable enterprise and how to architect it....

  17. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  18. Application of an improved cDNA competition technique to identify prostate cancer-associated gene.

    Science.gov (United States)

    Rinaldy, A R; Steiner, M S

    1999-11-01

    A technique to improve cDNA library screening was developed by using mixed probes derived from two closely related cDNA populations of high-metastatic MAT-LyLu and low-metastatic AT-1 Dunning R3227 rat prostate cancer sublines. The technique required the generation of a cDNA library from each subline followed by polymerase chain reaction (PCR) amplification of the cDNA insert population. The PCR products derived from the first library were radiolabeled and mixed with an excess amount of PCR products from the second library. The mixture and an excess amount of both the lambda and pBluescript DNA were used as a probe to screen the first cDNA library. This mixed probe (designated the competition probe) differentially cross-hybridized with the plaque lift of the screened first cDNA library. Weak radioactive signals indicated the cross-hybridization of cDNA sequences common to the competition probe mixture and the first cDNA library, whereas strong signals implied unhybridized unique or abundant cDNA sequences in the first cDNA library. The reproducibility of this technique was confirmed by showing that the full-length cDNA clones were associated with the phenotype of the screened first cell line. The isolated clones were characterized as rat nucleolar protein, rat mitochondrial genes coding for 16S and 12S rRNAs, and rat tRNAs specific for valine and phenyl-alanine. This result is consistent with the fact that the first cell line, MAT-LyLu, is metabolically more active than are AT-1 cells because of higher gene dosage or amplification of nucleolar and mitochondrial RNA and its associated genes. Another clone which had a strong signal represented a novel gene associated with the MAT-LyLu cancer phenotype.

  19. An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

    DEFF Research Database (Denmark)

    Bag, Satyabrata; Saha, Bipasa; Mehta, Ojasvi

    2016-01-01

    To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity...... and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental...... methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved...

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2010-01-01

    For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...

  1. Improved osteoblasts growth on osteomimetic hydroxyapatite/BaTiO{sub 3} composites with aligned lamellar porous structure

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Beilei [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); Chen, Liangjian, E-mail: jian007040@sina.com [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083 (China); Shao, Chunsheng [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); Zhang, Fuqiang; Zhou, Kechao [State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083 (China); Cao, Jun [Department of Stomatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013 (China); Zhang, Dou, E-mail: dzhang@csu.edu.cn [State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083 (China)

    2016-04-01

    Osteoblasts growing into bone substitute is an important step of bone regeneration. This study prepared porous hydroxyapatite (HA)/BaTiO{sub 3} piezoelectric composites with porosity of 40%, 50% and 60% by ice-templating method. Effects of HA/BaTiO{sub 3} composites with different porosities, with and without polarizing treatment on adhesion, proliferation and differentiation of osteoblasts were investigated in vitro. Results revealed that cell densities of the porous groups were significantly higher than those of the dense group (p < 0.05), so did the alkaline phosphate (ALP) and bone gla protein (BGP) activities. Porosity of 50% group exhibited higher ALP activity and BGP activity than those of the 40% and 60% groups. Scanning electron microscopy (SEM) observations revealed that osteoblasts adhered and stretched better on porous HA/BaTiO{sub 3} than on the dense one, especially HA/BaTiO{sub 3} with porosity of 50% and 60%. However, there was no significant difference in the cell morphology, cell densities, ALP and BGP activities between the polarized group and the non-polarized group (p > 0.05). The absence of mechanical loading on the polarized samples may account for this. The results indicated that hierarchically porous HA/BaTiO{sub 3} played a favorable part in osteoblasts proliferation, differentiation and adhesion process and is a promising bone substitute material. - Graphical abstract: Aligned porous structure of HA/BaTiO{sub 3} piezoelectric composites prepared by ice-templating method was similar to the lamellar Haversian system in bone tissue. When co-cultured with human osteosarcoma cells (MG63), porous HA/BaTiO{sub 3} composites exhibited remarkable biological activity in promoting proliferation, differentiation and adhesion of MG63 cells. - Highlights: • The aligned porous structure of HA/BaTiO{sub 3} composite was similar to the lamellar Haversian system in bone tissue. • The piezoelectric d{sub 33} coefficient of HA/BaTiO{sub 3} with porosity

  2. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K., E-mail: jonathan.doye@chem.ox.ac.uk [Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Randisi, Ferdinando [Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU (United Kingdom); Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Šulc, Petr [Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065 (United States); Ouldridge, Thomas E. [Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom); Tsukanov, Roman; Nir, Eyal [Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva (Israel); Louis, Ard A. [Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  3. RAPID SCREENING OF AN ARRAYED cDNA LIBRARY BY IMPROVED PCR-BASED METHOD

    Institute of Scientific and Technical Information of China (English)

    杜光伟; 潘美辉; 袁建刚; 周彦; 强伯勤; 梁植权

    1998-01-01

    Tbe present study reports an improved PCR-based technique that allows quick and effecfive screening of eDNA libraries. First, the eDNA library was arrayed as follows: about 3×106 cDNA clones were multiplied as individual plsques on solid medium in 24-well culture dishes at 1 200 plaque forming units per well.The phage suspension of each well was transferred to an individual micrccentrifuge tube in 72-tube box. Then,box pool, row pools and column pools were set up that respectively represent a 72-tube box,rows and columns within the box. To screen a specific target cDNA,primers specific for novel ESTs obtained in our laboratory were eznployed to conduct PCR in a fiierarchy mode. PCR began with the box pools, resulting in the identification of some positive box pools. Then PCR went down to the row and column pools of the positive box. Tbe intersection of the positive row(s) and column(s) revealed the candidate positive tubes. The specificity of PCR products were meanwhile checked hy restriction enzyme digestion. Finally, hybridization was carried out to get single specific eDNA clones-from the positive tlabes. This PCR-hased technique features high specificity, high efficiency and Les-cost in large-scale cDNA library screening. Our initial implementation of the technique resulted in the isolation of three longer different cDNA clones from a hnman fetal brain eDNA library. Thus this improved technique can serve as an alternative to the time-consuming and laborious conventional hybridization-hased metfiod for screening cDNA library.

  4. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  5. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    M. Dallavalle

    2013-01-01

    A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...

  6. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    Erik van Nimwegen

    2006-04-01

    Full Text Available Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5' and 3' ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non

  7. Quantitative Transcript Analysis in Plants: Improved First-strand cDNA Synthesis

    Institute of Scientific and Technical Information of China (English)

    Nai-Zhong XIAO; Lei BA; Preben Bach HOLM; Xing-Zhi WANG; Steve BOWRA

    2005-01-01

    The quantity and quality of first-strand cDNA directly influence the accuracy of transcriptional analysis and quantification. Using a plant-derived α-tubulin as a model system, the effect of oligo sequence and DTT on the quality and quantity of first-strand cDNA synthesis was assessed via a combination of semi-quantitative PCR and real-time PCR. The results indicated that anchored oligo dT significantly improved the quantity and quality of α-tubulin cDNA compared to the conventional oligo dT. Similarly, omitting DTT from the first-strand cDNA synthesis also enhanced the levels of transcript. This is the first time that a comparative analysis has been undertaken for a plant system and it shows conclusively that small changes to current protocols can have very significant impact on transcript analysis.

  8. The twilight zone of cis element alignments.

    Science.gov (United States)

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-02-01

    Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

  9. Post-coital vaginal sampling with nylon flocked swabs improves DNA typing.

    Science.gov (United States)

    Benschop, Corina C G; Wiebosch, Danielle C; Kloosterman, Ate D; Sijen, Titia

    2010-02-01

    In the examination of sexual assault cases, DNA typing of vaginal samples mostly occurs after differential DNA extraction. Notwithstanding the differential extraction method, the DNA profiles from the seminal fraction often show the male alleles at low-level in combination with female alleles. This unfavorable ratio male to female DNA is due to a limited amount of sperm cells and an overwhelming quantity of female cells. In this study, we compared standard cotton and nylon flocked swabs for post-coital vaginal sampling. Twelve couples donated 88 vaginal swabs - 44 cotton, 44 nylon flocked - which were taken with a time since intercourse (TSI) up to 84 h. These vaginal swabs were sorted into categories on the basis of the TSI and submitted to (1) microscopic examination for the presence of male cells, (2) presumptive tests for the detection of seminal fluid and (3) DNA typing. Cellular elution was found to be 6-fold more efficient from the nylon flocked swabs. This makes microscopic analysis less time consuming as the higher cell yield and better cell morphology simplify detection of male cells. Both swab types reveal similar results regarding presumptive tests and male DNA typing. Positive presumptive tests (RSID-semen and PSA) were obtained up to 60 h TSI and male autosomal profiles up to 72 h TSI. Interestingly, over 50% of the samples negative for both presumptive tests resulted in informative male STR profiles. After differential extraction, less DNA was left on the nylon flocked swabs and more male DNA was isolated. Our results imply that the use of nylon flocked swabs for vaginal sampling will improve microscopic analysis and DNA typing in the medical forensic investigation of sexual assault cases.

  10. An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

    Directory of Open Access Journals (Sweden)

    Jitendra Kumar

    2016-12-01

    Full Text Available Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23 kb metagenomic DNA (260/280 ratio >1.8 with a good yield (55.8 ± 3.8 ng/mg of feces. We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes = 227.9:1 in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.

  11. Improved DNA condensation, stability, and transfection with alkyl sulfonyl-functionalized PAMAM G2

    Energy Technology Data Exchange (ETDEWEB)

    Rata-Aguilar, Azahara, E-mail: azahara@ugr.es; Maldonado-Valderrama, Julia; Jódar-Reyes, Ana Belén; Ortega-Vinuesa, Juan Luis [University of Granada, Biocolloid and Fluid Physics Group, Department of Applied Physics (Spain); Santoyo-Gonzalez, Francisco [University of Granada, Organic Chemistry Department, Institute of Biotechnology (Spain); Martín-Rodríguez, Antonio [University of Granada, Biocolloid and Fluid Physics Group, Department of Applied Physics (Spain)

    2015-04-15

    In this work, we have used a second-generation PAMAM grafted with octadecyl sulfonyl chains to condense plasmid DNA. The influence of this modification at different levels was investigated by comparison with original PAMAM G2. The condensation process and temporal stability of the complexes was studied with DLS, finding that the aliphatic chains influence DNA compaction via hydrophobic forces and markedly improve the formation and temporal stability of a single populated system with a hydrodynamic diameter below 100 nm. Interaction with a cell membrane model was also evaluated with a pendant drop tensiometer, resulting in further incorporation of the C18-PAMAM dendriplexes onto the interface. The improvement observed in transfection with our C18 grafted PAMAM is ascribed to the size, stability, and interfacial behavior of the complexes, which in turn are consequence of the DNA condensation process and the interactions involved.

  12. Optimizing hyaluronidase dose and plasmid DNA delivery greatly improves gene electrotransfer efficiency in rat skeletal muscle

    DEFF Research Database (Denmark)

    Åkerström, Thorbjörn; Vedel, Kenneth; Needham Andersen, Josefine;

    2015-01-01

    delivery across the muscle by increasing the number of plasmid DNA injections further enhanced transfection efficiency whereas increasing plasmid dose from 0.2 to 1.6. μg/g b.w. or vehicle volume had no effect. The optimized protocol resulted in ~80% (CI95%: 79-84%) transfected muscle fibers......Transfection of rat skeletal muscle in vivo is a widely used research model. However, gene electrotransfer protocols have been developed for mice and yield variable results in rats. We investigated whether changes in hyaluronidase pre-treatment and plasmid DNA delivery can improve transfection...... with a homogenous distribution. We also show that transfection was stable over five weeks of regular exercise or inactivity. Our findings show that species-specific plasmid DNA delivery and hyaluronidase pre-treatment greatly improves transfection efficiency in rat skeletal muscle....

  13. Combining bleach and mild predigestion improves ancient DNA recovery from bones

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Hanghøj, Kristian Ebbesen; Nistelberger, Heidi M.

    2017-01-01

    aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high...

  14. An Improved Method for Soil DNA Extraction to Study the Microbial Assortment within Rhizospheric Region.

    Science.gov (United States)

    Fatima, Faria; Pathak, Neelam; Rastogi Verma, Smita

    2014-01-01

    The need for identification of soil microbial community mainly depends on direct extraction of DNA from soil, a multifaceted environment that is a major pool for microbial genetic diversity. The soil DNA extraction procedures usually suffer from two major problems, namely, inappropriate rupturing of cells and contamination with humic substances. In the present study, five protocols for single type of rhizospheric soil were investigated and their comparison indicated that the inclusion of 120 mM phosphate buffered saline (PBS) for washing and mannitol in the lysis buffer allowed the processing of soil sample in minimal time with no specific equipment requirement. Furthermore, DNA purity and yield were also improved, which allowed the exploitation of genetic potential of soil microbes within soil sample thereby facilitating the amplification of metagenomic DNA. The effectiveness of methods was analyzed using random amplification of polymorphic DNA. The banding patterns revealed that both the abundance and the composition of indigenous microbial community depend on the DNA recovery method.

  15. An improved DNA isolation technique for PCR detection of Strongyloides stercoralis in stool samples.

    Science.gov (United States)

    Repetto, S A; Alba Soto, C D; Cazorla, S I; Tayeldin, M L; Cuello, S; Lasala, M B; Tekiel, V S; González Cappa, S M

    2013-05-01

    Strongyloides stercoralis is a nematode that causes severe infections in immunocompromised patients. The low parasitic burden of chronically infected patients makes diagnosis difficult to achieve by conventional methods. Here, an in-house (IH) method for the isolation of parasite DNA from stools and a PCR assay for the molecular diagnosis of S. stercoralis were optimized. DNA yield and purity improved with the IH method which included a step of incubation of stool samples with a glycine-SDS buffer and mechanical disruption prior to DNA extraction. For the PCR assay, the addition of bovine serum albumin was required to neutralize inhibitors present in stool. The analytical sensitivity of the PCR using DNA as template, isolated with the IH method, was superior to the commercial one. This study demonstrates that a combined method that adds the step of glycine-SDS buffer incubation plus mechanical disruption prior to DNA isolation with the commercial kit increased PCR sensitivity to levels of the IH method. Finally, our assay was tested on 17 clinical samples. With the IH method for DNA isolation, a S. stercoralis specific band was detected by PCR in the first stool sample in all patients (17/17), while with the commercial kit, our S. stercoralis-specific band was only observed in 7 samples. The superior efficiency of the IH and combined methods over the commercial kit was demonstrated when applied to clinical samples with low parasitic burden. These results show that the DNA extraction procedure is a key to increase sensitivity of the S. stercoralis PCR assay in stool samples. The method developed here could help to improve the molecular diagnosis of S. stercoralis.

  16. Self-entanglement of long linear DNA vectors using transient non-B-DNA attachment points: a new concept for improvement of non-viral therapeutic gene delivery.

    Science.gov (United States)

    Tolmachov, Oleg E

    2012-05-01

    topoisomerases. The technology for such self-entanglement can be an avenue for the improvement of gene delivery with high-molecular-weight naked DNA using therapeutically important methods associated with considerable shear stress. Priority applications include in vivo muscle electroporation and sonoporation for Duchenne muscular dystrophy patients, aerosol inhalation to reach the target lung cells of cystic fibrosis patients and bio-ballistic delivery to skin melanomas with the vector DNA adsorbed on gold or tungsten projectiles.

  17. Cross-axis adaptation improves 3D vestibulo-ocular reflex alignment during chronic stimulation via a head-mounted multichannel vestibular prosthesis.

    Science.gov (United States)

    Dai, Chenkai; Fridman, Gene Y; Chiang, Bryce; Davidovics, Natan S; Melvin, Thuy-Anh; Cullen, Kathleen E; Della Santina, Charles C

    2011-05-01

    By sensing three-dimensional (3D) head rotation and electrically stimulating the three ampullary branches of a vestibular nerve to encode head angular velocity, a multichannel vestibular prosthesis (MVP) can restore vestibular sensation to individuals disabled by loss of vestibular hair cell function. However, current spread to afferent fibers innervating non-targeted canals and otolith end organs can distort the vestibular nerve activation pattern, causing misalignment between the perceived and actual axis of head rotation. We hypothesized that over time, central neural mechanisms can adapt to correct this misalignment. To test this, we rendered five chinchillas vestibular deficient via bilateral gentamicin treatment and unilaterally implanted them with a head-mounted MVP. Comparison of 3D angular vestibulo-ocular reflex (aVOR) responses during 2 Hz, 50°/s peak horizontal sinusoidal head rotations in darkness on the first, third, and seventh days of continual MVP use revealed that eye responses about the intended axis remained stable (at about 70% of the normal gain) while misalignment improved significantly by the end of 1 week of prosthetic stimulation. A comparable time course of improvement was also observed for head rotations about the other two semicircular canal axes and at every stimulus frequency examined (0.2-5 Hz). In addition, the extent of disconjugacy between the two eyes progressively improved during the same time window. These results indicate that the central nervous system rapidly adapts to multichannel prosthetic vestibular stimulation to markedly improve 3D aVOR alignment within the first week after activation. Similar adaptive improvements are likely to occur in other species, including humans.

  18. Field Test Results from Lidar Measured Yaw Control for Improved Yaw Alignment with the NREL Controls Advanced Research Turbine: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Scholbrock, A.; Fleming, P.; Wright, A.; Slinger, C.; Medley, J.; Harris, M.

    2014-12-01

    This paper describes field tests of a light detection and ranging (lidar) device placed forward looking on the nacelle of a wind turbine and used as a wind direction measurement to directly control the yaw position of a wind turbine. Conventionally, a wind turbine controls its yaw direction using a nacelle-mounted wind vane. If there is a bias in the measurement from the nacelle-mounted wind vane, a reduction in power production will be observed. This bias could be caused by a number of issues such as: poor calibration, electromagnetic interference, rotor wake, or other effects. With a lidar mounted on the nacelle, a measurement of the wind could be made upstream of the wind turbine where the wind is not being influenced by the rotor's wake or induction zone. Field tests were conducted with the lidar measured yaw system and the nacelle wind vane measured yaw system. Results show that a lidar can be used to effectively measure the yaw error of the wind turbine, and for this experiment, they also showed an improvement in power capture because of reduced yaw misalignment when compared to the nacelle wind vane measured yaw system.

  19. Parallel progressive multiple sequence alignment on reconfigurable meshes

    Directory of Open Access Journals (Sweden)

    Nguyen Ken D

    2011-12-01

    Full Text Available Abstract Background One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand. Results We design O(1 run-time solutions for both local and global dynamic programming pair-wise alignment algorithms on reconfigurable mesh computing model. To align m sequences with max length n, we combining the parallel pair-wise dynamic programming solutions with newly designed parallel components. We successfully reduce the progressive multiple sequence alignment algorithm's run-time complexity from O(m × n4 to O(m using O(m × n3 processing units for scoring schemes that use three distinct values for match/mismatch/gap-extension. The general solution to multiple sequence alignment algorithm takes O(m × n4 processing units and completes in O(m time. Conclusions To our knowledge, this is the first time the progressive multiple sequence alignment algorithm is completely parallelized with O(m run-time. We also provide a new parallel algorithm for the Longest Common Subsequence (LCS with O(1 run-time using O(n3 processing units. This is a big improvement over the current best constant-time algorithm that uses O(n4 processing units.

  20. Experimental conditions improving in-solution target enrichment for ancient DNA.

    Science.gov (United States)

    Cruz-Dávalos, Diana I; Llamas, Bastien; Gaunitz, Charleen; Fages, Antoine; Gamba, Cristina; Soubrier, Julien; Librado, Pablo; Seguin-Orlando, Andaine; Pruvost, Mélanie; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Scheu, Amelie; Beneke, Norbert; Ludwig, Arne; Cooper, Alan; Willerslev, Eske; Orlando, Ludovic

    2016-08-27

    High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.

  1. Oral antioxidant treatment partly improves integrity of human sperm DNA in infertile grade I varicocele patients.

    Science.gov (United States)

    Gual-Frau, Josep; Abad, Carlos; Amengual, María J; Hannaoui, Naim; Checa, Miguel A; Ribas-Maynou, Jordi; Lozano, Iris; Nikolaou, Alexandros; Benet, Jordi; García-Peiró, Agustín; Prats, Juan

    2015-09-01

    Infertile males with varicocele have the highest percentage of sperm cells with damaged DNA, compared to other infertile groups. Antioxidant treatment is known to enhance the integrity of sperm DNA; however, there are no data on the effects in varicocele patients. We thus investigated the potential benefits of antioxidant treatment specifically in grade I varicocele males. Twenty infertile patients with grade I varicocele were given multivitamins (1500 mg L-Carnitine, 60 mg vitamin C, 20 mg coenzyme Q10, 10 mg vitamin E, 200 μg vitamin B9, 1 μg vitamin B12, 10 mg zinc, 50 μg selenium) daily for three months. Semen parameters including total sperm count, concentration, progressive motility, vitality, and morphology were determined before and after treatment. In addition, sperm DNA fragmentation and the amount of highly degraded sperm cells were analyzed by Sperm Chromatin Dispersion. After treatment, patients showed an average relative reduction of 22.1% in sperm DNA fragmentation (p = 0.02) and had 31.3% fewer highly degraded sperm cells (p = 0.07). Total numbers of sperm cells were increased (p = 0.04), but other semen parameters were unaffected. These data suggest that sperm DNA integrity in grade I varicocele patients may be improved by oral antioxidant treatment.

  2. Improved method for measuring the ensemble average of strand breaks in genomic DNA.

    Science.gov (United States)

    Bespalov, V A; Conconi, A; Zhang, X; Fahy, D; Smerdon, M J

    2001-01-01

    The cis-syn cyclobutane pyrimidine dimer (CPD) is the major photoproduct induced in DNA by low wavelength ultraviolet radiation. An improved method was developed to detect CPD formation and removal in genomic DNA that avoids the problems encountered with the standard method of endonuclease detection of these photoproducts. Since CPD-specific endonucleases make single-strand cuts at CPD sites, quantification of the frequency of CPDs in DNA is usually done by denaturing gel electrophoresis. The standard method of ethidium bromide staining and gel photography requires more than 10 microg of DNA per gel lane, and correction of the photographic signal for the nonlinear film response. To simplify this procedure, a standard Southern blot protocol, coupled with phosphorimage analysis, was developed. This method uses random hybridization probes to detect genomic sequences with minimal sequence bias. Because of the vast linearity range of phosphorimage detection, scans of the signal profiles for the heterogeneous population of DNA fragments can be integrated directly to determine the number-average size of the population.

  3. Solvent-Assisted Oxygen Incorporation of Vertically Aligned MoS2 Ultrathin Nanosheets Decorated on Reduced Graphene Oxide for Improved Electrocatalytic Hydrogen Evolution.

    Science.gov (United States)

    Liu, Aiping; Zhao, Li; Zhang, Junma; Lin, Liangxu; Wu, Huaping

    2016-09-28

    Three-dimensional oxygen-incorporated MoS2 ultrathin nanosheets decorated on reduced graphene oxide (O-MoS2/rGO) had been successfully fabricated through a facile solvent-assisted hydrothermal method. The origin of the incorporated oxygen and its incorporation mechanism into MoS2 were carefully investigated. We found that the solvent N,N-dimethylformamide (DMF) was the key as the reducing agent and the oxygen donor, expanding interlayer spaces and improving intrinsic conductivity of MoS2 sheets (modulating its electronic structure and vertical edge sites). These O dopants, vertically aligned edges and decoration with rGO gave effectively improved double-layer capacitance and catalytic performance for hydrogen evolution reaction (HER) of MoS2. The prepared O-MoS2/rGO catalysts showed an exceptional small Tafel slope of 40 mV/decade, a high current density of 20 mA/cm(2) at the overpotential of 200 mV and remarkable stability even after 2000th continuous HER test in the acid media.

  4. Improving the Analysis of Dinoflagellate Phylogeny based on rDNA

    DEFF Research Database (Denmark)

    Murray, Shauna; Jørgensen, Mårten Flø; Ho, Simon Y.W.

    2005-01-01

    that may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non...

  5. Improving molecular detection of Candida DNA in whole blood: comparison of seven fungal DNA extraction protocols using real-time PCR.

    Science.gov (United States)

    Metwally, L; Fairley, D J; Coyle, P V; Hay, R J; Hedderwick, S; McCloskey, B; O'Neill, H J; Webb, C H; Elbaz, W; McMullan, R

    2008-03-01

    The limitations of classical diagnostic methods for invasive Candida infections have led to the development of molecular techniques such as real-time PCR to improve diagnosis. However, the detection of low titres of Candida DNA in blood from patients with candidaemia requires the use of extraction methods that efficiently lyse yeast cells and recover small amounts of DNA suitable for amplification. In this study, a Candida-specific real-time PCR assay was used to detect Candida albicans DNA in inoculated whole blood specimens extracted using seven different extraction protocols. The yield and quality of total nucleic acids were estimated using UV absorbance, and specific recovery of C. albicans genomic DNA was estimated quantitatively in comparison with a reference (Qiagen kit/lyticase) method currently in use in our laboratory. The extraction protocols were also compared with respect to sensitivity, cost and time required for completion. The TaqMan PCR assay used to amplify the DNA extracts achieved high levels of specificity, sensitivity and reproducibility. Of the seven extraction protocols evaluated, only the MasterPure yeast DNA extraction reagent kit gave significantly higher total nucleic acid yields than the reference method, although nucleic acid purity was highest using either the reference or YeaStar genomic DNA kit methods. More importantly, the YeaStar method enabled C. albicans DNA to be detected with highest sensitivity over the entire range of copy numbers evaluated, and appears to be an optimal method for extracting Candida DNA from whole blood.

  6. The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

    Science.gov (United States)

    Jordan, Gregory; Goldman, Nick

    2012-04-01

    When detecting positive selection in proteins, the prevalence of errors resulting from misalignment and the ability of alignment filters to mitigate such errors are not well understood, but filters are commonly applied to try to avoid false positive results. Focusing on the sitewise detection of positive selection across a wide range of divergence levels and indel rates, we performed simulation experiments to quantify the false positives and false negatives introduced by alignment error and the ability of alignment filters to improve performance. We found that some aligners led to many false positives, whereas others resulted in very few. False negatives were a problem for all aligners, increasing with sequence divergence. Of the aligners tested, PRANK's codon-based alignments consistently performed the best and ClustalW performed the worst. Of the filters tested, GUIDANCE performed the best and Gblocks performed the worst. Although some filters showed good ability to reduce the error rates from ClustalW and MAFFT alignments, none were found to substantially improve the performance of PRANK alignments under most conditions. Our results revealed distinct trends in error rates and power levels for aligners and filters within a biologically plausible parameter space. With the best aligner, a low false positive rate was maintained even with extremely divergent indel-prone sequences. Controls using the true alignment and an optimal filtering method suggested that performance improvements could be gained by improving aligners or filters to reduce the prevalence of false negatives, especially at higher divergence levels and indel rates.

  7. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair

    DEFF Research Database (Denmark)

    Akbari, Mansour; Keijzers, Guido; Maynard, Scott;

    2014-01-01

    by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional......Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial...... DNA replication and transcription and generate mutations. We carried out BER analysis in highly purified mitochondrial extracts from human cell lines U2OS and HeLa, and mouse brain using a circular DNA substrate containing a lesion at a specific position. We found that DNA ligation is significantly...

  8. Improved model for statistical alignment

    Energy Technology Data Exchange (ETDEWEB)

    Miklos, I.; Toroczkai, Z. (Zoltan)

    2001-01-01

    The statistical approach to molecular sequence evolution involves the stochastic modeling of the substitution, insertion and deletion processes. Substitution has been modeled in a reliable way for more than three decades by using finite Markov-processes. Insertion and deletion, however, seem to be more difficult to model, and thc recent approaches cannot acceptably deal with multiple insertions and deletions. A new method based on a generating function approach is introduced to describe the multiple insertion process. The presented algorithm computes the approximate joint probability of two sequences in 0(13) running time where 1 is the geometric mean of the sequence lengths.

  9. 提高MIMO信道BER性能的干扰对齐方案%Interference Alignment Scheme for Improving BER Performance of MIMO Channel

    Institute of Scientific and Technical Information of China (English)

    周强; 吴玉成

    2012-01-01

    To improve the Bit Error Rate(BER) performance of Multi Input Multi Output(MIMQ) X channel, this paper proposes an Interference Alignment(IA) scheme. It transmits data symbols according to Alamouti scheme at senders, and changes the operation mode of reconfigurable antennas at receivers. The final equivalent channel matrix is orthogonal, thus interference can be eliminated through matrix operation, and low complexity Partial Interference Cancellation(PIC) group decoding can be employed. Simulation results proves the validity of the scheme.%为提高多输入多输出(MIMO)X信道的比特误码率(BER)性能,提出一种干扰对齐方案.在发送端将数据按照Alamouti编码方案重复发送,在接收端通过重新配置天线工作模式改变信道系数,构成具有正交结构的等效信道矩阵,通过矩阵运算消除干扰,并采用低复杂度的PIC群译码算法进行译码.仿真结果验证了该方案的有效性.

  10. Magnetic alignment and the Poisson alignment reference system

    Science.gov (United States)

    Griffith, L. V.; Schenz, R. F.; Sommargren, G. E.

    1990-08-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This article begins with a review of the motivation for developing an alignment system that will assure better than 100-μm accuracy in the alignment of the magnetic axis throughout an FEL. The 100-μm accuracy is an error circle about an ideal axis for 300 m or more. The article describes techniques for identifying the magnetic axes of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development of a straight-line reference based on the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. The Poisson alignment reference system should be accurate to 25 μm over 300 m, which is believed to be a factor-of-4 improvement over earlier techniques. An error budget shows that only 25% of the total budgeted tolerance is used for the alignment reference system, so the remaining tolerances should fall within the allowable range for FEL alignment.

  11. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library

    Science.gov (United States)

    Arculeo, Marco; Bonello, Juan J.; Bonnici, Leanne; Cannas, Rita; Carbonara, Pierluigi; Cau, Alessandro; Charilaou, Charis; El Ouamari, Najib; Fiorentino, Fabio; Follesa, Maria Cristina; Garofalo, Germana; Golani, Daniel; Guarniero, Ilaria; Hanner, Robert; Hemida, Farid; Kada, Omar; Lo Brutto, Sabrina; Mancusi, Cecilia; Morey, Gabriel; Schembri, Patrick J.; Serena, Fabrizio; Sion, Letizia; Stagioni, Marco; Tursi, Angelo; Vrgoc, Nedo; Steinke, Dirk; Tinti, Fausto

    2017-01-01

    Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions. PMID:28107413

  12. Improvement of Hydrodynamics-Based Gene Transfer of Nonviral DNA Targeted to Murine Hepatocytes

    Directory of Open Access Journals (Sweden)

    Shingo Nakamura

    2013-01-01

    Full Text Available The liver is an important organ for supporting the life of an individual. Gene transfer toward this organ has been attempted in many laboratories to date; however, there have been few reports on improved liver-targeted gene delivery by using a nonviral vector. In this study, we examined the effect of various types of gene delivery carriers on enhancing the uptake and gene expression of exogenous DNA in murine hepatocytes when a hydrodynamics-based gene delivery (HGD is performed via tail-vein injection. Mice were singly injected with a large amount of phosphate-buffered saline containing reporter plasmid DNA and/or with a gene delivery carrier. One day after the gene delivery, the animals' livers were dissected and subjected to biochemical, histochemical, and molecular biological analyses. The strongest signal from the reporter plasmid DNA was observed when the DNA was mixed with a polyethylenimine- (PEI- based reagent. Coinjection with pCRTEIL (a loxP-floxed reporter construct and pTR/NCre (a liver-specific Cre expression vector resulted in the liver-specific recombination of pCRTEIL. The combination of PEI with HGD would thus be a valuable tool for liver-specific manipulation to examine the function of a gene of interest in the liver and for creating liver disease models.

