Schizosaccharomyces pombe MutSα and MutLα Maintain Stability of Tetra-Nucleotide Repeats and Msh3 of Hepta-Nucleotide Repeats

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Desirée Villahermosa

2017-05-01

Full Text Available Defective mismatch repair (MMR in humans is associated with colon cancer and instability of microsatellites, that is, DNA sequences with one or several nucleotides repeated. Key factors of eukaryotic MMR are the heterodimers MutSα (Msh2-Msh6, which recognizes base-base mismatches and unpaired nucleotides in DNA, and MutLα (Mlh1-Pms1, which facilitates downstream steps. In addition, MutSβ (Msh2-Msh3 recognizes DNA loops of various sizes, although our previous data and the data presented here suggest that Msh3 of Schizosaccharomyces pombe does not play a role in MMR. To test microsatellite stability in S. pombe and hence DNA loop repair, we have inserted tetra-, penta-, and hepta-nucleotide repeats in the ade6 gene and determined their Ade+ reversion rates and spectra in wild type and various mutants. Our data indicate that loops with four unpaired nucleotides in the nascent and the template strand are the upper limit of MutSα- and MutLα-mediated MMR in S. pombe. Stability of hepta-nucleotide repeats requires Msh3 and Exo1 in MMR-independent processes as well as the DNA repair proteins Rad50, Rad51, and Rad2FEN1. Most strikingly, mutation rates in the double mutants msh3 exo1 and msh3 rad51 were decreased when compared to respective single mutants, indicating that Msh3 prevents error prone processes carried out by Exo1 and Rad51. We conclude that Msh3 has no obvious function in MMR in S. pombe, but contributes to DNA repeat stability in MMR-independent processes.

Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges.

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Jensen, Michael A; Davis, Ronald W

2018-03-27

There is a growing demand for sustainable methods in research and development, where instead of hazardous chemicals, an aqueous medium is chosen to perform biological reactions. In this Perspective, we examine the history and current methodology of using enzymes to generate artificial single-stranded DNA. By using traditional solid-phase phosphoramidite chemistry as a metric, we also explore criteria for the method of template-independent enzymatic oligonucleotide synthesis (TiEOS). As its key component, we delve into the biology of one of the most enigmatic enzymes, terminal deoxynucleotidyl transferase (TdT). As TdT is found to exponentially increase antigen receptor diversity in the vertebrate immune system by adding nucleotides in a template-free manner, researchers have exploited this function as an alternative to the phosphoramidite synthesis method. Though TdT is currently the preferred enzyme for TiEOS, its random nucleotide incorporation presents a barrier in synthesis automation. Taking a closer look at the TiEOS cycle, particularly the coupling step, we find it is comprised of additions > n+1 and deletions. By tapping into the physical and biochemical properties of TdT, we strive to further elucidate its mercurial behavior and offer ways to better optimize TiEOS for production-grade oligonucleotide synthesis.

Additive-manufactured patient-specific titanium templates for thoracic pedicle screw placement: novel design with reduced contact area.

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Takemoto, Mitsuru; Fujibayashi, Shunsuke; Ota, Eigo; Otsuki, Bungo; Kimura, Hiroaki; Sakamoto, Takeshi; Kawai, Toshiyuki; Futami, Tohru; Sasaki, Kiyoyuki; Matsushita, Tomiharu; Nakamura, Takashi; Neo, Masashi; Matsuda, Shuich

2016-06-01

Image-based navigational patient-specific templates (PSTs) for pedicle screw (PS) placement have been described. With recent advances in three-dimensional computer-aided designs and additive manufacturing technology, various PST designs have been reported, although the template designs were not optimized. We have developed a novel PST design that reduces the contact area without sacrificing stability. It avoids susceptibility to intervening soft tissue, template geometric inaccuracy, and difficulty during template fitting. Fourteen candidate locations on the posterior aspect of the vertebra were evaluated. Among them, locations that had high reproducibility on computed tomography (CT) images and facilitated accurate PS placement were selected for the final PST design. An additive manufacturing machine (EOSINT M270) fabricated the PSTs using commercially pure titanium powder. For the clinical study, 36 scoliosis patients and 4 patients with ossification of the posterior longitudinal ligament (OPLL) were treated with thoracic PSs using our newly developed PSTs. We intraoperatively and postoperatively evaluated the accuracy of the PS hole created by the PST. Based on the segmentation reproducibility and stability analyses, we selected seven small, round contact points for our PST: bilateral superior and inferior points on the transverse process base, bilateral inferior points on the laminar, and a superior point on the spinous process. Clinically, the success rates of PS placement using this PST design were 98.6 % (414/420) for scoliosis patients and 100 % (46/46) for OPLL patients. This study provides a useful design concept for the development and introduction of patient-specific navigational templates for placing PSs.

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World.

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Ye Eun Kim

2016-11-01

Full Text Available It is believed that life passed through an RNA World stage in which replication was sustained by catalytic RNAs (ribozymes. The two most obvious types of ribozymes are a polymerase, which uses a neighbouring strand as a template to make a complementary sequence to the template, and a nucleotide synthetase, which synthesizes monomers for use by the polymerase. When a chemical source of monomers is available, the polymerase can survive on its own. When the chemical supply of monomers is too low, nucleotide production by the synthetase is essential and the two ribozymes can only survive when they are together. Here we consider a computational model to investigate conditions under which coexistence and cooperation of these two types of ribozymes is possible. The model considers six types of strands: the two functional sequences, the complementary strands to these sequences (which are required as templates, and non-functional mutants of the two sequences (which act as parasites. Strands are distributed on a two-dimensional lattice. Polymerases replicate strands on neighbouring sites and synthetases produce monomers that diffuse in the local neighbourhood. We show that coexistence of unlinked polymerases and synthetases is possible in this spatial model under conditions in which neither sequence could survive alone; hence, there is a selective force for increasing complexity. Coexistence is dependent on the relative lengths of the two functional strands, the strand diffusion rate, the monomer diffusion rate, and the rate of deleterious mutations. The sensitivity of this two-ribozyme system suggests that evolution of a system of many types of ribozymes would be difficult in a purely spatial model with unlinked genes. We therefore speculate that linkage of genes onto mini-chromosomes and encapsulation of strands in protocells would have been important fairly early in the history of life as a means of enabling more complex systems to evolve.

A non-parametric 2D deformable template classifier

DEFF Research Database (Denmark)

Schultz, Nette; Nielsen, Allan Aasbjerg; Conradsen, Knut

2005-01-01

feature space the ship-master will be able to interactively define a segmentation map, which is refined and optimized by the deformable template algorithms. The deformable templates are defined as two-dimensional vector-cycles. Local random transformations are applied to the vector-cycles, and stochastic...

Non-nucleotide Agonists Triggering P2X7 Receptor Activation and Pore Formation

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Francesco Di Virgilio

2018-02-01

Full Text Available The P2X7 receptor (P2X7R is a ligand-gated plasma membrane ion channel belonging to the P2X receptor subfamily activated by extracellular nucleotides. General consensus holds that the physiological (and maybe the only agonist is ATP. However, scattered evidence generated over the last several years suggests that ATP might not be the only agonist, especially at inflammatory sites. Solid data show that NAD+ covalently modifies the P2X7R of mouse T lymphocytes, thus lowering the ATP threshold for activation. Other structurally unrelated agents have been reported to activate the P2X7R via a poorly understood mechanism of action: (a the antibiotic polymyxin B, possibly a positive allosteric P2X7R modulator, (b the bactericidal peptide LL-37, (c the amyloidogenic β peptide, and (d serum amyloid A. Some agents, such as Alu-RNA, have been suggested to activate the P2X7R acting on the intracellular N- or C-terminal domains. Mode of P2X7R activation by these non-nucleotide ligands is as yet unknown; however, these observations raise the intriguing question of how these different non-nucleotide ligands may co-operate with ATP at inflammatory or tumor sites. New information obtained from the cloning and characterization of the P2X7R from exotic mammalian species (e.g., giant panda and data from recent patch-clamp studies are strongly accelerating our understanding of P2X7R mode of operation, and may provide hints to the mechanism of activation of P2X7R by non-nucleotide ligands.

Templated sequence insertion polymorphisms in the human genome

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Onozawa, Masahiro; Aplan, Peter

2016-11-01

Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including 1) target-site duplication (TSD), 2) polyadenylation 10-30 nucleotides downstream of a “cryptic” polyadenylation signal, and 3) preference for insertion at a 5’-TTTT/A-3’ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25-30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.

Graphene Emerges as a Versatile Template for Materials Preparation.

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Li, Zhengjie; Wu, Sida; Lv, Wei; Shao, Jiao-Jing; Kang, Feiyu; Yang, Quan-Hong

2016-05-01

Graphene and its derivatives are emerging as a class of novel but versatile templates for the controlled preparation and functionalization of materials. In this paper a conceptual review on graphene-based templates is given, highlighting their versatile roles in materials preparation. Graphene is capable of acting as a low-dimensional hard template, where its two-dimensional morphology directs the formation of novel nanostructures. Graphene oxide and other functionalized graphenes are amphiphilic and may be seen as soft templates for formatting the growth or inducing the controlled assembly of nanostructures. In addition, nanospaces in restacked graphene can be used for confining the growth of sheet-like nanostructures, and assemblies of interlinked graphenes can behave either as skeletons for the formation of composite materials or as sacrificial templates for novel materials with a controlled network structure. In summary, flexible graphene and its derivatives together with an increasing number of assembled structures show great potentials as templates for materials production. Many challenges remain, for example precise structural control of such novel templates and the removal of the non-functional remaining templates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cloning nanocrystal morphology with soft templates

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Thapa, Dev Kumar; Pandey, Anshu

2016-08-01

In most template directed preparative methods, while the template decides the nanostructure morphology, the structure of the template itself is a non-general outcome of its peculiar chemistry. Here we demonstrate a template mediated synthesis that overcomes this deficiency. This synthesis involves overgrowth of silica template onto a sacrificial nanocrystal. Such templates are used to copy the morphologies of gold nanorods. After template overgrowth, gold is removed and silver is regrown in the template cavity to produce a single crystal silver nanorod. This technique allows for duplicating existing nanocrystals, while also providing a quantifiable breakdown of the structure - shape interdependence.

New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage.

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Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

2014-01-01

The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (-ΔG°37) in the presence of 20 wt% PEG was more than 8.2 kcal mol(-1). Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.

A facile template method to synthesize significantly improved LiNi0.5Mn1.5O4 using corn stalk as a bio-template

International Nuclear Information System (INIS)

Liu, Guiyang; Kong, Xin; Sun, Hongyan; Wang, Baosen; Yi, Zhongzhou; Wang, Quanbiao

2014-01-01

In order to simplify the template method for the synthesis of cathode materials for lithium ion batteries, a facile template method using plant stalks as bio-templates has been introduced. Based on this method, LiNi 0.5 Mn 1.5 O 4 spinel with a significantly improved electrochemical performance has been synthesized using corn stalk as a template. X-ray diffraction (XRD), Fourier transform infrared pectroscopy (FTIR) and scanning electron microscope (SEM) have been used to investigate the phase composition and micro-morphologies of the products. Charge-discharge measurements in lithium cells, cyclic voltammetry (CV) and Electrochemical impedance spectroscopy (EIS) have been used to study the electrochemical performance of the products. The results indicate that the templated product exhibits higher crystallinity than that of non-templated product. Both of the templated product and the non-templated product are combination of the ordered space group P4 3 32 and the disordered Fd-3 m. The specific BET surface area of the templated product is about twice larger than that of the non-templated product. Moreover, the electrochemical performances of the templated product including specific capacity, cycling stability and rate capability are significantly improved as compared with the non-templated product, due to its higher crystallinity, larger Li + diffusion coefficient and lower charge transfer resistance

The possible role of human milk nucleotides as sleep inducers.

Science.gov (United States)

Sánchez, Cristina L; Cubero, Javier; Sánchez, Javier; Chanclón, Belén; Rivero, Montserrat; Rodríguez, Ana B; Barriga, Carmen

2009-02-01

Breast-milk contains a potent mixture of diverse components, such as the non-protein nitrogen fraction which includes nucleotides, whose variation in levels is evident throughout lactation. In addition, these substances play an important role in sleep homeostasis. In the present study, human milk samples were analyzed using a capillary electrophoresis system. The rhythmicity of each nucleotide was studied by cosinor analysis. It was found that the nucleotides 5'AMP, 5'GMP, 5'CMP, and 5'IMP have significant (P inducing the 'hypnotic' action of breast-milk at night in the infant.

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

International Nuclear Information System (INIS)

Wang Zhan-Feng; Liu Yu-Ru; Wang Peng-Ye; Xie Ping

2017-01-01

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson–Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA–RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP. (paper)

Pyridine nucleotides in regulation of cell death and survival by redox and non-redox reactions.

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Novak Kujundžić, Renata; Žarković, Neven; Gall Trošelj, Koraljka

2014-01-01

Changes of the level and ratios of pyridine nucleotides determine metabolism- dependent cellular redox status and the activity of poly(ADP-ribose) polymerases (PARPs) and sirtuins, thereby influencing several processes closely related to cell survival and death. Pyridine nucleotides participate in numerous metabolic reactions whereby their net cellular level remains constant, but the ratios of NAD+/NADP+ and NADH/NADPH oscillate according to metabolic changes in response to diverse stress signals. In non-redox reactions, NAD+ is degraded and quickly, afterward, resynthesized in the NAD+ salvage pathway, unless overwhelming activation of PARP-1 consumes NAD+ to the point of no return, when the cell can no longer generate enough ATP to accommodate NAD+ resynthesis. The activity of PARP-1 is mandatory for the onset of cytoprotective autophagy on sublethal stress signals. It has become increasingly clear that redox status, largely influenced by the metabolism-dependent composition of the pyridine nucleotides pool, plays an important role in the synthesis of pro-apoptotic and anti-apoptotic sphingolipids. Awareness of the involvement of the prosurvival sphingolipid, sphingosine-1-phosphate, in transition from inflammation to malignant transformation has recently emerged. Here, the participation of pyridine nucleotides in redox and non-redox reactions, sphingolipid metabolism, and their role in cell fate decisions is reviewed.

Template Dimerization Promotes an Acceptor Invasion-Induced Transfer Mechanism during Human Immunodeficiency Virus Type 1 Minus-Strand Synthesis

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Balakrishnan, Mini; Roques, Bernard P.; Fay, Philip J.; Bambara, Robert A.

2003-01-01

The biochemical mechanism of template switching by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and the role of template dimerization were examined. Homologous donor-acceptor template pairs derived from the HIV-1 untranslated leader region and containing the wild-type and mutant dimerization initiation sequences (DIS) were used to examine the efficiency and distribution of transfers. Inhibiting donor-acceptor interaction was sufficient to reduce transfers in DIS-containing template pairs, indicating that template dimerization, and not the mere presence of the DIS, promotes efficient transfers. Additionally, we show evidence that the overall transfer process spans an extended region of the template and proceeds through a two-step mechanism. Transfer is initiated through an RNase H-facilitated acceptor invasion step, while synthesis continues on the donor template. The invasion then propagates towards the primer terminus by branch migration. Transfer is completed with the translocation of the primer terminus at a site distant from the invasion point. In our system, most invasions initiated before synthesis reached the DIS. However, transfer of the primer terminus predominantly occurred after synthesis through the DIS. The two steps were separated by 60 to 80 nucleotides. Sequence markers revealed the position of primer terminus switch, whereas DNA oligomers designed to block acceptor-cDNA interactions defined sites of invasion. Within the region of homology, certain positions on the template were inherently more favorable for invasion than others. In templates with DIS, the proximity of the acceptor facilitates invasion, thereby enhancing transfer efficiency. Nucleocapsid protein enhanced the overall efficiency of transfers but did not alter the mechanism. PMID:12663778

DNA incorporation of 6-thioguanine nucleotides during maintenance therapy of childhood acute lymphoblastic leukaemia and non-Hodgkin lymphoma

DEFF Research Database (Denmark)

Hedeland, Rikke L; Hvidt, Kristian; Nersting, Jacob

2010-01-01

To explore the DNA incorporation of 6-thioguanine nucleotide levels (DNA-6TGN) during 6-mercaptopurine (6MP) therapy of childhood acute lymphoblastic leukaemia (ALL) and non-Hodgkin lymphoma (NHL) and its relation to erythrocyte levels of their metabolites: 6-thioguanine-nucleotides (E-6TGN...

Comparison of Nucleotide Sequence of P2C Region in Diabetogenic and Non-Diabetogenic Coxsackie Virus B5 Isolates

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Cheng-Chong Chou

2004-11-01

Full Text Available Enteroviruses are environmental triggers in the pathogenesis of type 1 diabetes mellitus (DM. A sequence of six identical amino acids (PEVKEK is shared by the 2C protein of Coxsackie virus B and the glutamic acid decarboxylase (GAD molecules. Between 1995 and 2002, we investigated 22 Coxsackie virus B5 (CVB5 isolates from southern Taiwan. Four of these isolates were obtained from four new-onset type 1 DM patients with diabetic ketoacidosis. We compared a 300 nucleotide sequence in the 2C protein gene (p2C in 24 CVB5 isolates (4 diabetogenic, 18 non-diabetogenic and 2 prototype. We found 0.3-10% nucleotide differences. In the four isolates from type 1 DM patients, there was only 2.4-3.4% nucleotide difference, and there was only 1.7-7.1% nucleotide difference between type 1 DM isolates and non-diabetogenic isolates. Comparison of the nucleotide sequence between prototype virus and 22 CVB5 isolates revealed 18.4-24.1% difference. Twenty-one CVB5 isolates from type 1 DM and non-type 1 DM patients contained the PEVKEK sequence, as shown by the p2C nucleotide sequence. Our data showed that the viral p2C sequence with homology with GAD is highly conserved in CVB5 isolates. There was no difference between diabetogenic and non-diabetogenic CVB5 isolates. All four type 1 DM patients had at least one of the genetic susceptibility alleles HLA-DR, DQA1, DQB1. Other genetic and autoimmune factors such as HLA genetic susceptibility and GAD may also play important roles in the pathogenesis in type 1 DM.

Strand displacement by DNA polymerase III occurs through a tau-psi-chi link to single-stranded DNA-binding protein coating the lagging strand template.

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Yuan, Quan; McHenry, Charles S

2009-11-13

In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of gamma-complex to support the reaction in the absence of tau. However, if gamma-complex is present to load beta(2), a truncated tau protein containing only domains III-V will suffice. This truncated protein is sufficient to bind both the alpha subunit of DNA polymerase (Pol) III and chipsi. This is reminiscent of the minimal requirements for Pol III to replicate short single-stranded DNA-binding protein (SSB)-coated templates where tau is only required to serve as a scaffold to hold Pol III and chi in the same complex (Glover, B., and McHenry, C. (1998) J. Biol. Chem. 273, 23476-23484). We propose a model in which strand displacement by DNA polymerase III holoenzyme depends upon a Pol III-tau-psi-chi-SSB binding network, where SSB is bound to the displaced strand, stabilizing the Pol III-template interaction. The same interaction network is probably important for stabilizing the leading strand polymerase interactions with authentic replication forks. The specificity constant (k(cat)/K(m)) for the strand displacement reaction is approximately 300-fold less favorable than reactions on single-stranded templates and proceeds with a slower rate (150 nucleotides/s) and only moderate processivity (approximately 300 nucleotides). PriA, the initiator of replication restart on collapsed or misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoing reaction.

High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny.

Science.gov (United States)

Conboy, Michael J; Karasov, Ariela O; Rando, Thomas A

2007-05-01

Decades ago, the "immortal strand hypothesis" was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer, while continuing to proliferate for the life of an organism. Originally based on observations in embryonic cells, and later studied in terms of stem cell self-renewal, this hypothesis has remained largely unaccepted because of few additional reports, the rarity of the cells displaying template strand segregation, and alternative interpretations of experiments involving single labels or different types of labels to follow template strands. Using sequential pulses of halogenated thymidine analogs (bromodeoxyuridine [BrdU], chlorodeoxyuridine [CldU], and iododeoxyuridine [IdU]), and analyzing stem cell progeny during induced regeneration in vivo, we observed extraordinarily high frequencies of segregation of older and younger template strands during a period of proliferative expansion of muscle stem cells. Furthermore, template strand co-segregation was strongly associated with asymmetric cell divisions yielding daughters with divergent fates. Daughter cells inheriting the older templates retained the more immature phenotype, whereas daughters inheriting the newer templates acquired a more differentiated phenotype. These data provide compelling evidence of template strand co-segregation based on template age and associated with cell fate determination, suggest that template strand age is monitored during stem cell lineage progression, and raise important caveats for the interpretation of label-retaining cells.

High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny.

Directory of Open Access Journals (Sweden)

Michael J Conboy

2007-05-01

Full Text Available Decades ago, the "immortal strand hypothesis" was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer, while continuing to proliferate for the life of an organism. Originally based on observations in embryonic cells, and later studied in terms of stem cell self-renewal, this hypothesis has remained largely unaccepted because of few additional reports, the rarity of the cells displaying template strand segregation, and alternative interpretations of experiments involving single labels or different types of labels to follow template strands. Using sequential pulses of halogenated thymidine analogs (bromodeoxyuridine [BrdU], chlorodeoxyuridine [CldU], and iododeoxyuridine [IdU], and analyzing stem cell progeny during induced regeneration in vivo, we observed extraordinarily high frequencies of segregation of older and younger template strands during a period of proliferative expansion of muscle stem cells. Furthermore, template strand co-segregation was strongly associated with asymmetric cell divisions yielding daughters with divergent fates. Daughter cells inheriting the older templates retained the more immature phenotype, whereas daughters inheriting the newer templates acquired a more differentiated phenotype. These data provide compelling evidence of template strand co-segregation based on template age and associated with cell fate determination, suggest that template strand age is monitored during stem cell lineage progression, and raise important caveats for the interpretation of label-retaining cells.

Molecular Properties of Poliovirus Isolates: Nucleotide Sequence Analysis, Typing by PCR and Real-Time RT-PCR.

Science.gov (United States)

Burns, Cara C; Kilpatrick, David R; Iber, Jane C; Chen, Qi; Kew, Olen M

2016-01-01

Virologic surveillance is essential to the success of the World Health Organization initiative to eradicate poliomyelitis. Molecular methods have been used to detect polioviruses in tissue culture isolates derived from stool samples obtained through surveillance for acute flaccid paralysis. This chapter describes the use of realtime PCR assays to identify and serotype polioviruses. In particular, a degenerate, inosine-containing, panpoliovirus (panPV) PCR primer set is used to distinguish polioviruses from NPEVs. The high degree of nucleotide sequence diversity among polioviruses presents a challenge to the systematic design of nucleic acid-based reagents. To accommodate the wide variability and rapid evolution of poliovirus genomes, degenerate codon positions on the template were matched to mixed-base or deoxyinosine residues on both the primers and the TaqMan™ probes. Additional assays distinguish between Sabin vaccine strains and non-Sabin strains. This chapter also describes the use of generic poliovirus specific primers, along with degenerate and inosine-containing primers, for routine VP1 sequencing of poliovirus isolates. These primers, along with nondegenerate serotype-specific Sabin primers, can also be used to sequence individual polioviruses in mixtures.

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae.

Science.gov (United States)

Rosinski-Chupin, Isabelle; Sauvage, Elisabeth; Sismeiro, Odile; Villain, Adrien; Da Cunha, Violette; Caliot, Marie-Elise; Dillies, Marie-Agnès; Trieu-Cuot, Patrick; Bouloc, Philippe; Lartigue, Marie-Frédérique; Glaser, Philippe

2015-05-30

Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing. Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively. This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools.

Hydrogen-Bonding Capability of a Templating Difluorotoluene Nucleotide Residue in an RB69 DNA Polymerase Ternary Complex

Energy Technology Data Exchange (ETDEWEB)

Xia, Shuangluo; Konigsberg, William H.; Wang, Jimin (Yale)

2011-08-29

Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 {angstrom}-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.

Multi-template polymerase chain reaction.

Science.gov (United States)

Kalle, Elena; Kubista, Mikael; Rensing, Christopher

2014-12-01

PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

Non-thiolate ligation of nickel by nucleotide-free UreG of Klebsiella aerogenes

Energy Technology Data Exchange (ETDEWEB)

Martin-Diaconescu, Vlad; Joseph, Crisjoe A.; Boer, Jodi L.; Mulrooney, Scott B.; Hausinger, Robert P.; Maroney, Michael J.

2016-12-21

Nickel-dependent ureases are activated by a multiprotein complex that includes the GTPase UreG. Prior studies showed that nucleotide-free UreG from Klebsiella aerogenes is monomeric and binds one nickel or zinc ion with near-equivalent affinity using an undefined binding site, whereas nucleotide-free UreG from Helicobacter pylori selectively binds one zinc ion per dimer via a universally conserved Cys-Pro-His motif in each protomer. Iodoacetamide-treated K. aerogenes UreG was nearly unaffected in nickel binding compared to non-treated sample, suggesting the absence of thiolate ligands to the metal. X-ray absorption spectroscopy of nickel-bound UreG showed the metal possessed four-coordinate geometry with all O/N donor ligands including one imidazole, thus confirming the absence of thiolate ligation. The nickel site in Strep-tag II-modified protein possessed six-coordinate geometry, again with all O/N donor ligands, but now including two or three imidazoles. An identical site was noted for the Strep-tag II-modified H74A variant, substituted in the Cys-Pro-His motif, ruling out coordination by this His residue. These results are consistent with metal binding to both His6 and a His residue of the fusion peptide in Strep-tagged K. aerogenes UreG. We conclude that the nickel- and zinc-binding site in nucleotide-free K. aerogenes UreG is distinct from that of nucleotide-free H. pylori UreG and does not involve the Cys-Pro-His motif. Further, we show the Strep-tag II can perturb metal coordination of this protein.

Titanium template for scaphoid reconstruction.

Science.gov (United States)

Haefeli, M; Schaefer, D J; Schumacher, R; Müller-Gerbl, M; Honigmann, P

2015-06-01

Reconstruction of a non-united scaphoid with a humpback deformity involves resection of the non-union followed by bone grafting and fixation of the fragments. Intraoperative control of the reconstruction is difficult owing to the complex three-dimensional shape of the scaphoid and the other carpal bones overlying the scaphoid on lateral radiographs. We developed a titanium template that fits exactly to the surfaces of the proximal and distal scaphoid poles to define their position relative to each other after resection of the non-union. The templates were designed on three-dimensional computed tomography reconstructions and manufactured using selective laser melting technology. Ten conserved human wrists were used to simulate the reconstruction. The achieved precision measured as the deviation of the surface of the reconstructed scaphoid from its virtual counterpart was good in five cases (maximal difference 1.5 mm), moderate in one case (maximal difference 3 mm) and inadequate in four cases (difference more than 3 mm). The main problems were attributed to the template design and can be avoided by improved pre-operative planning, as shown in a clinical case. © The Author(s) 2014.

Performance of peaky template matching under additive white Gaussian noise and uniform quantization

Science.gov (United States)

Horvath, Matthew S.; Rigling, Brian D.

2015-05-01

Peaky template matching (PTM) is a special case of a general algorithm known as multinomial pattern matching originally developed for automatic target recognition of synthetic aperture radar data. The algorithm is a model- based approach that first quantizes pixel values into Nq = 2 discrete values yielding generative Beta-Bernoulli models as class-conditional templates. Here, we consider the case of classification of target chips in AWGN and develop approximations to image-to-template classification performance as a function of the noise power. We focus specifically on the case of a uniform quantization" scheme, where a fixed number of the largest pixels are quantized high as opposed to using a fixed threshold. This quantization method reduces sensitivity to the scaling of pixel intensities and quantization in general reduces sensitivity to various nuisance parameters difficult to account for a priori. Our performance expressions are verified using forward-looking infrared imagery from the Army Research Laboratory Comanche dataset.

Multi-template polymerase chain reaction

Directory of Open Access Journals (Sweden)

Elena Kalle

2014-12-01

Full Text Available PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

The Saccharomyces cerevisiae RAD18 gene encodes a protein that contains potential zinc finger domains for nucleic acid binding and a putative nucleotide binding sequence

Energy Technology Data Exchange (ETDEWEB)

Jones, J.S.; Prakash, L. (Univ. of Rochester School of Medicine, NY (USA)); Weber, S. (Kodak Research Park, Rochester, NY (USA))

1988-07-25

The RAD18 gene of Saccharomyces cerevisiae is required for postreplication repair of UV damaged DNA. The authors have isolated the RAD18 gene, determined its nucleotide sequence and examined if deletion mutations of this gene show different or more pronounced phenotypic effects than the previously described point mutations. The RAD18 gene open reading frame encodes a protein of 487 amino acids, with a calculated molecular weight of 55,512. The RAD18 protein contains three potential zinc finger domains for nucleic acid binding, and a putative nucleotide binding sequence that is present in many proteins that bind and hydrolyze ATP. The DNA binding and nucleotide binding activities could enable the RAD18 protein to bind damaged sites in the template DNA with high affinity. Alternatively, or in addition, RAD18 protein may be a transcriptional regulator. The RAD18 deletion mutation resembles the previously described point mutations in its effects on viability, DNA repair, UV mutagenesis, and sporulation.

Sites of termination of in vitro DNA synthesis on psoralen phototreated single-stranded templates

International Nuclear Information System (INIS)

Piette, J.; Hearst, J.

1985-01-01

Single-stranded DNA has been photochemically induced to react with 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and used as substrate for DNA replication with E. coli DNA polymerase I large fragment. By using the dideoxy sequencing procedure, it is possible to map the termination sites on the template photoreacted with HMT. These sites occur at the nucleotides preceding each thymine residue (and a few cytosine residues), emphasizing the fact that in a single-stranded stretch of DNA, HMT reacts with each thymine residue without any specificity regarding the flanking base sequence of the thymine residues. In addition, termination of DNA synthesis due to psoralen-adducted thymine is not influenced by the efficiency of the 3'-5' exonuclease proof-reading activity of the DNA polymerase. (author)

Synthesis of Mesoporous ?-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading

OpenAIRE

Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

2016-01-01

This paper reports the synthetic route of 3-D network shape ?-Fe2O3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of ?-Fe2O3, particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constitue...

Enhancement of non-specific immune response, resistance and growth of (Litopenaeus vannamei by oral administration of nucleotide

Directory of Open Access Journals (Sweden)

Henky Manoppo

2011-01-01

Full Text Available This research evaluated the nonspecific immune responsse, resistance, and growth of Litopenaeus vannamei fed nucleotide diet. Shrimp juveniles (mean weight 5.39±0.56 g were reared in two groups of glass aquaria, each with three replications. Shrimps in group one and group two were fed nucleotide diet and basal diet each for four weeks. Total haemocyte count (THC and PO activity were evaluated at the end of feeding while growth was measured at two weeks interval. At the end of feeding trial, the shrimps were intramuscularly injected with Vibrio harveyi 0.1x106 cfu.shrimp-1. THC of shrimp fed nucleotide diet significantly increased (P-1 diet showed positive effect on the enhancement of nonspecific immune responsse, resistance, and growth of L. vannamei.  Key words: Litopenaeus vannamei, nucleotide, THC, PO activity, resistance   ABSTRAK Penelitian bertujuan untuk mengevaluasi respons imun non-spesifik dan resistensi udang vaname (Litopenaeus vannamei yang diberi pakan nukleotida.  Juvenil (5,39±0,56 g dipelihara dalam dua kelompok akuarium kaca masing-masing dengan 3 ulangan.  Udang dalam dalam kelompok pertama diberi pakan nukleotida sedangkan udang dalam kelompok kedua diberi pakan standar selama 4 minggu. Total haemocyte count (THC dan aktivitas phenoloxidase (PO diukur pada akhir pemberian pakan sedangkan pertumbuhan udang diukur setiap dua minggu. Pada akhir periode pemberian pakan perlakuan, udang diuji tantang secara injeksi intramuskular dengan bakteri Vibrio harveyi 0,1x106 cfu.udang-1. THC udang yang diberi pakan nukleotida meningkat secara signifikan (P-1 pakan selama 4 minggu memberi pengaruh positif terhadap peningkatan respons imun non-spesifik, resistensi dan pertumbuhan udang vaname. Kata kunci: Litopenaeus vannamei, nukleotida, THC, aktivitas PO, resistensi

Light Weight Biomorphous Cellular Ceramics from Cellulose Templates

Science.gov (United States)

Singh, Mrityunjay; Yee, Bo-Moon; Gray, Hugh R. (Technical Monitor)

2003-01-01

Bimorphous ceramics are a new class of materials that can be fabricated from the cellulose templates derived from natural biopolymers. These biopolymers are abundantly available in nature and are produced by the photosynthesis process. The wood cellulose derived carbon templates have three- dimensional interconnectivity. A wide variety of non-oxide and oxide based ceramics have been fabricated by template conversion using infiltration and reaction-based processes. The cellular anatomy of the cellulose templates plays a key role in determining the processing parameters (pyrolysis, infiltration conditions, etc.) and resulting ceramic materials. The processing approach, microstructure, and mechanical properties of the biomorphous cellular ceramics (silicon carbide and oxide based) have been discussed.

Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers

DEFF Research Database (Denmark)

Su, Guosheng; Christensen, Ole Fredslund; Ostersen, Tage

2012-01-01

of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects...

Non-additive measure and integral

CERN Document Server

Denneberg, Dieter

1994-01-01

Non-Additive Measure and Integral is the first systematic approach to the subject. Much of the additive theory (convergence theorems, Lebesgue spaces, representation theorems) is generalized, at least for submodular measures which are characterized by having a subadditive integral. The theory is of interest for applications to economic decision theory (decisions under risk and uncertainty), to statistics (including belief functions, fuzzy measures) to cooperative game theory, artificial intelligence, insurance, etc. Non-Additive Measure and Integral collects the results of scattered and often isolated approaches to non-additive measures and their integrals which originate in pure mathematics, potential theory, statistics, game theory, economic decision theory and other fields of application. It unifies, simplifies and generalizes known results and supplements the theory with new results, thus providing a sound basis for applications and further research in this growing field of increasing interest. It also co...

First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor

International Nuclear Information System (INIS)

Sharma, Ajeet K; Chowdhury, Debashish

2013-01-01

A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. However, whenever it commits an error by misincorporating an incorrect nucleotide, it can switch to an exonuclease mode. In the latter mode it excises the wrong nucleotide before switching back to its polymerase mode. We develop a stochastic kinetic model of DNA replication that mimics an in vitro experiment where single-stranded DNA, subjected to a mechanical tension F, is converted to double-stranded DNA by a single DNAP. The F-dependence of the average rate of replication, which depends on the rates of both polymerase and exonuclease activities of the DNAP, is in good qualitative agreement with the corresponding experimental results. We introduce nine novel distinct conditional dwell times of a DNAP. Using the method of first-passage times, we also derive the exact analytical expressions for the probability distributions of these conditional dwell times. The predicted F-dependences of these distributions are, in principle, accessible to single-molecule experiments. (paper)

Making Deformable Template Models Operational

DEFF Research Database (Denmark)

Fisker, Rune

2000-01-01

for estimation of the model parameters, which applies a combination of a maximum likelihood and minimum distance criterion. Another contribution is a very fast search based initialization algorithm using a filter interpretation of the likelihood model. These two methods can be applied to most deformable template......Deformable template models are a very popular and powerful tool within the field of image processing and computer vision. This thesis treats this type of models extensively with special focus on handling their common difficulties, i.e. model parameter selection, initialization and optimization....... A proper handling of the common difficulties is essential for making the models operational by a non-expert user, which is a requirement for intensifying and commercializing the use of deformable template models. The thesis is organized as a collection of the most important articles, which has been...

Perl Template Toolkit

CERN Document Server

Chamberlain, Darren; Cross, David; Torkington, Nathan; Diaz, tatiana Apandi

2004-01-01

Among the many different approaches to "templating" with Perl--such as Embperl, Mason, HTML::Template, and hundreds of other lesser known systems--the Template Toolkit is widely recognized as one of the most versatile. Like other templating systems, the Template Toolkit allows programmers to embed Perl code and custom macros into HTML documents in order to create customized documents on the fly. But unlike the others, the Template Toolkit is as facile at producing HTML as it is at producing XML, PDF, or any other output format. And because it has its own simple templating language, templates

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

Science.gov (United States)

Kupriushkin, M S; Pyshnyĭ, D V

2012-01-01

Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

Template Composite Dark Matter

DEFF Research Database (Denmark)

Drach, Vincent; Hietanen, Ari; Pica, Claudio

2015-01-01

We present a non perturbative study of SU(2) gauge theory with two fundamental Dirac flavours. We discuss how the model can be used as a template for composite Dark Matter (DM). We estimate one particular interaction of the DM candidate with the Standard Model : the interaction through photon...

Cyclic nucleotides and radioresistnace

International Nuclear Information System (INIS)

Kulinskij, V.I.; Mikheeva, G.A.; Zel'manovich, B.M.

1982-01-01

The addition of glucose to meat-peptone broth does not change the radiosensitizing effect (RSE) of cAMP at the logarithmic phase (LP) and the radioprotective effect (RPE) at the stationary phase (SP), but sensitization, characteristic of cGMP, disappears in SP and turns into RPE in LP. Introduction of glucose into the broth for 20 min eliminates all the effects of both cyclic nucleotides in the cya + strain while cya - mutant exhibits RSE. RSE of both cyclic nucleotides is only manifested on minimal media. These data brought confirmation of the dependence of the influence of cyclic media. These data brought confirmation of the dependence of the influence of cyclic nucleotides on radioresistance upon the metabolic status of the cell [ru

Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials.

Science.gov (United States)

Pu, Fang; Ren, Jinsong; Qu, Xiaogang

2018-02-21

The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.

Facilitating 3D Virtual World Learning Environments Creation by Non-Technical End Users through Template-Based Virtual World Instantiation

Science.gov (United States)

Liu, Chang; Zhong, Ying; Ozercan, Sertac; Zhu, Qing

2013-01-01

This paper presents a template-based solution to overcome technical barriers non-technical computer end users face when developing functional learning environments in three-dimensional virtual worlds (3DVW). "iVirtualWorld," a prototype of a platform-independent 3DVW creation tool that implements the proposed solution, facilitates 3DVW…

A template bank to search for gravitational waves from inspiralling compact binaries: II. Phenomenological model

International Nuclear Information System (INIS)

Cokelaer, T

2007-01-01

Matched filtering is used to search for gravitational waves emitted by inspiralling compact binaries in data from ground-based interferometers. One of the key aspects of the detection process is the deployment of a set of templates, also called a template bank, to cover the astrophysically interesting region of the parameter space. In a companion paper, we described the template bank algorithm used in the analysis of Laser Interferometer Gravitational-Wave Observatory (LIGO) data to search for signals from non-spinning binaries made of neutron star and/or stellar-mass black holes; this template bank is based upon physical template families. In this paper, we describe the phenomenological template bank that was used to search for gravitational waves from non-spinning black hole binaries (from stellar mass formation) in the second, third and fourth LIGO science runs. We briefly explain the design of the bank, whose templates are based on a phenomenological detection template family. We show that this template bank gives matches greater than 95% with the physical template families that are expected to be captured by the phenomenological templates

Design Automation Using Script Languages. High-Level CAD Templates in Non-Parametric Programs

Science.gov (United States)

Moreno, R.; Bazán, A. M.

2017-10-01

The main purpose of this work is to study the advantages offered by the application of traditional techniques of technical drawing in processes for automation of the design, with non-parametric CAD programs, provided with scripting languages. Given that an example drawing can be solved with traditional step-by-step detailed procedures, is possible to do the same with CAD applications and to generalize it later, incorporating references. In today’s modern CAD applications, there are striking absences of solutions for building engineering: oblique projections (military and cavalier), 3D modelling of complex stairs, roofs, furniture, and so on. The use of geometric references (using variables in script languages) and their incorporation into high-level CAD templates allows the automation of processes. Instead of repeatedly creating similar designs or modifying their data, users should be able to use these templates to generate future variations of the same design. This paper presents the automation process of several complex drawing examples based on CAD script files aided with parametric geometry calculation tools. The proposed method allows us to solve complex geometry designs not currently incorporated in the current CAD applications and to subsequently create other new derivatives without user intervention. Automation in the generation of complex designs not only saves time but also increases the quality of the presentations and reduces the possibility of human errors.

Non-volatile flash memory with discrete bionanodot floating gate assembled by protein template

International Nuclear Information System (INIS)

Miura, Atsushi; Yamashita, Ichiro; Uraoka, Yukiharu; Fuyuki, Takashi; Tsukamoto, Rikako; Yoshii, Shigeo

2008-01-01

We demonstrated non-volatile flash memory fabrication by utilizing uniformly sized cobalt oxide (Co 3 O 4 ) bionanodot (Co-BND) architecture assembled by a cage-shaped supramolecular protein template. A fabricated high-density Co-BND array was buried in a metal-oxide-semiconductor field-effect-transistor (MOSFET) structure to use as the charge storage node of a floating nanodot gate memory. We observed a clockwise hysteresis in the drain current-gate voltage characteristics of fabricated BND-embedded MOSFETs. Observed hysteresis obviously indicates a memory operation of Co-BND-embedded MOSFETs due to the charge confinement in the embedded BND and successful functioning of embedded BNDs as the charge storage nodes of the non-volatile flash memory. Fabricated Co-BND-embedded MOSFETs showed good memory properties such as wide memory windows, long charge retention and high tolerance to repeated write/erase operations. A new pathway for device fabrication by utilizing the versatile functionality of biomolecules is presented

Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools

Science.gov (United States)

Waisertreiger, Irina S.-R.; Liston, Victoria G.; Menezes, Miriam R.; Kim, Hyun-Min; Lobachev, Kirill S.; Stepchenkova, Elena I.; Tahirov, Tahir H.; Rogozin, Igor B.; Pavlov, Youri. I.

2014-01-01

The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ε, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair. PMID:23055184

A non-catalytic N-terminal domain negatively influences the nucleotide exchange activity of translation elongation factor 1Bα.

Science.gov (United States)

Trosiuk, Tetiana V; Shalak, Vyacheslav F; Szczepanowski, Roman H; Negrutskii, Boris S; El'skaya, Anna V

2016-02-01

Eukaryotic translation elongation factor 1Bα (eEF1Bα) is a functional homolog of the bacterial factor EF-Ts, and is a component of the macromolecular eEF1B complex. eEF1Bα functions as a catalyst of guanine nucleotide exchange on translation elongation factor 1A (eEF1A). The C-terminal domain of eEF1Bα is necessary and sufficient for its catalytic activity, whereas the N-terminal domain interacts with eukaryotic translation elongation factor 1Bγ (eEF1Bγ) to form a tight complex. However, eEF1Bγ has been shown to enhance the catalytic activity of eEF1Bα attributed to the C-terminal domain of eEF1Bα. This suggests that the N-terminal domain of eEF1Bα may in some way influence the guanine nucleotide exchange process. We have shown that full-length recombinant eEF1Bα and its truncated forms are non-globular proteins with elongated shapes. Truncation of the N-terminal domain of eEF1Bα, which is dispensable for catalytic activity, resulted in acceleration of the rate of guanine nucleotide exchange on eEF1A compared to full-length eEF1Bα. A similar effect on the catalytic activity of eEF1Bα was observed after its interaction with eEF1Bγ. We suggest that the non-catalytic N-terminal domain of eEF1Bα may interfere with eEF1A binding to the C-terminal catalytic domain, resulting in a decrease in the overall rate of the guanine nucleotide exchange reaction. Formation of a tight complex between the eEF1Bγ and eEF1Bα N-terminal domains abolishes this inhibitory effect. © 2015 FEBS.

Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli

Science.gov (United States)

Isogawa, Asako; Fujii, Shingo

2017-01-01

It is generally assumed that most point mutations are fixed when damage containing template DNA undergoes replication, either right at the fork or behind the fork during gap filling. Here we provide genetic evidence for a pathway, dependent on Nucleotide Excision Repair, that induces mutations when processing closely spaced lesions. This pathway, referred to as Nucleotide Excision Repair-induced Mutagenesis (NERiM), exhibits several characteristics distinct from mutations that occur within the course of replication: i) following UV irradiation, NER-induced mutations are fixed much more rapidly (t ½ ≈ 30 min) than replication dependent mutations (t ½ ≈ 80–100 min) ii) NERiM specifically requires DNA Pol IV in addition to Pol V iii) NERiM exhibits a two-hit dose-response curve that suggests processing of closely spaced lesions. A mathematical model let us define the geometry (infer the structure) of the toxic intermediate as being formed when NER incises a lesion that resides in close proximity of another lesion in the complementary strand. This critical NER intermediate requires Pol IV / Pol II for repair, it is either lethal if left unrepaired or mutation-prone when repaired. Finally, NERiM is found to operate in stationary phase cells providing an intriguing possibility for ongoing evolution in the absence of replication. PMID:28686598

Partial nucleotide sequence analysis of 18S ribosomal RNA gene of the four genotypes of Trypanosoma congolense

International Nuclear Information System (INIS)

Osanya, A.; Majiwa, P.A.O.; Kinyanjui, P.W.

2006-01-01

Specific oligonucleotide primers based on conserved nucleotide sequences of 18s ribisomal RNA (18s rRNA) gene of Trypanosoma brucei, Leishmania donovani, Triponema aequale and Lagenidium gigantum have been designed and used in the ploymerase chain reaction (PCR) to amplify genomic DNA from four different clones each representing a different genotypic group of T. congolence. PCR products of approximately 1Kb were generated using as template DNA from each of the trypanosomes. The PCR products cross-hybridized with genomic DNA from T.brucei, T. simiae and the four genotypes of T.congolense implying significant sequence homology of 18S rRNA gene among trypanosomes. The nucleotide sequence of a segment of the PCR products were determined by direct sequencing to provide partial nucleotide sequence of the 18s rRNA gene in each T.congolense genotypic group. The sequences obtained together with those that have been published for T.brucei reveals that although most regions show inter and intra species nucleotide identity, there are several sites where deletions, insertions and base changes have occured in nucleotide sequence of of T.brucei and the four genotypes of T.congolense.(author)

Statistical properties and fractals of nucleotide clusters in DNA sequences

International Nuclear Information System (INIS)

Sun Tingting; Zhang Linxi; Chen Jin; Jiang Zhouting

2004-01-01

Statistical properties of nucleotide clusters in DNA sequences and their fractals are investigated in this paper. The average size of nucleotide clusters in non-coding sequence is larger than that in coding sequence. We investigate the cluster-size distribution P(S) for human chromosomes 21 and 22, and the results are different from previous works. The cluster-size distribution P(S 1 +S 2 ) with the total size of sequential Pu-cluster and Py-cluster S 1 +S 2 is studied. We observe that P(S 1 +S 2 ) follows an exponential decay both in coding and non-coding sequences. However, we get different results for human chromosomes 21 and 22. The probability distribution P(S 1 ,S 2 ) of nucleotide clusters with the size of sequential Pu-cluster and Py-cluster S 1 and S 2 respectively, is also examined. In the meantime, some of the linear correlations are obtained in the double logarithmic plots of the fluctuation F(l) versus nucleotide cluster distance l along the DNA chain. The power spectrums of nucleotide clusters are also discussed, and it is concluded that the curves are flat and hardly changed and the 1/3 frequency is neither observed in coding sequence nor in non-coding sequence. These investigations can provide some insights into the nucleotide clusters of DNA sequences

MRI non-uniformity correction through interleaved bias estimation and B-spline deformation with a template.

Science.gov (United States)

Fletcher, E; Carmichael, O; Decarli, C

2012-01-01

We propose a template-based method for correcting field inhomogeneity biases in magnetic resonance images (MRI) of the human brain. At each algorithm iteration, the update of a B-spline deformation between an unbiased template image and the subject image is interleaved with estimation of a bias field based on the current template-to-image alignment. The bias field is modeled using a spatially smooth thin-plate spline interpolation based on ratios of local image patch intensity means between the deformed template and subject images. This is used to iteratively correct subject image intensities which are then used to improve the template-to-image deformation. Experiments on synthetic and real data sets of images with and without Alzheimer's disease suggest that the approach may have advantages over the popular N3 technique for modeling bias fields and narrowing intensity ranges of gray matter, white matter, and cerebrospinal fluid. This bias field correction method has the potential to be more accurate than correction schemes based solely on intrinsic image properties or hypothetical image intensity distributions.

MRI Non-Uniformity Correction Through Interleaved Bias Estimation and B-Spline Deformation with a Template*

Science.gov (United States)

Fletcher, E.; Carmichael, O.; DeCarli, C.

2013-01-01

We propose a template-based method for correcting field inhomogeneity biases in magnetic resonance images (MRI) of the human brain. At each algorithm iteration, the update of a B-spline deformation between an unbiased template image and the subject image is interleaved with estimation of a bias field based on the current template-to-image alignment. The bias field is modeled using a spatially smooth thin-plate spline interpolation based on ratios of local image patch intensity means between the deformed template and subject images. This is used to iteratively correct subject image intensities which are then used to improve the template-to-image deformation. Experiments on synthetic and real data sets of images with and without Alzheimer’s disease suggest that the approach may have advantages over the popular N3 technique for modeling bias fields and narrowing intensity ranges of gray matter, white matter, and cerebrospinal fluid. This bias field correction method has the potential to be more accurate than correction schemes based solely on intrinsic image properties or hypothetical image intensity distributions. PMID:23365843

Code Generation with Templates

CERN Document Server

Arnoldus, Jeroen; Serebrenik, A

2012-01-01

Templates are used to generate all kinds of text, including computer code. The last decade, the use of templates gained a lot of popularity due to the increase of dynamic web applications. Templates are a tool for programmers, and implementations of template engines are most times based on practical experience rather than based on a theoretical background. This book reveals the mathematical background of templates and shows interesting findings for improving the practical use of templates. First, a framework to determine the necessary computational power for the template metalanguage is presen

Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

Science.gov (United States)

Kleinbaum, Daniel J; Miller, Gregory P; Kool, Eric T

2010-06-16

Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore. Three potential double displacement architectures, all possessing two fluorescence quencher/leaving groups (dabsylate groups), were synthesized and evaluated for templated reaction with nucleophile (phosphorothioate) probes both in vitro and in intact bacterial cells. All three DD probe designs provided substantially better initial quenching than a single-Dabsyl control. In isothermal templated reactions in vitro, double displacement probes yielded considerably lower background signal than previous single displacement probes; investigation into the mechanism revealed that one dabsylate acts as a sacrificial leaving group, reacting nonspecifically with water, but yielding little signal because another quencher group remains. Templated reaction with the specific nucleophile probe is required to activate a signal. The double displacement probes provided a ca. 80-fold turn-on signal and yielded a 2-4-fold improvement in signal/background over single Dabsyl probes. The best-performing probe architecture was demonstrated in a two-color, FRET-based two-allele discrimination system in vitro and was shown to be capable of discriminating between two closely related species of bacteria differing by a single nucleotide at an rRNA target site.

White emission from non-planar InGaN/GaN MQW LEDs grown on GaN template with truncated hexagonal pyramids.