  13. NAD(+) Replenishment Improves Lifespan and Healthspan in Ataxia Telangiectasia Models via Mitophagy and DNA Repair.

    Science.gov (United States)

    Fang, Evandro Fei; Kassahun, Henok; Croteau, Deborah L; Scheibye-Knudsen, Morten; Marosi, Krisztina; Lu, Huiming; Shamanna, Raghavendra A; Kalyanasundaram, Sumana; Bollineni, Ravi Chand; Wilson, Mark A; Iser, Wendy B; Wollman, Bradley N; Morevati, Marya; Li, Jun; Kerr, Jesse S; Lu, Qiping; Waltz, Tyler B; Tian, Jane; Sinclair, David A; Mattson, Mark P; Nilsen, Hilde; Bohr, Vilhelm A

    2016-10-11

    Ataxia telangiectasia (A-T) is a rare autosomal recessive disease characterized by progressive neurodegeneration and cerebellar ataxia. A-T is causally linked to defects in ATM, a master regulator of the response to and repair of DNA double-strand breaks. The molecular basis of cerebellar atrophy and neurodegeneration in A-T patients is unclear. Here we report and examine the significance of increased PARylation, low NAD(+), and mitochondrial dysfunction in ATM-deficient neurons, mice, and worms. Treatments that replenish intracellular NAD(+) reduce the severity of A-T neuropathology, normalize neuromuscular function, delay memory loss, and extend lifespan in both animal models. Mechanistically, treatments that increase intracellular NAD(+) also stimulate neuronal DNA repair and improve mitochondrial quality via mitophagy. This work links two major theories on aging, DNA damage accumulation, and mitochondrial dysfunction through nuclear DNA damage-induced nuclear-mitochondrial signaling, and demonstrates that they are important pathophysiological determinants in premature aging of A-T, pointing to therapeutic interventions.

  14. Alignment method for solar collector arrays

    Science.gov (United States)

    Driver, Jr., Richard B

    2012-10-23

    The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

  15. Improvement of reliability of molecular DNA computing: solution of inverse problem of Raman spectroscopy using artificial neural networks

    Science.gov (United States)

    Dolenko, T. A.; Burikov, S. A.; Vervald, E. N.; Efitorov, A. O.; Laptinskiy, K. A.; Sarmanova, O. E.; Dolenko, S. A.

    2017-02-01

    Elaboration of methods for the control of biochemical reactions with deoxyribonucleic acid (DNA) strands is necessary for the solution of one of the basic problems in the creation of biocomputers—improvement in the reliability of molecular DNA computing. In this paper, the results of the solution of the four-parameter inverse problem of laser Raman spectroscopy—the determination of the type and concentration of each of the DNA nitrogenous bases in multi-component solutions—are presented.

  16. MUSE alignment onto VLT

    Science.gov (United States)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  17. Improved reproducibility in genome-wide DNA methylation analysis for PAXgene® fixed samples compared to restored FFPE DNA

    DEFF Research Database (Denmark)

    Andersen, Gitte Brinch; Hager, Henrik; Hansen, Lise Lotte;

    2014-01-01

    , precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap......Chip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better...... compared with restored FFPE DNA in genome-wide DNA methylation analysis. In addition, DNA from PAXgene tissue can be directly used on the array without prior restoration, rendering the analytical process significantly more time- and cost-effective....

  18. Improving Griffith's protocol for co-extraction of microbial DNA and RNA in adsorptive soils

    DEFF Research Database (Denmark)

    Paulin, Mélanie Marie; Nicolaisen, Mette Haubjerg; Jacobsen, Carsten Suhr

    2013-01-01

    -time PCR on both the RNA (after conversion to cDNA) and the DNA fraction of the extracts. Non-adsorptive soils were characterized by low clay content and/or high phosphate content, whereas adsorptive soils had clay contents above 20% and/or a strong presence of divalent Ca in combination with high p......Quantification of microbial gene expression is increasingly being used to study key functions in soil microbial communities, yet major limitations still exist for efficient extraction of nucleic acids, especially RNA for transcript analysis, from this complex matrix. We present an improved...... extraction protocol that was optimized by: i) including an adsorption-site competitor prior to cell lysis to decrease adsorption of nucleic acids to soil particles, and ii) optimizing the PEG concentration used for nucleic acid precipitation. The extraction efficiency was determined using quantitative real...

  19. Routes to improving the reliability of low level DNA analysis using real-time PCR

    Directory of Open Access Journals (Sweden)

    Burns Malcolm J

    2006-07-01

    Full Text Available Abstract Background Accurate quantification of DNA using quantitative real-time PCR at low levels is increasingly important for clinical, environmental and forensic applications. At low concentration levels (here referring to under 100 target copies DNA quantification is sensitive to losses during preparation, and suffers from appreciable valid non-detection rates for sampling reasons. This paper reports studies on a real-time quantitative PCR assay targeting a region of the human SRY gene over a concentration range of 0.5 to 1000 target copies. The effects of different sample preparation and calibration methods on quantitative accuracy were investigated. Results At very low target concentrations of 0.5–10 genome equivalents (g.e. eliminating any replicates within each DNA standard concentration with no measurable signal (non-detects compromised calibration. Improved calibration could be achieved by eliminating all calibration replicates for any calibration standard concentration with non-detects ('elimination by sample'. Test samples also showed positive bias if non-detects were removed prior to averaging; less biased results were obtained by converting to concentration, including non-detects as zero concentration, and averaging all values. Tube plastic proved to have a strongly significant effect on DNA quantitation at low levels (p = 1.8 × 10-4. At low concentrations (under 10 g.e., results for assays prepared in standard plastic were reduced by about 50% compared to the low-retention plastic. Preparation solution (carrier DNA or stabiliser was not found to have a significant effect in this study. Detection probabilities were calculated using logistic regression. Logistic regression over large concentration ranges proved sensitive to non-detected replicate reactions due to amplification failure at high concentrations; the effect could be reduced by regression against log (concentration or, better, by eliminating invalid responses

  20. 基于正逆向与降噪的捷联惯导改进快速对准方法%Improved fast alignment method of strapdown INS using bidirectional processes and denoising

    Institute of Scientific and Technical Information of China (English)

    覃方君; 李安; 许江宁

    2014-01-01

    针对捷联惯性导航系统(INS)的快速对准问题,基于双向过程和惯性传感器的降噪方法,提出了一种改进的对准方法。利用双向过程(前向和逆向)反复处理保存的惯性测量单元(IMU)的数据序列实现快速对准,推导了一种新的前向与逆向对准关系。为了减少角随机游走误差的影响,基于小波变换的降噪方法抑制光纤陀螺(FOGs)和加速度计噪声,给出陀螺罗经回路的改进方法的整个流程,并在自研的光纤陀螺捷联惯导系统上进行测试。实测数据实验结果表明,经正逆向与降噪改进后的快速对准方法具有更快的收敛速度,能在不到3 min内完成对准任务,同时也具有更好的对准精度。%To solve fast alignment problem for strapdown inertial navigation system(INS), an improved alignment method is proposed using bidirectional processes and inertial sensors denoising. It is proved that repeatedly making use of the bidirectional processes(forward and backward ) to process the saved inertial measurement unit(IMU) data sequence could help fast alignment. A new relationship between forward and backward processes for alignment is deviated. In order to reduce the effect of angular random walk error, a wavelet-based demoising method is adopted to suppress the noises of fiber optical gyroscopes(FOGs) and accelerometers. And the whole procedure of the improved method based on gyrocompassing loop is given. The fast alignment method has been tested on a self-made FOG strapdown INS. The experiment results show that the improved method has great advantage in alignment speed, which costs less than 3 min to complete the alignment mission, and also has higher alignment accuracy after offline denoising the inertial sensors.

  1. Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE

    Directory of Open Access Journals (Sweden)

    Ile Kristina E

    2003-07-01

    Full Text Available Abstract Background The ADGE technique is a method designed to magnify the ratios of gene expression before detection. It improves the detection sensitivity to small change of gene expression and requires small amount of starting material. However, the throughput of ADGE is low. We integrated ADGE with DNA microarray (ADGE microarray and compared it with regular microarray. Results When ADGE was integrated with DNA microarray, a quantitative relationship of a power function between detected and input ratios was found. Because of ratio magnification, ADGE microarray was better able to detect small changes in gene expression in a drug resistant model cell line system. The PCR amplification of templates and efficient labeling reduced the requirement of starting material to as little as 125 ng of total RNA for one slide hybridization and enhanced the signal intensity. Integration of ratio magnification, template amplification and efficient labeling in ADGE microarray reduced artifacts in microarray data and improved detection fidelity. The results of ADGE microarray were less variable and more reproducible than those of regular microarray. A gene expression profile generated with ADGE microarray characterized the drug resistant phenotype, particularly with reference to glutathione, proliferation and kinase pathways. Conclusion ADGE microarray magnified the ratios of differential gene expression in a power function, improved the detection sensitivity and fidelity and reduced the requirement for starting material while maintaining high throughput. ADGE microarray generated a more informative expression pattern than regular microarray.

  2. A recoding method to improve the humoral immune response to an HIV DNA vaccine.

    Directory of Open Access Journals (Sweden)

    Yaoxing Huang

    Full Text Available This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon optimized consensus gag gene, we recode the nucleotide sequence so as to remove these motifs without modifying the amino acid sequence. Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version. We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model. Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine.

  3. Electroporative transfection with KGF-1 DNA improves wound healing in a diabetic mouse model.

    Science.gov (United States)

    Marti, G; Ferguson, M; Wang, J; Byrnes, C; Dieb, R; Qaiser, R; Bonde, P; Duncan, M D; Harmon, J W

    2004-12-01

    We recently demonstrated that electroporation enhances transfection in a mouse wound-healing model. Keratinocyte growth factor (KGF) is an inducer of epithelial cell proliferation and differentiation and has been shown to be under expressed in the wounds of diabetic individuals. We hypothesized that KGF delivered into an excisional wound via naked DNA injection with subsequent electroporation would be a novel and potentially effective method to enhance wound closure in a diabetic mouse model. ELISA assays confirmed production of KGF protein in cultured mouse cells and RT-PCR assays confirmed KGF mRNA in skin samples taken from mice. In all, 32 genetically diabetic mice were given two identical excisional wounds of their dorsum and split into two groups with one group receiving KGF DNA injection and electroporation with the other group receiving no treatment. Over 90% of wounds healed in the presence of KGF and electroporation versus 40% in the untreated group by day 12. Histological analysis of the wounds demonstrated that untreated wounds contained microulcers with thin or incomplete epithelium with unresolved inflammation as compared to treated wounds where intact and mature epithelium was observed. Taken together these findings suggest that a single injection of KGF DNA encoded on a plasmid coupled with electroporation improves and accelerates wound closure in a delayed wound-healing model.

  4. Improvement in Lithography Alignment with Thick Aluminum Manufacture Process%厚铝芯片制造工艺的光刻对准效果改善

    Institute of Scientific and Technical Information of China (English)

    马万里

    2011-01-01

    对于厚铝芯片的制造工艺,由于光刻对准标记上覆盖了厚的铝层,对准标记形貌轮廓会变得模糊,这会导致光刻对准出现困难,对偏的问题将变得常见.为了解决此问题,提出了多种改善方法,首先采用叠加标记法,通过将不同层次的对准标记进行叠加,增大了标记的台阶,对准标记的轮廓变得比原来清晰.其次是局部溅射法,通过夹具保护对准标记,确保标记不被厚铝覆盖,因此厚铝将不会对对准标记产生任何影响.最后是剥离工艺法,通过光刻胶保护对准标记,使之不被厚铝覆盖,因此,对准标记形貌将会保持清晰.这些方法在工艺和原理上是不同的,它们适用于不同的环境.通过这些方法,基本可以解决厚铝工艺中光刻对准困难的问题.%For manufacture process with thick aluminum, the profile of alignment mark will become blur because of being covered by thick aluminum. It will lead to have difficulty in photo alignment, and misalignment will be common. For the sake of resolving this problem, several methods are put forward. Firstly, with the alignment mark for overlapping, the step of alignment mark is enlarged by overlapping the marks of different layers. The profile of alignment mark become clear than ever. Secondly, through metal sputtering locally, alignment mark is protected by the clamp from being covered by thick aluminum. So thick aluminum will have no effect on the alignment mark. Finally, by lift off process, photo resistor protects alignment mark from being covered by thick aluminum. So the profile of alignment mark will be clear. These methods are different in process and principle and adapt to different conditions. All of misalignment problem for thick aluminum can be resolved by these methods.

  5. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Science.gov (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  6. 一种改善胆固醇液晶排列的简易方法%One Method for Improving the Alignment of Cholesteric Liquid Crystal

    Institute of Scientific and Technical Information of China (English)

    罗吉祥; 黄玉华; 晋敏

    2014-01-01

    Because a lot of defects will be formed in thick cholesteric liquid crystals (CLC),which destroys its photonic bandgap structure and dramatically reduces the transmissivity,its applications in photonics have been dramatically limited.In order to overcome this problem,we developed a method to improve the alignment of the liquid crystal (LC) molecules in the CLC sample.The procedure is as follows:firstly,high enough AC voltage with 1 kHz is applied to swithch on the CLC sample.After switching on and off the sample at this voltage for several times,massage is done on the CLC surface for a while.The results show that after massage,the defects inside the CLC sample can be dramatically reduced,therefore the planar structure of CLC is greatly improved,and the transmission is drastically increased.It indicates that this method can be used for fabricating thicker CLC samples.Above all,it provides a useful fabrication basis for the CLC's applications in photonics.%胆固醇液晶在厚的液晶盒中会形成大量缺陷,以至于其光子晶体结构被破坏,透射率急剧降低,严重影响了晶体光学性质及其应用.针对此提出了一种能有效改善胆固醇液晶分子排列的简易方法,其过程为先通过给胆固醇液晶施加足以驱动胆固醇液晶分子的交流电压,并在该交流电压下开关数次后对其进行摩擦处理.结果表明经过摩擦处理后,胆固醇液晶样品的内部缺陷明显减少了,其平面结构相应得到了较大的改善,样品的透射率显著提高,由摩擦前的模糊变成摩擦后的透明.表明该方法可以用于制备高质量的厚胆固醇液晶样品,从而为胆固醇液晶在光学领域的应用提供了必要条件.

  7. Technical improvements in the DNA analysis of the myotonic dystrophy (DM) mutation

    Energy Technology Data Exchange (ETDEWEB)

    Leblond, S.; Lehev, D.; Barcelo, J. [Children`s Hospital of Eastern Ontario, Ottawa (Canada)] [and others

    1994-09-01

    It has become increasingly clear that widespread clinical application of routine DNA diagnosis requires robust and easily replicated methodologies. Mutation analysis in DM involves detection of a CTG expansion which may increase in size between generations within a family. DNA testing has required two distinct methods: genomic and PCR DNA Southern blotting. Genomic Southerns visualize from E1 (hundreds of repeats) to the very largest E4 (thousands of repeats in congenital DM). PCR Southerns permit detection of the smallest mutations (E0, protomutations associated with minimal if any clinical signs) to E3, but E4 is not uniformly visualized. In order to improve the DM testing such that even the largest expansions are visualized by a single PCR test, we have altered the PCR conditions. Since the PCR conditions do not substantially affect the normal allele of less than 200 bp, CTG expansion must be directly monitored by hybridization with a labelled (CTG){sub 10} oligonucleotide. Unlike PCR of the CGG expansion in fragile X, addition of deazaGTP reduced visualization of the DM expansion. Addition of single-stranded protein and DMSO significantly improved PCR up to ten-fold such that E4s were visualized. The CTG expansion was very sensitive to the denaturing cycle temperature (which does not affect the intensity of the normal allele). Thus, 96{degrees}C on the Perkin Elmer 480 was optimal in our hands, with 98{degrees}C and 94{degrees}C actually causing loss of even the intermediate sized E1 and E2 expansions. This has implications when setting up the DM test on different thermocyclers where digital readings may not reflect actual block temperature. These PCR `tune-ups` will support more reliable and streamlined analyses, as more expansion mutations are recognized and routinely offered for clinical use.

  8. FSH treatment in infertile males candidate to assisted reproduction improved sperm DNA fragmentation and pregnancy rate.

    Science.gov (United States)

    Garolla, Andrea; Ghezzi, Marco; Cosci, Ilaria; Sartini, Barbara; Bottacin, Alberto; Engl, Bruno; Di Nisio, Andrea; Foresta, Carlo

    2016-07-27

    The purpose of this study is to evaluate whether follicle-stimulating hormone treatment improves sperm DNA parameters and pregnancy outcome in infertile male candidates to in-vitro fertilization.Observational study in 166 infertile male partners of couples undergoing in-vitro fertilization. Eighty-four patients were receiving follicle-stimulating hormone treatment (cases) and 82 refused treatment (controls). Semen parameters, sexual hormones, and sperm nucleus (fluorescence in-situ hybridization, acridine orange, TUNEL, and γH2AX) were evaluated at baseline (T0) and after 3 months (T1), when all subjects underwent assisted reproduction techniques. Statistical analysis was performed by analysis of variance.Compared to baseline, cases showed significant improvements in seminal parameters and DNA fragmentation indexes after follicle-stimulating hormone therapy (all P fragmentation index and lower double strand breaks (P fragmentation, which in turn leads to increased pregnancy rates in infertile males undergoing in-vitro fertilization. In particular, double strand breaks (measured with γH2AX test) emerged as the most sensible parameter to follicle-stimulating hormone treatment in predicting reproductive outcome.

  9. Vibrating wire alignment technique

    CERN Document Server

    Xiao-Long, Wang; lei, Wu; Chun-Hua, Li

    2013-01-01

    Vibrating wire alignment technique is a kind of method which through measuring the spatial distribution of magnetic field to do the alignment and it can achieve very high alignment accuracy. Vibrating wire alignment technique can be applied for magnet fiducialization and accelerator straight section components alignment, it is a necessary supplement for conventional alignment method. This article will systematically expound the international research achievements of vibrating wire alignment technique, including vibrating wire model analysis, system frequency calculation, wire sag calculation and the relation between wire amplitude and magnetic induction intensity. On the basis of model analysis this article will introduce the alignment method which based on magnetic field measurement and the alignment method which based on amplitude and phase measurement. Finally, some basic questions will be discussed and the solutions will be given.

  10. Conjugation of benzylvanillin and benzimidazole structure improves DNA binding with enhanced antileukemic properties.

    Science.gov (United States)

    Al-Mudaris, Zena A; Majid, Aman S A; Ji, Dan; Al-Mudarris, Ban A; Chen, Shih-Hsun; Liang, Po-Huang; Osman, Hasnah; Jamal Din, Shah Kamal Khan; Abdul Majid, Amin M S

    2013-01-01

    Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy)-3-methoxybenzaldehyde) compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl)-2-(2-benzyloxy-3-methoxyphenyl)-1H-benzimidazole, 2XP, and (R) and (S)-1-(2-benzyloxy-3-methoxyphenyl)-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1), the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1) has weak anticancer activity even after it was combined with the benzimidazole (2MP), but after addition of another benzylvanillin structure (2XP), stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS) significantly improved the

  11. Conjugation of benzylvanillin and benzimidazole structure improves DNA binding with enhanced antileukemic properties.

    Directory of Open Access Journals (Sweden)

    Zena A Al-Mudaris

    Full Text Available Benzyl-o-vanillin and benzimidazole nucleus serve as important pharmacophore in drug discovery. The benzyl vanillin (2-(benzyloxy-3-methoxybenzaldehyde compound shows anti-proliferative activity in HL60 leukemia cancer cells and can effect cell cycle progression at G2/M phase. Its apoptosis activity was due to disruption of mitochondrial functioning. In this study, we have studied a series of compounds consisting of benzyl vanillin and benzimidazole structures. We hypothesize that by fusing these two structures we can produce compounds that have better anticancer activity with improved specificity particularly towards the leukemia cell line. Here we explored the anticancer activity of three compounds namely 2-(2-benzyloxy-3-methoxyphenyl-1H-benzimidazole, 2MP, N-1-(2-benzyloxy-3-methoxybenzyl-2-(2-benzyloxy-3-methoxyphenyl-1H-benzimidazole, 2XP, and (R and (S-1-(2-benzyloxy-3-methoxyphenyl-2, 2, 2-trichloroethyl benzenesulfonate, 3BS and compared their activity to 2-benzyloxy-3-methoxybenzaldehyde, (Bn1, the parent compound. 2XP and 3BS induces cell death of U937 leukemic cell line through DNA fragmentation that lead to the intrinsic caspase 9 activation. DNA binding study primarily by the equilibrium binding titration assay followed by the Viscosity study reveal the DNA binding through groove region with intrinsic binding constant 7.39 µM/bp and 6.86 µM/bp for 3BS and 2XP respectively. 2XP and 3BS showed strong DNA binding activity by the UV titration method with the computational drug modeling showed that both 2XP and 3BS failed to form any electrostatic linkages except via hydrophobic interaction through the minor groove region of the nucleic acid. The benzylvanillin alone (Bn1 has weak anticancer activity even after it was combined with the benzimidazole (2MP, but after addition of another benzylvanillin structure (2XP, stronger activity was observed. Also, the combination of benzylvanillin with benzenesulfonate (3BS significantly improved

  12. Engagement, Alignment, and Rigor as Vital Signs of High-Quality Instruction: A Classroom Visit Protocol for Instructional Improvement and Research

    Science.gov (United States)

    Early, Diane M.; Rogge, Ronald D.; Deci, Edward L.

    2014-01-01

    This paper investigates engagement (E), alignment (A), and rigor (R) as vital signs of high-quality teacher instruction as measured by the EAR Classroom Visit Protocol, designed by the Institute for Research and Reform in Education (IRRE). Findings indicated that both school leaders and outside raters could learn to score the protocol with…

  13. Improved Collision Detection Algorithm Based on Axis- Aligned Bounding Box%基于改进轴向包围盒的碰撞检测算法

    Institute of Scientific and Technical Information of China (English)

    孙毅刚; 段晓晔; 张红颖

    2011-01-01

    Airport emergency rescue is an important field of civil aviation, and the emergency rescue in the virtual scene can save resources largely.In order to improve the authenticity and accuracy of collision detection in the virtual scene, this paper proposed a collision deteetion algorithm based on feature - triangle.By adding the feature elements of vertex, edges and face in the triangle, feature -triangle was formed to solve the issue of queries in the triangulated model; then axis - aligned bounding box combined with feature - triangle was used to complete collision detection,and accurate intersection calculation was performed in the final stage of the algorithm to provide more collision informarion for the collision response.Experimental results show that the proposed algorithm can save time and has better performance.%研究机场应急救援是民航领域的问题.为防止机场地面车辆拥堵,要求在虚拟场景下的应急演练可全方位测试系统.为增强虚拟演练场景中碰撞检测的真实性与精确性,提出了一种基于特征三角形的碰撞检测算法.在基于三角形的模型中,通过在三角形中添加特征元素(点、边、面)形成特征三角形,利用特征三角形可以有效解决重复查询;通过轴向包围盒结合特征三角形,更好地完成碰撞检测,最后进行精确求交计算,为碰撞响应提供更多的碰撞信息.实验结果表明,算法可以缩短计算时间,提高检测精度,具有实际指导价值.

  14. Accelerated large-scale multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Lloyd Scott

    2011-12-01

    Full Text Available Abstract Background Multiple sequence alignment (MSA is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware. Results We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor. Conclusions Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from http://dna.cs.byu.edu/msa/.

  15. Alignment-free phylogenetics and population genetics.

    Science.gov (United States)

    Haubold, Bernhard

    2014-05-01

    Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

    Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

  17. Improving molecular detection of fungal DNA in formalin-fixed paraffin-embedded tissues: comparison of five tissue DNA extraction methods using panfungal PCR.

    Science.gov (United States)

    Muñoz-Cadavid, C; Rudd, S; Zaki, S R; Patel, M; Moser, S A; Brandt, M E; Gómez, B L

    2010-06-01

    DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissues is difficult and requires special protocols in order to extract small amounts of DNA suitable for amplification. Most described methods report an amplification success rate between 60 and 80%; therefore, there is a need to improve molecular detection and identification of fungi in FFPE tissue. Eighty-one archived FFPE tissues with a positive Gomori methenamine silver (GMS) stain were evaluated using five different commercial DNA extraction kits with some modifications. Three different panfungal PCR assays were used to detect fungal DNA, and two housekeeping genes were used to assess the presence of amplifiable DNA and to detect PCR inhibitors. The sensitivities of the five extraction protocols were compared, and the quality of DNA detection (calculated for each kit as the number of housekeeping gene PCR-positive samples divided by the total number of samples) was 60 to 91% among the five protocols. The efficiencies of the three different panfungals used (calculated as the number of panfungal-PCR-positive samples divided by the number of housekeeping gene PCR-positive samples) were 58 to 93%. The panfungal PCR using internal transcribed spacer 3 (ITS3) and ITS4 primers yielded a product in most FFPE tissues. Two of the five DNA extraction kits (from TaKaRa and Qiagen) showed similar and promising results. However, one method (TaKaRa) could extract fungal DNA from 69 of the 74 FFPE tissues from which a housekeeping gene could be amplified and was also cost-effective, with a nonlaborious protocol. Factors such as sensitivity, cost, and labor will help guide the selection of the most appropriate method for the needs of each laboratory.

  18. Improved rolling circle amplification (RCA) of hepatitis B virus (HBV) relaxed-circular serum DNA (RC-DNA).

    Science.gov (United States)

    Martel, Nora; Gomes, Selma A; Chemin, Isabelle; Trépo, Christian; Kay, Alan

    2013-11-01

    For functional analysis of HBV isolates, epidemiological studies and correct identification of recombinant genomes, the amplification of complete genomes is necessary. A method for completely in vitro amplification of full-length HBV genomes starting from serum RC-DNA is described. This uses in vitro completion/ligation of plus-strand HBV RC-DNA and amplification using Rolling-Circle Amplification, eventually followed by a genomic PCR. The method can amplify complete HBV genomes from sera with viral loads ranging from >1.0E+8 IU/ml down to 1.0E+3 IU/ml. The method can be applied to archived sera that have undergone long-term storage or to archived DNA serum extracts. The genomes can easily be cloned. HBV genotypes A-G can all be amplified with no apparent problems. A recombinant subgenotype A3/genotype E genome was identified and fully sequenced.

  19. Effects of Sperm DNA Fragmentation on Semen Parameters and ICSI Outcome Determined by an Improved SCD Test,Halosperm

    Directory of Open Access Journals (Sweden)

    Asuman Demiroglu Zergeroğlu

    2010-01-01

    Full Text Available Background: Sperm DNA fragmentation is known as an important cause of male infertility.The influence of sperm DNA damage on reproductive potential has been subject of many studiesindicating various results and remaining the subject controversial. In this study, we investigateddifferences of the semen parameters and intracytoplasmic sperm injection (ICSI outcome accordingto sperm DNA fragmentation levels (DFLs of patients.Materials and Methods: The DFLs were determined by Halosperm, a new improved spermchromatin dispersion (SCD test. Patients were grouped as low DNA fragmentation group (LFG≤30% and high fragmentation group (HFG >30%.Results: Our analysis showed that semen parameters including concentration of untreated spermand motility of prepared semen were low in HGF, whereas other parameters were not different.Sperm DNA fragmentation levels decreased in both groups after semen preparation by densitygradient technique.Conclusion: No difference was detected on ICSI outcomes (fertilization, embryo development,embryo cleavage, embryo quality and pregnancy rates between two group.

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and J. Pivarski

    2011-01-01

    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  1. Improved high-throughput DNA fragment analyzer employing horizontal ultrathin gel electrophoresis

    Science.gov (United States)

    Brumley, Robert L., Jr.; Luckey, John A.

    1996-04-01

    We are currently developing a significantly improved gel electrophoresis and detection system that will allow more than an order of magnitude enhancement in the speed of DNA fragment analysis. This system is based upon the technique of horizontal ultrathin gel electrophoresis (HUGE) which employs denaturing polyacrylamide gels that are 75 microns thick. Because of the thinness of the gel, very high electric field strengths may be applied without deleterious thermal effects on resolution. Our proprietary fluorescence detector that scans the gel during electrophoresis allows for the simultaneous detection of up to four fluorophores. Because of the efficiency of the system of light collection, the gel can be scanned at speeds fast enough to generate high resolution gel images despite the high speed of separations. In addition, we are able to increase sample density by collecting 500 datapoints across the width of the gel. The resulting instrument has the capability to separate and resolve single-stranded DNA molecules that are between 25 and 300 bases in length from each of 60 lanes in less than 45 minutes. With the advent of 96 lane gels and attendant automation, this instrument will have the ability to analyze 18,432 genotypes per day.

  2. Locus Reference Genomic sequences: An improved basis for describing human DNA variants

    KAUST Repository

    Dalgleish, Raymond

    2010-04-15

    As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

  3. Directed Molecular Evolution Improves the Immunogenicity and Protective Efficacy of a Venezuelan Equine Encephalitis Virus DNA Vaccine

    Science.gov (United States)

    2009-05-01

    developed by serial passage of the virulent Trinidad donkey strain in cultures of guinea pig heart cells [5]. Although TC-83 is gen- erally safe and...vaccinated with plasmid DNA 18]. In addition, improvements in the immunogenicity and cross- eactivity of DNA vaccine candidates for HIV -1 and the malaria...antibodies to the VEEV E2 protein. Consequently, we used pools of the day 63 pre-challenge sera from each vaccination group of the pathogen challenge

  4. Instructional Alignment under No Child Left Behind

    Science.gov (United States)

    Polikoff, Morgan S.

    2012-01-01

    The alignment of instruction with the content of standards and assessments is the key mediating variable separating the policy of standards-based reform (SBR) from the outcome of improved student achievement. Few studies have investigated SBR's effects on instructional alignment, and most have serious methodological limitations. This research uses…

  5. Selection of normal spermatozoa with a vacuole-free head (x6300) improves selection of spermatozoa with intact DNA in patients with high sperm DNA fragmentation rates.

    Science.gov (United States)

    Hammoud, I; Boitrelle, F; Ferfouri, F; Vialard, F; Bergere, M; Wainer, B; Bailly, M; Albert, M; Selva, J

    2013-06-01

    Intracytoplasmic morphologically selected sperm injection (IMSI, 6300× magnification with Nomarski contrast) of a normal spermatozoon with a vacuole-free head could improve the embryo's ability to grow to the blastocyst stage and then implant. However, the most relevant indications for IMSI remain to be determined. To evaluate the potential value of IMSI for patients with a high degree of sperm DNA fragmentation (n = 8), different types of spermatozoa were analysed in terms of DNA fragmentation. Motile normal spermatozoa with a vacuole-free head selected at 6300× magnification had a significantly lower mean DNA fragmentation rate (4.1 ± 1.1%, n = 191) than all other types of spermatozoa: non-selected spermatozoa (n = 8000; 26.1 ± 1.5% versus 4.1 ± 1.1%; P sperm DNA fragmentation rates, selection of normal spermatozoa with a vacuole-free head (6300×) yields the greatest likelihood of obtaining spermatozoa with non-fragmented DNA.

  6. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

  7. An improved method with a wider applicability to isolate plant mitochondria for mtDNA extraction

    OpenAIRE

    2015-01-01

    Background Mitochondria perform a principal role in eukaryotic cells. Mutations in mtDNA can cause mitochondrial dysfunction and are frequently associated with various abnormalities during plant development. Extraction of plant mitochondria and mtDNA is the basic requirement for the characterization of mtDNA mutations and other molecular studies. However, currently available methods for mitochondria isolation are either tissue specific or species specific. Extracted mtDNA may contain substant...

  8. Microbial DNA extraction from intestinal biopsies is improved by avoiding mechanical cell disruption

    Science.gov (United States)

    Carbonero, Franck; Nava, Gerardo M.; Benefiel, Ann C.; Greenberg, Eugene; Gaskins, H. Rex

    2011-01-01

    Currently, standard protocols for microbial DNA extraction from intestinal tissues do not exist. We assessed the efficiency of a commercial kit with and without mechanical disruption. Better quality DNA was obtained without mechanical disruption. Thus, it appears that bead-beating is not required for efficient microbial DNA extraction from intestinal biopsies. PMID:21820015

  9. TREHALOSE-BASED ADDITIVE IMPROVED INTER-PRIMER BINDING SITE REACTIONS FOR DNA ISOLATED FROM RECALCITRANT PLANTS

    Directory of Open Access Journals (Sweden)

    Veronika Lancíková

    2014-02-01

    Full Text Available Trehalose-based (TBT-PAR additive was tested in order to optimize PCR amplification for DNA isolated from recalcitrant plants. Retrotransposon-based inter-primer binding site reactions were significantly improved with TBT-PAR solution using genomic DNA isolated from flax (Linum usitatissimum L., genotypes Kyivskyi, Bethune grown in radio-contaminated and non-radioactive remediated Chernobyl experimental fields. Additionally, similar improvements were observed using 19 recalcitrant genotypes of maize (Zea mays L. and three genotypes of yacon (Smallanthus sonchifolius, Poepp. et Endl., genotypes PER05, ECU45, BOL22 grown in standard field conditions.

  10. ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Kim Taeho

    2010-09-01

    Full Text Available Abstract Background There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC environment with a greatly extended data storage capacity. Results We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA. The new editing option and the graphical user interface (GUI provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets. Conclusions ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1 the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2 Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3 Support for both single PC and distributed cluster systems.

  11. Multiple data sources improve DNA-based mark-recapture population estimates of grizzly bears.

    Science.gov (United States)

    Boulanger, John; Kendall, Katherine C; Stetz, Jeffrey B; Roon, David A; Waits, Lisette P; Paetkau, David

    2008-04-01

    A fundamental challenge to estimating population size with mark-recapture methods is heterogeneous capture probabilities and subsequent bias of population estimates. Confronting this problem usually requires substantial sampling effort that can be difficult to achieve for some species, such as carnivores. We developed a methodology that uses two data sources to deal with heterogeneity and applied this to DNA mark-recapture data from grizzly bears (Ursus arctos). We improved population estimates by incorporating additional DNA "captures" of grizzly bears obtained by collecting hair from unbaited bear rub trees concurrently with baited, grid-based, hair snag sampling. We consider a Lincoln-Petersen estimator with hair snag captures as the initial session and rub tree captures as the recapture session and develop an estimator in program MARK that treats hair snag and rub tree samples as successive sessions. Using empirical data from a large-scale project in the greater Glacier National Park, Montana, USA, area and simulation modeling we evaluate these methods and compare the results to hair-snag-only estimates. Empirical results indicate that, compared with hair-snag-only data, the joint hair-snag-rub-tree methods produce similar but more precise estimates if capture and recapture rates are reasonably high for both methods. Simulation results suggest that estimators are potentially affected by correlation of capture probabilities between sample types in the presence of heterogeneity. Overall, closed population Huggins-Pledger estimators showed the highest precision and were most robust to sparse data, heterogeneity, and capture probability correlation among sampling types. Results also indicate that these estimators can be used when a segment of the population has zero capture probability for one of the methods. We propose that this general methodology may be useful for other species in which mark-recapture data are available from multiple sources.

  12. Improved recovery of bisulphite-treated cell-free DNA in plasma

    DEFF Research Database (Denmark)

    Pedersen, Inge Søkilde; Krarup, H.B.; Thorlacius-Ussing, O.;

    Detection of cell-free methylated DNA in plasma is a promising tool for tumour diagnosis and monitoring. Due to the very low amount of cell-free DNA in plasma, sensitivity of the detection methods are of utmost importance. The vast majority of currently available methods for analysing DNA...... of PCR amplifying methylated and umethylated MEST. This procedure allows low levels of DNA to be easily and reliably analysed, a prerequisite for the clinical usefulness of cell-free methylated DNA detection in plasma........ The analytical sensitivity of the method was analysed by detection of methylated/unmethylated copies of the imprinted (and hemimethylated) gene MEST in a dilution series of plasma DNA. The method is based on an accelerated deamination step and magnetic silica purification of DNA in combination with a first round...

  13. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Science.gov (United States)

    He, Xin; Ling, Xu; Sinha, Saurabh

    2009-03-01

    Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs) and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs) and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i) the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii) binding sites in distal bound sequences (relative to transcription start sites) tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context.

  14. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Directory of Open Access Journals (Sweden)

    Xin He

    2009-03-01

    Full Text Available Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii binding sites in distal bound sequences (relative to transcription start sites tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis, ready to be applied in a broad biological context.

  15. cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer

    Directory of Open Access Journals (Sweden)

    Jesionek-Kupnicka Dorota

    2009-08-01

    Full Text Available Abstract Background Recently published data showed discrepancies beteween P53 cDNA and DNA sequencing in glioblastomas. We hypothesised that similar discrepancies may be observed in other human cancers. Methods To this end, we analyzed 23 colorectal cancers for P53 mutations and gene expression using both DNA and cDNA sequencing, real-time PCR and immunohistochemistry. Results We found P53 gene mutations in 16 cases (15 missense and 1 nonsense. Two of the 15 cases with missense mutations showed alterations based only on cDNA, and not DNA sequencing. Moreover, in 6 of the 15 cases with a cDNA mutation those mutations were difficult to detect in the DNA sequencing, so the results of DNA analysis alone could be misinterpreted if the cDNA sequencing results had not also been available. In all those 15 cases, we observed a higher ratio of the mutated to the wild type template by cDNA analysis, but not by the DNA analysis. Interestingly, a similar overexpression of P53 mRNA was present in samples with and without P53 mutations. Conclusion In terms of colorectal cancer, those discrepancies might be explained under three conditions: 1, overexpression of mutated P53 mRNA in cancer cells as compared with normal cells; 2, a higher content of cells without P53 mutation (normal cells and cells showing K-RAS and/or APC but not P53 mutation in samples presenting P53 mutation; 3, heterozygous or hemizygous mutations of P53 gene. Additionally, for heterozygous mutations unknown mechanism(s causing selective overproduction of mutated allele should also be considered. Our data offer new clues for studying discrepancy in P53 cDNA and DNA sequencing analysis.

  16. Improvement in fetal DNA extraction from maternal plasma. Evaluation of the NucliSens Magnetic Extraction system and the QIAamp DSP Virus Kit in comparison with the QIAamp DNA Blood Mini Kit

    DEFF Research Database (Denmark)

    Clausen, Frederik Banch; Krog, Grethe Risum; Rieneck, Klaus

    2007-01-01

    Prenatal diagnostic assays have been developed using free fetal DNA circulating in the maternal blood of pregnant women. Efficient DNA extraction is crucial for a robust analysis. To improve fetal DNA yield, we tested two manual extraction methods--the NucliSens Magnetic Extraction (NMAG) system...... and the QIAamp DSP Virus Kit (QDSP)--against our current standard method, the widely used QIAamp DNA Blood Mini Kit (QDNA)....

  17. A pillow of 8 cm height did not improve laryngeal view and alignment of airway axes but increased anesthesiologist discomfort compared to a pillow of 4 cm height during tracheal intubation in adult patients

    Science.gov (United States)

    Hong, Hyo Ju; Kim, Sung Hoon; Hwang, Jung Won; Lee, Hyung Chul

    2016-01-01

    Background Neck flexion by head elevation using an 8 to 10 cm thick pillow and head extension has been suggested to align the laryngeal, pharyngeal and oral axis and facilitate tracheal intubation. Presently, the laryngeal view and discomfort for tracheal intubation were evaluated according to two different degrees of head elevation in adult patients. Methods This prospective randomized, controlled study included 50 adult patients aged 18 to 90 years. After induction of anesthesia, the Cormack Lehane grade was evaluated in 25 patients using a direct laryngoscope while the patient's head was elevated with a 4 cm pillow (4 cm group) and then an 8 cm pillow (8 cm group). In the other 25 patients, the grades were evaluated in the opposite sequence and tracheal intubation was performed. The success rate and anesthesiologist's discomfort score for tracheal intubation, and laryngeal, pharyngeal and oral axes were assessed. Results There were no differences in the laryngeal view and success rate for tracheal intubation between the two groups. The discomfort score during tracheal intubation was higher in the 8 cm group when the patient's head was elevated 4 cm first and then 8 cm. The alignment of laryngeal, pharyngeal and oral axes were not different between the two degrees of head elevation. Conclusions A pillow of 8 cm height did not improve laryngeal view and alignment of airway axes but increased the anesthesiologist discomfort, compared to a pillow of 4 cm height, during tracheal intubation in adult patients. PMID:27066204

  18. Improvement in efficacy of DNA vaccine encoding HIV-1 Vif by LIGHT gene adjuvant.

    Science.gov (United States)

    Du, Jiani; Wu, Xiaoyu; Long, Fengying; Wen, Jiejun; Hao, Wenli; Chen, Ran; Kong, Xiaobo; Qian, Min; Jiang, Wenzheng

    2013-02-01

    DNA vaccine can induce the prolonged immune responses against the encoded antigen with the appropriate adjuvant. To study the immunogenicity of the HIV-1 vif DNA vaccine in inducing the humoral and cellular immune responses and the immunoadjuvant effect of LIGHT, which is a member of TNF superfamily and can stimulate the proliferation of naïve T cells as a co-stimulatory molecule, DNA vaccine plasmid pcDNA-Vif was constructed by inserting HIV-1 vif gene into the downstream of CMV promoter in eukaryotic expression vector pcDNA3.1(+). In vitro expression of HIV-1 Vif in pcDNA-Vif-transfected HeLa cells was confirmed in transcriptional and protein level by RT-PCR and Western blot, respectively. After BALB/c mice were injected muscularly with DNA vaccines for three times, the specific immune responses were analyzed. The data showed that anti-Vif antibody response, Vif-specific T cell proliferation, and CTL activities were induced in the mice that were inoculated with HIV-1 vif DNA vaccine plasmid. Interestingly, stronger humoral and cellular immune responses were detected in mice that were immunized with plasmid pcDNA-Vif and pcDNA-LIGHT together compared to the single immunization with plasmid pcDNA-Vif alone. Together, the results of the study suggest that candidate HIV-1 DNA vaccine can elicit HIV-1 Vif-specific immune responses in mice and that LIGHT plays the role of immunoadjuvant in co-immunization with DNA vaccine.

  19. Improving Business Investment Confidence in Culture-Aligned Indigenous Economies in Remote Australian Communities: A Business Support Framework to Better Inform Government Programs

    Directory of Open Access Journals (Sweden)

    Ann E. Fleming

    2015-06-01

    Full Text Available There is significant evidence that culture-aligned economies are more effective in engaging remote-living Indigenous Australians in work long-term. Despite this evidence, governments remain resistant to investing substantially in these economies, with the result that low employment rates persist. This article argues that governmental systems of organisation are not designed to support non-mainstream economies and this position is unlikely to change. Similarly, the commercial sector lacks confidence that investing in culture-aligned economies will generate financial returns. This article presents a localised, pragmatic approach to Indigenous business support that works within existing systems of government, business and culture. Most unsuccessful programs fail to recognise the full suite of critical factors for sustained market engagement by both business and Indigenous people. This article reports on work to bring all critical factors together into a business support framework to inform the design and implementation of an aquaculture development program in a remote Indigenous Australian community.

  20. Ontology alignment with OLA

    OpenAIRE

    Euzenat, Jérôme; Loup, David; Touzani, Mohamed; Valtchev, Petko

    2004-01-01

    euzenat2004d; International audience; Using ontologies is the standard way to achieve interoperability of heterogeneous systems within the Semantic web. However, as the ontologies underlying two systems are not necessarily compatible, they may in turn need to be aligned. Similarity-based approaches to alignment seems to be both powerful and flexible enough to match the expressive power of languages like OWL. We present an alignment tool that follows the similarity-based paradigm, called OLA. ...

  1. Long-term bezafibrate treatment improves skin and spleen phenotypes of the mtDNA mutator mouse.

    Directory of Open Access Journals (Sweden)

    Lloye M Dillon

    Full Text Available Pharmacological agents, such as bezafibrate, that activate peroxisome proliferator-activated receptors (PPARs and PPAR γ coactivator-1α (PGC-1α pathways have been shown to improve mitochondrial function and energy metabolism. The mitochondrial DNA (mtDNA mutator mouse is a mouse model of aging that harbors a proofreading-deficient mtDNA polymerase γ. These mice develop many features of premature aging including hair loss, anemia, osteoporosis, sarcopenia and decreased lifespan. They also have increased mtDNA mutations and marked mitochondrial dysfunction. We found that mutator mice treated with bezafibrate for 8-months had delayed hair loss and improved skin and spleen aging-like phenotypes. Although we observed an increase in markers of fatty acid oxidation in these tissues, we did not detect a generalized increase in mitochondrial markers. On the other hand, there were no improvements in muscle function or lifespan of the mutator mouse, which we attributed to the rodent-specific hepatomegaly associated with fibrate treatment. These results showed that despite its secondary effects in rodent's liver, bezafibrate was able to improve some of the aging phenotypes in the mutator mouse. Because the associated hepatomegaly is not observed in primates, long-term bezafibrate treatment in humans could have beneficial effects on tissues undergoing chronic bioenergetic-related degeneration.

  2. Improving efficiency and reliability of environmental DNA analysis for silver carp

    Science.gov (United States)

    Amberg, Jon J.; McCalla, S. Grace; Monroe, Emy; Lance, Richard; Baerwaldt, Kelly; Gaikowski, Mark P.

    2015-01-01

    Natural resource agencies have established surveillance programs which use environmental DNA (eDNA) for the early detection of bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix before they establish populations within the Great Lakes. This molecular monitoring technique must be highly accurate and precise for confident interpretation and also efficient, both in detection threshold and cost. Therefore, we compared two DNA extraction techniques and compared a new quantitative PCR (qPCR) assay with the conventional PCR (cPCR) assay used by monitoring programs. Both the qPCR and cPCR assays were able to amplify the DNA of silver carp present in environmental samples taken from locations where mixed populations of bigheaded carps existed. However, the qPCR assay had substantially fewer PCR positive samples which were subsequently determined not to contain DNA of bigheaded carps than the cPCR assay. Additionally, the qPCR assay was able to amplify the DNA of bigheaded carps even in the presence of inhibitors that blocked amplification with cPCR. Also, the selection of an appropriate DNA extraction method can significantly alter the efficiency of eDNA surveillance programs by lowering detection limits and by decreasing costs associated with sample processing. The results reported herein are presently being incorporated into eDNA surveillance programs to decrease the costs, increase DNA yield and increase the confidence that assays are amplifying the target DNA. These results are critical to enhancing our ability to accurately and confidently interpret the results reported from monitoring programs using eDNA for early detection of invasive species.

  3. Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis.

    Directory of Open Access Journals (Sweden)

    Irvan Luhung

    Full Text Available As bioaerosol research attracts increasing attention, there is a need for additional efforts that focus on method development to deal with different environmental samples. Bioaerosol environmental samples typically have very low biomass concentrations in the air, which often leaves researchers with limited options in choosing the downstream analysis steps, especially when culture-independent methods are intended.This study investigates the impacts of three important factors that can influence the performance of culture-independent DNA-based analysis in dealing with bioaerosol environmental samples engaged in this study. The factors are: 1 enhanced high temperature sonication during DNA extraction; 2 effect of sampling duration on DNA recoverability; and 3 an alternative method for concentrating composite samples. In this study, DNA extracted from samples was analysed using the Qubit fluorometer (for direct total DNA measurement and quantitative polymerase chain reaction (qPCR.The findings suggest that additional lysis from high temperature sonication is crucial: DNA yields from both high and low biomass samples increased up to 600% when the protocol included 30-min sonication at 65°C. Long air sampling duration on a filter media was shown to have a negative impact on DNA recoverability with up to 98% of DNA lost over a 20-h sampling period. Pooling DNA from separate samples during extraction was proven to be feasible with margins of error below 30%.

  4. Improving herpetological surveys in eastern North America using the environmental DNA method.

    Science.gov (United States)

    Lacoursière-Roussel, Anaïs; Dubois, Yohann; Normandeau, Eric; Bernatchez, Louis

    2016-11-01

    Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

  5. DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae.

    Directory of Open Access Journals (Sweden)

    Kurt Jordaens

    Full Text Available The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera. The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ / Maximum Likelihood (ML analysis, and using SpeciesIdentifier. Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low ( 0.03 maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02, and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.

  6. Paricalcitol may improve oxidative DNA damage on experimental amikacin-induced nephrotoxicity model.

    Science.gov (United States)

    Bulut, Gulay; Basbugan, Yildiray; Ari, Elif; Erten, Remzi; Bektas, Havva; Alp, Hamit Hakan; Bayram, Irfan

    2016-06-01

    This study aimed to investigate the possible protective effect of paricalcitol on experimental amikacin-induced nephrotoxicity model in rats. Wistar albino rats (n = 32) were allocated into four equal groups of eight each, the control (Group C), paricalcitol (Group P), amikacin-induced nephrotoxicity (Group A), and paricalcitol-treated amikacin-induced nephrotoxicity (Group A + P) groups. Paricalcitol was given intra-peritoneally at a dose of 0.4 μg/kg/d for 5 consecutive days prior to induction of amikacin-induced nephrotoxicity. Intra-peritoneal amikacin (1.2 g/kg) was used to induce nephrotoxicity at day 4. Renal function parameters, oxidative stress biomarkers, oxidative DNA damage (8-hydroxy-2'-deoxyguanosine/deoxyguanosine ratio), kidney histology, and vascular endothelial growth factor (VEGF) immunoexpression were determined. Group A + P had lower mean fractional sodium excretion (p < 0.001) as well as higher creatinine clearance (p = 0.026) than the amikacin group (Group A). Renal tissue malondialdehyde levels (p = 0.035) and serum 8-hydroxy-2'-deoxyguanosine/deoxyguanosine ratio (8-OHdG/dG ratio) (p < 0.001) were significantly lower; superoxide dismutase (p = 0.024) and glutathione peroxidase (p = 0.007) activities of renal tissue were significantly higher in group A + P than in group A. The mean scores of tubular necrosis (p = 0.024), proteinaceous casts (p = 0.038), medullary congestion (p = 0.035), and VEGF immunoexpression (p = 0.018) were also lower in group A + P when compared with group A. This study demonstrates the protective effect of paricalcitol in the prevention of amikacin-induced nephrotoxicity in an experimental model. Furthermore, it is the first study to demonstrate that paricalcitol improves oxidative DNA damage in an experimental acute kidney injury model.

  7. Improved photoluminescence of vertically aligned ZnO nanorods grown on BaSrTiO{sub 3} by pulsed laser deposition

    Energy Technology Data Exchange (ETDEWEB)

    Varanasi, C V [University of Dayton Research Institute, Dayton, OH 45469 (United States); Leedy, K D; Tomich, D H [Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433 (United States); Subramanyam, G [University of Dayton, Dayton, OH 45469 (United States); Look, D C, E-mail: Chakrapani.Varanasi@wpafb.af.mi [Semiconductor Research Center, Wright State University, Dayton, OH 45435 (United States)

    2009-09-23

    ZnO nanorods were grown on a variety of substrates such as Si, SiO{sub 2}/Si and sapphire in a large-area pulsed laser deposition chamber designed for sensor device fabrication. Processing conditions were optimized to grow ZnO nanorods with or without seed layers. Au, Cr and BaSrTiO{sub 3} (BST) seed layers were investigated to compare their effects on the diameter and orientation of ZnO nanorods. ZnO nanorods were observed to align better when grown on sapphire, Cr or BST seed layers as compared to Au or Si layers. The highest quality nanorods were those grown on BST seed layers, as shown by 4 K photoluminescence donor-bound-exciton linewidths of only 0.5 meV.

  8. Organic extraction of bone lysates improves DNA purification with silica beads.

    Science.gov (United States)

    Desmyter, Stijn; De Cock, Greet; Moulin, Sabine; Noël, Fabrice

    2017-04-01

    In our standard protocol for DNA extraction from skeletal remains of unidentified bodies, bone lysates resulting from decalcification and Proteinase K treatment were purified with the DNA IQ™ Casework Pro Kit for Maxwell(®)16 automate (Promega, WI). Despite its success in the majority of cases, the DNA purification with paramagnetic silica beads failed in some challenging samples. This failure in DNA recovery was often associated with filter clogging during the required volume reduction of the lysate to enable loading on the automate. Two modifications to the standard method were tested for a more efficient filtering and purification. Adding collagenase to the lysate reduced the filter lead time but did not enhance DNA yield, while organic extraction of the crude lysate solved the filter clogging and resulted in successful DNA purification. The modified method in which a phenol treated lysate was loaded on the automate resulted in successful STR-profiling of the skeletal remains of all 13 unidentified bodies tested, which showed a wide variety in post mortem interval and preservation conditions. The variation in DNA yield between the 28 samples tested showed the importance of bone type selection and multiple sampling in successful STR-profiling of skeletal remains. Despite the disadvantages inherent to phenol, the organic extraction of crude bone lysates enhanced the efficiency of DNA purification with paramagnetic silica beads. The combined method of organic extraction and purification with silica beads resulted in STR-profiling of challenging bone samples.

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

    The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  11. Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques.

    Science.gov (United States)

    Xu, Chao; Dong, Wenpan; Shi, Shuo; Cheng, Tao; Li, Changhao; Liu, Yanlei; Wu, Ping; Wu, Hongkun; Gao, Peng; Zhou, Shiliang

    2015-11-01

    A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400-500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.

  12. SPEAR3 Construction Alignment

    Energy Technology Data Exchange (ETDEWEB)

    LeCocq, Catherine; Banuelos, Cristobal; Fuss, Brian; Gaudreault, Francis; Gaydosh, Michael; Griffin, Levirt; Imfeld, Hans; McDougal, John; Perry, Michael; Rogers,; /SLAC

    2005-08-17

    An ambitious seven month shutdown of the existing SPEAR2 synchrotron radiation facility was successfully completed in March 2004 when the first synchrotron light was observed in the new SPEAR3 ring, SPEAR3 completely replaced SPEAR2 with new components aligned on a new highly-flat concrete floor. Devices such as magnets and vacuum chambers had to be fiducialized and later aligned on girder rafts that were then placed into the ring over pre-aligned support plates. Key to the success of aligning this new ring was to ensure that the new beam orbit matched the old SPEAR2 orbit so that existing experimental beamlines would not have to be reoriented. In this presentation a pictorial summary of the Alignment Engineering Group's surveying tasks for the construction of the SPEAR3 ring is provided. Details on the networking and analysis of various surveys throughout the project can be found in the accompanying paper.

  13. Physics of Grain Alignment

    CERN Document Server

    Lazarian, A

    2000-01-01

    Aligned grains provide one of the easiest ways to study magnetic fields in diffuse gas and molecular clouds. How reliable our conclusions about the inferred magnetic field depends critically on our understanding of the physics of grain alignment. Although grain alignment is a problem of half a century standing recent progress achieved in the field makes us believe that we are approaching the solution of this mystery. I review basic physical processes involved in grain alignment and show why mechanisms that were favored for decades do not look so promising right now. I also discuss why the radiative torque mechanism ignored for more than 20 years looks right now the most powerful means of grain alignment.

  14. Bayesian Species Identification under the Multispecies Coalescent Provides Significant Improvements to DNA Barcoding Analyses.

    Science.gov (United States)

    Yang, Ziheng; Rannala, Bruce

    2017-03-09

    DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between-species divergence from within-species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single-locus or multi-loci sequence data. Here we use simulations to demonstrate three features of an MSC method implemented in the program bpp. First, we show that with one locus, MSC can accurately assign individuals to species without the need for arbitrarily determined distance thresholds (as required for barcoding methods). We provide an example in which no single threshold or barcoding gap exists that can be used to assign all specimens without incurring high error rates. Second, we show that bpp can identify cryptic species that may be mis-identified as a single species within the library, potentially improving the accuracy of barcoding libraries. Third, we show that taxon rarity does not present any particular problems for species assignments using bpp, and that accurate assignments can be achieved even when only one or a few loci are available. Thus, concerns that have been raised that MSC methods may have problems analyzing rare taxa (singletons) are unfounded. Currently barcoding methods enjoy a huge computational advantage over MSC methods and may be the only approach feasible for massively large datasets, but MSC methods may offer a more stringent test for species that are tentatively assigned by barcoding. This article is protected by copyright. All rights reserved.

  15. Improved sensitivity of circulating tumor DNA measurement using short PCR amplicons

    DEFF Research Database (Denmark)

    Andersen, Rikke Fredslund; Spindler, Karen-Lise Garm; Brandslund, Ivan

    2015-01-01

    , however, presents a number of challenges that require attention. The amount of DNA is low and highly fragmented and analyses need to be optimized accordingly. KRAS ARMS-qPCR assays with amplicon lengths of 120 and 85 base pairs, respectively, were compared using positive control material (PCR fragments......) and plasma samples from 46 colorectal cancer patients known to harbor a tumor KRAS mutation. KRAS mutated DNA was detected in significantly more clinical samples using the short amplicon assays compared to the long amplicon assays (74% vs. 61%, p=0.03). The level of mutated DNA in plasma was on average three...

  16. Better estimation of protein-DNA interaction parameters improve prediction of functional sites

    Directory of Open Access Journals (Sweden)

    O'Flanagan Ruadhan A

    2008-12-01

    Full Text Available Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment method designed to produce many such sequences. Results We analyzed low stringency SELEX data for E. coli Catabolic Activator Protein (CAP, and we show here that appropriate quantitative analysis improves our ability to predict in vitro affinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Roulet et al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones in the E. coli genome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related species S. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites. Conclusion We think that training binding site detection

  17. Bag model for DNA migration during pulsed-field electrophoresis.

    OpenAIRE

    Chu, G

    1991-01-01

    A model for pulsed-field electrophoresis was developed by picturing large DNA as a deformable "bag" that (i) moves with limiting mobility in a continuous electric field, (ii) adopts an orientation aligned with the field direction, and (iii) reorients after a change in field direction in a size-dependent manner. The model correctly predicted the resolution of large DNA in a pulsed field including the surprising phenomena of mobility inversion, lateral band spreading, and improved resolution fo...

  18. Electroporation mediated DNA vaccination directly to a mucosal surface results in improved immune responses

    OpenAIRE

    Kichaev, Gleb; Mendoza, Janess M; Amante, Dinah; Smith, Trevor RF; McCoy, Jay R; Sardesai, Niranjan Y.; Kate E. Broderick

    2013-01-01

    In vivo electroporation (EP) has been shown to be a highly efficient non-viral method for enhancing DNA vaccine delivery and immunogenicity, when the site of immunization is the skin or muscle of animals and humans. However, the route of entry for many microbial pathogens is via the mucosal surfaces of the human body. We have previously reported on minimally invasive, surface and contactless EP devices for enhanced DNA delivery to dermal tissue. Robust antibody responses were induced followin...

  19. Technical note: improved DNA extraction from ancient bones using silica-based spin columns.

    Science.gov (United States)

    Yang, D Y; Eng, B; Waye, J S; Dudar, J C; Saunders, S R

    1998-04-01

    We describe a simple method for extracting polymerase chain reaction-amplifiable DNA from ancient bones without the use of organic solvents. Bone powders are digested with proteinase K, and the DNA is purified directly using silica-based spin columns (QIAquick3, QIAGEN). The efficiency of this protocol is demonstrated using human bone samples ranging in age from 15 to 5,000 years old.

  20. Development of Well-Aligned TiO2 Nanotube Arrays to Improve Electron Transport in Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Kyung-Ho Chung

    2012-01-01

    Full Text Available We fabricated well-aligned one-dimensional (1-D titania nanotubes (TNT on transparent conducting oxide (TCO by anodization of Ti foil. Different lengths of TNTs were prepared by varying the applied potential (70 V time, and we investigated the performance of these TNTs in dye-sensitized solar cells (DSSCs, transplanted onto a 6 μm TNP adhesion layer. The fabricated TNTs arrays (length 15 μm photoelectrode showed 24% increased efficiency compared to the TNP photoelectrode of 17 μm thickness. We further investigated the performances of DSSCs for the TNTs (1 wt% incorporated TNP photoelectrode and obtained 22% increased efficiency. The increased efficiency of the pure TNTs arrays and TNT-mixed TNP photoelectrodes was attributed to the directional electron movement of TNTs and light scattering effect of the TNT with the decreased rate of back electron transfer. The anodized and fabricated TNTs and DSSCs were characterized by X-ray diffraction (XRD, scanning electron microscopy (SEM, transmission electron microscope (TEM, and electrochemical impedance spectroscopy (EIS.

  1. An Improved DNA Extraction Method for Efficient and Quantitative Recovery of Phytoplankton Diversity in Natural Assemblages.

    Directory of Open Access Journals (Sweden)

    Jian Yuan

    Full Text Available Marine phytoplankton are highly diverse with different species possessing different cell coverings, posing challenges for thoroughly breaking the cells in DNA extraction yet preserving DNA integrity. While quantitative molecular techniques have been increasingly used in phytoplankton research, an effective and simple method broadly applicable to different lineages and natural assemblages is still lacking. In this study, we developed a bead-beating protocol based on our previous experience and tested it against 9 species of phytoplankton representing different lineages and different cell covering rigidities. We found the bead-beating method enhanced the final yield of DNA (highest as 2 folds in comparison with the non-bead-beating method, while also preserving the DNA integrity. When our method was applied to a field sample collected at a subtropical bay located in Xiamen, China, the resultant ITS clone library revealed a highly diverse assemblage of phytoplankton and other micro-eukaryotes, including Archaea, Amoebozoa, Chlorophyta, Ciliphora, Bacillariophyta, Dinophyta, Fungi, Metazoa, etc. The appearance of thecate dinoflagellates, thin-walled phytoplankton and "naked" unicellular organisms indicates that our method could obtain the intact DNA of organisms with different cell coverings. All the results demonstrate that our method is useful for DNA extraction of phytoplankton and environmental surveys of their diversity and abundance.

  2. Galaxy alignments: An overview

    CERN Document Server

    Joachimi, Benjamin; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais

    2015-01-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  3. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    2009-01-01

    The alignment of shape data to a common mean before its subsequent processing is an ubiquitous step within the area shape analysis. Current approaches to shape analysis or, as more specifically considered in this work, shape classification perform the alignment in a fully unsupervised way......, not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two......-dimensional shapes from a two-class recognition problem....

  4. Coelostat and heliostat - Theory of alignment

    Science.gov (United States)

    Demianski, M.; Pasachoff, J. M.

    1984-06-01

    For perfectly aligned heliostats and coelostats tracking at the solar rate and half the solar rate, respectively, the solar beam has no translational motion. But, particularly in the field at eclipses, it is not possible to align heliostats and coelostats with infinite precision. The authors derive the effect of small misalignments on the translational motion of the beam, and give tables to allow the calculation of the accuracy to which the instruments must be mounted and adjusted to attain a desired accuracy over a given duration. Further, it is shown how to derive the necessary adjustments to improve alignment, given measurements of the tracking error.

  5. Fine-tuning structural RNA alignments in the twilight zone

    Directory of Open Access Journals (Sweden)

    Schirmer Stefanie

    2010-04-01

    Full Text Available Abstract Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

  6. Algorithms for Automatic Alignment of Arrays

    Science.gov (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

    1996-01-01

    Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

  7. Splign: algorithms for computing spliced alignments with identification of paralogs

    Directory of Open Access Journals (Sweden)

    Tatusova Tatiana

    2008-05-01

    Full Text Available Abstract Background The computation of accurate alignments of cDNA sequences against a genome is at the foundation of modern genome annotation pipelines. Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms. Results We describe a set of algorithms behind a tool called Splign for computing cDNA-to-Genome alignments. The algorithms include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a refined sequence alignment. In a series of tests, Splign has produced more accurate results than other tools commonly used to compute spliced alignments, in a reasonable amount of time. Conclusion Splign's ability to deal with various issues complicating the spliced alignment problem makes it a helpful tool in eukaryotic genome annotation processes and alternative splicing studies. Its performance is enough to align the largest currently available pools of cDNA data such as the human EST set on a moderate-sized computing cluster in a matter of hours. The duplications identification (compartmentization algorithm can be used independently in other areas such as the study of pseudogenes. Reviewers This article was reviewed by: Steven Salzberg, Arcady Mushegian and Andrey Mironov (nominated by Mikhail Gelfand.

  8. Unscented Kalman filter for SINS alignment

    Institute of Scientific and Technical Information of China (English)

    Zhou Zhanxin; Gao Yanan; Chen Jiabin

    2007-01-01

    In order to improve the filter accuracy for the nonlinear error model of strapdown inertial navigation system (SINS) alignment, Unscented Kalman Filter (UKF) is presented for simulation with stationary base and moving base of SINS alignment.Simulation results show the superior performance of this approach when compared with classical suboptimal techniques such as extended Kalman filter in cases of large initial misalignment.The UKF has good performance in case of small initial misalignment.

  9. Optimal Nonlinear Filter for INS Alignment

    Institute of Scientific and Technical Information of China (English)

    赵瑞; 顾启泰

    2002-01-01

    All the methods to handle the inertial navigation system (INS) alignment were sub-optimal in the past. In this paper, particle filtering (PF) as an optimal method is used for solving the problem of INS alignment. A sub-optimal two-step filtering algorithm is presented to improve the real-time performance of PF. The approach combines particle filtering with Kalman filtering (KF). Simulation results illustrate the superior performance of these approaches when compared with extended Kalman filtering (EKF).

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

  11. RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

    Science.gov (United States)

    Navarro, Elisabeth; Fabrègue, Olivier; Scorretti, Riccardo; Reboulet, Jérémy; Simonet, Pascal; Dawson, Lorna; Demanèche, Sandrine

    2015-12-01

    Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.