Science.gov (United States)

Lee, Ming-Lun; Yeh, Yu-Hsiang; Tu, Shang-Ju; Chen, P C; Lai, Wei-Chih; Sheu, Jinn-Kong

2015-04-06

Non-planar InGaN/GaN multiple quantum well (MQW) structures are grown on a GaN template with truncated hexagonal pyramids (THPs) featuring c-plane and r-plane surfaces. The THP array is formed by the regrowth of the GaN layer on a selective-area Si-implanted GaN template. Transmission electron microscopy shows that the InGaN/GaN epitaxial layers regrown on the THPs exhibit different growth rates and indium compositions of the InGaN layer between the c-plane and r-plane surfaces. Consequently, InGaN/GaN MQW light-emitting diodes grown on the GaN THP array emit multiple wavelengths approaching near white light.

Generating XML schemas for DICOM structured reporting templates.

Science.gov (United States)

Zhao, Luyin; Lee, Kwok Pun; Hu, Jingkun

2005-01-01

In this paper, the authors describe a methodology to transform programmatically structured reporting (SR) templates defined by the Digital Imaging and Communications for Medicine (DICOM) standard into an XML schema representation. Such schemas can be used in the creation and validation of XML-encoded SR documents that use templates. Templates are a means to put additional constraints on an SR document to promote common formats for specific reporting applications or domains. As the use of templates becomes more widespread in the production of SR documents, it is important to ensure validity of such documents. The work described in this paper is an extension of the authors' previous work on XML schema representation for DICOM SR. Therefore, this paper inherits and partially modifies the structure defined in the earlier work.

Non-additive measures theory and applications

CERN Document Server

Narukawa, Yasuo; Sugeno, Michio; 9th International Conference on Modeling Decisions for Artificial Intelligence (MDAI 2012)

2014-01-01

This book provides a comprehensive and timely report in the area of non-additive measures and integrals. It is based on a panel session on fuzzy measures, fuzzy integrals and aggregation operators held during the 9th International Conference on Modeling Decisions for Artificial Intelligence (MDAI 2012) in Girona, Spain, November 21-23, 2012. The book complements the MDAI 2012 proceedings book, published in Lecture Notes in Computer Science (LNCS) in 2012. The individual chapters, written by key researchers in the field, cover fundamental concepts and important definitions (e.g. the Sugeno integral, definition of entropy for non-additive measures) as well some important applications (e.g. to economics and game theory) of non-additive measures and integrals. The book addresses students, researchers and practitioners working at the forefront of their field.  

Modes of DNA repair and replication

International Nuclear Information System (INIS)

Hanawalt, P.; Kondo, S.

1979-01-01

Modes of DNA repair and replication require close coordination as well as some overlap of enzyme functions. Some classes of recovery deficient mutants may have defects in replication rather than repair modes. Lesions such as the pyrimidine dimers produced by ultraviolet light irradiation are the blocks to normal DNA replication in vivo and in vitro. The DNA synthesis by the DNA polymerase 1 of E. coli is blocked at one nucleotide away from the dimerized pyrimidines in template strands. Thus, some DNA polymerases seem to be unable to incorporate nucleotides opposite to the non-pairing lesions in template DNA strands. The lesions in template DNA strands may block the sequential addition of nucleotides in the synthesis of daughter strands. Normal replication utilizes a constitutive ''error-free'' mode that copies DNA templates with high fidelity, but which may be totally blocked at a lesion that obscures the appropriate base pairing specificity. It might be expected that modified replication system exhibits generally high error frequency. The error rate of DNA polymerases may be controlled by the degree of phosphorylation of the enzyme. Inducible SOS system is controlled by recA genes that also control the pathways for recombination. It is possible that SOS system involves some process other than the modification of a blocked replication apparatus to permit error-prone transdimer synthesis. (Yamashita, S.)

Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay.

Science.gov (United States)

Rotherham, D; Harbison, S A

2011-04-15

Cannabis sativa is both an illegal drug and a legitimate crop. The differentiation of illegal drug Cannabis from non-drug forms of Cannabis is relevant in the context of the growth of fibre and seed oil varieties of Cannabis for commercial purposes. This differentiation is currently determined based on the levels of tetrahydrocannabinol (THC) in adult plants. DNA based methods have the potential to assay Cannabis material unsuitable for analysis using conventional means including seeds, pollen and severely degraded material. The purpose of this research was to develop a single nucleotide polymorphism (SNP) assay for the differentiation of "drug" and "non-drug"Cannabis plants. An assay was developed based on four polymorphisms within a 399 bp fragment of the tetrahydrocannabinolic acid (THCA) synthase gene, utilising the snapshot multiplex kit. This SNP assay was tested on 94 Cannabis plants, which included 10 blind samples, and was able to differentiate between "drug" and "non-drug"Cannabis in all cases, while also differentiating between Cannabis and other species. Non-drug plants were found to be homozygous at the four sites assayed while drug Cannabis plants were either homozygous or heterozygous. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Gamma Radiation-Induced Template Polymerization Technique

International Nuclear Information System (INIS)

Siyam, T.

2005-01-01

Gamma radiation induced copolymerization of acrylamide sodiumacrylate (AM-AANa) in the presence and absence of the polymer additive was studied at low monomer concentration(1.4M/l). The results showed that the exponents of the dose rate for the polymerization rate was found to be 1.3 and 1.4 in the absence and in the presence of the polymer additive respectively. The molecular weight of the formed polymer increased by addition of the polymer to the system. In the presence of the polymer the comonomers polymerize on the added polymer. In the absence of the added polymer the comonomers polymerize according to the copolymerization process at the initial stage of the copolymerization. While at high conversion the residual comonomers polymerize on the formed macromolecular chains of the produced polymer. These studies showed that the copolymerization in the presence of added polymer is completely template copolymerization while in the absence of the polymer the copolymerization process is only template process with a high conversion

Multi-template tensor-based morphometry: application to analysis of Alzheimer's disease.

Science.gov (United States)

Koikkalainen, Juha; Lötjönen, Jyrki; Thurfjell, Lennart; Rueckert, Daniel; Waldemar, Gunhild; Soininen, Hilkka

2011-06-01

In this paper methods for using multiple templates in tensor-based morphometry (TBM) are presented and compared to the conventional single-template approach. TBM analysis requires non-rigid registrations which are often subject to registration errors. When using multiple templates and, therefore, multiple registrations, it can be assumed that the registration errors are averaged and eventually compensated. Four different methods are proposed for multi-template TBM. The methods were evaluated using magnetic resonance (MR) images of healthy controls, patients with stable or progressive mild cognitive impairment (MCI), and patients with Alzheimer's disease (AD) from the ADNI database (N=772). The performance of TBM features in classifying images was evaluated both quantitatively and qualitatively. Classification results show that the multi-template methods are statistically significantly better than the single-template method. The overall classification accuracy was 86.0% for the classification of control and AD subjects, and 72.1% for the classification of stable and progressive MCI subjects. The statistical group-level difference maps produced using multi-template TBM were smoother, formed larger continuous regions, and had larger t-values than the maps obtained with single-template TBM. Copyright © 2011 Elsevier Inc. All rights reserved.

Degradation of brown adipocyte purine nucleotides regulates uncoupling protein 1 activity

Directory of Open Access Journals (Sweden)

Tobias Fromme

2018-02-01

Full Text Available Objective: Non-shivering thermogenesis in mammalian brown adipose tissue depends on thermogenic uncoupling protein 1. Its activity is triggered by free fatty acids while purine nucleotides mediate inhibition. During activation, it is thought that free fatty acids overcome purine-mediated inhibition. We measured the cellular concentration and the release of purine nucleotide metabolites to uncover a possible role of purine nucleotide degradation in uncoupling protein 1 activation. Methods: With mass spectrometry, purine nucleotide metabolites were quantified in cellular homogenates and supernatants of cultured primary brown adipocytes. We also determined oxygen consumption in response to a β-adrenergic agonist. Results: Upon adrenergic activation, brown adipocytes decreased the intracellular concentration of inhibitory nucleotides (ATP, ADP, GTP and GDP and released the respective degradation products. At the same time, an increase in cellular calcium occurred. None of these phenomena occurred in white adipocytes or myotubes. The brown adipocyte expression of enzymes implicated in purine metabolic remodeling is altered upon cold exposure. Pharmacological and genetic interference of purine metabolism altered uncoupling protein 1 mediated uncoupled respiration. Conclusion: Adrenergic stimulation of brown adipocytes lowers the intracellular concentration of purine nucleotides, thereby contributing to uncoupling protein 1 activation. Keywords: Purine nucleotides, Uncoupling protein 1, Brown adipose tissue, Non-shivering thermogenesis, HILIC-MS/MS, Guanosine monophosphate reductase

Stochastic Template Bank for Gravitational Wave Searches for Precessing Neutron Star-Black Hole Coalescence Events

Science.gov (United States)

Indik, Nathaniel; Haris, K.; Dal Canton, Tito; Fehrmann, Henning; Krishnan, Badri; Lundgren, Andrew; Nielsen, Alex B.; Pai, Archana

2017-01-01

Gravitational wave searches to date have largely focused on non-precessing systems. Including precession effects greatly increases the number of templates to be searched over. This leads to a corresponding increase in the computational cost and can increase the false alarm rate of a realistic search. On the other hand, there might be astrophysical systems that are entirely missed by non-precessing searches. In this paper we consider the problem of constructing a template bank using stochastic methods for neutron star-black hole binaries allowing for precession, but with the restrictions that the total angular momentum of the binary is pointing toward the detector and that the neutron star spin is negligible relative to that of the black hole. We quantify the number of templates required for the search, and we explicitly construct the template bank. We show that despite the large number of templates, stochastic methods can be adapted to solve the problem. We quantify the parameter space region over which the non-precessing search might miss signals.

Computer-aided modelling template: Concept and application

DEFF Research Database (Denmark)

Fedorova, Marina; Sin, Gürkan; Gani, Rafiqul

2015-01-01

decomposition technique which identifies generic steps and workflow involved, the computer-aided template concept has been developed. This concept is implemented as a software tool, which provides a user-friendly interface for following the workflow steps and guidance through the steps providing additional......Modelling is an important enabling technology in modern chemical engineering applications. A template-based approach is presented in this work to facilitate the construction and documentation of the models and enable their maintenance for reuse in a wider application range. Based on a model...

Report Template

DEFF Research Database (Denmark)

Bjørn, Anders; Laurent, Alexis; Owsianiak, Mikołaj

2018-01-01

To ensure consistent reporting of life cycle assessment (LCA), we provide a report template. The report includes elements of an LCA study as recommended but the ILCD Handbook. Illustrative case study reported according to this template is presented in Chap. 39 ....

LDH nanocages synthesized with MOF templates and their high performance as supercapacitors

Science.gov (United States)

Jiang, Zhen; Li, Zhengping; Qin, Zhenhua; Sun, Haiyan; Jiao, Xiuling; Chen, Dairong

2013-11-01

Layered double hydroxides (LDHs) are currently attracting intense research interest for their various applications. Three LDH hollow nano-polyhedra are synthesized with zeolitic imidazolate framework-67 (ZIF-67) nanocrystals as the templates. The nanocages well inherit the rhombic dodecahedral shape of the ZIF-67 templates, and the shell is composed of nanosheets assembled with an edge-to-face stacking. This is the first synthesis of the LDH non-spherical structures. And the mechanism of utilizing metal-organic framework (MOF) nanocrystals as templates is explored. Control of the simultaneous reactions, the precipitation of the shells and the template etching, is extremely crucial to the preparation of the perfect nanocages. And the Ni-Co LDH nanocages exhibit superior pseudocapacitance property due to their novel hierarchical and submicroscopic structures.Layered double hydroxides (LDHs) are currently attracting intense research interest for their various applications. Three LDH hollow nano-polyhedra are synthesized with zeolitic imidazolate framework-67 (ZIF-67) nanocrystals as the templates. The nanocages well inherit the rhombic dodecahedral shape of the ZIF-67 templates, and the shell is composed of nanosheets assembled with an edge-to-face stacking. This is the first synthesis of the LDH non-spherical structures. And the mechanism of utilizing metal-organic framework (MOF) nanocrystals as templates is explored. Control of the simultaneous reactions, the precipitation of the shells and the template etching, is extremely crucial to the preparation of the perfect nanocages. And the Ni-Co LDH nanocages exhibit superior pseudocapacitance property due to their novel hierarchical and submicroscopic structures. Electronic supplementary information (ESI) available: Experimental details, XRD, TEM, SEM, and XPS images. See DOI: 10.1039/c3nr03829g

Searching for gravitational-wave signals emitted by eccentric compact binaries using a non-eccentric template bank: implications for ground-based detectors

Energy Technology Data Exchange (ETDEWEB)

Cokelaer, T; Pathak, D, E-mail: Thomas.Cokelaer@astro.cf.ac.u, E-mail: Devanka.Pathak@astro.cf.ac.u [School of Physics and Astronomy, Cardiff University, Cardiff CF24 3AA (United Kingdom)

2009-02-21

Most of the inspiralling compact binaries are expected to be circularized by the time their gravitational-wave signals enter the frequency band of ground-based detectors such as LIGO or VIRGO. However, it is not excluded that some of these binaries might still possess a significant eccentricity at a few tens of hertz. Despite this possibility, current search pipelines-based on matched filtering techniques-consider only non-eccentric templates. The effect of such an approximation on the loss of signal-to-noise ratio (SNR) has been investigated by Martel and Poisson (1999 Phys. Rev. D 60 124008) in the context of initial LIGO detector. They ascertained that non-eccentric templates will be successful at detecting eccentric signals. We revisit their work by incorporating current and future ground-based detectors and precisely quantify the exact loss of SNR. In order to be more faithful to an actual search, we maximized the SNR over a template bank, whose minimal match is set to 95%. For initial LIGO detector, we claim that the initial eccentricity does not need to be taken into account in our searches for any system with total mass M element of [2-45]M{sub o-dot} if e{sub 0} approx< 0.05 because the loss of SNR (about 5%) is consistent with the discreteness of the template bank. Similarly, this statement is also true for systems with M element of [6-35]M{sub o-dot} and e{sub 0} approx< 0.10. However, by neglecting the eccentricity in our searches, significant loss of detection (larger than 10%) may arise as soon as e{sub 0} >= 0.05 for neutron-star binaries. We also provide exhaustive results for VIRGO, Advanced LIGO and Einstein Telescope detectors. It is worth noting that for Einstein Telescope, neutron star binaries with e{sub 0} >= 0.02 lead to a 10% loss of detection.

Palindromic nucleotide analysis in human T cell receptor rearrangements.

Directory of Open Access Journals (Sweden)

Santosh K Srivastava

Full Text Available Diversity of T cell receptor (TCR genes is primarily generated by nucleotide insertions upon rearrangement from their germ line-encoded V, D and J segments. Nucleotide insertions at V-D and D-J junctions are random, but some small subsets of these insertions are exceptional, in that one to three base pairs inversely repeat the sequence of the germline DNA. These short complementary palindromic sequences are called P nucleotides. We apply the ImmunoSeq deep-sequencing assay to the third complementarity determining region (CDR3 of the β chain of T cell receptors, and use the resulting data to study P nucleotides in the repertoire of naïve and memory CD8(+ and CD4(+ T cells. We estimate P nucleotide distributions in a cross section of healthy adults and different T cell subtypes. We show that P nucleotide frequency in all T cell subtypes ranges from 1% to 2%, and that the distribution is highly biased with respect to the coding end of the gene segment. Classification of observed palindromic sequences into P nucleotides using a maximum conditional probability model shows that single base P nucleotides are very rare in VDJ recombination; P nucleotides are primarily two bases long. To explore the role of P nucleotides in thymic selection, we compare P nucleotides in productive and non-productive sequences of CD8(+ naïve T cells. The naïve CD8(+ T cell clones with P nucleotides are more highly expanded.

Welding template

International Nuclear Information System (INIS)

Ben Venue, R.J. of.

1976-01-01

A welding template is described which is used to weld strip material into a cellular grid structure for the accommodation of fuel elements in a nuclear reactor. On a base plate the template carries a multitude of cylindrical pins whose upper half is narrower than the bottom half and only one of which is attached to the base plate. The others are arrested in a hexagonal array by oblong webs clamped together by chuck jaws which can be secured by means of screws. The parts are ground very accurately. The template according to the invention is very easy to make. (UWI) [de

Sacrificial template method of fabricating a nanotube

Science.gov (United States)

Yang, Peidong [Berkeley, CA; He, Rongrui [Berkeley, CA; Goldberger, Joshua [Berkeley, CA; Fan, Rong [El Cerrito, CA; Wu, Yi-Ying [Albany, CA; Li, Deyu [Albany, CA; Majumdar, Arun [Orinda, CA

2007-05-01

Methods of fabricating uniform nanotubes are described in which nanotubes were synthesized as sheaths over nanowire templates, such as using a chemical vapor deposition process. For example, single-crystalline zinc oxide (ZnO) nanowires are utilized as templates over which gallium nitride (GaN) is epitaxially grown. The ZnO templates are then removed, such as by thermal reduction and evaporation. The completed single-crystalline GaN nanotubes preferably have inner diameters ranging from 30 nm to 200 nm, and wall thicknesses between 5 and 50 nm. Transmission electron microscopy studies show that the resultant nanotubes are single-crystalline with a wurtzite structure, and are oriented along the direction. The present invention exemplifies single-crystalline nanotubes of materials with a non-layered crystal structure. Similar "epitaxial-casting" approaches could be used to produce arrays and single-crystalline nanotubes of other solid materials and semiconductors. Furthermore, the fabrication of multi-sheath nanotubes are described as well as nanotubes having multiple longitudinal segments.

Programmable imprint lithography template

Science.gov (United States)

Cardinale, Gregory F [Oakland, CA; Talin, Albert A [Livermore, CA

2006-10-31

A template for imprint lithography (IL) that reduces significantly template production costs by allowing the same template to be re-used for several technology generations. The template is composed of an array of spaced-apart moveable and individually addressable rods or plungers. Thus, the template can be configured to provide a desired pattern by programming the array of plungers such that certain of the plungers are in an "up" or actuated configuration. This arrangement of "up" and "down" plungers forms a pattern composed of protruding and recessed features which can then be impressed onto a polymer film coated substrate by applying a pressure to the template impressing the programmed configuration into the polymer film. The pattern impressed into the polymer film will be reproduced on the substrate by subsequent processing.

The role of achiral pyrazolidinone templates in enantioselective Diels-Alder reactions: scope, limitations, and conformational insights.

Science.gov (United States)

Sibi, Mukund P; Stanley, Levi M; Nie, Xiaoping; Venkatraman, Lakshmanan; Liu, Mei; Jasperse, Craig P

2007-01-17

We have evaluated the role of achiral pyrazolidinone templates in conjunction with chiral Lewis acids in room temperature, enantioselective Diels-Alder cycloadditions. The role of the fluxional N(1) substituent was examined, with the bulky 1-naphthylmethyl group providing enantioselectivities up to 99% ee, while templates with smaller fluxional groups gave lower selectivities. High selectivities were also observed in reactions of 7d with chiral Lewis acids derived from relatively small chiral ligands, suggesting the pyrazolidinone templates are capable of relaying stereochemical information from the ligand to the reaction center. Lewis acids capable of adapting square planar geometries, such as Cu(OTf)2, Cu(ClO4)2, and Pd(ClO4)2, were found to be particularly effective at providing high selectivities. Additionally, substitution at the C-5 position of the pyrazolidinone templates has been shown to be critical for optimal selectivity. Reactions of the optimal pyrazolidinone appended with a number of common dienophiles and various dienes demonstrate the utility of this achiral template. Furthermore, catalytic loadings could be lowered to 2.5 mol % with essentially no loss in selectivity. Pi-Pi interactions were evaluated as a means to explain the unusually high selectivity observed at room temperature. Finally, non-C2-symmetric ligands were employed as a test to determine if chiral relay was operative.

Colloidal micro- and nano-particles as templates for polyelectrolyte multilayer capsules.

Science.gov (United States)

Parakhonskiy, Bogdan V; Yashchenok, Alexey M; Konrad, Manfred; Skirtach, Andre G

2014-05-01

Colloidal particles play an important role in various areas of material and pharmaceutical sciences, biotechnology, and biomedicine. In this overview we describe micro- and nano-particles used for the preparation of polyelectrolyte multilayer capsules and as drug delivery vehicles. An essential feature of polyelectrolyte multilayer capsule preparations is the ability to adsorb polymeric layers onto colloidal particles or templates followed by dissolution of these templates. The choice of the template is determined by various physico-chemical conditions: solvent needed for dissolution, porosity, aggregation tendency, as well as release of materials from capsules. Historically, the first templates were based on melamine formaldehyde, later evolving towards more elaborate materials such as silica and calcium carbonate. Their advantages and disadvantages are discussed here in comparison to non-particulate templates such as red blood cells. Further steps in this area include development of anisotropic particles, which themselves can serve as delivery carriers. We provide insights into application of particles as drug delivery carriers in comparison to microcapsules templated on them. Copyright © 2014 Elsevier B.V. All rights reserved.

Contribution of mesopores in MgO-templated mesoporous carbons to capacitance in non-aqueous electrolytes

Science.gov (United States)

Kado, Yuya; Soneda, Yasushi; Yoshizawa, Noriko

2015-02-01

MgO-templated mesoporous carbons were fabricated by annealing trimagnesium dicitrate nonahydrate at various temperatures from 700 to 1000 °C with subsequent acid leaching of MgO. The obtained carbons contained a large amount of mesopores. Performances of electric double-layer capacitors using these carbons were examined for propylene carbonate electrolyte containing 1 M tetraethylammonium tetrafluoroborate. The mesoporous carbons synthesized at higher temperatures showed better rate capabilities. AC impedance measurements indicated that high-temperature annealing of the carbon precursors and the presence of mesopores were important for high rate performance. In addition, the contribution of mesopores to capacitance was more significant at higher current densities of 30 A g-1.

Effects of dietary nucleotides on growth, non-specific immune response and disease resistance of sea cucumber Apostichopus japonicas.

Science.gov (United States)

Wei, Zehong; Yi, Lina; Xu, Wei; Zhou, Huihui; Zhang, Yanjiao; Zhang, Wenbing; Mai, Kangsen

2015-11-01

A 9-week feeding trial was conducted to investigate the effects of dietary nucleotides (NT) on growth, immune response and disease resistance of sea cucumber Apostichopus japonicas (initial weight: 5.87 ± 0.03 g). Four graded levels of dietary NT were designed as 0, 150, 375 and 700 mg/kg, respectively. After the feeding trial, sea cucumbers were challenged with Vibrio splendidus for the determination of disease resistance. The results showed that the specific growth rates were significantly higher in sea cucumber fed the diet with 375 mg/kg NT than those fed the basal diet without NT supplementation (P sea cucumber fed diets with nucleotides (≥ 375 mg/kg) had significantly higher phagocytic activities in coelomic fluid (P 0.05). After being challenged with V. splendidus, the cumulative mortalities of sea cucumber fed diets with 150 and 375 mg/kg NT were significantly lower than that in the treatment without dietary nucleotide supplementation (P sea cucumber in vivo. In conclusion, it was showed that dietary NT does increase the growth performance, non-specific immunity and disease resistance of sea cucumber. The optimum dietary NT supplementation level for sea cucumber was found to be 375 mg/kg. The application of dietary NT may present a novel strategy for health management in sea cucumber's aquaculture. Copyright © 2015 Elsevier Ltd. All rights reserved.

Non-autoclaved aerated concrete with mineral additives

Science.gov (United States)

Il'ina, L. V.; Rakov, M. A.

2016-01-01

We investigated the effect of joint grinding of Portland cement clinker, silica and carbonate components and mineral additives to specific surface of 280 - 300 m2/kg on the properties (strength, average density and thermal conductivity) of non-autoclaved aerated concrete, and the porosity of the hardened cement paste produced from Portland cement clinker with mineral additives. The joint grinding of the Portland cement clinker with silica and carbonate components and mineral additives reduces the energy consumption of non-autoclaved aerated concrete production. The efficiency of mineral additives (diopside, wollastonite) is due to the closeness the composition, the type of chemical bonds, physical and chemical characteristics (specific enthalpy of formation, specific entropy) to anhydrous clinker minerals and their hydration products. Considering the influence of these additions on hydration of clinker minerals and formation of hardened cement paste structure, dispersed wollastonite and diopside should be used as mineral additives. The hardness and, consequently, the elastic modulus of diopside are higher than that of hardened cement paste. As a result, there is a redistribution of stresses in the hardened cement paste interporous partitions and hardening, both the partitions and aerated concrete on the whole. The mineral additives introduction allowed to obtain the non-autoclaved aerated concrete with average density 580 kg/m3, compressive strength of 3.3 MPa and thermal conductivity of 0.131 W/(m.°C).

Efficiency of template banks for binary black-hole detection

International Nuclear Information System (INIS)

Cokelaer, Thomas; Babak, Stas; Sathyaprakash, B S

2004-01-01

In the framework of matched filtering theory, which is the most promising method for the detection of gravitational waves emitted by coalescing binaries, we report on the ability of a template bank to catch a simulated binary black-hole gravitational wave signal. If we suppose that the incoming signal waveform is known a priori, then both the (simulated) signal and the templates can be based on the same physical model and therefore the template bank can be optimal in the sense of Wiener filtering. This turns out to be true for the case of neutron star binaries but not necessarily for the black-hole case. When the templates and the signal are based on different physical models the detection bank may still remain efficient. Nonetheless, it might be a judicious choice to use a phenomenological template family such as the so-called BCV templates to catch all the different physical models. In the first part of that report, we illustrate in a non-exhaustive study, by using Monte Carlo simulations, the efficiency of a template bank based on the stationary phase approximation and show how it catches simulated signals based on the same physical model but fails to catch signals built using other models (Pade, EOB, ...) especially in the case of high mass binaries. In the second part, we construct a BCV-template bank and test its validity by injecting simulated signals based on different physical models such as the PN-approximants, Pade-approximant and the effective one-body method. We show that it is suitable for a search pipeline since it gives a match higher than 95% for all the different physical models. The range of individual mass which has been used is [3-20]M o-dot

A nucleotide-analogue-induced gain of function corrects the error-prone nature of human DNA polymerase iota.

Science.gov (United States)

Ketkar, Amit; Zafar, Maroof K; Banerjee, Surajit; Marquez, Victor E; Egli, Martin; Eoff, Robert L

2012-06-27

Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota

Science.gov (United States)

Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L

2012-01-01

Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2′-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2′-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (χ), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase. PMID:22632140

Electrochemical impedance spectroscopy of nanoporous anodic alumina template

International Nuclear Information System (INIS)

Shahzad, K.

2010-01-01

Room temperature EIS characterization of nanoporous anodic alumina prepared at 40 V and 60 V has been done in 0.3 M oxalic acid solution. Rapid decrease in impedance was observed for the template prepared at 40 V. EIS study of porous anodic alumina template prepared in 0.3 M oxalic acid has been done in different electrolytes. Templates prepared in 0.3 M sulfuric acid solution were also characterized for comparison. Rapid decrease in the thickness of nonporous anodic film was observed with an increase of aggressiveness of electrolyte. Temperature based systematic study of EIS measurement has been done for porous anodic alumina template at different temperatures. Formation of micropores was observed in the nanoporous anodic alumina film formed on aluminum in 0.3 M oxalic acid solution which accelerates the dissolution rate with increase of measurement temperature. In addition to these, electropolishing behavior of pure aluminum has also been studied in different electrolytes and it was observed that electropolishing conditions prior to anodization are extremely important. (author)

Computing layouts with deformable templates

KAUST Repository

Peng, Chi-Han

2014-07-22

In this paper, we tackle the problem of tiling a domain with a set of deformable templates. A valid solution to this problem completely covers the domain with templates such that the templates do not overlap. We generalize existing specialized solutions and formulate a general layout problem by modeling important constraints and admissible template deformations. Our main idea is to break the layout algorithm into two steps: a discrete step to lay out the approximate template positions and a continuous step to refine the template shapes. Our approach is suitable for a large class of applications, including floorplans, urban layouts, and arts and design. Copyright © ACM.

Computing layouts with deformable templates

KAUST Repository

Peng, Chi-Han; Yang, Yongliang; Wonka, Peter

2014-01-01

In this paper, we tackle the problem of tiling a domain with a set of deformable templates. A valid solution to this problem completely covers the domain with templates such that the templates do not overlap. We generalize existing specialized solutions and formulate a general layout problem by modeling important constraints and admissible template deformations. Our main idea is to break the layout algorithm into two steps: a discrete step to lay out the approximate template positions and a continuous step to refine the template shapes. Our approach is suitable for a large class of applications, including floorplans, urban layouts, and arts and design. Copyright © ACM.

The immediate nucleotide precursor, guanosine triphosphate, in the riboflavin biosynthetic pathway

International Nuclear Information System (INIS)

Mitsuda, Hisateru; Nakajima, Kenji; Nadamoto, Tomonori

1977-01-01

In the present paper, the nucleotide precursor of riboflavin was investigated by experiments with labeled purines using non-growing cells of Eremothecium ashbyii. The added purines, at 10 -4 M, were effectively incorporated into riboflavin at an early stage of riboflavin biosynthesis under the experimental conditions. In particular, both labeled xanthine and labeled guanine were specifically transported to guanosine nucleotides, GMP, GDP, GDP-Mannose and GTP, in the course of the riboflavin biosynthesis. A comparison of specific activities of labeled guanosine nucleotides and labeled riboflavin indicated that the nucleotide precursor of riboflavin is guanosine triphosphate. From the results obtained, a biosynthetic pathway of riboflavin is proposed. (auth.)

A Deformable Template Model, with Special Reference to Elliptical Templates

DEFF Research Database (Denmark)

Hobolth, Asger; Pedersen, Jan; Jensen, Eva Bjørn Vedel

2002-01-01

This paper suggests a high-level continuous image model for planar star-shaped objects. Under this model, a planar object is a stochastic deformation of a star-shaped template. The residual process, describing the difference between the radius-vector function of the template and the object...

Automated PET-only quantification of amyloid deposition with adaptive template and empirically pre-defined ROI

Science.gov (United States)

Akamatsu, G.; Ikari, Y.; Ohnishi, A.; Nishida, H.; Aita, K.; Sasaki, M.; Yamamoto, Y.; Sasaki, M.; Senda, M.

2016-08-01

Amyloid PET is useful for early and/or differential diagnosis of Alzheimer’s disease (AD). Quantification of amyloid deposition using PET has been employed to improve diagnosis and to monitor AD therapy, particularly in research. Although MRI is often used for segmentation of gray matter and for spatial normalization into standard Montreal Neurological Institute (MNI) space where region-of-interest (ROI) template is defined, 3D MRI is not always available in clinical practice. The purpose of this study was to examine the feasibility of PET-only amyloid quantification with an adaptive template and a pre-defined standard ROI template that has been empirically generated from typical cases. A total of 68 subjects who underwent brain 11C-PiB PET were examined. The 11C-PiB images were non-linearly spatially normalized to the standard MNI T1 atlas using the same transformation parameters of MRI-based normalization. The automatic-anatomical-labeling-ROI (AAL-ROI) template was applied to the PET images. All voxel values were normalized by the mean value of cerebellar cortex to generate the SUVR-scaled images. Eleven typical positive images and eight typical negative images were normalized and averaged, respectively, and were used as the positive and negative template. Positive and negative masks which consist of voxels with SUVR  ⩾1.7 were extracted from both templates. Empirical PiB-prone ROI (EPP-ROI) was generated by subtracting the negative mask from the positive mask. The 11C-PiB image of each subject was non-rigidly normalized to the positive and negative template, respectively, and the one with higher cross-correlation was adopted. The EPP-ROI was then inversely transformed to individual PET images. We evaluated differences of SUVR between standard MRI-based method and PET-only method. We additionally evaluated whether the PET-only method would correctly categorize 11C-PiB scans as positive or negative. Significant correlation was observed between the SUVRs

Co-occurring nonnative woody shrubs have additive and non-additive soil legacies.

Science.gov (United States)

Kuebbing, Sara E; Patterson, Courtney M; Classen, Aimée T; Simberloff, Daniel

2016-09-01

To maximize limited conservation funds and prioritize management projects that are likely to succeed, accurate assessment of invasive nonnative species impacts is essential. A common challenge to prioritization is a limited knowledge of the difference between the impacts of a single nonnative species compared to the impacts of nonnative species when they co-occur, and in particular predicting when impacts of co-occurring nonnative species will be non-additive. Understanding non-additivity is important for management decisions because the management of only one co-occurring invader will not necessarily lead to a predictable reduction in the impact or growth of the other nonnative plant. Nonnative plants are frequently associated with changes in soil biotic and abiotic characteristics, which lead to plant-soil interactions that influence the performance of other species grown in those soils. Whether co-occurring nonnative plants alter soil properties additively or non-additively relative to their effects on soils when they grow in monoculture is rarely addressed. We use a greenhouse plant-soil feedback experiment to test for non-additive soil impacts of two common invasive nonnative woody shrubs, Lonicera maackii and Ligustrum sinense, in deciduous forests of the southeastern United States. We measured the performance of each nonnative shrub, a native herbaceous community, and a nonnative woody vine in soils conditioned by each shrub singly or together in polyculture. Soils conditioned by both nonnative shrubs had non-additive impacts on native and nonnative performance. Root mass of the native herbaceous community was 1.5 times lower and the root mass of the nonnative L. sinense was 1.8 times higher in soils conditioned by both L. maackii and L. sinense than expected based upon growth in soils conditioned by either shrub singly. This result indicates that when these two nonnative shrubs co-occur, their influence on soils disproportionally favors persistence

Pre-Steady State Kinetic Investigation of the Incorporation of Anti-Hepatitis B Nucleotide Analogs Catalyzed by Non-Canonical Human DNA Polymerases

Science.gov (United States)

Brown, Jessica A.; Pack, Lindsey R.; Fowler, Jason D.; Suo, Zucai

2011-01-01

Antiviral nucleoside analogs have been developed to inhibit the enzymatic activities of the hepatitis B virus (HBV) polymerase, thereby preventing the replication and production of HBV. However, the usage of these analogs can be limited by drug toxicity because the 5′-triphosphates of these nucleoside analogs (nucleotide analogs) are potential substrates for human DNA polymerases to incorporate into host DNA. Although they are poor substrates for human replicative DNA polymerases, it remains to be established whether these nucleotide analogs are substrates for the recently discovered human X- and Y-family DNA polymerases. Using pre-steady state kinetic techniques, we have measured the substrate specificity values for human DNA polymerases β, λ, η, ι, κ, and Rev1 incorporating the active forms of the following anti-HBV nucleoside analogs approved for clinical use: adefovir, tenofovir, lamivudine, telbivudine, and entecavir. Compared to the incorporation of a natural nucleotide, most of the nucleotide analogs were incorporated less efficiently (2 to >122,000) by the six human DNA polymerases. In addition, the potential for entecavir and telbivudine, two drugs which possess a 3′-hydroxyl, to become embedded into human DNA was examined by primer extension and DNA ligation assays. These results suggested that telbivudine functions as a chain terminator while entecavir was efficiently extended by the six enzymes and was a substrate for human DNA ligase I. Our findings suggested that incorporation of anti-HBV nucleotide analogs catalyzed by human X- and Y-family polymerases may contribute to clinical toxicity. PMID:22132702

Bi-template assisted synthesis of mesoporous manganese oxide nanostructures: Tuning properties for efficient CO oxidation.

Science.gov (United States)

Roy, Mouni; Basak, Somjyoti; Naskar, Milan Kanti

2016-02-21

A simple soft bi-templating process was used for the synthesis of mesoporous manganese oxide nanostructures using KMnO4 as a precursor and polyethylene glycol and cetyltrimethylammonium bromide as templates in the presence of benzaldehyde as an organic additive in alkaline media, followed by calcination at 400 °C. X-ray diffraction and Raman spectroscopic analysis of the calcined products confirmed the existence of stoichiometric (MnO2 and Mn5O8) and non-stoichiometric mixed phases (MnO2 + Mn5O8) of Mn oxides obtained by tuning the concentration of the additive and the synthesis time. The surface properties of the prepared Mn oxides were determined by X-ray photoelectron spectroscopy. The mesoporosity of the samples was confirmed by N2 adsorption-desorption. Different synthetic conditions resulted in the formation of different morphologies of the Mn oxides (α-MnO2, Mn5O8, and α-MnO2 + Mn5O8), such as nanoparticles, nanorods, and nanowires. The synthesized mesoporous Mn oxide nanostructures were used for the catalytic oxidation of the harmful air pollutant carbon monoxide. The Mn5O8 nanoparticles with the highest Brunauer-Emmett-Teller surface area and the non-stoichiometric manganese oxide (α-MnO2 + Mn5O8) nanorods with a higher Mn(3+) concentration had the best catalytic efficiency.

NUCLEOTIDES IN INFANT FEEDING

Directory of Open Access Journals (Sweden)

L.G. Mamonova

2007-01-01

Full Text Available The article reviews the application of nucleotides-metabolites, playing a key role in many biological processes, for the infant feeding. The researcher provides the date on the nucleotides in the women's milk according to the lactation stages. She also analyzes the foreign experience in feeding newborns with nucleotides-containing milk formulas. The article gives a comparison of nucleotides in the adapted formulas represented in the domestic market of the given products.Key words: children, feeding, nucleotides.

Nucleotide Metabolism

DEFF Research Database (Denmark)

Martinussen, Jan; Willemoës, M.; Kilstrup, Mogens

2011-01-01

Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolis...

Synthesis of Mesoporous α-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading

Science.gov (United States)

Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

2016-12-01

This paper reports the synthetic route of 3-D network shape α-Fe2O3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of α-Fe2O3, particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constituents. The synthesized nanocrystal at this condition had a narrow pore size distribution and high surface area compared to the bulk α-Fe2O3 or the one synthesized from lower pH conditions. The hydrocracking performance was tested over the synthesized iron oxide catalysts with different morphologies. The worm-like shape of iron oxide showed a superior performance, including overall yield of liquid fuel product and coke formation, over the hydrocracking of heavy petroleum oil.

Biometric Template Security

Directory of Open Access Journals (Sweden)

Abhishek Nagar

2008-03-01

Full Text Available Biometric recognition offers a reliable solution to the problem of user authentication in identity management systems. With the widespread deployment of biometric systems in various applications, there are increasing concerns about the security and privacy of biometric technology. Public acceptance of biometrics technology will depend on the ability of system designers to demonstrate that these systems are robust, have low error rates, and are tamper proof. We present a high-level categorization of the various vulnerabilities of a biometric system and discuss countermeasures that have been proposed to address these vulnerabilities. In particular, we focus on biometric template security which is an important issue because, unlike passwords and tokens, compromised biometric templates cannot be revoked and reissued. Protecting the template is a challenging task due to intrauser variability in the acquired biometric traits. We present an overview of various biometric template protection schemes and discuss their advantages and limitations in terms of security, revocability, and impact on matching accuracy. A template protection scheme with provable security and acceptable recognition performance has thus far remained elusive. Development of such a scheme is crucial as biometric systems are beginning to proliferate into the core physical and information infrastructure of our society.

Functional Programming with C++ Template Metaprograms

Science.gov (United States)

Porkoláb, Zoltán

Template metaprogramming is an emerging new direction of generative programming. With the clever definitions of templates we can force the C++ compiler to execute algorithms at compilation time. Among the application areas of template metaprograms are the expression templates, static interface checking, code optimization with adaption, language embedding and active libraries. However, as template metaprogramming was not an original design goal, the C++ language is not capable of elegant expression of metaprograms. The complicated syntax leads to the creation of code that is hard to write, understand and maintain. Although template metaprogramming has a strong relationship with functional programming, this is not reflected in the language syntax and existing libraries. In this paper we give a short and incomplete introduction to C++ templates and the basics of template metaprogramming. We will enlight the role of template metaprograms, and some important and widely used idioms. We give an overview of the possible application areas as well as debugging and profiling techniques. We suggest a pure functional style programming interface for C++ template metaprograms in the form of embedded Haskell code which is transformed to standard compliant C++ source.

Looking sharp: Becoming a search template boosts precision and stability in visual working memory.

Science.gov (United States)

Rajsic, Jason; Ouslis, Natasha E; Wilson, Daryl E; Pratt, Jay

2017-08-01

Visual working memory (VWM) plays a central role in visual cognition, and current work suggests that there is a special state in VWM for items that are the goal of visual searches. However, whether the quality of memory for target templates differs from memory for other items in VWM is currently unknown. In this study, we measured the precision and stability of memory for search templates and accessory items to determine whether search templates receive representational priority in VWM. Memory for search templates exhibited increased precision and probability of recall, whereas accessory items were remembered less often. Additionally, while memory for Templates showed benefits when instances of the Template appeared in search, this benefit was not consistently observed for Accessory items when they appeared in search. Our results show that becoming a search template can substantially affect the quality of a representation in VWM.

Animated pose templates for modeling and detecting human actions.

Science.gov (United States)

Yao, Benjamin Z; Nie, Bruce X; Liu, Zicheng; Zhu, Song-Chun

2014-03-01

This paper presents animated pose templates (APTs) for detecting short-term, long-term, and contextual actions from cluttered scenes in videos. Each pose template consists of two components: 1) a shape template with deformable parts represented in an And-node whose appearances are represented by the Histogram of Oriented Gradient (HOG) features, and 2) a motion template specifying the motion of the parts by the Histogram of Optical-Flows (HOF) features. A shape template may have more than one motion template represented by an Or-node. Therefore, each action is defined as a mixture (Or-node) of pose templates in an And-Or tree structure. While this pose template is suitable for detecting short-term action snippets in two to five frames, we extend it in two ways: 1) For long-term actions, we animate the pose templates by adding temporal constraints in a Hidden Markov Model (HMM), and 2) for contextual actions, we treat contextual objects as additional parts of the pose templates and add constraints that encode spatial correlations between parts. To train the model, we manually annotate part locations on several keyframes of each video and cluster them into pose templates using EM. This leaves the unknown parameters for our learning algorithm in two groups: 1) latent variables for the unannotated frames including pose-IDs and part locations, 2) model parameters shared by all training samples such as weights for HOG and HOF features, canonical part locations of each pose, coefficients penalizing pose-transition and part-deformation. To learn these parameters, we introduce a semi-supervised structural SVM algorithm that iterates between two steps: 1) learning (updating) model parameters using labeled data by solving a structural SVM optimization, and 2) imputing missing variables (i.e., detecting actions on unlabeled frames) with parameters learned from the previous step and progressively accepting high-score frames as newly labeled examples. This algorithm belongs to a

Development of Self-Assembled Nanoscale Templates via Microphase Separation Induced by Polymer Brushes

Science.gov (United States)

Chu, Elza

Phase separation in soft matter has been the crucial element in generating hybrid materials, such as polymer blends and mixed polymer brushes. This dissertation discusses two methods of developing self-assembled nanoscale templates via microphase separation induced by polymer brush synthesis. This work introduces a novel soft substrate approach with renewable grafting sites where polyacrylamide is "grafted through" chitosan soft substrates. The mechanism of grafting leads to ordered arrays of filament-like nanostructures spanning the chitosan-air interface. Additionally, the chemical composition of the filaments allows for post-chemical modification to change the physical properties of the filaments, and subsequently tailor surfaces for specific application. Unlike traditional materials, multi-functional or "smart" materials, such as binary polymer brushes (BPB) are capable of spontaneously changing the spatial distribution of functional groups and morphology at the surface upon external stimuli. Although promising in principle, the limited range of available complementary polymers with common non-selective solvents confines the diversity of usable materials and restricts any further advancement in the field. This dissertation also covers the fabrication and characterization of responsive nanoscale polystyrene templates or "mosaic" brushes that are capable of changing interfacial composition upon exposure to varying solvent qualities. Using a "mosaic" brush template is a unique approach that allows the fabrication of strongly immiscible polymer BPB without the need for a common solvent. The synthesis of such BPB is exemplified by two strongly immiscible polymers, i.e. polystyrene (polar) and polyacrylamide (non-polar), where polyacrylamide brush is "graft through" a Si-substrate modified with the polystyrene collapsed "mosaic" brush. The surface exhibits solvent-triggered responses, as well as application potential for anti-biofouling.

Templates, Numbers & Watercolors.

Science.gov (United States)

Clemesha, David J.

1990-01-01

Describes how a second-grade class used large templates to draw and paint five-digit numbers. The lesson integrated artistic knowledge and vocabulary with their mathematics lesson in place value. Students learned how draftspeople use templates, and they studied number paintings by Charles Demuth and Jasper Johns. (KM)

A TSR Visual Servoing System Based on a Novel Dynamic Template Matching Method

Directory of Open Access Journals (Sweden)

Jia Cai

2015-12-01

Full Text Available The so-called Tethered Space Robot (TSR is a novel active space debris removal system. To solve its problem of non-cooperative target recognition during short-distance rendezvous events, this paper presents a framework for a real-time visual servoing system using non-calibrated monocular-CMOS (Complementary Metal Oxide Semiconductor. When a small template is used for matching with a large scene, it always leads to mismatches, so a novel template matching algorithm to solve the problem is presented. Firstly, the novel matching algorithm uses a hollow annulus structure according to a FAST (Features from Accelerated Segment algorithm and makes the method be rotation-invariant. Furthermore, the accumulative deviation can be decreased by the hollow structure. The matching function is composed of grey and gradient differences between template and object image, which help it reduce the effects of illumination and noises. Then, a dynamic template update strategy is designed to avoid tracking failures brought about by wrong matching or occlusion. Finally, the system synthesizes the least square integrated predictor, realizing tracking online in complex circumstances. The results of ground experiments show that the proposed algorithm can decrease the need for sophisticated computation and improves matching accuracy.

The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase

Directory of Open Access Journals (Sweden)

Yusuke Takezawa

2016-06-01

Full Text Available A metal-mediated base pair, composed of two ligand-bearing nucleotides and a bridging metal ion, is one of the most promising components for developing DNA-based functional molecules. We have recently reported an enzymatic method to synthesize hydroxypyridone (H-type ligand-bearing artificial DNA strands. Terminal deoxynucleotidyl transferase (TdT, a template-independent DNA polymerase, was found to oligomerize H nucleotides to afford ligand-bearing DNAs, which were subsequently hybridized through copper-mediated base pairing (H–CuII–H. In this study, we investigated the effects of a metal cofactor, MgII ion, on the TdT-catalyzed polymerization of H nucleotides. At a high MgII concentration (10 mM, the reaction was halted after several H nucleotides were appended. In contrast, at lower MgII concentrations, H nucleotides were further appended to the H-tailed product to afford longer ligand-bearing DNA strands. An electrophoresis mobility shift assay revealed that the binding affinity of TdT to the H-tailed DNAs depends on the MgII concentration. In the presence of excess MgII ions, TdT did not bind to the H-tailed strands; thus, further elongation was impeded. This is possibly because the interaction with MgII ions caused folding of the H-tailed strands into unfavorable secondary structures. This finding provides an insight into the enzymatic synthesis of longer ligand-bearing DNA strands.

Synthesis of non-siliceous mesoporous oxides.

Science.gov (United States)

Gu, Dong; Schüth, Ferdi

2014-01-07

Mesoporous non-siliceous oxides have attracted great interest due to their unique properties and potential applications. Since the discovery of mesoporous silicates in 1990s, organic-inorganic assembly processes by using surfactants or block copolymers as soft templates have been considered as a feasible path for creating mesopores in metal oxides. However, the harsh sol-gel conditions and low thermal stabilities have limited the expansion of this method to various metal oxide species. Nanocasting, using ordered mesoporous silica or carbon as a hard template, has provided possibilities for preparing novel mesoporous materials with new structures, compositions and high thermal stabilities. This review concerns the synthesis, composition, and parameter control of mesoporous non-siliceous oxides. Four synthesis routes, i.e. soft-templating (surfactants or block copolymers as templates), hard-templating (mesoporous silicas or carbons as sacrificial templates), colloidal crystal templating (3-D ordered colloidal particles as a template), and super lattice routes, are summarized in this review. Mesoporous metal oxides with different compositions have different properties. Non-siliceous mesoporous oxides are comprehensively described, including a discussion of constituting elements, synthesis, and structures. General aspects concerning pore size control, atomic scale crystallinity, and phase control are also reviewed.

Nucleotide sequence of tomato ringspot virus RNA-2.

Science.gov (United States)

Rott, M E; Tremaine, J H; Rochon, D M

1991-07-01

The sequence of tomato ringspot virus (TomRSV) RNA-2 has been determined. It is 7273 nucleotides in length excluding the 3' poly(A) tail and contains a single long open reading frame (ORF) of 5646 nucleotides in the positive sense beginning at position 78 and terminating at position 5723. A second in-frame AUG at position 441 is in a more favourable context for initiation of translation and may act as a site for initiation of translation. The TomRSV RNA-2 3' noncoding region is 1550 nucleotides in length. The coat protein is located in the C-terminal region of the large polypeptide and shows significant but limited amino acid sequence similarity to the putative coat proteins of the nepoviruses tomato black ring (TBRV), Hungarian grapevine chrome mosaic (GCMV) and grapevine fanleaf (GFLV). Comparisons of the coding and non-coding regions of TomRSV RNA-2 and the RNA components of TBRV, GCMV, GFLV and the comovirus cowpea mosaic virus revealed significant similarity for over 300 amino acids between the coding region immediately to the N-terminal side of the putative coat proteins of TomRSV and GFLV; very little similarity could be detected among the non-coding regions of TomRSV and any of these viruses.

软模板法合成纳米材料的研究进展%The Progress of Nanomaterials Prepared in the Presence of Soft Template

Institute of Scientific and Technical Information of China (English)

阮秀; 董磊; 于晶; 于良民; 防玉臻

2012-01-01

The progress of research on synthesis of nanomaterials with polymer templating method, biomacro-molecule templating method, surfactant templating method and small molecule organic additives templating method are summarized, with emphasis on the scheme about synthesis of nanomaterials with different morphologies and structures that template induce. Because of simple synthetic method and flexible structure design of polymer templating, non-polluting and precisely regulating the nanostructures of biomacromolecule templating, so they are reviewed detailedly.%介绍了近年来合成高分子模板法、生物高分子模板法、表面活性剂模板法、有机小分子添加剂模板法制备纳米材料的研究进展,重点介绍了模板剂诱导不同形貌和结构的纳米材料形成的作用机理.因合成高分子模板制备简单,结构设计灵活,生物高分子模板绿色环保,能更精确调控纳米材料结构,故详细综述了这2种方法.

Design reflowable digital book template

Science.gov (United States)

Prasetya, Didik Dwi; Widiyaningtyas, Triyanna; Arifin, M. Zainal; Wahyu Sakti G., I.

2017-09-01

Electronic books (e-books or digital books) increasingly in demand and continue to grow in the form of future books. One of the standard format electronic books that potential is EPUB (electronic publication) published by the International Digital Publishing Forum (IDPF). This digital book has major advantages are able to provide interactive and reflowable content, which are not found in another book format, such as PDF. Reflowable content allows the book can be accessed through a variety of reader device, like desktop and mobile with a fit and comfort view. However, because the generating process of an EPUB digital book is not as easy a PDF, so this format is less popular. Therefore, in order to help overcome the existing problems, this paper develops digital reflowable text book templates to support electronic learning, especially in Indonesia. This template can be used by anyone to produce a standard digital book quickly and easily without requiring additional specialized knowledge.