  12. Incremental Alignment Manifold Learning

    Institute of Scientific and Technical Information of China (English)

    Zhi Han; De-Yu Meng; Zong-Sen Xu; Nan-Nan Gu

    2011-01-01

    A new manifold learning method, called incremental alignment method (IAM), is proposed for nonlinear dimensionality reduction of high dimensional data with intrinsic low dimensionality. The main idea is to incrementally align low-dimensional coordinates of input data patch-by-patch to iteratively generate the representation of the entire dataset. The method consists of two major steps, the incremental step and the alignment step. The incremental step incrementally searches neighborhood patch to be aligned in the next step, and the alignment step iteratively aligns the low-dimensional coordinates of the neighborhood patch searched to generate the embeddings of the entire dataset. Compared with the existing manifold learning methods, the proposed method dominates in several aspects: high efficiency, easy out-of-sample extension, well metric-preserving, and averting of the local minima issue. All these properties are supported by a series of experiments performed on the synthetic and real-life datasets. In addition, the computational complexity of the proposed method is analyzed, and its efficiency is theoretically argued and experimentally demonstrated.

  13. Improving the Spatial Alignment in PET/CT Using Amplitude-Based Respiration-Gated PET and Respiration-Triggered CT

    NARCIS (Netherlands)

    Vos, C.S. van der; Grootjans, W.; Osborne, D.R.; Meeuwis, A.P.; Hamill, J.J.; Acuff, S.; Geus-Oei, L.F. de; Visser, E.P.

    2015-01-01

    Respiratory motion during PET can cause inaccuracies in the quantification of radiotracer uptake, which negatively affects PET-guided radiotherapy planning. Quantitative accuracy can be improved by respiratory gating. However, additional miscalculation of standardized uptake value (SUV) in PET image

  14. In silico engineering and optimization of Transcription Activator-Like Effectors and their derivatives for improved DNA binding predictions.

    KAUST Repository

    Piatek, Marek J.

    2015-12-01

    Transcription Activator-Like Effectors (TALEs) can be used as adaptable DNAbinding modules to create site-specific chimeric nucleases or synthetic transcriptional regulators. The central repeat domain mediates specific DNA binding via hypervariable repeat di-residues (RVDs). This DNA-Binding Domain can be engineered to bind preferentially to any user-selected DNA sequence if engineered appropriately. Therefore, TALEs and their derivatives have become indispensable molecular tools in site-specific manipulation of genes and genomes. This thesis revolves around two problems: in silico design and improved binding site prediction of TALEs. In the first part, a study is shown where TALEs are successfully designed in silico and validated in laboratory to yield the anticipated effects on selected genes. Software is developed to accompany the process of designing and prediction of binding sites. I expanded the functionality of the software to be used as a more generic set of tools for the design, target and offtarget searching. Part two contributes a method and associated toolkit developed to allow users to design in silico optimized synthetic TALEs with user-defined specificities for various experimental purposes. This method is based on a mutual relationship of three consecutive tandem repeats in the DNA-binding domain. This approach revealed positional and compositional bias behind the binding of TALEs to DNA. In conclusion, I developed methods, approaches, and software to enhance the functionality of synthetic TALEs, which should improve understanding of TALEs biology and will further advance genome-engineering applications in various organisms and cell types.

  15. Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia

    Directory of Open Access Journals (Sweden)

    Zuiter Afnan

    2012-08-01

    Full Text Available Abstract Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Findings Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. Conclusion To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants.

  16. HAMSA: Highly Accelerated Multiple Sequence Aligner

    Directory of Open Access Journals (Sweden)

    Naglaa M. Reda

    2016-06-01

    Full Text Available For biologists, the existence of an efficient tool for multiple sequence alignment is essential. This work presents a new parallel aligner called HAMSA. HAMSA is a bioinformatics application designed for highly accelerated alignment of multiple sequences of proteins and DNA/RNA on a multi-core cluster system. The design of HAMSA is based on a combination of our new optimized algorithms proposed recently of vectorization, partitioning, and scheduling. It mainly operates on a distance vector instead of a distance matrix. It accomplishes similarity computations and generates the guide tree in a highly accelerated and accurate manner. HAMSA outperforms MSAProbs with 21.9- fold speedup, and ClustalW-MPI of 11-fold speedup. It can be considered as an essential tool for structure prediction, protein classification, motive finding and drug design studies.

  17. DNA methyltransferase inhibitors improve the effect of chemotherapeutic agents in SW48 and HT-29 colorectal cancer cells.

    Directory of Open Access Journals (Sweden)

    Sylwia Flis

    Full Text Available DNA methylation is an epigenetic phenomenon known to play an important role in the development and progression of human cancer. Enzyme responsible for this process is DNA methyltransferase 1 (DNMT1 that maintains an altered methylation pattern by copying it from parent to daughter DNA strands after replication. Aberrant methylation of the promoter regions of genes critical for normal cellular functions is potentially reversible. Therefore, inactivation of DNMT1 seems to be a valuable target for the development of cancer therapies. Currently, the most popular DNMT inhibitors (DNMTi are cytidine analogues like 5-azacytidine, 5-aza-2'-deoxycytidine (decitabine and pyrimidin-2-one ribonucleoside (zebularine. In colorectal cancer, epigenetic modifications play an essential role at each step of carcinogenesis. Therefore, we have addressed the hypothesis that DNA methyltransferase inhibitors may potentiate inhibitory effects of classical chemotherapeutic agents, such as oxaliplatin and 5-fluorouracil (5-FU, commonly used in colorectal cancer therapy. Here, our report shows that DNMTi can have positive interactions with standard chemotherapeutics in colorectal cancer treatment. Using pharmacological models for the drug-drug interaction analysis, we have revealed that the combination of decitabine with 5-FU or oxaliplatin shows the most attractive interaction (synergism, whereas the effect of zebularine in combinations with chemotherapeutics is moderate and may be depended on genetic/epigenetic background of a cell line or secondary drug used in combination. Our results suggest that DNMTi administered in combination with standard chemotherapeutics might improve the treatment of patients with colorectal cancers.

  18. Ethanol fuel improves arthropod capture in pitfall traps and preserves DNA

    Directory of Open Access Journals (Sweden)

    Neucir Szinwelski

    2012-05-01

    Full Text Available We tested the value of ethanol fuel as a killing solution in terms of sampling efficiency (species richness and accumulated abundance and DNA preservation of Ensifera ground-dwelling specimens. Sampling efficiency was evaluated comparing abundance and species richness of pitfall sampling using 100% ethanol fuel, with two alternative killing solutions. We evaluated the DNA preservation efficiency of the killing solutions and of alternative storage solutions. Ethanol fuel was the most efficient killing solution, and allowed successful DNA preservation. This solution is cheaper than other preserving liquids, and is easily acquired near field study sites since it is available at every fuel station in Brazil and at an increasing number of fuel stations in the U.S. We recommend the use of ethanol fuel as a killing and storage solution, because it is a cheap and efficient alternative for large-scale arthropod sampling, both logistically and for DNA preservation. For open habitat sampling with high day temperatures, we recommend doubling the solution volume to cope with high evaporation, increasing its efficacy over two days.

  19. NAD(+) Replenishment Improves Lifespan and Healthspan in Ataxia Telangiectasia Models via Mitophagy and DNA Repair

    DEFF Research Database (Denmark)

    Fang, Evandro Fei; Kassahun, Henok; Croteau, Deborah L

    2016-01-01

    Ataxia telangiectasia (A-T) is a rare autosomal recessive disease characterized by progressive neurodegeneration and cerebellar ataxia. A-T is causally linked to defects in ATM, a master regulator of the response to and repair of DNA double-strand breaks. The molecular basis of cerebellar atrophy...

  20. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.

    Science.gov (United States)

    Guilinger, John P; Pattanayak, Vikram; Reyon, Deepak; Tsai, Shengdar Q; Sander, Jeffry D; Joung, J Keith; Liu, David R

    2014-04-01

    Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have activity against related off-target sequences. To better understand TALEN specificity, we profiled 30 unique TALENs with different target sites, array length and domain sequences for their abilities to cleave any of 10(12) potential off-target DNA sequences using in vitro selection and high-throughput sequencing. Computational analysis of the selection results predicted 76 off-target substrates in the human genome, 16 of which were accessible and modified by TALENs in human cells. The results suggest that (i) TALE repeats bind DNA relatively independently; (ii) longer TALENs are more tolerant of mismatches yet are more specific in a genomic context; and (iii) excessive DNA-binding energy can lead to reduced TALEN specificity in cells. Based on these findings, we engineered a TALEN variant that exhibits equal on-target cleavage activity but tenfold lower average off-target activity in human cells.

  1. Improvement of in vivo transfer of plasmid DNA in muscle : Comparison of electroporation versus ultrasound

    NARCIS (Netherlands)

    Kusumanto, Yoka H.; Mulder, Nanno H.; Dam, Wendy A.; Losen, Mario H.; Meijer, Coby; Hospers, Geke A. P.

    2007-01-01

    Plasmid-based gene delivery to muscle is a treatment strategy for many diseases with potential advantages above viral-based gene delivery methods, however, with a relative low transfection efficiency. We compared two physical methods-electroporation and ultrasound-that facilitate DNA uptake into cel

  2. Improving DNA data exchange: validation studies on a single 6 dye STR kit with 24 loci.

    Science.gov (United States)

    Martín, Pablo; de Simón, Lourdes Fernández; Luque, Gracia; Farfán, María José; Alonso, Antonio

    2014-11-01

    The idea of developing a new multiplex STR amplification system was conceived in 2011 as an effective way to implement the new European standard set (ESS) of 12 STR markers adopted by The Council of the European Union in 2009 while maintaining an effective compatibility and information exchange with the historical DNA profiles contained in the Spanish national DNA database (around 200,000 DNA profiles) mainly based on the 13 CODIS core STR loci plus D19S433 and D2S1338 markers. With this goal in mind we proposed to test and validate a single STR amplification system for simultaneous analysis of 21 STR markers covering both CODIS and ESS core STR loci plus three additional markers (D19S433, D2S1338, and SE33) also contained in commonly used STR kits and national DNA databases. In 2012, we started the first beta-testing with a 6-dye STR kit prototype containing 24 loci (now known as the GlobalFiler™ PCR Amplification Kit) developed by Life Technologies in response to the CODIS Core Loci Working Group's recommendation to expand the CODIS Core Loci. This prototype included our proposal of 21 autosomal STR markers and two Y-chromosome markers (DYS391 and Y-indel) and maximizes concordance with established databases and previously analyzed samples by maintaining primer sequences of previous Identifiler(®)/NGM SElect™ kits for the 21 STR markers except for TPOX. This paper describes the validation studies conducted with the first commercial available 6-dye STR kit for casework using a 3500 genetic analyzer for fragment detection that included the analysis of the following parameters and aspects: analytical threshold, sensitivity & stochastic threshold, heterozygous balance, stutter threshold, precision and accuracy, repeatability and reproducibility, genotype concordance, DNA mixtures, species specificity, and stability studies with case type samples. The studies demonstrated that the GlobalFiler™ system provided equivalent overall performance to previous forensic

  3. Genomic multiple sequence alignments: refinement using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2005-08-01

    Full Text Available Abstract Background Genomic sequence data cannot be fully appreciated in isolation. Comparative genomics – the practice of comparing genomic sequences from different species – plays an increasingly important role in understanding the genotypic differences between species that result in phenotypic differences as well as in revealing patterns of evolutionary relationships. One of the major challenges in comparative genomics is producing a high-quality alignment between two or more related genomic sequences. In recent years, a number of tools have been developed for aligning large genomic sequences. Most utilize heuristic strategies to identify a series of strong sequence similarities, which are then used as anchors to align the regions between the anchor points. The resulting alignment is globally correct, but in many cases is suboptimal locally. We describe a new program, GenAlignRefine, which improves the overall quality of global multiple alignments by using a genetic algorithm to improve local regions of alignment. Regions of low quality are identified, realigned using the program T-Coffee, and then refined using a genetic algorithm. Because a better COFFEE (Consistency based Objective Function For alignmEnt Evaluation score generally reflects greater alignment quality, the algorithm searches for an alignment that yields a better COFFEE score. To improve the intrinsic slowness of the genetic algorithm, GenAlignRefine was implemented as a parallel, cluster-based program. Results We tested the GenAlignRefine algorithm by running it on a Linux cluster to refine sequences from a simulation, as well as refine a multiple alignment of 15 Orthopoxvirus genomic sequences approximately 260,000 nucleotides in length that initially had been aligned by Multi-LAGAN. It took approximately 150 minutes for a 40-processor Linux cluster to optimize some 200 fuzzy (poorly aligned regions of the orthopoxvirus alignment. Overall sequence identity increased only

  4. Improved method for Mica functionalization used in single molecule imaging of DNA with atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Hana Zapletalová

    2016-07-01

    Full Text Available The modified procedure of 1-(3-aminopropylsilatrane (APS compound synthesis based on a new derivative (3‑aminopropyltrimethoxysilane for the purpose of DNA immobilization for AFM single imaging is described. New reaction pathway based on kinetically driven reaction approach is described. Necessity of two‑step purification process is proved; ability of purified APS to provide four times smoother surfaces in comparison with a crude product is demonstrated. Various analytical methods such mass spectroscopy and 1H NMR were used to show structure and enhanced purity of the APS product. APS mediates fixation of DNA molecules to mica substrates to be used for DNA imaging under Atomic Force Microscope. The use of an APS compound for simple and rapid silanization of mica surface is demonstrated. The advantages of APS‑based method are based mainly on low roughness of modified mica and homogeneous surface coverage by short sequence dsDNA (246 bp. The product obtained by the condensation reaction was purified in a two step process whose effectiveness was demonstrated not only by reduction of the silanized surface roughness, but also by mass spectroscopy (MS‑ESi, MALDI‑TOF method and proton magnetic resonance spectroscopy. Experiments demonstrate that 1‑(3‑aminopropylsilatrane can be used to fix dsDNA molecules to a mica surface to be visualized by either the tapping mode or the force‑volume mode of AFM microscopy, as demonstrated by experiments. Moreover, necessity of advanced purification protocol is demonstrated by AFM based roughness measurements – pure vs crude APS product. The kinetics of APS‑layer aging, caused by silicon oxide growth on silanized layers, was studied by water contact angle measurements and is discussed.

  5. DNA barcoding using skin exuviates can improve identification and biodiversity studies of snakes.

    Science.gov (United States)

    Khedkar, Trupti; Sharma, Rashmi; Tiknaik, Anita; Khedkar, Gulab; Naikwade, Bhagwat S; Ron, Tetsuzan Benny; Haymer, David

    2016-01-01

    Snakes represent a taxonomically underdeveloped group of animals in India with a lack of experts and incomplete taxonomic descriptions being the main deterrents to advances in this area. Molecular taxonomic approaches using DNA barcoding could aid in snake identification as well as studies of biodiversity. Here a non-invasive sampling method using DNA barcoding is tested using skin exuviates. Taxonomically authenticated samples were collected and tested for validation and comparisons to unknown snake exuviate samples. This approach was also used to construct the first comprehensive study targeting the snake species from Maharashtra state in India. A total of 92 skin exuviate samples were collected and tested for this study. Of these, 81 samples were successfully DNA barcoded and compared with unknown samples for assignment of taxonomic identity. Good quality DNA was obtained irrespective of age and quality of the exuviate material, and all unknown samples were successfully identified. A total of 23 species of snakes were identified, six of which were in the list of Endangered species (Red Data Book). Intra- and inter-specific distance values were also calculated, and these were sufficient to allow discrimination among species and between species without ambiguity in most cases. Two samples were suspected to represent cryptic species based on deep K2P divergence values (>3%), and one sample could be identified to the genus level only. Eleven samples failed to amplify COI sequences, suggesting the need for alternative PCR primer pairs. This study clearly documents how snake skin exuviates can be used for DNA barcoding, estimates of diversity and population genetic structuring in a noninvasive manner.

  6. A novel approach to multiple sequence alignment using hadoop data grids.

    Science.gov (United States)

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

  7. Optimizing System and Software Assurance in the Engineering Trade Space - Aligning Governance, Engineering Practice, and Engineering Economics to Reduce Risk and Improve Value

    Science.gov (United States)

    2011-05-01

    14]; – Environmental/Contextual-Oriented Models, like Balanced Scorecard [15]; and – Quantitative Estimation Models, like CoCoMo II with Security...Grembergen and S. De Haes. Measuring and Improving IT Governance Through the Balanced Scorecard , Information Systems Control Journal, Volume 2

  8. Improvement of Finite Element Analysis in the Propulsion Shaft Alignment%船舶推进轴系校中有限元法的改进及软件实现

    Institute of Scientific and Technical Information of China (English)

    周瑞平; 徐禄俊; 李冰融; 张昇平

    2005-01-01

    详细论述了有限元的基本理论,根据实际情况,考虑船舶推进轴系校中计算中剪切变形的影响,对有限元法的刚度矩阵进行了改进.利用VB.NET开发了船舶推进轴系校中计算通用软件,通过与没有考虑剪切变形的国内外同类计算软件计算结果的比较以及实际中的应用,表明了这种改进是合理的且可以获得更准确的结果.所开发的计算软件,界面友好,功能完善,操作简单,满足轴系设计计算、校核计算的需要,进一步完善了船舶推进轴系校中计算模型,便于二次开发与深入研究.%The basic theory of the Finite Element Method is presented in detail. According to the practice of the propulsion shaft alignment,some improvements are made in the stiffness matrix due to taking the shear deformation effect into consideration. Based on the presented algorithm,the propulsion shaft alignment calculation program is developed in VB.NET language. By comparing calculation results with the output of other similar software without considering the shear deformation effect and the application in practice,it is proved that these improvements in the Finite Element Method are reasonable and can obtain more accurate results. The user-friendly interfaces,perfect functions and simple operations are included in the software,which meets the need of the checkout of the marine propulsion shaft and consummates the propulsion shaft alignment calculation model. It is convenient for the further redevelopment and study.

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  10. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef

    2010-01-01

    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  11. Alignment free characterization of 2D gratings

    CERN Document Server

    Madsen, Morten Hannibal; Hansen, Poul-Erik; Jørgensen, Jan Friis

    2015-01-01

    Fast characterization of 2-dimensional gratings is demonstrated using a Fourier lens optical system and a differential optimization algorithm. It is shown that both the grating specific parameters such as the basis vectors and the angle between them and the alignment of the sample, such as the rotation of the sample around the x-, y-, and z-axis, can be deduced from a single measurement. More specifically, the lattice vectors and the angle between them have been measured, while the corrections of the alignment parameters are used to improve the quality of the measurement, and hence reduce the measurement uncertainty. Alignment free characterization is demonstrated on both a 2D hexagonal grating with a period of 700 nm and a checkerboard grating with a pitch of 3000 nm. The method can also be used for both automatic alignment and in-line characterization of gratings.

  12. Alignment of the ATLAS Inner Tracking System during LHC Run 2

    CERN Document Server

    Kozakai, Chihiro; The ATLAS collaboration

    2016-01-01

    The inner detector of the ATLAS experiment requires high precision alignment to improve tracking quality. This poster discusses how the alignment for Run 2 has been improved by IBL bowing correction and weak-mode studies.

  13. Strategic Alignment of Business Intelligence

    OpenAIRE

    Cederberg, Niclas

    2010-01-01

    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  14. Orientation and Alignment Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Hartmann, J -M; Faucher, O; Gershnabel, E; Prior, Y; Averbukh, I Sh

    2015-01-01

    We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses.

  15. Group Based Interference Alignment

    CERN Document Server

    Ma, Yanjun; Chen, Rui; Yao, Junliang

    2010-01-01

    in $K$-user single-input single-output (SISO) frequency selective fading interference channels, it is shown that the achievable multiplexing gain is almost surely $K/2$ by using interference alignment (IA). However when the signaling dimensions is limited, allocating all the resource to all the users simultaneously is not optimal. According to this problem, a group based interference alignment (GIA) scheme is proposed and a search algorithm is designed to get the group patterns and the resource allocation among them. Analysis results show that our proposed scheme achieves a higher multiplexing gain when the resource is limited.

  16. PILOT optical alignment

    Science.gov (United States)

    Longval, Y.; Mot, B.; Ade, P.; André, Y.; Aumont, J.; Baustista, L.; Bernard, J.-Ph.; Bray, N.; de Bernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Charra, M.; Chaigneau, M.; Crane, B.; Crussaire, J.-P.; Douchin, F.; Doumayrou, E.; Dubois, J.-P.; Engel, C.; Etcheto, P.; Gélot, P.; Griffin, M.; Foenard, G.; Grabarnik, S.; Hargrave, P..; Hughes, A.; Laureijs, R.; Lepennec, Y.; Leriche, B.; Maestre, S.; Maffei, B.; Martignac, J.; Marty, C.; Marty, W.; Masi, S.; Mirc, F.; Misawa, R.; Montel, J.; Montier, L.; Narbonne, J.; Nicot, J.-M.; Pajot, F.; Parot, G.; Pérot, E.; Pimentao, J.; Pisano, G.; Ponthieu, N.; Ristorcelli, I.; Rodriguez, L.; Roudil, G.; Salatino, M.; Savini, G.; Simonella, O.; Saccoccio, M.; Tapie, P.; Tauber, J.; Torre, J.-P.; Tucker, C.

    2016-07-01

    PILOT is a balloon-borne astronomy experiment designed to study the polarization of dust emission in the diffuse interstellar medium in our Galaxy at wavelengths 240 μm with an angular resolution about two arcminutes. Pilot optics is composed an off-axis Gregorian type telescope and a refractive re-imager system. All optical elements, except the primary mirror, are in a cryostat cooled to 3K. We combined the optical, 3D dimensional measurement methods and thermo-elastic modeling to perform the optical alignment. The talk describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015.

  17. Improving DNA double-strand repair inhibitor KU55933 therapeutic index in cancer radiotherapy using nanoparticle drug delivery

    Science.gov (United States)

    Tian, Xi; Lara, Haydee; Wagner, Kyle T.; Saripalli, Srinivas; Hyder, Syed Nabeel; Foote, Michael; Sethi, Manish; Wang, Edina; Caster, Joseph M.; Zhang, Longzhen; Wang, Andrew Z.

    2015-11-01

    Radiotherapy is a key component of cancer treatment. Because of its importance, there has been high interest in developing agents and strategies to further improve the therapeutic index of radiotherapy. DNA double-strand repair inhibitors (DSBRIs) are among the most promising agents to improve radiotherapy. However, their clinical translation has been limited by their potential toxicity to normal tissue. Recent advances in nanomedicine offer an opportunity to overcome this limitation. In this study, we aim to demonstrate the proof of principle by developing and evaluating nanoparticle (NP) formulations of KU55933, a DSBRI. We engineered a NP formulation of KU55933 using nanoprecipitation method with different lipid polymer nanoparticle formulation. NP KU55933 using PLGA formulation has the best loading efficacy as well as prolonged drug release profile. We demonstrated that NP KU55933 is a potent radiosensitizer in vitro using clonogenic assay and is more effective as a radiosensitizer than free KU55933 in vivo using mouse xenograft models of non-small cell lung cancer (NSCLC). Western blots and immunofluorescence showed NP KU55933 exhibited more prolonged inhibition of DNA repair pathway. In addition, NP KU55933 leads to lower skin toxicity than KU55933. Our study supports further investigations using NP to deliver DSBRIs to improve cancer radiotherapy treatment.

  18. Oral administration of an immunostimulatory DNA sequence from Bifidobacterium longum improves Th1/Th2 balance in a murine model.

    Science.gov (United States)

    Takahashi, Noritoshi; Kitazawa, Haruki; Iwabuchi, Noriyuki; Xiao, Jin-Zhong; Miyaji, Kazuhiro; Iwatsuki, Keiji; Saito, Tadao

    2006-08-01

    We have reported the antiallergic activities of the immunostimulatory oligodeoxynucleotide (ODN) BL07S, identified from genomic DNA of Bifidobacterium longum BB536 from in vitro and in vivo studies. The present study evaluated the efficiency of ODN BL07S in preventing allergic responses by oral administration. Oral administration of BL07S suppressed serum ovalbumin (OVA)-specific immunoglobulin (Ig) E levels and improved the OVA-specific IgG2a/IgG1 ratio. ODN BL07S increased Th1 cytokine and decreased Th2 cytokine production in splenocytes. These results suggest that immunostimulatory ODNs are potentially associated with the antiallergic effects of probiotics.

  19. Quality standards for DNA sequence variation databases to improve clinical management under development in Australia

    Directory of Open Access Journals (Sweden)

    B. Bennetts

    2014-09-01

    Full Text Available Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA in collaboration with the Human Genetics Society of Australasia (HGSA, and the Human Variome Project (HVP is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.

  20. The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology.

    Science.gov (United States)

    Derkx, Patrick M F; Janzen, Thomas; Sørensen, Kim I; Christensen, Jeffrey E; Stuer-Lauridsen, Birgitte; Johansen, Eric

    2014-08-29

    The food industry is constantly striving to develop new products to fulfil the ever changing demands of consumers and the strict requirements of regulatory agencies. For foods based on microbial fermentation, this pushes the boundaries of microbial performance and requires the constant development of new starter cultures with novel properties. Since the use of ingredients in the food industry is tightly regulated and under close scrutiny by consumers, the use of recombinant DNA technology to improve microbial performance is currently not an option. As a result, the focus for improving strains for microbial fermentation is on classical strain improvement methods. Here we review the use of these techniques to improve the functionality of lactic acid bacteria starter cultures for application in industrial-scale food production. Methods will be described for improving the bacteriophage resistance of specific strains, improving their texture forming ability, increasing their tolerance to stress and modulating both the amount and identity of acids produced during fermentation. In addition, approaches to eliminating undesirable properties will be described. Techniques include random mutagenesis, directed evolution and dominant selection schemes.

  1. Aligning Theory with Practice

    Science.gov (United States)

    Kurz, Terri L.; Batarelo, Ivana

    2009-01-01

    This article describes a structure to help preservice teachers get invaluable field experience by aligning theory with practice supported by the integration of elementary school children into their university mathematics methodology course. This course structure allowed preservice teachers to learn about teaching mathematics in a nonthreatening…

  2. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    2014-01-01

    The emergence of patient-centered eHealth systems introduces new challenges, where patients come to play an increasingly important role. Realizing the promises requires an in-depth understanding of not only the technology, but also the needs of both clinicians and patients. However, insights from...... as a design rationale for successful eHealth, termed 'alignment of concerns'....

  3. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko

    2013-01-01

    This work introduces a framework that implements asymmetric communication theory proposed by Sperber and Wilson [1]. The framework applies a generalization model known as the Bayesian model of generalization (BMG) [2] for aligning knowledge possessed by two communicating parties. The work focuses...

  4. INFORMATION TECHNOLOGY STRATEGIC ALIGNMENT: ANALYSIS OF ALIGNMENT MODELS AND PROPOSALS FOR FUTURE RESEARCH

    Directory of Open Access Journals (Sweden)

    Fabrício Sobrosa Affeldt

    2009-10-01

    Full Text Available Information Technology (IT is a resource capable of supporting businesses, which provides agile operations and mobility and decision support tools. The link between IT and business strategy has been studied regarding the best fitted model to improve company performance. This paper analyzes, through bibliographic research, the strategic alignment concept and the evolution of the strategic alignment theoretical models that are considered references in this area. The paper presents a comparison between these referential models and some perspectives for future research related IT strategic alignment.

  5. Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches

    Energy Technology Data Exchange (ETDEWEB)

    Dogget, N.; Myers, G. [Los Alamos National Lab., NM (United States); Wills, C.J. [Univ. of California, San Diego, CA (United States)

    1998-12-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

  6. Comparison of pathogen DNA isolation methods from large volumes of whole blood to improve molecular diagnosis of bloodstream infections.

    Directory of Open Access Journals (Sweden)

    Anne J M Loonen

    Full Text Available For patients suffering from bloodstream infections (BSI molecular diagnostics from whole blood holds promise to provide fast and adequate treatment. However, this approach is hampered by the need of large blood volumes. Three methods for pathogen DNA isolation from whole blood were compared, i.e. an enzymatic method (MolYsis, 1-5 ml, the novel non-enzymatic procedure (Polaris, 1-5 ml, and a method that does not entail removal of human DNA (Triton-Tris-EDTA EasyMAG, 200 µl. These methods were evaluated by processing blood spiked with 0-1000 CFU/ml of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans. Downstream detection was performed with real-time PCR assays. Polaris and MolYsis processing followed by real-time PCRs enabled pathogen detection at clinically relevant concentrations of 1-10 CFU/ml blood. By increasing sample volumes, concurrent lower cycle threshold (Ct values were obtained at clinically relevant pathogen concentrations, demonstrating the benefit of using larger blood volumes. A 100% detection rate at a concentration of 10 CFU/ml for all tested pathogens was obtained with the Polaris enrichment, whereas comparatively lower detection rates were measured for MolYsis (50-67% and EasyMAG (58-79%. For the samples with a concentration of 1 CFU/ml Polaris resulted in most optimal detection rates of 70-75% (MolYsis 17-50% and TTE-EasyMAG 20-36%. The Polaris method was more reproducible, less labour intensive, and faster (45 minutes (including Qiagen DNA extraction vs. 2 hours (MolYsis. In conclusion, Polaris and MolYsis enrichment followed by DNA isolation and real-time PCR enables reliable and sensitive detection of bacteria and fungi from 5 ml blood. With Polaris results are available within 3 hours, showing potential for improved BSI diagnostics.

  7. Scaling statistical multiple sequence alignment to large datasets

    Directory of Open Access Journals (Sweden)

    Michael Nute

    2016-11-01

    Full Text Available Abstract Background Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest. While many alignment methods exist, the most accurate alignments are likely to be based on stochastic models where sequences evolve down a tree with substitutions, insertions, and deletions. While some methods have been developed to estimate alignments under these stochastic models, only the Bayesian method BAli-Phy has been able to run on even moderately large datasets, containing 100 or so sequences. A technique to extend BAli-Phy to enable alignments of thousands of sequences could potentially improve alignment and phylogenetic tree accuracy on large-scale data beyond the best-known methods today. Results We use simulated data with up to 10,000 sequences representing a variety of model conditions, including some that are significantly divergent from the statistical models used in BAli-Phy and elsewhere. We give a method for incorporating BAli-Phy into PASTA and UPP, two strategies for enabling alignment methods to scale to large datasets, and give alignment and tree accuracy results measured against the ground truth from simulations. Comparable results are also given for other methods capable of aligning this many sequences. Conclusions Extensions of BAli-Phy using PASTA and UPP produce significantly more accurate alignments and phylogenetic trees than the current leading methods.

  8. General space-efficient sampling algorithm for suboptimal alignment

    Institute of Scientific and Technical Information of China (English)

    CHEN; Yi; BAI; Yan-qin

    2009-01-01

    Suboptimal alignments always reveal additional interesting biological features and have been successfully used to informally estimate the significance of an optimal alignment. Besides, traditional dynamic programming algorithms for sequence comparison require quadratic space, and hence are infeasible for long protein or DNA sequences. In this paper, a space-efficient sampling algorithm for computing suboptimal alignments is described. The algorithm uses a general gap model, where the cost associated with gaps is given by an affine score, and randomly selects an alignment according to the distribution of weights of all potential alignments. If x and y are two sequences with lengths n and m, respectively, then the space requirement of this algorithm is linear to the sum of n and m. Finally, an example illustrates the utility of the algorithm.

  9. Alignment and Integration of Lightweight Mirror Segments

    Science.gov (United States)

    Evans, Tyler; Biskach, Michael; Mazzarella, Jim; McClelland, Ryan; Saha, Timo; Zhang, Will; Chan, Kai-Wing

    2011-01-01

    The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc-seconds. These mirror segments are 0.4 mm thick, and 200 to 400 mm in size, which makes it difficult not to impart distortion at the sub-arc-second level. This paper outlines the precise alignment, permanent bonding, and verification testing techniques developed at NASA's Goddard Space Flight Center (GSFC). Improvements in alignment include new hardware and automation software. Improvements in bonding include two module new simulators to bond mirrors into, a glass housing for proving single pair bonding, and a Kovar module for bonding multiple pairs of mirrors. Three separate bonding trials were x-ray tested producing results meeting the requirement of sub ten arc-second alignment. This paper will highlight these recent advances in alignment, testing, and bonding techniques and the exciting developments in thin x-ray optic technology development.

  10. Aligning component upgrades

    Directory of Open Access Journals (Sweden)

    Roberto Di Cosmo

    2011-08-01

    Full Text Available Modern software systems, like GNU/Linux distributions or Eclipse-based development environment, are often deployed by selecting components out of large component repositories. Maintaining such software systems by performing component upgrades is a complex task, and the users need to have an expressive preferences language at their disposal to specify the kind of upgrades they are interested in. Recent research has shown that it is possible to develop solvers that handle preferences expressed as a combination of a few basic criteria used in the MISC competition, ranging from the number of new components to the freshness of the final configuration. In this work we introduce a set of new criteria that allow the users to specify their preferences for solutions with components aligned to the same upstream sources, provide an efficient encoding and report on the experimental results that prove that optimising these alignment criteria is a tractable problem in practice.

  11. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  12. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    E-health promises to enable and support active patient participation in chronic care. However, these fairly recent innovations are complicated matters and emphasize significant challenges, such as patients’ and clinicians’ different ways of conceptualizing disease and illness. Informed by insight...... from medical phenomenology and our own empirical work in telemonitoring and medical care of heart patients, we propose a design rationale for e-health systems conceptualized as the ‘alignment of concerns’....

  13. An improved SELEX technique for selection of DNA aptamers binding to M-type 11 of Streptococcus pyogenes.

    Science.gov (United States)

    Hamula, Camille L A; Peng, Hanyong; Wang, Zhixin; Tyrrell, Gregory J; Li, Xing-Fang; Le, X Chris

    2016-03-15

    Streptococcus pyogenes is a clinically important pathogen consisting of various serotypes determined by different M proteins expressed on the cell surface. The M type is therefore a useful marker to monitor the spread of invasive S. pyogenes in a population. Serotyping and nucleic acid amplification/sequencing methods for the identification of M types are laborious, inconsistent, and usually confined to reference laboratories. The primary objective of this work is to develop a technique that enables generation of aptamers binding to specific M-types of S. pyogenes. We describe here an in vitro technique that directly used live bacterial cells and the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) strategy. Live S. pyogenes cells were incubated with DNA libraries consisting of 40-nucleotides randomized sequences. Those sequences that bound to the cells were separated, amplified using polymerase chain reaction (PCR), purified using gel electrophoresis, and served as the input DNA pool for the next round of SELEX selection. A specially designed forward primer containing extended polyA20/5Sp9 facilitated gel electrophoresis purification of ssDNA after PCR amplification. A counter-selection step using non-target cells was introduced to improve selectivity. DNA libraries of different starting sequence diversity (10(16) and 10(14)) were compared. Aptamer pools from each round of selection were tested for their binding to the target and non-target cells using flow cytometry. Selected aptamer pools were then cloned and sequenced. Individual aptamer sequences were screened on the basis of their binding to the 10 M-types that were used as targets. Aptamer pools obtained from SELEX rounds 5-8 showed high affinity to the target S. pyogenes cells. Tests against non-target Streptococcus bovis, Streptococcus pneumoniae, and Enterococcus species demonstrated selectivity of these aptamers for binding to S. pyogenes. Several aptamer sequences were found to bind

  14. Nuclear reactor alignment plate configuration

    Energy Technology Data Exchange (ETDEWEB)

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  15. Orbit IMU alignment: Error analysis

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  16. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

    The first full-scale tests of the ATLAS Muon Spectrometer are about to begin in Prévessin. The set-up includes several layers of Monitored Drift Tubes Chambers (MDTs) and will allow tests of the performance of the detectors and of their highly accurate alignment system.   Monitored Drift Chambers in Building 887 in Prévessin, where they are just about to be tested. Muon chambers are keeping the ATLAS Muon Spectrometer team quite busy this summer. Now that most people go on holiday, the beam and alignment tests for these chambers are just starting. These chambers will measure with high accuracy the momentum of high-energy muons, and this implies very demanding requirements for their alignment. The MDT chambers consist of drift tubes, which are gas-filled metal tubes, 3 cm in diameter, with wires running down their axes. With high voltage between the wire and the tube wall, the ionisation due to traversing muons is detected as electrical pulses. With careful timing of the pulses, the position of the muon t...

  17. RECAT - Redundant Channel Alignment Technique

    Science.gov (United States)

    2016-06-07

    distribution unlimited 13. SUPPLEMENTARY NOTES NUWC2015 14. ABSTRACT A problem in the analog-to- digital , (A/D), conversion of broadband tape recorded...Alignment Technique, is used to align data taken on one pass with data from any other pass. The accuracy of this alignment is a function of the digital ...Redundant Channel Alignment Technique; analog-to- digital ; A/D; Broadband Bearing Time Processing 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

  18. Improvement of FISH mapping resolution on combed DNA molecules by iterative constrained deconvolution: a quantitative study.

    Science.gov (United States)

    Monier, K; Heliot, L; Rougeulle, C; Heard, E; Robert-Nicoud, M; Vourc'h, C; Bensimon, A; Usson, Y

    2001-01-01

    Image restoration approaches, such as digital deconvolution, are becoming widely used for improving the quality of microscopic images. However, no quantification of the gain in resolution of fluorescence images is available. We show that, after iterative constrained deconvolution, fluorescent cosmid signals appear to be 25% smaller, and 1.2-kb fragment signals on combed molecules faithfully display the expected length.

  19. Velocity-aligned Doppler spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Z.; Koplitz, B.; Wittig, C.

    1989-03-01

    The technique of velocity-aligned Doppler spectrosocopy (VADS) is presented and discussed. For photolysis/probe experiments with pulsed initiation, VADS can yield Doppler profiles for nascent photofragments that allow detailed center-of-mass (c.m.) kinetic energy distributions to be extracted. When compared with traditional forms of Doppler spectroscopy, the improvement in kinetic energy resolution is dramatic. Changes in the measured profiles are a consequence of spatial discrimination (i.e., focused and overlapping photolysis and probe beams) and delayed observation. These factors result in the selective detection of species whose velocities are aligned with the wave vector of the probe radiation k/sub pr/, thus revealing the speed distribution along k/sub pr/ rather than the distribution of nascent velocity components projected upon this direction. Mathematical details of the procedure used to model VADS are given, and experimental illustrations for HI, H/sub 2/S, and NH/sub 3/ photodissociation are presented. In these examples, pulsed photodissociation produces H atoms that are detected by sequential two-photon, two-frequency ionization via Lyman-..cap alpha.. with a pulsed laser (121.6+364.7 nm), and measuring the Lyman-..cap alpha.. Doppler profile as a function of probe delay reveals both internal and c.m. kinetic energy distributions for the photofragments. Strengths and weaknesses of VADS as a tool for investigating photofragmentation phenomena are also discussed.

  20. Improvement and Check on the mtDNA extract techniques for termites%白蚁 mtDNA 提取方法改良及检测

    Institute of Scientific and Technical Information of China (English)

    姜丽红; 邹湘武; 宁涤非; 席在星

    2013-01-01

      利用mtDNA多态性进行种类鉴定是一种分子生物学常用方法,从DNA水平对白蚁进行物种鉴别并探讨物种的进化,其必要前提是提取到一定数量和质量的mtDNA.在分离得到线粒体后,分别采用CTAB、SDS 2种方法提取mtDNA.紫外分光光度计检测DNA纯度及浓度,用mtDNA 特异性引物进行PCR 扩增检测.试验证明2种方法均能成功提取白蚁的mtDNA, SDS法提取效果较好.%Species identification with mtDNA polymorphisms is an usual method in molecular biology. To identify the species and to explore the evolution of the termites from the DNA level, it is necessary to extract the mtDNA with enough quantity and good quality. In this study, mitochondria of termites is firstly isolated, then CTAB and SDS methods were employed for the extraction of mtDNA, respectively. Purity and concentration of mtDNA were determined by UV spectrophotometer. PCR amplification of mtDNA was executed by specific primers. Results shows that both CTAB the SDS methods can successfully extracted termite mtDNA, but SDS method shows better performance than CTAB method.

  1. Method for alignment of microwires

    Energy Technology Data Exchange (ETDEWEB)

    Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

    2017-01-24

    A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

  2. Improved reproducibility in genome-wide DNA methylation analysis for PAXgene-fixed samples compared with restored formalin-fixed and paraffin-embedded DNA.

    Science.gov (United States)

    Andersen, Gitte Brinch; Hager, Henrik; Hansen, Lise Lotte; Tost, Jörg

    2015-01-01

    Formalin fixation has been the standard method for conservation of clinical specimens for decades. However, a major drawback is the high degradation of nucleic acids, which complicates its use in genome-wide analyses. Unbiased identification of biomarkers, however, requires genome-wide studies, precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap-freezing is the PAXgene Tissue System, developed for simultaneous preservation of morphology, proteins, and nucleic acids. In the current study, we compared the performance of DNA from either PAXgene or formalin-fixed tissues to snap-frozen material for genome-wide DNA methylation analysis using the Illumina 450K BeadChip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better compared with restored FFPE DNA in genome-wide DNA methylation analysis. In addition, DNA from PAXgene tissue can be directly used on the array without prior restoration, rendering the analytical process significantly more time- and cost-effective.

  3. An Epitope-Substituted DNA Vaccine Improves Safety and Immunogenicity against Dengue Virus Type 2.

    Directory of Open Access Journals (Sweden)

    Chung-Tao Tang

    Full Text Available Dengue virus (DENV, a global disease, is divided into four serotypes (DENV1-4. Cross-reactive and non-neutralizing antibodies against envelope (E protein of DENV bind to the Fcγ receptors (FcγR of cells, and thereby exacerbate viral infection by heterologous serotypes via antibody-dependent enhancement (ADE. Identification and modification of enhancing epitopes may mitigate enhancement of DENV infection. In this study, we characterized the cross-reactive DB21-6 and DB39-2 monoclonal antibodies (mAbs against domain I-II of DENV; these antibodies poorly neutralized and potently enhanced DENV infection both in vitro and in vivo. In addition, two enhancing mAbs, DB21-6 and DB39-2, were observed to compete with sera antibodies from patients infected with dengue. The epitopes of these enhancing mAbs were identified using phage display, structural prediction, and mapping of virus-like particle (VLP mutants. N8, R9, V12, and E13 are the reactive residues of DB21-6, while N8, R9, and E13 are the reactive residues of DB39-2. N8 substitution tends to maintain VLP secretion, and decreases the binding activity of DB21-6 and DB39-2. The immunized sera from N8 substitution (N8R DNA vaccine exerted greater neutralizing and protective activity than wild-type (WT-immunized sera, both in vitro and in vivo. Furthermore, treatment with N8R-immunized sera reduced the enhancement of mortality in AG129 mice. These results support identification and substitution of enhancing epitope as a novel strategy for developing safe dengue vaccines.

  4. Transfer alignment of shipborne inertial-guided weapon systems

    Institute of Scientific and Technical Information of China (English)

    Sun Changyue; Deng Zhenglong

    2009-01-01

    The transfer alignment problem of the shipborne weapon inertial navigation system (INS) is addressed. Specifically, two transfer alignment algorithms subjected to the ship motions induced by the waves are discussed. To consider the limited maneuver level performed by the ship, a new filter algorithm for transfer alignment methods using velocity and angular rate matching is first derived. And then an improved method using integrated velocity and integrated angular rate matching is introduced to reduce the effect of the ship body flexure. The simulation results show the feasibility and validity of the proposed transfer alignment algorithms.

  5. Anchor-based English-Chinese Bilingual Chunk Alignment Model

    Institute of Scientific and Technical Information of China (English)

    WU We-lin; CHENG Chang-sheng; XU Liang-xian; LU Ru-zhan

    2005-01-01

    Chunk alignment for the bilingual corpus is the base of Example-based Machine Translation. An anchor-based English-Chinese bilingual chunk alignment model and the corresponding algorithm of alignment are presented in this paper. It can effectively overcome the sparse data problem due to the limited size of the bilingual corpus. In this model, the chunk segmentation disambiguation is delayed to the alignment process, and hence the accuracy of chunk segmentation is improved. The experimental results demonstrate the feasibility and viability of this model.

  6. Double positivity for HPV DNA/p16 in tonsillar and base of tongue cancer improves prognostication

    DEFF Research Database (Denmark)

    Garnaes, Emilie; Frederiksen, Kirsten; Kiss, Katalin

    2016-01-01

    of tongue squamous cell carcinoma (BSCC) when stratifying for HPV DNA status, p16 expression and combined HPV/p16 status. We included all patients (n = 797) diagnosed with TSCCs and BSCCs in Eastern Denmark as registered in the Danish Head and Neck Cancer Group (DAHANCA) database and the Danish Pathology...... Databank, 2000–2010. Patients were treated according to national guidelines (radiotherapy +/− concomitant cisplatin). All specimens were analysed using HPV DNA PCR and p16 immunohistochemistry. Clinical information was retrieved from the DAHANCA database and the Danish National Patient Registry....... Information on vital status was obtained from the Danish Civil Registration System. We observed improved OS for HPV+/p16+ BSCCs compared to HPV−/p16− (hazard ratio for death [HR], 0.15; 95% CI, 0.09–0.24). Among STSCCs, HPV+/p16+ showed the lowest HR (0.19, 95% CI, 0.13–0.29); whereas, HPV−/p16+ showed...

  7. Aligning Business Needs and Instructional Assets (Recycling Instructional Assets)

    Science.gov (United States)

    Gendelman, Joel

    2009-01-01

    High-performing organizations and performance improvement professionals frequently speak about the alignment of their instructional curricula with the needs of the business. However, they often lack a systematic methodology for performing that alignment. This article presents such a method. The process provides the ability to better support…

  8. Chunk Alignment for Corpus-Based Machine Translation

    Science.gov (United States)

    Kim, Jae Dong

    2011-01-01

    Since sub-sentential alignment is critically important to the translation quality of an Example-Based Machine Translation (EBMT) system, which operates by finding and combining phrase-level matches against the training examples, we developed a new alignment algorithm for the purpose of improving the EBMT system's performance. This new…

  9. Vaxfectin adjuvant improves antibody responses of juvenile rhesus macaques to a DNA vaccine encoding the measles virus hemagglutinin and fusion proteins.

    Science.gov (United States)

    Lin, Wen-Hsuan W; Vilalta, Adrian; Adams, Robert J; Rolland, Alain; Sullivan, Sean M; Griffin, Diane E

    2013-06-01

    DNA vaccines formulated with the cationic lipid-based adjuvant Vaxfectin induce protective immunity in macaques after intradermal (i.d.) or intramuscular (i.m.) delivery of 0.5 to 1 mg of codon-optimized DNA encoding the hemagglutinin (H) and fusion (F) proteins of measles virus (MeV). To characterize the effect of Vaxfectin at lower doses of H+F DNA, rhesus macaques were vaccinated twice with 20 μg of DNA plus Vaxfectin i.d., 100 μg of DNA plus Vaxfectin i.d., 100 μg of DNA plus Vaxfectin i.m. or 100 μg of DNA plus phosphate-buffered saline (PBS) i.m. using a needleless Biojector device. The levels of neutralizing (P = 0.036) and binding (P = 0.0001) antibodies were higher after 20 or 100 μg of DNA plus Vaxfectin than after 100 μg of DNA plus PBS. Gamma interferon (IFN-γ)-producing T cells were induced more rapidly than antibody, but were not improved with Vaxfectin. At 18 months after vaccination, monkeys were challenged with wild-type MeV. None developed rash or viremia, but all showed evidence of infection. Antibody levels increased, and IFN-γ- and interleukin-17-producing T cells, including cells specific for the nucleoprotein absent from the vaccine, were induced. At 3 months after challenge, MeV RNA was detected in the leukocytes of two monkeys. The levels of antibody peaked 2 to 4 weeks after challenge and then declined in vaccinated animals reflecting low numbers of bone marrow-resident plasma cells. Therefore, Vaxfectin was dose sparing and substantially improved the antibody response to the H+F DNA vaccine. This immune response led to protection from disease (rash/viremia) but not from infection. Antibody responses after challenge were more transient in vaccinated animals than in an unvaccinated animal.

  10. 早食李基因组DNA提取方法的改进%Improvement of Technique for Extraction of Total DNA from "Zaoshi" Plum

    Institute of Scientific and Technical Information of China (English)

    谢志亮; 何业华

    2013-01-01

    以改进的CTAB法对三华李品种群中的早食李叶片基因组DNA的提取进行了试验.结果表明,改进的CTAB法适于高质量三华李品种群基因组DNA的提取,提取的早食李基因组DNA完整性较好,无降解,OD260/OD280的比值在1.9~2.0之间,多糖类杂质去除较为干净.经SRAP检验,条带清晰,多态性良好,说明改良CTAB法提取的基因组DNA质量较好,适于三华李高质量基因组DNA的提取.不同时期的不同成熟度的叶片都可以提取到基因组DNA,但以各期的嫩叶(梢)产量最高,效率最好.%The DNA extraction experiment on "Zaoshi" plum was carried out by improved CTAB DNA extraction method. The results indicated that the improved CTAB DNA extraction method was suitable for extraction of high quality DNA from the "Sanhua" plum cultivar group. The extracted "Zaoshi" plum DNA was in good integrality and without degradation. The OD260/OD280 radio was between 1. 9~2. 0, and the polysaccharide was dislodged clearly. The SRAP test produced clear polymorphic patterns, which indicated that the improved CTAB DNA extraction method was suitable for high quality DNA extraction from "Sanhua" plum cultivar group. The leaves at different development stage were also suitable for DNA extraction, but the young leaves (shoots) were the most suitable.

  11. BBMap: A Fast, Accurate, Splice-Aware Aligner

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

    Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].

  12. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

    Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  13. Enabling Process Alignment for IT Entrepreneurship

    Directory of Open Access Journals (Sweden)

    Sonia D. Bot

    2012-11-01

    Full Text Available All firms use information technology (IT. Larger firms have IT organizations whose business function is to supply and manage IT infrastructure and applications to support the firm's business objectives. Regardless of whether the IT function has been outsourced or is resident within a firm, the objectives of the IT organization must be aligned to the strategic needs of the business. It is often a challenge to balance the demand for IT against the available supply within the firm. Most IT organizations have little capacity to carry out activities that go beyond the incremental ones that are needed to run the immediate needs of the business. A process-ambidexterity framework for IT improves the IT organization's entrepreneurial ability, which in turn, better aligns the IT function with the business functions in the firm. Process ambidexterity utilizes both process alignment and process adaptability. This article presents a framework for process alignment in IT. This is useful for understanding how the processes in Business Demand Management, a core component of the process-ambidexterity framework for IT, relate to those in IT Governance and IT Supply Chain Management. The framework is presented through three lenses (governance, business, and technology along with real-world examples from major firms in the USA. Enabling process alignment in the IT function, and process ambidexterity overall, benefits those who govern IT, the executives who lead IT, as well as their peers in the business functions that depend on IT.

  14. An improved method for the isolation of rat alveolar type II lung cells: Use in the Comet assay to determine DNA damage induced by cigarette smoke.

    Science.gov (United States)

    Dalrymple, Annette; Ordoñez, Patricia; Thorne, David; Dillon, Debbie; Meredith, Clive

    2015-06-01

    Smoking is a cause of serious diseases, including lung cancer, emphysema, chronic bronchitis and heart disease. DNA damage is thought to be one of the mechanisms by which cigarette smoke (CS) initiates disease in the lung. Indeed, CS induced DNA damage can be measured in vitro and in vivo. The potential of the Comet assay to measure DNA damage in isolated rat lung alveolar type II epithelial cells (AEC II) was explored as a means to include a genotoxicity end-point in rodent sub-chronic inhalation studies. In this study, published AEC II isolation methods were improved to yield viable cells suitable for use in the Comet assay. The improved method reduced the level of basal DNA damage and DNA repair in isolated AEC II. CS induced DNA damage could also be quantified in isolated cells following a single or 5 days CS exposure. In conclusion, the Comet assay has the potential to determine CS or other aerosol induced DNA damage in AEC II isolated from rodents used in sub-chronic inhalation studies.

  15. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection

    Directory of Open Access Journals (Sweden)

    María Fernanda Loayza

    2015-01-01

    • The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium.

  16. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider at CERN. In order to achieve its physics goals, the ATLAS tracking requires that the positions of the silicon detector elements have to be known to a precision better than 10 μm. Several track-based alignment algorithms have been developed for the Inner Detector. An extensive validation has been performed with simulated events and real data coming from the ATLAS. Results from such validation are reported in this paper.

  17. CELT optics Alignment Procedure

    Science.gov (United States)

    Mast, Terry S.; Nelson, Jerry E.; Chanan, Gary A.; Noethe, Lothar

    2003-01-01

    The California Extremely Large Telescope (CELT) is a project to build a 30-meter diameter telescope for research in astronomy at visible and infrared wavelengths. The current optical design calls for a primary, secondary, and tertiary mirror with Ritchey-Chretién foci at two Nasmyth platforms. The primary mirror is a mosaic of 1080 actively-stabilized hexagonal segments. This paper summarizes a CELT report that describes a step-by-step procedure for aligning the many degrees of freedom of the CELT optics.

  18. TSGC and JSC Alignment

    Science.gov (United States)

    Sanchez, Humberto

    2013-01-01

    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  19. All about alignment

    CERN Multimedia

    2006-01-01

    The ALICE absorbers, iron wall and superstructure have been installed with great precision. The ALICE front absorber, positioned in the centre of the detector, has been installed and aligned. Weighing more than 400 tonnes, the ALICE absorbers and the surrounding support structures have been installed and aligned with a precision of 1-2 mm, hardly an easy task but a very important one. The ALICE absorbers are made of three parts: the front absorber, a 35-tonne cone-shaped structure, and two small-angle absorbers, long straight cylinder sections weighing 18 and 40 tonnes. The three pieces lined up have a total length of about 17 m. In addition to these, ALICE technicians have installed a 300-tonne iron filter wall made of blocks that fit together like large Lego pieces and a surrounding metal support structure to hold the tracking and trigger chambers. The absorbers house the vacuum chamber and are also the reference surface for the positioning of the tracking and trigger chambers. For this reason, the ab...

  20. Testing the tidal alignment model of galaxy intrinsic alignment

    CERN Document Server

    Blazek, Jonathan; Seljak, Uros

    2011-01-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w_{g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes (the latter of which is zero in the linear tidal alignment theory); (4) the alignment correlation function, w_g(r_p,theta), a recently developed statistic that generalizes the galaxy correlation func...

  1. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  2. LHCb's Time-Real Alignment in RunII

    CERN Multimedia

    Batozskaya, Varvara

    2015-01-01

    LHCb has introduced a novel real-time detector alignment and calibration strategy for LHC Run 2. Data collected at the start of the fill will be processed in a few minutes and used to update the alignment, while the calibration constants will be evaluated for each run. This procedure will improve the quality of the online alignment. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. This offers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configur...

  3. Research on the risk assessment of route alignment based on the improved AHP%基于改进AHP法的道路选线风险评估研究

    Institute of Scientific and Technical Information of China (English)

    李军; 蒋世琼

    2013-01-01

    阐述了现行道路选线设计中存在的不确定因素对整体选线设计造成的影响,分析了在道路选线设计中引入风险评估思想,以风险估计结果作为选线设计可行性分析的一个重要参数的可行性和实用性.通过逆向风险识别思维,提出选线设计风险“隐因子”的概念,建立了风险识别HOI模型,即隐因子风险识别模型.基于该风险识别模型构建相应的风险指标层次结构体系,利用层次分析法与BP神经网络相结合的优化AHP法,结合各指标对选线风险的影响权值进行风险评价分析,对该类不确定因素进行综合评估.实例证明,风险评估的引入能够为选线设计可行性研究阶段线路方案的评价提供参考.%This paper presents an improved risk assessment method in the design of road alignment. As is known, risk assessment can help the road designers to heighten the comprehensive view of their designing approach and ameliorate their subjective analysis of the environmental and economic uncertainties. It is from these actual needs that we would like to describe the impacts of uncertainties in route selection and its relation to the entire work of road design. It is just for these purposes and other inclinations concerned, we should like to present our discussion on the feasibility and practicality of the risk assessment to be taken into account as an important reference to the feasibility analysis of the route alignment. Starting from this point, we have first of all put forward the ideas on fully considering on how to i-dentify "hidden factors" in the risk assessment process and the concept of reverse risk identification. The concept is by nature closely connected with the environmental and economic uncertainty in the stage of route selection. And, then, we have established the identification model, named "HOI" model, based on which we have built up the corresponding hierarchy of risk indicators. And, afterwards, we have

  4. Onorbit IMU alignment error budget

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  5. Lunar Alignments - Identification and Analysis

    Science.gov (United States)

    González-García, A. César

    Lunar alignments are difficult to establish given the apparent lack of written accounts clearly pointing toward lunar alignments for individual temples. While some individual cases are reviewed and highlighted, the weight of the proof must fall on statistical sampling. Some definitions for the lunar alignments are provided in order to clarify the targets, and thus, some new tools are provided to try to test the lunar hypothesis in several cases, especially in megalithic astronomy.

  6. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  7. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection

    Science.gov (United States)

    Loayza, María Fernanda; Villavicencio, Fernando Xavier; Santander, Stephanie Carolina; Baldeón, Manuel; Ponce, Lourdes Karina; Salvador, Iván; Vivar Díaz, Nicolás

    2014-01-01

    To assess the molecular events exerted by Helicobacter pylori interacting directly with gastric epithelial cells, an improved procedure for microbial DNA isolation from stained hematoxilin-eosin gastric biopsies was developed based on laser micro-dissection (LM) [1]. Few articles have described the use of LM to select and detect H. pylori genome from formalin-fixed paraffin embedded gastric tissue [2]. To improve the yield and quality of DNA isolated from H. pylori contacting intestinal epithelial cells, the following conditions were established after modification of the QIAamp DNA Micro kit. • Use of at least 25 cut sections of 10–20 μm of diameter and 3 μm thick with more than 10 bacteria in each cut. • Lysis with 30 μL of tissue lysis buffer and 20 μL of proteinase K (PK) with the tube in an upside-down position. • The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium. PMID:26150965

  8. Improved method for extraction and detection of Helicobacter pylori DNA in formalin-fixed paraffin embedded gastric biopsies using laser micro-dissection.

    Science.gov (United States)

    Loayza, María Fernanda; Villavicencio, Fernando Xavier; Santander, Stephanie Carolina; Baldeón, Manuel; Ponce, Lourdes Karina; Salvador, Iván; Vivar Díaz, Nicolás

    2015-01-01

    To assess the molecular events exerted by Helicobacter pylori interacting directly with gastric epithelial cells, an improved procedure for microbial DNA isolation from stained hematoxilin-eosin gastric biopsies was developed based on laser micro-dissection (LM) [1]. Few articles have described the use of LM to select and detect H. pylori genome from formalin-fixed paraffin embedded gastric tissue [2]. To improve the yield and quality of DNA isolated from H. pylori contacting intestinal epithelial cells, the following conditions were established after modification of the QIAamp DNA Micro kit. •Use of at least 25 cut sections of 10-20 μm of diameter and 3 μm thick with more than 10 bacteria in each cut.•Lysis with 30 μL of tissue lysis buffer and 20 μL of proteinase K (PK) with the tube in an upside-down position.•The use of thin purification columns with 35 μL of elution buffer. The mean of DNA concentration obtained from 25 LM cut sections was 1.94± 0 .16 ng/μL, and it was efficiently amplified with qPCR in a Bio Rad iCycler instrument. The LM can improve the sample selection and DNA extraction for molecular analysis of H. pylori associated with human gastric epithelium.

  9. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    Full Text Available BACKGROUND: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY: We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS: We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

  10. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  11. Moving State Marine SINS Initial Alignment Based on High Degree CKF

    Directory of Open Access Journals (Sweden)

    Yong-Gang Zhang

    2014-01-01

    Full Text Available A new moving state marine initial alignment method of strap-down inertial navigation system (SINS is proposed based on high-degree cubature Kalman filter (CKF, which can capture higher order Taylor expansion terms of nonlinear alignment model than the existing third-degree CKF, unscented Kalman filter and central difference Kalman filter, and improve the accuracy of initial alignment under large heading misalignment angle condition. Simulation results show the efficiency and advantage of the proposed initial alignment method as compared with existing initial alignment methods for the moving state SINS initial alignment with large heading misalignment angle.

  12. Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament.

    KAUST Repository

    Fornander, Louise H

    2013-12-03

    The Swi5-Sfr1 heterodimer protein stimulates the Rad51-promoted DNA strand exchange reaction, a crucial step in homologous recombination. To clarify how this accessory protein acts on the strand exchange reaction, we have analyzed how the structure of the primary reaction intermediate, the Rad51/single-stranded DNA (ssDNA) complex filament formed in the presence of ATP, is affected by Swi5-Sfr1. Using flow linear dichroism spectroscopy, we observe that the nucleobases of the ssDNA are more perpendicularly aligned to the filament axis in the presence of Swi5-Sfr1, whereas the bases are more randomly oriented in the absence of Swi5-Sfr1. When using a modified version of the natural protein where the N-terminal part of Sfr1 is deleted, which has no affinity for DNA but maintained ability to stimulate the strand exchange reaction, we still observe the improved perpendicular DNA base orientation. This indicates that Swi5-Sfr1 exerts its activating effect through interaction with the Rad51 filament mainly and not with the DNA. We propose that the role of a coplanar alignment of nucleobases induced by Swi5-Sfr1 in the presynaptic Rad51/ssDNA complex is to facilitate the critical matching with an invading double-stranded DNA, hence stimulating the strand exchange reaction.

  13. Aligned-Braided Nanofibrillar Scaffold with Endothelial Cells Enhances Arteriogenesis.

    Science.gov (United States)

    Nakayama, Karina H; Hong, Guosong; Lee, Jerry C; Patel, Jay; Edwards, Bryan; Zaitseva, Tatiana S; Paukshto, Michael V; Dai, Hongjie; Cooke, John P; Woo, Y Joseph; Huang, Ngan F

    2015-07-28

    The objective of this study was to enhance the angiogenic capacity of endothelial cells (ECs) using nanoscale signaling cues from aligned nanofibrillar scaffolds in the setting of tissue ischemia. Thread-like nanofibrillar scaffolds with porous structure were fabricated from aligned-braided membranes generated under shear from liquid crystal collagen solution. Human ECs showed greater outgrowth from aligned scaffolds than from nonpatterned scaffolds. Integrin α1 was in part responsible for the enhanced cellular outgrowth on aligned nanofibrillar scaffolds, as the effect was abrogated by integrin α1 inhibition. To test the efficacy of EC-seeded aligned nanofibrillar scaffolds in improving neovascularization in vivo, the ischemic limbs of mice were treated with EC-seeded aligned nanofibrillar scaffold; EC-seeded nonpatterned scaffold; ECs in saline; aligned nanofibrillar scaffold alone; or no treatment. After 14 days, laser Doppler blood spectroscopy demonstrated significant improvement in blood perfusion recovery when treated with EC-seeded aligned nanofibrillar scaffolds, in comparison to ECs in saline or no treatment. In ischemic hindlimbs treated with scaffolds seeded with human ECs derived from induced pluripotent stem cells (iPSC-ECs), single-walled carbon nanotube (SWNT) fluorophores were systemically delivered to quantify microvascular density after 28 days. Near infrared-II (NIR-II, 1000-1700 nm) imaging of SWNT fluorophores demonstrated that iPSC-EC-seeded aligned scaffolds group showed significantly higher microvascular density than the saline or cells groups. These data suggest that treatment with EC-seeded aligned nanofibrillar scaffolds improved blood perfusion and arteriogenesis, when compared to treatment with cells alone or scaffold alone, and have important implications in the design of therapeutic cell delivery strategies.

  14. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  15. Modified "DMC" technique for stretching DNA molecules

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A modified "dynamic molecular combing"(DMC)technique used for stretching double-strandedDNA is reported. DNA molecules were stretched on the silanized mica surface by thistechnique, its speed being precisely controlled with a computer. This approachcombinedthe precise DNA stretching method with high resolution AFM imaging at nanometer scale,thusmaking it useful for DNA alignment manipulation and subsequent gene research.

  16. Metabolic network alignment in large scale by network compression

    Directory of Open Access Journals (Sweden)

    Ay Ferhat

    2012-03-01

    Full Text Available Abstract Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far limited their use to moderately sized networks. In this paper, we address the problem of aligning two metabolic networks, particularly when both of them are too large to be dealt with using existing methods. We develop a generic framework that can significantly improve the scale of the networks that can be aligned in practical time. Our framework has three major phases, namely the compression phase, the alignment phase and the refinement phase. For the first phase, we develop an algorithm which transforms the given networks to a compressed domain where they are summarized using fewer nodes, termed supernodes, and interactions. In the second phase, we carry out the alignment in the compressed domain using an existing network alignment method as our base algorithm. This alignment results in supernode mappings in the compressed domain, each of which are smaller instances of network alignment problem. In the third phase, we solve each of the instances using the base alignment algorithm to refine the alignment results. We provide a user defined parameter to control the number of compression levels which generally determines the tradeoff between the quality of the alignment versus how fast the algorithm runs. Our experiments on the networks from KEGG pathway database demonstrate that the compression method we propose reduces the sizes of metabolic networks by almost half at each compression level which provides an expected speedup of more than an order of magnitude. We also observe that the alignments obtained by only one level of compression capture the original alignment results with high accuracy. Together, these suggest that our

  17. Mask alignment system for semiconductor processing

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.

    2017-02-14

    A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.