Emergency department documentation templates: variability in template selection and association with physical examination and test ordering in dizziness presentations

Directory of Open Access Journals (Sweden)

Meurer William J

2011-03-01

Full Text Available Abstract Background Clinical documentation systems, such as templates, have been associated with process utilization. The T-System emergency department (ED templates are widely used but lacking are analyses of the templates association with processes. This system is also unique because of the many different template options available, and thus the selection of the template may also be important. We aimed to describe the selection of templates in ED dizziness presentations and to investigate the association between items on templates and process utilization. Methods Dizziness visits were captured from a population-based study of EDs that use documentation templates. Two relevant process outcomes were assessed: head computerized tomography (CT scan and nystagmus examination. Multivariable logistic regression was used to estimate the probability of each outcome for patients who did or did not receive a relevant-item template. Propensity scores were also used to adjust for selection effects. Results The final cohort was 1,485 visits. Thirty-one different templates were used. Use of a template with a head CT item was associated with an increase in the adjusted probability of head CT utilization from 12.2% (95% CI, 8.9%-16.6% to 29.3% (95% CI, 26.0%-32.9%. The adjusted probability of documentation of a nystagmus assessment increased from 12.0% (95%CI, 8.8%-16.2% when a nystagmus-item template was not used to 95.0% (95% CI, 92.8%-96.6% when a nystagmus-item template was used. The associations remained significant after propensity score adjustments. Conclusions Providers use many different templates in dizziness presentations. Important differences exist in the various templates and the template that is used likely impacts process utilization, even though selection may be arbitrary. The optimal design and selection of templates may offer a feasible and effective opportunity to improve care delivery.

Chronic low-dose ultraviolet-induced mutagenesis in nucleotide excision repair-deficient cells.

Science.gov (United States)

Haruta, Nami; Kubota, Yoshino; Hishida, Takashi

2012-09-01

UV radiation induces two major types of DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidine photoproducts, which are both primarily repaired by nucleotide excision repair (NER). Here, we investigated how chronic low-dose UV (CLUV)-induced mutagenesis occurs in rad14Δ NER-deficient yeast cells, which lack the yeast orthologue of human xeroderma pigmentosum A (XPA). The results show that rad14Δ cells have a marked increase in CLUV-induced mutations, most of which are C→T transitions in the template strand for transcription. Unexpectedly, many of the CLUV-induced C→T mutations in rad14Δ cells are dependent on translesion synthesis (TLS) DNA polymerase η, encoded by RAD30, despite its previously established role in error-free TLS. Furthermore, we demonstrate that deamination of cytosine-containing CPDs contributes to CLUV-induced mutagenesis. Taken together, these results uncover a novel role for Polη in the induction of C→T transitions through deamination of cytosine-containing CPDs in CLUV-exposed NER deficient cells. More generally, our data suggest that Polη can act as both an error-free and a mutagenic DNA polymerase, depending on whether the NER pathway is available to efficiently repair damaged templates.

DNA Nucleotides Detection via capacitance properties of Graphene

Science.gov (United States)

Khadempar, Nahid; Berahman, Masoud; Yazdanpanah, Arash

2016-05-01

In the present paper a new method is suggested to detect the DNA nucleotides on a first-principles calculation of the electronic features of DNA bases which chemisorbed to a graphene sheet placed between two gold electrodes in a contact-channel-contact system. The capacitance properties of graphene in the channel are surveyed using non-equilibrium Green's function coupled with the Density Functional Theory. Thus, the capacitance properties of graphene are theoretically investigated in a biological environment, and, using a novel method, the effect of the chemisorbed DNA nucleotides on electrical charges on the surface of graphene is deciphered. Several parameters in this method are also extracted including Electrostatic energy, Induced density, induced electrostatic potential, Electron difference potential and Electron difference density. The qualitative and quantitative differences among these parameters can be used to identify DNA nucleotides. Some of the advantages of this approach include its ease and high accuracy. What distinguishes the current research is that it is the first experiment to investigate the capacitance properties of gaphene changes in the biological environment and the effect of chemisorbed DNA nucleotides on the surface of graphene on the charge.

Hard template synthesis of metal nanowires

Science.gov (United States)

Kawamura, Go; Muto, Hiroyuki; Matsuda, Atsunori

2014-11-01

Metal nanowires (NWs) have attracted much attention because of their high electron conductivity, optical transmittance and tunable magnetic properties. Metal NWs have been synthesized using soft templates such as surface stabilizing molecules and polymers, and hard templates such as anodic aluminum oxide, mesoporous oxide, carbon nanotubes. NWs prepared from hard templates are composites of metals and the oxide/carbon matrix. Thus, selecting appropriate elements can simplify the production of composite devices. The resulting NWs are immobilized and spatially arranged, as dictated by the ordered porous structure of the template. This avoids the NWs from aggregating, which is common for NWs prepared with soft templates in solution. Herein, the hard template synthesis of metal NWs is reviewed, and the resulting structures, properties and potential applications are discussed.

A new template matching method based on contour information

Science.gov (United States)

Cai, Huiying; Zhu, Feng; Wu, Qingxiao; Li, Sicong

2014-11-01

Template matching is a significant approach in machine vision due to its effectiveness and robustness. However, most of the template matching methods are so time consuming that they can't be used to many real time applications. The closed contour matching method is a popular kind of template matching methods. This paper presents a new closed contour template matching method which is suitable for two dimensional objects. Coarse-to-fine searching strategy is used to improve the matching efficiency and a partial computation elimination scheme is proposed to further speed up the searching process. The method consists of offline model construction and online matching. In the process of model construction, triples and distance image are obtained from the template image. A certain number of triples which are composed by three points are created from the contour information that is extracted from the template image. The rule to select the three points is that the template contour is divided equally into three parts by these points. The distance image is obtained here by distance transform. Each point on the distance image represents the nearest distance between current point and the points on the template contour. During the process of matching, triples of the searching image are created with the same rule as the triples of the model. Through the similarity that is invariant to rotation, translation and scaling between triangles, the triples corresponding to the triples of the model are found. Then we can obtain the initial RST (rotation, translation and scaling) parameters mapping the searching contour to the template contour. In order to speed up the searching process, the points on the searching contour are sampled to reduce the number of the triples. To verify the RST parameters, the searching contour is projected into the distance image, and the mean distance can be computed rapidly by simple operations of addition and multiplication. In the fine searching process

iTemplate: A template-based eye movement data analysis approach.

Science.gov (United States)

Xiao, Naiqi G; Lee, Kang

2018-02-08

Current eye movement data analysis methods rely on defining areas of interest (AOIs). Due to the fact that AOIs are created and modified manually, variances in their size, shape, and location are unavoidable. These variances affect not only the consistency of the AOI definitions, but also the validity of the eye movement analyses based on the AOIs. To reduce the variances in AOI creation and modification and achieve a procedure to process eye movement data with high precision and efficiency, we propose a template-based eye movement data analysis method. Using a linear transformation algorithm, this method registers the eye movement data from each individual stimulus to a template. Thus, users only need to create one set of AOIs for the template in order to analyze eye movement data, rather than creating a unique set of AOIs for all individual stimuli. This change greatly reduces the error caused by the variance from manually created AOIs and boosts the efficiency of the data analysis. Furthermore, this method can help researchers prepare eye movement data for some advanced analysis approaches, such as iMap. We have developed software (iTemplate) with a graphic user interface to make this analysis method available to researchers.

CPU and GPU (Cuda Template Matching Comparison

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Evaldas Borcovas

2014-05-01

Full Text Available Image processing, computer vision or other complicated opticalinformation processing algorithms require large resources. It isoften desired to execute algorithms in real time. It is hard tofulfill such requirements with single CPU processor. NVidiaproposed CUDA technology enables programmer to use theGPU resources in the computer. Current research was madewith Intel Pentium Dual-Core T4500 2.3 GHz processor with4 GB RAM DDR3 (CPU I, NVidia GeForce GT320M CUDAcompliable graphics card (GPU I and Intel Core I5-2500K3.3 GHz processor with 4 GB RAM DDR3 (CPU II, NVidiaGeForce GTX 560 CUDA compatible graphic card (GPU II.Additional libraries as OpenCV 2.1 and OpenCV 2.4.0 CUDAcompliable were used for the testing. Main test were made withstandard function MatchTemplate from the OpenCV libraries.The algorithm uses a main image and a template. An influenceof these factors was tested. Main image and template have beenresized and the algorithm computing time and performancein Gtpix/s have been measured. According to the informationobtained from the research GPU computing using the hardwarementioned earlier is till 24 times faster when it is processing abig amount of information. When the images are small the performanceof CPU and GPU are not significantly different. Thechoice of the template size makes influence on calculating withCPU. Difference in the computing time between the GPUs canbe explained by the number of cores which they have.

Hard template synthesis of metal nanowires

Directory of Open Access Journals (Sweden)

Go eKawamura

2014-11-01

Full Text Available Metal nanowires (NWs have attracted much attention because of their high electron conductivity, optical transmittance and tunable magnetic properties. Metal NWs have been synthesized using soft templates such as surface stabilizing molecules and polymers, and hard templates such as anodic aluminum oxide, mesoporous oxide, carbon nanotubes. NWs prepared from hard templates are composites of metals and the oxide/carbon matrix. Thus, selecting appropriate elements can simplify the production of composite devices. The resulting NWs are immobilized and spatially arranged, as dictated by the ordered porous structure of the template. This avoids the NWs from aggregating, which is common for NWs prepared with soft templates in solution. Herein, the hard template synthesis of metal NWs is reviewed, and the resulting structures, properties and potential applications are discussed.

Photometric redshifts for the next generation of deep radio continuum surveys - I. Template fitting

Science.gov (United States)

Duncan, Kenneth J.; Brown, Michael J. I.; Williams, Wendy L.; Best, Philip N.; Buat, Veronique; Burgarella, Denis; Jarvis, Matt J.; Małek, Katarzyna; Oliver, S. J.; Röttgering, Huub J. A.; Smith, Daniel J. B.

2018-01-01

We present a study of photometric redshift performance for galaxies and active galactic nuclei detected in deep radio continuum surveys. Using two multiwavelength data sets, over the NOAO Deep Wide Field Survey Boötes and COSMOS fields, we assess photometric redshift (photo-z) performance for a sample of ∼4500 radio continuum sources with spectroscopic redshifts relative to those of ∼63 000 non-radio-detected sources in the same fields. We investigate the performance of three photometric redshift template sets as a function of redshift, radio luminosity and infrared/X-ray properties. We find that no single template library is able to provide the best performance across all subsets of the radio-detected population, with variation in the optimum template set both between subsets and between fields. Through a hierarchical Bayesian combination of the photo-z estimates from all three template sets, we are able to produce a consensus photo-z estimate that equals or improves upon the performance of any individual template set.

The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions.

Science.gov (United States)

Yates, Christopher M; Sternberg, Michael J E

2013-11-01

Non-synonymous single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino acid sequence of the encoded protein. Many of these variants are associated with disease, so nsSNPs have been well studied, with studies looking at the effects of nsSNPs on individual proteins, for example, on stability and enzyme active sites. In recent years, the impact of nsSNPs upon protein-protein interactions has also been investigated, giving a greater insight into the mechanisms by which nsSNPs can lead to disease. In this review, we summarize these studies, looking at the various mechanisms by which nsSNPs can affect protein-protein interactions. We focus on structural changes that can impair interaction, changes to disorder, gain of interaction, and post-translational modifications before looking at some examples of nsSNPs at human-pathogen protein-protein interfaces and the analysis of nsSNPs from a network perspective. © 2013.

Effect of template-induced surface species on electronic structure and photocatalytic activity of g-C{sub 3}N{sub 4}

Energy Technology Data Exchange (ETDEWEB)

Shen, Yu; Guo, Xiaojuan; Bo, Xiangkun; Wang, Yongzheng [Key Lab of Mesoscopic Chemistry MOE, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023 (China); Guo, Xiangke [Key Lab of Mesoscopic Chemistry MOE, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023 (China); Hubei Key Laboratory for Processing and Application of Catalytic Materials, Huanggang Normal University, Huanggang 438000 (China); Xie, Mingjiang, E-mail: xiemingjiang@hotmail.com [Key Lab of Mesoscopic Chemistry MOE, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023 (China); Guo, Xuefeng, E-mail: guoxf@nju.edu.cn [Key Lab of Mesoscopic Chemistry MOE, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023 (China); Hubei Key Laboratory for Processing and Application of Catalytic Materials, Huanggang Normal University, Huanggang 438000 (China)

2017-02-28

Highlights: • The effect of template on the surface chemistry of g-C{sub 3}N{sub 4} were investigated. • Template induces more non-graphitic species (sp{sup 3}−C−C− and −NH{sub x}) on g-C{sub 3}N{sub 4}. • Non-graphitic species influence electronic structure and performance of g-C{sub 3}N{sub 4}. - Abstract: In view of the fact that the photocatalytic activity of graphitic carbon nitride (g-C{sub 3}N{sub 4}) is greatly influenced by its electronic structure, herein, effect of templates induced surface species variation on the electronic structure and photocatalytic activity of the templated g-C{sub 3}N{sub 4} was investigated. By mixing the precursor of cyanamide with different templates (SiO{sub 2}, Al{sub 2}O{sub 3} and template-free) in the preparation of graphitic carbon nitride (g-C{sub 3}N{sub 4}), carbon nitrides with different surface species were obtained. The obtained carbon nitride (g-C{sub 3}N{sub 4}-Si) templated by SiO{sub 2} nanoparticles exhibits enlarged band gap (3.26 eV) and enhanced photo-degradation ability towards Methyl Orange (MO) compared to that of bulk g-C{sub 3}N{sub 4} (2.67 eV) synthesized from direct condensation/carbonization of melamine and Al{sub 2}O{sub 3}-templated g-C{sub 3}N{sub 4}-Al (2.76 eV). Detailed characterizations confirm that the introduction of templates in the synthesis process resulted in more non-graphitic species (sp{sup 3}−C−C− and −NH{sub x}) on the surface of the derived carbon nitrides, exerting remarkable effect on the electronic structure and photocatalytic performance.

Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation.

Science.gov (United States)

E, Chao; Duan, Baogen; Yu, Jin

2017-04-20

Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 k B T) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.

The nucleotide sequence of satellite RNA in grapevine fanleaf virus, strain F13.

Science.gov (United States)

Fuchs, M; Pinck, M; Serghini, M A; Ravelonandro, M; Walter, B; Pinck, L

1989-04-01

The nucleotide sequence of cDNA copies of grapevine fanleaf virus (strain F13) satellite RNA has been determined. The primary structure obtained was 1114 nucleotides in length, excluding the poly(A) tail, and contained only one long open reading frame encoding a 341 residue, highly hydrophilic polypeptide of Mr37275. The coding sequence was bordered by a leader of 14 nucleotides and a 3'-terminal non-coding region of 74 nucleotides. No homology has been found with small satellite RNAs associated with other nepoviruses. Two limited homologies of eight nucleotides have been detected between the satellite RNA in grapevine fanleaf virus and those in tomato black ring virus, and a consensus sequence U.G/UGAAAAU/AU/AU/A at the 5' end of nepovirus RNAs is reported. A less extended consensus exists in this region in comovirus and picornavirus RNA.

Electrostatic assembly of CTAB-capped silver nanoparticles along predefined λ-DNA template

International Nuclear Information System (INIS)

Wei Gang; Wang Li; Zhou Hualan; Liu Zhiguo; Song Yonghai; Li Zhuang

2005-01-01

Cetyltrimethylammonium bromide (CTAB)-capped positively-charged silver nanoparticles synthesized in water-ethanol system was electrostatic assembled on predefined aligned λ-DNA template. Silver nanowire can be obtained by changing the reaction time and the particles concentration. In our work, the length of the silver nanowire obtained is about 10 μm, and the dimension of the wires is about 20 nm. AFM data reveal that the assembly of CTAB-capped silver nanoparticles on DNA is ordered, but there is space between two particles absorbed on the DNA template. X-ray photoelectron spectroscopy (XPS) was applied to characterize the linear silver clusters, which provides an additional proof that the silver particles were assembled onto DNA template with fine order

Novel simple templates for reproducible positioning of skin applicators in brachytherapy

Directory of Open Access Journals (Sweden)

Silvia Rodríguez Villalba

2016-08-01

Full Text Available Purpose : Esteya and Valencia surface applicators are designed to treat skin tumors using brachytherapy. In clinical practice, in order to avoid errors that may affect the treatment outcome, there are two issues that need to be carefully addressed. First, the selected applicator for the treatment should provide adequate margin for the target, and second, the applicator has to be precisely positioned before each treatment fraction. In this work, we describe the development and use of a new acrylic templates named Template La Fe-ITIC. They have been designed specifically to help the clinical user in the selection of the correct applicator, and to assist the medical staff in reproducing the positioning of the applicator. These templates are freely available upon request. Material and methods: Templates that were developed by University and Polytechnic Hospital La Fe (La Fe and Hospital Clínica Benidorm (ITIC in cooperation with Elekta, consist of a thin sheet made of transparent acrylic. For each applicator, a crosshair and two different circles are drawn on these templates: the inner one corresponds to the useful beam, while the outer one represents the external perimeter of the applicator. The outer circle contains slits that facilitate to draw a circle on the skin of the patient for exact positioning of the applicator. In addition, there are two perpendicular rulers to define the adequate margin. For each applicator size, a specific template was developed. Results: The templates have been used successfully in our institutions for more than 50 patients’ brachytherapy treatments. They are currently being used for Esteya and Valencia applicators. Conclusions : The template La Fe-ITIC is simple and practical. It improves both the set-up time and reproducibility. It helps to establish the adequate margins, an essential point in the clinical outcome.

A template bank to search for gravitational waves from inspiralling compact binaries: I. Physical models

International Nuclear Information System (INIS)

Babak, S; Balasubramanian, R; Churches, D; Cokelaer, T; Sathyaprakash, B S

2006-01-01

Gravitational waves from coalescing compact binaries are searched for using the matched filtering technique. As the model waveform depends on a number of parameters, it is necessary to filter the data through a template bank covering the astrophysically interesting region of the parameter space. The choice of templates is defined by the maximum allowed drop in signal-to-noise ratio due to the discreteness of the template bank. In this paper we describe the template-bank algorithm that was used in the analysis of data from the Laser Interferometer Gravitational Wave Observatory (LIGO) and GEO 600 detectors to search for signals from binaries consisting of non-spinning compact objects. Using Monte Carlo simulations, we study the efficiency of the bank and show that its performance is satisfactory for the design sensitivity curves of ground-based interferometric gravitational wave detectors GEO 600, initial LIGO, advanced LIGO and Virgo. The bank is efficient in searching for various compact binaries such as binary primordial black holes, binary neutron stars, binary black holes, as well as a mixed binary consisting of a non-spinning black hole and a neutron star

From scores to face templates: a model-based approach.

Science.gov (United States)

Mohanty, Pranab; Sarkar, Sudeep; Kasturi, Rangachar

2007-12-01

Regeneration of templates from match scores has security and privacy implications related to any biometric authentication system. We propose a novel paradigm to reconstruct face templates from match scores using a linear approach. It proceeds by first modeling the behavior of the given face recognition algorithm by an affine transformation. The goal of the modeling is to approximate the distances computed by a face recognition algorithm between two faces by distances between points, representing these faces, in an affine space. Given this space, templates from an independent image set (break-in) are matched only once with the enrolled template of the targeted subject and match scores are recorded. These scores are then used to embed the targeted subject in the approximating affine (non-orthogonal) space. Given the coordinates of the targeted subject in the affine space, the original template of the targeted subject is reconstructed using the inverse of the affine transformation. We demonstrate our ideas using three, fundamentally different, face recognition algorithms: Principal Component Analysis (PCA) with Mahalanobis cosine distance measure, Bayesian intra-extrapersonal classifier (BIC), and a feature-based commercial algorithm. To demonstrate the independence of the break-in set with the gallery set, we select face templates from two different databases: Face Recognition Grand Challenge (FRGC) and Facial Recognition Technology (FERET) Database (FERET). With an operational point set at 1 percent False Acceptance Rate (FAR) and 99 percent True Acceptance Rate (TAR) for 1,196 enrollments (FERET gallery), we show that at most 600 attempts (score computations) are required to achieve a 73 percent chance of breaking in as a randomly chosen target subject for the commercial face recognition system. With similar operational set up, we achieve a 72 percent and 100 percent chance of breaking in for the Bayesian and PCA based face recognition systems, respectively. With

A SCHEME FOR TEMPLATE SECURITY AT FEATURE FUSION LEVEL IN MULTIMODAL BIOMETRIC SYSTEM

Directory of Open Access Journals (Sweden)

Arvind Selwal

2016-09-01

Full Text Available Biometric is the science of human recognition based upon using their biological, chemical or behavioural traits. These systems are used in many real life applications simply from biometric based attendance system to providing security at very sophisticated level. A biometric system deals with raw data captured using a sensor and feature template extracted from raw image. One of the challenges being faced by designers of these systems is to secure template data extracted from the biometric modalities of the user and protect the raw images. To minimize spoof attacks on biometric systems by unauthorised users one of the solutions is to use multi-biometric systems. Multi-modal biometric system works by using fusion technique to merge feature templates generated from different modalities of the human. In this work a new scheme is proposed to secure template during feature fusion level. Scheme is based on union operation of fuzzy relations of templates of modalities during fusion process of multimodal biometric systems. This approach serves dual purpose of feature fusion as well as transformation of templates into a single secured non invertible template. The proposed technique is cancelable and experimentally tested on a bimodal biometric system comprising of fingerprint and hand geometry. Developed scheme removes the problem of an attacker learning the original minutia position in fingerprint and various measurements of hand geometry. Given scheme provides improved performance of the system with reduction in false accept rate and improvement in genuine accept rate.

The Role of Cyclic Nucleotide Signaling Pathways in Cancer: Targets for Prevention and Treatment

Energy Technology Data Exchange (ETDEWEB)

Fajardo, Alexandra M.; Piazza, Gary A. [Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Ave, Suite 3029, Mobile, AL 36604 (United States); Tinsley, Heather N., E-mail: htinsley@montevallo.edu [Department of Biology, Chemistry, and Mathematics, University of Montevallo, Station 6480, Montevallo, AL 35115 (United States)

2014-02-26

For more than four decades, the cyclic nucleotides cyclic AMP (cAMP) and cyclic GMP (cGMP) have been recognized as important signaling molecules within cells. Under normal physiological conditions, cyclic nucleotides regulate a myriad of biological processes such as cell growth and adhesion, energy homeostasis, neuronal signaling, and muscle relaxation. In addition, altered cyclic nucleotide signaling has been observed in a number of pathophysiological conditions, including cancer. While the distinct molecular alterations responsible for these effects vary depending on the specific cancer type, several studies have demonstrated that activation of cyclic nucleotide signaling through one of three mechanisms—induction of cyclic nucleotide synthesis, inhibition of cyclic nucleotide degradation, or activation of cyclic nucleotide receptors—is sufficient to inhibit proliferation and activate apoptosis in many types of cancer cells. These findings suggest that targeting cyclic nucleotide signaling can provide a strategy for the discovery of novel agents for the prevention and/or treatment of selected cancers.

Templated Dry Printing of Conductive Metal Nanoparticles

Science.gov (United States)

Rolfe, David Alexander

Printed electronics can lower the cost and increase the ubiquity of electrical components such as batteries, sensors, and telemetry systems. Unfortunately, the advance of printed electronics has been held back by the limited minimum resolution, aspect ratio, and feature fidelity of present printing techniques such as gravure, screen printing and inkjet printing. Templated dry printing offers a solution to these problems by patterning nanoparticle inks into templates before drying. This dissertation shows advancements in two varieties of templated dry nanoprinting. The first, advective micromolding in vapor-permeable templates (AMPT) is a microfluidic approach that uses evaporation-driven mold filling to create submicron features with a 1:1 aspect ratio. We will discuss submicron surface acoustic wave (SAW) resonators made through this process, and the refinement process in the template manufacturing process necessary to make these devices. We also present modeling techniques that can be applied to future AMPT templates. We conclude with a modified templated dry printing that improves throughput and isolated feature patterning by transferring dry-templated features with laser ablation. This method utilizes surface energy-defined templates to pattern features via doctor blade coating. Patterned and dried features can be transferred to a polymer substrate with an Nd:YAG MOPA fiber laser, and printed features can be smaller than the laser beam width.

A population MRI brain template and analysis tools for the macaque.

Science.gov (United States)

Seidlitz, Jakob; Sponheim, Caleb; Glen, Daniel; Ye, Frank Q; Saleem, Kadharbatcha S; Leopold, David A; Ungerleider, Leslie; Messinger, Adam

2018-04-15

The use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previous in vivo templates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the "National Institute of Mental Health Macaque Template", or NMT for short. The NMT is a high-resolution in vivo MRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies. Copyright © 2017 ElsevierCompany. All rights reserved.

Liquid foam templating - A route to tailor-made polymer foams.

Science.gov (United States)

Andrieux, Sébastien; Quell, Aggeliki; Stubenrauch, Cosima; Drenckhan, Wiebke

2018-06-01

Solid foams with pore sizes between a few micrometres and a few millimetres are heavily exploited in a wide range of established and emerging applications. While the optimisation of foam applications requires a fine control over their structural properties (pore size distribution, pore opening, foam density, …), the great complexity of most foaming processes still defies a sound scientific understanding and therefore explicit control and prediction of these parameters. We therefore need to improve our understanding of existing processes and also develop new fabrication routes which we understand and which we can exploit to tailor-make new porous materials. One of these new routes is liquid templating in general and liquid foam templating in particular, to which this review article is dedicated. While all solid foams are generated from an initially liquid(-like) state, the particular notion of liquid foam templating implies the specific condition that the liquid foam has time to find its "equilibrium structure" before it is solidified. In other words, the characteristic time scales of the liquid foam's stability and its solidification are well separated, allowing to build on the vast know-how on liquid foams established over the last 20 years. The dispersed phase of the liquid foam determines the final pore size and pore size distribution, while the continuous phase contains the precursors of the desired porous scaffold. We review here the three key challenges which need to be addressed by this approach: (1) the control of the structure of the liquid template, (2) the matching of the time scales between the stability of the liquid template and solidification, and (3) the preservation of the structure of the template throughout the process. Focusing on the field of polymer foams, this review gives an overview of recent research on the properties of liquid foam templates and summarises a key set of studies in the emerging field of liquid foam templating. It

IRF6 rs2235375 single nucleotide polymorphism is associated with isolated non-syndromic cleft palate but not with cleft lip with or without palate in south Indian population.

Science.gov (United States)

Gurramkonda, Venkatesh Babu; Syed, Altaf Hussain; Murthy, Jyotsna; Lakkakula, Bhaskar V K S

2017-06-26

Transcription factors are very diverse family of proteins involved in activating or repressing the transcription of a gene at a given time. Several studies using animal models demonstrated the role of transcription factor genes in craniofacial development. We aimed to investigate the association of IRF6 intron-6 polymorphism in the non-syndromic cleft lip with or without Palate in a south Indian population. 173 unrelated nonsyndromic cleft lip with or without Palate patients and 176 controls without clefts patients were genotyped for IRF6 rs2235375 variant by allele-specific amplification using the KASPar single nucleotide polymorphism genotyping system. The association between interferon regulatory factor-6 gene intron-6 dbSNP208032210:g.G>C (rs2235375) single nucleotide polymorphism and non-syndromic cleft lip with or without palate risk was investigated by chi-square test. There were significant differences in genotype or allele frequencies of rs2235375 single nucleotide polymorphism between controls and cases with non-syndromic cleft lip with or without palate. IRF6 rs2235375 variant was significantly associated with increased risk of non-syndromic cleft lip with or without palate in co-dominant, dominant (OR: 1.19; 95% CI 1.03-2.51; p=0.034) and allelic models (OR: 1.40; 95% CI 1.04-1.90; p=0.028). When subset analysis was applied significantly increased risk was observed in cleft palate only group (OR dominant: 4.33; 95% CI 1.44-12.97; p=0.005). These results suggest that IRF6 rs2235375 SNP play a major role in the pathogenesis and risk of developing non-syndromic cleft lip with or without palate. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Biometric template revocation

Science.gov (United States)

Arndt, Craig M.

2004-08-01

Biometric are a powerful technology for identifying humans both locally and at a distance. In order to perform identification or verification biometric systems capture an image of some biometric of a user or subject. The image is then converted mathematical to representation of the person call a template. Since we know that every human in the world is different each human will have different biometric images (different fingerprints, or faces, etc.). This is what makes biometrics useful for identification. However unlike a credit card number or a password to can be given to a person and later revoked if it is compromised and biometric is with the person for life. The problem then is to develop biometric templates witch can be easily revoked and reissued which are also unique to the user and can be easily used for identification and verification. In this paper we develop and present a method to generate a set of templates which are fully unique to the individual and also revocable. By using bases set compression algorithms in an n-dimensional orthogonal space we can represent a give biometric image in an infinite number of equally valued and unique ways. The verification and biometric matching system would be presented with a given template and revocation code. The code will then representing where in the sequence of n-dimensional vectors to start the recognition.

Development of Total Knee Replacement Digital Templating Software

Science.gov (United States)

Yusof, Siti Fairuz; Sulaiman, Riza; Thian Seng, Lee; Mohd. Kassim, Abdul Yazid; Abdullah, Suhail; Yusof, Shahril; Omar, Masbah; Abdul Hamid, Hamzaini

In this study, by taking full advantage of digital X-ray and computer technology, we have developed a semi-automated procedure to template knee implants, by making use of digital templating method. Using this approach, a software system called OrthoKneeTMhas been designed and developed. The system is to be utilities as a study in the Department of Orthopaedic and Traumatology in medical faculty, UKM (FPUKM). OrthoKneeTMtemplating process employs uses a technique similar to those used by many surgeons, using acetate templates over X-ray films. Using template technique makes it easy to template various implant from every Implant manufacturers who have with a comprehensive database of templates. The templating functionality includes, template (knee) and manufactures templates (Smith & Nephew; and Zimmer). From an image of patient x-ray OrthoKneeTMtemplates help in quickly and easily reads to the approximate template size needed. The visual templating features then allow us quickly review multiple template sizes against the X-ray and thus obtain the nearly precise view of the implant size required. The system can assist by templating on one patient image and will generate reports that can accompany patient notes. The software system was implemented in Visual basic 6.0 Pro using the object-oriented techniques to manage the graphics and objects. The approaches for image scaling will be discussed. Several of measurement in orthopedic diagnosis process have been studied and added in this software as measurement tools features using mathematic theorem and equations. The study compared the results of the semi-automated (using digital templating) method to the conventional method to demonstrate the accuracy of the system.

Template Assembly for Detailed Urban Reconstruction

KAUST Repository

Nan, Liangliang

2015-05-04

We propose a new framework to reconstruct building details by automatically assembling 3D templates on coarse textured building models. In a preprocessing step, we generate an initial coarse model to approximate a point cloud computed using Structure from Motion and Multi View Stereo, and we model a set of 3D templates of facade details. Next, we optimize the initial coarse model to enforce consistency between geometry and appearance (texture images). Then, building details are reconstructed by assembling templates on the textured faces of the coarse model. The 3D templates are automatically chosen and located by our optimization-based template assembly algorithm that balances image matching and structural regularity. In the results, we demonstrate how our framework can enrich the details of coarse models using various data sets.

The Design of a Templated C++ Small Vector Class for Numerical Computing

Science.gov (United States)

Moran, Patrick J.

2000-01-01

We describe the design and implementation of a templated C++ class for vectors. The vector class is templated both for vector length and vector component type; the vector length is fixed at template instantiation time. The vector implementation is such that for a vector of N components of type T, the total number of bytes required by the vector is equal to N * size of (T), where size of is the built-in C operator. The property of having a size no bigger than that required by the components themselves is key in many numerical computing applications, where one may allocate very large arrays of small, fixed-length vectors. In addition to the design trade-offs motivating our fixed-length vector design choice, we review some of the C++ template features essential to an efficient, succinct implementation. In particular, we highlight some of the standard C++ features, such as partial template specialization, that are not supported by all compilers currently. This report provides an inventory listing the relevant support currently provided by some key compilers, as well as test code one can use to verify compiler capabilities.

Matched filtering of numerical relativity templates of spinning binary black holes

International Nuclear Information System (INIS)

Vaishnav, Birjoo; Hinder, Ian; Herrmann, Frank; Shoemaker, Deirdre

2007-01-01

Tremendous progress has been made towards the solution of the binary-black-hole problem in numerical relativity. The waveforms produced by numerical relativity will play a role in gravitational wave detection as either test beds for analytic template banks or as template banks themselves. As the parameter space explored by numerical relativity expands, the importance of quantifying the effect that each parameter has on first the detection of gravitational waves and then the parameter estimation of their sources increases. In light of this, we present a study of equal-mass, spinning binary-black-hole evolutions through matched filtering techniques commonly used in data analysis. We study how the match between two numerical waveforms varies with numerical resolution, initial angular momentum of the black holes, and the inclination angle between the source and the detector. This study is limited by the fact that the spinning black-hole binaries are oriented axially and the waveforms only contain approximately two and a half orbits before merger. We find that for detection purposes, spinning black holes require the inclusion of the higher harmonics in addition to the dominant mode, a condition that becomes more important as the black-hole spins increase. In addition, we conduct a preliminary investigation of how well a template of fixed spin and inclination angle can detect target templates of arbitrary but nonprecessing spin and inclination for the axial case considered here

Crossbreeding to increase beef production: additive and non ...

African Journals Online (AJOL)

GScholtz

2013-06-06

Jun 6, 2013 ... Crossbreeding to increase beef production: additive and non-additive effects on weight traits ... total weight of weaned calves. ... Weight traits are not all equally important to efficiency ... values to model total herd productivity. ..... The maintenance requirement of a cow is affected by her weight: the larger the.

Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms.

Science.gov (United States)

Van, K; Onoda, S; Kim, M Y; Kim, K D; Lee, S-H

2008-03-01

The Waxy (Wx) gene product controls the formation of a straight chain polymer of amylose in the starch pathway. Dominance/recessiveness of the Wx allele is associated with amylose content, leading to non-waxy/waxy phenotypes. For a total of 113 foxtail millet accessions, agronomic traits and the molecular differences of the Wx gene were surveyed to evaluate genetic diversities. Molecular types were associated with phenotypes determined by four specific primer sets (non-waxy, Type I; low amylose, Type VI; waxy, Type IV or V). Additionally, the insertion of transposable element in waxy was confirmed by ex1/TSI2R, TSI2F/ex2, ex2int2/TSI7R and TSI7F/ex4r. Seventeen single nucleotide polymorphims (SNPs) were observed from non-coding regions, while three SNPs from coding regions were non-synonymous. Interestingly, the phenotype of No. 88 was still non-waxy, although seven nucleotides (AATTGGT) insertion at 2,993 bp led to 78 amino acids shorter. The rapid decline of r (2) in the sequenced region (exon 1-intron 1-exon 2) suggested a low level of linkage disequilibrium and limited haplotype structure. K (s) values and estimation of evolutionary events indicate early divergence of S. italica among cereal crops. This study suggested the Wx gene was one of the targets in the selection process during domestication.

The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family.

Directory of Open Access Journals (Sweden)

Lonneke van der Linden

2015-03-01

Full Text Available The genus Enterovirus of the family Picornaviridae contains many important human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and enterovirus 71 for which no antiviral drugs are available. The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy. Nucleoside-based inhibitors have broad-spectrum activity but often exhibit off-target effects. Most non-nucleoside inhibitors (NNIs target surface cavities, which are structurally more flexible than the nucleotide-binding pocket, and hence have a more narrow spectrum of activity and are more prone to resistance development. Here, we report a novel NNI, GPC-N114 (2,2'-[(4-chloro-1,2-phenylenebis(oxy]bis(5-nitro-benzonitrile with broad-spectrum activity against enteroviruses and cardioviruses (another genus in the picornavirus family. Surprisingly, coxsackievirus B3 (CVB3 and poliovirus displayed a high genetic barrier to resistance against GPC-N114. By contrast, EMCV, a cardiovirus, rapidly acquired resistance due to mutations in 3Dpol. In vitro polymerase activity assays showed that GPC-N114 i inhibited the elongation activity of recombinant CVB3 and EMCV 3Dpol, (ii had reduced activity against EMCV 3Dpol with the resistance mutations, and (iii was most efficient in inhibiting 3Dpol when added before the RNA template-primer duplex. Elucidation of a crystal structure of the inhibitor bound to CVB3 3Dpol confirmed the RNA-binding channel as the target for GPC-N114. Docking studies of the compound into the crystal structures of the compound-resistant EMCV 3Dpol mutants suggested that the resistant phenotype is due to subtle changes that interfere with the binding of GPC-N114 but not of the RNA template-primer. In conclusion, this study presents the first NNI that targets the RNA template channel of the picornavirus polymerase and identifies a new pocket that can be used for the design of broad-spectrum inhibitors. Moreover, this study provides important new insight

Response of non-added solutes during nutrient addition experiments in streams

Science.gov (United States)

Rodriguez-Cardona, B.; Wymore, A.; Koenig, L.; Coble, A. A.; McDowell, W. H.

2015-12-01

Nutrient addition experiments, such as Tracer Additions for Spiraling Curve Characterization (TASCC), have become widely popular as a means to study nutrient uptake dynamics in stream ecosystems. However, the impact of these additions on ambient concentrations of non-added solutes is often overlooked. TASCC addition experiments are ideal for assessing interactions among solutes because it allows for the characterization of multiple solute concentrations across a broad range of added nutrient concentrations. TASCC additions also require the addition of a conservative tracer (NaCl) to track changes in conductivity during the experimental manipulation. Despite its use as a conservative tracer, chloride (Cl) and its associated sodium (Na) might change the concentrations of other ions and non-added nutrients through ion exchange or other processes. Similarly, additions of biologically active solutes might change the concentrations of other non-added solutes. These methodological issues in nutrient addition experiments have been poorly addressed in the literature. Here we examine the response of non-added solutes to pulse additions (i.e. TASCC) of NaCl plus nitrate (NO3-), ammonium, and phosphate across biomes including temperate and tropical forests, and arctic taiga. Preliminary results demonstrate that non-added solutes respond to changes in the concentration of these added nutrients. For example, concentrations of dissolved organic nitrogen (DON) in suburban headwater streams of New Hampshire both increase and decrease in response to NO3- additions, apparently due to biotic processes. Similarly, cations such as potassium, magnesium, and calcium also increase during TASCC experiments, likely due to cation exchange processes associated with Na addition. The response of non-added solutes to short-term pulses of added nutrients and tracers needs to be carefully assessed to ensure that nutrient uptake metrics are accurate, and to detect biotic interactions that may

Effects of polyamines and methylglyoxal bis(guanylhydrazone) on hepatic nuclear structure and deoxyribonucleic acid template activity.

Science.gov (United States)

Brown, K B; Nelson, N F; Brown, D G

1975-12-01

1. The interaction of polyamines and methylglyoxal bis(guanythydrazone) (1, 1'-[(methylethanediylidene)-dinitrilo]diguanidine) with isolated rat liver nuclei was investigated by electron microscopy. 2. At 4mM, putrescine was without effect; however, spermidine, spermine or methylglyoxal bis(guanythydrazone) resulted in dispersed chromatin and alterations in nucleolar structure. In addition, spermidine or methylglyoxal bis(guanylhydrazone) caused marked aggregation of interchromatin granules. 3. The DNA template property of calf thymus DNA was examined by using DNA polymerases from Escherichia coli, Micrococcus lysodeikticus and calf thymus in the presence of 0-5 mM-amine. 4. In the presence of DNA polymerase, spermine or methylglyoxal bis(guanylhydrazone) inhibited activity, whereas putrescine or spermidine had much less effect or in some cases stimulated [3H]dTMP incorporation. 5. Template activity which was inhibited by spermine or methylglyoxal bis(guanylhydrazone) could be partially restored by additional DNA or enzyme. 6. When mixed with calf thymus DNA, calf thymus histone inhibited template activity as measured with E. coli DNA polymerase. The template activity of such a 'histone-nucleate' could not be restored by putrescine, spermidine, spermine or methylglyoxal bis(guanylhydrazone). 7. DNA template activity of isolated rat liver nuclei was tested by using E. coli DNA polymerase. None of the amines was able to increase the template activity of the nuclear DNA in vitro.

Studies on the formation of hierarchical zeolite T aggregates with well-defined morphology in different template systems

Science.gov (United States)

Yin, Xiaoyan; Chu, Naibo; Lu, Xuewei; Li, Zhongfang; Guo, Hong

2016-01-01

In this paper, the disk-like and pumpkin-like hierarchical zeolite T aggregates consisted of primary nano-grains have been hydrothermally synthesized with and without the aid of the second template. The first template is used with tetramethylammonium hydroxide (TMAOH) and the second template is used with triethanolamine (TEA) or polyving akohol (PVA). A combination of characterization techniques, including XRD, SEM, TEM and N2 adsorption-desorption to examine the crystal crystallinity, morphology and surface properties of hierarchical zeolite T aggregates. In the single-template preparation process, the two-step varying-temperature treatment has been used to improve the meso-porosity of zeolite T aggregates. In the double-template preparation process, the amounts of PVA or TEA on the crystallinity, morphology and meso-porosity of zeolite T aggregates have been studied. It has been proved that the interstitial voids between the primary grains of aggregates are the origin of additional mesopores of samples. The micro- and meso-porosities of samples prepared with and without the second template have been contrasted in detail at last. In particular, the sample synthesized with the addition of PVA presents a hierarchical pore structure with the highest Sext value of 122 m2/g and Vmeso value of 0.255 cm3/g.

Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1.

Science.gov (United States)

Le Gall, O; Candresse, T; Brault, V; Dunez, J

1989-10-11

The nucleotide sequence of the RNA1 of hungarian grapevine chrome mosaic virus, a nepovirus very closely related to tomato black ring virus, has been determined from cDNA clones. It is 7212 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame extending from nucleotides 216 to 6971. The presumably encoded polyprotein is 2252 amino acids in length with a molecular weight of 250 kDa. The primary structure of the polyprotein was compared with that of other viral polyproteins, revealing the same general genetic organization as that of other picorna-like viruses (comoviruses, potyviruses and picornaviruses), except that an additional protein is suspected to occupy the N-terminus of the polyprotein.

2D vector-cyclic deformable templates

DEFF Research Database (Denmark)

Schultz, Nette; Conradsen, Knut

1998-01-01

In this paper the theory of deformable templates is a vector cycle in 2D is described. The deformable template model originated in (Grenander, 1983) and was further investigated in (Grenander et al., 1991). A template vector distribution is induced by parameter distribution from transformation...... matrices applied to the vector cycle. An approximation in the parameter distribution is introduced. The main advantage by using the deformable template model is the ability to simulate a wide range of objects trained by e.g. their biological variations, and thereby improve restoration, segmentation...... and probabillity measurement. The case study concerns estimation of meat percent in pork carcasses. Given two cross-sectional images - one at the front and one near the ham of the carcass - the areas of lean and fat and a muscle in the lean area are measured automatically by the deformable templates....

Antinociceptive effect of purine nucleotides.

Science.gov (United States)

Mello, C F; Begnini, J; De-La-Vega, D D; Lopes, F P; Schwartz, C C; Jimenez-Bernal, R E; Bellot, R G; Frussa-Filho, R

1996-10-01

The antinociceptive effect of purine nucleotides administered systematically (sc) was determined using the formalin and writhing tests in adult male albino mice. The mechanisms underlying nucleotide-induced antinociception were investigated by preinjecting the animals (sc) with specific antagonists for opioid (naloxone, 1 mg/kg), purinergic P1 (caffeine, 5, 10, of 30 mg/kg); theophylline, 10 mg/kg) or purinergic P2 receptors (suramin, 100 mg/kg; Coomassie blue, 30-300 mg/kg; quinidine, 10 mg/kg). Adenosine, adenosine monophosphate (AMP), diphosphate (ADP) and triphosphate (ATP) caused a reduction in the number of writhes and in the time of licking the formalin-injected paw. Naloxone had no effect on adenosine- or adenine nucleotide-induced antinociception. Caffeine (30 mg/kg) and theophylline (10 mg/kg) reversed the antinociceptive action of adenosine and adenine nucleotide derivatives in both tests. P2 antagonists did not reverse adenine nucleotide-induced antinociception. These results suggest that antinociceptive effect of adenine nucleotides is mediated by adenosine.

Accuracy of templating the acetabular cup size in Total Hip Replacement using conventional acetate templates on digital radiographs.

Science.gov (United States)

Krishnamoorthy, Vignesh P; Perumal, Rajamani; Daniel, Alfred J; Poonnoose, Pradeep M

2015-12-01

Templating of the acetabular cup size in Total Hip Replacement (THR) is normally done using conventional radiographs. As these are being replaced by digital radiographs, it has become essential to create a technique of templating using digital films. We describe a technique that involves templating the digital films using the universally available acetate templates for THR without the use of special software. Preoperative digital radiographs of the pelvis were taken with a 30 mm diameter spherical metal ball strapped over the greater trochanter. Using standard acetate templates provided by the implant company on magnified digital radiographs, the size of the metal ball (X mm) and acetabular cup (Y mm) were determined. The size of the acetabular cup to be implanted was estimated using the formula 30*Y/X. The estimated size was compared with the actual size of the cup used at surgery. Using this technique, it was possible to accurately predict the acetabular cup size in 28/40 (70%) of the hips. When the accuracy to within one size was considered, templating was correct in 90% (36/40). When assessed by two independent observers, there was good intra-observer and inter-observer reliability with intra-class correlation coefficient values greater than 0.8. It was possible to accurately and reliably predict the size of the acetabular cup, using acetate templates on digital films, without any digital templates.

Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs)

DEFF Research Database (Denmark)

Udatha, D B R K Gupta; Rasmussen, Simon; Sicheritz-Pontén, Thomas

2013-01-01

The non-synonymous SNPs, the so-called non-silent SNPs, which are single-nucleotide variations in the coding regions that give "birth" to amino acid mutations, are often involved in the modulation of protein function. Understanding the effect of individual amino acid mutations on a protein...

Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

Energy Technology Data Exchange (ETDEWEB)

Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland); Co, Nguyen Truong [Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam); Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam); Nguyen, Phuong H. [Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan, E-mail: masli@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)

2015-04-14

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

Preparation of micro/nanostructure TiO2 spheres by controlling pollen as hard template and soft template.

Science.gov (United States)

Yang, Xiaohui; Xu, Bin; Zhang, Xuehong; Song, Xiuqin; Chen, Rufen

2014-09-01

In this paper, micro/nanostructure TiO2 spheres were synthesized by a sunflower pollen induced and self-assembly mineralization process, in which a titania precursor and pollen reacted in one-pot at normal pressure. In this paper, the bio-template advantage, as hard and soft template is fully demonstrated. The superiority of our synthesis is that we not only can control pollen as hard template, but also can control it as soft template only by changing reactions temperature. Under 80 degrees C of water bath, TiO2 microspheres which replicated the morphology of pollen were prepared by controlling pollen as hard template. Under 100 degrees C, hierarchical TiO2 spheres with complicated morphology, different from pollen template, were synthesized by using pollen as soft template. At the same time, judicious choice of the amount of pollen affords the synthesis of hierarchical structures spheres with adjustable morphology and crystal structure. The morphology can be tuned from microspheres constructed from TiO2 nanorods to nanospheres constructed from TiO2 nanoparticles, and the crystal structure can be tuned from rutile to anatase. More over this anatase phase can be keep better even at high temperature of 1000 degrees C. The as-prepared micro/nano structure photocatalysts not only have high photocatalytic activities, but also have good separability and reuse performance.

The arabidopsis cyclic nucleotide interactome

KAUST Repository

Donaldson, Lara Elizabeth

2016-05-11

Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

Biometric templates selection and update using quality measures

Science.gov (United States)

Abboud, Ali J.; Jassim, Sabah A.

2012-06-01

To deal with severe variation in recording conditions, most biometric systems acquire multiple biometric samples, at the enrolment stage, for the same person and then extract their individual biometric feature vectors and store them in the gallery in the form of biometric template(s), labelled with the person's identity. The number of samples/templates and the choice of the most appropriate templates influence the performance of the system. The desired biometric template(s) selection technique must aim to control the run time and storage requirements while improving the recognition accuracy of the biometric system. This paper is devoted to elaborating on and discussing a new two stages approach for biometric templates selection and update. This approach uses a quality-based clustering, followed by a special criterion for the selection of an ultimate set of biometric templates from the various clusters. This approach is developed to select adaptively a specific number of templates for each individual. The number of biometric templates depends mainly on the performance of each individual (i.e. gallery size should be optimised to meet the needs of each target individual). These experiments have been conducted on two face image databases and their results will demonstrate the effectiveness of proposed quality-guided approach.

Optimizing preventive maintenance with maintenance templates

International Nuclear Information System (INIS)

Dozier, I.J.

1996-01-01

Rising operating costs has caused maintenance professionals to rethink their strategy for preventive maintenance (PM) programs. Maintenance Templates are pre-engineered PM task recommendations for a component type based on application of the component. Development of the maintenance template considers the dominant failure cause of the component and the type of preventive maintenance that can predict or prevent the failure from occurring. Maintenance template development also attempts to replace fixed frequency tasks with condition monitoring tasks such as vibration analysis or thermography. For those components that have fixed frequency PM intervals, consideration is given to the maintenance drivers such as criticality, environment and usage. This helps to maximize the PM frequency intervals and maximize the component availability. Maintenance Templates have been used at PECO Energy's Limerick Generating Station during the Reliability Centered Maintenance (RCM) Process to optimize their PM program. This paper describes the development and uses of the maintenance templates

Single nucleotide polymorphisms as susceptibility, prognostic, and therapeutic markers of nonsmall cell lung cancer

Directory of Open Access Journals (Sweden)

Zienolddiny S

2011-12-01

Full Text Available Shanbeh Zienolddiny, Vidar SkaugSection for Toxicology and Biological Work Environment, National Institute of Occupational Health, Oslo, NorwayAbstract: Lung cancer is a major public health problem throughout the world. Among the most frequent cancer types (prostate, breast, colorectal, stomach, lung, lung cancer is the leading cause of cancer-related deaths worldwide. Among the two major subtypes of small cell lung cancer and nonsmall cell lung cancer (NSCLC, 85% of tumors belong to the NSCLC histological types. Small cell lung cancer is associated with the shortest survival time. Although tobacco smoking has been recognized as the major risk factor for lung cancer, there is a great interindividual and interethnic difference in risk of developing lung cancer given exposure to similar environmental and lifestyle factors. This may indicate that in addition to chemical and environmental factors, genetic variations in the genome may contribute to risk modification. A common type of genetic variation in the genome, known as single nucleotide polymorphism, has been found to be associated with susceptibility to lung cancer. Interestingly, many of these polymorphisms are found in the genes that regulate major pathways of carcinogen metabolism (cytochrome P450 genes, detoxification (glutathione S-transferases, adduct removal (DNA repair genes, cell growth/apoptosis (TP53/MDM2, the immune system (cytokines/chemokines, and membrane receptors (nicotinic acetylcholine and dopaminergic receptors. Some of these polymorphisms have been shown to alter the level of mRNA, and protein structure and function. In addition to being susceptibility markers, several of these polymorphisms are emerging to be important for response to chemotherapy/radiotherapy and survival of patients. Therefore, it is hypothesized that single nucleotide polymorphisms will be valuable genetic markers in individual-based prognosis and therapy in future. Here we will review some of the most

Adsorption of nucleotides onto ferromagnesian phyllosilicates: Significance for the origin of life

Science.gov (United States)

Pedreira-Segade, Ulysse; Feuillie, Cécile; Pelletier, Manuel; Michot, Laurent J.; Daniel, Isabelle

2016-03-01

saturation of lateral surfaces. Below pH 4, swelling clays also adsorb nucleotides through cation exchange on basal surfaces, whereas non-swelling phyllosilicates do not. However, at high surface loadings an additional mechanism stabilizing adsorption occurs. Given the proposed adsorption mechanisms, the possibility of a favorable polymerization at the mineral-water interface is discussed. We propose that Fe-Mg rich phyllosilicates tightly bind nucleotides, under ambient conditions, and concentrate them up to 1000 times the solution concentration upon saturation. Nontronites have the most diverse and favorable adsorption behaviors and could have helped to the concentration and polymerization of nucleotides under primitive Earth-like conditions.