  18. Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp..

    Directory of Open Access Journals (Sweden)

    Cameron R Turner

    Full Text Available Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp., an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

  19. Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).

    Science.gov (United States)

    Turner, Cameron R; Miller, Derryl J; Coyne, Kathryn J; Corush, Joel

    2014-01-01

    Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

  20. Effects of Sperm DNA Fragmentation on Semen Parameters and ICSI Outcome Determined by an Improved SCD Test,Halosperm

    OpenAIRE

    Asuman Demiroglu Zergeroğlu; Seda Yılmaz; Pelin Kutlu; Nuri Delikara; Kenan Sofuoglu

    2010-01-01

    Background: Sperm DNA fragmentation is known as an important cause of male infertility.The influence of sperm DNA damage on reproductive potential has been subject of many studiesindicating various results and remaining the subject controversial. In this study, we investigateddifferences of the semen parameters and intracytoplasmic sperm injection (ICSI) outcome accordingto sperm DNA fragmentation levels (DFLs) of patients.Materials and Methods: The DFLs were determined by Halosperm, a new im...

  1. Evaluation of methods to improve the extraction and recovery of DNA from cotton swabs for forensic analysis.

    Science.gov (United States)

    Adamowicz, Michael S; Stasulli, Dominique M; Sobestanovich, Emily M; Bille, Todd W

    2014-01-01

    Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C) as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations.

  2. Evaluation of methods to improve the extraction and recovery of DNA from cotton swabs for forensic analysis.

    Directory of Open Access Journals (Sweden)

    Michael S Adamowicz

    Full Text Available Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations.

  3. An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment

    NARCIS (Netherlands)

    Bauer, M.; Klau, G.W.; Reinert, K.

    2008-01-01

    One of the main tasks in computational biology is the computation of alignments of genomic sequences to reveal their commonalities. In case of DNA or protein sequences, sequence information alone is usually sufficient to compute reliable alignments. RNA molecules, however, build spatial confor

  4. SVM with discriminative dynamic time alignment

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In the past several years, support vector machines (SVM) have achieved a huge success in many field, especially in pattern recognition. But the standard SVM cannot deal with length-variable vectors, which is one severe obstacle for its applications to some important areas, such as speech recognition and part-of-speech tagging. The paper proposed a novel SVM with discriminative dynamic time alignment (DDTA-SVM) to solve this problem. When training DDTA-SVM classifier, according to the category information of the training Samples, different time alignment strategies were adopted to manipulate them in the kernel functions, which contributed to great improvement for training speed and generalization capability of the classifier. Since the alignment operator was embedded in kernel functions, the training algorithms of standard SVM were still compatible in DDTA-SVM. In order to increase the reliability of the classification, a new classification algorithm was suggested. The preliminary experimental results on Chinese confusable syllables speech classification task show that DDTA-SVM obtains faster convergence speed and better classification performance than dynamic time alignment kernel SVM (DTAK-SVM).Moreover, DDTA-SVM also gives higher classification precision compared to the conventional HMM. This proves that the proposed method is effective, especially for confusable lengthvariable pattern classification tasks.

  5. A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction.

    Science.gov (United States)

    Yang, Yuedong; Zhan, Jian; Zhao, Huiying; Zhou, Yaoqi

    2012-08-01

    A structure alignment program aligns two structures by optimizing a scoring function that measures structural similarity. It is highly desirable that such scoring function is independent of the sizes of proteins in comparison so that the significance of alignment across different sizes of the protein regions aligned is comparable. Here, we developed a new score called SP-score that fixes the cutoff distance at 4 Å and removed the size dependence using a normalization prefactor. We further built a program called SPalign that optimizes SP-score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding. For fold discrimination, SPalign improves sensitivity over TMalign for the chain-level comparison by 12% and over DALI for the domain-level comparison by 13% at the same specificity of 99.6%. The difference between TMalign and SPalign at the chain level is due to the inability of TMalign to detect single domain similarity between multidomain proteins. For recognizing nucleic acid binding proteins, SPalign consistently improves over TMalign by 12% and DALI by 31% in average value of Mathews correlation coefficients for four datasets. SPalign with default setting is 14% faster than TMalign. SPalign is expected to be useful for function prediction and comparing structures with or without domains defined. The source code for SPalign and the server are available at http://sparks.informatics.iupui.edu.

  6. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp and Aspergillus niger phytase gene phyA (1404 bp. Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  7. S/MAR-containing DNA nanoparticles promote persistent RPE gene expression and improvement in RPE65-associated LCA.

    Science.gov (United States)

    Koirala, Adarsha; Makkia, Rasha S; Conley, Shannon M; Cooper, Mark J; Naash, Muna I

    2013-04-15

    Mutations in genes in the retinal pigment epithelium (RPE) cause or contribute to debilitating ocular diseases, including Leber's congenital amaurosis (LCA). Genetic therapies, particularly adeno-associated viruses (AAVs), are a popular choice for monogenic diseases; however, the limited payload capacity of AAVs combined with the large number of retinal disease genes exceeding that capacity make the development of alternative delivery methods critical. Here, we test the ability of compacted DNA nanoparticles (NPs) containing a plasmid with a scaffold matrix attachment region (S/MAR) and vitelliform macular dystrophy 2 (VMD2) promoter to target the RPE, drive long-term, tissue-specific gene expression and mediate proof-of-principle rescue in the rpe65(-/-) model of LCA. We show that the S/MAR-containing plasmid exhibited reporter gene expression levels several fold higher than plasmid or NPs without S/MARs. Importantly, this expression was highly persistent, lasting up to 2 years (last timepoint studied). We therefore selected this plasmid for testing in the rpe65(-/-) mouse model and observe that NP or plasmid VMD2-hRPE65-S/MAR led to structural and functional improvements in the LCA disease phenotype. These results indicate that the non-viral delivery of hRPE65 vectors can result in persistent, therapeutically efficacious gene expression in the RPE.

  8. A simple and accurate two-step long DNA sequences synthesis strategy to improve heterologous gene expression in pichia.

    Science.gov (United States)

    Yang, Jiang-Ke; Chen, Fang-Yuan; Yan, Xiang-Xiang; Miao, Li-Hong; Dai, Jiang-Hong

    2012-01-01

    In vitro gene chemical synthesis is a powerful tool to improve the expression of gene in heterologous system. In this study, a two-step gene synthesis strategy that combines an assembly PCR and an overlap extension PCR (AOE) was developed. In this strategy, the chemically synthesized oligonucleotides were assembled into several 200-500 bp fragments with 20-25 bp overlap at each end by assembly PCR, and then an overlap extension PCR was conducted to assemble all these fragments into a full length DNA sequence. Using this method, we de novo designed and optimized the codon of Rhizopus oryzae lipase gene ROL (810 bp) and Aspergillus niger phytase gene phyA (1404 bp). Compared with the original ROL gene and phyA gene, the codon-optimized genes expressed at a significantly higher level in yeasts after methanol induction. We believe this AOE method to be of special interest as it is simple, accurate and has no limitation with respect to the size of the gene to be synthesized. Combined with de novo design, this method allows the rapid synthesis of a gene optimized for expression in the system of choice and production of sufficient biological material for molecular characterization and biotechnological application.

  9. Fecal Collection and Stabilization Methods for Improved Fecal DNA Test for Colorectal Cancer in a Screening Setting

    Directory of Open Access Journals (Sweden)

    Francesca Maria Carozzi

    2013-01-01

    Full Text Available Early detection of CRC and adenomas reduces CRC-related mortality. The optimal screening test for CRC is still a subject of debate, and molecular stool sample analysis could provide a valid alternative to conventional methods in terms of compliance and practicability. Seven fecal DNA storage systems were evaluated in two successive phases. In the first phase of the study was selected the preservative buffer able to ensure the best human DNA recovery. In the second phase was evaluated human DNA stability, amplificability and integrity in DNA extracted from selected buffer. Results showed that the best performance was obtained in samples stored in 100 mM EDTA buffer and Genefec buffer. Likewise buffer addition yielded a significant increase in DNA stability and integrity without PCR inhibition, compared to the matched aliquots with no buffer added. Our study shows that samples collected in stabilization solution stabilize DNA so that intact nucleic acids, are more effectively detectable in the molecular assay. DNA buffer preservation and storage conditions could be useful to guarantee the most consistent yield in human DNA. Stabilization buffer addition to stool samples prior to transport presents an easily implemented solution that appears to be highly effective. Overall DNA extracted from faeces preserved in preservative buffer can feasibility been used for molecular analysis leading to an increase of assay sensitivity.

  10. An improved method for genomic DNA extraction from strawberry leaves Otimização de um método para extração de DNA genômico a partir de folhas de morangueiro

    Directory of Open Access Journals (Sweden)

    Claudinéia Ferreira Nunes

    2011-08-01

    Full Text Available Several extraction methods of genomic DNA for identification and characterization of genetic diversity in different plant species are routinely applied during molecular analysis. However, the presence of undesirable compounds such as polyphenols and polysaccharides is one of the biggest problems faced during the isolation and purification of high quality DNA in plants. Therefore, achievement of fast and accurate methods for DNA extraction is crucial in order to produce pure samples. Leaves of strawberry genotypes (Fragaria ananassa have high contents of polysaccharides and polyphenols which increase the sample viscosity and decrease the DNA quality, interfering with the PCR performance. Thereby, in this study we evaluated the quality and amount of genomic DNA extracted from young leaves of strawberry after tissue lyophilization and maceration in presence of polivinilpirrolidone (PVP. The CTAB method was used as reference procedure and it was modified to improve the DNA extraction. The modifications consisted of tissue lyophilization overnight until it was completely freeze-dried and addition of PVP during the tissue maceration in liquid nitrogen. The results showed the efficiency and reliability of the modified method compared to the unmodified method, indicating that combination of lyophilization and PVP improve the quality and amount of the DNA extracted from strawberry leaves.Vários métodos de extração de DNA genômico para a identificação e caracterização da diversidade genética em diferentes espécies de plantas são rotineiramente aplicados durante a análise molecular. Entretanto, a presença de compostos indesejáveis, tais como polifenóis e polissacarídeos, é um dos maiores problemas que ocorrem durante o isolamento e purificação de DNA de alta qualidade em plantas. Dessa forma, o sucesso no desenvolvimento de métodos de extração de DNA rápidos e acurados é crucial para produzir amostras puras. Folhas de genótipos de

  11. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

    Full Text Available High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1 a top-level summary of the top candidate sequences aligned to each reference sequence, 2 a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3 a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  12. CATO: The Clone Alignment Tool.

    Science.gov (United States)

    Henstock, Peter V; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  13. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and alig...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter.......Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... two or more sequences. The advantage of this algorithm over those that separate the folding and alignment steps is that it makes better predictions. The disadvantage is that it is slower and requires more computer memory to run. The amount of computational resources needed to run the Sankoff algorithm...

  14. Lexical alignment in triadic communication.

    Science.gov (United States)

    Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

    2015-01-01

    Lexical alignment refers to the adoption of one's interlocutor's lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants' lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment.

  15. Vacuum Alignment with more Flavors

    DEFF Research Database (Denmark)

    Ryttov, Thomas

    2014-01-01

    We study the alignment of the vacuum in gauge theories with $N_f$ Dirac fermions transforming according to a complex representation of the gauge group. The alignment of the vacuum is produced by adding a small mass perturbation to the theory. We study in detail the $N_f=2,3$ and $4$ case. For $N...

  16. Study on compound ultra-precision alignment technique

    Institute of Scientific and Technical Information of China (English)

    Zhang Jinlong; Yang Ankang; Liu Jingnan; Yoshiyuki Uchida

    2007-01-01

    A nano-displacement measurement system with duo-gratings is analyzed by using optics theory, a mathematic model for the system is established, and the characteristic of laser Moiré signals is studied through CAD simulation. To improve signal sensitivity and positioning accuracy, two methods of precision positioning are brought forward: differential Moiré positioning method and modified Moiré positioning method. A compound control system for precision positioning is set up by combining these 2 Moiré alignment methods, in which the modified Moiré alignment technique is used for coarse alignment and the differential Moiré alignment technique is used for fine alignment, and the system obtains positioning accuracy of ±10 nm in ±500 μm positioning range with shot response time.

  17. A context dependent pair hidden Markov model for statistical alignment

    CERN Document Server

    Arribas-Gil, Ana

    2011-01-01

    This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation of two homologous sequences. The procedure is based on a generalized pair-hidden Markov structure, where conditional on the alignment path, the nucleotide sequences follow a Markov distribution. We use a stochastic approximation expectation maximization (saem) algorithm to give accurate estimators of parameters and alignments. We provide results both on simulated data and vertebrate genomes, which are known to have a high mutation rate from CG dinucleotide. In particular, we establish that the method improves the accuracy of the alignment of a human pseudogene and its functional gene.

  18. The Laser Shaft Alignment System with Dual PSDs

    Institute of Scientific and Technical Information of China (English)

    JIAO Guohua; LI Yulin; ZHANG Dongbo; LI Tonghai; HU Baowen

    2006-01-01

    Shaft alignment is an important technique during installation and maintenance of a rotating machine. A high-precision laser alignment system has been designed with dual PSDs (Position Sensing Detector) to change traditional manual way of shaft alignment and to make the measurement easier and more accurate. The system is comprised of two small measuring units (laser transmitter and detector) and a PDA (Personal Digital Assistant) with the measurement software. The laser alignment system with dual PSDs was improved on a single PSD system, and it gets higher measurement accuracy than the previous design, and it has been succeeded in designing and implement for actual shaft alignment. In the system, the range of offset measurement is ±4 mm, and the resolution is 1.5 μm, and the accuracy is less than 2 μm.

  19. A laser shaft alignment system with dual PSDs

    Institute of Scientific and Technical Information of China (English)

    JIAO Guo-hua; LI Yu-lin; ZHANG Dong-bo; LI Tong-hai; HU Bao-wen

    2006-01-01

    Shaft alignment is an important technique during installation and maintenance of a rotating machine. A high-precision laser alignment system has been designed with dual PSDs (Position Sensing Detector) to change traditional manual way of shaft alignment and to make the measurement easier and more accurate. The system is comprised of two small measuring units (laser transmitter and detector) and a PDA (Personal Digital Assistant) with measurement software. The laser alignment system with dual PSDs was improved on a single PSD system, and yields higher measurement accuracy than the previous design, and has been successful for designing and implements actual shaft alignment. In the system, the range of offset measurement is ±4 mm, and the resolution is 1.5 μm, with accuracy being less than 2 μm.

  20. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  1. Alignment of flexible protein structures.

    Science.gov (United States)

    Shatsky, M; Fligelman, Z Y; Nussinov, R; Wolfson, H J

    2000-01-01

    We present two algorithms which align flexible protein structures. Both apply efficient structural pattern detection and graph theoretic techniques. The FlexProt algorithm simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. It does it by efficiently detecting maximal congruent rigid fragments in both molecules and calculating their optimal arrangement which does not violate the protein sequence order. The FlexMol algorithm is sequence order independent, yet requires as input the hypothesized hinge positions. Due its sequence order independence it can also be applied to protein-protein interface matching and drug molecule alignment. It aligns the rigid parts of the molecule using the Geometric Hashing method and calculates optimal connectivity among these parts by graph-theoretic techniques. Both algorithms are highly efficient even compared with rigid structure alignment algorithms. Typical running times on a standard desktop PC (400 MHz) are about 7 seconds for FlexProt and about 1 minute for FlexMol.

  2. Alignments in the nobelium isotopes

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Zie; XU Fu-Rong; YUAN Cen-Xi; QI Chong

    2009-01-01

    Total-Routhian-Surface calculations have been performed to investigate the deformation and align-ment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, align-ments develop at hω=0.2-0.3 MeV. Our calculations show that the occupation of the vj orbital plays an important role in the alignments of the No isotopes.

  3. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

    Science.gov (United States)

    Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Cheatham, Thomas E; Galindo-Murillo, Rodrigo; Jurečka, Petr

    2015-12-01

    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

  4. An improved method to extract DNA from 1 ml of uncultured amniotic fluid from patients at less than 16 weeks' gestation.

    Directory of Open Access Journals (Sweden)

    Anne-Laure Mosca-Boidron

    Full Text Available The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003. All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.

  5. Downlink Interference Alignment

    CERN Document Server

    Suh, Changho; Tse, David

    2010-01-01

    We develop an interference alignment (IA) technique for a downlink cellular system. In the uplink, IA schemes need channel-state-information exchange across base-stations of different cells, but our downlink IA technique requires feedback only within a cell. As a result, the proposed scheme can be implemented with a few changes to an existing cellular system where the feedback mechanism (within a cell) is already being considered for supporting multi-user MIMO. Not only is our proposed scheme implementable with little effort, it can in fact provide substantial gain especially when interference from a dominant interferer (base-station) is significantly stronger than the remaining interference: it is shown that in the two-isolated cell layout, our scheme provides four-fold gain in throughput performance over a standard multi-user MIMO technique. We show through simulations that our technique provides respectable gain under more realistic scenarios: it gives approximately 55% and 20% gain for a linear cell layou...

  6. Interference Alignment for Secrecy

    CERN Document Server

    Koyluoglu, Onur Ozan; Lai, Lifeng; Poor, H Vincent

    2008-01-01

    This paper studies the frequency/time selective $K$-user Gaussian interference channel with secrecy constraints. Two distinct models, namely the interference channel with confidential messages and the one with an external eavesdropper, are analyzed. The key difference between the two models is the lack of channel state information (CSI) about the external eavesdropper. Using interference alignment along with secrecy pre-coding, it is shown that each user can achieve non-zero secure Degrees of Freedom (DoF) for both cases. More precisely, the proposed coding scheme achieves $\\frac{K-2}{2K-2}$ secure DoF {\\em with probability one} per user in the confidential messages model. For the external eavesdropper scenario, on the other hand, it is shown that each user can achieve $\\frac{K-2}{2K}$ secure DoF {\\em in the ergodic setting}. Remarkably, these results establish the {\\em positive impact} of interference on the secrecy capacity region of wireless networks.

  7. Space Mirror Alignment System

    Science.gov (United States)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.

    2011-01-01

    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  8. Sample selection algorithm to improve quality of genotyping from plasma-derived DNA: to separate the wheat from the chaff.

    Science.gov (United States)

    Schoenborn, Veit; Gohlke, Henning; Heid, Iris M; Illig, Thomas; Utermann, Gerd; Kronenberg, Florian

    2007-11-01

    Plasma and serum samples were often the only biological material collected for earlier epidemiological studies. These studies have a huge informative content, especially due to their long follow-up and would be an invaluable treasure for genetic investigations. However, often no banked DNA is available. To use the small amounts of DNA present in plasma, in a first step, we applied magnetic bead technology to extract this DNA, followed by a whole-genome amplification (WGA) using phi29-polymerase. We assembled 88 sample pairs, each consisting of WGA plasma DNA and the corresponding whole-blood DNA. We genotyped nine highly polymorphic short tandem repeats (STRs) and 23 SNPs in both DNA sources. The average within-pair discordance was 3.8% for SNPs and 15.9% for STR genotypes, respectively. We developed an algorithm based on one-half of the sample pairs and validated on the other one-half to identify the samples with high WGA plasma DNA quality to assure low genotyping error and to exclude plasma DNA samples with insufficient quality: excluding samples showing homozygosity at five or more of the nine STR loci yielded exclusion of 22.7% of all samples and decreased average discordance for STR and SNP markers to 3.92% and 0.63%, respectively. For SNPs, this is very close to the error observed for genomic DNA in many laboratories. Our workflow and sample selection algorithm offers new opportunities to recover reliable DNA from stored plasma material. This algorithm is superior to testing the amount of input DNA.

  9. Phylogenetic inference under varying proportions of indel-induced alignment gaps

    Directory of Open Access Journals (Sweden)

    Gadagkar Sudhindra R

    2009-08-01

    Full Text Available Abstract Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation to reflect indel (insertion/deletion events during the evolution of DNA sequences. The resulting (true alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1 In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2 gaps resulting from deletions (as opposed to insertions contributed more to the inaccuracy of phylogenetic inference, (3 the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP performed better at most levels of gap percentage when compared to parsimony (MP and distance (NJ methods, with Bayesian analysis being clearly the best, (4 methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method, and (5 in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1 alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2 the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3 methods that

  10. Physical Pre-Treatment Improves Efficient DNA Extraction and qPCR Sensitivity from Clostridium Difficile Spores in Faecal Swine Specimens.

    Science.gov (United States)

    Grześkowiak, Łukasz; Zentek, Jürgen; Vahjen, Wilfried

    2016-11-01

    A considerable fraction of the faecal microbiota is spore-forming. Molecular quantification of bacteria may be underestimated if preceded with nucleic acid extraction without special treatment to extract recalcitrant bacterial spores. The objective of this study was to improve the DNA extraction regarding the presence of Clostridium difficile spores in faecal swine specimens. Sow faeces were inoculated with spores of C. difficile (10(6) CFU), frozen at - 30 °C overnight and subjected to DNA extraction. As a preceding step to a standard DNA extraction method (QIAamp DNA stool Mini kit), different physical treatments such as microwave oven heating and repeated bead-beating techniques and a combination of both were applied and compared with each other by means of qPCR. Using a standard DNA extraction method only, C. difficile spores were quantified at 4.96 log copy number/200 mg of faeces. A repeated bead-beating at 6 m/s for 10 min followed by a standard DNA extraction resulted in 5.77 log copy number of spores in inoculated faeces. Heating in a microwave oven at 800 W for 1, 3, 5 and 10 min followed by a standard DNA extraction resulted in a gene quantification of up to 4.89 log copy number. A combination of both methods resulted in the bacterial gene quantity of 5.37 log copy number. Pre-treatment with repeated bead-beating led to the highest quantification of bacteria, and therefore it can be applied for more efficient DNA extraction from spores of C. difficile in faecal specimens.

  11. An Improved Method for DNA Extraction from the Faeces of Cervus elaphus%一种从马鹿粪便中提取DNA的改进方法

    Institute of Scientific and Technical Information of China (English)

    日沙来提·吐尔地; 艾斯卡尔·买买提; 日孜汗·阿布地艾尼; 阿米拉·阿布来提; 马合木提·哈力克

    2012-01-01

    [目的]介绍一种从马鹿粪便中提取DNA的改进方法.[方法]在传统的CTAB裂解法的基础下,根据马鹿粪便的特征进行改进所得的DNA提取方法.[结果]采用该方法从天山马鹿粪便中提取了高质量的粪便DNA并扩增出了天山马鹿线粒体细胞色素b基因片段,通过测序检测,同时以提取的马鹿肌肉和皮毛样品DNA作为对照,进一步证实了提取的可靠性.[结论]该方法提取过程中无需使用蛋白酶K;所提取的DNA无需使用DNA纯化试剂盒纯化,可直接用于PCR扩增,因此,试验费用很低.%[ Objective ] To introduce an improved method for DNA extraction from the faeces of red deer. [ Method ] Based on the traditional method of CTAB lysis,we proposed an improved DNA extraction method according to the characteristics of red deer feces. [ Result] The improved method extracted high-quality fecal DNA from Tianshan red deer and amplified the mitochondrial cytochrome b gene. The sequencing detection, using the muscle and skin DNA of red deer ad the control, further confirmed the reliability of the method. [ Conclusion ] The method requires no proteinase K in the process of extraction, and the extracted DNA can be used for PCR amplification directly without the purification of DNA purification kit,thus,the cost for the test is very low.

  12. An Improved Method for DNA Extraction from the Faeces of Red Deer%一种从马鹿粪便中提取DNA的改进方法

    Institute of Scientific and Technical Information of China (English)

    日沙来提·吐尔地; 艾斯卡尔·买买提; 日孜汗·阿布地艾尼; 阿米拉·阿布来提; 马合木提·哈力克

    2012-01-01

    [Objective] To introduce an improved method for DNA extraction from the faeces of red deer. [Method] Based on the traditional method of CTAB lysis, we proposed an improved DNA extraction method according to the characteristics of red deer faeces. [Result] This improved method extracted high-quality fecal DNA from Tianshan red deer and amplified the mitochondrial cytochrome b gene. With the muscle and fur DNA of red deer as the control, the sequencing results further con- firmed the reliability of the method. [Conclusion] The method requires no proteinase K in the process of extraction, and the extracted DNA can be used for PCR ampli- fication directly without the purification of DNA purification kit, thus, it is cost-saving.%[目的]介绍一个从马鹿粪便中提取DNA的改进方法。[方法]本实验采用的是,在传统的CTAB裂解法的基础下,根据马鹿粪便的特征摸索出来的改进方法。[结果]采用该方法从天山马鹿粪便中提取了高质量的粪便DNA并扩增了天山马鹿线粒体细胞色素b基因片段,通过测序检测,同时提取马鹿肌肉和皮毛样品的DNA作为对照,进一步证实了提取的可靠性。[结论]该方法提取过程中不需要用蛋白酶K;所提取的DNA不需要州DNA纯化试剂盒纯化,可直接用PCR扩增,因此,费用量很低。

  13. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

    Science.gov (United States)

    Hart, Katarina; Foloppe, Nicolas; Baker, Christopher M; Denning, Elizabeth J; Nilsson, Lennart; Mackerell, Alexander D

    2012-01-10

    The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles ε and ζ (BI = ε-ζ 0). BI is the most populated state, but the population of the BII state, which is sequence dependent, is significant and accumulating evidence shows that BII affects the overall structure of DNA, and thus influences protein-DNA recognition. This work presents a reparametrization of the CHARMM27 additive nucleic acid force field to increase the sampling of the BII form in MD simulations of DNA. In addition, minor modifications of sugar puckering were introduced to facilitate sampling of the A form of DNA under the appropriate environmental conditions. Parameter optimization was guided by quantum mechanical data on model compounds, followed by calculations on several DNA duplexes in the condensed phase. The selected optimized parameters were then validated against a number of DNA duplexes, with the most extensive tests performed on the EcoRI dodecamer, including comparative calculations using the Amber Parm99bsc0 force field. The new CHARMM model better reproduces experimentally observed sampling of the BII conformation, including sampling as a function of sequence. In addition, the model reproduces the A form of the 1ZF1 duplex in 75 % ethanol, and yields a stable Z-DNA conformation of duplex (GTACGTAC) in its crystal environment. The resulting model, in combination with a recent reoptimization of the CHARMM27 force field for RNA, will be referred to as CHARMM36.

  14. Extracting Total DNA from Guava(Psidium guajava L.) Leaves by Improved CTAB Method%改良CTAB法提取番石榴叶片总DNA

    Institute of Scientific and Technical Information of China (English)

    王家保; 杜中军; 雷新涛; 徐碧玉

    2006-01-01

    目的:从番石榴叶片中快速提取高质量的总DNA.方法:改良CTAB法.主要改进之处在于不用液氮,而是直接研磨硅胶干燥样品;用高浓度CTAB、低浓度乙醇与NaCl盐析相结合等方法去除多糖.结果:应用改良后的方法可以快速提取番石榴叶片总DNA,有效去除组织中的多糖、蛋白质,抑制提取过程中的组织褐变.提取的DNA可用于限制性内切酶酶切和PCR扩增.结论:传统CTAB法经过改良,可用于快速提取番石榴高质量DNA.

  15. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    Science.gov (United States)

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  16. A improved method for extracting genomic DNA from reserved blood%改良碘化钾法提取冻存外周血基因组 DNA 的方法探讨

    Institute of Scientific and Technical Information of China (English)

    蔡雪梅; 李穗雯; 胡大春

    2013-01-01

    Objective To explore the modified potassium iodide method (Improved method) for extracting the long-term cryopreservation of peripheral blood genomic DNA. Methods The potassium iodide (KI) method was improved by increasing the blood volume from 100μL to 200μL, replacing the sterile distilled water with 0.9% NH4CL solution for destruction the red blood cells, increasing the 5 mol/L KI solution dosage(70μL) for cracking the white cells membrane, and centrifuging at low temperature(4℃ ). The modified potassium iodide method was used for extracting the genomic DNA from 82 blood samples reserved in -80℃, and the concentration and purity of the extracted DNA was compared with the KI method. Meanwhile the extracted DNA was used as the template to amplify CYP2C19 gene by PCR. Results The extracted DNA concentration and A260/A280 of the KI method and the improved method were 128.2±34.9μg/mL, 1.74±0.08 and 220±91.29μg/mL, 1.87±0.12, respectively. The DNA purity of improved method was higher, and there were significant statistically different (P<0.01). The amount of DNA extracted by the modified method was more than that of KI method. The genomic DNA extracted by improved method were amplified using PCR, which result were stable. Conclusion The genomic DNA extracted from the long-term cryopreservation of peripheral blood using improved KI method had higher quality, which were able to meet the demand on the clinical study of cryopreserved samples.%  目的探讨用改良碘化钾法(改良法)提取长期冻存外周血基因组 DNA 的方法.方法对碘化钾(KI)法加以改良,包括:血量由100μL 增加到200μL;使用0.9% NH4CL 溶液代替无菌重蒸馏水裂解红细胞;增加裂解白细胞膜的5 mol/L KI 溶液的用量(为70μL);低温(4℃)离心.然后用改良碘化钾法从82份-80℃冻存外周血标本中提取基因组 DNA.同时使用碘化钾法提取其中的30份血标本,比对两种方法提取 DNA

  17. Aligning for Innovation - Alignment Strategy to Drive Innovation

    Science.gov (United States)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  18. GATA: a graphic alignment tool for comparative sequence analysis

    Directory of Open Access Journals (Sweden)

    Nix David A

    2005-01-01

    Full Text Available Abstract Background Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments. Results To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA http://gata.sourceforge.net/. GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF file. Conclusions GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA

  19. Controle da qualidade no laboratório clínico: alinhando melhoria de processos, confiabilidade e segurança do paciente Quality control in clinical laboratory: aligning process improvement, reliability and patient safety

    Directory of Open Access Journals (Sweden)

    Fernando de Almeida Berlitz

    2010-10-01

    has been widely pursued as a theoretical basis for this issue is high reliability organization (HRO. In this paper we propose a new approach to analytical quality control (AQC, based on HRO principles and focused on patient safety improvement. OBJECTIVES: To propose a new approach to AQC system, aligned with HRO theory and focused on patient safety improvement. MATERIALS AND METHODS: In order to optimize the traditional AQC approach and make feasible the long term assessment of system stability, we propose a model based on evaluation of random and systematic error by means of advanced control charts. We used real data obtained from the routine to validate the simulated model (glucose, Vitros FS 5.1, OCD. RESULTS: The studied assay was evaluated in terms of long term performance and showed an adequate performance (4.1 sigma for its diagnostic use. DISCUSSION: The proposed model suggests an alternative tool based on expertise already widely applied in statistical process control in order to control long-term stability of laboratory methods. CONCLUSION: The new proposed approach, which is a complement to the traditional quality control system and involves the sequential and associated use of different statistical tools, proved to be a valid and useful model for effective performance evaluation and its ongoing performance stability.

  20. Magnetic axis alignment and the Poisson alignment reference system

    Science.gov (United States)

    Griffith, Lee V.; Schenz, Richard F.; Sommargren, Gary E.

    1989-01-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This paper begins with a review of the motivation for developing an alignment system that will assure better than 100 micrometer accuracy in the alignment of the magnetic axis throughout an FEL. The paper describes techniques for identifying the magnetic axis of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development and use of the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. An error budget shows that the Poisson alignment reference system will make it possible to meet the alignment tolerances for an FEL.

  1. DNA barcoding as an effective tool in improving a digital plant identification system: a case study for the area of Mt. Valerio, Trieste (NE Italy.

    Directory of Open Access Journals (Sweden)

    Ilaria Bruni

    Full Text Available BACKGROUND: Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting. DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy. The core barcode markers (plastidial rbcL and matK, plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios. CONCLUSIONS/SIGNIFICANCE: Our results show that the core barcode markers univocally identify most species of our local flora (96%. The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant

  2. Evryscope Robotilter automated camera / ccd alignment system

    Science.gov (United States)

    Ratzloff, Jeff K.; Law, Nicholas M.; Fors, Octavi; Ser, Daniel d.; Corbett, Henry T.

    2016-08-01

    We have deployed a new class of telescope, the Evryscope, which opens a new parameter space in optical astronomy - the ability to detect short time scale events across the entire sky simultaneously. The system is a gigapixel-scale array camera with an 8000 sq. deg. field of view, 13 arcsec per pixel sampling, and the ability to detect objects brighter than g = 16 in each 2-minute exposure. The Evryscope is designed to find transiting exoplanets around exotic stars, as well as detect nearby supernovae and provide continuous records of distant relativistic explosions like gamma-ray-bursts. The Evryscope uses commercially available CCDs and optics; the machine and assembly tolerances inherent in the mass production of these parts introduce problematic variations in the lens / CCD alignment which degrades image quality. We have built an automated alignment system (Robotilters) to solve this challenge. In this paper we describe the Robotilter system, mechanical and software design, image quality improvement, and current status.

  3. Interference Alignment with Analog Channel State Feedback

    CERN Document Server

    Ayach, Omar El

    2010-01-01

    Interference alignment (IA) is a multiplexing gain optimal transmission strategy for the interference channel with an arbitrary number of users. While the achieved sum rate with IA is much higher than previously thought possible, the improvement comes at the cost of requiring network channel state information at the transmitters. This can be achieved by explicit feedback, a flexible yet costly approach that incurs large overhead and limits throughput. We propose using analog feedback as an alternative to limited feedback or reciprocity based alignment. We show that the full multiplexing gain observed with perfect channel knowledge is preserved by analog feedback and the mean loss in sum rate is bounded by a constant when signal-to-noise ratio is comparable in both forward and feedback channels. When such feedback quality is not quite possible, a fraction of the degrees of freedom is achieved. We consider the overhead of training and feedback and use this framework to optimize the system's effective throughput...

  4. Kinetics of DNA tile dimerization.

    Science.gov (United States)

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  5. Score distributions of gapped multiple sequence alignments down to the low-probability tail

    Science.gov (United States)

    Fieth, Pascal; Hartmann, Alexander K.

    2016-08-01

    Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10-160, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments.

  6. Improved DNA extraction efficiency from low level cell numbers using a silica monolith based micro fluidic device.

    Science.gov (United States)

    Kashkary, Loay; Kemp, Cordula; Shaw, Kirsty J; Greenway, Gillian M; Haswell, Stephen J

    2012-10-31

    The evaluation of a micro fluidic system with an integrated silica monolith for performing DNA extraction from limited biological samples has been carried out. Low DNA target concentrations usually require the addition of carrier RNA to ensure desired extraction efficiencies. Here, we demonstrate a micro fluidic extraction system with increasingly efficient extraction performances for biological samples containing extracted DNA showed successful amplification via the polymerase chain reaction demonstrating both the effectiveness of the proposed system at removing potential inhibitors and yielding good quality DNA. The work presented here beneficially identifies reduced sample volumes/concentrations as suitable for processing with respect to downstream analysis by enabling pre-concentration of the biological sample, particularly important when dealing with clinical or forensic specimens.

  7. PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif

    Science.gov (United States)

    Böhlke, Kristina; Pisani, Francesca M.; Vorgias, Constantinos E.; Frey, Bruno; Sobek, Harald; Rossi, Mosè; Antranikian, Garabed

    2000-01-01

    The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of the tyrosine at position 387 (Tyr387→Phe, Tyr387→Trp, Tyr387→His, Tyr387→Asn and Tyr387→Ser) revealed that an aromatic ring system is crucial for the synthetic activity of the enzyme. Amino acids at this position lacking the ring system (Ser and Asn) led to a significant decrease in polymerase activity and to enhanced exonuclease activity, which resulted in improved enzyme fidelity. Exchange of tyrosine to phenylalanine, tryptophan or histidine led to phenotypes with wild-type-like fidelity but enhanced PCR performance that could be related to a higher velocity of polymerisation. With the help of a modelled structure of T.aggregans DNA polymerase, the biochemical data were interpreted proposing that the conformation of the flexible loop containing the Y-GG/A motif is an important factor for the equilibrium between DNA polymerisation and exonucleolysis. PMID:11024170

  8. A fast and accurate initial alignment method for strapdown inertial navigation system on stationary base

    Institute of Scientific and Technical Information of China (English)

    Xinlong WANG; Gongxun SHEN

    2005-01-01

    In this work,a fast and accurate stationary alignment method for strapdown inertial navigation system (SINS) is proposed.It has been demonstrated that the stationary alignment of SINS can be improved by employing the multiposition technique,but the alignment time of the azimuth error is relatively longer.Over here,the two-position alignment principle is presented.On the basis of this SINS error model,a fast estimation algorithm of the azimuth error for the initial alignment of SINS on stationary base is derived fully from the horizontal velocity outputs and the output rates,and the novel azimuth error estimation algorithm is used for the two-position alignment.Consequently,the speed and accuracy of the SINS's initial alignment is enhanced greatly.The computer simulation results illustrate the efficiency of this alignment method.

  9. RF Jitter Modulation Alignment Sensing

    Science.gov (United States)

    Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

    2017-01-01

    We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

  10. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole

    2007-12-01

    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  11. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.

    Directory of Open Access Journals (Sweden)

    Bédis Dridi

    Full Text Available BACKGROUND: The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool. METHODOLOGY/PRINCIPAL FINDINGS: Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens (15 for M. smithii and 15 for M. stadtmanae yielded a sequence similarity of 99-100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences. CONCLUSIONS/SIGNIFICANCE: In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome.

  12. Context dependent DNA evolutionary models

    DEFF Research Database (Denmark)

    Jensen, Jens Ledet

    This paper is about stochastic models for the evolution of DNA. For a set of aligned DNA sequences, connected in a phylogenetic tree, the models should be able to explain - in probabilistic terms - the differences seen in the sequences. From the estimates of the parameters in the model one can...

  13. Ribosomal DNA analysis of tsetse and non-tsetse transmitted Ethiopian Trypanosoma vivax strains in view of improved molecular diagnosis.

    Science.gov (United States)

    Fikru, Regassa; Matetovici, Irina; Rogé, Stijn; Merga, Bekana; Goddeeris, Bruno Maria; Büscher, Philippe; Van Reet, Nick

    2016-04-15

    Animal trypanosomosis caused by Trypanosoma vivax (T. vivax) is a devastating disease causing serious economic losses. Most molecular diagnostics for T. vivax infection target the ribosomal DNA locus (rDNA) but are challenged by the heterogeneity among T. vivax strains. In this study, we investigated the rDNA heterogeneity of Ethiopian T. vivax strains in relation to their presence in tsetse-infested and tsetse-free areas and its effect on molecular diagnosis. We sequenced the rDNA loci of six Ethiopian (three from tsetse-infested and three from tsetse-free areas) and one Nigerian T. vivax strain. We analysed the obtained sequences in silico for primer-mismatches of some commonly used diagnostic PCR assays and for GC content. With these data, we selected some rDNA diagnostic PCR assays for evaluation of their diagnostic accuracy. Furthermore we constructed two phylogenetic networks based on sequences within the smaller subunit (SSU) of 18S and within the 5.8S and internal transcribed spacer 2 (ITS2) to assess the relatedness of Ethiopian T. vivax strains to strains from other African countries and from South America. In silico analysis of the rDNA sequence showed important mismatches of some published diagnostic PCR primers and high GC content of T. vivax rDNA. The evaluation of selected diagnostic PCR assays with specimens from cattle under natural T. vivax challenge showed that this high GC content interferes with the diagnostic accuracy of PCR, especially in cases of mixed infections with T. congolense. Adding betain to the PCR reaction mixture can enhance the amplification of T. vivax rDNA but decreases the sensitivity for T. congolense and Trypanozoon. The networks illustrated that Ethiopian T. vivax strains are considerably heterogeneous and two strains (one from tsetse-infested and one from tsetse-free area) are more related to the West African and South American strains than to the East African strains. The rDNA locus sequence of six Ethiopian T. vivax

  14. Fish DNA-modified clays: Towards highly flame retardant polymer nanocomposite with improved interfacial and mechanical performance

    Science.gov (United States)

    Zabihi, Omid; Ahmadi, Mojtaba; Khayyam, Hamid; Naebe, Minoo

    2016-12-01

    Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1.2 nm for pristine clay to ~1.9 nm for clay modified with DNA (d-clay). Compared to epoxy nanocomposite containing 2.5%wt of Nanomer I.28E organoclay (m-clay), it was found that at 2.5%wt d-clay loading, significant enhancements of ~14%, ~6% and ~26% in tensile strength, tensile modulus, and fracture toughness of epoxy nanocomposite can be achieved, respectively. Effect of DNA as clay modifier on thermal performance of epoxy nanocomposite containing 2.5%wt d-clay was evaluated using TGA and cone calorimetry analysis, revealing significant decreases of ~4000 kJ/m2 and ~78 kW/m2 in total heat release and peak of heat release rate, respectively, in comparison to that containing 2.5%wt of m-clay.

  15. An oral chitosan DNA vaccine against nodavirus improves transcription of cell-mediated cytotoxicity and interferon genes in the European sea bass juveniles gut and survival upon infection.

    Science.gov (United States)

    Valero, Yulema; Awad, Elham; Buonocore, Francesco; Arizcun, Marta; Esteban, M Ángeles; Meseguer, José; Chaves-Pozo, Elena; Cuesta, Alberto

    2016-12-01

    Vaccines for fish need to be improved for the aquaculture sector, with DNA vaccines and the oral administration route providing the most promising improvements. In this study, we have created an oral chitosan-encapsulated DNA vaccine (CP-pNNV) for the nodavirus (NNV) in order to protect the very susceptible European sea bass (Dicentrarchus labrax). Our data show that the oral CP-pNNV vaccine failed to induce serum circulating or neutralizing specific antibodies (immunoglobulin M) or to up-regulate their gene expression in the posterior gut. However, the vaccine up-regulated the expression of genes related to the cell-mediated cytotoxicity (CMC; tcrb and cd8a) and the interferon pathway (IFN; ifn, mx and ifng). In addition, 3 months after vaccination, challenged fish showed a retarded onset of fish death and lower cumulative mortality with a relative survival of 45%. Thus, we created a chitosan-encapsulated DNA vaccine against NNV that is partly protective to European sea bass juveniles and up-regulates the transcription of genes related to CMC and IFN. However, further studies are needed to improve the anti-NNV vaccine and to understand its mechanisms.

  16. Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

    Institute of Scientific and Technical Information of China (English)

    ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida

    2001-01-01

    Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

  17. Product Grammars for Alignment and Folding.

    Science.gov (United States)

    Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Stadler, Peter F

    2015-01-01

    We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple "atomic" grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in L(A)T(E)X for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf. uni-leipzig.de/Software/gramprod/.

  18. DNA media storage

    Institute of Scientific and Technical Information of China (English)

    Christy M.Bogard; Eric C.Rouchka; Benjamin Arazi

    2008-01-01

    In 1994. University of Southern California computer scientist,Dr.Leonard Adleman solved the Hamiltonian path problem using DNA as a computational mechanism.He proved the principle that DNA computing could be used to solve computationally complex problems.Because of the limitations in discovery time,resource requirements,and sequence mismatches,DNA computing has not yet become a commonly accepted practice.However,advancements are continually being discovered that are evolving the field of DNA computing.Practical applications of DNA are not restricted to computation alone.This research presents a novel approach in which DNA could be used as a means of storing files.Through the use of multiple sequence alignment combined with intelligent heuristics,the most probabilistic file contents can be determined with minimal errors.

  19. DNA Media Storage.

    Science.gov (United States)

    Bogard, Christy M; Rouchka, Eric C

    2007-09-01

    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field of DNA Computing. Practical applications of DNA are not restricted to computation alone. This research presents a novel approach in which DNA could be used as a means of storing files. Through the use of Multiple Sequence Alignment combined with intelligent heuristics, the most probabilistic file contents can be determined with minimal errors.

  20. Functionalization of vertically aligned carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Eloise Van Hooijdonk

    2013-02-01

    Full Text Available This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs. The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs.

  1. Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae

    Directory of Open Access Journals (Sweden)

    Jephris Gere

    2013-12-01

    Full Text Available Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.

  2. Improved rapid and efficient method for Staphylococcus aureus DNA extraction from milk for identification of mastitis pathogens.

    Science.gov (United States)

    Unno, Hirotaka; Inada, Mika; Nakamura, Akiyoshi; Hashimoto, Michie; Ito, Keiko; Hashimoto, Koji; Nikaido, Masaru; Hayashi, Tomohito; Hata, Eiji; Katsuda, Ken; Kiku, Yoshio; Tagawa, Yuichi; Kawai, Kazuhiro

    2015-08-01

    A rapid and efficient DNA extraction method was developed for detecting mastitis pathogens in milk. The first critical step involved cell wall disruption by bead-beating, as physical disruption using beads was more effective for DNA extraction from Gram-positive bacteria, such as Staphylococcus aureus, than enzymatic disruption using proteinase K. The second critical step involves the use of acetic acid and ammonium sulfate in the purification process, as these reagents effectively and efficiently remove the lipids and proteins in milk. Using these methods, DNA suitable for loop-mediated isothermal amplification was obtained within 30 min. Also, the rapid and sensitive detection of S. aureus in milk was possible at levels as low as 200 cfu/ml.

  3. A single portion of blueberry (Vaccinium corymbosum L) improves protection against DNA damage but not vascular function in healthy male volunteers

    DEFF Research Database (Denmark)

    Del Bo, Cristian; Riso, Patrizia; Campolo, Jonica;

    2013-01-01

    It has been suggested that anthocyanin-rich foods may exert antioxidant effects and improve vascular function as demonstrated mainly in vitro and in the animal model. Blueberries are rich sources of anthocyanins and we hypothesized that their intake could improve cell protection against oxidative...... were collected and used to evaluate anthocyanin absorption (through mass spectrometry), endogenous and H(2)O(2)-induced DNA damage in blood mononuclear cells (through the comet assay), and plasma nitric oxide concentrations (through a fluorometric assay). Peripheral arterial function was assessed...

  4. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

    Directory of Open Access Journals (Sweden)

    Grossman Lawrence I

    2007-09-01

    Full Text Available Abstract Background Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence. Results Here we report an online codon-preserved alignment tool (OCPAT that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved. Conclusion The OCPAT program facilitates large-scale evolutionary and

  5. Electrospun nanofiber reinforcement of dental composites with electromagnetic alignment approach

    Energy Technology Data Exchange (ETDEWEB)

    Uyar, Tansel [Department of Biomedical Engineering, Başkent University Bağlıca Campus, 06530 Ankara (Turkey); Çökeliler, Dilek, E-mail: cokeliler@baskent.edu.tr [Department of Biomedical Engineering, Başkent University Bağlıca Campus, 06530 Ankara (Turkey); Doğan, Mustafa [Department of Electrical and Electronics Engineering, Başkent University, Ankara 06180 (Turkey); Koçum, Ismail Cengiz [Department of Biomedical Engineering, Başkent University Bağlıca Campus, 06530 Ankara (Turkey); Karatay, Okan [Department of Electrical and Electronics Engineering, Başkent University, Ankara 06180 (Turkey); Denkbaş, Emir Baki [Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara (Turkey)

    2016-05-01

    Polymethylmethacrylate (PMMA) is commonly used as a base acrylic denture material with benefits of rapid and easy handling, however, when it is used in prosthetic dentistry, fracturing or cracking problems can be seen due to the relatively low strength issues. Besides, acrylic resin is the still prominent material for denture fabrication due to its handy and low cost features. Numerous proposed fillers that are used to produce PMMA composites, however electrospun polyvinylalcohol (PVA) nanofiber fillers for production of PMMA composite resins are not studied as much as the others. The other focus of the practice is to compare both mechanical properties and efficiency of aligned fibers versus non-aligned PVA nanofibers in PMMA based dental composites. Field-controlled electrospinning system is manufactured and provided good alignment in lab scale as one of contributions. Some novel auxiliary electrodes in controlled structure are augmented to obtain different patterns of alignment with a certain range of fiber diameters. Scanning electron microscopy is used for physical characterization to determine the range of fiber diameters. Non-woven fiber has no unique pattern due to chaotic nature of electrospinning process, but aligned fibers have round pattern or crossed lines. These produced fibers are structured as layer-by-layer form with different features, and these features are used in producing PMMA dental composites with different volume ratios. The maximum flexural strength figure shows that fiber load by weight of 0.25% w/w and above improves in the maximum level. As a result, mechanical properties of PMMA dental composites are improved by using PVA nanofibers as a filler, however the improvement was higher when aligned PVA nanofibers are used. The maximum values were 5.1 MPa (flexural strength), 0.8 GPa (elastic modulus), and 170 kJ/m{sup 3} (toughness) in three-point bending test. In addition to the positive results of aligned and non-aligned nanofibers it was

  6. Spontaneous magnetic alignment behaviour in free-living lizards

    Science.gov (United States)

    Diego-Rasilla, Francisco J.; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

    2017-04-01

    Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards ( Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

  7. DIDA: Distributed Indexing Dispatched Alignment.

    Directory of Open Access Journals (Sweden)

    Hamid Mohamadi

    Full Text Available One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA, and is free for academic use.

  8. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains.

    Directory of Open Access Journals (Sweden)

    Alvaro L Pérez-Quintero

    Full Text Available Transcription Activators-Like Effectors (TALEs belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.

  9. General Alignment Concept of the CMS experiment

    CERN Document Server

    Lampen, T

    2006-01-01

    Efficient and accurate track reconstruction requires proper alignment of the tracking devices used. Here we describe the general alignment strategy envisaged for the CMS experiment. The hardware alignment devices of CMS are presented as well as the different track based alignment approaches.

  10. Photosensitive Polymers for Liquid Crystal Alignment

    Science.gov (United States)

    Mahilny, U. V.; Stankevich, A. I.; Trofimova, A. V.; Muravsky, A. A.; Murauski, A. A.

    The peculiarities of alignment of liquid crystal (LC) materials by the layers of photocrosslinkable polymers with side benzaldehyde groups are considered. The investigation of mechanism of photostimulated alignment by rubbed benzaldehyde layer is performed. The methods of creation of multidomain aligning layers on the basis of photostimulated rubbing alignment are described.

  11. An improved method of DNA isolation suitable for PCR-based detection of begomoviruses from jute and other mucilaginous plants.

    Science.gov (United States)

    Ghosh, Raju; Paul, Sujay; Ghosh, Subrata Kumar; Roy, Anirban

    2009-07-01

    A relatively quick and inexpensive modified cetyl trimethylammonium bromide method for extraction of DNA from leaf materials containing large quantities of mucilage is described. The modification including use of more volume of extraction buffer and dissolving crude nucleic acid pellet in 1 M NaCl, reduced markedly the viscosity of the mucilage and thus in the final purification step yielded a larger quantity of mucilage-free DNA suitable for subsequent PCR-based detection of begomoviruses. The method was standardized with jute samples with yellow mosaic disease and validated with different other mucilaginous-hosts with low titre of begomoviruses. DNA isolated using this method showed consistency in yield and compatibility with PCR for detection of begomoviruses from different mucilaginous plant species. The method was compared for efficacy with other reported methods and it was found to be superior over the existing methods described for isolation of DNA from mucilaginous hosts. Thus the method described could be used on a wider scale for reliable and consistent detection of begomoviruses from mucilaginous hosts for characterization and variability study.

  12. Improved electrochemical performances of polyaniline nanotubes-poly-L-lysine composite for label-free impedance detection of DNA hybridization

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A sensitive label-free DNA hybridization biosensing platform was fabricated based on the synergistic effect of polyaniline nanotubes (PANInt) and poly-L-lysine (pLys).The composite of pLys and PANInt was coated onto the carbon paste electrode (CPE) to form a uniform and very stable nanocomposite membrane.The pLys in the composite film not only acts as a membrane to retain good electron transfer capability of PANInt even at physiological pH,but also possesses fine biocompatibility for bio-analytes.DNA probes with negatively charged phosphate groups were readily linked to the positively charged pLys surface due to the strong electrostatic affinity.The synergistic effect of PANInt and pLys could significantly enhance the sensitivity of DNA hybridization recognition.The phosphinothricin acetyltransferase (PAT) gene fragment from transgenic corn and the polymerase chain reaction amplification of the terminator of nopaline synthase gene from the real sample of a kind of transgenic soybean were detected by this DNA electrochemical biosensor via label-free impedance method.This stable composite gives convenient permselectivity properties as a transducer material for the design of modern electrochemical impedance biosensor using [Fe(CN)6]3-/4as an indicator.

  13. Targeting hepatitis B virus antigens to dendritic cells by heat shock protein to improve DNA vaccine potency

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    AIM: To investigate a novel DNA vaccination based upon expression of the HBV e antigen fused to a heat shock protein (HSP) as a strategy to enhance DNA vaccine potency.METHODS: A pCMV-HBeAg-HSP DNA vaccine and a control DNA vaccine were generated. Mice were immunized with these different construct. Immune responses were measured 2 wk after a second immunization by a T cell response assay, CTL cytotoxicity assay, and an antibody assay in C57BL/6 and BALB/c mice. CT26-HBeAg tumor cell challenge test in vivo was performed in BALB/c mice to monitor anti-tumor immune responses.RESULTS: In the mice immunized with pCMV-HBe-HSP DNA, superior CTL activity to target HBV-positive target cells was observed in comparison with mice immunized with pCMV-HBeAg (44% ± 5% vs 30% ± 6% in E: T > 50:1, P < 0.05). ELISPOT assays showed a stronger T-cell response from mice immunized with pCMV-HBe-HSP than that from pCMV-HBeAg immunized animals when stimulated either with MHC class Ⅰ or class Ⅱ epitopes derived from HBeAg (74% ± 9% vs 31% ± 6%, P < 0.01). ELISA assays revealed an enhanced HBeAg antibody response from mice immunized with pCMV-HBe-HSP than from those immunized with pCMV-HBeAg. The lowest tumor incidence and the slowest tumor growth were observed in mice immunized with pCMV-HBe-HSP when challenged with CT26-HBeAg.CONCLUSION: The results of this study demonstrate a broad enhancement of antigen-specific CD4+ helper,CD8+ cytotoxic T-cell, and B-cell responses by a novel DNA vaccination strategy. They also proved a stronger antigen-specific immune memory, which may be superior to currently described HBV DNA vaccination strategies for the treatment of chronic HBV infection.

  14. Study of wafer pre-aligning approaches

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Wafer pre-aligning system is an important component in IC manufacturing industry. A wafer prealigning platform with a CCD sensor is presented in this paper. The centering and notch detecting approaches are extended based on this platform. Least square circle fitting approach is adopted to calculate the center and radius of the wafer, and a formula for calculating the fitting error is derived. An approach called edge variation rate is also proposed to detect the range of wafer notch, and the fiducial is calculated by curve fitting approach. These approaches can improve the accuracy effectively as indicated by experiments.

  15. Alignment method for parabolic trough solar concentrators

    Science.gov (United States)

    Diver, Richard B.

    2010-02-23

    A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

  16. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  17. Laser shaft alignment measurement model

    Science.gov (United States)

    Mo, Chang-tao; Chen, Changzheng; Hou, Xiang-lin; Zhang, Guoyu

    2007-12-01

    Laser beam's track which is on photosensitive surface of the a receiver will be closed curve, when driving shaft and the driven shaft rotate with same angular velocity and rotation direction. The coordinate of arbitrary point which is on the curve is decided by the relative position of two shafts. Basing on the viewpoint, a mathematic model of laser alignment is set up. By using a data acquisition system and a data processing model of laser alignment meter with single laser beam and a detector, and basing on the installation parameter of computer, the state parameter between two shafts can be obtained by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated. This will instruct us to move the apparatus to align the shafts.

  18. Error Analysis and Compensation of Gyrocompass Alignment for SINS on Moving Base

    Directory of Open Access Journals (Sweden)

    Bo Xu

    2014-01-01

    Full Text Available An improved method of gyrocompass alignment for strap-down inertial navigation system (SINS on moving base assisted with Doppler velocity log (DVL is proposed in this paper. After analyzing the classical gyrocompass alignment principle on static base, implementation of compass alignment on moving base is given in detail. Furthermore, based on analysis of velocity error, latitude error, and acceleration error on moving base, two improvements are introduced to ensure alignment accuracy and speed: (1 the system parameters are redesigned to decrease the acceleration interference and (2 a data repeated calculation algorithm is used in order to shorten the prolonged alignment time caused by changes in parameters. Simulation and test results indicate that the improved method can realize the alignment on moving base quickly and effectively.

  19. BarraCUDA - a fast short read sequence aligner using graphics processing units

    Directory of Open Access Journals (Sweden)

    Klus Petr

    2012-01-01

    Full Text Available Abstract Background With the maturation of next-generation DNA sequencing (NGS technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU, extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net

  20. BarraCUDA - a fast short read sequence aligner using graphics processing units

    LENUS (Irish Health Repository)

    Klus, Petr

    2012-01-13

    Abstract Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http:\\/\\/seqbarracuda.sf.net

  1. The alignment-distribution graph

    Science.gov (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  2. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  3. Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

    Science.gov (United States)

    Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; McCallum, R. W.; McCall, Scott K.; Kramer, M. J.; Paranthaman, M. Parans

    2017-01-01

    Considerations for achieving high degree of alignment in polymer bonded permanent magnets are presented via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. The thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.

  4. Convergent algorithms for protein structural alignment

    Directory of Open Access Journals (Sweden)

    Martínez José

    2007-08-01

    Full Text Available Abstract Background Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually successful for detecting structural similarities. However, current practical methods are seldom supported by convergence theories. In particular, although the goal of each algorithm is to maximize some scoring function, there is no practical method that theoretically guarantees score maximization. A practical algorithm with solid convergence properties would be useful for the refinement of protein folding maps, and for the development of new scores designed to be correlated with functional similarity. Results In this work, the maximization of scoring functions in protein alignment is interpreted as a Low Order Value Optimization (LOVO problem. The new interpretation provides a framework for the development of algorithms based on well established methods of continuous optimization. The resulting algorithms are convergent and increase the scoring functions at every iteration. The solutions obtained are critical points of the scoring functions. Two algorithms are introduced: One is based on the maximization of the scoring function with Dynamic Programming followed by the continuous maximization of the same score, with respect to the protein position, using a smooth Newtonian method. The second algorithm replaces the Dynamic Programming step by a fast procedure for computing the correspondence between Cα atoms. The algorithms are shown to be very effective for the maximization of the STRUCTAL score. Conclusion The interpretation of protein alignment as a LOVO problem provides a new theoretical framework for the development of convergent protein alignment algorithms. These algorithms are shown to be very reliable for the maximization of the STRUCTAL score, and other distance-dependent scores may be optimized with same strategy. The improved score optimization

  5. Mutation by DNA shuffling of 5-enolpyruvylshikimate-3-phosphate synthase from Malus domestica for improved glyphosate resistance.

    Science.gov (United States)

    Tian, Yong-Sheng; Xu, Jing; Peng, Ri-He; Xiong, Ai-Sheng; Xu, Hu; Zhao, Wei; Fu, Xiao-Yan; Han, Hong-Juan; Yao, Quan-Hong

    2013-09-01

    A new 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene from Malus domestica (MdEPSPS) was cloned and characterized by rapid amplification of cDNA ends to identify an EPSPS gene appropriate for the development of transgenic glyphosate-tolerant plants. However, wild-type MdEPSPS is not suitable for the development of transgenic glyphosate-tolerant plants because of its poor glyphosate resistance. Thus, we performed DNA shuffling on MdEPSPS, and one highly glyphosate-resistant mutant with mutations in eight amino acids (N63D, N86S, T101A, A187T, D230G, H317R, Y399R and C413A.) was identified after five rounds of DNA shuffling and screening. Among the eight amino acid substitutions on this mutant, only two residue changes (T101A and A187T) were identified by site-directed mutagenesis as essential and additive in altering glyphosate resistance, which was further confirmed by kinetic analyses. The single-site A187T mutation has also never been previously reported as an important residue for glyphosate resistance. Furthermore, transgenic rice was used to confirm the potential of MdEPSPS mutant in developing glyphosate-resistant crops.

  6. The Rigors of Aligning Performance

    Science.gov (United States)

    2015-06-01

    organization must consider and work closely with its many stakeholders so as to guarantee satisfaction ; this idea is especially important as there is no...define success. Methodology includes a literature review, employee and customer surveys and a Strength, Weaknesses, Opportunities, Threats...bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment, which is vital to highlight the

  7. Aligning Assessments for COSMA Accreditation

    Science.gov (United States)

    Laird, Curt; Johnson, Dennis A.; Alderman, Heather

    2015-01-01

    Many higher education sport management programs are currently in the process of seeking accreditation from the Commission on Sport Management Accreditation (COSMA). This article provides a best-practice method for aligning student learning outcomes with a sport management program's mission and goals. Formative and summative assessment procedures…

  8. Aligned natural inflation with modulations

    Directory of Open Access Journals (Sweden)

    Kiwoon Choi

    2016-08-01

    Full Text Available The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  9. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

    Full Text Available Abstract Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mismatch scores.

  10. Fusion-Expressed CTB Improves Both Systemic and Mucosal T-Cell Responses Elicited by an Intranasal DNA Priming/Intramuscular Recombinant Vaccinia Boosting Regimen

    Directory of Open Access Journals (Sweden)

    Sugan Qiu

    2014-01-01

    Full Text Available Previous study showed that CTB (Cholera toxin subunit B can be used as a genetic adjuvant to enhance the systemic immune responses. To further investigate whether it can also be used as a genetic adjuvant to improve mucosal immune responses, we constructed DNA and recombinant Tiantan vaccinia (rTTV vaccines expressing OVA-CTB fusion antigen. Female C57BL/6 mice were immunized with an intranasal DNA priming/intramuscular rTTV boosting regimen. OVA specific T-cell responses were measured by IFN-γ ELISPOT and specific antibody responses were determined by ELISA. Compared to the nonadjuvant group (pSV-OVA intranasal priming/rTTV-OVA intramuscular boosting, pSV-OVA-CTB intranasal priming/rTTV-OVA-CTB intramuscular boosting group significantly improved the magnitudes of T-cell responses at spleen (1562±567 SFCs/106 splenocytes versus 330±182 SFCs/106 splenocytes, P<0.01, mesenteric LN (96±83 SFCs/106 lymphocytes versus 1±2 SFCs/106 lymphocytes, P<0.05, draining LNs of respiratory tract (109±60 SFCs/106 lymphocytes versus 2±2 SFCs/106 lymphocytes, P<0.01 and female genital tract (89±48 SFCs/106 lymphocytes versus 23±21 SFCs/106 lymphocytes, P<0.01. These results collectively demonstrated that fusion-expressed CTB could act as a potent adjuvant to improve both systemic and mucosal T-cell responses.

  11. A Hybrid Parallel Strategy Based on String Graph Theory to Improve De Novo DNA Assembly on the TianHe-2 Supercomputer.

    Science.gov (United States)

    Zhang, Feng; Liao, Xiangke; Peng, Shaoliang; Cui, Yingbo; Wang, Bingqiang; Zhu, Xiaoqian; Liu, Jie

    2016-06-01

    ' The de novo assembly of DNA sequences is increasingly important for biological researches in the genomic era. After more than one decade since the Human Genome Project, some challenges still exist and new solutions are being explored to improve de novo assembly of genomes. String graph assembler (SGA), based on the string graph theory, is a new method/tool developed to address the challenges. In this paper, based on an in-depth analysis of SGA we prove that the SGA-based sequence de novo assembly is an NP-complete problem. According to our analysis, SGA outperforms other similar methods/tools in memory consumption, but costs much more time, of which 60-70 % is spent on the index construction. Upon this analysis, we introduce a hybrid parallel optimization algorithm and implement this algorithm in the TianHe-2's parallel framework. Simulations are performed with different datasets. For data of small size the optimized solution is 3.06 times faster than before, and for data of middle size it's 1.60 times. The results demonstrate an evident performance improvement, with the linear scalability for parallel FM-index construction. This results thus contribute significantly to improving the efficiency of de novo assembly of DNA sequences.

  12. An improved and robust DNA immunization method to develop antibodies against extracellular loops of multi-transmembrane proteins.

    Science.gov (United States)

    Hazen, Meredith; Bhakta, Sunil; Vij, Rajesh; Randle, Steven; Kallop, Dara; Chiang, Vicki; Hötzel, Isidro; Jaiswal, Bijay S; Ervin, Karen E; Li, Bing; Weimer, Robby M; Polakis, Paul; Scheller, Richard H; Junutula, Jagath R; Hongo, Jo-Anne S

    2014-01-01

    Multi-transmembrane proteins are especially difficult targets for antibody generation largely due to the challenge of producing a protein that maintains its native conformation in the absence of a stabilizing membrane. Here, we describe an immunization strategy that successfully resulted in the identification of monoclonal antibodies that bind specifically to extracellular epitopes of a 12 transmembrane protein, multi-drug resistant protein 4 (MRP4). These monoclonal antibodies were developed following hydrodynamic tail vein immunization with a cytomegalovirus (CMV) promoter-based plasmid expressing MRP4 cDNA and were characterized by flow cytometry. As expected, the use of the immune modulators fetal liver tyrosine kinase 3 ligand (Flt3L) and granulocyte-macrophage colony-stimulating factor positively enhanced the immune response against MRP4. Imaging studies using CMV-based plasmids expressing luciferase showed that the in vivo half-life of the target antigen was less than 48 h using CMV-based plasmids, thus necessitating frequent boosting with DNA to achieve an adequate immune response. We also describe a comparison of plasmids, which contained MRP4 cDNA with either the CMV or CAG promoters, used for immunizations. The observed luciferase activity in this comparison demonstrated that the CAG promoter-containing plasmid pCAGGS induced prolonged constitutive expression of MRP4 and an increased anti-MRP4 specific immune response even when the plasmid was injected less frequently. The method described here is one that can be broadly applicable as a general immunization strategy to develop antibodies against multi-transmembrane proteins, as well as target antigens that are difficult to express or purify in native and functionally active conformation.