Selection of appropriate template for spatial normalization of brain images: tensor based morphometry

Energy Technology Data Exchange (ETDEWEB)

Lee, Jae Sung; Lee, Dong Soo; Kim, Yu Kyeong; Chung, June Key; Lee, Myung Chul [College of Medicine, Seoul National University, Seoul (Korea, Republic of)

2004-07-01

Although there have been remarkable advances in spatial normalization techniques, the differences in the shape of the hemispheres and the sulcal pattern of brains relative to age, gender, races, and diseases cannot be fully overcome by the nonlinear spatial normalization techniques. T1 SPGR MR images in 16 elderly male normal volunteers (>55 y. mean age: = 61.8 {+-} 3.5 y) were spatially normalized onto the age/gender specific Korean templates, and the Caucasian MNI template and the extent of the deformations were compared. These particular subjects were never included in the development of the templates. First , the images were matched into the templates using an affine transformation to eliminate the global difference between the templates and source images. Second the affine registration was followed by an estimation of nonlinear deformation. Determinants of the Jacobian matrices of the nonlinear deformation were then calculated for every voxel to estimate the regional volume change during the nonlinear transformation Jacobian determinant images highlighted the great magnitude of the relative local volume changes obtained when the elderly brains were spatially normalized onto the young/midlife male or female templates. They reflect the enlargement of CSF space in the lateral ventricles, sylvian fissures and cisterna magna, and the shrinkage of the cortex noted mainly in frontal, insular and lateral temporal cortexes, and the cerebellums in the aged brains. In the Jacobian determinant images, a regional shrinkage of the brain in the left middle prefrontal cortex was observed in addition to the regional expansion in the ventricles and sylvian fissures, which may be due to the age differences between the template and source images. The regional anatomical difference between template and source images could impose an extreme deformation of the source images during the spatial normalization and therefore. Individual brains should be placed into the appropriate

Selection of appropriate template for spatial normalization of brain images: tensor based morphometry

International Nuclear Information System (INIS)

Lee, Jae Sung; Lee, Dong Soo; Kim, Yu Kyeong; Chung, June Key; Lee, Myung Chul

2004-01-01

Although there have been remarkable advances in spatial normalization techniques, the differences in the shape of the hemispheres and the sulcal pattern of brains relative to age, gender, races, and diseases cannot be fully overcome by the nonlinear spatial normalization techniques. T1 SPGR MR images in 16 elderly male normal volunteers (>55 y. mean age: = 61.8 ± 3.5 y) were spatially normalized onto the age/gender specific Korean templates, and the Caucasian MNI template and the extent of the deformations were compared. These particular subjects were never included in the development of the templates. First , the images were matched into the templates using an affine transformation to eliminate the global difference between the templates and source images. Second the affine registration was followed by an estimation of nonlinear deformation. Determinants of the Jacobian matrices of the nonlinear deformation were then calculated for every voxel to estimate the regional volume change during the nonlinear transformation Jacobian determinant images highlighted the great magnitude of the relative local volume changes obtained when the elderly brains were spatially normalized onto the young/midlife male or female templates. They reflect the enlargement of CSF space in the lateral ventricles, sylvian fissures and cisterna magna, and the shrinkage of the cortex noted mainly in frontal, insular and lateral temporal cortexes, and the cerebellums in the aged brains. In the Jacobian determinant images, a regional shrinkage of the brain in the left middle prefrontal cortex was observed in addition to the regional expansion in the ventricles and sylvian fissures, which may be due to the age differences between the template and source images. The regional anatomical difference between template and source images could impose an extreme deformation of the source images during the spatial normalization and therefore. Individual brains should be placed into the appropriate template

Different effects of guanine nucleotides (GDP and GTP) on protein-mediated mitochondrial proton leak.

Science.gov (United States)

Woyda-Ploszczyca, Andrzej M; Jarmuszkiewicz, Wieslawa

2014-01-01

In this study, we compared the influence of GDP and GTP on isolated mitochondria respiring under conditions favoring oxidative phosphorylation (OXPHOS) and under conditions excluding this process, i.e., in the presence of carboxyatractyloside, an adenine nucleotide translocase inhibitor, and/or oligomycin, an FOF1-ATP synthase inhibitor. Using mitochondria isolated from rat kidney and human endothelial cells, we found that the action of GDP and GTP can differ diametrically depending on the conditions. Namely, under conditions favoring OXPHOS, both in the absence and presence of linoleic acid, an activator of uncoupling proteins (UCPs), the addition of 1 mM GDP resulted in the state 4 (non-phosphorylating respiration)-state 3 (phosphorylating respiration) transition, which is characteristic of ADP oxidative phosphorylation. In contrast, the addition of 1 mM GTP resulted in a decrease in the respiratory rate and an increase in the membrane potential, which is characteristic of UCP inhibition. The stimulatory effect of GDP, but not GTP, was also observed in inside-out submitochondrial particles prepared from rat kidney mitochondria. However, the effects of GDP and GTP were more similar in the presence of OXPHOS inhibitors. The importance of these observations in connection with the action of UCPs, adenine nucleotide translocase (or other carboxyatractyloside-sensitive carriers), carboxyatractyloside- and purine nucleotide-insensitive carriers, as well as nucleoside-diphosphate kinase (NDPK) are considered. Because the measurements favoring oxidative phosphorylation better reflect in vivo conditions, our study strongly supports the idea that GDP cannot be considered a significant physiological inhibitor of UCP. Moreover, it appears that, under native conditions, GTP functions as a more efficient UCP inhibitor than GDP and ATP.

[The template principle: paradigm of modern genetics].

Science.gov (United States)

Inge-Vechtomov, S G

2013-01-01

The idea of continuity in living systems, which was initially developed in mid-19th century, reached its peak in 1928 thanks to N.K. Koltsov, who proposed the template principle in chromosome reproduction. The determination of genetic functions of nucleic acids and the advent of molecular genetics led to F. Crick's statement of the central dogma of molecular biology in 1958. This dogma became a contemporary version of the template principle (templates of the first order). The discovery of "protein inheritance" underlay the notion of steric or conformational templates (second order) for reproducing conformation in a number of proteins. The template principle supplemented by this notion claims to be the main paradigm of modern genetics.

Hard template synthesis of metal nanowires

OpenAIRE

Kawamura, Go; Muto, Hiroyuki; Matsuda, Atsunori

2014-01-01

Metal nanowires (NWs) have attracted much attention because of their high electron conductivity, optical transmittance, and tunable magnetic properties. Metal NWs have been synthesized using soft templates such as surface stabilizing molecules and polymers, and hard templates such as anodic aluminum oxide, mesoporous oxide, carbon nanotubes. NWs prepared from hard templates are composites of metals and the oxide/carbon matrix. Thus, selecting appropriate elements can simplify the production o...

An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

Science.gov (United States)

Valdés-Hernández, Pedro Antonio; Sumiyoshi, Akira; Nonaka, Hiroi; Haga, Risa; Aubert-Vásquez, Eduardo; Ogawa, Takeshi; Iturria-Medina, Yasser; Riera, Jorge J.; Kawashima, Ryuta

2011-01-01

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies. PMID:22275894

An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats.

Science.gov (United States)

Valdés-Hernández, Pedro Antonio; Sumiyoshi, Akira; Nonaka, Hiroi; Haga, Risa; Aubert-Vásquez, Eduardo; Ogawa, Takeshi; Iturria-Medina, Yasser; Riera, Jorge J; Kawashima, Ryuta

2011-01-01

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies.

Learning templates for artistic portrait lighting analysis.

Science.gov (United States)

Chen, Xiaowu; Jin, Xin; Wu, Hongyu; Zhao, Qinping

2015-02-01

Lighting is a key factor in creating impressive artistic portraits. In this paper, we propose to analyze portrait lighting by learning templates of lighting styles. Inspired by the experience of artists, we first define several novel features that describe the local contrasts in various face regions. The most informative features are then selected with a stepwise feature pursuit algorithm to derive the templates of various lighting styles. After that, the matching scores that measure the similarity between a testing portrait and those templates are calculated for lighting style classification. Furthermore, we train a regression model by the subjective scores and the feature responses of a template to predict the score of a portrait lighting quality. Based on the templates, a novel face illumination descriptor is defined to measure the difference between two portrait lightings. Experimental results show that the learned templates can well describe the lighting styles, whereas the proposed approach can assess the lighting quality of artistic portraits as human being does.

Template Generation and Selection Algorithms

NARCIS (Netherlands)

Guo, Y.; Smit, Gerardus Johannes Maria; Broersma, Haitze J.; Heysters, P.M.; Badaway, W.; Ismail, Y.

The availability of high-level design entry tooling is crucial for the viability of any reconfigurable SoC architecture. This paper presents a template generation method to extract functional equivalent structures, i.e. templates, from a control data flow graph. By inspecting the graph the algorithm

Bioinformatic Analysis of Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs in the Coding Regions of Human Prion Protein Gene (PRNP

Directory of Open Access Journals (Sweden)

Kourosh Bamdad

2016-12-01

Full Text Available Background & Objective: Single nucleotide polymorphisms are the cause of genetic variation to living organisms. Single nucleotide polymorphisms alter residues in the protein sequence. In this investigation, the relationship between prion protein gene polymorphisms and its relevance to pathogenicity was studied. Material & Method: Amino acid sequence of the main isoform from the human prion protein gene (PRNP was extracted from UniProt database and evaluated by FoldAmyloid and AmylPred servers. All non-synonymous single nucleotide polymorphisms (nsSNPs from SNP database (dbSNP were further analyzed by bioinformatics servers including SIFT, PolyPhen-2, I-Mutant-3.0, PANTHER, SNPs & GO, PHD-SNP, Meta-SNP, and MutPred to determine the most damaging nsSNPs. Results: The results of the first structure analyses by FoldAmyloid and AmylPerd servers implied that regions including 5-15, 174-178, 180-184, 211-217, and 240-252 were the most sensitive parts of the protein sequence to amyloidosis. Screening all nsSNPs of the main protein isoform using bioinformatic servers revealed that substitution of Aspartic acid with Valine at position 178 (ID code: rs11538766 was the most deleterious nsSNP in the protein structure. Conclusion:  Substitution of the Aspartic acid with Valine at position 178 (D178V was the most pathogenic mutation in the human prion protein gene. Analyses from the MutPred server also showed that beta-sheets’ increment in the secondary structure was the main reason behind the molecular mechanism of the prion protein aggregation.

Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator.

Science.gov (United States)

Fenati, Renzo A; Connolly, Ashley R; Ellis, Amanda V

2017-02-15

Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded-DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP-Cytosine > TPP-Thymine > TPP-Adenine ≥ TPP-Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80-90% quenching), compared to 25-30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. Copyright © 2016 Elsevier B.V. All rights reserved.

images_template

Data.gov (United States)

National Aeronautics and Space Administration — Images for the website template go here. It will not change their names or locations, but will hopefully help to organize them. Oh, but for a directory structure...

Synthesis of platinum nanowheels using a bicellar template.

Science.gov (United States)

Song, Yujiang; Dorin, Rachel M; Garcia, Robert M; Jiang, Ying-Bing; Wang, Haorong; Li, Peng; Qiu, Yan; van Swol, Frank; Miller, James E; Shelnutt, John A

2008-09-24

Disk-like surfactant bicelles provide a unique meso-structured reaction environment for templating the wet-chemical reduction of platinum(II) salt by ascorbic acid to produce platinum nanowheels. The Pt wheels are 496 +/-55 nm in diameter and possess thickened centers and radial dendritic nanosheets (about 2-nm in thickness) culminating in flared dendritic rims. The structural features of the platinum wheels arise from confined growth of platinum within the bilayer that is also limited at edges of the bicelles. The size of CTAB/FC7 bicelles is observed to evolve with the addition of Pt(II) complex and ascorbic acid. Synthetic control is demonstrated by varying the reaction parameters including metal salt concentration, temperature, and total surfactant concentration. This study opens up opportunities for the use of other inhomogeneous soft templates for synthesizing metals, metal alloys, and possibly semiconductors with complex nanostructures.

Computational Analysis of Single Nucleotide Polymorphisms Associated with Altered Drug Responsiveness in Type 2 Diabetes

Directory of Open Access Journals (Sweden)

Valerio Costa

2016-06-01

Full Text Available Type 2 diabetes (T2D is one of the most frequent mortality causes in western countries, with rapidly increasing prevalence. Anti-diabetic drugs are the first therapeutic approach, although many patients develop drug resistance. Most drug responsiveness variability can be explained by genetic causes. Inter-individual variability is principally due to single nucleotide polymorphisms, and differential drug responsiveness has been correlated to alteration in genes involved in drug metabolism (CYP2C9 or insulin signaling (IRS1, ABCC8, KCNJ11 and PPARG. However, most genome-wide association studies did not provide clues about the contribution of DNA variations to impaired drug responsiveness. Thus, characterizing T2D drug responsiveness variants is needed to guide clinicians toward tailored therapeutic approaches. Here, we extensively investigated polymorphisms associated with altered drug response in T2D, predicting their effects in silico. Combining different computational approaches, we focused on the expression pattern of genes correlated to drug resistance and inferred evolutionary conservation of polymorphic residues, computationally predicting the biochemical properties of polymorphic proteins. Using RNA-Sequencing followed by targeted validation, we identified and experimentally confirmed that two nucleotide variations in the CAPN10 gene—currently annotated as intronic—fall within two new transcripts in this locus. Additionally, we found that a Single Nucleotide Polymorphism (SNP, currently reported as intergenic, maps to the intron of a new transcript, harboring CAPN10 and GPR35 genes, which undergoes non-sense mediated decay. Finally, we analyzed variants that fall into non-coding regulatory regions of yet underestimated functional significance, predicting that some of them can potentially affect gene expression and/or post-transcriptional regulation of mRNAs affecting the splicing.

A Nucleotide Phosphatase Activity in the Nucleotide Binding Domain of an Orphan Resistance Protein from Rice*

Science.gov (United States)

Fenyk, Stepan; de San Eustaquio Campillo, Alba; Pohl, Ehmke; Hussey, Patrick J.; Cann, Martin J.

2012-01-01

Plant resistance proteins (R-proteins) are key components of the plant immune system activated in response to a plethora of different pathogens. R-proteins are P-loop NTPase superfamily members, and current models describe their main function as ATPases in defense signaling pathways. Here we show that a subset of R-proteins have evolved a new function to combat pathogen infection. This subset of R-proteins possesses a nucleotide phosphatase activity in the nucleotide-binding domain. Related R-proteins that fall in the same phylogenetic clade all show the same nucleotide phosphatase activity indicating a conserved function within at least a subset of R-proteins. R-protein nucleotide phosphatases catalyze the production of nucleoside from nucleotide with the nucleotide monophosphate as the preferred substrate. Mutation of conserved catalytic residues substantially reduced activity consistent with the biochemistry of P-loop NTPases. Kinetic analysis, analytical gel filtration, and chemical cross-linking demonstrated that the nucleotide-binding domain was active as a multimer. Nuclear magnetic resonance and nucleotide analogues identified the terminal phosphate bond as the target of a reaction that utilized a metal-mediated nucleophilic attack by water on the phosphoester. In conclusion, we have identified a group of R-proteins with a unique function. This biochemical activity appears to have co-evolved with plants in signaling pathways designed to resist pathogen attack. PMID:22157756

A nucleotide phosphatase activity in the nucleotide binding domain of an orphan resistance protein from rice.

Science.gov (United States)

Fenyk, Stepan; Campillo, Alba de San Eustaquio; Pohl, Ehmke; Hussey, Patrick J; Cann, Martin J

2012-02-03

Plant resistance proteins (R-proteins) are key components of the plant immune system activated in response to a plethora of different pathogens. R-proteins are P-loop NTPase superfamily members, and current models describe their main function as ATPases in defense signaling pathways. Here we show that a subset of R-proteins have evolved a new function to combat pathogen infection. This subset of R-proteins possesses a nucleotide phosphatase activity in the nucleotide-binding domain. Related R-proteins that fall in the same phylogenetic clade all show the same nucleotide phosphatase activity indicating a conserved function within at least a subset of R-proteins. R-protein nucleotide phosphatases catalyze the production of nucleoside from nucleotide with the nucleotide monophosphate as the preferred substrate. Mutation of conserved catalytic residues substantially reduced activity consistent with the biochemistry of P-loop NTPases. Kinetic analysis, analytical gel filtration, and chemical cross-linking demonstrated that the nucleotide-binding domain was active as a multimer. Nuclear magnetic resonance and nucleotide analogues identified the terminal phosphate bond as the target of a reaction that utilized a metal-mediated nucleophilic attack by water on the phosphoester. In conclusion, we have identified a group of R-proteins with a unique function. This biochemical activity appears to have co-evolved with plants in signaling pathways designed to resist pathogen attack.

The INIA19 template and NeuroMaps atlas for primate brain image parcellation and spatial normalization

Directory of Open Access Journals (Sweden)

Torsten eRohlfing

2012-12-01

Full Text Available The INIA19 is a new, high-quality template for imaging-based studies of non-human primate brains created from high-resolution T1-weighted magnetic resonance (MR images of 19 rhesus macaque (Macaca mulatta animals. Combined with the comprehensive cortical and subcortical label map of the NeuroMaps atlas, the INIA19 is equally suitable for studies requiring both spatial normalization and atlas label propagation. Population-averaged template images are provided for both the brain and the whole head, to allow alignment of the atlas with both skull-stripped and unstripped data, and thus to facilitate its use for skull stripping of new images. This article describes the construction of the template using freely-available software tools, as well as the template itself, which is being made available to the scientific community (http://nitrc.org/projects/inia19/.

Effects of Dietary Nucleotides on Growth Rate and Disease ...

African Journals Online (AJOL)

Nucleotides are low molecular weight biological compounds, which are ... nutrition and disease aspects of crustaceans (Overton and Bland 1981 .... additives on growth and disease resistance. Effects of ... metabolically active cells during stressful conditions ... in humans supplemented with Uracyl, which resulted in optimal ...

Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D.

Science.gov (United States)

Zhu, Hui; Bhattarai, Hitesh; Yan, Han-Guang; Shuman, Stewart; Glickman, Michael S

2012-12-21

Mycobacteria exploit nonhomologous end-joining (NHEJ) to repair DNA double-strand breaks. The core NHEJ machinery comprises the homodimeric DNA end-binding protein Ku and DNA ligase D (LigD), a modular enzyme composed of a C-terminal ATP-dependent ligase domain (LIG), a central 3'-phosphoesterase domain (PE), and an N-terminal polymerase domain (POL). LigD POL is proficient at adding templated and nontemplated deoxynucleotides and ribonucleotides to DNA ends in vitro and is the catalyst in vivo of unfaithful NHEJ events involving nontemplated single-nucleotide additions to blunt DSB ends. Here, we identify two mycobacterial proteins, PolD1 and PolD2, as stand-alone homologues of the LigD POL domain. Biochemical characterization of PolD1 and PolD2 shows that they resemble LigD POL in their monomeric quaternary structures, their ability to add templated and nontemplated nucleotides to primer-templates and blunt ends, and their preference for rNTPs versus dNTPs. Deletion of polD1, polD2, or both from a Mycobacterium smegmatis strain carrying an inactivating mutation in LigD POL failed to reveal a role for PolD1 or PolD2 in templated nucleotide additions during NHEJ of 5'-overhang DSBs or in clastogen resistance. Whereas our results document the existence and characteristics of new stand-alone members of the LigD POL family of RNA/DNA polymerases, they imply that other polymerases can perform fill-in synthesis during mycobacterial NHEJ.

Non-additive dissipation in open quantum networks out of equilibrium

Science.gov (United States)

Mitchison, Mark T.; Plenio, Martin B.

2018-03-01

We theoretically study a simple non-equilibrium quantum network whose dynamics can be expressed and exactly solved in terms of a time-local master equation. Specifically, we consider a pair of coupled fermionic modes, each one locally exchanging energy and particles with an independent, macroscopic thermal reservoir. We show that the generator of the asymptotic master equation is not additive, i.e. it cannot be expressed as a sum of contributions describing the action of each reservoir alone. Instead, we identify an additional interference term that generates coherences in the energy eigenbasis, associated with the current of conserved particles flowing in the steady state. Notably, non-additivity arises even for wide-band reservoirs coupled arbitrarily weakly to the system. Our results shed light on the non-trivial interplay between multiple thermal noise sources in modular open quantum systems.

Study of excess carrier dynamics in polar, semi-polar, and non-polar (In,Ga)N epilayers and QWs

Energy Technology Data Exchange (ETDEWEB)

Aleksiejunas, R. [Institute of Applied Research, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Laser Research Center, Vilnius University, Sauletekio Ave. 10, 10222 Vilnius (Lithuania); Lubys, L.; Jarasiunas, K. [Institute of Applied Research, Vilnius University, Sauletekio Ave. 9-III, 10222 Vilnius (Lithuania); Vengris, M. [Laser Research Center, Vilnius University, Sauletekio Ave. 10, 10222 Vilnius (Lithuania); Wernicke, T.; Hoffmann, V.; Netzel, C.; Knauer, A.; Weyers, M. [Ferdinand-Braun-Institut, Leibniz-Institut fuer Hoechstfrequenztechnik, Gustav-Kirchhoff-Str. 4, 12498 Berlin (Germany); Kneissl, M. [Ferdinand-Braun-Institut, Leibniz-Institut fuer Hoechstfrequenztechnik, Gustav-Kirchhoff-Str. 4, 12498 Berlin (Germany); Institute of Solid State Physics, Technische Universitaet Berlin, Hardenbergstr. 36, 10623 Berlin (Germany)

2011-07-15

We studied carrier recombination and diffusion in GaN/sapphire templates, (In,Ga)N layers, and (In,Ga)N quantum well structures oriented along the polar [0001], semi-polar [11-22], and non-polar [11-20] orientations by means of light induced transient grating, differential transmission, and photoluminescence optical techniques. We show that the lifetime of excess carriers drops by orders of magnitude when changing the orientation from polar to non-polar, both in GaN templates and (In,Ga)N layers. We attribute the shorter lifetime to carrier trapping by extended structural defects that are more abundant in non-polar grown samples. In addition, we observe pronounced carrier localization effects in the semi- and non-polar layers. We show that thick (In,Ga)N layers inherit the properties of the GaN templates. However, the thin quantum well structures show a lower carrier trapping activity. So, a better electrical quality can be assumed as compared to the thick (In,Ga)N layers. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Non-invasive prenatal detection of trisomy 21 using tandem single nucleotide polymorphisms.

Directory of Open Access Journals (Sweden)

Sujana Ghanta

Full Text Available BACKGROUND: Screening tests for Trisomy 21 (T21, also known as Down syndrome, are routinely performed for the majority of pregnant women. However, current tests rely on either evaluating non-specific markers, which lead to false negative and false positive results, or on invasive tests, which while highly accurate, are expensive and carry a risk of fetal loss. We outline a novel, rapid, highly sensitive, and targeted approach to non-invasively detect fetal T21 using maternal plasma DNA. METHODS AND FINDINGS: Highly heterozygous tandem Single Nucleotide Polymorphism (SNP sequences on chromosome 21 were analyzed using High-Fidelity PCR and Cycling Temperature Capillary Electrophoresis (CTCE. This approach was used to blindly analyze plasma DNA obtained from peripheral blood from 40 high risk pregnant women, in adherence to a Medical College of Wisconsin Institutional Review Board approved protocol. Tandem SNP sequences were informative when the mother was heterozygous and a third paternal haplotype was present, permitting a quantitative comparison between the maternally inherited haplotype and the paternally inherited haplotype to infer fetal chromosomal dosage by calculating a Haplotype Ratio (HR. 27 subjects were assessable; 13 subjects were not informative due to either low DNA yield or were not informative at the tandem SNP sequences examined. All results were confirmed by a procedure (amniocentesis/CVS or at postnatal follow-up. Twenty subjects were identified as carrying a disomy 21 fetus (with two copies of chromosome 21 and seven subjects were identified as carrying a T21 fetus. The sensitivity and the specificity of the assay was 100% when HR values lying between 3/5 and 5/3 were used as a threshold for normal subjects. CONCLUSIONS: In summary, a targeted approach, based on calculation of Haplotype Ratios from tandem SNP sequences combined with a sensitive and quantitative DNA measurement technology can be used to accurately detect fetal

Deficiency in nucleotide excision repair family gene activity, especially ERCC3, is associated with non-pigmented hair fiber growth.

Directory of Open Access Journals (Sweden)

Mei Yu

Full Text Available We conducted a microarray study to discover gene expression patterns associated with a lack of melanogenesis in non-pigmented hair follicles (HF by microarray. Pigmented and non-pigmented HFs were collected and micro-dissected into the hair bulb (HB and the upper hair sheaths (HS including the bulge region. In comparison to pigmented HS and HBs, nucleotide excision repair (NER family genes ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, XPA, NTPBP, HCNP, DDB2 and POLH exhibited statistically significantly lower expression in non- pigmented HS and HBs. Quantitative PCR verified microarray data and identified ERCC3 as highly differentially expressed. Immunohistochemistry confirmed ERCC3 expression in HF melanocytes. A reduction in ERCC3 by siRNA interference in human melanocytes in vitro reduced their tyrosinase production ability. Our results suggest that loss of NER gene function is associated with a loss of melanin production capacity. This may be due to reduced gene transcription and/or reduced DNA repair in melanocytes which may eventually lead to cell death. These results provide novel information with regard to melanogenesis and its regulation.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

Science.gov (United States)

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Bio-fabrication and physiological self-release of tissue equivalents using smart peptide amphiphile templates.

Science.gov (United States)

Gouveia, Ricardo M; Hamley, Ian W; Connon, Che J

2015-10-01

In this study we applied a smart biomaterial formed from a self-assembling, multi-functional synthetic peptide amphiphile (PA) to coat substrates with various surface chemistries. The combination of PA coating and alignment-inducing functionalised substrates provided a template to instruct human corneal stromal fibroblasts to adhere, become aligned and then bio-fabricate a highly-ordered, multi-layered, three-dimensional tissue by depositing an aligned, native-like extracellular matrix. The newly-formed corneal tissue equivalent was subsequently able to eliminate the adhesive properties of the template and govern its own complete release via the action of endogenous proteases. Tissues recovered through this method were structurally stable, easily handled, and carrier-free. Furthermore, topographical and mechanical analysis by atomic force microscopy showed that tissue equivalents formed on the alignment-inducing PA template had highly-ordered, compact collagen deposition, with a two-fold higher elastic modulus compared to the less compact tissues produced on the non-alignment template, the PA-coated glass. We suggest that this technology represents a new paradigm in tissue engineering and regenerative medicine, whereby all processes for the bio-fabrication and subsequent self-release of natural, bio-prosthetic human tissues depend solely on simple template-tissue feedback interactions.

Preparation of tailored carbons with meso- and micro- porosity via template synthesis route

Directory of Open Access Journals (Sweden)

Howard. M. Williams

2009-02-01

Full Text Available A low cost templating approach to making non-ordered carbons with a tailored meso/micropore structure is described. A series of mesoporous carbons was prepared from polyfurfuryl alcohol and phenolic resin precursors by a templating route, using a variety of commercially available silica gels as the template material. Carbons were produced with mesopore volumes up to 1 cm3 g-1, mesopore sizes in the range of 4 nm to 8 nm and surface areas in the range of 300 to 700 m2 g-1. These mesoporous carbons were subsequently activated in CO2 to add controlled amounts of microporosity to produce carbons with both a micro and mesoporous structure. Significantly, the activation process did not appreciably change the mesopore size distribution of the carbons. By altering the activation time, it was possible to tailor the micropore: mesopore volume ratios within wide limits.

Microporous silica prepared by organic templating: relationship between the molecular template and pore structure

International Nuclear Information System (INIS)

Brinker, C. Jeffrey; Cao, Guozhong; Kale, Rahul P.; Lopez, Gabriel P.; Lu, Yunfeng; Prabakar, S.

1999-01-01

Microporous silica materials with a controlled pore size and a narrow pore size distribution have been prepared by sol-gel processing using an organic-templating approach. Microporous networks were formed by pyrolytic removal of organic ligands (methacryloxypropyl groups) from organic/inorganic hybrid materials synthesized by copolymerization of 3-methacryloxypropylsilane (MPS) and tetraethoxysilane (TEOS). Molecular simulations and experimental measurements were conducted to examine the relationship between the microstructural characteristics of the porous silica (e.g., pore size, total pore volume, and pore connectivity) and the size and amount of organic template ligands added. Adsorption measurements suggest that the final porosity of the microporous silica is due to both primary pores (those present in the hybrid materials prior to pyrolysis) and secondary pores (those created by pyrolytic removal of organic templates). Primary pores were inaccessible to N(sub 2) at 77 K but accessible to CO(sub 2) at 195 K; secondary pores were accessible to both N(sub 2) (at 77 K) and CO(sub 2) (at 195 K) in adsorption measurements. Primary porosity decreases with the amount of organic ligands added because of the enhanced densification of MPS/TEOS hybrid materials as the mole fraction of trifunctional MPS moieties increases. pore volumes measured by nitrogen adsorption experiments at 77 K suggest that the secondary (template-derived) porosity exhibits a percolation behavior as the template concentration is increased. Gas permeation experiments indicate that the secondary pores are approximately 5(angstrom) in diameter, consistent with predictions based on molecular simulations

Smart Contract Templates: foundations, design landscape and research directions

OpenAIRE

Clack, Christopher D.; Bakshi, Vikram A.; Braine, Lee

2016-01-01

In this position paper, we consider some foundational topics regarding smart contracts (such as terminology, automation, enforceability, and semantics) and define a smart contract as an automatable and enforceable agreement. We explore a simple semantic framework for smart contracts, covering both operational and non-operational aspects, and describe templates and agreements for legally-enforceable smart contracts, based on legal documents. Building upon the Ricardian Contract, we identify op...

A light meson translatable template

International Nuclear Information System (INIS)

Allgower, C.E.; Peaslee, D.C.

2002-01-01

Recently surveyed (mass)2 values for I = 0, JPC = 2++ light mesons can be assembled into repeating patterns of 4 states, dubbed 'templates'. Within error, both internal and external template spacings approximate simple multiples of Δm2 ≅ 0.35 GeV2. Hopefully, this feature will be useful in predicting the positions of higher isoscalar 2++ states

PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

Science.gov (United States)

Belotserkovskii, Boris P; Hanawalt, Philip C

2015-11-01

Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

Adsorption of nucleotides onto Fe-Mg-Al rich swelling clays

Science.gov (United States)

Feuillie, Cécile; Daniel, Isabelle; Michot, Laurent J.; Pedreira-Segade, Ulysse

2013-11-01

Mineral surfaces may have played a role in the origin of the first biopolymers, by concentrating organic monomers from a dilute ocean. Swelling clays provide a high surface area for the concentration of prebiotic monomers, and have therefore been the subject of numerous investigations. In that context, montmorillonite, the most abundant swelling clay in modern environments, has been extensively studied with regard to adsorption and polymerization of nucleic acids. However, montmorillonite was probably rather marginal on the primitive ocean floor compared to iron-magnesium rich phyllosilicates such as nontronite that results from the hydrothermal alteration of a mafic or ultramafic oceanic crust. In the present paper, we study the adsorption of nucleotides on montmorillonite and nontronite, at various pH and ionic strength conditions plausible for Archean sea-water. A thorough characterization of the mineral surfaces shows that nucleotide adsorb mainly on the edge faces of the smectites by ligand exchange between the phosphate groups of the nucleotides and the -OH groups from the edge sites over a wide pH range (4-10). Nontronite is more reactive than montmorillonite. At low pH, additional ion exchange may play a role as the nucleotides become positively charged.

The arabidopsis cyclic nucleotide interactome

KAUST Repository

Donaldson, Lara Elizabeth; Meier, Stuart Kurt; Gehring, Christoph A

2016-01-01

Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms

Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

Science.gov (United States)

Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

2017-09-01

In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

Nucleotide Selectivity in Abiotic RNA Polymerization Reactions.

Science.gov (United States)

Coari, Kristin M; Martin, Rebecca C; Jain, Kopal; McGown, Linda B

2017-09-01

In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

New insights into the promoterless transcription of DNA coligo templates by RNA polymerase III.

Science.gov (United States)

Lama, Lodoe; Seidl, Christine I; Ryan, Kevin

2014-01-01

Chemically synthesized DNA can carry small RNA sequence information but converting that information into small RNA is generally thought to require large double-stranded promoters in the context of plasmids, viruses and genes. We previously found evidence that circularized oligodeoxynucleotides (coligos) containing certain sequences and secondary structures can template the synthesis of small RNA by RNA polymerase III in vitro and in human cells. By using immunoprecipitated RNA polymerase III we now report corroborating evidence that this enzyme is the sole polymerase responsible for coligo transcription. The immobilized polymerase enabled experiments showing that coligo transcripts can be formed through transcription termination without subsequent 3' end trimming. To better define the determinants of productive transcription, a structure-activity relationship study was performed using over 20 new coligos. The results show that unpaired nucleotides in the coligo stem facilitate circumtranscription, but also that internal loops and bulges should be kept small to avoid secondary transcription initiation sites. A polymerase termination sequence embedded in the double-stranded region of a hairpin-encoding coligo stem can antagonize transcription. Using lessons learned from new and old coligos, we demonstrate how to convert poorly transcribed coligos into productive templates. Our findings support the possibility that coligos may prove useful as chemically synthesized vectors for the ectopic expression of small RNA in human cells.

Review of Research on Template Methods in Preparation of Nanomaterials

Directory of Open Access Journals (Sweden)

Yadian Xie

2016-01-01

Full Text Available The nanomaterials have been widely used in various fields, such as photonics, catalysis, and adsorption, because of their unique physical and chemical properties. Therefore, their production methods are of utmost importance. Compared with traditional synthetic methods, the template method can effectively control the morphology, particle size, and structure during the preparation of nanomaterials, which is an effective method for their synthesis. The key for the template method is to choose different templates, which are divided into hard template and soft template according to their different structures. In this paper, the effects of different types of templates on the morphology of nanomaterials during their preparation are investigated from two aspects: hard template and soft template, combined with the mechanism of action.

Molecular recognition of nucleotides in micelles and the development and expansion of a chemistry outreach program

Science.gov (United States)

Schechinger, Linda Sue

I. To investigate the delivery of nucleotide-based drugs, we are studying molecular recognition of nucleotide derivatives in environments that are similar to cell membranes. The Nowick group previously discovered that membrane-like surfactant micelles tetradecyltrimethylammonium bromide (TTAB) micelle facilitate molecular of adenosine monophosphate (AMP) recognition. The micelles bind nucleotides by means of electrostatic interactions and hydrogen bonding. We observed binding by following 1H NMR chemical shift changes of unique hexylthymine protons upon addition of AMP. Cationic micelles are required for binding. In surfactant-free or sodium dodecylsulfate solutions, no hydrogen bonding is observed. These observations suggest that the cationic surfactant headgroups bind the nucleotide phosphate group, while the intramicellar base binds the nucleotide base. The micellar system was optimized to enhance binding and selectivity for adenosine nucleotides. The selectivity for adenosine and the number of phosphate groups attached to the adenosine were both investigated. Addition of cytidine, guanidine, or uridine monophosphates, results in no significant downfield shifting of the NH resonance. Selectivity for the phosphate is limited, since adenosine mono-, di-, and triphosphates all have similar binding constants. We successfully achieved molecular recognition of adenosine nucleotides in micellar environments. There is significant difference in the binding interactions between the adenosine nucleotides and three other natural nucleotides. II. The UCI Chemistry Outreach Program (UCICOP) addresses the declining interest of the nations youth for science. UCICOP brings fun and exciting chemistry experiments to local high schools, to remind students that science is fun and has many practical uses. Volunteer students and alumni of UCI perform the demonstrations using scripts and material provided by UCICOP. The preparation of scripts and materials is done by two coordinators

Template based parallel checkpointing in a massively parallel computer system

Science.gov (United States)

Archer, Charles Jens [Rochester, MN; Inglett, Todd Alan [Rochester, MN

2009-01-13

A method and apparatus for a template based parallel checkpoint save for a massively parallel super computer system using a parallel variation of the rsync protocol, and network broadcast. In preferred embodiments, the checkpoint data for each node is compared to a template checkpoint file that resides in the storage and that was previously produced. Embodiments herein greatly decrease the amount of data that must be transmitted and stored for faster checkpointing and increased efficiency of the computer system. Embodiments are directed to a parallel computer system with nodes arranged in a cluster with a high speed interconnect that can perform broadcast communication. The checkpoint contains a set of actual small data blocks with their corresponding checksums from all nodes in the system. The data blocks may be compressed using conventional non-lossy data compression algorithms to further reduce the overall checkpoint size.

MgO-templated carbon as a negative electrode material for Na-ion capacitors

Science.gov (United States)

Kado, Yuya; Soneda, Yasushi

2016-12-01

In this study, MgO-templated carbon with different pore structures was investigated as a negative electrode material for Na-ion capacitors. With increasing the Brunauer-Emmett-Teller surface area, the irreversible capacity increased, and the coulombic efficiency of the 1st cycle decreased because of the formation of solid electrolyte interface layers. MgO-templated carbon annealed at 1000 °C exhibited the highest capacity and best rate performance, suggesting that an appropriate balance between surface area and crystallinity is imperative for fast Na-ion storage, attributed to the storage mechanism: combination of non-faradaic electric double-layer capacitance and faradaic Na intercalation in the carbon layers. Finally, a Na-ion capacitor cell using MgO-templated carbon and activated carbon as the negative and positive electrodes, respectively, exhibited an energy density at high power density significantly greater than that exhibited by the cell using a commercial hard carbon negative electrode.

Between and beyond additivity and non-additivity : the statistical modelling of genotype by environment interaction in plant breeding

OpenAIRE

Eeuwijk, van, F.A.

1996-01-01

In plant breeding it is a common observation to see genotypes react differently to environmental changes. This phenomenon is called genotype by environment interaction. Many statistical approaches for analysing genotype by environment interaction rely heavily on the analysis of variance model. Genotype by environment interaction is then taken to be equivalent to non-additivity. This thesis criticizes the analysis of variance approach. Modelling genotype by environment interaction by non-addit...

Template for safety reports with descriptive example

International Nuclear Information System (INIS)

1995-12-01

This report provides a template for future safety reports on long-term safety in support of important decisions and permit applications in connection with the construction of a deep repository system. The template aims at providing a uniform structure for describing long-term safety, after the repository has been closed and sealed. The availability of such a structure will simplify both preparation and review of the safety reports, and make it possible to follow how safety assessments are influenced by the progressively more detailed body of data that emerges. A separate section containing 'descriptive examples' has been appended to the template. This section illustrates what the different chapters of the template should contain. 279 refs

Template for safety reports with descriptive example

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-12-01

This report provides a template for future safety reports on long-term safety in support of important decisions and permit applications in connection with the construction of a deep repository system. The template aims at providing a uniform structure for describing long-term safety, after the repository has been closed and sealed. The availability of such a structure will simplify both preparation and review of the safety reports, and make it possible to follow how safety assessments are influenced by the progressively more detailed body of data that emerges. A separate section containing `descriptive examples` has been appended to the template. This section illustrates what the different chapters of the template should contain. 279 refs.

Screening for templates that promote crystallization

NARCIS (Netherlands)

Urbanus, J.; Roelands, C.P.M.; Horst, J.H. ter; Verdoes, D.; Jansens, P.J.

2008-01-01

In Situ Product Recovery (ISPR) applied in fermentation processes leads to improved yield and productivity of these processes. In principle, ISPR can be achieved using Template Induced Crystallization (TIC), which is one possible ISPR technique. With TIC, templates are added to the solution as a

Prediction of Nucleotide Binding Peptides Using Star Graph Topological Indices.

Science.gov (United States)

Liu, Yong; Munteanu, Cristian R; Fernández Blanco, Enrique; Tan, Zhiliang; Santos Del Riego, Antonino; Pazos, Alejandro

2015-11-01

The nucleotide binding proteins are involved in many important cellular processes, such as transmission of genetic information or energy transfer and storage. Therefore, the screening of new peptides for this biological function is an important research topic. The current study proposes a mixed methodology to obtain the first classification model that is able to predict new nucleotide binding peptides, using only the amino acid sequence. Thus, the methodology uses a Star graph molecular descriptor of the peptide sequences and the Machine Learning technique for the best classifier. The best model represents a Random Forest classifier based on two features of the embedded and non-embedded graphs. The performance of the model is excellent, considering similar models in the field, with an Area Under the Receiver Operating Characteristic Curve (AUROC) value of 0.938 and true positive rate (TPR) of 0.886 (test subset). The prediction of new nucleotide binding peptides with this model could be useful for drug target studies in drug development. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Subtle Distinctions: How Attentional Templates Influence EEG Parameters of Cognitive Control in a Spatial Cuing Paradigm

Directory of Open Access Journals (Sweden)

Christine Mertes

2018-03-01

Full Text Available Using event-related potentials (ERPs of the electroencephalogram, we investigated how cognitive control is altered by the scope of an attentional template currently activated in visual working memory. Participants performed a spatial cuing task where an irrelevant color singleton cue was presented prior to a target array. Blockwise, the target was either a red circle or a gray square and had to be searched within homogenous (gray circles or heterogeneous non-targets (differently colored circles or various shapes. Thereby we aimed to trigger the adoption of different attentional templates: a broader singleton or a narrower, more specific feature template. ERP markers of attentional selection and inhibitory control showed that the amount of cognitive control was overall enhanced when participants searched on the basis of a feature-specific template: the analysis revealed reduced selection (N2pc, frontal P2 and pronounced inhibition (negative shift of frontal N2 of the irrelevant color cue when participants searched for a feature target. On behavioral level attentional capture was most pronounced in the color condition with no differentiation between the task-induced scopes of the attentional template.

Rate in template-directed polymer synthesis.

Science.gov (United States)

Saito, Takuya

2014-06-01

We discuss the temporal efficiency of template-directed polymer synthesis, such as DNA replication and transcription, under a given template string. To weigh the synthesis speed and accuracy on the same scale, we propose a template-directed synthesis (TDS) rate, which contains an expression analogous to that for the Shannon entropy. Increasing the synthesis speed accelerates the TDS rate, but the TDS rate is lowered if the produced sequences are diversified. We apply the TDS rate to some production system models and investigate how the balance between the speed and the accuracy is affected by changes in the system conditions.

Templated Control of Au nanospheres in Silica Nanowires

Energy Technology Data Exchange (ETDEWEB)

Tringe, J W; Vanamu, G; Zaidi, S H

2007-03-15

The formation of regularly-spaced metal nanostructures in selectively-placed insulating nanowires is an important step toward realization of a wide range of nano-scale electronic and opto-electronic devices. Here we report templated synthesis of Au nanospheres embedded in silica nanowires, with nanospheres consistently spaced with a period equal to three times their diameter. Under appropriate conditions, nanowires form exclusively on Si nanostructures because of enhanced local oxidation and reduced melting temperatures relative to templates with larger dimensions. We explain the spacing of the nanospheres with a general model based on a vapor-liquid-solid mechanism, in which an Au/Si alloy dendrite remains liquid in the nanotube until a critical Si concentration is achieved locally by silicon oxide-generated nanowire growth. Additional Si oxidation then locally reduces the surface energy of the Au-rich alloy by creating a new surface with minimum area inside of the nanotube. The isolated liquid domain subsequently evolves to become an Au nanosphere, and the process is repeated.

Improving your target-template alignment with MODalign

OpenAIRE

Barbato, Alessandro; Benkert, Pascal; Schwede, Torsten; Tramontano, Anna; Kosinski, Jan

2012-01-01

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-di...

Template analysis for the MAGIC telescopes

Energy Technology Data Exchange (ETDEWEB)

Menzel, Uta [Max-Planck-Institut fuer Physik, Muenchen (Germany); Collaboration: MAGIC-Collaboration

2016-07-01

The MAGIC telescopes are two 17-m-diameter Imaging Air Cherenkov Telescopes located on the Canary island of La Palma. They record the Cherenkov light from air showers induced by very high energy photons. The current data analysis uses a parametrization of the two shower images (including Hillas parameters) to determine the characteristics of the primary particle. I am implementing an advanced analysis method that compares shower images on a pixel basis with template images based on Monte Carlo simulations. To reduce the simulation effort the templates contain only pure shower images that are convolved with the telescope response later in the analysis. The primary particle parameters are reconstructed by maximizing the likelihood of the template. By using all the information available in the shower images, the performance of MAGIC is expected to improve. In this presentation I will explain the general idea of a template-based analysis and show the first results of the implementation.

Multimodal biometric approach for cancelable face template generation

Science.gov (United States)

Paul, Padma Polash; Gavrilova, Marina

2012-06-01

Due to the rapid growth of biometric technology, template protection becomes crucial to secure integrity of the biometric security system and prevent unauthorized access. Cancelable biometrics is emerging as one of the best solutions to secure the biometric identification and verification system. We present a novel technique for robust cancelable template generation algorithm that takes advantage of the multimodal biometric using feature level fusion. Feature level fusion of different facial features is applied to generate the cancelable template. A proposed algorithm based on the multi-fold random projection and fuzzy communication scheme is used for this purpose. In cancelable template generation, one of the main difficulties is keeping interclass variance of the feature. We have found that interclass variations of the features that are lost during multi fold random projection can be recovered using fusion of different feature subsets and projecting in a new feature domain. Applying the multimodal technique in feature level, we enhance the interclass variability hence improving the performance of the system. We have tested the system for classifier fusion for different feature subset and different cancelable template fusion. Experiments have shown that cancelable template improves the performance of the biometric system compared with the original template.

Highly conductive templated-graphene fabrics for lightweight, flexible and foldable supercapacitors

Science.gov (United States)

Zhang, Ping; Zhang, Hanzhi; Yan, Casey; Zheng, Zijian; Yu, You

2017-07-01

The templated-rGO fabric, featuring high conductivity (<1.0 Ω □-1) and low density (160 mg cm-2), is prepared by a simple dip-coating technique with sequentially coating nickel via polymer-assisted metal deposition (PAMD) and reduced-graphene oxide (rGO) on textile fabric templates at very mild conditions and is used in the fabrication of energy storage devices. As a proof of concept, both the layered and planar supercapacitors (SCs) are successfully fabricated using the rGO fabrics as templates, and both exhibit excellent electrochemical performance, ultrahigh stability with 2000 charge-discharge cycles and mechanical flexibility at bending (r  =  3 mm) and even folding states. It is found that the material of textile fabric used has a profound effect on the electrochemical property of SCs. The comparison result reveals that loose natural cotton fabrics are more suitable than tight man-made nylon fabrics for preparing high-performance SCs. In addition, such supercapacitor can be sewed into commercial textiles and powers a LED light, indicating promising applications in wearable electronics.

Speed-up Template Matching through Integral Image based Weak Classifiers

NARCIS (Netherlands)

Wu, t.; Toet, A.

2014-01-01

Template matching is a widely used pattern recognition method, especially in industrial inspection. However, the computational costs of traditional template matching increase dramatically with both template-and scene imagesize. This makes traditional template matching less useful for many (e.g.

Non-additive non-interacting kinetic energy of rare gas dimers

Science.gov (United States)

Jiang, Kaili; Nafziger, Jonathan; Wasserman, Adam

2018-03-01

Approximations of the non-additive non-interacting kinetic energy (NAKE) as an explicit functional of the density are the basis of several electronic structure methods that provide improved computational efficiency over standard Kohn-Sham calculations. However, within most fragment-based formalisms, there is no unique exact NAKE, making it difficult to develop general, robust approximations for it. When adjustments are made to the embedding formalisms to guarantee uniqueness, approximate functionals may be more meaningfully compared to the exact unique NAKE. We use numerically accurate inversions to study the exact NAKE of several rare-gas dimers within partition density functional theory, a method that provides the uniqueness for the exact NAKE. We find that the NAKE decreases nearly exponentially with atomic separation for the rare-gas dimers. We compute the logarithmic derivative of the NAKE with respect to the bond length for our numerically accurate inversions as well as for several approximate NAKE functionals. We show that standard approximate NAKE functionals do not reproduce the correct behavior for this logarithmic derivative and propose two new NAKE functionals that do. The first of these is based on a re-parametrization of a conjoint Perdew-Burke-Ernzerhof (PBE) functional. The second is a simple, physically motivated non-decomposable NAKE functional that matches the asymptotic decay constant without fitting.

Fabrication of Nanostructures Using Self-Assembled Peptides as Templates

DEFF Research Database (Denmark)

Castillo, Jaime

2015-01-01

the advantages of diphenylalanine are explained step by step offering new alternatives to fabricate nanostructures in a simple and rapid way. The chapter is complemented with techniques to manipulate the self-assembled diphenylalanine nanostructures without changing its properties during the manipulation process.......This chapter evaluates the use of a short-aromatic dipeptide, diphenylalanine, as a template in the fabrication of new nanostructures (nanowires, coaxial nanocables, nanochannels) using materials such as silicon, conducting and non-conducting polymers. Diphenylalanine self...

Synthesis of Hybrid Conducting Nanowire Using AAO Template

Science.gov (United States)

2006-09-28

oxide and alujminum oxide in anodized aluminum oxide ( AAO ) template with various aspect ratio and...than 3 nm. 2. Experimentals Anodized aluminum oxide ( AAO ) template was prepared from 99.999% purity aluminum foil by performing the following...to prepare uniform dimension of nanomaterials is to use anodized alumina membrane as template. The work emphasized self-organized arrangement of

Nucleic Acid Templated Reactions for Chemical Biology.

Science.gov (United States)

Di Pisa, Margherita; Seitz, Oliver

2017-06-21

Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Biocompatibility of Soft-Templated Mesoporous Carbons

Energy Technology Data Exchange (ETDEWEB)

Gencoglu, Maria F. [Michigan Technological Univ., Houghton, MI (United States). Dept. of Chemical Engineering; Spurri, Amanda [Widener Univ., Chester, PA (United States). Dept. of Chemical Engineering; Franko, Mitchell [Widener Univ., Chester, PA (United States). Dept. of Chemical Engineering; Chen, Jihua [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Hensley, Dale K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Heldt, Caryn L. [Michigan Technological Univ., Houghton, MI (United States). Dept. of Chemical Engineering; Saha, Dipendu [Widener Univ., Chester, PA (United States). Dept. of Chemical Engineering

2014-08-21

We report that soft-templated mesoporous carbon is morphologically a non-nano type of carbon. It is a relatively newer variety of biomaterial, which has already demonstrated its successful role in drug delivery applications. To investigate the toxicity and biocompatibility, we introduced three types of mesoporous carbons with varying synthesis conditions and pore textural properties. We compared the Brunauer–Emmett–Teller (BET) surface area and pore width and performed cytotoxicity experiments with HeLa cells, cell viability studies with fibroblast cells and hemocomapatibility studies. Cytotoxicity tests reveal that two of the carbons are not cytotoxic, with cell survival over 90%. The mesoporous carbon with the highest surface area showed slight toxicity (~70% cell survival) at the highest carbon concentration of 500 μg/mL. Fibroblast cell viability assays suggested high and constant viability of over 98% after 3 days with no apparent relation with materials property and good visible cell-carbon compatibility. No hemolysis (<1%) was confirmed for all the carbon materials. Protein adsorption experiments with bovine serum albumin (BSA) and fibrinogen revealed a lower protein binding capacity of 0.2–0.6 mg/m² and 2–4 mg/m² for BSA and fibrinogen, respectively, with lower binding associated with an increase in surface area. The results of this study confirm the biocompatibility of soft-templated mesoporous carbons.

Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes

NARCIS (Netherlands)

Maijenburg, A.W.

2014-01-01

This thesis is entitled “Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes”. Templated electrodeposition is the synthesis technique that was used throughout this thesis, and it comprises the use of a template with specific shape and dimensions for the

A color based face detection system using multiple templates

Institute of Scientific and Technical Information of China (English)

王涛; 卜佳俊; 陈纯

2003-01-01

A color based system using multiple templates was developed and implemented for detecting human faces in color images. The algorithm consists of three image processing steps. The first step is human skin color statistics. Then it separates skin regions from non-skin regions. After that, it locates the frontal human face(s) within the skin regions. In the first step, 250 skin samples from persons of different ethnicities are used to determine the color distribution of human skin in chromatic color space in order to get a chroma chart showing likelihoods of skin colors. This chroma chart is used to generate, from the original color image, a gray scale image whose gray value at a pixel shows its likelihood of representing the skin. The algorithm uses an adaptive thresholding process to achieve the optimal threshold value for dividing the gray scale image into separate skin regions from non skin regions. Finally, multiple face templates matching is used to determine if a given skin region represents a frontal human face or not. Test of the system with more than 400 color images showed that the resulting detection rate was 83%, which is better than most color-based face detection systems. The average speed for face detection is 0.8 second/image (400×300 pixels) on a Pentium 3 (800MHz) PC.

A color based face detection system using multiple templates

Institute of Scientific and Technical Information of China (English)

王涛; 卜佳酸; 陈纯

2003-01-01

A color based system using multiple templates was developed and implemented for detecting hu-man faces in color images.The algorithm comsists of three image processing steps.The first step is human skin color statistics.Then it separates skin regions from non-skin regions.After that,it locates the frontal human face(s) within the skin regions.In the first step,250 skin samples from persons of different ethnicities are used to determine the color distribution of human skin in chromatic color space in order to get a chroma chart showing likelihoods of skin colors.This chroma chart is used to generate,from the original color image,a gray scale image whose gray value at a pixel shows its likelihood of representing the shin,The algorithm uses an adaptive thresholding process to achieve the optimal threshold value for dividing the gray scale image into sep-arate skin regions from non skin regions.Finally,multiple face templates matching is used to determine if a given skin region represents a frontal human face or not.Test of the system with more than 400 color images showed that the resulting detection rate was 83%,which is better than most colou-based face detection sys-tems.The average speed for face detection is 0.8 second/image(400×300pixels) on a Pentium 3(800MHz) PC.

Nanowires and nanostructures fabrication using template methods

DEFF Research Database (Denmark)

Mátéfi-Tempfli, Stefan; Mátéfi-Tempfli, M.; Vlad, A.

2009-01-01

One of the great challenges of today is to find reliable techniques for the fabrication of nanomaterials and nanostructures. Methods based on template synthesis and on self organization are the most promising due to their easiness and low cost. This paper focuses on the electrochemical synthesis ...... of nanowires and nanostructures using nanoporous host materials such as supported anodic aluminum considering it as a key template for nanowires based devices. New ways are opened for applications by combining such template synthesis methods with nanolithographic techniques....

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Barry J Grant

2009-03-01

Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

GaN epilayers on nanopatterned GaN/Si(1 1 1) templates: Structural and optical characterization

International Nuclear Information System (INIS)

Wang, L.S.; Tripathy, S.; Wang, B.Z.; Chua, S.J.

2006-01-01

Template-based nanoscale epitaxy has been explored to realize high-quality GaN on Si(1 1 1) substrates. We have employed polystyrene-based nanosphere lithography to form the nano-hole array patterns on GaN/Si(1 1 1) template and then, subsequent regrowth of GaN is carried out by metalorganic chemical vapor deposition (MOCVD). During the initial growth stage of GaN on such nanopatterned substrates, we have observed formation of nanoislands with hexagonal pyramid shape due to selective area epitaxy. With further epitaxial regrowth, these nanoislands coalesce and form continuous GaN film. The overgrown GaN on patterned and non-patterned regions is characterized by high-resolution X-ray diffraction (HRXRD) and high-spatial resolution optical spectroscopic methods. Micro-photoluminescence (PL), micro-Raman scattering and scanning electron microscopy (SEM) have been used to assess the microstructural and optical properties of GaN. Combined PL and Raman data analyses show improved optical quality when compared to GaN simultaneously grown on non-patterned bulk Si(1 1 1). Such thicker GaN templates would be useful to achieve III-nitride-based opto- and electronic devices integrated on Si substrates

The retained templates as "helpers" for the spherical meso-silica in adsorption of heavy metals and impacts of solution chemistry.

Science.gov (United States)

Liang, Zhijie; Shi, Wenxin; Zhao, Zhiwei; Sun, Tianyi; Cui, Fuyi

2017-06-15

The spherical mesoporous silica (meso-silica) MCM-41 and those with different dosage of the retained templates were prepared and characterized. Particularly, effects of the retained template and its dosage on the adsorption of typical heavy metals (Cu 2+ and Cd 2+ ) in the synthesized materials were investigated. The results indicated that the retained templates acted as "helpers" for the adsorption of Cu 2+ and Cd 2+ in the spherical meso-silica MCM-41, and the maximum adsorption capacities (Q max ) increased with the increase of the retained template dosage. The interaction between the metal ions and the cationic heads of the templates contributed to the enhancement effect due to the anions (Cl - and OH - ) electronically adsorbed on the interface of the template micelles. Additionally, the presented results indicated that the adsorption of Cu 2+ and Cd 2+ depended on pH and high ion strength of the solution but not on the coexisted humic acid. Copyright © 2017 Elsevier Inc. All rights reserved.

Three-dimensional metallic opals fabricated by double templating

International Nuclear Information System (INIS)

Yan Qingfeng; Nukala, Pavan; Chiang, Yet-Ming; Wong, C.C.

2009-01-01

We report a simple and cost-effective double templating method for fabricating large-area three-dimensional metallic photonic crystals of controlled thickness. A self-assembled polystyrene opal was used as the first template to fabricate a silica inverse opal on a gold-coated glass substrate via sol-gel processing. Gold was subsequently infiltrated to the pores of the silica inverse opal using electrochemical deposition. A high-quality three-dimensional gold photonic crystal was obtained after removal of the secondary template (silica inverse opal). The effects of template sphere size and deposition current density on the gold growth rate, and the resulting morphology and growth mechanism of the gold opal, were investigated.

Megathrust Earthquake Swarms Contemporaneous to Slow Slip and Non-Volcanic Tremor in Southern Mexico, Detected and Analyzed through a Template Matching Approach

Science.gov (United States)

Holtkamp, S.; Brudzinski, M. R.; Cabral-Cano, E.; Arciniega-Ceballos, A.

2012-12-01

An outstanding question in geophysics is the degree to which the newly discovered types of slow fault slip are related to their destructive cousin - the earthquake. Here, we utilize a local network along the Oaxacan segment of the Middle American subduction zone to investigate the potential relationship between slow slip, non-volcanic tremor (NVT), and earthquakes along the subduction megathrust. We have developed a multi-station "template matching" waveform cross correlation technique which is able to detect and locate events several orders of magnitude smaller than would be possible using more traditional techniques. Also, our template matching procedure is capable of consistently locate events which occur during periods of increased background activity (e.g., during productive NVT, loud cultural noise, or after larger earthquakes) because the multi-station detector is finely tuned to events with similar hypocentral location and focal mechanism. The local network in the Oaxaca region allows us to focus on documented megathrust earthquake swarms, which we focus on because slow slip is hypothesized to be the cause for earthquake swarms in some tectonic environments. We identify a productive earthquake swarm in July 2006 (~600 similar earthquakes detected), which occurred during a week-long episode of productive tremor and slow slip. Families of events in this sequence were also active during larger and longer slow slip events, which provides a potential link between slow slip in the transition zone and earthquakes at the downdip end of the seismogenic portion of the megathrust. Because template matching techniques only detect similar signals, detected waveforms can be stacked together to produce higher signal to noise ratios or cross correlated against each other to produce precise relative phase arrival times. We are using the refined signals to look for evidence of expansion or propagation of hypocenters during these earthquake swarms, which could be used as a

PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space.

Science.gov (United States)

De Leener, Benjamin; Fonov, Vladimir S; Collins, D Louis; Callot, Virginie; Stikov, Nikola; Cohen-Adad, Julien

2018-01-15

Template-based analysis of multi-parametric MRI data of the spinal cord sets the foundation for standardization and reproducibility, thereby helping the discovery of new biomarkers of spinal-related diseases. While MRI templates of the spinal cord have been recently introduced, none of them cover the entire spinal cord. In this study, we introduced an unbiased multimodal MRI template of the spinal cord and the brainstem, called PAM50, which is anatomically compatible with the ICBM152 brain template and uses the same coordinate system. The PAM50 template is based on 50 healthy subjects, covers the full spinal cord (C1 to L2 vertebral levels) and the brainstem, is available for T1-, T2-and T2*-weighted MRI contrasts and includes a probabilistic atlas of the gray matter and white matter tracts. Template creation accuracy was assessed by computing the mean and maximum distance error between each individual spinal cord centerline and the PAM50 centerline, after registration to the template. Results showed high accuracy for both T1- (mean = 0.37 ± 0.06 mm; max = 1.39 ± 0.58 mm) and T2-weighted (mean = 0.11 ± 0.03 mm; max = 0.71 ± 0.27 mm) contrasts. Additionally, the preservation of the spinal cord topology during the template creation process was verified by comparing the cross-sectional area (CSA) profile, averaged over all subjects, and the CSA profile of the PAM50 template. The fusion of the PAM50 and ICBM152 templates will facilitate group and multi-center studies of combined brain and spinal cord MRI, and enable the use of existing atlases of the brainstem compatible with the ICBM space. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Durable diamond-like carbon templates for UV nanoimprint lithography

International Nuclear Information System (INIS)

Tao, L; Ramachandran, S; Nelson, C T; Overzet, L J; Goeckner, M; Lee, G; Hu, W; Lin, M; Willson, C G; Wu, W

2008-01-01

The interaction between resist and template during the separation process after nanoimprint lithography (NIL) can cause the formation of defects and damage to the templates and resist patterns. To alleviate these problems, fluorinated self-assembled monolayers (F-SAMs, i.e. tridecafluoro-1,1,2,2,tetrahydrooctyl trichlorosilane or FDTS) have been employed as template release coatings. However, we find that the FDTS coating undergoes irreversible degradation after only 10 cycles of UV nanoimprint processes with SU-8 resist. The degradation includes a 28% reduction in surface F atoms and significant increases in the surface roughness. In this paper, diamond-like carbon (DLC) films were investigated as an alternative material not only for coating but also for direct fabrication of nanoimprint templates. DLC films deposited on quartz templates in a plasma enhanced chemical vapor deposition system are shown to have better chemical and physical stability than FDTS. After the same 10 cycles of UV nanoimprints, the surface composition as well as the roughness of DLC films were found to be unchanged. The adhesion energy between the DLC surface and SU-8 is found to be smaller than that of FDTS despite the slightly higher total surface energy of DLC. DLC templates with 40 nm features were fabricated using e-beam lithography followed by Cr lift-off and reactive ion etching. UV nanoimprinting using the directly patterned DLC templates in SU-8 resist demonstrates good pattern transfer fidelity and easy template-resist separation. These results indicate that DLC is a promising material for fabricating durable templates for UV nanoimprint lithography

Business Process Variability : A Tool for Declarative Template Design

NARCIS (Netherlands)

Bulanov, P.; Groefsema, H.; Aiello, M.

2012-01-01

To lower both implementation time and cost, many Business Process Management tools use process templates to implement highly recurring processes. However, in order for such templates to be used, a process has to adhere substantially to the template. Therefore, current practice for processes which

Transcription of Nanofibrous Cerium Phosphate Using a pH-Sensitive Lipodipeptide Hydrogel Template

Directory of Open Access Journals (Sweden)

Mario Llusar

2017-06-01

Full Text Available A novel and simple transcription strategy has been designed for the template-synthesis of CePO4·xH2O nanofibers having an improved nanofibrous morphology using a pH-sensitive nanofibrous hydrogel (glycine-alanine lipodipeptide as structure-directing scaffold. The phosphorylated hydrogel was employed as a template to direct the mineralization of high aspect ratio nanofibrous cerium phosphate, which in-situ formed by diffusion of aqueous CeCl3 and subsequent drying (60 °C and annealing treatments (250, 600 and 900 °C. Dried xerogels and annealed CePO4 powders were characterized by conventional thermal and thermogravimetric analysis (DTA/TG, and Wide-Angle X-ray powder diffraction (WAXD and X-ray powder diffraction (XRD techniques. A molecular packing model for the formation of the fibrous xerogel template was proposed, in accordance with results from Fourier-Transformed Infrarred (FTIR and WAXD measurements. The morphology, crystalline structure and composition of CePO4 nanofibers were characterized by electron microscopy techniques (Field-Emission Scanning Electron Microscopy (FE-SEM, Transmission Electron Microscopy/High-Resolution Transmission Electron Microscopy (TEM/HRTEM, and Scanning Transmission Electron Microscopy working in High Angle Annular Dark-Field (STEM-HAADF with associated X-ray energy-dispersive detector (EDS and Scanning Transmission Electron Microscopy-Electron Energy Loss (STEM-EELS spectroscopies. Noteworthy, this templating approach successfully led to the formation of CePO4·H2O nanofibrous bundles of rather co-aligned and elongated nanofibers (10–20 nm thick and up to ca. 1 μm long. The formed nanofibers consisted of hexagonal (P6222 CePO4 nanocrystals (at 60 and 250 °C, with a better-grown and more homogeneous fibrous morphology with respect to a reference CePO4 prepared under similar (non-templated conditions, and transformed into nanofibrous monoclinic monazite (P21/n around 600 °C. The nanofibrous morphology

Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins

International Nuclear Information System (INIS)

Wnęk, M; Stockley, P G; Górzny, M Ł; Evans, S D; Ward, M B; Brydson, R; Wälti, C; Davies, A G

2013-01-01

The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating. (paper)

Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins

Science.gov (United States)

Wnęk, M.; Górzny, M. Ł.; Ward, M. B.; Wälti, C.; Davies, A. G.; Brydson, R.; Evans, S. D.; Stockley, P. G.

2013-01-01

The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating.

MOCVD epitaxy of InAlN on different templates

International Nuclear Information System (INIS)

Yun Lijun; Wei Tongbo; Yan Jianchang; Liu Zhe; Wang Junxi; Li Jinmin

2011-01-01

InAlN epilayers were grown on high quality GaN and AlN templates with the same growth parameters. Measurement results showed that two samples had the same In content of ∼ 16%, while the crystal quality and surface topography of the InAlN epilayer grown on the AlN template, with 282.3 (002) full width at half maximum (FWHM) of rocking curve, 313.5 (102) FWHM, surface roughness of 0.39 nm and V-pit density of 2.8 x 10 8 cm -2 , were better than that of the InAlN epilayer grown on the GaN template, 309.3, 339.1, 0.593 nm and 4.2 x 10 8 cm -2 . A primary conclusion was proposed that both the crystal quality and the surface topography of the InAlN epilayer grown on the AlN template were better than that of the InAlN epilayer grown on the GaN template. Therefore, the AlN template was a better choice than the GaN template for getting high quality InAlN epilayers. (semiconductor materials)

Joomla! 3 template essentials

CERN Document Server

Frankowski, Pawel

2013-01-01

Using this hands-on, step-by step tutorial filled with practical examples, the readers will be able to create beautiful templates and themes for your websites that will make them stand out from others.This book is written for all of you who wish to create your own unique templates for Joomla! 3.x. This book can be used by Joomla! administrators or visual designers (with no programming experience) or those of you who are used to working with common web developer tools like HTML/CSS editors for coding purposes. You would need basic knowledge of Joomla! and some knowledge of CSS and HTML.

FTA liver impressions as DNA template for detecting and genotyping fowl adenovirus.

Science.gov (United States)

Moscoso, Hugo; Bruzual, Jose J; Sellers, Holly; Hofacre, Charles L

2007-03-01

The feasibility of using liver impressions on Flinders Technology Associates (FTA filter paper for the collection, inactivation, and molecular analysis of fowl adenovirus (FAV) was evaluated. FAV I European Union (EU) serotype 1 spotted on FTA was shown to be inactivated using specific-pathogen-free (SPF) primary chicken embryo liver cell culture as indicated by absence of cytopathic effect. Sensitivity of the polymerase chain reaction (PCR) test using tenfold dilutions of allantoic fluid from 100 to 10-4 for the detection of adenovirus serotype 1 on FTA cards was determined to be 0.0005 mean tissue culture infectious dose per FTA spot. The stability of the DNA from liver impressions on the FTA was found to be 198 days when stored at -20 degrees C. In a trial, inclusion body hepatitis (IBH) was experimentally reproduced in SPF chickens inoculated with FAV I EU serogroup 1, 4, 8, or 11, which presented weakness, pallor, depression, dehydration, and mortality within 6 days after inoculation. PCR performed on FTA liver impressions from the inoculated birds was able to detect all four viruses, and the nucleotide sequence analysis of the amplified PCR products (1219 bp of the hexone gene) revealed the expected serotypes. In addition to the trial, 55 clinical samples were analyzed from liver impressions on FTA cards, and FAV was detected in 11 of 55 (20%). Sequencing analysis showed that the viruses were EU serotypes 4, 5, 9, and 10. The results demonstrate that FTA filter paper inactivates the FAV I and maintains the DNA template for molecular analysis.

Synthesis and NMR characterization of SAPO-35 from non-aqueous systems using hexamethyleneimine template

International Nuclear Information System (INIS)

Venkatathri, N.

2005-01-01

SAPO-35 was synthesized using hexamethyleneimine template in non-aqueous systems. X-ray diffraction and scanning electron micrograph analysis shows the synthesized sample is pure and well crystalline. Presence of four stages (1.6%, 0.8%, 7.8% and 8.4%) of weight loss is observed by TG/DTA analysis. FT-IR analysis in the framework region shows the presence of tetrahedral T-O-T vibrations is similar to the other known aluminophosphate molecular sieves. FT-IR spectrum in the -OH region shows stretching vibrations at 3631, 3604 and 3580 cm -1 can be assigned to OH groups in bigger cages near S6R, in bigger cages near D6R and those actually confined inside the D6R, respectively. The spectra for the as-synthesized sample show a single symmetrical 27 Al MAS NMR line at δ = 36.26 indicating the presence of a single tetrahedral aluminium species. Where as 29 Si and 31 P MAS NMR shows the presence of two peaks in both at (-89.9 and -95.15 ppm) and (-34.01 and -40.45 ppm) due to the Si substitution of P present in two different locations in double 6 ring (D6R) and in single 6 ring (S6R). 27 Al 3Q-MAS NMR shows two peaks for environmentally different tetrahedral aluminium atoms. This is the first time we are showing such a fact which is not observable using ordinary MAS NMR

Broadband infrared metamaterial absorber based on anodic aluminum oxide template

Science.gov (United States)

Yang, Jingfan; Qu, Shaobo; Ma, Hua; Wang, Jiafu; Yang, Shen; Pang, Yongqiang

2018-05-01

In this work, a broadband infrared metamaterial absorber is proposed based on trapezoid-shaped anodic aluminum oxide (AAO) template. Unlike traditional metamaterial absorber constructed from metal-dielectric-metal sandwich structure, our proposed absorber is composed of trapezoid-shaped AAO template with metallic nanowires inside. The infrared absorption efficiency is numerically calculated and the mechanism analysis is given in the paper. Owing to the superposition of multiple resonances produced by the nanowires with different heights, the infrared metamatrial absorber can keep high absorption efficiency during broad working wavelength band from 3.4 μm to 6.1 μm. In addition, the resonance wavelength is associated with the height of nanowires, which indicates that the resonance wavelength can be modulated flexibly through changing the heights of nanowires. This kind of design can also be adapted to other wavelength regions.

Silver nanowires-templated metal oxide for broadband Schottky photodetector

Energy Technology Data Exchange (ETDEWEB)

Patel, Malkeshkumar; Kim, Hong-Sik; Kim, Joondong, E-mail: joonkim@inu.ac.kr [Photoelectric and Energy Device Application Lab (PEDAL) and Department of Electrical Engineering, Incheon National University, 119 Academy Rd. Yeonsu, Incheon 406772 (Korea, Republic of); Park, Hyeong-Ho [Applied Device and Material Lab., Device Technology Division, Korea Advanced Nano Fab Center (KANC), Suwon 443270 (Korea, Republic of)

2016-04-04

Silver nanowires (AgNWs)-templated transparent metal oxide layer was applied for Si Schottky junction device, which remarked the record fastest photoresponse of 3.4 μs. Self-operating AgNWs-templated Schottky photodetector showed broad wavelength photodetection with high responsivity (42.4 A W{sup −1}) and detectivity (2.75 × 10{sup 15} Jones). AgNWs-templated indium-tin-oxide (ITO) showed band-to-band excitation due to the internal photoemission, resulting in significant carrier collection performances. Functional metal oxide layer was formed by AgNWs-templated from ITO structure. The grown ITO above AgNWs has a cylindrical shape and acts as a thermal protector of AgNWs for high temperature environment without any deformation. We developed thermal stable AgNWs-templated transparent oxide devices and demonstrated the working mechanism of AgNWs-templated Schottky devices. We may propose the high potential of hybrid transparent layer design for various photoelectric applications, including solar cells.

Comparison of template registration methods for multi-site meta-analysis of brain morphometry

Science.gov (United States)

Faskowitz, Joshua; de Zubicaray, Greig I.; McMahon, Katie L.; Wright, Margaret J.; Thompson, Paul M.; Jahanshad, Neda

2016-03-01

Neuroimaging consortia such as ENIGMA can significantly improve power to discover factors that affect the human brain by pooling statistical inferences across cohorts to draw generalized conclusions from populations around the world. Voxelwise analyses such as tensor-based morphometry also allow an unbiased search for effects throughout the brain. Even so, such consortium-based analyses are limited by a lack of high-powered methods to harmonize voxelwise information across study populations and scanners. While the simplest approach may be to map all images to a single standard space, the benefits of cohort-specific templates have long been established. Here we studied methods to pool voxel-wise data across sites using templates customized for each cohort but providing a meaningful common space across all studies for voxelwise comparisons. As non-linear 3D MRI registrations represent mappings between images at millimeter resolution, we need to consider the reliability of these mappings. To evaluate these mappings, we calculated test-retest statistics on the volumetric maps of expansion and contraction. Further, we created study-specific brain templates for ten T1-weighted MRI datasets, and a common space from four study-specific templates. We evaluated the efficacy of using a two-step registration framework versus a single standard space. We found that the two-step framework more reliably mapped subjects to a common space.

View-Invariant Gait Recognition Through Genetic Template Segmentation

Science.gov (United States)

Isaac, Ebenezer R. H. P.; Elias, Susan; Rajagopalan, Srinivasan; Easwarakumar, K. S.

2017-08-01

Template-based model-free approach provides by far the most successful solution to the gait recognition problem in literature. Recent work discusses how isolating the head and leg portion of the template increase the performance of a gait recognition system making it robust against covariates like clothing and carrying conditions. However, most involve a manual definition of the boundaries. The method we propose, the genetic template segmentation (GTS), employs the genetic algorithm to automate the boundary selection process. This method was tested on the GEI, GEnI and AEI templates. GEI seems to exhibit the best result when segmented with our approach. Experimental results depict that our approach significantly outperforms the existing implementations of view-invariant gait recognition.

Morphology-dependent enhancement of the pseudocapacitance of template-guided tunable polyaniline nanostructures

KAUST Repository

Chen, Wei

2013-07-25

Polyaniline is one of the most investigated conducting polymers as supercapacitor material for energy storage applications. The preparation of nanostructured polyaniline with well-controlled morphology is crucial to obtaining good supercapacitor performance. We present here a facile chemical process to produce polyaniline nanostructures with three different morphologies (i.e., nanofibers, nanospheres, and nanotubes) by utilizing the corresponding tunable morphology of MnO2 reactive templates. A growth mechanism is proposed to explain the evolution of polyaniline morphology based on the reactive templates. The morphology-induced improvement in the electrochemical performance of polyaniline pseudocapacitors is as large as 51% due to the much enhanced surface area and the porous nature of the template-guided polyaniline nanostructures. In addition, and for the first time, a redox-active electrolyte is applied to the polyaniline pseudocapacitors to achieve significant enhancement of pseudocapacitance. Compared to the conventional electrolyte, the enhancement of pseudocapacitance in the redox-active electrolyte is 49%-78%, depending on the specific polyaniline morphology, reaching the highest reported capacitance of 896 F/g for polyaniline full cells so far. © 2013 American Chemical Society.

Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

Energy Technology Data Exchange (ETDEWEB)

Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke; Lam, Angela M.; Grice, Rena L.; Du, Jinfa; Sofia, Michael J.; Furman, Philip A.; Otto, Michael J. (Pharmasset); (Emerald)

2012-08-01

The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.

Morphology-dependent enhancement of the pseudocapacitance of template-guided tunable polyaniline nanostructures

KAUST Repository

Chen, Wei; Baby, Rakhi Raghavan; Alshareef, Husam N.

2013-01-01

Polyaniline is one of the most investigated conducting polymers as supercapacitor material for energy storage applications. The preparation of nanostructured polyaniline with well-controlled morphology is crucial to obtaining good supercapacitor performance. We present here a facile chemical process to produce polyaniline nanostructures with three different morphologies (i.e., nanofibers, nanospheres, and nanotubes) by utilizing the corresponding tunable morphology of MnO2 reactive templates. A growth mechanism is proposed to explain the evolution of polyaniline morphology based on the reactive templates. The morphology-induced improvement in the electrochemical performance of polyaniline pseudocapacitors is as large as 51% due to the much enhanced surface area and the porous nature of the template-guided polyaniline nanostructures. In addition, and for the first time, a redox-active electrolyte is applied to the polyaniline pseudocapacitors to achieve significant enhancement of pseudocapacitance. Compared to the conventional electrolyte, the enhancement of pseudocapacitance in the redox-active electrolyte is 49%-78%, depending on the specific polyaniline morphology, reaching the highest reported capacitance of 896 F/g for polyaniline full cells so far. © 2013 American Chemical Society.

Template-directed synthesis of MS (M=Cd, Zn) hollow microsphere via hydrothermal method

Science.gov (United States)

Wang, Shi-Ming; Wang, Qiong-Sheng; Wan, Qing-Li

2008-05-01

CdS, ZnS hollow microspheres were prepared with chitosan as the synthesis template at 140 and 150 °C, respectively, by hydrothermal method. The resultant products were characterized by X-ray diffraction (XRD) measurements in order to determine the crystalline phase of the products. The structural and morphological features of the nanoparticles were investigated by transmission electron microscopy (TEM) and ultraviolet-visible diffuse reflection spectroscopy (DRS). The experimental results indicated that all the nanoparticles aggregated into hollow microspheres and chitosan as a template played an important role in the formation of hollow microspheres. In addition, an intermediate complex structure-controlling possible reaction mechanism was proposed in this paper.

Efficiency and Fidelity of Human DNA Polymerases λ and β during Gap-Filling DNA Synthesis

Science.gov (United States)

Brown, Jessica A.; Pack, Lindsey R.; Sanman, Laura E.; Suo, Zucai

2010-01-01

The base excision repair (BER) pathway coordinates the replacement of 1 to 10 nucleotides at sites of single-base lesions. This process generates DNA substrates with various gap sizes which can alter the catalytic efficiency and fidelity of a DNA polymerase during gap-filling DNA synthesis. Here, we quantitatively determined the substrate specificity and base substitution fidelity of human DNA polymerase λ (Pol λ), an enzyme proposed to support the known BER DNA polymerase β (Pol β), as it filled 1- to 10-nucleotide gaps at 1-nucleotide intervals. Pol λ incorporated a correct nucleotide with relatively high efficiency until the gap size exceeded 9 nucleotides. Unlike Pol λ, Pol β did not have an absolute threshold on gap size as the catalytic efficiency for a correct dNTP gradually decreased as the gap size increased from 2 to 10 nucleotides and then recovered for non-gapped DNA. Surprisingly, an increase in gap size resulted in lower polymerase fidelity for Pol λ, and this downregulation of fidelity was controlled by its non-enzymatic N-terminal domains. Overall, Pol λ was up to 160-fold more error-prone than Pol β, thereby suggesting Pol λ would be more mutagenic during long gap-filling DNA synthesis. In addition, dCTP was the preferred misincorporation for Pol λ and its N-terminal domain truncation mutants. This nucleotide preference was shown to be dependent upon the identity of the adjacent 5′-template base. Our results suggested that both Pol λ and Pol β would catalyze nucleotide incorporation with the highest combination of efficiency and accuracy when the DNA substrate contains a single-nucleotide gap. Thus, Pol λ, like Pol β, is better suited to catalyze gap-filling DNA synthesis during short-patch BER in vivo, although, Pol λ may play a role in long-patch BER. PMID:20961817

I - Template Metaprogramming for Massively Parallel Scientific Computing - Expression Templates

CERN Multimedia

CERN. Geneva

2016-01-01

Large scale scientific computing raises questions on different levels ranging from the fomulation of the problems to the choice of the best algorithms and their implementation for a specific platform. There are similarities in these different topics that can be exploited by modern-style C++ template metaprogramming techniques to produce readable, maintainable and generic code. Traditional low-level code tend to be fast but platform-dependent, and it obfuscates the meaning of the algorithm. On the other hand, object-oriented approach is nice to read, but may come with an inherent performance penalty. These lectures aim to present he basics of the Expression Template (ET) idiom which allows us to keep the object-oriented approach without sacrificing performance. We will in particular show to to enhance ET to include SIMD vectorization. We will then introduce techniques for abstracting iteration, and introduce thread-level parallelism for use in heavy data-centric loads. We will show to to apply these methods i...

Photon signature analysis using template matching

Energy Technology Data Exchange (ETDEWEB)

Bradley, D.A., E-mail: d.a.bradley@surrey.ac.uk [Department of Physics, University of Surrey, Guildford GU2 7XH (United Kingdom); Hashim, S., E-mail: suhairul@utm.my [Department of Physics, Universiti Teknologi Malaysia, 81310 Skudai, Johor (Malaysia); Saripan, M.I. [Faculty of Engineering, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Wells, K. [Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH (United Kingdom); Dunn, W.L. [Department of Mechanical and Nuclear Engineering, Kansas State University, 3002 Rathbone Hall, Manhattan, KS 66506 (United States)

2011-10-01

We describe an approach to detect improvised explosive devices (IEDs) by using a template matching procedure. This approach relies on the signature due to backstreaming {gamma} photons from various targets. In this work we have simulated cylindrical targets of aluminum, iron, copper, water and ammonium nitrate (nitrogen-rich fertilizer). We simulate 3.5 MeV source photons distributed on a plane inside a shielded area using Monte Carlo N-Particle (MCNP{sup TM}) code version 5 (V5). The 3.5 MeV source gamma rays yield 511 keV peaks due to pair production and scattered gamma rays. In this work, we simulate capture of those photons that backstream, after impinging on the target element, toward a NaI detector. The captured backstreamed photons are expected to produce a unique spectrum that will become part of a simple signal processing recognition system based on the template matching method. Different elements were simulated using different sets of random numbers in the Monte Carlo simulation. To date, the sum of absolute differences (SAD) method has been used to match the template. In the examples investigated, template matching was found to detect all elements correctly.

Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota.

Science.gov (United States)

Makarova, Alena V; Ignatov, Artem; Miropolskaya, Nataliya; Kulbachinskiy, Andrey

2014-10-01

Human DNA polymerase iota (Pol ι) is a Y-family polymerase that can bypass various DNA lesions but possesses very low fidelity of DNA synthesis in vitro. Structural analysis of Pol ι revealed a narrow active site that promotes noncanonical base-pairing during catalysis. To better understand the structure-function relationships in the active site of Pol ι we investigated substitutions of individual amino acid residues in its fingers domain that contact either the templating or the incoming nucleotide. Two of the substitutions, Y39A and Q59A, significantly decreased the catalytic activity but improved the fidelity of Pol ι. Surprisingly, in the presence of Mn(2+) ions, the wild-type and mutant Pol ι variants efficiently incorporated nucleotides opposite template purines containing modifications that disrupted either Hoogsteen or Watson-Crick base-pairing, suggesting that Pol ι may use various types of interactions during nucleotide addition. In contrast, in Mg(2+) reactions, wild-type Pol ι was dependent on Hoogsteen base-pairing, the Y39A mutant was essentially inactive, and the Q59A mutant promoted Watson-Crick interactions with template purines. The results suggest that Pol ι utilizes distinct mechanisms of nucleotide incorporation depending on the metal cofactor and reveal important roles of specific residues from the fingers domain in base-pairing and catalysis. Copyright © 2014 Elsevier B.V. All rights reserved.

A Convenient and Templated Method for the Fabrication of Monodisperse Micrometer Hollow Titania Spheres

Directory of Open Access Journals (Sweden)

Haibo Yao

2013-01-01

Full Text Available A simple and widely applicable methodology was presented to synthesize monodisperse micrometer hollow titania spheres (HTS based on the templating method. It was performed by using the preformed poly(styrene-acrylic acid (PSA as template spheres which was mixed with tetrabutyltitanate (TBOT in an ethanol solvent under steam treatment. The HTS which were obtained by the calcination of PSA/TiO2 composite core-shell spheres had a narrow particle size distribution and commendable surface topography characterized by SEM. The calcined HTS at 500°C displayed crystalline reflection peaks that were characteristic to the anatase phase by XRD. Moreover, some key influencing factors including TBOT concentration and reaction time were analyzed. As expected, the diameter of HTS could be readily controlled by altering the size of PSA template spheres. In addition, the approach was also applied to fabricate hollow zirconia spheres and other inorganic spheres.

DNA Three-Way Junction for Differentiation of Single-Nucleotide Polymorphisms with Fluorescent Copper Nanoparticles.

Science.gov (United States)

Sun, Feifei; You, Ying; Liu, Jie; Song, Quanwei; Shen, Xiaotong; Na, Na; Ouyang, Jin

2017-05-23

A label- and enzyme-free fluorescent sensor for the detection of single-nucleotide polymorphisms (SNPs) at room temperature is proposed, using new copper nanoparticles (CuNPs) as fluorescent reporters. The CuNPs were constructed by using a DNA three-way junction (3WJ) template. In this assay, two complementary adenine/thymine-rich probes can hybridize with the wild-type target simultaneously to construct a 3WJ structure, serving as an efficient scaffold for the generation of CuNPs. However, the CuNPs produce weak fluorescence when the probes bind with a mutant-type target. SNPs can be identified by the difference in fluorescence intensity of the CuNPs. This SNPs detection strategy is straightforward, cost-effective, and avoids the complicated procedures of labeling or enzymatic reactions. The fluorescent sensor is versatile and can be applied to all types of mutation because the probes are programmable. Moreover, the sensor exhibits good detection performance in biological samples. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlling macro- and mesostructures with hierarchical porosity through combined hard and soft templating.

Science.gov (United States)

Petkovich, Nicholas D; Stein, Andreas

2013-05-07

Rigid, porous objects and surfactants serve as powerful templates for the formation of mesoporous and macroporous materials. When both types of template are combined in a single synthesis, materials with intricate architectures and hierarchical porosity can be obtained. In this tutorial review, we explain how to conduct syntheses with both soft and hard templates; moreover, we describe methods to control the final structure present in the templated material. Much of the foundation for multiple templating lies in the study of materials made with only one type of template. To establish a foundation in this area, a description of hard and soft templating is given, delving into the templates available and the steps required for effective templating. This leads into an extended discussion about materials templated with both hard and soft templates. Through the use of recent examples in the literature, we aim to show the diversity of structures possible through multiple templating and the advantages these structures can provide for a wide range of applications. An emphasis is placed on how various factors-such as the type of template, type of precursor, heat-treatment temperature, confinement within a small space, and template-template interactions-impact morphology.

Nucleotide sequence preservation of human mitochondrial DNA

International Nuclear Information System (INIS)

Monnat, R.J. Jr.; Loeb, L.A.

1985-01-01

Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

Synthesis of Porous Carbon Monoliths Using Hard Templates.

Science.gov (United States)

Klepel, Olaf; Danneberg, Nina; Dräger, Matti; Erlitz, Marcel; Taubert, Michael

2016-03-21

The preparation of porous carbon monoliths with a defined shape via template-assisted routes is reported. Monoliths made from porous concrete and zeolite were each used as the template. The porous concrete-derived carbon monoliths exhibited high gravimetric specific surface areas up to 2000 m²·g -1 . The pore system comprised macro-, meso-, and micropores. These pores were hierarchically arranged. The pore system was created by the complex interplay of the actions of both the template and the activating agent as well. On the other hand, zeolite-made template shapes allowed for the preparation of microporous carbon monoliths with a high volumetric specific surface area. This feature could be beneficial if carbon monoliths must be integrated into technical systems under space-limited conditions.

Solubilization and reconstitution of the formylmethionylleucylphenylalanine receptor coupled to guanine nucleotide regulatory protein

International Nuclear Information System (INIS)

Williamson, K.; Dickey, B.F.; Pyun, H.Y.; Navarro, J.

1988-01-01

The authors describe the solubilization, resolution, and reconstitution of the formylmethionylleucylphenylalanine (fMet-Leu-Phe) receptor and guanine nucleotide regulatory proteins (G-proteins). The receptor was solubilized with 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate. Guanine nucleotides decreased the number of high-affinity binding sites and accelerated the rate of dissociation of the receptor-ligand complex, suggesting that the solubilized receptor remained coupled to endogenous G-proteins. The solubilized receptor was resolved from endogenous G-proteins by fractionation on a wheat germ agglutinin (WGA)-Sepharose 4B column. High-affinity [ 3 H]fMet-Leu-Phe binding to the WGA-purified receptor was diminished and exhibited reduced guanine nucleotide sensitivity. High-affinity [ 3 H]fMET-Leu-Phe binding and guanine nucleotide sensitivity were reconstituted upon the addition of purified brain G-proteins. Similar results were obtained when the receptor was reconstituted with brain G-proteins into phospholipid vesicles by gel filtration chromatography. In addition, they also demonstrated fMET-Leu-Phe-dependent GTP hydrolysis in the reconstituted vesicles. The results of this work indicate that coupling of the fMet-Leu-Phe receptor to G-proteins converts the receptor to a high-affinity binding state and that agonist produces activation of G-proteins. The resolution and functional reconstitution of this receptor should provide an important step toward the elucidation of the molecular mechanism of the fMet-Leu-Phe transduction system in neutrophils

Improved cellular infiltration into nanofibrous electrospun cross-linked gelatin scaffolds templated with micrometer-sized polyethylene glycol fibers

International Nuclear Information System (INIS)

Skotak, Maciej; Ragusa, Jorge; Gonzalez, Daniela; Subramanian, Anuradha

2011-01-01

Gelatin-based nanofibrous scaffolds with a mean fiber diameter of 300 nm were prepared with and without micrometer-sized polyethylene glycol (PEG) fibers that served as sacrificial templates. Upon fabrication of the scaffolds via electrospinning, the gelatin fibers were crosslinked with glutaraldehyde, and the PEG templates were removed using tert-butanol to yield nanofibrous scaffolds with pore diameters ranging from 10 to 100 μm, as estimated with mercury intrusion porosimetry. Non-templated gelatin-based nanofibrous matrices had an average pore size of 1 μm. Fibroblasts were seeded onto both types of the gelatin-based nanofibrous surfaces and cultured for 14 days. For comparative purposes, chitosan-based and polyurethane-based macroporous scaffolds with pore sizes of 100 and 170 μm, respectively, were also included. The number of cells as a function of the depth into the scaffold was judged and quantitatively assessed using nuclei staining. Cell penetration up to a depth of 250 and 90 μm was noted in gelatin scaffolds prepared with sacrificial templates and gelatin-only nanofibrous scaffolds. Noticeably, scaffold preparation protocol presented here allowed the structural integrity to be maintained even with high template content (95%) and can easily be extended toward other classes of electrospun polymer matrices for tissue engineering.

Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection.

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David G Nickens

Full Text Available BACKGROUND: In vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive RNA species. While nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' OH of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated. METHODOLOGY/PRINCIPAL FINDINGS: This study demonstrates the ability of T4 DNA ligase to capture RNA strands in which a tethered monodeoxynucleoside has acquired a 5' phosphate. The ligation reaction therefore mimics the partition step of a selection for nucleoside kinase (deoxyribozymes. Ligation with tethered substrates was considerably slower than with nicked, fully duplex DNA, even though the deoxynucleotides at the ligation junction were Watson-Crick base paired in the tethered substrate. Ligation increased markedly when the bridging template strand contained unpaired spacer nucleotides across from the flexible tether, according to the trends: A(2>A(1>A(3>A(4>A(0>A(6>A(8>A(10 and T(2>T(3>T(4>T(6 approximately T(1>T(8>T(10. Bridging T's generally gave higher yield of ligated product than bridging A's. ATP concentrations above 33 microM accumulated adenylated intermediate and decreased yields of the gap-sealed product, likely due to re-adenylation of dissociated enzyme. Under optimized conditions, T4 DNA ligase efficiently (>90% joined a correctly paired, or TratioG wobble-paired, substrate on the 3' side of the ligation junction while discriminating approximately 100-fold against most mispaired substrates. Tethered dC and dG gave the highest ligation rates and yields, followed by tethered deoxyinosine (dI and dT, with the slowest reactions for tethered dA. The same kinetic trends were observed in ligase-mediated capture in complex reaction mixtures with multiple substrates. The "universal" analog 5-nitroindole (dNI did not support ligation when

A Fully Non-Metallic Gas Turbine Engine Enabled by Additive Manufacturing

Science.gov (United States)

Grady, Joseph E.; Halbig, Michael C.; Singh, Mrityunjay

2015-01-01

In a NASA Aeronautics Research Institute (NARI) sponsored program entitled "A Fully Non-Metallic Gas Turbine Engine Enabled by Additive Manufacturing", evaluation of emerging materials and additive manufacturing technologies was carried out. These technologies may enable fully non-metallic gas turbine engines in the future. This paper highlights the results of engine system trade studies which were carried out to estimate reduction in engine emissions and fuel burn enabled due to advanced materials and manufacturing processes. A number of key engine components were identified in which advanced materials and additive manufacturing processes would provide the most significant benefits to engine operation. In addition, feasibility of using additive manufacturing technologies to fabricate gas turbine engine components from polymer and ceramic matrix composite were demonstrated. A wide variety of prototype components (inlet guide vanes (IGV), acoustic liners, engine access door) were additively manufactured using high temperature polymer materials. Ceramic matrix composite components included first stage nozzle segments and high pressure turbine nozzle segments for a cooled doublet vane. In addition, IGVs and acoustic liners were tested in simulated engine conditions in test rigs. The test results are reported and discussed in detail.

gel template method

Indian Academy of Sciences (India)

TiO2 nanotubes have been synthesized by sol–gel template method using alumina membrane. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, UV absorption spectrum and X-ray diffraction techniques have been used to investigate the structure, morphology and optical ...

Additive non-uniform random sampling in superimposed fiber Bragg grating strain gauge

Science.gov (United States)

Ma, Y. C.; Liu, H. Y.; Yan, S. B.; Yang, Y. H.; Yang, M. W.; Li, J. M.; Tang, J.

2013-05-01

This paper demonstrates an additive non-uniform random sampling and interrogation method for dynamic and/or static strain gauge using a reflection spectrum from two superimposed fiber Bragg gratings (FBGs). The superimposed FBGs are designed to generate non-equidistant space of a sensing pulse train in the time domain during dynamic strain gauge. By combining centroid finding with smooth filtering methods, both the interrogation speed and accuracy are improved. A 1.9 kHz dynamic strain is measured by generating an additive non-uniform randomly distributed 2 kHz optical sensing pulse train from a mean 500 Hz triangular periodically changing scanning frequency.

Nanostructured gold deposited in gelatin template applied for electrochemical assay of glucose in serum

Czech Academy of Sciences Publication Activity Database

Juřík, T.; Podešva, Pavel; Farka, Z.; Kovář, D.; Skládal, P.; Foret, František

2016-01-01

Roč. 188, JAN (2016), s. 277-285 ISSN 0013-4686 R&D Projects: GA ČR(CZ) GA15-15479S Institutional support: RVO:68081715 Keywords : gold nanostructures * gelatin template * glucose electrooxidation * blood analysis * non-enzymatic sensor Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.798, year: 2016

Finger multibiometric cryptosystems: fusion strategy and template security

Science.gov (United States)

Peng, Jialiang; Li, Qiong; Abd El-Latif, Ahmed A.; Niu, Xiamu

2014-03-01

We address two critical issues in the design of a finger multibiometric system, i.e., fusion strategy and template security. First, three fusion strategies (feature-level, score-level, and decision-level fusions) with the corresponding template protection technique are proposed as the finger multibiometric cryptosystems to protect multiple finger biometric templates of fingerprint, finger vein, finger knuckle print, and finger shape modalities. Second, we theoretically analyze different fusion strategies for finger multibiometric cryptosystems with respect to their impact on security and recognition accuracy. Finally, the performance of finger multibiometric cryptosystems at different fusion levels is investigated on a merged finger multimodal biometric database. The comparative results suggest that the proposed finger multibiometric cryptosystem at feature-level fusion outperforms other approaches in terms of verification performance and template security.

MOVPE of InN films on GaN templates grown on sapphire and silicon(111) substrates

International Nuclear Information System (INIS)

Jamil, Muhammad; Arif, Ronald A.; Ee, Yik-Khoon; Tong, Hua; Tansu, Nelson; Higgins, John B.

2008-01-01

This paper reports the study of MOVPE of InN on GaN templates grown on sapphire and silicon(111) substrates. Thermodynamic analysis of MOVPE of InN performed using NH 3 as nitrogen source and the experimental findings support the droplet-free epitaxial growth of InN under high V/III ratios of input precursors. At a growth pressure of 500 Torr, the optimum growth temperature and V/III ratio of the InN film are 575-650 C and >3 x 10 5 , respectively. The surface RMS roughness of InN film grown GaN/sapphire template is ∝0.3 nm on 2 μm x 2 μm area, while the RMS roughness of the InN film grown on GaN/Si(111) templates is found as ∝0.7 nm. The X-ray diffraction (XRD) measurement reveals the (0002) texture of the InN film on GaN/sapphire template with a FWHM of 281 arcsec of the InN(0002) ω rocking curve. For the film grown on GaN/Si template under identical growth conditions, the XRD measurements show the presence of metallic In, in addition to the (0002) orientation of InN layer. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity

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Ivaylo P. Ivanov

2017-06-01

Full Text Available Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs in its >700-nucleotide (nt 5′ leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5′ region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5′ conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro. In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression.

The need of appropriate brain SPECT templates for SPM comparisons

International Nuclear Information System (INIS)

Morbelli, S.; Altrinetti, V.; Piccardo, A.; Rodriguez, G.; Brugnolo, A.; Nobili, F.; Mignone, A.; Pupi, A.; Koulibaly, P.M.

2008-01-01

Statistical parametric mapping (SPM) is used worldwide to compare brain perfusion single photon emission computed tomography (SPECT) data. The default template within the SPM package used for SPECT image normalization includes images of a group of healthy subjects studied with 99m TcHMPAO. Since [ 99m Tc] HMPAO and [ 99m Tc] ECD have shown to distribute differently in SPECT studies, we formulated the hypothesis that comparing set of [ 99m Tc]ECD data normalized by means of a [ 99m Tc]HMPAO template may lead to incorrect results. A customized [ 99m Tc]ECD template was built with SPECT and magnetic resonance imaging (MRI) images of 22 neurologically healthy women. Then, two sets of subjects, i.e. a group of patients with very early Alzheimer's disease (eAD) and a matched control group, studied by means of [ 99m Tc]ECD SPECT, were chosen for comparisons. The same statistical approach (t-test between eAD patients and controls and correlation analysis between brain SPECT and a cognitive score) was applied twice, i.e. after normalization with either the default [ 99m Tc]HMPAO template or the customized [ 99m Tc]ECD template. In the comparison between eAD and controls, a cluster of difference in the posterior-cingulate gyrus of both hemispheres was only highlighted when using the customized [ 99m Tc]ECD template, but was missed when using the default [ 99m Tc]HMPAO template. In the correlation between brain perfusion and a cognitive score, the significant cluster was more significant and far more extended, also including the right superior temporal gyrus, using the customized [ 99m Tc]ECD template than using the default [ 99m Tc]HMPAO template. These data suggest the need of customized, radiopharmaceutical-matched SPECT templates to be used within the SPM package. The present customized [ 99m Tc]ECD template is now freely available on the web. (authors)

Regulation of Ca2+ release from mitochondria by the oxidation-reduction state of pyridine nucleotides

Science.gov (United States)

Lehninger, Albert L.; Vercesi, Anibal; Bababunmi, Enitan A.