  13. Aligned Layers of Silver Nano-Fibers

    Directory of Open Access Journals (Sweden)

    Andrii B. Golovin

    2012-02-01

    Full Text Available We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

  14. Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA.

    Science.gov (United States)

    Ruan, Thomas L; Davis, Supriya J; Powell, Barrett M; Harbeck, Cole P; Habdas, Jan; Habdas, Piotr; Yatsunyk, Liliya A

    2017-01-01

    Ligands that stabilize non-canonical DNA structures called G-quadruplexes (GQs) might have applications in medicine as anti-cancer agents, due to the involvement of GQ DNA in a variety of cancer-related biological processes. Five derivatives of 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4), where a N-methylpyridyl group was replaced with phenyl (4P3), 4-aminophenyl (PN3M), 4-phenylamidoproline (PL3M), or 4-carboxyphenyl (PC3M and P2C2M) were investigated for their interactions with human telomeric DNA (Tel22) using fluorescence resonance energy transfer (FRET) assay, and UV-visible and circular dichroism spectroscopies in K(+) buffer. The molecules are cationic or zwitterionic with an overall charge of 3+ (4P3, PN3M, and PL3M), 2+ (PC3M) or neutral (P2C2M). All porphyrins except P2C2M stabilize human telomeric DNA in FRET assays by ∼20 °C at 5 eq CD melting experiments suggest that 4P3 is the most stabilizing ligand with a stabilization temperature of 16.8 °C at 4 eq. Importantly, 4P3, PC3M and PL3M demonstrate excellent selectivity for quadruplexes, far superior to that of TMPyP4. Binding constants, determined using UV-vis titrations, correlate with charge: triply cationic 4P3, PN3M and PL3M display Ka of 5-9 μM(-1), doubly cationic PC3M displays Ka of 1 μM(-1), and neutral P2C2M displays weak-to-no binding. UV-vis data suggest that binding interactions are driven by electrostatic attractions and that the binding mode may be base-stacking (or end-stacking) judging by the high values of red shift (15-20 nm) and hypochromicity (40-50%). We conclude that lowering the charge on TMPyP4 to 3+ can achieve the desired balance between stabilizing ability, affinity, and high selectivity required for an excellent quadruplex ligand.

  15. 植物总DNA的提取方法的改进%The Improvement of Plant Total DNA Extraction Protocol

    Institute of Scientific and Technical Information of China (English)

    黄永莲; 刘媛; 黄真池

    2007-01-01

    改进了以CTAB法为基础的植物总DNA的提取方法.通过对实验材料的暗处理、4 ℃放置、加入蛋白酶K、提高提取缓冲液中β-巯基乙醇用量,增加氯仿/ 异戊醇的量和使用次数,以及缩短异丙醇沉淀DNA的时间,成功地从富含酚类和多糖的榕树叶片中提取到高质量的总DNA.

  16. The impact of shared domain knowledge on strategic information systems planning and alignment

    Directory of Open Access Journals (Sweden)

    Simla Maharaj

    2015-02-01

    Full Text Available Background: Lack of alignment or harmony between information technology (IT and business imperatives continues to plague organisations despite decades of research. Strategic information systems planning (SISP is the process of coordinating the relationship between IT and the business in order to steer alignment. Shared domain knowledge (SDK is a factor that is posited as important for improving both SISP and alignment, which is theorised to be the main outcome of SISP. Objectives: The aim of this article is to examine the impact of SDK on SISP and alignment. Method: Data were gathered from management consultants in a large, global IT organisation, through the use of a structured questionnaire, and analysed. Results: It was shown that SDK positively influences SISP characteristics and the alignment outcome. Specifically, it was found that high levels of rationality in SISP positively influenced the intellectual dimension of alignment, whilst IT manager participation in business planning influenced the social dimension of alignment. SDK was found to have a bearing on all of the SISP characteristics measured (i.e. rationality, adaptation, business planning-SISP integration and IT manager participation in business planning. SDK was also found to positively impact both the intellectual and social dimensions of alignment.Conclusion: The implications of the findings are that fostering a knowledge sharing environment in organisations will help improve alignment, as well as the formal processes designed to steer alignment such as SISP.

  17. 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...

  18. TMO: time and memory optimized algorithm applicable for more accurate alignment of trinucleotide repeat disorders associated genes

    Directory of Open Access Journals (Sweden)

    Done Stojanov

    2016-03-01

    Full Text Available In this study, time and memory optimized (TMO algorithm is presented. Compared with Smith–Waterman's algorithm, TMO is applicable for a more accurate detection of continuous insertion/deletions (indels in genes’ fragments, associated with disorders caused by over-repetition of a certain codon. The improvement comes from the tendency to pinpoint indels in the least preserved nucleotide pairs. All nucleotide pairs that occur less frequently are classified as less preserved and they are considered as mutated codons whose mid-nucleotides were deleted. Other benefit of the proposed algorithm is its general tendency to maximize the number of matching nucleotides included per alignment, regardless of any specific alignment metrics. Since the structure of the solution, when applying Smith–Waterman, depends on the adjustment of the alignment parameters and, therefore, an incomplete (shortened solution may be derived, our algorithm does not reject any of the consistent matching nucleotides that can be included in the final solution. In terms of computational aspects, our algorithm runs faster than Smith–Waterman for very similar DNA and requires less memory than the most memory efficient dynamic programming algorithms. The speed up comes from the reduced number of nucleotide comparisons that have to be performed, without having to imperil the completeness of the solution. Due to the fact that four integers (16 Bytes are required for tracking matching fragment, regardless its length, our algorithm requires less memory than Huang's algorithm.

  19. Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM)

    Science.gov (United States)

    Coghlan, Megan L.; Maker, Garth; Crighton, Elly; Haile, James; Murray, Dáithí C.; White, Nicole E.; Byard, Roger W.; Bellgard, Matthew I.; Mullaney, Ian; Trengove, Robert; Allcock, Richard J. N.; Nash, Christine; Hoban, Claire; Jarrett, Kevin; Edwards, Ross; Musgrave, Ian F.; Bunce, Michael

    2015-12-01

    Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological and heavy metal screening by separation techniques and mass spectrometry (MS) to provide a comprehensive audit. Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit. The study showed 92% of the TCMs examined were found to have some form of contamination and/or substitution. This study demonstrates that a combination of molecular methodologies can provide an effective means by which to audit complementary and alternative medicines.

  20. LHCb’s Real-Time Alignment in Run II

    CERN Document Server

    Batozskaya, Varvara

    2015-01-01

    The LHCb collaboration has introduced a novel real-time detector alignment and calibration strategy for LHC Run II. The data collected at the start of the fill will be processed in a few minutes and used to update the alignment, while the calibration constants will be evaluated for each run. This procedure will improve the quality of the online alignment. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and oine reconstruction, thus improving the correlation between triggered and oine selected events. This oers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configu...

  1. DNA adductomics.

    Science.gov (United States)

    Balbo, Silvia; Turesky, Robert J; Villalta, Peter W

    2014-03-17

    Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology.

  2. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    Science.gov (United States)

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples.

  3. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Klarissa; Lueg, Rainer; Lauridsen, Ole

    2016-01-01

    Changes in public policy, such as the Bologna Process, require students to be equipped with multifunctional competencies to master relevant tasks in unfamiliar situations. Achieving this goal might imply a change in many curricula toward deeper learning. As a didactical means to achieve deep...... learning results, the authors suggest reciprocal peer tutoring (RPT); as a conceptual framework the authors suggest the SOLO (Structure of Observed Learning Outcomes) taxonomy and constructive alignment as suggested by Biggs and Tang. Our study presents results from the introduction of RPT in a large...... course. The authors find that RPT produces satisfying learning outcomes, active students, and ideal constructive alignments of the seminar content with the exam, the intended learning outcomes, and the requirements of the Bologna Process. Our data, which comprise surveys and evaluations from both faculty...

  4. Prism Window for Optical Alignment

    Science.gov (United States)

    Tang, Hong

    2008-01-01

    A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

  5. Shuttle onboard IMU alignment methods

    Science.gov (United States)

    Henderson, D. M.

    1976-01-01

    The current approach to the shuttle IMU alignment is based solely on the Apollo Deterministic Method. This method is simple, fast, reliable and provides an accurate estimate for the present cluster to mean of 1,950 transformation matrix. If four or more star sightings are available, the application of least squares analysis can be utilized. The least squares method offers the next level of sophistication to the IMU alignment solution. The least squares method studied shows that a more accurate estimate for the misalignment angles is computed, and the IMU drift rates are a free by-product of the analysis. Core storage requirements are considerably more; estimated 20 to 30 times the core required for the Apollo Deterministic Method. The least squares method offers an intermediate solution utilizing as much data that is available without a complete statistical analysis as in Kalman filtering.

  6. Aligned mesoporous architectures and devices.

    Energy Technology Data Exchange (ETDEWEB)

    Brinker, C. Jeffrey; Lu, Yunfeng (University of California Los Angeles, Los Angeles, CA)

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  7. The Cluster Substructure - Alignment Connection

    OpenAIRE

    Plionis, Manolis

    2001-01-01

    Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically young clusters are more clustered than the overall cluster population. These are strong indications that cluster develop in ...

  8. Delivery of plasmid DNA expression vector for keratinocyte growth factor-1 using electroporation to improve cutaneous wound healing in a septic rat model.

    Science.gov (United States)

    Lin, Michael P; Marti, Guy P; Dieb, Rami; Wang, Jiaai; Ferguson, Mark; Qaiser, Rabia; Bonde, Pramod; Duncan, Mark D; Harmon, John W

    2006-01-01

    We have previously shown that wound healing was improved in a diabetic mouse model of impaired wound healing following transfection with keratinocyte growth factor-1 (KGF-1) cDNA. We now extend these findings to the characterization of the effects of DNA plasmid vectors delivered to rats using electroporation (EP) in vivo in a sepsis-based model of impaired wound healing. To assess plasmid transfection and wound healing, gWIZ luciferase and PCDNA3.1/KGF-1 expression vectors were used, respectively. Cutaneous wounds were produced using an 8 mm-punch biopsy in Sprague-Dawley rats in which healing was impaired by cecal ligation-induced sepsis. We used National Institutes of Health image analysis software and histologic assessment to analyze wound closure and found that EP increased expression of gWIZ luciferase vector up to 53-fold compared with transfection without EP (p < 0.001). EP-assisted plasmid transfection was found to be localized to skin. Septic rats had a 4.7 times larger average wound area on day 9 compared with control (p < 0.001). Rats that underwent PCDNA3.1/KGF-1 transfection with EP had 60% smaller wounds on day 12 compared with vector without EP (p < 0.009). Quality of healing with KGF-1 vector plus EP scored 3.0 +/- 0.3 and was significantly better than that of 1.8 +/- 0.3 for treatment with vector alone (p < 0.05). We conclude that both the rate and quality of healing were improved with DNA plasmid expression vector for growth factor delivered with EP to septic rats.

  9. Inhibition of Histone Deacetylation and DNA Methylation Improves Gene Expression Mediated by the Adeno-Associated Virus/Phage in Cancer Cells

    Directory of Open Access Journals (Sweden)

    Amin Hajitou

    2013-10-01

    Full Text Available Bacteriophage (phage, viruses that infect bacteria only, have become promising vectors for targeted systemic delivery of genes to cancer, although, with poor efficiency. We previously designed an improved phage vector by incorporating cis genetic elements of adeno-associated virus (AAV. This novel AAV/phage hybrid (AAVP specifically targeted systemic delivery of therapeutic genes into tumors. To advance the AAVP vector, we recently introduced the stress-inducible Grp78 tumor specific promoter and found that this dual tumor-targeted AAVP provides persistent gene expression, over time, in cancer cells compared to silenced gene expression from the CMV promoter in the parental AAVP. Herein, we investigated the effect of histone deacetylation and DNA methylation on AAVP-mediated gene expression in cancer cells and explored the effect of cell confluence state on AAVP gene expression efficacy. Using a combination of AAVP expressing the GFP reporter gene, flow cytometry, inhibitors of histone deacetylation, and DNA methylation, we have demonstrated that histone deacetylation and DNA methylation are associated with silencing of gene expression from the CMV promoter in the parental AAVP. Importantly, inhibitors of histone deacetylases boost gene expression in cancer cells from the Grp78 promoter in the dual tumor-targeted AAVP. However, cell confluence had no effect on AAVP-guided gene expression. Our findings prove that combination of histone deacetylase inhibitor drugs with the Grp78 promoter is an effective approach to improve AAVP-mediated gene expression in cancer cells and should be considered for AAVP-based clinical cancer gene therapy.

  10. Double positivity for HPV DNA/p16 in tonsillar and base of tongue cancer improves prognostication: Insights from a large population-based study.

    Science.gov (United States)

    Garnaes, Emilie; Frederiksen, Kirsten; Kiss, Katalin; Andersen, Luise; Therkildsen, Marianne H; Franzmann, Maria B; Specht, Lena; Andersen, Elo; Norrild, Bodil; Kjaer, Susanne K; von Buchwald, Christian

    2016-12-01

    The aim was to explore the overall survival (OS) for palatine tonsillar squamous cell carcinoma (TSCC), subdivided, according to certainty of tonsillar tumour origin, into specified tonsillar squamous cell carcinomas (STSCCs) and nonspecified tonsillar squamous cell carcinomas (NSTSCCs), and base of tongue squamous cell carcinoma (BSCC) when stratifying for HPV DNA status, p16 expression and combined HPV/p16 status. We included all patients (n = 797) diagnosed with TSCCs and BSCCs in Eastern Denmark as registered in the Danish Head and Neck Cancer Group (DAHANCA) database and the Danish Pathology Databank, 2000-2010. Patients were treated according to national guidelines (radiotherapy +/- concomitant cisplatin). All specimens were analysed using HPV DNA PCR and p16 immunohistochemistry. Clinical information was retrieved from the DAHANCA database and the Danish National Patient Registry. Information on vital status was obtained from the Danish Civil Registration System. We observed improved OS for HPV+/p16+ BSCCs compared to HPV-/p16- (hazard ratio for death [HR], 0.15; 95% CI, 0.09-0.24). Among STSCCs, HPV+/p16+ showed the lowest HR (0.19, 95% CI, 0.13-0.29); whereas, HPV-/p16+ showed an intermediate HR (0.39; 95% CI, 0.22-0.70). For NSTSCCs, HPV+/p16+ and HPV-/p16+ showed similar OS (HRs, 0.39; 95% CI, 0.26-0.59; and 0.48; 95% CI, 0.24-0.95, respectively). Combined HPV+/p16+ was a significantly better prognostic marker in BSCCs and STSCCs than HPV DNA and p16, alone (all p-values p16 (p = 0.53), alone. In conclusion, double positivity for HPV/p16 in conjunction with the certainty of tumour site improved prognosis.

  11. Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.

    Science.gov (United States)

    Stamm, Marcus; Forrest, Lucy R

    2015-09-01

    Protein structure alignment methods are used for the detection of evolutionary and functionally related positions in proteins. A wide array of different methods are available, but the choice of the best method is often not apparent to the user. Several studies have assessed the alignment accuracy and consistency of structure alignment methods, but none of these explicitly considered membrane proteins, which are important targets for drug development and have distinct structural features. Here, we compared 13 widely used pairwise structural alignment methods on a test set of homologous membrane protein structures (called HOMEP3). Each pair of structures was aligned and the corresponding sequence alignment was used to construct homology models. The model accuracy compared to the known structures was assessed using scoring functions not incorporated in the tested structural alignment methods. The analysis shows that fragment-based approaches such as FR-TM-align are the most useful for aligning structures of membrane proteins. Moreover, fragment-based approaches are more suitable for comparison of protein structures that have undergone large conformational changes. Nevertheless, no method was clearly superior to all other methods. Additionally, all methods lack a measure to rate the reliability of a position within a structure alignment. To solve both of these problems, we propose a consensus-type approach, combining alignments from four different methods, namely FR-TM-align, DaliLite, MATT, and FATCAT. Agreement between the methods is used to assign confidence values to each position of the alignment. Overall, we conclude that there remains scope for the improvement of structural alignment methods for membrane proteins.

  12. Colour stabilities of three types of orthodontic clear aligners exposed to staining agents

    Institute of Scientific and Technical Information of China (English)

    Chen-Lu Liu; Wen-Tian Sun; Wen Liao; Wen-Xin Lu; Qi-Wen Li; Yunho Jeong; Jun Liu; Zhi-He Zhao

    2016-01-01

    The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I’Eclairage L*a*b*colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higherΔE*values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE*values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, Po0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties.

  13. Grain alignment in starless cores

    Energy Technology Data Exchange (ETDEWEB)

    Jones, T. J.; Bagley, M. [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Krejny, M. [Cree Inc., 4600 Silicon Dr., Durham, NC (United States); Andersson, B.-G. [SOFIA Science Center, USRA, Moffett Field, CA (United States); Bastien, P., E-mail: tjj@astro.umn.edu [Centre de recherche en astrophysique du Québec and Départment de Physique, Université de Montréal, Montréal (Canada)

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A{sub V}∼48. We find that P{sub K}/τ{sub K} continues to decline with increasing A{sub V} with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A{sub V}≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A{sub V}∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  14. Student conceptions about the DNA structure within a hierarchical organizational level: Improvement by experiment- and computer-based outreach learning.

    Science.gov (United States)

    Langheinrich, Jessica; Bogner, Franz X

    2015-01-01

    As non-scientific conceptions interfere with learning processes, teachers need both, to know about them and to address them in their classrooms. For our study, based on 182 eleventh graders, we analyzed the level of conceptual understanding by implementing the "draw and write" technique during a computer-supported gene technology module. To give participants the hierarchical organizational level which they have to draw, was a specific feature of our study. We introduced two objective category systems for analyzing drawings and inscriptions. Our results indicated a long- as well as a short-term increase in the level of conceptual understanding and in the number of drawn elements and their grades concerning the DNA structure. Consequently, we regard the "draw and write" technique as a tool for a teacher to get to know students' alternative conceptions. Furthermore, our study points the modification potential of hands-on and computer-supported learning modules.

  15. Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites.

    Science.gov (United States)

    Adachi, J; Hasegawa, M

    1995-06-01

    The internal branch lengths estimated by distance methods such as neighbor-joining are shown to be biased to be short when the evolutionary rate differs among sites. The variable-invariable model for site heterogeneity fits the amino acid sequence data encoded by the mitochondrial DNA from Hominoidea remarkably well. By assuming the orangutan separation to be 13 or 16 Myr old, a maximum-likelihood analysis estimates a young date of 3.6 +/- 0.6 or 4.4 +/- 0.7 Myr (+/- 1 SE) for the human/chimpanzee separation, and these estimates turn out to be robust against differences in the assumed model for amino acid substitutions. Although some uncertainties still exist in our estimates, this analysis suggests that humans separated from chimpanzees some 4-5 Myr ago.

  16. Assessing business-IT alignment in networked organizations

    NARCIS (Netherlands)

    Santana Tapia, Roberto Guadalupe

    2009-01-01

    Concerns such as identifying ways to control costs, improve quality, increase effectiveness, and manage risk have become increasingly important for organizations as they face more and more pressure to gain and maintain their competitive edge. Business-IT alignment (B-ITa) is recognized as a solution

  17. Cactus: Algorithms for genome multiple sequence alignment

    OpenAIRE

    Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David

    2011-01-01

    Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms...

  18. Robustly Aligning a Shape Model and Its Application to Car Alignment of Unknown Pose.

    Science.gov (United States)

    Li, Yan; Gu, Leon; Kanade, Takeo

    2011-09-01

    Precisely localizing in an image a set of feature points that form a shape of an object, such as car or face, is called alignment. Previous shape alignment methods attempted to fit a whole shape model to the observed data, based on the assumption of Gaussian observation noise and the associated regularization process. However, such an approach, though able to deal with Gaussian noise in feature detection, turns out not to be robust or precise because it is vulnerable to gross feature detection errors or outliers resulting from partial occlusions or spurious features from the background or neighboring objects. We address this problem by adopting a randomized hypothesis-and-test approach. First, a Bayesian inference algorithm is developed to generate a shape-and-pose hypothesis of the object from a partial shape or a subset of feature points. For alignment, a large number of hypotheses are generated by randomly sampling subsets of feature points, and then evaluated to find the one that minimizes the shape prediction error. This method of randomized subset-based matching can effectively handle outliers and recover the correct object shape. We apply this approach on a challenging data set of over 5,000 different-posed car images, spanning a wide variety of car types, lighting, background scenes, and partial occlusions. Experimental results demonstrate favorable improvements over previous methods on both accuracy and robustness.

  19. Physician-Hospital Alignment in Orthopedic Surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery.

  20. An Overview of Multiple Sequence Alignment Systems

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    An overview of current multiple alignment systems to date are described.The useful algorithms, the procedures adopted and their limitations are presented.We also present the quality of the alignments obtained and in which cases(kind of alignments, kind of sequences etc) the particular systems are useful.

  1. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao;

    2007-01-01

    sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...

  2. Inferring comprehensible business/ICT alignment rules

    NARCIS (Netherlands)

    Cumps, B.; Martens, D.; De Backer, M.; Haesen, R.; Viaene, S.; Dedene, G.; Baesens, B.; Snoeck, M.

    2009-01-01

    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputati

  3. Shift dynamics of capillary self-alignment

    NARCIS (Netherlands)

    Arutinov, G.; Mastrangeli, M.; Smits, E.C.P.; Heck, G.V.; Schoo, H.F.M.; Toonder, J.J.M. den; Dietzel, A.H.

    2014-01-01

    This paper describes the dynamics of capillary self-alignment of components with initial shift offsets from matching receptor sites. The analysis of the full uniaxial self-alignment dynamics of foil-based mesoscopic dies from pre-alignment to final settling evidenced three distinct, sequential regim

  4. Alignment of lower-limb prostheses.

    Science.gov (United States)

    Zahedi, M S; Spence, W D; Solomonidis, S E; Paul, J P

    1986-04-01

    Alignment of a prosthesis is defined as the position of the socket relative to the other prosthetic components of the limb. During dynamic alignment the prosthetist, using subjective judgment and feedback from the patient, aims to achieve the most suitable limb geometry for best function and comfort. Until recently it was generally believed that a patient could only be satisfied with a unique "optimum alignment." The purpose of this systematic study of lower-limb alignment parameters was to gain an understanding of the factors that make a limb configuration or optimum alignment, acceptable to the patient, and to obtain a measure of the variation of this alignment that would be acceptable to the amputee. In this paper, the acceptable range of alignments for 10 below- and 10 above-knee amputees are established. Three prosthetists were involved in the majority of the 183 below-knee and 100 above-knee fittings, although several other prosthetists were also involved. The effects of each different prosthetist on the established range of alignment for each patient are reported to be significant. It is now established that an amputee can tolerate several alignments ranging in some parameters by as much as 148 mm in shifts and 17 degrees in tilts. This paper describes the method of defining and measuring the alignment of lower-limb prostheses. It presents quantitatively established values for bench alignment position and the range of adjustment required for incorporation into the design of new alignment units.

  5. Aligning Projection Images from Binary Volumes

    NARCIS (Netherlands)

    Bleichrodt, F.; Beenhouwer, J. de; Sijbers, J.; Batenburg, K.J.

    2014-01-01

    In tomography, slight differences between the geometry of the scanner hardware and the geometric model used in the reconstruction lead to alignment artifacts. To exploit high-resolution detectors used in many applications of tomography, alignment of the projection data is essential. Markerless align

  6. Vertically aligned nanostructure scanning probe microscope tips

    Science.gov (United States)

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  7. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry

    2012-01-01

    Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment o...

  8. 一种从石蜡包埋组织中获取高质量基因组DNA的改良方法%An improved method to recover high quality genomic DNA from paraffin-embedded tissues

    Institute of Scientific and Technical Information of China (English)

    夏米西努尔·伊力克; 杨曦; 武贵臻; 马琦; 阿布力孜·阿布杜拉

    2009-01-01

    Objective To establish a high quality genomic DNA preparation method from formalin fixed and paraffin embedded tissues (FFPET) by integrating previous DNA extraction methods. Methods We combined classical genomic DNA extraction methods and commercially available DNA affinity column, replaced the de-waxing by dimethylbenzene with water-bath, designed a fast and improved genomic DNA preparation method. We also extracted genomic DNA from paraffin embedded cervical cancer tissues, and checked the quality of DNA by agarose gel electrophoresis and polymerase chain reaction detection. Results The improved genomic DNA extraction method combined the advantages of the water-bath de-waxing and DNA affinity column, making it possible to get high quality genomic DNA from paraffin embedded cervical cancer tissues, and especially efficient to recover genomic DNA fragments larger than 20 kb. Conclusion The improved DNA extraction method is fast and convenient to recover high quality genomic DNA from paraffin embedded tissues.%目的:比较现有的DNA制备方法,建立一种从甲醛固定石蜡包埋组织(formalin-fixed paraffin-embedded tissues,FFPET)提取高质量基因组DNA的方法.方法:将传统基因组DNA提取方法与市场供应的DNA亲和层析柱结合在一起,以水浴脱腊法替代二甲苯脱腊法,设计一种改良的基因组DNA快速提取方法,从石蜡包埋宫颈癌组织标本提取基因组DNA,并用琼脂糖凝胶电泳法和聚合酶链式反应法进行鉴定.结果:改良的基因组DNA提取法整合了水浴脱蜡与DNA亲和层析柱的优点,从石蜡包埋宫颈癌组织中获得了高质量的基因组DNA,特别是能以很高的效率回收大于20 kb的基因组DNA大片段.结论:改良的基因组DNA提取方法简单快捷,是一种从石蜡包埋组织中回收高质量基因组DNA的有效途径.

  9. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Marcelo Bento (New York, NY); Bonaldo, Maria de Fatima (New York, NY)

    1998-01-01

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods.

  10. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    Energy Technology Data Exchange (ETDEWEB)

    Soares, M.B.; Fatima Bonaldo, M. de

    1998-12-08

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.

  11. Functionally informed cortex based alignment: an integrated approach for whole-cortex macro-anatomical and ROI-based functional alignment.

    Science.gov (United States)

    Frost, Martin A; Goebel, Rainer

    2013-12-01

    Due to anatomical variability across subjects many brain mapping experiments have analysis focused on a few particular regions of interest so as to circumvent the problem of sub-optimal statistics resulting from the lack of anatomical correspondence across subjects. Since the topographic distribution of experimental effects across the cortex is also often of interest, two separate analyses are often conducted, one on the regions of interest alone, as well as a separate 'whole brain' analysis with sub-optimal spatial correspondence across brains. In this paper we present a new group alignment procedure which incorporates, from each subject, both macro-anatomical (curvature) information and functional information from standard localizer experiments. After specifying appropriate parameters to weight anatomical and functional alignment forces, we were able to create a group cortical reconstruction which was well aligned in terms of both anatomical and functional areas. We observed an increase in the overlap of functional areas as well as an improvement in group statistics following this integrated alignment procedure. We propose that, using this alignment scheme, two separate analyses may not be necessary as both analyses can be integrated into a single procedure. After an integrated structural and functional alignment one is able to carry out a whole brain analysis with improved statistical sensitivity due to the reduction in spatial variation in the location of functional regions of interest which fCBA accomplishes. Furthermore, regions in the vicinity of localised and aligned regions-of-interest will also benefit from the integrated alignment.

  12. Fuzzy adaptive strong tracking scaled unscented Kalman filter for initial alignment of large misalignment angles.

    Science.gov (United States)

    Li, Jing; Song, Ningfang; Yang, Gongliu; Jiang, Rui

    2016-07-01

    In the initial alignment process of strapdown inertial navigation system (SINS), large misalignment angles always bring nonlinear problem, which can usually be processed using the scaled unscented Kalman filter (SUKF). In this paper, the problem of large misalignment angles in SINS alignment is further investigated, and the strong tracking scaled unscented Kalman filter (STSUKF) is proposed with fixed parameters to improve convergence speed, while these parameters are artificially constructed and uncertain in real application. To further improve the alignment stability and reduce the parameters selection, this paper proposes a fuzzy adaptive strategy combined with STSUKF (FUZZY-STSUKF). As a result, initial alignment scheme of large misalignment angles based on FUZZY-STSUKF is designed and verified by simulations and turntable experiment. The results show that the scheme improves the accuracy and convergence speed of SINS initial alignment compared with those based on SUKF and STSUKF.

  13. Fuzzy adaptive strong tracking scaled unscented Kalman filter for initial alignment of large misalignment angles

    Science.gov (United States)

    Li, Jing; Song, Ningfang; Yang, Gongliu; Jiang, Rui

    2016-07-01

    In the initial alignment process of strapdown inertial navigation system (SINS), large misalignment angles always bring nonlinear problem, which can usually be processed using the scaled unscented Kalman filter (SUKF). In this paper, the problem of large misalignment angles in SINS alignment is further investigated, and the strong tracking scaled unscented Kalman filter (STSUKF) is proposed with fixed parameters to improve convergence speed, while these parameters are artificially constructed and uncertain in real application. To further improve the alignment stability and reduce the parameters selection, this paper proposes a fuzzy adaptive strategy combined with STSUKF (FUZZY-STSUKF). As a result, initial alignment scheme of large misalignment angles based on FUZZY-STSUKF is designed and verified by simulations and turntable experiment. The results show that the scheme improves the accuracy and convergence speed of SINS initial alignment compared with those based on SUKF and STSUKF.

  14. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

    DEFF Research Database (Denmark)

    Lindgreen, Stinus; Gardner, Paul P; Krogh, Anders

    2007-01-01

    , it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. RESULT: We present a novel solution to the problem of simultaneous structure prediction...... and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost...

  15. Mobile and replicated alignment of arrays in data-parallel programs

    Science.gov (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

  16. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.;

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  17. Subsonic Mechanical Alignment of Irregular Grains

    CERN Document Server

    Lazarian, Alex

    2007-01-01

    We show that grains can be efficiently aligned by interacting with a subsonic gaseous flow. The alignment arises from grains having irregularities that scatter atoms with different efficiency in the right and left directions. The grains tend to align with long axes perpendicular to magnetic field, which corresponds to Davis-Greenstein predictions, but does not involve magnetic field. For rather conservative factors characterizing the grain helicity and scattering efficiency of impinging atoms, the alignment of helical grains is much more efficient than the Gold-type alignment processes.

  18. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    Science.gov (United States)

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.

  19. Novel Real-time Calibration and Alignment Procedure for LHCb Run II

    CERN Multimedia

    Prouve, Claire

    2016-01-01

    In order to achieve optimal detector performance the LHCb experiment has introduced a novel real-time detector alignment and calibration strategy for Run II of the LHC. For the alignment tasks, data is collected and processed at the beginning of each fill while the calibrations are performed for each run. This real time alignment and calibration allows the same constants being used in both the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. Additionally the newly computed alignment and calibration constants can be instantly used in the trigger, making it more efficient. The online alignment and calibration of the RICH detectors also enable the use of hadronic particle identification in the trigger. The computing time constraints are met through the use of a new dedicated framework using the multi-core farm infrastructure for the LHCb trigger. An overview of all alignment and calibration tasks is presented and their performance is shown.

  20. Mutual Understanding Determinants for Effective Communication in Business and IT Strategic Alignment Planning

    Directory of Open Access Journals (Sweden)

    Nurul `Izzati Mohmad Adnan

    2016-12-01

    Full Text Available Business and IT strategic alignment is continuously explored from different facets motivated by the demands for organisation to be well aligned in its business and IT strategies for business continuity. The management aspect rather than technological issues often causes misalignment in business and IT strategies more significantly. One of the issues is the communication ineffectiveness between business and IT people involved in planning the business and IT strategic alignment. Difficulty to achieve mutual understanding between these two teams is a critical problem in communication and hinders the successful alignment. Therefore, a set of determinants for mutual understanding is proposed. Extensive analysis on literature has been carried out to identify and define the determining factors. The review can serve as a reference for business and IT executives to improve in their communication effectiveness towards achieving well aligned business and IT strategic alignment.