1978-01-01

Mitochondria from normal rat liver and heart, and also Ehrlich tumor cells, respiring on succinate as energy source in the presence of rotenone (to prevent net electron flow to oxygen from the endogenous pyridine nucleotides), rapidly take up Ca2+ and retain it so long as the pyridine nucleotides are kept in the reduced state. When acetoacetate is added to bring the pyridine nucleotides into a more oxidized state, Ca2+ is released to the medium. A subsequent addition of a reductant of the pyridine nucleotides such as β-hydroxybutyrate, glutamate, or isocitrate causes reuptake of the released Ca2+. Successive cycles of Ca2+ release and uptake can be induced by shifting the redox state of the pyridine nucleotides to more oxidized and more reduced states, respectively. Similar observations were made when succinate oxidation was replaced as energy source by ascorbate oxidation or by the hydrolysis of ATP. These and other observations form the basis of a hypothesis for feedback regulation of Ca2+-dependent substrate- or energy-mobilizing enzymatic reactions by the uptake or release of mitochondrial Ca2+, mediated by the cytosolic phosphate potential and the ATP-dependent reduction of mitochondrial pyridine nucleotides by reversal of electron transport. Images PMID:25436

POROUS MEMBRANE TEMPLATED SYNTHESIS OF POLYMER PILLARED LAYER

Institute of Scientific and Technical Information of China (English)

Zhong-wei Niu; Dan Li; Zhen-zhong Yang

2003-01-01

The anodic porous alumina membranes with a definite pore diameter and aspect ratio were used as templates to synthesize polymer pillared layer structures. The pillared polymer was produced in the template membrane pores, and the layer on the template surfaces. Rigid cured epoxy resin, polystyrene and soft hydrogel were chosen to confirm the methodology. The pillars were in the form of either tubes or fibers, which were controlled by the alumina membrane pore surface wettability. The structural features were confirmed by scanning electron microscopy results.

The Affordance Template ROS Package for Robot Task Programming

Science.gov (United States)

Hart, Stephen; Dinh, Paul; Hambuchen, Kimberly

2015-01-01

This paper introduces the Affordance Template ROS package for quickly programming, adjusting, and executing robot applications in the ROS RViz environment. This package extends the capabilities of RViz interactive markers by allowing an operator to specify multiple end-effector waypoint locations and grasp poses in object-centric coordinate frames and to adjust these waypoints in order to meet the run-time demands of the task (specifically, object scale and location). The Affordance Template package stores task specifications in a robot-agnostic XML description format such that it is trivial to apply a template to a new robot. As such, the Affordance Template package provides a robot-generic ROS tool appropriate for building semi-autonomous, manipulation-based applications. Affordance Templates were developed by the NASA-JSC DARPA Robotics Challenge (DRC) team and have since successfully been deployed on multiple platforms including the NASA Valkyrie and Robonaut 2 humanoids, the University of Texas Dreamer robot and the Willow Garage PR2. In this paper, the specification and implementation of the affordance template package is introduced and demonstrated through examples for wheel (valve) turning, pick-and-place, and drill grasping, evincing its utility and flexibility for a wide variety of robot applications.

Children’s Non-symbolic, Symbolic Addition and Their Mapping Capacity at 4–7 Years Old

Directory of Open Access Journals (Sweden)

Yanjun Li

2017-07-01

Full Text Available The study aimed to examine the developmental trajectories of non-symbolic and symbolic addition capacities in children and the mapping ability between these two. We assessed 106 4- to 7-year-old children and found that 4-year-olds were able to do non-symbolic addition but not symbolic addition. Five-year-olds and older were able to do symbolic addition and their performance in symbolic addition exceeded non-symbolic addition in grade 1 (approximate age 7. These results suggested non-symbolic addition ability emerges earlier and is less affected by formal mathematical education than symbolic addition. Meanwhile, we tested children’s bi-directional mapping ability using a novel task and found that children were able to map between symbolic and non-symbolic representations of number at age 5. Their ability in mapping non-symbolic to symbolic number became more proficient in grade 1 (approximate age 7. This suggests children at age 7 have developed a relatively mature symbolic representation system.

Classifying Coding DNA with Nucleotide Statistics

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Nicolas Carels

2009-10-01

Full Text Available In this report, we compared the success rate of classification of coding sequences (CDS vs. introns by Codon Structure Factor (CSF and by a method that we called Universal Feature Method (UFM. UFM is based on the scoring of purine bias (Rrr and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i the stop codon distribution, (ii the product of purine probabilities in the three positions of nucleotide triplets, (iii the product of Cytosine (C, Guanine (G, and Adenine (A probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv the probabilities of G in 1st and 2nd position of triplets and (v the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives of Homo sapiens (>250 bp, Drosophila melanogaster (>250 bp and Arabidopsis thaliana (>200 bp are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.

Can Non-HLA Single Nucleotide Polymorphisms Help Stratify Risk in TrialNet Relatives at Risk for Type 1 Diabetes?

Science.gov (United States)

Steck, Andrea K; Xu, Ping; Geyer, Susan; Redondo, Maria J; Antinozzi, Peter; Wentworth, John M; Sosenko, Jay; Onengut-Gumuscu, Suna; Chen, Wei-Min; Rich, Stephen S; Pugliese, Alberto

2017-08-01

Genome-wide association studies identified >50 type 1 diabetes (T1D) associated non-human leukocyte antigens (non-HLA) loci. The purpose of this study was to assess the contribution of non-HLA single nucleotide polymorphisms (SNPs) to risk of disease progression. The TrialNet Pathway to Prevention Study follows relatives of T1D patients for development of autoantibodies (Abs) and T1D. Using the Immunochip, we analyzed 53 diabetes-associated, non-HLA SNPs in 1016 Ab-positive, at-risk non-Hispanic white relatives. Effect of SNPs on the development of multiple Abs and T1D. Cox proportional analyses included all substantial non-HLA SNPs, HLA genotypes, relationship to proband, sex, age at initial screening, initial Ab type, and number. Factors involved in progression from single to multiple Abs included age at screening, relationship to proband, HLA genotypes, and rs3087243 (cytotoxic T lymphocyte antigen-4). Significant factors for diabetes progression included age at screening, Ab number, HLA genotypes, rs6476839 [GLIS family zinc finger 3 (GLIS3)], and rs3184504 [SH2B adaptor protein 3 (SH2B3)]. When glucose area under the curve (AUC) was included, factors involved in disease progression included glucose AUC, age at screening, Ab number, relationship to proband, HLA genotypes, rs6476839 (GLIS3), and rs7221109 (CCR7). In stratified analyses by age, glucose AUC, age at screening, sibling, HLA genotypes, rs6476839 (GLIS3), and rs4900384 (C14orf64) were significantly associated with progression to diabetes in participants <12 years old, whereas glucose AUC, sibling, rs3184504 (SH2B3), and rs4900384 (C14orf64) were significant in those ≥12. In conclusion, we identified five non-HLA SNPs associated with increased risk of progression from Ab positivity to disease that may improve risk stratification for prevention trials. Copyright © 2017 by the Endocrine Society

Pengenalan Angka Pada Sistem Operasi Android Dengan Menggunakan Metode Template Matching

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Abdi Pandu Kusuma

2016-07-01

Full Text Available AbstrakUsia dini merupakan usia yang efektif untuk mengembangkan berbagai potensi yang dimiliki oleh anak. Upaya pengembangan potensi dapat dilakukan melalui berbagai cara termasuk dengan cara bermain. Bermain bagi anak merupakan cara yang tepat untuk belajar. Berdasarkan fenomena tersebut, maka perlu dibuat sebuah aplikasi pengenalan angka yang interaktif dengan unsur edukasi. Aplikasi tersebut diharapkan dapat mengambil keputusan secara otomatis apa yang ditulis anak itu bernilai benar atau salah dan juga dapat membangkitkan semangat belajar anak dalam mengenal pola angka. Solusi yang sesuai agar aplikasi tersebut dapat memberikan jawaban salah atau benar digunakan satu metode yaitu template matching. Pengenalan angka dengan menggunakan metode template matching dilakukan dengan cara membandingkan citra masukan dengan citra template. Hasil template matching dihitung dari banyaknya titik pada citra masukan yang sesuai dengan citra template. Template disediakan pada database untuk memberikan contoh cara penulisan pola angka. Uji coba dilakukan pada aplikasi sebanyak 40 kali dengan pola yang berbeda. Dari hasil uji coba didapat prosentase keberhasilan aplikasi ini mencapai 75,75%.Kata kunci: Belajar, bermain, Template Matching, dan pola. AbstractEarly childhood is an effective age to develop the potential of the child. Potential development efforts can be done through various ways, including by playing. Playing for children is a great way to learn. Based on this phenomenon, it should be made an introduction to the numbers interactive application with elements of education. The application is expected to take decisions automatically what the child is written is true or false, and also can encourage a child's learning in recognizing number patterns. Appropriate solutions so that the app can give an answer right or wrong to use the methods that template matching. The introduction of the numbers by using template matching is done by comparing the

DNA-templated antibody conjugation for targeted drug delivery to cancer cells

DEFF Research Database (Denmark)

Liu, Tianqiang

2016-01-01

-templated organic synthesis due to the wide existence of the 3-histidine cluster in most wild-type proteins. In this thesis, three projects that relate to targeted drug delivery to cancer cells based on the DTPC method is described. The first project was a delivery system which uses transferrin as the targeting....... The study shows that DNA is a highly useful tool for the assembly of proteins with potential therapeutic applications. The DNA-templated protein conjugation shows a promising application in constructing antibody-toxin conjugates or antibody-drug conjugates. In addition, DNA strands used for antibody...... either antibody engineering or special expression systems and are both time and labor consuming. To avoid the drawbacks caused by conventional chemical modification and recombinant methodologies, an ideal site specific conjugation technique would use natural amino acid residues to the protein by a new...

A lightweight approach for biometric template protection

Science.gov (United States)

Al-Assam, Hisham; Sellahewa, Harin; Jassim, Sabah

2009-05-01

Privacy and security are vital concerns for practical biometric systems. The concept of cancelable or revocable biometrics has been proposed as a solution for biometric template security. Revocable biometric means that biometric templates are no longer fixed over time and could be revoked in the same way as lost or stolen credit cards are. In this paper, we describe a novel and an efficient approach to biometric template protection that meets the revocability property. This scheme can be incorporated into any biometric verification scheme while maintaining, if not improving, the accuracy of the original biometric system. However, we shall demonstrate the result of applying such transforms on face biometric templates and compare the efficiency of our approach with that of the well-known random projection techniques. We shall also present the results of experimental work on recognition accuracy before and after applying the proposed transform on feature vectors that are generated by wavelet transforms. These results are based on experiments conducted on a number of well-known face image databases, e.g. Yale and ORL databases.

Organic or organometallic template mediated clay synthesis

Science.gov (United States)

Gregar, Kathleen C.; Winans, Randall E.; Botto, Robert E.

1994-01-01

A method for incorporating diverse Varieties of intercalants or templates directly during hydrothermal synthesis of clays such as hectorite or montmorillonite-type layer-silicate clays. For a hectorite layer-silicate clay, refluxing a gel of silica sol, magnesium hydroxide sol and lithium fluoride for two days in the presence of an organic or organometallic intercalant or template results in crystalline products containing either (a) organic dye molecules such as ethyl violet and methyl green, (b) dye molecules such as alcian blue that are based on a Cu(II)-phthalocyannine complex, or (c) transition metal complexes such as Ru(II)phenanthroline and Co(III)sepulchrate or (d) water-soluble porphyrins and metalloporphyrins. Montmorillonite-type clays are made by the method taught by U.S. Pat. No. 3,887,454 issued to Hickson, Jun. 13, 1975; however, a variety of intercalants or templates may be introduced. The intercalants or templates should have (i) water-solubility, (ii) positive charge, and (iii) thermal stability under moderately basic (pH 9-10) aqueous reflux conditions or hydrothermal pressurized conditions for the montmorillonite-type clays.

Herpesvirus telomerase RNA (vTR with a mutated template sequence abrogates herpesvirus-induced lymphomagenesis.

Directory of Open Access Journals (Sweden)

Benedikt B Kaufer

2011-10-01

Full Text Available Telomerase reverse transcriptase (TERT and telomerase RNA (TR represent the enzymatically active components of telomerase. In the complex, TR provides the template for the addition of telomeric repeats to telomeres, a protective structure at the end of linear chromosomes. Human TR with a mutation in the template region has been previously shown to inhibit proliferation of cancer cells in vitro. In this report, we examined the effects of a mutation in the template of a virus encoded TR (vTR on herpesvirus-induced tumorigenesis in vivo. For this purpose, we used the oncogenic avian herpesvirus Marek's disease virus (MDV as a natural virus-host model for lymphomagenesis. We generated recombinant MDV in which the vTR template sequence was mutated from AATCCCAATC to ATATATATAT (vAU5 by two-step Red-mediated mutagenesis. Recombinant viruses harboring the template mutation replicated with kinetics comparable to parental and revertant viruses in vitro. However, mutation of the vTR template sequence completely abrogated virus-induced tumor formation in vivo, although the virus was able to undergo low-level lytic replication. To confirm that the absence of tumors was dependent on the presence of mutant vTR in the telomerase complex, a second mutation was introduced in vAU5 that targeted the P6.1 stem loop, a conserved region essential for vTR-TERT interaction. Absence of vTR-AU5 from the telomerase complex restored virus-induced lymphoma formation. To test if the attenuated vAU5 could be used as an effective vaccine against MDV, we performed vaccination-challenge studies and determined that vaccination with vAU5 completely protected chickens from lethal challenge with highly virulent MDV. Taken together, our results demonstrate 1 that mutation of the vTR template sequence can completely abrogate virus-induced tumorigenesis, likely by the inhibition of cancer cell proliferation, and 2 that this strategy could be used to generate novel vaccine candidates

Enantioselective conjugate addition of hydroxylamines to pyrazolidinone acrylamides.

Science.gov (United States)

Sibi, M P; Liu, M

2001-12-27

Chiral relay templates provide amplification of selectivity in conjugate addition reactions. Reversal of stereochemistry of the product isoxazolidinones has also been demonstrated by a simple change of the Lewis acid. [reaction: see text

Additive non-uniform random sampling in superimposed fiber Bragg grating strain gauge

International Nuclear Information System (INIS)

Ma, Y C; Liu, H Y; Yan, S B; Li, J M; Tang, J; Yang, Y H; Yang, M W

2013-01-01

This paper demonstrates an additive non-uniform random sampling and interrogation method for dynamic and/or static strain gauge using a reflection spectrum from two superimposed fiber Bragg gratings (FBGs). The superimposed FBGs are designed to generate non-equidistant space of a sensing pulse train in the time domain during dynamic strain gauge. By combining centroid finding with smooth filtering methods, both the interrogation speed and accuracy are improved. A 1.9 kHz dynamic strain is measured by generating an additive non-uniform randomly distributed 2 kHz optical sensing pulse train from a mean 500 Hz triangular periodically changing scanning frequency. (paper)

Characterization of nickel nanocones routed by electrodeposition without any template.

Science.gov (United States)

Hang, Tao; Li, Ming; Fei, Qin; Mao, Dali

2008-01-23

This work reports the synthesis of Ni nanocones by a one-step electrodeposition method without any template. With the addition of ethylenediamine dihydrochloride (EDA·2HCl) in the nickel plating solution, the novel Ni conical structure can be easily deposited onto different metal surfaces. The as-prepared nickel nanocones grow preferentially along [Formula: see text] directions with very sharp tips. The conical structures are single crystalline without any disruption of the lattice planes. In addition, the Ni nanocone structure is demonstrated to show magnetocrystalline anisotropy and enhance the magnetic properties when compared with other Ni nanostructures.

Single nucleotide primer extension to detect genetic diseases: Experimental application to hemophilia B (factor IX) and cystic fibrosis genes

International Nuclear Information System (INIS)

Kuppuswamy, M.N.; Hoffmann, J.W.; Spitzer, S.G.; Groce, S.L.; Bajaj, S.P.; Kasper, C.K.

1991-01-01

In this report, the authors describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then prepared. Each contains the amplified fragment, a primer (18-mer or longer) whose sequence is identical to the coding sequence of the normal gene immediately flanking the 5' end of the mutation site, and either an α- 32 P-labeled nucleotide corresponding to the normal coding sequence at the mutation site or an α- 32 P-labeled nucleotide corresponding to the mutant sequence. An essential feature of the present methodology is that the base immediately 3' to the template-bound primer is one of those altered in the mutant, since in this way an extension of the primer by a single base will give an extended molecule characteristic of either the mutant or the wild type. The method is rapid and should be useful in carrier detection and prenatal diagnosis of every genetic disease with a known sequence variation

Synthetic opal as a template for nanostructured materials

Science.gov (United States)

White, Paul A.; Heales, Lindsey; Barber, Richard L.; Turney, Terence W.

2001-04-01

Synthetic opal has been used as a template for making 3D inverse opals of silica, titania and silicone rubber. The materials are mesoporous with connected pores and channels and have better opalescence than the opal templates they replace. Thin films of synthetic opal have been grown onto glass substrates by spin coating and these have also been used as templates for making thin films of inverse opal and as masks for depositing metal nanodots. This method produced hexagonally patterned 50 nm gold dots on a flat graphite substrate.

Factor 11 single-nucleotide variants in women with heavy menstrual bleeding

NARCIS (Netherlands)

Wiewel-Verschueren, Sophie; Mulder, Andre B.; Meijer, Karina; Mulder, Rene

2017-01-01

In a previous study it was shown that lower factor XI (FXI) levels in women with heavy menstrual bleeding (HMB). Our aim was to determine the single-nucleotide variants (SNVs) in the F11 gene in women with HMB. In addition, an extensive literature search was performed to determine the clinical

Proline-catalysed asymmetric ketol cyclizations: The template ...

Indian Academy of Sciences (India)

Unknown

Abstract. A modified template mechanism based on modelling studies of energy minimised complexes is presented for the asymmetric proline-catalysed cyclization of triketones 1, 2 and 3 to the 2S,3S-ketols. 1a, 2a and 3a respectively. The template model involves a three-point contact as favoured in enzyme– substrate ...

Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator

International Nuclear Information System (INIS)

Fenati, Renzo A.; Connolly, Ashley R.; Ellis, Amanda V.

2017-01-01

Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded–DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP–Cytosine > TPP–Thymine > TPP–Adenine ≥ TPP–Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80–90% quenching), compared to 25–30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. - Highlights: • Fluorophores and DNA intercalators effect the rate of toehold-mediated strand displacement. • Ethidium bromide had a destabilizing effect on mismatches that contained cytosine. • A cationic fluorophore and Black Hole Quencher 1 strand displacement system was 2–3 times faster than a FRET system. • This enabled SNP detection using toehold-mediated strand displacement in 15 min.

Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator

Energy Technology Data Exchange (ETDEWEB)

Fenati, Renzo A.; Connolly, Ashley R. [Flinders Centre for Nanoscale Science and Technology, Flinders University, Sturt Road, Bedford Park, Adelaide, South Australia 5042 (Australia); Ellis, Amanda V., E-mail: amanda.ellis@flinders.edu.au [Flinders Centre for Nanoscale Science and Technology, Flinders University, Sturt Road, Bedford Park, Adelaide, South Australia 5042 (Australia); Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010 (Australia)

2017-02-15

Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded–DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP–Cytosine > TPP–Thymine > TPP–Adenine ≥ TPP–Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80–90% quenching), compared to 25–30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. - Highlights: • Fluorophores and DNA intercalators effect the rate of toehold-mediated strand displacement. • Ethidium bromide had a destabilizing effect on mismatches that contained cytosine. • A cationic fluorophore and Black Hole Quencher 1 strand displacement system was 2–3 times faster than a FRET system. • This enabled SNP detection using toehold-mediated strand displacement in 15 min.

Fabrication of a Ni nano-imprint stamp for an anti-reflective layer using an anodic aluminum oxide template.

Science.gov (United States)

Park, Eun-Mi; Lim, Seung-Kyu; Ra, Senug-Hyun; Suh, Su-Jung

2013-11-01

Aluminum anodizing can alter pore diameter, density distribution, periodicity and layer thickness in a controlled way. Because of this property, porous type anodic aluminum oxide (AAO) was used as a template for nano-structure fabrication. The alumina layer generated at a constant voltage increased the pore size from 120 nm to 205 nm according to an increasing process time from 60 min to 150 min. The resulting fabricated AAO templates had pore diameters at or less than 200 nm. Ni was sputtered as a conductive layer onto this AAO template and electroplated using DC and pulse power. Comparing these Ni stamps, those generated from electroplating using on/reverse/off pulsing had an ordered pillar array and maintained the AAO template morphology. This stamp was used for nano-imprinting on UV curable resin coated glass wafer. Surface observations via electron microscopy showed that the nano-imprinted patterned had the same shape as the AAO template. A soft mold was subsequently fabricated and nano-imprinted to form a moth-eye structure on the glass wafer. An analysis of the substrate transmittance using UV-VIS/NIR spectroscopy showed that the transmittance of the substrate with the moth-eye structure was 5% greater that the non-patterned substrate.

Cytosolic nucleotides block and regulate the Arabidopsis vacuolar anion channel AtALMT9.

Science.gov (United States)

Zhang, Jingbo; Martinoia, Enrico; De Angeli, Alexis

2014-09-12

The aluminum-activated malate transporters (ALMTs) form a membrane protein family exhibiting different physiological roles in plants, varying from conferring tolerance to environmental Al(3+) to the regulation of stomatal movement. The regulation of the anion channels of the ALMT family is largely unknown. Identifying intracellular modulators of the activity of anion channels is fundamental to understanding their physiological functions. In this study we investigated the role of cytosolic nucleotides in regulating the activity of the vacuolar anion channel AtALMT9. We found that cytosolic nucleotides modulate the transport activity of AtALMT9. This modulation was based on a direct block of the pore of the channel at negative membrane potentials (open channel block) by the nucleotide and not by a phosphorylation mechanism. The block by nucleotides of AtALMT9-mediated currents was voltage dependent. The blocking efficiency of intracellular nucleotides increased with the number of phosphate groups and ATP was the most effective cellular blocker. Interestingly, the ATP block induced a marked modification of the current-voltage characteristic of AtALMT9. In addition, increased concentrations of vacuolar anions were able to shift the ATP block threshold to a more negative membrane potential. The block of AtALMT9-mediated anion currents by ATP at negative membrane potentials acts as a gate of the channel and vacuolar anion tune this gating mechanism. Our results suggest that anion transport across the vacuolar membrane in plant cells is controlled by cytosolic nucleotides and the energetic status of the cell. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Cytosolic Nucleotides Block and Regulate the Arabidopsis Vacuolar Anion Channel AtALMT9*

Science.gov (United States)

Zhang, Jingbo; Martinoia, Enrico; De Angeli, Alexis

2014-01-01

The aluminum-activated malate transporters (ALMTs) form a membrane protein family exhibiting different physiological roles in plants, varying from conferring tolerance to environmental Al3+ to the regulation of stomatal movement. The regulation of the anion channels of the ALMT family is largely unknown. Identifying intracellular modulators of the activity of anion channels is fundamental to understanding their physiological functions. In this study we investigated the role of cytosolic nucleotides in regulating the activity of the vacuolar anion channel AtALMT9. We found that cytosolic nucleotides modulate the transport activity of AtALMT9. This modulation was based on a direct block of the pore of the channel at negative membrane potentials (open channel block) by the nucleotide and not by a phosphorylation mechanism. The block by nucleotides of AtALMT9-mediated currents was voltage dependent. The blocking efficiency of intracellular nucleotides increased with the number of phosphate groups and ATP was the most effective cellular blocker. Interestingly, the ATP block induced a marked modification of the current-voltage characteristic of AtALMT9. In addition, increased concentrations of vacuolar anions were able to shift the ATP block threshold to a more negative membrane potential. The block of AtALMT9-mediated anion currents by ATP at negative membrane potentials acts as a gate of the channel and vacuolar anion tune this gating mechanism. Our results suggest that anion transport across the vacuolar membrane in plant cells is controlled by cytosolic nucleotides and the energetic status of the cell. PMID:25028514

Assessing usefulness and researcher satisfaction with consent form templates.

Science.gov (United States)

Larson, Elaine L; Teller, Alan; Aguirre, Alejandra N; Jackson, Jhia; Meyer, Dodi

2017-08-01

We aimed to improve the research consenting process by developing and evaluating simplified consent forms. Four templates written at the eighth-tenth grade reading level were developed and trialed by a group of experts in clinical research, health literacy, national regulatory requirements, and end users. Researchers from protocols which had received expedited review were surveyed at 2 time points regarding their use and assessment of the templates. At baseline 18/86 (20.9%) responding researchers had heard of the templates and 5 (5.8%) reported that they had used them; 2 years later, 54.2% (32/59) had heard of the templates and 87.5% (28/32) had used them ( p Consent form templates may be one mechanism to improve patient comprehension of research protocols as well as efficiency of the review process, but require considerable time for development and implementation, and one key to their success is involvement and support from the IRB and technical staff.

Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes

OpenAIRE

Maijenburg, A.W.

2014-01-01

This thesis is entitled “Templated electrodeposition of functional nanostructures: nanowires, nanotubes and nanocubes”. Templated electrodeposition is the synthesis technique that was used throughout this thesis, and it comprises the use of a template with specific shape and dimensions for the formation of different types of nanostructures. Throughout this thesis, three different nanostructures were made: nanowires (Chapters 2 to 6), nanotubes (Chapters 2 and 5) and nanocubes (Chapters 7 and ...

Supplementary Material for: The arabidopsis cyclic nucleotide interactome

KAUST Repository

Donaldson, Lara; Meier, Stuart; Gehring, Christoph A

2016-01-01

Abstract Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

MULTIDIRECTIONAL BUILDING DETECTION IN AERIAL IMAGES WITHOUT SHAPE TEMPLATES

Directory of Open Access Journals (Sweden)

A. Manno-Kovacs

2013-05-01

Full Text Available The aim of this paper is to exploit orientation information of an urban area for extracting building contours without shape templates. Unlike using shape templates, these given contours describe more variability and reveal the fine details of the building outlines, resulting in a more accurate detection process, which is beneficial for many tasks, like map updating and city planning. According to our assumption, orientation of the closely located buildings is coherent, it is related to the road network, therefore adaptation of this information can lead to more efficient building detection results. The introduced method first extracts feature points for representing the urban area. Orientation information in the feature point neighborhoods is analyzed to define main orientations. Based on orientation information, the urban area is classified into different directional clusters. The edges of the classified building groups are then emphasized with shearlet based edge detection method, which is able to detect edges only in the main directions, resulting in an efficient connectivity map. In the last step, with the fusion of the feature points and connectivity map, building contours are detected with a non-parametric active contour method.

Ordered Nanomaterials Thin Films via Supported Anodized Alumina Templates

Directory of Open Access Journals (Sweden)

Mohammed eES-SOUNI

2014-10-01

Full Text Available Supported anodized alumina template films with highly ordered porosity are best suited for fabricating large area ordered nanostructures with tunable dimensions and aspect ratios. In this paper we first discuss important issues for the generation of such templates, including required properties of the Al/Ti/Au/Ti thin film heterostructure on a substrate for high quality templates. We then show examples of anisotropic nanostructure films consisting of noble metals using these templates, discuss briefly their optical properties and their applications to molecular detection using surface enhanced Raman spectroscopy. Finally we briefly address the possibility to make nanocomposite films, exemplary shown on a plasmonic-thermochromic nanocomposite of VO2-capped Au-nanorods.

Modification of TiO2 nanoparticles through lanthanum doping and PEG templating

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Marija Milanovic

2014-12-01

Full Text Available Pure and lanthanum doped titania nanopowders were synthesized through a room temperature sol-gel method using a template of polyethylene glycol (PEG. The progress of the synthesis in terms of phase formation and size of nanoparticles was monitored by X-ray diffraction, FTIR spectroscopy and SEM analysis. After calcination at 450 °C in air, the results have shown the presence of small particles crystallized predominantly in the form of anatase phase, with significant agglomeration. Nitrogen adsorption-desorption measurements confirmed that all prepared powders are mesoporous with an average pore diameter in range 3.1–3.8 nm. The addition of lanthanum ions leads to the nanopowders with the highest specific surface (BET area (203 m2/g. The obtained powders were compared to TiO2 prepared without a template.

Template-mediated, Hierarchical Engineering of Ordered Mesoporous Films and Powders

Science.gov (United States)

Tian, Zheng

Hierarchical control over pore size, pore topology, and meso/mictrostructure as well as material morphology (e.g., powders, monoliths, thin films) is crucial for meeting diverse materials needs among applications spanning next generation catalysts, sensors, batteries, sorbents, etc. The overarching goal of this thesis is to establish fundamental mechanistic insight enabling new strategies for realizing such hierarchical textural control for carbon materials that is not currently achievable with sacrificial pore formation by 'one-pot' surfactant-based 'soft'-templating or multi-step inorganic 'hard-templating. While 'hard'-templating is often tacitly discounted based upon its perceived complexity, it offers potential for overcoming key 'soft'-templating challenges, including bolstering pore stability, accommodating a more versatile palette of replica precursors, realizing ordered/spanning porosity in the case of porous thin films, simplifying formation of bi-continuous pore topologies, and inducing microstructure control within porous replica materials. In this thesis, we establish strategies for hard-templating of hierarchically porous and structured carbon powders and tunable thin films by both multi-step hard-templating and a new 'one-pot' template-replica precursor co-assembly process. We first develop a nominal hard-templating technique to successfully prepare three-dimensionally ordered mesoporous (3DOm) and 3DOm-supported microporous carbon thin films by exploiting our ability to synthesize and assemble size-tunable silica nanoparticles into scalable, colloidal crystalline thin film templates of tunable mono- to multi-layer thickness. This robust thin film template accommodates liquid and/or vapor-phase infiltration, polymerization, and pyrolysis of various carbon sources without pore contraction and/or collapse upon template sacrifice. The result is robust, flexible 3DOm or 3DOm-supported ultra-thin microporous films that can be transferred by stamp

Computational resources to filter gravitational wave data with P-approximant templates

International Nuclear Information System (INIS)

Porter, Edward K

2002-01-01

The prior knowledge of the gravitational waveform from compact binary systems makes matched filtering an attractive detection strategy. This detection method involves the filtering of the detector output with a set of theoretical waveforms or templates. One of the most important factors in this strategy is knowing how many templates are needed in order to reduce the loss of possible signals. In this study, we calculate the number of templates and computational power needed for a one-step search for gravitational waves from inspiralling binary systems. We build on previous works by first expanding the post-Newtonian waveforms to 2.5-PN order and second, for the first time, calculating the number of templates needed when using P-approximant waveforms. The analysis is carried out for the four main first-generation interferometers, LIGO, GEO600, VIRGO and TAMA. As well as template number, we also calculate the computational cost of generating banks of templates for filtering GW data. We carry out the calculations for two initial conditions. In the first case we assume a minimum individual mass of 1 M o-dot and in the second, we assume a minimum individual mass of 5 M o-dot . We find that, in general, we need more P-approximant templates to carry out a search than if we use standard PN templates. This increase varies according to the order of PN-approximation, but can be as high as a factor of 3 and is explained by the smaller span of the P-approximant templates as we go to higher masses. The promising outcome is that for 2-PN templates, the increase is small and is outweighed by the known robustness of the 2-PN P-approximant templates

The effect of a new communication template on anticipated willingness to initiate or resume allergen immunotherapy

DEFF Research Database (Denmark)

Calderon, Moises A; Cox, Linda; Casale, Thomas B

2015-01-01

to validate the new communication template and to assess its impact on anticipated willingness to initiate or resume allergen immunotherapy. RESULTS: We surveyed a total of 261 patients (France: 57; Germany: 51; Spain: 52; USA: 51; Russia: 50), comprising 127 "early abandoners" and 134 "non...

Hidden correlations entailed by q-non additivity render the q-monoatomic gas highly non trivial

Science.gov (United States)

Plastino, A.; Rocca, M. C.

2018-01-01

It ts known that Tsallis' q-non-additivity entails hidden correlations. It has also been shown that even for a monoatomic gas, both the q-partition function Z and the mean energy 〈 U 〉 diverge and, in particular, exhibit poles for certain values of the Tsallis non additivity parameter q. This happens because Z and 〈 U 〉 both depend on a Γ-function. This Γ, in turn, depends upon the spatial dimension ν. We encounter three different regimes according to the argument A of the Γ-function. (1) A > 0, (2) A 0 outside the poles. (3) A displays poles and the physics is obtained via dimensional regularization. In cases (2) and (3) one discovers gravitational effects and quartets of particles. Moreover, bound states and gravitational effects emerge as a consequence of the hidden q-correlations.

Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides

Directory of Open Access Journals (Sweden)

Wang Yanli

2007-02-01

Full Text Available Abstract Background 8-Oxoguanine (8-oxoG is a common oxidative lesion frequently encountered by DNA polymerases such as the repair enzyme DNA polymerase β (pol β. To interpret in atomic and energetic detail how pol β processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol β 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. Results Our analyses show that the closing pathways of the 8-oxoG complexes are different from one another and from the nonlesioned analogues in terms of the individual transition states along each pathway, associated energies, and the stability of each pathway's closed state relative to the corresponding open state. In particular, the closed-to-open state stability difference in each system establishes a hierarchy of stability (from high to low as G:C > 8-oxoG:C > 8-oxoG:A > G:A, corresponding to -3, -2, 2, 9 kBT, respectively. This hierarchy of closed state stability parallels the experimentally observed processing efficiencies for the four pairs. Network models based on the calculated rate constants in each pathway indicate that the closed species are more populated than the open species for 8-oxoG:dCTP, whereas the opposite is true for 8-oxoG:dATP. Conclusion These results suggest that the lower insertion efficiency (larger Km for dATP compared to dCTP opposite 8-oxoG is caused by a less stable closed-form of pol β, destabilized by unfavorable interactions between Tyr271 and the mispair. This stability of the closed vs. open form can also explain the higher insertion efficiency for 8-oxoG:dATP compared to the nonlesioned G:dATP pair, which also has a higher overall conformational barrier. Our study offers atomic details of the complexes at different states, in addition to helping interpret the different insertion efficiencies of dATP and dCTP opposite 8-oxoG and G.

Enzymatic activities of the GB virus-B RNA-dependent RNA polymerase

International Nuclear Information System (INIS)

Ranjith-Kumar, C.T.; Santos, Jan Lee; Gutshall, Lester L.; Johnston, Victor K.; Juili, L.-G.; Kim, M.-J.; Porter, David J.; Maley, Derrick; Greenwood, Cathy; Earnshaw, David L.; Baker, Audrey; Gu Baohua; Silverman, Carol; Sarisky, Robert T.; Kao Cheng

2003-01-01

The GB virus-B (GBV-B) nonstructural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp) with greater than 50% sequence similarity to the hepatitis C virus (HCV) NS5B. Recombinant GBV-B NS5B was reported to possess RdRp activity (W. Zhong et al., 2000, J. Viral Hepat. 7, 335-342). In this study, the GBV-B RdRp was examined more thoroughly for different RNA synthesis activities, including primer-extension, de novo initiation, template switch, terminal nucleotide addition, and template specificity. The results can be compared with previous characterizations of the HCV RdRp. The two RdRps share similarities in terms of metal ion and template preference, the abilities to add nontemplated nucleotides, perform both de novo initiation and extension from a primer, and switch templates. However, several differences in RNA synthesis between the GBV-B and HCV RdRps were observed, including (i) optimal temperatures for activity, (ii) ranges of Mn 2+ concentration tolerated for activity, and (iii) cation requirements for de novo RNA synthesis and terminal transferase activity. To assess whether the recombinant GBV-B RdRp may represent a relevant surrogate system for testing HCV antiviral agents, two compounds demonstrated to be active at nanomolar concentrations against HCV NS5B were tested on the GBV RdRp. A chain terminating nucleotide analog could prevent RNA synthesis, while a nonnucleoside HCV inhibitor was unable to affect RNA synthesis by the GBV RdRp

The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf

Directory of Open Access Journals (Sweden)

Geldner Niko

2005-02-01

Full Text Available Abstract Background Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs that stimulate the exchange of the tightly bound GDP nucleotide by GTP. The catalytic domain responsible for nucleotide exchange is in general associated with non-catalytic domains that define the spatio-temporal conditions of activation. In the case of small G proteins of the Arf subfamily, which are major regulators of membrane trafficking, GEFs form a heterogeneous family whose only common characteristic is the well-characterized Sec7 catalytic domain. In contrast, the function of non-catalytic domains and how they regulate/cooperate with the catalytic domain is essentially unknown. Results Based on Sec7-containing sequences from fully-annotated eukaryotic genomes, including our annotation of these sequences from Paramecium, we have investigated the domain architecture of large ArfGEFs of the BIG and GBF subfamilies, which are involved in Golgi traffic. Multiple sequence alignments combined with the analysis of predicted secondary structures, non-structured regions and splicing patterns, identifies five novel non-catalytic structural domains which are common to both subfamilies, revealing that they share a conserved modular organization. We also report a novel ArfGEF subfamily with a domain organization so far unique to alveolates, which we name TBS (TBC-Sec7. Conclusion Our analysis unifies the BIG and GBF subfamilies into a higher order subfamily, which, together with their being the only subfamilies common to all eukaryotes, suggests that they descend from a common ancestor from which species-specific ArfGEFs have subsequently evolved. Our identification of a conserved modular architecture provides a background for future functional investigation of non-catalytic domains.

Fast Template-based Shape Analysis using Diffeomorphic Iterative Centroid

OpenAIRE

Cury , Claire; Glaunès , Joan Alexis; Chupin , Marie; Colliot , Olivier

2014-01-01

International audience; A common approach for the analysis of anatomical variability relies on the estimation of a representative template of the population, followed by the study of this population based on the parameters of the deformations going from the template to the population. The Large Deformation Diffeomorphic Metric Mapping framework is widely used for shape analysis of anatomical structures, but computing a template with such framework is computationally expensive. In this paper w...

Strand Displacement by DNA Polymerase III Occurs through a τ-ψ-χ Link to Single-stranded DNA-binding Protein Coating the Lagging Strand Template*

OpenAIRE

Yuan, Quan; McHenry, Charles S.

2009-01-01

In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of γ-complex to support the reaction in the absence of τ. However, if γ-complex is p...

Creating Shape Templates for Patient Specific Biventricular Modeling in Congenital Heart Disease

Science.gov (United States)

Gilbert, Kathleen; Farrar, Genevieve; Cowan, Brett R.; Suinesiaputra, Avan; Occleshaw, Christopher; Pontré, Beau; Perry, James; Hegde, Sanjeet; Marsden, Alison; Omens, Jeff; McCulloch, Andrew; Young, Alistair A.

2018-01-01

Survival rates for infants with congenital heart disease (CHD) are improving, resulting in a growing population of adults with CHD. However, the analysis of left and right ventricular function is very time-consuming owing to the variety of congenital morphologies. Efficient customization of patient geometry and function depends on high quality shape templates specifically designed for the application. In this paper, we combine a method for creating finite element shape templates with an interactive template customization to patient MRI examinations. This enables different templates to be chosen depending on patient morphology. To demonstrate this pipeline, a new biventricular template with 162 elements was created and tested in place of an existing 82-element template. The method was able to provide fast interactive biventricular analysis with 0.31 sec per edit response time. The new template was customized to 13 CHD patients with similar biventricular topology, showing improved performance over the previous template and good agreement with clinical indices. PMID:26736353

Structural insight of dopamine β-hydroxylase, a drug target for complex traits, and functional significance of exonic single nucleotide polymorphisms.

Directory of Open Access Journals (Sweden)

Abhijeet Kapoor

Full Text Available Human dopamine β-hydroxylase (DBH is an important therapeutic target for complex traits. Several single nucleotide polymorphisms (SNPs have also been identified in DBH with potential adverse physiological effect. However, difficulty in obtaining diffractable crystals and lack of a suitable template for modeling the protein has ensured that neither crystallographic three-dimensional structure nor computational model for the enzyme is available to aid rational drug design, prediction of functional significance of SNPs or analytical protein engineering.Adequate biochemical information regarding human DBH, structural coordinates for peptidylglycine alpha-hydroxylating monooxygenase and computational data from a partial model of rat DBH were used along with logical manual intervention in a novel way to build an in silico model of human DBH. The model provides structural insight into the active site, metal coordination, subunit interface, substrate recognition and inhibitor binding. It reveals that DOMON domain potentially promotes tetramerization, while substrate dopamine and a potential therapeutic inhibitor nepicastat are stabilized in the active site through multiple hydrogen bonding. Functional significance of several exonic SNPs could be described from a structural analysis of the model. The model confirms that SNP resulting in Ala318Ser or Leu317Pro mutation may not influence enzyme activity, while Gly482Arg might actually do so being in the proximity of the active site. Arg549Cys may cause abnormal oligomerization through non-native disulfide bond formation. Other SNPs like Glu181, Glu250, Lys239 and Asp290 could potentially inhibit tetramerization thus affecting function.The first three-dimensional model of full-length human DBH protein was obtained in a novel manner with a set of experimental data as guideline for consistency of in silico prediction. Preliminary physicochemical tests validated the model. The model confirms, rationalizes and

Structural insight of dopamine β-hydroxylase, a drug target for complex traits, and functional significance of exonic single nucleotide polymorphisms.

Science.gov (United States)

Kapoor, Abhijeet; Shandilya, Manish; Kundu, Suman

2011-01-01

Human dopamine β-hydroxylase (DBH) is an important therapeutic target for complex traits. Several single nucleotide polymorphisms (SNPs) have also been identified in DBH with potential adverse physiological effect. However, difficulty in obtaining diffractable crystals and lack of a suitable template for modeling the protein has ensured that neither crystallographic three-dimensional structure nor computational model for the enzyme is available to aid rational drug design, prediction of functional significance of SNPs or analytical protein engineering. Adequate biochemical information regarding human DBH, structural coordinates for peptidylglycine alpha-hydroxylating monooxygenase and computational data from a partial model of rat DBH were used along with logical manual intervention in a novel way to build an in silico model of human DBH. The model provides structural insight into the active site, metal coordination, subunit interface, substrate recognition and inhibitor binding. It reveals that DOMON domain potentially promotes tetramerization, while substrate dopamine and a potential therapeutic inhibitor nepicastat are stabilized in the active site through multiple hydrogen bonding. Functional significance of several exonic SNPs could be described from a structural analysis of the model. The model confirms that SNP resulting in Ala318Ser or Leu317Pro mutation may not influence enzyme activity, while Gly482Arg might actually do so being in the proximity of the active site. Arg549Cys may cause abnormal oligomerization through non-native disulfide bond formation. Other SNPs like Glu181, Glu250, Lys239 and Asp290 could potentially inhibit tetramerization thus affecting function. The first three-dimensional model of full-length human DBH protein was obtained in a novel manner with a set of experimental data as guideline for consistency of in silico prediction. Preliminary physicochemical tests validated the model. The model confirms, rationalizes and provides

The Utility of Template Analysis in Qualitative Psychology Research.

Science.gov (United States)

Brooks, Joanna; McCluskey, Serena; Turley, Emma; King, Nigel

2015-04-03

Thematic analysis is widely used in qualitative psychology research, and in this article, we present a particular style of thematic analysis known as Template Analysis. We outline the technique and consider its epistemological position, then describe three case studies of research projects which employed Template Analysis to illustrate the diverse ways it can be used. Our first case study illustrates how the technique was employed in data analysis undertaken by a team of researchers in a large-scale qualitative research project. Our second example demonstrates how a qualitative study that set out to build on mainstream theory made use of the a priori themes (themes determined in advance of coding) permitted in Template Analysis. Our final case study shows how Template Analysis can be used from an interpretative phenomenological stance. We highlight the distinctive features of this style of thematic analysis, discuss the kind of research where it may be particularly appropriate, and consider possible limitations of the technique. We conclude that Template Analysis is a flexible form of thematic analysis with real utility in qualitative psychology research.

Fabrication of high quality ordered porous anodic aluminum oxide templates

International Nuclear Information System (INIS)

Liu Kai; Du Kai; Chen Jing; Zhou Lan; Zhang Lin; Fang Yu

2010-01-01

The preparation of porous anodic aluminum oxide (AAO) templates has been studied with oxalic acid as electrolyte. The morphology of the as-prepared templates has been characterized by field-emission scanning electron microscope (FE-SEM). The pores distributed orderly and uniformly with the diameter ranging from 40 nm to 70 nm. The experimental results indicate that electrolyte concentration, oxidation voltage, oxidation temperature and oxidation time affect the structure of AAO templates. Ordered porous AAO templates can be derived without annealing and finishing. X-ray diffraction (XRD) analysis indicates that the aluminum oxide film is mainly composed of amorphous Al 2 O 3 . (authors)

Polymeric Bicontinuous Microemulsions as Templates for Nanostructured Materials

Science.gov (United States)

Jones, Brad Howard

Ternary blends of two homopolymers and a diblock copolymer can self-assemble into interpenetrating, three dimensionally-continuous networks with a characteristic length scale of ˜ 100 nm. In this thesis, it is shown that these liquid phases, known as polymeric bicontinuous microemulsions (BμE), can be designed as versatile precursors to nanoporous materials having pores with uniform sizes of ˜ 100 nm. The model blends from which the porous materials are derived are composed of polyethylene (PE) and a sacrificial polyolefin. The liquid BμE structure is captured by crystallization of the PE, and a three-dimensionally continuous pore network with a narrow pore size distribution is generated by selective extraction of the sacrificial component. The original BμE structure is retained in the resultant nanoporous PE. This monolithic material is then used as a template in the synthesis of other nanoporous materials for which structural control at the nm scale has traditionally been difficult to achieve. These materials, which include a high-temperature ceramic, polymeric thermosets, and a conducting polymer, are produced by a simple nanocasting process, providing an inverse replica of the PE template. On account of the BμE structure of the template, the product materials also possess three-dimensionally continuous pore networks with narrow size distributions centered at ˜ 100 nm. The PE template is further used as a template for the production of hierarchically structured inorganic and polymeric materials by infiltration of mesostructured compounds into its pore network. In the former case, a hierarchically porous SiO2 material is demonstrated, simultaneously possessing two discrete, bicontinuous pore networks with sizes differing by over an order of magnitude. Finally, the templating procedures are extended to thin films supported on substrates and novel conductive polymer films are synthesized. The work described herein represents an unprecedented suite of

Template polymerization of N-vinylimidazole along poly(methacrylic acid) in water

NARCIS (Netherlands)

Grampel, Hendrik Theodorus van de

1990-01-01

Template polymerisaties zijn polymerisaties waarbij radicalen gedurende het grootste gedeelte van hun bestaan langs het template polymeer groeien. In het algemeen kan de template invloed hebben op de polymerisatiesnelheid, als ook op het molecuulgewicht en de tacticiteit van het bijgevormde

Biosynthesis of a hypermodified nucleotide in Saccharomyces carlsbergensis 17S and HeLa-cell 18S ribosomal ribonucleic acid.

Science.gov (United States)

Brand, R C; Klootwijk, J; Planta, R J; Maden, B E

1978-01-01

The biosynthesis of a hypermodified nucleotide, similar to or identical with 3-(3-amino-3-carboxypropyl)-1-methylpseudouridine monophosphate, present in Saccharomyces carlsbergensis 17S and HeLa-cell 18S rRNA, was investigated with respect to the sequence of reactions required for synthesis and their timing in ribosome maturation. In both yeast and HeLa cells methylation precedes attachment of the 3-amino-3-carboxypropyl group. In yeast the methylated precursor nucleotide was tentatively characterized as 1-methylpseudouridine. This precursor nucleotide was demonstrated in both 37S and most of the cytoplasmic 18S pre-rRNA (rRNA precursor) molecules. The synthesis of the hypermodified nucleotide is completed just before the final cleavage of 18S pre-rRNA to give 17S rRNA, so that the final addition of the 3-amino-3-carboxypropyl group is a cytoplasmic event. Comparable experiments with HeLa cells indicated that formation of 1-methylpseudouridine occurs at the level of 45S RNA and addition of the 3-amino-3-carboxypropyl group occurs in the cytoplasm on newly synthesized 18S RNA.

A Hybrid Approach to Protect Palmprint Templates

Directory of Open Access Journals (Sweden)

Hailun Liu

2014-01-01

Full Text Available Biometric template protection is indispensable to protect personal privacy in large-scale deployment of biometric systems. Accuracy, changeability, and security are three critical requirements for template protection algorithms. However, existing template protection algorithms cannot satisfy all these requirements well. In this paper, we propose a hybrid approach that combines random projection and fuzzy vault to improve the performances at these three points. Heterogeneous space is designed for combining random projection and fuzzy vault properly in the hybrid scheme. New chaff point generation method is also proposed to enhance the security of the heterogeneous vault. Theoretical analyses of proposed hybrid approach in terms of accuracy, changeability, and security are given in this paper. Palmprint database based experimental results well support the theoretical analyses and demonstrate the effectiveness of proposed hybrid approach.

Uranyl Sulfate Nanotubules Templated by N-phenylglycine

Directory of Open Access Journals (Sweden)

Oleg I. Siidra

2018-04-01

Full Text Available The synthesis, structure, and infrared spectroscopy properties of the new organically templated uranyl sulfate Na(phgH+7[(UO26(SO410](H2O3.5 (1, obtained at room temperature by evaporation from aqueous solution, are reported. Its structure contains unique uranyl sulfate [(UO26(SO410]8− nanotubules templated by protonated N-phenylglycine (C6H5NH2CH2COOH+. Their internal diameter is 1.4 nm. Each of the nanotubules is built from uranyl sulfate rings sharing common SO4 tetrahedra. The template plays an important role in the formation of the complex structure of 1. The aromatic rings are stacked parallel to each other due to the effect of π–π interaction with their side chains extending into the gaps between the nanotubules.

Application of Carbohydrate-Templated Asymmetric Diels-Alder Reaction to the Syntheses of ent-Penicillones A and B.

Science.gov (United States)

Weng, Chia-Hao; Hsu, Day-Shin; Liao, Chun-Chen

2016-11-18

Total syntheses of ent-penicillones A (ent-1) and B (ent-2) from 3,5-dimethylcatechol (3) were accomplished in 10 and 9 synthetic steps, respectively. A carbohydrate-templated asymmetric intramolecular Diels-Alder reaction of a masked o-benzoquinone (MOB) 9 and an aqueous acid-catalyzed intramolecular aldol reaction are the key synthetic steps. In addition, the absolute configurations of the bicyclo[2.2.2]oct-5-en-2-one core obtained from the per-O-benzylated α-d-glucopyranosyl as a carbohydrate template in the intramolecular Diels-Alder reaction of MOBs were revised.

Removal of carbamazepine and clofibric acid from water using double templates-molecularly imprinted polymers.

Science.gov (United States)

Dai, Chao-meng; Zhang, Juan; Zhang, Ya-lei; Zhou, Xue-fei; Duan, Yan-ping; Liu, Shu-guang

2013-08-01

A novel double templates-molecularly imprinted polymer (MIP) was prepared by precipitation polymerization using carbamazepine (CBZ) and clofibric acid (CA) as the double templates molecular and 2-vinylpyridine as functional monomer. The equilibrium data of MIP was well described by the Freundlich isotherm model. Two kinetic models were adopted to describe the experimental data, and the pseudo second-order model well-described adsorption of CBZ and CA on the MIP. Adsorption experimental results showed that the MIP had good selectivity and adsorption capacity for CBZ and CA in the presence of competitive compounds compared with non-imprinted polymer, commercial powdered activated carbon, and C18 adsorbents. The feasibility of removing CBZ and CA from water by the MIP was demonstrated using tap water, lake water, and river water.

Non toxic additives for improved fabric filter performance

Energy Technology Data Exchange (ETDEWEB)

Bustard, C.J.; Baldrey, K.E.; Ebner, T.G. [ADA Technologies, Inc., Englewood, CO (United States)] [and others

1995-11-01

The overall objective of this three-phase Small Business innovative Research (SBIR) program funded by the Department of Energy pittsburgh Energy Technology Center (PETC) is to commercialize a technology based upon the use of non-toxic, novel flue gas conditioning agents to improve particulate air toxic control and overall fabric filter performance. The ultimate objective of the Phase II program currently in progress is to demonstrate that the candidate additives are successful at full-scale on flue gas from a coal-fired utility boiler. This paper covers bench-scale field tests conducted during the period February through May, 1995. The bench-scale additives testing was conducted on a flue gas slipstream taken upstream of the existing particulate control device at a utility power plant firing a Texas lignite coal. These tests were preceded by extensive testing with additives in the laboratory using a simulated flue gas stream and re-dispersed flyash from the same power plant. The bench-scale field testing was undertaken to demonstrate the performance with actual flue gas of the bet candidate additives previously identified in the laboratory. Results from the bench-scale tests will be used to establish operating parameters for a larger-scale demonstration on either a single baghouse compartment or a full baghouse at the same site.

Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases

Science.gov (United States)

Buey, Rubén M.; Ledesma-Amaro, Rodrigo; Velázquez-Campoy, Adrián; Balsera, Mónica; Chagoyen, Mónica; de Pereda, José M.; Revuelta, José L.

2015-11-01

Inosine-5'-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.

Template protection and its implementation in 3D face recognition systems

Science.gov (United States)

Zhou, Xuebing

2007-04-01

As biometric recognition systems are widely applied in various application areas, security and privacy risks have recently attracted the attention of the biometric community. Template protection techniques prevent stored reference data from revealing private biometric information and enhance the security of biometrics systems against attacks such as identity theft and cross matching. This paper concentrates on a template protection algorithm that merges methods from cryptography, error correction coding and biometrics. The key component of the algorithm is to convert biometric templates into binary vectors. It is shown that the binary vectors should be robust, uniformly distributed, statistically independent and collision-free so that authentication performance can be optimized and information leakage can be avoided. Depending on statistical character of the biometric template, different approaches for transforming biometric templates into compact binary vectors are presented. The proposed methods are integrated into a 3D face recognition system and tested on the 3D facial images of the FRGC database. It is shown that the resulting binary vectors provide an authentication performance that is similar to the original 3D face templates. A high security level is achieved with reasonable false acceptance and false rejection rates of the system, based on an efficient statistical analysis. The algorithm estimates the statistical character of biometric templates from a number of biometric samples in the enrollment database. For the FRGC 3D face database, the small distinction of robustness and discriminative power between the classification results under the assumption of uniquely distributed templates and the ones under the assumption of Gaussian distributed templates is shown in our tests.

II - Template Metaprogramming for Massively Parallel Scientific Computing - Vectorization with Expression Templates

CERN Multimedia

CERN. Geneva

2016-01-01

Large scale scientific computing raises questions on different levels ranging from the fomulation of the problems to the choice of the best algorithms and their implementation for a specific platform. There are similarities in these different topics that can be exploited by modern-style C++ template metaprogramming techniques to produce readable, maintainable and generic code. Traditional low-level code tend to be fast but platform-dependent, and it obfuscates the meaning of the algorithm. On the other hand, object-oriented approach is nice to read, but may come with an inherent performance penalty. These lectures aim to present he basics of the Expression Template (ET) idiom which allows us to keep the object-oriented approach without sacrificing performance. We will in particular show to to enhance ET to include SIMD vectorization. We will then introduce techniques for abstracting iteration, and introduce thread-level parallelism for use in heavy data-centric loads. We will show to to apply these methods i...

Non-Archimedean Hyers-Ulam Stability of an Additive-Quadratic Mapping

Directory of Open Access Journals (Sweden)

Hassan Azadi Kenary

2012-01-01

Full Text Available Using fixed point method and direct method, we prove the Hyers-Ulam stability of the following additive-quadratic functional equation 2((++/+2((−+/+2((+−/+2((−++/=4(+4(+4(, where is a positive real number, in non-Archimedean normed spaces.

NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform

Directory of Open Access Journals (Sweden)

Barker Michael S

2010-08-01

Full Text Available Abstract Background There is increasing demand to test hypotheses that contrast the evolution of genes and gene families among genomes, using simulations that work across these levels of organization. The EvolSimulator program was developed recently to provide a highly flexible platform for forward simulations of amino acid evolution in multiple related lineages of haploid genomes, permitting copy number variation and lateral gene transfer. Synonymous nucleotide evolution is not currently supported, however, and would be highly advantageous for comparisons to full genome, transcriptome, and single nucleotide polymorphism (SNP datasets. In addition, EvolSimulator creates new genomes for each simulation, and does not allow the input of user-specified sequences and gene family information, limiting the incorporation of further biological realism and/or user manipulations of the data. Findings We present modified C++ source code for the EvolSimulator platform, which we provide as the extension module NU-IN. With NU-IN, synonymous and non-synonymous nucleotide evolution is fully implemented, and the user has the ability to use real or previously-simulated sequence data to initiate a simulation of one or more lineages. Gene family membership can be optionally specified, as well as gene retention probabilities that model biased gene retention. We provide PERL scripts to assist the user in deriving this information from previous simulations. We demonstrate the features of NU-IN by simulating genome duplication (polyploidy in the presence of ongoing copy number variation in an evolving lineage. This example is initiated with real genomic data, and produces output that we analyse directly with existing bioinformatic pipelines. Conclusions The NU-IN extension module is a publicly available open source software (GNU GPLv3 license extension to EvolSimulator. With the NU-IN module, users are now able to simulate both drift and selection at the nucleotide

High aspect ratio 10-nm-scale nanoaperture arrays with template-guided metal dewetting.

Science.gov (United States)

Wang, Ying Min; Lu, Liangxing; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Zhang, Yong Wei; Yang, Joel K W

2015-04-10

We introduce an approach to fabricate ordered arrays of 10-nm-scale silica-filled apertures in a metal film without etching or liftoff. Using low temperature (dewetting of metal films guided by nano-patterned templates, apertures with aspect ratios up to 5:1 are demonstrated. Apertures form spontaneously during the thermal process without need for further processing. Although the phenomenon of dewetting has been well studied, this is the first demonstration of its use in the fabrication of nanoapertures in a spatially controllable manner. In particular, the achievement of 10-nm length-scale patterning at high aspect ratio with thermal dewetting is unprecedented. By varying the nanotemplate design, we show its strong influence over the positions and sizes of the nanoapertures. In addition, we construct a three-dimensional phase field model of metal dewetting on nano-patterned substrates. The simulation data obtained closely corroborates our experimental results and reveals new insights to template dewetting at the nanoscale. Taken together, this fabrication method and simulation model form a complete toolbox for 10-nm-scale patterning using template-guided dewetting that could be extended to a wide range of material systems and geometries.

Roles of phosphorylation and nucleotide binding domains in calcium transport by sarcoplasmic reticulum adenosinetriphosphatase

International Nuclear Information System (INIS)

Teruel, J.A.; Inesi, G.

1988-01-01

The roles of the phosphorylation (phosphorylated enzyme intermediate) and nucleotide binding domains in calcium transport were studied by comparing acetyl phosphate and ATP as substrates for the Ca 2+ -ATPase of sarcoplasmic reticulum vesicles. The authors found that the maximal level of phosphoenzyme obtained with either substrate is approximately 4 nmol/mg of protein, corresponding to the stoichiometry of catalytic sites in their preparation. The initial burst of phosphoenzyme formation observed in the transient state, following addition of either substrate, is accompanied by internalization of 2 mol of calcium per mole of phosphoenzyme. The internalized calcium is then translocated with a sequential pattern, independent of the substrate used. Following a rate-limiting step, the phosphoenzyme undergoes hydrolytic cleavage and proceeds to the steady-state activity which is soon back inhibited by the rise of Ca 2+ concentration in the lumen of the vesicles. When the back inhibition is released by the addition of oxalate, substrate utilization and calcium transport occur with a ratio of 1:2, independent of the substrate and its concentration. When the nucleotide binding site is derivatized with FITP, the enzyme can still utilize acetyl phosphate (but not ATP) for calcium transport. These observations demonstrate that the basic coupling mechanism of catalysis and calcium transport involves the phosphorylation and calcium binding domains, and not the nucleotide binding domain. On the other hand, occupancy of the FITC-sensitive nucleotide site is involved in kinetic regulation not only with respect to utilization of substrate for the phosphoryl transfer reaction but also for subsequent steps related to calcium translocation and phosphoenzyme turnover

Templates for Cross-Cultural and Culturally Specific Usability Testing

DEFF Research Database (Denmark)

Clemmensen, Torkil

2011-01-01

The cultural diversity of users of technology challenges our methods for usability testing. This article suggests templates for cross-culturally and culturally specific usability testing, based on studies of usability testing in companies in Mumbai, Beijing, and Copenhagen. Study 1 was a cross...... tests. The result was the construction of templates for usability testing. The culturally specific templates were in Mumbai “user-centered evaluation,” Copenhagen “client-centered evaluation,” and Beijing “evaluator-centered evaluation.” The findings are compared with related research...

Ebselen induces mitochondrial permeability transition because of its interaction with adenine nucleotide translocase.

Science.gov (United States)

Pavón, Natalia; Correa, Francisco; Buelna-Chontal, Mabel; Hernández-Esquivel, Luz; Chávez, Edmundo

2015-10-15

Mitochondrial permeability transition is a process established through massive Ca(2+) load in addition to an inducer reagent. Ebselen (Ebs), an antioxidant seleno compound, has been introduced as a reagent which inhibits mitochondrial dysfunction induced by permeability transition. Paradoxically enough, it has been shown that Ebs may also be able to induce the opening of the mitochondrial non-selective pores. This study was performed with the purpose of establishing the membrane system involved in Ebs-induced pore opening. Permeability transition was appraised by analyzing the following: i) matrix Ca(2+) release, and mitochondrial swelling, ii) efflux of cytochrome c, and iii) the inhibition of superoxide dismutase. All of these adverse reactions were inhibited by N-ethylmaleimide and cyclosporin A. At concentrations from 5 to 20 μM, we found that Ebs induces non-specific membrane permeability. Remarkably, Ebs blocks the binding of the fluorescent reagent eosin-5-maleimide to the thiol groups of the adenine nucleotide translocase. Based on the above, it is tempting to hypothesize that Ebs induces pore opening through its binding to the ADP/ATP carrier. Copyright © 2015 Elsevier Inc. All rights reserved.

Template-based automatic breast segmentation on MRI by excluding the chest region

International Nuclear Information System (INIS)

Lin, Muqing; Chen, Jeon-Hor; Wang, Xiaoyong; Su, Min-Ying; Chan, Siwa; Chen, Siping

2013-01-01

total error by adding the inclusion and exclusion errors ranged from 0.16% to 11.8%, with a mean of 2.89% ± 2.55%. Conclusions: The automatic chest template-based breast MRI segmentation method worked well for cases with different body and breast shapes and different density patterns. Compared to the radiologist-established truth, the mean difference in segmented breast volume was approximately 1%, and the total error by considering the additive inclusion and exclusion errors was approximately 3%. This method may provide a reliable tool for MRI-based segmentation of breast density

Template-based automatic breast segmentation on MRI by excluding the chest region

Energy Technology Data Exchange (ETDEWEB)

Lin, Muqing [Tu and Yuen Center for Functional Onco-Imaging, Department of Radiological Sciences, University of California, Irvine, California 92697-5020 and National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, 518060 China (China); Chen, Jeon-Hor [Tu and Yuen Center for Functional Onco-Imaging, Department of Radiological Sciences, University of California, Irvine, California 92697-5020 and Department of Radiology, E-Da Hospital and I-Shou University, Kaohsiung 82445, Taiwan (China); Wang, Xiaoyong; Su, Min-Ying, E-mail: msu@uci.edu [Tu and Yuen Center for Functional Onco-Imaging, Department of Radiological Sciences, University of California, Irvine, California 92697-5020 (United States); Chan, Siwa [Department of Radiology, Taichung Veterans General Hospital, Taichung 40407, Taiwan (China); Chen, Siping [National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, 518060 China (China)

2013-12-15

.03%. The total error by adding the inclusion and exclusion errors ranged from 0.16% to 11.8%, with a mean of 2.89% ± 2.55%. Conclusions: The automatic chest template-based breast MRI segmentation method worked well for cases with different body and breast shapes and different density patterns. Compared to the radiologist-established truth, the mean difference in segmented breast volume was approximately 1%, and the total error by considering the additive inclusion and exclusion errors was approximately 3%. This method may provide a reliable tool for MRI-based segmentation of breast density.

Calculating the weight of evidence in low-template forensic DNA casework.

Science.gov (United States)

Lohmueller, Kirk E; Rudin, Norah

2013-01-01

Interpreting and assessing the weight of low-template DNA evidence presents a formidable challenge in forensic casework. This report describes a case in which a similar mixed DNA profile was obtained from four different bloodstains. The defense proposed that the low-level minor profile came from an alternate suspect, the defendant's mistress. The strength of the evidence was assessed using a probabilistic approach that employed likelihood ratios incorporating the probability of allelic drop-out. Logistic regression was used to model the probability of drop-out using empirical validation data from the government laboratory. The DNA profile obtained from the bloodstain described in this report is at least 47 billion times more likely if, in addition to the victim, the alternate suspect was the minor contributor, than if another unrelated individual was the minor contributor. This case illustrates the utility of the probabilistic approach for interpreting complex low-template DNA profiles. © 2012 American Academy of Forensic Sciences.

Ferritin-Templated Quantum-Dots for Quantum Logic Gates

Science.gov (United States)

Choi, Sang H.; Kim, Jae-Woo; Chu, Sang-Hyon; Park, Yeonjoon; King, Glen C.; Lillehei, Peter T.; Kim, Seon-Jeong; Elliott, James R.

2005-01-01

Quantum logic gates (QLGs) or other logic systems are based on quantum-dots (QD) with a stringent requirement of size uniformity. The QD are widely known building units for QLGs. The size control of QD is a critical issue in quantum-dot fabrication. The work presented here offers a new method to develop quantum-dots using a bio-template, called ferritin, that ensures QD production in uniform size of nano-scale proportion. The bio-template for uniform yield of QD is based on a ferritin protein that allows reconstitution of core material through the reduction and chelation processes. One of the biggest challenges for developing QLG is the requirement of ordered and uniform size of QD for arrays on a substrate with nanometer precision. The QD development by bio-template includes the electrochemical/chemical reconsitution of ferritins with different core materials, such as iron, cobalt, manganese, platinum, and nickel. The other bio-template method used in our laboratory is dendrimers, precisely defined chemical structures. With ferritin-templated QD, we fabricated the heptagonshaped patterned array via direct nano manipulation of the ferritin molecules with a tip of atomic force microscope (AFM). We also designed various nanofabrication methods of QD arrays using a wide range manipulation techniques. The precise control of the ferritin-templated QD for a patterned arrangement are offered by various methods, such as a site-specific immobilization of thiolated ferritins through local oxidation using the AFM tip, ferritin arrays induced by gold nanoparticle manipulation, thiolated ferritin positioning by shaving method, etc. In the signal measurements, the current-voltage curve is obtained by measuring the current through the ferritin, between the tip and the substrate for potential sweeping or at constant potential. The measured resistance near zero bias was 1.8 teraohm for single holoferritin and 5.7 teraohm for single apoferritin, respectively.

A multibiometric face recognition fusion framework with template protection

Science.gov (United States)

Chindaro, S.; Deravi, F.; Zhou, Z.; Ng, M. W. R.; Castro Neves, M.; Zhou, X.; Kelkboom, E.

2010-04-01

In this work we present a multibiometric face recognition framework based on combining information from 2D with 3D facial features. The 3D biometrics channel is protected by a privacy enhancing technology, which uses error correcting codes and cryptographic primitives to safeguard the privacy of the users of the biometric system at the same time enabling accurate matching through fusion with 2D. Experiments are conducted to compare the matching performance of such multibiometric systems with the individual biometric channels working alone and with unprotected multibiometric systems. The results show that the proposed hybrid system incorporating template protection, match and in some cases exceed the performance of corresponding unprotected equivalents, in addition to offering the additional privacy protection.

Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis

Directory of Open Access Journals (Sweden)

Suravajhala P

2017-06-01

Full Text Available Prashanth Suravajhala,1 Alfredo Benso2 1Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark; 2Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy Abstract: Next-generation sequencing technology has provided resources to easily explore and identify candidate single-nucleotide polymorphisms (SNPs and variants. However, there remains a challenge in identifying and inferring the causal SNPs from sequence data. A problem with different methods that predict the effect of mutations is that they produce false positives. In this hypothesis, we provide an overview of methods known for identifying causal variants and discuss the challenges, fallacies, and prospects in discerning candidate SNPs. We then propose a three-point classification strategy, which could be an additional annotation method in identifying causalities. Keywords: clinical mastitis, single-nucleotide polymorphisms, variants, associations, diseases, linkage disequilibrium, GWAS

Constructing inverse V-type TiO{sub 2}-based photocatalyst via bio-template approach to enhance the photosynthetic water oxidation

Energy Technology Data Exchange (ETDEWEB)

Jiang, Jinghui; Zhou, Han; Ding, Jian; Zhang, Fan; Fan, Tongxiang, E-mail: txfan@sjtu.edu.cn; Zhang, Di

2015-08-30

Graphical abstract: Inverse V-type TiO{sub 2}-based photocatalyst was synthesized by using cross-linked titanium precursor to duplicate bio-template. - Highlights: • Cross-linked titanium precursor can facilitate an accurate duplication of templates. • In situ deposition of Ag{sup 0} from AgBr can maintain the completeness of surface structure. • Perfect inverse V-type Ag{sup 0}/TiO{sub 2} can achieve efficient water oxidation. - Abstract: Bio-template approach was employed to construct inverse V-type TiO{sub 2}-based photocatalyst with well distributed AgBr in TiO{sub 2} matrix by making dead Troides Helena wings with inverse V-type scales as the template. A cross-linked titanium precursor with homogenous hydrolytic rate, good liquidity, and low viscosity was employed to facilitate a perfect duplication of the template and the dispersion of AgBr based on appropriate pretreatment of the template by alkali and acid. The as-synthesized inverse V-type TiO{sub 2}/AgBr can be turned into inverse V-type TiO{sub 2}/Ag{sup 0} from AgBr photolysis during photocatalysis to achieve in situ deposition of Ag{sup 0} in TiO{sub 2} matrix, by this approach, to avoid the deformation of surface microstructure inherited from the template. The result showed that the cooperation of perfect inverse V-type structure and the well distributed TiO{sub 2}/Ag{sup 0} microstructures can efficiently boost the photosynthetic water oxidation compared to non-inverse V-type TiO{sub 2}/Ag{sup 0} and TiO{sub 2}/Ag{sup 0} without using template. The anti-reflection function of inverse V-type structure and the plasmatic effect of Ag{sup 0} might be able to account for the enhanced photon capture and efficient photoelectric conversion.

Formation of novel morphologies of aragonite induced by inorganic template

International Nuclear Information System (INIS)

Wang, Xiaoming; Nan, Zhaodong

2011-01-01

Graphical abstract: Glass-slices were used as a template to induce formation and assembly of aragonite. Different morphologies, such as hemisphere, twinborn hemisphere and flower-shaped particles, were produced by direction of the glass-slices. Highlights: → Glass-slices were used as a template to induce formation and assembly of aragonite. → Hemisphere, twinborn hemisphere and flower-shaped particles were produced by direction of the glass-slices. → Planes were always appeared in these as-synthesized samples. → Thermodynamic theory was applied to explain the production of the aragonite. -- Abstract: A glass-slice was used as a template to induce formation and assembly of aragonite. Thermodynamic theory was applied to explain the production of the aragonite. Transformation of three-dimensional nucleation to template-based two-dimensional surface nucleation caused the production of aragonite. Hemisphere, twinborn hemisphere and flower-shaped particles were produced by direction of the glass-slices. Planes were always appeared in these as-synthesized samples because the nucleation and the growth of these samples were adsorbed at the surfaces of the glass-slices. The formation mechanism of the as-formed sample was proposed. Compared with organic template, the present study provides a facile method to apply inorganic template to prepare functional materials.

A Novel Surgical Template Design in Staged Dental Implant Rehabilitations

Directory of Open Access Journals (Sweden)

Michael Patras

2012-05-01

Full Text Available Background: The philosophy of a gradual transition to an implant retained prosthesis in cases of full-mouth or extensive rehabilitation usually involves a staged treatment concept. In this therapeutic approach, the placement of implants may sometimes be divided into phases. During a subsequent surgical phase of treatment, the pre-existing implants can serve as anchors for the surgical template. Those modified surgical templates help in the precise transferring of restorative information into the surgical field and guide the optimal three-dimensional implant positioning. Methods: This article highlights the rationale of implant-retained surgical templates and illustrates them through the presentation of two clinical cases. The templates are duplicates of the provisional restorations and are secured to the existing implants through the utilization of implant mounts. Results: This template design in such staged procedures provided stability in the surgical field and enhanced the accuracy in implant positioning based upon the planned restoration, thus ensuring predictable treatment outcomes.Conclusions: Successful rehabilitation lies in the correct sequence of surgical and prosthetic procedures. Whenever a staged approach of implant placement is planned, the clinician can effectively use the initially placed implants as anchors for the surgical template during the second phase of implant surgery.

Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

Science.gov (United States)

Hwang, Hanshin; Taylor, John-Stephen

2005-03-29

We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the

Deregulation of ocular nucleotide homeostasis in patients with diabetic retinopathy.

Science.gov (United States)

Loukovaara, Sirpa; Sandholm, Jouko; Aalto, Kristiina; Liukkonen, Janne; Jalkanen, Sirpa; Yegutkin, Gennady G

2017-02-01

Clear signaling roles for ATP and adenosine have been established in all tissues, including the eye. The magnitude of signaling responses is governed by networks of enzymes; however, little is known about the regulatory mechanisms of purinergic signaling in the eye. By employing thin-layer chromatographic assays with 3 H-labeled substrates, this study aimed to evaluate the role of nucleotide homeostasis in the pathogenesis of vitreoretinal diseases in humans. We have identified soluble enzymes ecto-5'-nucleotidase/CD73, adenylate kinase-1, and nucleoside diphosphate kinase in the vitreous fluid that control active cycling between pro-inflammatory ATP and anti-inflammatory adenosine. Strikingly, patients with proliferative form of diabetic retinopathy (DR) had higher adenylate kinase activity and ATP concentration, when compared to non-proliferative DR eyes and non-diabetic controls operated for rhegmatogenous retinal detachment, macular hole, and pucker. The non-parametric correlation analysis revealed positive correlations between intravitreal adenylate kinase and concentrations of ATP, ADP, and other angiogenic (angiopoietins-1 and -2), profibrotic (transforming growth factor-β1), and proteolytic (matrix metalloproteinase-9) factors but not erythropoietin and VEGF. Immunohistochemical staining of postmortem human retina additionally revealed selective expression of ecto-5'-nucleotidase/CD73 on the rod-and-cone-containing photoreceptor cells. Collectively, these findings provide novel insights into the regulatory mechanisms that influence purinergic signaling in diseased eye and open up new possibilities in the development of enzyme-targeted therapeutic approaches for prevention and treatment of DR. Ecto-5'-nucleotidase/CD73 and adenylate kinase-1 circulate in human vitreous fluid. Adenylate kinase activity is high in diabetic eyes with proliferative retinopathy. Diabetic eyes display higher intravitreal ATP/ADP ratio than non-diabetic controls. Soluble adenylate

Template matching techniques in computer vision theory and practice

CERN Document Server

Brunelli, Roberto

2009-01-01

The detection and recognition of objects in images is a key research topic in the computer vision community.  Within this area, face recognition and interpretation has attracted increasing attention owing to the possibility of unveiling human perception mechanisms, and for the development of practical biometric systems. This book and the accompanying website, focus on template matching, a subset of object recognition techniques of wide applicability, which has proved to be particularly effective for face recognition applications. Using examples from face processing tasks throughout the book to illustrate more general object recognition approaches, Roberto Brunelli: examines the basics of digital image formation, highlighting points critical to the task of template matching;presents basic and  advanced template matching techniques, targeting grey-level images, shapes and point sets;discusses recent pattern classification paradigms from a template matching perspective;illustrates the development of a real fac...

Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

Science.gov (United States)

Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

2017-11-01

Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele

Photoelectron spectroscopic study on electronic structure of butterfly-templated ZnO

Energy Technology Data Exchange (ETDEWEB)

Kamada, Masao; Sugiyama, Harue; Takahashi, Kazutoshi; Guo, Qixin [Synchrotron Light Application Center, Saga University, Honjo 1, Saga 840-8502 (Japan); Gu, Jiajun; Zhang, Wang; Fan, Tongxiang; Zhang, Di [State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200030 (China)

2010-06-15

Biological systems have complicated hierarchical architecture involving nano-structures inside, and are expected as another candidate for new nano-templates. The present work reports the photoelectron spectroscopic study on electronic structure of the butterfly-templated ZnO that were successfully produced from butterfly wings. Ultraviolet Photoelectron Spectrum (UPS) of the butterfly-templated ZnO shows clearly the valence band and a Zn-3d peak, indicating that the butterfly-templated ZnO has the same electronic structure as bulk ZnO. However, the details show that the energy positions of the Zn-3d level and the valence-band structure are different between them. The present results indicate that the bonding interaction between Zn-4sp and O-2p orbitals is stronger in the butterfly-templated ZnO, probably due to the nano-structures inside. Important parameters such as band bending and electron affinity are also obtained. The larger band bending and the lower electron affinity are found in the butterfly-templated ZnO (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

An integrated semiconductor device enabling non-optical genome sequencing.

Science.gov (United States)

Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James

2011-07-20

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

Adenine nucleotide depletion from endothelial cells exposed to xanthine oxidase

International Nuclear Information System (INIS)

Aalto, T.K.; Raivio, K.O.

1990-01-01

Hypoxia causes breakdown of cellular nucleotides, accumulation of hypoxanthine (HX), and conversion of xanthine dehydrogenase into xanthine oxidase (XO). Upon reoxygenation, the HX-XO reaction generates free radicals, one potential mechanism of tissue damage. Because endothelial cells contain XO and are exposed to circulating HX, they are a likely target for damage. We studied the effect of XO and/or HX at physiologically relevant concentrations on nucleotide metabolism of cultured endothelial cells from human umbilical veins. Cells were labeled with [14C]adenine and incubated for up to 6 h with HX, XO, or both, in the absence or presence of serum. Adenine nucleotides from cell extracts and nucleotide breakdown products (HX, xanthine, and urate) from the medium were separated and counted. HX alone had no effect. XO (80 mU/ml) alone caused a 70% (no serum) or 40% (with serum) fall in adenine nucleotides and an equivalent increase of xanthine and urate. The combination of HX and XO caused a 90% (no serum) or 70% (with serum) decrease in nucleotides, decrease in energy charge, and detachment of cells from the culture plate. Nucleotide depletion was not accounted for by proteolytic activity in the XO preparation. Albumin was only half as effective as serum in preventing nucleotide loss. Thus exogenous XO, in the presence of endogenous HX, triggers adenine nucleotide catabolism, but endogenous XO activity is too low to influence nucleotide levels even at high exogenous HX concentrations. Serum limits the catabolic effect of XO and thus protects cells from free radical damage

Computer-Aided Template for Model Reuse, Development and Maintenance

DEFF Research Database (Denmark)

Fedorova, Marina; Sin, Gürkan; Gani, Rafiqul

2014-01-01

A template-based approach for model development is presented in this work. Based on a model decomposition technique, the computer-aided template concept has been developed. This concept is implemented as a software tool , which provides a user-friendly interface for following the workflow steps...

Comparison of high-accuracy numerical simulations of black-hole binaries with stationary-phase post-Newtonian template waveforms for initial and advanced LIGO

International Nuclear Information System (INIS)

Boyle, Michael; Brown, Duncan A; Pekowsky, Larne

2009-01-01

We study the effectiveness of stationary-phase approximated post-Newtonian waveforms currently used by ground-based gravitational-wave detectors to search for the coalescence of binary black holes by comparing them to an accurate waveform obtained from numerical simulation of an equal-mass non-spinning binary black hole inspiral, merger and ringdown. We perform this study for the initial- and advanced-LIGO detectors. We find that overlaps between the templates and signal can be improved by integrating the match filter to higher frequencies than used currently. We propose simple analytic frequency cutoffs for both initial and advanced LIGO, which achieve nearly optimal matches, and can easily be extended to unequal-mass, spinning systems. We also find that templates that include terms in the phase evolution up to 3.5 post-Newtonian (pN) order are nearly always better, and rarely significantly worse, than 2.0 pN templates currently in use. For initial LIGO we recommend a strategy using templates that include a recently introduced pseudo-4.0 pN term in the low-mass (M ≤ 35 M o-dot ) region, and 3.5 pN templates allowing unphysical values of the symmetric reduced mass η above this. This strategy always achieves overlaps within 0.3% of the optimum, for the data used here. For advanced LIGO we recommend a strategy using 3.5 pN templates up to M = 12 M o-dot , 2.0 pN templates up to M = 21 M o-dot , pseudo-4.0 pN templates up to 65 M o-dot , and 3.5 pN templates with unphysical η for higher masses. This strategy always achieves overlaps within 0.7% of the optimum for advanced LIGO.

Main: Nucleotide Analysis [KOME

Lifescience Database Archive (English)

Full Text Available Nucleotide Analysis Japonica genome blast search result Result of blastn search against jap...onica genome sequence kome_japonica_genome_blast_search_result.zip kome_japonica_genome_blast_search_result ...

Patterned FePt nanostructures using ultrathin self-organized templates

Science.gov (United States)

Deng, Chen Hua; Zhang, Min; Wang, Fang; Xu, Xiao Hong

2018-02-01

Patterned magnetic thin films are both scientifically interesting and technologically useful. Ultrathin self-organized anodic aluminum oxide (AAO) template can be used to fabricate large area nanodot and antidot arrays. The magnetic properties of these nanostructures may be tuned by the morphology of the AAO template, which in turn can be controlled by synthetic parameters. In this work, ultrathin AAO templates were used as etching masks for the fabrication of both FePt nanodot and antidot arrays with high areal density. The perpendicular magnetic anisotropy of L10 FePt thin films are preserved in the nanostructures.

Anodic Aluminum Oxide Templates for Nano wires Array Fabrication

International Nuclear Information System (INIS)

Nur Ubaidah Saidin; Kok, K.Y.; Ng, I.K.

2011-01-01

This paper reports on the process developed to fabricate anodic aluminium oxide (AAO) templates suitable for the fabrication of nano wire arrays. Anodization process has been used to fabricate the AAO templates with pore diameters ranging from 15 nm to 30 nm. Electrodeposition of parallel arrays of high aspect ratio nickel nano wires were demonstrated using these fabricated AAO templates. The nano wires produced were characterized using X-ray diffraction (XRD) and scanning electron microscopy (SEM). It was found that the orientations of the electrodeposited nickel nano wires were governed by the deposition current and electrolyte conditions. (author)

Creation of structured documentation templates using Natural Language Processing techniques.

Science.gov (United States)

Kashyap, Vipul; Turchin, Alexander; Morin, Laura; Chang, Frank; Li, Qi; Hongsermeier, Tonya

2006-01-01

Structured Clinical Documentation is a fundamental component of the healthcare enterprise, linking both clinical (e.g., electronic health record, clinical decision support) and administrative functions (e.g., evaluation and management coding, billing). One of the challenges in creating good quality documentation templates has been the inability to address specialized clinical disciplines and adapt to local clinical practices. A one-size-fits-all approach leads to poor adoption and inefficiencies in the documentation process. On the other hand, the cost associated with manual generation of documentation templates is significant. Consequently there is a need for at least partial automation of the template generation process. We propose an approach and methodology for the creation of structured documentation templates for diabetes using Natural Language Processing (NLP).

Innovation in the planning of V-Y rotation advancement flaps: A template for flap design

Directory of Open Access Journals (Sweden)

Utku Can Dölen

2018-01-01

Full Text Available Local flaps exhibit excellent color matching that no other type of flap can compete with. Moreover, surgery using a local flap is easier and faster than surgery using a distant or free flap. However, local flaps can be much more difficult to design. We designed 2 templates to plan a V-Y rotation advancement flap. The template for a unilateral V-Y rotation advancement flap was used on the face (n=5, anterior tibia (n=1, posterior axilla (n=1, ischium (n=1, and trochanter (n=2. The template for a bilateral flap was used on the sacrum (n=8, arm (n=1, and anterior tibia (n=1. The causes of the defects were meningocele (n=3, a decubitus ulcer (n=5, pilonidal sinus (n=3, and skin tumor excision (n=10. The meningocele patients were younger than 8 days. The mean age of the adult patients was 50.4 years (range, 19–80 years. All the donor areas of the flaps were closed primarily. None of the patients experienced wound dehiscence or partial/total flap necrosis. The templates guided surgeons regarding the length and the placement of the incision for a V-Y rotation advancement flap according to the size of the wound. In addition, they could be used for the training of residents.

Template synthesis of indium nanowires using anodic aluminum oxide membranes.

Science.gov (United States)

Chen, Feng; Kitai, Adrian H

2008-09-01

Indium nanowires with diameters approximately 300 nm have been synthesized by a hydraulic pressure technique using anodic aluminum oxide (AAO) templates. The indium melt is injected into the AAO template and solidified to form nanostructures. The nanowires are dense, continuous and uniformly run through the entire approximately 60 microm thickness of the AAO template. X-ray diffraction (XRD) reveals that the nanowires are polycrystalline with a preferred orientation. SEM is performed to characterize the morphology of the nanowires.

Co-occurring nonnative woody shrubs have additive and non-additive soil legacies

DEFF Research Database (Denmark)

Kuebbing, Sara E.; Patterson, Courtney M.; Classen, Aimee Taylor

2016-01-01

shrubs, Lonicera maackii and Ligustrum sinense, in deciduous forests of the southeastern United States. We measured the performance of each nonnative shrub, a native herbaceous community, and a nonnative woody vine in soils conditioned by each shrub singly or together in polyculture. Soils conditioned...... by both nonnative shrubs had non-additive impacts on native and nonnative performance. Root mass of the native herbaceous community was 1.5 times lower and the root mass of the nonnative L. sinense was 1.8 times higher in soils conditioned by both L. maackii and L. sinense than expected based upon growth...... in soils conditioned by either shrub singly. This result indicates that when these two nonnative shrubs co-occur, their influence on soils disproportionally favors persistence of the nonnative L. sinense relative to this native herbaceous community, and could provide an explanation of why native species...

BPFlexTemplate: A Business Process template generation tool based on similarity and flexibility

Directory of Open Access Journals (Sweden)

Latifa Ilahi

2017-01-01

Full Text Available In large organizations with multiple organizational units, process variants emerge due to many aspects, including local management policies, resources or socio-technical limitations. Organizations then struggle to improve a business process which has no longer a single process model to redesign, implement and adjust. In this paper, we propose an approach to tackle these two challenges: decrease the proliferation of process variants in these organizations, and foresee, at the same time, the need of having flexible business processes that allow for a certain degree of adjustment. To validate our approach, we first conducted case studies where we collected six real-world business process variants from two organizational units of the same healthcare organization. We then proposed an algorithm to derive a template process model from all the variants, which includes common and flexible process elements. We implemented our approach in a software tool called BPFlexTemplate, and tested it with the elicited variants.

Single-Nucleotide Variations in Cardiac Arrhythmias: Prospects for Genomics and Proteomics Based Biomarker Discovery and Diagnostics

Directory of Open Access Journals (Sweden)

Ayman Abunimer

2014-03-01

Full Text Available Cardiovascular diseases are a large contributor to causes of early death in developed countries. Some of these conditions, such as sudden cardiac death and atrial fibrillation, stem from arrhythmias—a spectrum of conditions with abnormal electrical activity in the heart. Genome-wide association studies can identify single nucleotide variations (SNVs that may predispose individuals to developing acquired forms of arrhythmias. Through manual curation of published genome-wide association studies, we have collected a comprehensive list of 75 SNVs associated with cardiac arrhythmias. Ten of the SNVs result in amino acid changes and can be used in proteomic-based detection methods. In an effort to identify additional non-synonymous mutations that affect the proteome, we analyzed the post-translational modification S-nitrosylation, which is known to affect cardiac arrhythmias. We identified loss of seven known S-nitrosylation sites due to non-synonymous single nucleotide variations (nsSNVs. For predicted nitrosylation sites we found 1429 proteins where the sites are modified due to nsSNV. Analysis of the predicted S-nitrosylation dataset for over- or under-representation (compared to the complete human proteome of pathways and functional elements shows significant statistical over-representation of the blood coagulation pathway. Gene Ontology (GO analysis displays statistically over-represented terms related to muscle contraction, receptor activity, motor activity, cystoskeleton components, and microtubule activity. Through the genomic and proteomic context of SNVs and S-nitrosylation sites presented in this study, researchers can look for variation that can predispose individuals to cardiac arrhythmias. Such attempts to elucidate mechanisms of arrhythmia thereby add yet another useful parameter in predicting susceptibility for cardiac diseases.

The influence of polarity of additive molecules on micelle structures of polystyrene-block-poly(4-vinylpyridine) in the fabrication of nano-porous templates.

Science.gov (United States)

Chua, Kee Sze; Koh, Ai Peng; Lam, Yeng Ming

2010-11-01

Block copolymers are useful for in situ synthesis of nanoparticles as well as producing nanoporous templates. As such, the effects of precursors on the block copolymer micelle structure is important. In this study, we investigate the effects of polarity of molecules introduced into block copolymer micelle cores on the micelle structure. The molecular dipole moment of the additive molecules has been evaluated and their effects on the block copolymer micelles investigated using light scattering spectroscopy, small-angle X-ray scattering, transmission electron microscopy and atomic force microscopy. The molecule with the largest dipole moment resulted in spherical structures with a polydispersity of less than 0.06 in a fully translational diffusion system. Surprisingly, the less polar additive molecules produced elongated micelles and the aspect ratio increases with decreasing polarity. The change in structure from spherical to elongated structure was attributed to P4VP chain extension, where compounds with polarity most similar to P4VP induce the most chain extension. The second virial coefficients of the solutions with elongated micelles are lower than that for spherical micelle systems by up to one order in magnitude, indicating a strong tendency for micelles to coalesce. On rinsing the spin-cast films, pores were obtained from spherical micelles and ridges from elongated micelles, suggesting a viable alternative for morphology modification using mild conditions where external annealing treatments to the film are not preferred. The knowledge of polarity effects of additive molecules on micelle structure has wider implications for supramolecular block copolymer systems where, depending on the application requirements, changes to the shape of the micelle structure can be induced or avoided. Copyright 2010 Elsevier Inc. All rights reserved.

Hierarchically porous LaFeO3 perovskite prepared from the pomelo peel bio-template for catalytic oxidation of NO

Science.gov (United States)

Zhao, Shaojun; Wang, Li; Wang, Ying; Li, Xing

2018-05-01

In this paper, pomelo peel was used as biological template to obtain hierarchically porous LaFeO3 perovskite for the catalytic oxidation of NO to NO2. In addition, X-ray diffraction (XRD), scanning electron microscopy (SEM), N2 adsorption-desorption analyses, X-ray photoelectron spectra (XPS), NO temperature-programmed desorption (NO-TPD), oxygen temperature-programmed desorption (O2-TPD) and hydrogen temperature-programmed reduction (H2-TPR) were used to investigate the micro-structure and the redox properties of the hierarchically porous LaFeO3 perovskite prepared from pomelo peel biological template and the LaFeO3 perovskite without the biological template. The results indicated that the hierarchically porous LaFeO3 perovskite successfully replicated the porous structure of pomelo peel with high specific surface area. Compared to the LaFeO3 perovskite prepared without the pomelo peel template, the hierarchically porous LaFeO3 perovskite showed better catalytic oxidization of NO to NO2 under the same conditions. The maximum NO conversions for LaFeO3 prepared with and without template were 90% at 305 °C and 76% at 313 °C, respectively. This is mainly attributed to the higher ratio of Fe4+/Fe3+, the hierarchically porous structure with more adsorbed oxygen species and higher surface area for the hierarchically porous LaFeO3 perovskite compared with the sample prepared without the pomelo peel template.

PLGA nanoparticles from nano-emulsion templating as imaging agents: Versatile technology to obtain nanoparticles loaded with fluorescent dyes.

Science.gov (United States)

Fornaguera, C; Feiner-Gracia, N; Calderó, G; García-Celma, M J; Solans, C

2016-11-01

The interest in polymeric nanoparticles as imaging systems for biomedical applications has increased notably in the last decades. In this work, PLGA nanoparticles, prepared from nano-emulsion templating, have been used to prepare novel fluorescent imaging agents. Two model fluorescent dyes were chosen and dissolved in the oil phase of the nano-emulsions together with PLGA. Nano-emulsions were prepared by the phase inversion composition (PIC) low-energy method. Fluorescent dye-loaded nanoparticles were obtained by solvent evaporation of nano-emulsion templates. PLGA nanoparticles loaded with the fluorescent dyes showed hydrodynamic radii lower than 40nm; markedly lower than those reported in previous studies. The small nanoparticle size was attributed to the nano-emulsification strategy used. PLGA nanoparticles showed negative surface charge and enough stability to be used for biomedical imaging purposes. Encapsulation efficiencies were higher than 99%, which was also attributed to the nano-emulsification approach as well as to the low solubility of the dyes in the aqueous component. Release kinetics of both fluorescent dyes from the nanoparticle dispersions was pH-independent and sustained. These results indicate that the dyes could remain encapsulated enough time to reach any organ and that the decrease of the pH produced during cell internalization by the endocytic route would not affect their release. Therefore, it can be assumed that these nanoparticles are appropriate as systemic imaging agents. In addition, in vitro toxicity tests showed that nanoparticles are non-cytotoxic. Consequently, it can be concluded that the preparation of PLGA nanoparticles from nano-emulsion templating represents a very versatile technology that enables obtaining biocompatible, biodegradable and safe imaging agents suitable for biomedical purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

Emergence of a code in the polymerization of amino acids along RNA templates.

Directory of Open Access Journals (Sweden)

Jean Lehmann

2009-06-01

Full Text Available The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the tRNAs (the translation adaptors are not loaded selectively with amino acids, we show that an elementary translation governed by a Michaelis-Menten type of kinetics can follow different polymerization regimes: random polymerization, homopolymerization and coded polymerization. The regime under which the system is running is set by the relative concentrations of the amino acids and the kinetic constants involved. We point out that the coding regime can naturally occur under prebiotic conditions. It generates partially coded proteins through a mechanism which is remarkably robust against non-specific interactions (mismatches between the adaptors and the RNA template. Features of the genetic code support the existence of this early translation system.

Growth control of carbon nanotubes using by anodic aluminum oxide nano templates.

Science.gov (United States)

Park, Yong Seob; Choi, Won Seek; Yi, Junsin; Lee, Jaehyeong

2014-05-01

Anodic Aluminum Oxide (AAO) template prepared in acid electrolyte possess regular and highly anisotropic porous structure with pore diameter range from five to several hundred nanometers, and with a density of pores ranging from 10(9) to 10(11) cm(-2). AAO can be used as microfilters and templates for the growth of CNTs and metal or semiconductor nanowires. Varying anodizing conditions such as temperature, electrolyte, applied voltage, anodizing and widening time, one can control the diameter, the length, and the density of pores. In this work, we deposited Al thin film by radio frequency magnetron sputtering method to fabricate AAO nano template and synthesized multi-well carbon nanotubes on a glass substrate by microwave plasma-enhanced chemical vapor deposition (MPECVD). AAO nano-porous templates with various pore sizes and depths were introduced to control the dimension and density of CNT arrays. The AAO nano template was synthesize on glass by two-step anodization technique. The average diameter and interpore distance of AAO nano template are about 65 nm and 82 nm. The pore density and AAO nano template thickness are about 2.1 x 10(10) pores/cm2 and 1 microm, respectively. Aligned CNTs on the AAO nano template were synthesized by MPECVD at 650 degrees C with the Ni catalyst layer. The length and diameter of CNTs were grown 2 microm and 50 nm, respectively.

Template for success: using a resident-designed sign-out template in the handover of patient care.

Science.gov (United States)

Clark, Clancy J; Sindell, Sarah L; Koehler, Richard P

2011-01-01

Report our implementation of a standardized handover process in a general surgery residency program. The standardized handover process, sign-out template, method of implementation, and continuous quality improvement process were designed by general surgery residents with support of faculty and senior hospital administration using standard work principles and business models of the Virginia Mason Production System and the Toyota Production System. Nonprofit, tertiary referral teaching hospital. General surgery residents, residency faculty, patient care providers, and hospital administration. After instruction in quality improvement initiatives, a team of general surgery residents designed a sign-out process using an electronic template and standard procedures. The initial implementation phase resulted in 73% compliance. Using resident-driven continuous quality improvement processes, real-time feedback enabled residents to modify and improve this process, eventually attaining 100% compliance and acceptance by residents. The creation of a standardized template and protocol for patient handovers might eliminate communication failures. Encouraging residents to participate in this process can establish the groundwork for successful implementation of a standardized handover process. Integrating a continuous quality-improvement process into such an initiative can promote active participation of busy general surgery residents and lead to successful implementation of standard procedures. Copyright © 2011 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Template Directed Oligomer Ligation in Eutectic Phases in Water-Ice

DEFF Research Database (Denmark)

Dörr, Mark; Löffler, Philipp M. G.; Wieczorek, Rafal

2011-01-01

achieved, if small, activated, oligonucleotides are ligated on a template. A template directed ligation can lead to autocatalytic or cross- catalytic replication and thus maintain a certain pool of catalyitc species. Important for these processes is a destabilization of the formed douplex....../multiplex to overcome product inhibition. The latest results of our template directed ligation experiments in the eutectic ice phase are presented. Different activation strategies are compared and an outlook towards applications in molecular evolution and artifical cell systems (« protocells ») will be given. Figure 1....... (a) Reaction scheme of the condensation reaction of two oligoribonucleotides : The leaving group in this example is imidazole. (b) Illustration of a possible spatial arrangement of a template (15nt) directed ligation. The 7-mer is activated with imidazole at the 5' phosphate (apical moiety...

Template assisted solid state electrochemical growth of silver micro- and nanowires

International Nuclear Information System (INIS)

Peppler, Klaus; Janek, Juergen

2007-01-01

We report on a template based solid state electrochemical method for fabricating silver nanowires with predefined diameter, depending only on the pore diameter of the template. As templates we used porous silicon with pore diameters in the μm range and porous alumina with pore diameters in the nm range. The template pores were filled with silver sulfide (a mixed silver cation and electronic conductor) by direct chemical reaction of silver and sulfur. The filled template was then placed between a silver foil as anode (bottom side) and a microelectrode (top side) as cathode. An array of small cylindrical transference cells with diameters in the range of either micro- or nanometers was thus obtained. By applying a cathodic voltage to the microelectrode silver in the form of either micro- or nanowires was deposited at about 150 deg. C. The growth rate is controllable by the electric current

Tailoring silver nanoparticle construction using dendrimer templated silica networks

International Nuclear Information System (INIS)

Liu Xiaojun; Kakkar, Ashok

2008-01-01

We have examined the role of the internal environment of dendrimer templated silica networks in tailoring the construction of silver nanoparticle assemblies. Silica networks from which 3,5-dihydroxybenzyl alcohol based dendrimer templates have been completely removed, slowly wet with an aqueous solution of silver acetate. The latter then reacts with internal silica silanol groups, leading to chemisorption of silver ions, followed by the growth of silver oxide nanoparticles. Silica network constructed using generation 4 dendrimer contains residual dendrimer template, and mixes with aqueous silver acetate solution easily. Upon chemisorption, silver ions get photolytically reduced to silver metal under a stabilizing dendrimer environment, leading to the formation of silver metal nanoparticles

Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

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Arnett Donna

2009-08-01

Full Text Available Abstract Background Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years and compared them to similarly aged non-Hispanic whites (NHW (n = 597. Results Minor allele frequency (MAF distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusion These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans.

GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5·Vps9 system.

Science.gov (United States)

Uejima, Tamami; Ihara, Kentaro; Goh, Tatsuaki; Ito, Emi; Sunada, Mariko; Ueda, Takashi; Nakano, Akihiko; Wakatsuki, Soichi

2010-11-19

Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7·VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP β-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP β-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.

Priming and the guidance by visual and categorical templates in visual search

NARCIS (Netherlands)

Wilschut, A.M.; Theeuwes, J.; Olivers, C.N.L.

2014-01-01

Visual search is thought to be guided by top-down templates that are held in visual working memory. Previous studies have shown that a search-guiding template can be rapidly and strongly implemented from a visual cue, whereas templates are less effective when based on categorical cues. Direct visual

Supply-Chain Optimization Template

Science.gov (United States)

Quiett, William F.; Sealing, Scott L.

2009-01-01

The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

Iris Template Protection Based on Local Ranking

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Dongdong Zhao

2018-01-01

Full Text Available Biometrics have been widely studied in recent years, and they are increasingly employed in real-world applications. Meanwhile, a number of potential threats to the privacy of biometric data arise. Iris template protection demands that the privacy of iris data should be protected when performing iris recognition. According to the international standard ISO/IEC 24745, iris template protection should satisfy the irreversibility, revocability, and unlinkability. However, existing works about iris template protection demonstrate that it is difficult to satisfy the three privacy requirements simultaneously while supporting effective iris recognition. In this paper, we propose an iris template protection method based on local ranking. Specifically, the iris data are first XORed (Exclusive OR operation with an application-specific string; next, we divide the results into blocks and then partition the blocks into groups. The blocks in each group are ranked according to their decimal values, and original blocks are transformed to their rank values for storage. We also extend the basic method to support the shifting strategy and masking strategy, which are two important strategies for iris recognition. We demonstrate that the proposed method satisfies the irreversibility, revocability, and unlinkability. Experimental results on typical iris datasets (i.e., CASIA-IrisV3-Interval, CASIA-IrisV4-Lamp, UBIRIS-V1-S1, and MMU-V1 show that the proposed method could maintain the recognition performance while protecting the privacy of iris data.

Bacterial nucleotide-based second messengers.

Science.gov (United States)

Pesavento, Christina; Hengge, Regine

2009-04-01

In all domains of life nucleotide-based second messengers transduce signals originating from changes in the environment or in intracellular conditions into appropriate cellular responses. In prokaryotes cyclic di-GMP has emerged as an important and ubiquitous second messenger regulating bacterial life-style transitions relevant for biofilm formation, virulence, and many other bacterial functions. This review describes similarities and differences in the architecture of the cAMP, (p)ppGpp, and c-di-GMP signaling systems and their underlying signaling principles. Moreover, recent advances in c-di-GMP-mediated signaling will be presented and the integration of c-di-GMP signaling with other nucleotide-based signaling systems will be discussed.

Improvement of engineering soil properties using non -traditional additives

Directory of Open Access Journals (Sweden)

Waheed Mohanned

2018-01-01

Full Text Available Laboratory experiments are conducted to evaluate the effect of some non-traditional additives on the engineering properties of clayey soil, which show problematic phenomenon when used as a construction material. The conducted tests covered the influence of these additives on various parameters like consistency limits, compaction characteristics and CBR value. Two nontraditional stabilizers are selected in this study, polymers and phosphoric acid at three different percent which are (1%, 3% and 5% of the dry soil weight. It is concluded that addition of the polymer to the clayey soil results in a slight increase in plastic limit while the liquid limit is not affected accompanied by a marginal decrease in the dry unit weight while the optimum moisture content remains unaffected. The addition of phosphoric acid to the clayey soil has no effect on its Atterberg limits. In general, it is observed that polymer is found to be ineffective as a stabilizer to improve clayey soils, especially in small amounts of about (3%. The phosphoric acid treated soil gained better improvement for all amounts of additive used. For (3% acid treated soil the CBR is about (360% compared to that of untreated soil, for that, it can be concluded that the improvement using phosphoric acid in the clay soils is a promising option and can be applied to solve the geotechnical stabilization problems.

Template security analysis of multimodal biometric frameworks based on fingerprint and hand geometry

Directory of Open Access Journals (Sweden)

Arvind Selwal

2016-09-01

Full Text Available Biometric systems are automatic tools used to provide authentication during various applications of modern computing. In this work, three different design frameworks for multimodal biometric systems based on fingerprint and hand geometry modalities are proposed. An analysis is also presented to diagnose various types of template security issues in the proposed system. Fuzzy analytic hierarchy process (FAHP is applied with five decision parameters on all the designs and framework 1 is found to be better in terms of template data security, templates fusion and computational efficiency. It is noticed that template data security before storage in database is a challenging task. An important observation is that a template may be secured at feature fusion level and an indexing technique may be used to improve the size of secured templates.

Osteogenic Treatment Initiating a Tissue-Engineered Cartilage Template Hypertrophic Transition.

Science.gov (United States)

Fu, J Y; Lim, S Y; He, P F; Fan, C J; Wang, D A

2016-10-01

Hypertrophic chondrocytes play a critical role in endochondral bone formation as well as the progress of osteoarthritis (OA). An in vitro cartilage hypertrophy model can be used as a platform to study complex molecular mechanisms involved in these processes and screen new drugs for OA. To develop an in vitro cartilage hypertrophy model, we treated a tissue-engineered cartilage template, living hyaline cartilaginous graft (LhCG), with osteogenic medium for hypertrophic induction. In addition, endothelial progenitor cells (EPCs) were seeded onto LhCG constructs to mimic vascular invasion. The results showed that osteogenic treatment significantly inhibited the synthesis of endostatin in LhCG constructs and enhanced expression of hypertrophic marker-collagen type X (Col X) and osteogenic markers, as well as calcium deposition in vitro. Upon subcutaneous implantation, osteogenic medium-treated LhCG constructs all stained positive for Col X and showed significant calcium deposition and blood vessel invasion. Col X staining and calcium deposition were most obvious in osteogenic medium-treated only group, while there was no difference between EPC-seeded and non-seeded group. These results demonstrated that osteogenic treatment was of the primary factor to induce hypertrophic transition of LhCG constructs and this model may contribute to the establishment of an in vitro cartilage hypertrophy model.

Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part I: Template-Based Generic Programming

Directory of Open Access Journals (Sweden)

Roger P. Pawlowski

2012-01-01

Full Text Available An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.

Laparotomy operative note template constructed through a modified Delphi method.

Science.gov (United States)

Moore, Lolonya; Churley-Strom, Ruth; Singal, Bonita; O'Leary, Sharon

2009-05-01

An operative note is indispensable to physician documentation and decision-making; however, there are no accepted standards for operative note content. Our aim was to use a modified Delphi consensus-building method to construct a uniform operative note template for laparotomy. Using Joint Commission on Accreditation of Healthcare Organizations requirements, literature review, and feedback from 15 medical malpractice defense attorneys, we compiled a draft operative note template of 31 elements. We surveyed 37 Association of Professor of Gynecology and Obstetrics/Solvay scholars asking for their input on inclusion of each item as essential content of the operative note. Two iterations of the survey were required to reach a predetermined 75% level of consensus. Nine elements were eliminated from the template: 6 original and 3 expert-suggested elements. We provide an operative note template that was compiled through a Delphi process.

Biometric template data protection in mobile device environment using XML-database

DEFF Research Database (Denmark)

Thirumathyam, Rubathas; Derawi, Mohammad; Fischer, Paul

2010-01-01

recognition or gait recognition. To gain a real understanding of how it is possible to protect the biometric data, this paper first starts out with introducing a technique for security in a biometric system and emphasizes that template protection is important by going through the vulnerabilities and threats....... Furthermore, it points out requirements for template protection, a recital of various template protection schemes and a brief overview of biometric standards....

[Use of diagnostic templates at stages of prosthetics treatment with implant-retained restorations].

Science.gov (United States)

Gvetadze, R Sh; Abramyan, S V; Ivanov, A A; Nubaryan, A P

The comparative analysis of efficiency of various types of diagnostic templates for planning orthopedic treatment of 50 patients with partial or complete absence of teeth was performed. The patients were divided in 3 groups according to template manufacturing technique. All diagnostic templates made in accordance with clinical conditions allowed transfering digital data of the scheduled prosthetic construction for virtual implantation planning. Advantages and pitfalls of each template type are discussed.

Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population

DEFF Research Database (Denmark)

Fabbri, Elena; Caniglia, R.; Mucci, Nadia

2012-01-01

Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient geno....... We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring....

Synthesis and characterizations of Pt nanorods on electrospun polyamide-6 nanofibers templates

International Nuclear Information System (INIS)

Nirmala, R.; Navamathavan, R.; Won, Jeong Jin; Jeon, Kyung Soo; Yousef, Ayman; Kim, Hak Yong

2012-01-01

Highlights: ► Electrospun polyamide-6 nanofibers were used as the templates for synthesis Pt nanorods. ► Polyamide-6 nanofibers surfaces were plasma treated to coat Pt. ► High quality Pt nanorods were obtained by calcinations process. ► Pt nanorods with a diameter of few hundred nanometers were obtained. ► Polyamide-6 nanofibers template based Pt nanorods synthesis are a feasible method. - Abstract: We report on the synthesis of platinum (Pt) nanorods by using ultrafine polyamide-6 nanofibers templates produced via electrospinning technique. These ultrafine polyamide-6 nanofibers can be utilized as the templates for growing Pt nanorods after modifying them optimally by plasma passivations. The morphological, structural, optical and electrical properties of the template assisted Pt nanorods were studied by field-emission scanning electron microscopy (FE-SEM), high-resolution transmission electron microscopy (HR-TEM), X-ray diffraction (XRD), photoluminescence (PL) and current–voltage (I–V) characteristics. The ability to fabricate the ultrafine size controlled Pt nanorods on polyamide-6 templates with optimized growth parameters in real time can be utilized for the variety of technological applications. Therefore, it is possible to obtain high quality with size control Pt nanorods. Once obtaining the high quality metal nanorods on polymer templates, the same can be adapted for the electronic device fabrication.

Synthesis of Highly Reactive Subnano-sized Zero-valent Iron using Smectite Clay Templates

Science.gov (United States)

Gu, Cheng; Jia, Hanzhang; Li, Hui; Teppen, Brian J.; Boyd, Stephen A.

2010-01-01

A novel method was developed for synthesizing subnano-sized zero-valent iron (ZVI) using smectite clay layers as templates. Exchangeable Fe(III) cations compensating the structural negative charges of smectites were reduced with NaBH4, resulting in the formation of ZVI. The unique structure of smectite clay, in which isolated exchangeable Fe(III) cations reside near the sites of structural negative charges, inhibited the agglomeration of ZVI resulting in the formation of discrete regions of subnanoscale ZVI particles in the smectite interlayer regions. X-ray diffraction revealed an interlayer spacing of ~ 5 Å. The non-structural iron content of this clay yields a calculated ratio of two atoms of ZVI per three cation exchange sites, in full agreement with the XRD results since the diameter of elemental Fe is 2.5 Å. The clay-templated ZVI showed superior reactivity and efficiency compared to other previously reported forms of ZVI as indicated by the reduction of nitrobenzene; structural Fe within the aluminosilicate layers was nonreactive. At a 1:3 molar ratio of nitrobenzene:non-structural Fe, a reaction efficiency of 83% was achieved, and over 80% of the nitrobenzene was reduced within one minute. These results confirm that non-structural Fe from Fe(III)-smectite was reduced predominantly to ZVI which was responsible for the reduction of nitrobenzene to aniline. This new form of subnano-scale ZVI may find utility in the development of remediation technologies for persistent environmental contaminants, e.g. as components of constructed reactive domains such as reactive caps for contaminated sediments. PMID:20446730

Synthesis of highly reactive subnano-sized zero-valent iron using smectite clay templates.

Science.gov (United States)

Gu, Cheng; Jia, Hanzhong; Li, Hui; Teppen, Brian J; Boyd, Stephen A

2010-06-01

A novel method was developed for synthesizing subnano-sized zero-valent iron (ZVI) using smectite clay layers as templates. Exchangeable Fe(III) cations compensating the structural negative charges of smectites were reduced with NaBH(4), resulting in the formation of ZVI. The unique structure of smectite clay, in which isolated exchangeable Fe(III) cations reside near the sites of structural negative charges, inhibited the agglomeration of ZVI resulting in the formation of subnanoscale ZVI particles in the smectite interlayer regions. X-ray diffraction revealed an interlayer spacing of approximately 5 A. The non-structural iron content of this clay yields a calculated ratio of two atoms of ZVI per three cation exchange sites, in full agreement with the X-ray diffraction (XRD) results since the diameter of elemental Fe is 2.5 A. The clay-templated ZVI showed superior reactivity and efficiency compared to other previously reported forms of ZVI as indicated by the reduction of nitrobenzene; structural Fe within the aluminosilicate layers was nonreactive. At a 1:3 molar ratio of nitrobenzene/non-structural Fe, a reaction efficiency of 83% was achieved, and over 80% of the nitrobenzene was reduced within one minute. These results confirm that non-structural Fe from Fe(III)-smectite was reduced predominantly to ZVI which was responsible for the reduction of nitrobenzene to aniline. This new form of subnanoscale ZVI may find utility in the development of remediation technologies for persistent environmental contaminants, for example, as components of constructed reactive domains such as reactive caps for contaminated sediments.

BioAssay templates for the semantic web

Directory of Open Access Journals (Sweden)

Alex M. Clark

2016-05-01

Full Text Available Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object. With appropriate annotation, assays can be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1 defining a BioAssay Template (BAT data model; (2 creating a software tool for experts to create or modify templates to suit their needs; and (3 designing a common assay template (CAT to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples, and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template, in order to encourage community input and use within diverse projects, including but not limited to our own

Storage stability of milk-cans with the addition of maltodextrin

Directory of Open Access Journals (Sweden)

L. V. Golubeva

2016-01-01

Full Text Available The paper presents data on the study of the safety milk-containing canned food. The examine sample has multicomponent non-standard composition. The part of components is presented by food additives of a plant origin. The composition of product was varied for improvement of its properties and increase of storage stability. Starch treacly additives were widely expansion in the dairy industry. In milk-containing tinned was decided to replace partially a sweet component – sugar with maltodextrin. As maltodextrin possesses less sweet taste, the basic component was replaced partially. The manufacturing process of the product involves mixing the dry components in order to obtain the desired properties. The technology excludes process of evaporation and use of the expensive volume equipment. For comparison of properties of development investigated a reference template. The reference template s a product of a classical formulation which includes the origin of the components of milk and sugar. Organoleptic properties are studied of two samples. Defined that taste, a smell, appearance and a consistence of development and a control sample are similar on the first periods of storage. However, the consistence of a control sample is aggravating after 6 months of storage. In process of investigation is determined such parameters as the water activity, the dynamic viscosity and the active acidity. Values of these indicators for a new product are in rated limits, but they are much lower than the reference. Carried out the analysis of the received results. We concluded that milkcontaining tinned with maltodextrin have a high storage stability and better performance compared to the control sample.

Enzymatic primer-extension with glycerol-nucleoside triphosphates on DNA templates.

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Jesse J Chen

Full Text Available BACKGROUND: Glycerol nucleic acid (GNA has an acyclic phosphoglycerol backbone repeat-unit, but forms stable duplexes based on Watson-Crick base-pairing. Because of its structural simplicity, GNA is of particular interest with respect to the possibility of evolving functional polymers by in vitro selection. Template-dependent GNA synthesis is essential to any GNA-based selection system. PRINCIPAL FINDINGS: In this study, we investigated the ability of various DNA polymerases to use glycerol-nucleoside triphosphates (gNTPs as substrates for GNA synthesis on DNA templates. Therminator DNA polymerase catalyzes quantitative primer-extension by the incorporation of two glyceronucleotides, with much less efficient extension up to five glyceronucleotides. Steady-state kinetic experiments suggested that GNA synthesis by Therminator was affected by both decreased catalytic rates and weakened substrate binding, especially for pyrimidines. In an attempt to improve pyrimidine incorporation by providing additional stacking interactions, we synthesized two new gNTP analogs with 5-propynyl substituted pyrimidine nucleobases. This led to more efficient incorporation of gC, but not gT. CONCLUSIONS: We suggest that directed evolution of Therminator might lead to mutants with improved substrate binding and catalytic efficiency.

Micelle-template synthesis of hollow silica spheres for improving water vapor permeability of waterborne polyurethane membrane

Science.gov (United States)

Bao, Yan; Wang, Tong; Kang, Qiaoling; Shi, Chunhua; Ma, Jianzhong

2017-04-01

Hollow silica spheres (HSS) with special interior spaces, high specific surface area and excellent adsorption and permeability performance were synthesized via micelle-template method using cetyl trimethyl ammonium bromide (CTAB) micelles as soft template and tetraethoxysilane (TEOS) as silica precursor. SEM, TEM, FT-IR, XRD, DLS and BET-BJH were carried out to characterize the morphology and structure of as-obtained samples. The results demonstrated that the samples were amorphous with a hollow structure and huge specific surface area. The growth of HSS was an inward-growth mechanism along template. Notably, we have provided a new and interesting fundamental principle for HSS materials by precisely controlling the ethanol-to-water volume ratio. In addition, the as-obtained HSS were mixed with waterborne polyurethane (WPU) to prepare WPU/HSS composite membrane. Various characterizations (SEM, TEM, FT-IR and TGA) revealed the morphology, polydispersity and adherence between HSS and WPU. Performance tests showed that the introduction of HSS can improve the water vapor permeability of composite membrane, promoting its water resistance and mechanical performance at the same time.

The optical properties of ZnO films grown on porous Si templates

International Nuclear Information System (INIS)

Liu, Y L; Liu, Y C; Yang, H; Wang, W B; Ma, J G; Zhang, J Y; Lu, Y M; Shen, D Z; Fan, X W

2003-01-01

ZnO films were electrodeposited on porous silicon templates with different porosities. The photoluminescence (PL) spectra of the samples before and after deposition of ZnO were measured to study the effect of template porosity on the luminescence properties of ZnO/porous Si composites. As-prepared porous Si (PS) templates emit strong red light. The red PL peak of porous Si after deposition of ZnO shows an obvious blueshift, and the trend of blueshift increases with an increase in template porosity. A green emission at about 550 nm was also observed when the porosity of template increases, which is ascribed to the deep-level emission band of ZnO. A model-based band diagram of the ZnO/porous Si composite is suggested to interpret the properties of the composite

Efficacy of saccharides bio-template on structural, morphological, optical and antibacterial property of ZnO nanoparticles.

Science.gov (United States)

Dhanalakshmi, A; Palanimurugan, A; Natarajan, B

2018-09-01

Mono, di and polysaccharides of glucose (C 6 H 12 O 6 ), sucrose (C 12 H 24 O 12 ) and starch (C 6 H 12 O 6 ) n bio-template ZnO nanoparticles (NPs) has prepared by chemical precipitation method. Saccharides bio-template ZnO (SBts-ZnO) NPs were efficiently prepared for their structural and optical properties were examined by using XRD, FE-SEM, AFM, FTIR, UV and PL techniques. All the samples are polycrystalline nature with a preferential orientation depending on the (1 0 1) plane. The reduction of crystalline size by utilizing glucose, sucrose and starch bio-template of ZnO NPs. FE-SEM images revealed that the spherical and nano-rods like morphologies for ZnO and SBts-ZnO NPs respectively. AFM recorded images shows spherical features that confirmed and also the morphological changes were noticed with the addition of polymers. Interaction of bio-templated saccharides (glucose G 1 , sucrose S 2 & starch S n ) molecules was proved by FTIR study. Optical absorbance and emission behaviours were investigated using UV-Vis and photoluminescence techniques. The antibacterial study revealed that SBts-ZnO have excellent antibacterial effect than ZnO. The S n -ZnO sample has potent antibacterial activity against the Proteus vulgaris followed by Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus. Copyright © 2018 Elsevier B.V. All rights reserved.

Aluminum Templates of Different Sizes with Micro-, Nano- and Micro/Nano-Structures for Cell Culture

Directory of Open Access Journals (Sweden)

Ming-Liang Yen

2017-10-01

Full Text Available This study investigates the results of cell cultures on aluminum (Al templates with flat-structures, micro-structures, nano-structures and micro/nano-structures. An Al template with flat-structure was obtained by electrolytic polishing; an Al template with micro-structure was obtained by micro-powder blasting; an Al template with nano-structure was obtained by aluminum anodization; and an Al template with micro/nano-structure was obtained by micro-powder blasting and then anodization. Osteoblast-like cells were cultured on aluminum templates with various structures. The microculture tetrazolium test assay was utilized to assess the adhesion, elongation, and proliferation behaviors of cultured osteoblast-like cells on aluminum templates with flat-structures, micro-structures, nano-structures, and micro/nano-structures. The results showed that the surface characterization of micro/nano-structure of aluminum templates had superhydrophilic property, and these also revealed that an aluminum template with micro/nano-structure could provide the most suitable growth situation for cell culture.

Comparison of five-axis milling and rapid prototyping for implant surgical templates.

Science.gov (United States)

Park, Ji-Man; Yi, Tae-Kyoung; Koak, Jai-Young; Kim, Seong-Kyoon; Park, Eun-Jin; Heo, Seong-Joo

2014-01-01

This study aims to compare and evaluate the accuracy of surgical templates fabricated using coordinate synchronization processing with five-axis milling and design-related processing with rapid prototyping (RP). Master phantoms with 10 embedded gutta-percha cylinders hidden under artificial gingiva were fabricated and imaged using cone beam computed tomography. Vectors of the hidden cylinders were extracted and transferred to those of the planned implants through reverse engineering using virtual planning software. An RP-produced template was fabricated by stereolithography in photopolymer at the RP center according to planned data. Metal sleeves were bonded after holes were bored (group RP). For the milled template, milling coordinates were synchronized using the conversion process for the coordinate synchronization platform located on the model's bottom. Metal bushings were set on holes milled on the five-axis milling machine, on which the model was fixed through the coordinate synchronization plate, and the framework was constructed on the model using orthodontic resin (group CS). A computed tomography image was taken with templates firmly fixed on models using anchor pins (RP) or anchor screws (CS). The accuracy was analyzed via reverse engineering. Differences between the two groups were compared by repeated measures two-factor analysis. From the reverse-engineered image of the template on the experimental model, RP-produced templates showed significantly larger deviations than did milled surgical guides. Maximum deviations of the group RP were 1.58 mm (horizontal), 1.68 mm (vertical), and 8.51 degrees (angular); those of the group CS were 0.68 mm (horizontal), 0.41 mm (vertical), and 3.23 degrees (angular). A comparison of milling and RP template production methods showed that a vector-milled surgical guide had significantly smaller deviations than did an RP-produced template. The accuracy of computer-guided milled surgical templates was within the safety

Preparation of porous diatomite-templated carbons with large adsorption capacity and mesoporous zeolite K-H as a byproduct.

Science.gov (United States)

Liu, Dong; Yuan, Weiwei; Deng, Liangliang; Yu, Wenbin; Sun, Hongjuan; Yuan, Peng

2014-06-15

In this study, KOH activation was performed to enhance the porosity of the diatomite-templated carbon and to increase its adsorption capacity of methylene blue (MB). In addition to serving as the activation agent, KOH was also used as the etchant to remove the diatomite templates. Zeolite K-H was synthesized as a byproduct via utilization of the resultant silicon- and potassium-containing solutions created from the KOH etching of the diatomite templates. The obtained diatomite-based carbons were composed of macroporous carbon pillars and tubes, which were derived from the replication of the diatomite templates and were well preserved after KOH activation. The abundant micropores in the walls of the carbon pillars and tubes were derived from the break and reconfiguration of carbon films during both the removal of the diatomite templates and KOH activation. Compared with the original diatomite-templated carbons and CO2-activated carbons, the KOH-activated carbons had much higher specific surface areas (988 m(2)/g) and pore volumes (0.675 cm(3)/g). Moreover, the KOH-activated carbons possessed larger MB adsorption capacity (the maximum Langmuir adsorption capacity: 645.2 mg/g) than those of the original carbons and CO2-activated carbons. These results showed that KOH activation was a high effective activation method. The zeolite K-H byproduct was obtained by utilizing the silicon- and potassium-containing solution as the silicon and potassium sources. The zeolite exhibited a stick-like morphology and possessed nanosized particles with a mesopore-predominant porous structure which was observed by TEM for the first time. Copyright © 2014 Elsevier Inc. All rights reserved.

Controlling the anodizing conditions in preparation of an nanoporous anodic aluminium oxide template

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Nazemi, Azadeh; Abolfazl, Seyed; Sadjadi, Seyed

2014-12-01

Porous anodic aluminium oxide (AAO) template is commonly used in the synthesis of one-dimensional nanostructures, such as nanowires and nanorods, due to its simple fabrication process. Controlling the anodizing conditions is important because of their direct influence on the size of AAO template pores; it affects the size of nanostructures that are fabricated in AAO template. In present study, several alumina templates were fabricated by a two-step electrochemical anodization in different conditions, such as the time of first process, its voltage, and electrolyte concentration. The effect of these factors on pore diameters of AAO templates was investigated using scanning electron microscopy (SEM).

Effect of migration in a diffusion model for template coexistence in protocells.

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Fontanari, José F; Serva, Maurizio

2014-03-01

The compartmentalization of distinct templates in protocells and the exchange of templates between them (migration) are key elements of a modern scenario for prebiotic evolution. Here we use the diffusion approximation of population genetics to study analytically the steady-state properties of such a prebiotic scenario. The coexistence of distinct template types inside a protocell is achieved by a selective pressure at the protocell level (group selection) favoring protocells with a mixed template composition. In the degenerate case, where the templates have the same replication rate, we find that a vanishingly small migration rate suffices to eliminate the segregation effect of random drift and so to promote coexistence. In the nondegenerate case, a small migration rate greatly boosts coexistence as compared with the situation where there is no migration. However, increase of the migration rate beyond a critical value leads to the complete dominance of the more efficient template type (homogeneous regime). In this case, we find a continuous phase transition separating the homogeneous and the coexistence regimes, with the order parameter vanishing linearly with the distance to the transition point.

Method for priming and DNA sequencing

Energy Technology Data Exchange (ETDEWEB)

Mugasimangalam, R.C.; Ulanovsky, L.E.

1997-12-01

A method is presented for improving the priming specificity of an oligonucleotide primer that is non-unique in a nucleic acid template which includes selecting a continuous stretch of several nucleotides in the template DNA where one of the four bases does not occur in the stretch. This also includes bringing the template DNA in contract with a non-unique primer partially or fully complimentary to the sequence immediately upstream of the selected sequence stretch. This results in polymerase-mediated differential extension of the primer in the presence of a subset of deoxyribonucleotide triphosphates that does not contain the base complementary to the base absent in the selected sequence stretch. These reactions occur at a temperature sufficiently low for allowing the extension of the non-unique primer. The method causes polymerase-mediated extension reactions in the presence of all four natural deoxyribonucleotide triphosphates or modifications. At this high temperature discrimination occurs against priming sites of the non-unique primer where the differential extension has not made the primer sufficiently stable to prime. However, the primer extended at the selected stretch is sufficiently stable to prime.

Action video game play facilitates the development of better perceptual templates

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Bejjanki, Vikranth R.; Zhang, Ruyuan; Li, Renjie; Pouget, Alexandre; Green, C. Shawn; Lu, Zhong-Lin; Bavelier, Daphne

2014-01-01

The field of perceptual learning has identified changes in perceptual templates as a powerful mechanism mediating the learning of statistical regularities in our environment. By measuring threshold-vs.-contrast curves using an orientation identification task under varying levels of external noise, the perceptual template model (PTM) allows one to disentangle various sources of signal-to-noise changes that can alter performance. We use the PTM approach to elucidate the mechanism that underlies the wide range of improvements noted after action video game play. We show that action video game players make use of improved perceptual templates compared with nonvideo game players, and we confirm a causal role for action video game play in inducing such improvements through a 50-h training study. Then, by adapting a recent neural model to this task, we demonstrate how such improved perceptual templates can arise from reweighting the connectivity between visual areas. Finally, we establish that action gamers do not enter the perceptual task with improved perceptual templates. Instead, although performance in action gamers is initially indistinguishable from that of nongamers, action gamers more rapidly learn the proper template as they experience the task. Taken together, our results establish for the first time to our knowledge the development of enhanced perceptual templates following action game play. Because such an improvement can facilitate the inference of the proper generative model for the task at hand, unlike perceptual learning that is quite specific, it thus elucidates a general learning mechanism that can account for the various behavioral benefits noted after action game play. PMID:25385590

Action video game play facilitates the development of better perceptual templates.

Science.gov (United States)

Bejjanki, Vikranth R; Zhang, Ruyuan; Li, Renjie; Pouget, Alexandre; Green, C Shawn; Lu, Zhong-Lin; Bavelier, Daphne

2014-11-25

The field of perceptual learning has identified changes in perceptual templates as a powerful mechanism mediating the learning of statistical regularities in our environment. By measuring threshold-vs.-contrast curves using an orientation identification task under varying levels of external noise, the perceptual template model (PTM) allows one to disentangle various sources of signal-to-noise changes that can alter performance. We use the PTM approach to elucidate the mechanism that underlies the wide range of improvements noted after action video game play. We show that action video game players make use of improved perceptual templates compared with nonvideo game players, and we confirm a causal role for action video game play in inducing such improvements through a 50-h training study. Then, by adapting a recent neural model to this task, we demonstrate how such improved perceptual templates can arise from reweighting the connectivity between visual areas. Finally, we establish that action gamers do not enter the perceptual task with improved perceptual templates. Instead, although performance in action gamers is initially indistinguishable from that of nongamers, action gamers more rapidly learn the proper template as they experience the task. Taken together, our results establish for the first time to our knowledge the development of enhanced perceptual templates following action game play. Because such an improvement can facilitate the inference of the proper generative model for the task at hand, unlike perceptual learning that is quite specific, it thus elucidates a general learning mechanism that can account for the various behavioral benefits noted after action game play.

Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors.

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Jian Weng

Full Text Available Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group.

Dosimetry study of three-dimensional print template-guided precision 125I seed implantation

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Zhang Hongtao

2016-01-01

Conclusions: The postplan and preplan dose parameters of 3D print template-guided seed implantation were nearly consistent. The dose parameters of template group superior to the traditional group. The seeds can be implanted accurately with 3D print template.

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

NARCIS (Netherlands)

Xue, Li C; Garcia Lopes Maia Rodrigues, João; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2016-01-01

Although many advanced and sophisticatedab initioapproaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to

New immobilisation protocol for the template used in solid-phase synthesis of MIP nanoparticles

Science.gov (United States)

Chen, Lu; Muhammad, Turghun; Yakup, Burabiye; Piletsky, Sergey A.

2017-06-01

As a novel imprinting method, solid-phase synthesis has proven to be a promising approach to prepare polymer nanoparticles with specific recognition sites for a template molecule. In this method, imprinted polymer nanoparticles were synthesized using template immobilized on a solid support. Herein, preparation of immobilized templates on quartz chips through homogeneous route was reported as an efficient alternative strategy to heterogeneous one. The template molecule indole-3-butyric acid (IBA) was reacted with 3-aminopropyltriethoxysilane (APTES) to produce silylated template (IBA-APTES), and it was characterized by IR, 1H NMR and GC-MS. Then, the silylated template molecule was grafted onto the activated surfaces of quartz chip to prepare immobilized template (SiO2@IBA-APTES). The immobilization was confirmed by contact angle, XPS, UV and fluorescence measurement. Immobilization protocol has shown good reproducibility and stability of the immobilized template. MIP nanoparticles were prepared with high selectivity toward the molecule immobilized onto the solid surface. This provides a new approach for the development of molecularly imprinted nanoparticles.

III - Template Metaprogramming for massively parallel scientific computing - Templates for Iteration; Thread-level Parallelism

CERN Multimedia

CERN. Geneva

2016-01-01

Large scale scientific computing raises questions on different levels ranging from the fomulation of the problems to the choice of the best algorithms and their implementation for a specific platform. There are similarities in these different topics that can be exploited by modern-style C++ template metaprogramming techniques to produce readable, maintainable and generic code. Traditional low-level code tend to be fast but platform-dependent, and it obfuscates the meaning of the algorithm. On the other hand, object-oriented approach is nice to read, but may come with an inherent performance penalty. These lectures aim to present he basics of the Expression Template (ET) idiom which allows us to keep the object-oriented approach without sacrificing performance. We will in particular show to to enhance ET to include SIMD vectorization. We will then introduce techniques for abstracting iteration, and introduce thread-level parallelism for use in heavy data-centric loads. We will show to to apply these methods i...

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

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Yi Li

2017-01-01

Full Text Available Objective A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results A total of 18 (0, 15 (3, 12 (8, 15 (18, 11 (7, and 21 (1 SNPs were detected at the 5% chromosome (genome - wise level for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area (LMA and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29 were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA. Conclusion The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

Examining multi-component DNA-templated nanostructures as imaging agents

Science.gov (United States)

Jaganathan, Hamsa

2011-12-01

Magnetic resonance imaging (MRI) is the leading non-invasive tool for disease imaging and diagnosis. Although MRI exhibits high spatial resolution for anatomical features, the contrast resolution is low. Imaging agents serve as an aid to distinguish different types of tissues within images. Gadolinium chelates, which are considered first generation designs, can be toxic to health, while ultra-small, superparamagnetic nanoparticles (NPs) have low tissue-targeting efficiency and rapid bio-distribution, resulting to an inadequate detection of the MRI signal and enhancement of image contrast. In order to improve the utility of MRI agents, the challenge in composition and structure needs to be addressed. One-dimensional (1D), superparamagnetic nanostructures have been reported to enhance magnetic and in vivo properties and therefore has a potential to improve contrast enhancement in MRI images. In this dissertation, the structure of 1D, multi-component NP chains, scaffolded on DNA, were pre-clinically examined as potential MRI agents. First, research was focused on characterizing and understanding the mechanism of proton relaxation for DNA-templated NP chains using nuclear magnetic resonance (NMR) spectrometry. Proton relaxation and transverse relaxivity were higher in multi-component NP chains compared to disperse NPs, indicating the arrangement of NPs on a 1D structure improved proton relaxation sensitivity. Second, in vitro evaluation for potential issues in toxicity and contrast efficiency in tissue environments using a 3 Tesla clinical MRI scanner was performed. Cell uptake of DNA-templated NP chains was enhanced after encapsulating the nanostructure with layers of polyelectrolytes and targeting ligands. Compared to dispersed NPs, DNA-templated NP chains improved MRI contrast in both the epithelial basement membrane and colon cancer tumors scaffolds. The last part of the project was focused on developing a novel MRI agent that detects changes in DNA methylation

LipidPioneer : A Comprehensive User-Generated Exact Mass Template for Lipidomics

Science.gov (United States)

Ulmer, Candice Z.; Koelmel, Jeremy P.; Ragland, Jared M.; Garrett, Timothy J.; Bowden, John A.

2017-03-01

Lipidomics, the comprehensive measurement of lipid species in a biological system, has promising potential in biomarker discovery and disease etiology elucidation. Advances in chromatographic separation, mass spectrometric techniques, and novel substrate applications continue to expand the number of lipid species observed. The total number and type of lipid species detected in a given sample are generally indicative of the sample matrix examined (e.g., serum, plasma, cells, bacteria, tissue, etc.). Current exact mass lipid libraries are static and represent the most commonly analyzed matrices. It is common practice for users to manually curate their own lists of lipid species and adduct masses; however, this process is time-consuming. LipidPioneer, an interactive template, can be used to generate exact masses and molecular formulas of lipid species that may be encountered in the mass spectrometric analysis of lipid profiles. Over 60 lipid classes are present in the LipidPioneer template and include several unique lipid species, such as ether-linked lipids and lipid oxidation products. In the template, users can add any fatty acyl constituents without limitation in the number of carbons or degrees of unsaturation. LipidPioneer accepts naming using the lipid class level (sum composition) and the LIPID MAPS notation for fatty acyl structure level. In addition to lipid identification, user-generated lipid m/z values can be used to develop inclusion lists for targeted fragmentation experiments. Resulting lipid names and m/z values can be imported into software such as MZmine or Compound Discoverer to automate exact mass searching and isotopic pattern matching across experimental data.

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

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Tammy M K Cheng

Full Text Available Recent analyses of human genome sequences have given rise to impressive advances in identifying non-synonymous single nucleotide polymorphisms (nsSNPs. By contrast, the annotation of nsSNPs and their links to diseases are progressing at a much slower pace. Many of the current approaches to analysing disease-associated nsSNPs use primarily sequence and evolutionary information, while structural information is relatively less exploited. In order to explore the potential of such information, we developed a structure-based approach, Bongo (Bonds ON Graph, to predict structural effects of nsSNPs. Bongo considers protein structures as residue-residue interaction networks and applies graph theoretical measures to identify the residues that are critical for maintaining structural stability by assessing the consequences on the interaction network of single point mutations. Our results show that Bongo is able to identify mutations that cause both local and global structural effects, with a remarkably low false positive rate. Application of the Bongo method to the prediction of 506 disease-associated nsSNPs resulted in a performance (positive predictive value, PPV, 78.5% similar to that of PolyPhen (PPV, 77.2% and PANTHER (PPV, 72.2%. As the Bongo method is solely structure-based, our results indicate that the structural changes resulting from nsSNPs are closely associated to their pathological consequences.

Enzymatic Incorporation of Modified Purine Nucleotides in DNA.

Science.gov (United States)

Abu El Asrar, Rania; Margamuljana, Lia; Abramov, Mikhail; Bande, Omprakash; Agnello, Stefano; Jang, Miyeon; Herdewijn, Piet

2017-12-14

A series of nucleotide analogues, with a hypoxanthine base moiety (8-aminohypoxanthine, 1-methyl-8-aminohypoxanthine, and 8-oxohypoxanthine), together with 5-methylisocytosine were tested as potential pairing partners of N 8 -glycosylated nucleotides with an 8-azaguanine or 8-aza-9-deazaguanine base moiety by using DNA polymerases (incorporation studies). The best results were obtained with the 5-methylisocytosine nucleotide followed by the 1-methyl-8-aminohypoxanthine nucleotide. The experiments demonstrated that small differences in the structure (8-azaguanine versus 8-aza-9-deazaguanine) might lead to significant differences in recognition efficiency and selectivity, base pairing by Hoogsteen recognition at the polymerase level is possible, 8-aza-9-deazaguanine represents a self-complementary base pair, and a correlation exists between in vitro incorporation studies and in vivo recognition by natural bases in Escherichia coli, but this recognition is not absolute (exceptions were observed). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Junctional transfer in cultured vascular endothelium: II. Dye and nucleotide transfer

International Nuclear Information System (INIS)

Larson, D.M.; Sheridan, J.D.

1985-01-01

Vascular endothelial cultures, derived from large vessels, retain many of the characteristics of their in vivo counterparts. However, the observed reduction in size and complexity of intercellular gap and tight junctions in these cultured cells suggests that important functions, thought to be mediated by these structures, may be altered in vitro. In continuing studies on intercellular communication in vessel wall cells, the authors have quantitated the extent of junctional transfer of small molecular tracers (the fluorescent dye Lucifer Yellow CH and tritiated uridine nucleotides) in confluent cultures of calf aortic (BAEC) and umbilical vein (BVEC) endothelium. Both BAEC and BVEC show extensive (and quantitatively equivalent) dye and nucleotide transfer. As an analogue of intimal endothelium, the authors have also tested dye transfer in freshly isolated sheets of endothelium. Transfer in BAEC and BVEC sheets was more rapid, extensive and homogeneous than in the cultured cells, implying a reduction in molecular coupling as endothelium adapts to culture conditions. In addition, they have documented heterocellular nucleotide transfer between cultured endothelium and vascular smooth muscle cells, of particular interest considering the prevalence of ''myo-endothelial'' junctions in vivo. These data yield further information on junctional transfer in cultured vascular endothelium and have broad implications for the functional integration of the vessel wall in the physiology and pathophysiology of the vasculature

Investigation of (Y,Gd)Ba2Cu3O7-x grown by MOCVD on a simplified IBAD MgO template

International Nuclear Information System (INIS)

Stan, L; Holesinger, T G; Maiorov, B; Civale, L; DePaula, R F; Jia, Q X; Chen, Y; Xiong, X; Selvamanickam, V

2010-01-01

We have used an ion beam sputtered Y 2 O 3 -Al 2 O 3 (YALO) composite to simplify the architecture of high temperature superconducting (HTS) coated conductors (CCs) based on a IBAD MgO template. By implementing YALO, we have reduced the total non-superconducting layers between the polycrystalline metal substrate and the superconducting film from five (the standard architecture) to four. Well textured (Y,Gd)Ba 2 Cu 3 O 7-x ((Y, Gd)BCO) films have been successfully grown by MOCVD on this simplified template. The microstructural characterization revealed that all layers are continuous and uniform with sharp and clean interfaces. Additionally, the YALO maintained its amorphous nature after the deposition of the superconductive layer, which is a plus in terms of its efficiency as a diffusion barrier. The achievement of a self-field critical current of 230 A cm -1 at 75.5 K is another proof of the effectiveness of YALO as a diffusion barrier and nucleation seed for the MgO. The transport properties under an applied magnetic field of MOCVD grown (Y, Gd)BCO on LMO buffered MgO/YALO/Ni-alloy are comparable with those of (Y, Gd)BCO on a standard architecture, thus demonstrating good compatibility between the simplified template with the MOCVD grown (Y, Gd)BCO. The use of a single composite YALO layer instead of individual layers of Y 2 O 3 and Al 2 O 3 for the large scale fabrication of HTS CCs based on IBAD MgO provides advantages such as potentially reduced cost due to the reduced number of fabrication steps.

Improved dielectric functions in metallic films obtained via template stripping

Science.gov (United States)

Hyuk Park, Jong; Nagpal, Prashant; Oh, Sang-Hyun; Norris, David J.

2012-02-01

We compare the dielectric functions of silver interfaces obtained via thermal evaporation with those obtained with template stripping. Ellipsometry measurements show that the smoother template-stripped surfaces exhibit effective dielectric functions with a more negative real component and a smaller imaginary component, implying higher conductivity and less energy loss, respectively. These results agree with the relation between dielectric function and surface roughness derived from combining the effective-medium model and the Drude-Lorentz model. The improvement in the effective dielectric properties shows that metallic films prepared via template stripping can be favorable for applications in electronics, nanophotonics, and plasmonics.

External and semi-internal controls for PCR amplification of homologous sequences in mixed templates.

Science.gov (United States)

Kalle, Elena; Gulevich, Alexander; Rensing, Christopher

2013-11-01

In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory practice in different PCR assays. We propose the inclusion of an analogous approach as a quality control system for multi-template PCR applications. The amplification controls must take into account the characteristics of multi-template PCR and be able to effectively monitor particular assay performance. This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples. The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products. © 2013 Elsevier B.V. All rights reserved.

Preparation of Biomorphic TiO2 Ceramics from Rattan Templates

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Liangcun Qian

2015-05-01

Full Text Available In this work, biomorphic ceramics were produced from various rattan templates, and sol infiltration was used with vacuum/positive pressure technology. Finally, the samples were sintered to form TiO2 ceramics with a rattan microstructure. Through X-ray diffraction (XRD, thermogravimetric (TG data, dimensional variation analysis, and scanning electron microscopy (SEM images of biomorphic ceramics, the results of this experiment showed that the times of sol-gel infiltration were decreased due to use of the vacuum/positive pressure technology. In order to further supply the TiO2 content and fill the pyrolysis gaps in the charcoal/TiO2 composites sintered at 800 °C, it was necessary to repeat the sol-gel process. In the transverse section, ceramics for the rattan templates without the rattan edge, more perfect biomorphic features were achieved. Conversely, deformations occurred along the transverse section of the ceramics for the templates made with the rattan edge. Meanwhile, the fracture phenomenon took place along the ceramic axial section. The main reason for deformation and fracture was that the anisotropic structure of the template was stressed during the sintering process. Furthermore, the micrometer-sized pores were found in the ceramics along the axial section because of the removal of the charcoal templates.

Fabricating superhydrophobic polymer surfaces with excellent abrasion resistance by a simple lamination templating method.

Science.gov (United States)

Xu, Qian Feng; Mondal, Bikash; Lyons, Alan M

2011-09-01

Fabricating robust superhydrophobic surfaces for commercial applications is challenging as the fine-scale surface features, necessary to achieve superhydrophobicity, are susceptible to mechanical damage. Herein, we report a simple and inexpensive lamination templating method to create superhydrophobic polymer surfaces with excellent abrasion resistance and water pressure stability. To fabricate the surfaces, polyethylene films were laminated against woven wire mesh templates. After cooling, the mesh was peeled from the polymer creating a 3D array of ordered polymer microposts on the polymer surface. The resulting texture is monolithic with the polymer film and requires no chemical modification to exhibit superhydrophobicity. By controlling lamination parameters and mesh dimensions, polyethylene surfaces were fabricated that exhibit static contact angles of 160° and slip angles of 5°. Chemical and mechanical stability was evaluated using an array of manual tests as well as a standard reciprocating abraser test. Surfaces remained superhydrophobic after more than 5500 abrasion cycles at a pressure of 32.0 kPa. In addition, the surface remains dry after immersing into water for 5 h at 55 kPa. This method is environmental friendly, as it employs no solvents or harsh chemicals and may provide an economically viable path to manufacture large areas of mechanically robust superhydrophobic surfaces from inexpensive polymers and reusable templates.

Polymerization of amino acids containing nucleotide bases

Science.gov (United States)

Ben Cheikh, Azzouz; Orgel, Leslie E.

1990-01-01

The nucleoamino acids 1-(3'-amino,3'-carboxypropyl)uracil (3) and 9-(3'-amino,3'-carboxypropyl)adenine (4) have been prepared as (L)-en-antiomers and as racemic mixtures. When 3 or 4 is suspended in water and treated with N,N'-carbon-yldiimidazole, peptides are formed in good yield. The products formed from the (L)-enantiomers are hydrolyzed to the monomeric amino acids by pronase. Attempts to improve the efficiency of these oligomerizations by including a polyuridylate template in the reaction mixture were not successful. Similarly, oligomers derived from the (L)-enantiomer of 3 did not act as templates to facilitate the oligomerization of 4.

New natural shapes of non-Gaussianity from high-derivative interactions and their optimal limits from WMAP 9-year data

International Nuclear Information System (INIS)

Behbahani, Siavosh R.; Mirbabayi, Mehrdad; Senatore, Leonardo; Smith, Kendrick M.

2014-01-01

Given the fantastic experimental effort, it is important to thoroughly explore the signature space of inflationary models. The fact that higher derivative operators do not renormalize lower derivative ones allows us to find a large class of technically natural single-clock inflationary models where, in the context of the Effective Field Theory of Inflation, the leading interactions have many derivatives. We systematically explore the 3-point function induced by these models and their overlap with the standard equilateral and orthogonal templates. We find that in order to satisfactorily cover the signature space of these models, two new additional templates need to be included. We then perform the optimal analysis of the WMAP 9-year data for the resulting four templates, finding that the overall significance of a non-zero signal is between 2–2.5σ, depending on the choice of parameter space, partially driven by the preference for nonzero f NL orth in WMAP9

A novel ethanol templating synthesis of ordered lamellar superstructured crystalline zirconia

International Nuclear Information System (INIS)

Liu Chao; Wang Bin; Ji Xiujie; Zhao Shanshan; Wu Jie; Jia Jianlong; Ma Dongxia

2012-01-01

Soft template technique has attracted great interest, because it is a facile, inexpensive and efficient synthesis strategy for ordered superstructural systems. Here, a novel ethanol template was used to synthesize the ordered lamellar superstructured crystalline zirconia (Lα-ZrO 2 ) without post-treatments and surfactants. ZrOCl 2 and NaOH were served as Zr source and precipitant, respectively. XRD analysis showed that Lα-ZrO 2 is crystalline. XPS spectra indicated the physical adsorption of ethanol molecules in Lα-ZrO 2 . TEM further observed and proved the 1.36-nm period of superstructure detected and calculated by SAXRD (1.35 nm), which is composed of 0.68-nm thick ZrO 2 and pore alternatively. In contrast, the template-free ZrO 2 (TF-ZrO 2 ) presents no superstructure and is poorly crystallized. As a soft template, ethanol presents the roles of (i) inducing the growth of zirconia layers, (ii) directing the self-assembly of ordered lamellar superstructure, and (iii) decreasing the crystallization temperature. The possible mechanism of ethanol serving as a soft template was proposed and discussed in thermodynamics.

Functional interaction between the two halves of the photoreceptor-specific ATP binding cassette protein ABCR (ABCA4). Evidence for a non-exchangeable ADP in the first nucleotide binding domain.

Science.gov (United States)

Ahn, Jinhi; Beharry, Seelochan; Molday, Laurie L; Molday, Robert S

2003-10-10

ABCR, also known as ABCA4, is a member of the superfamily of ATP binding cassette transporters that is believed to transport retinal or retinylidene-phosphatidylethanolamine across photoreceptor disk membranes. Mutations in the ABCR gene are responsible for Stargardt macular dystrophy and related retinal dystrophies that cause severe loss in vision. ABCR consists of two tandemly arranged halves each containing a membrane spanning segment followed by a large extracellular/lumen domain, a multi-spanning membrane domain, and a nucleotide binding domain (NBD). To define the role of each NBD, we examined the nucleotide binding and ATPase activities of the N and C halves of ABCR individually and co-expressed in COS-1 cells and derived from trypsin-cleaved ABCR in disk membranes. When disk membranes or membranes from co-transfected cells were photoaffinity labeled with 8-azido-ATP and 8-azido-ADP, only the NBD2 in the C-half bound and trapped the nucleotide. Co-expressed half-molecules displayed basal and retinal-stimulated ATPase activity similar to full-length ABCR. The individually expressed N-half displayed weak 8-azido-ATP labeling and low basal ATPase activity that was not stimulated by retinal, whereas the C-half did not bind ATP and exhibited little if any ATPase activity. Purified ABCR contained one tightly bound ADP, presumably in NBD1. Our results indicate that only NBD2 of ABCR binds and hydrolyzes ATP in the presence or absence of retinal. NBD1, containing a bound ADP, associates with NBD2 to play a crucial, non-catalytic role in ABCR function.

Multi-template synthesis of hierarchically porous carbon spheres with potential application in supercapacitors

NARCIS (Netherlands)

Zhou, Weizheng; Lin, Zhixing; Tong, Gangsheng; Stoyanov, Simeon D.; Yan, Deyue; Mai, Yiyong; Zhu, Xinyuan

2016-01-01

A new and simple multi-template approach towards hierarchical porous carbon (HPC) materials was reported. HPC spheres were prepared by using hierarchical silica capsules (HSCs) as the hard template and triblock copolymer Pluronic P123 as the soft template. Three types of pores were tunably

78 FR 64925 - Request for Comments on Proposed Elimination of Patents Search Templates

Science.gov (United States)

2013-10-30

...] Request for Comments on Proposed Elimination of Patents Search Templates AGENCY: United States Patent and... Patents Search Templates from the USPTO Web site. In 2006, the United States Patent and Trademark Office (USPTO) implemented Patents Search Templates, which are United States Patent Classification (USPC...

Effect of template in MCM-41 on the adsorption of aniline from aqueous solution.

Science.gov (United States)

Yang, Xinxin; Guan, Qingxin; Li, Wei

2011-11-01

The effect of the surfactant template cetyltrimethylammonium bromide (CTAB) in MCM-41 on the adsorption of aniline was investigated. Various MCM-41 samples were prepared by controlling template removal using an extraction method. The samples were then used as adsorbents for the removal of aniline from aqueous solution. The results showed that the MCM-41 samples with the template partially removed (denoted as C-MCM-41) exhibited better adsorption performance than MCM-41 with the template completely removed (denoted as MCM-41). The reason for this difference may be that the C-MCM-41 samples had stronger hydrophobic properties and selectivity for aniline because of the presence of the template. The porosity and cationic sites generated by the template play an important role in the adsorption process. The optimal adsorbent with moderate template was achieved by changing the ratio of extractant; it has the potential for promising applications in the field of water pollution control. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Survey On Various Web Template Detection And Extraction Methods

Directory of Open Access Journals (Sweden)

Neethu Mary Varghese

2015-03-01

Full Text Available Abstract In todays digital world reliance on the World Wide Web as a source of information is extensive. Users increasingly rely on web based search engines to provide accurate search results on a wide range of topics that interest them. The search engines in turn parse the vast repository of web pages searching for relevant information. However majority of web portals are designed using web templates which are designed to provide consistent look and feel to end users. The presence of these templates however can influence search results leading to inaccurate results being delivered to the users. Therefore to improve the accuracy and reliability of search results identification and removal of web templates from the actual content is essential. A wide range of approaches are commonly employed to achieve this and this paper focuses on the study of the various approaches of template detection and extraction that can be applied across homogenous as well as heterogeneous web pages.

Template-assisted growth of nano structured functional materials

International Nuclear Information System (INIS)

Ying, K.K.; Nur Ubaidah Saidin; Khuan, N.I.; Suhaila Hani Ilias; Foo, C.T.

2012-01-01

Template-assisted growth is an important nano electrochemical deposition technique for synthesizing one-dimensional (1-D) nano structures with uniformly well-controlled shapes and sizes. A good template with well-defined dimensions is imperative for realizing this task. Porous anodic alumina (PAA) has been a favorable candidate for this purpose as it can be tailor-made with precise pore geometries, such as pore length and diameter as well as inter-pore distances, via the anodization of pure aluminium. This paper reports the fabrication of PAA templates and electrochemical synthesis of functional nano structures in the form of nano wires using PAA templates as scaffolds. Axial heterostructure and homogeneous nano wires formed by engineering materials configuration via composition and/ or layer thickness variations were fabricated for different functionalities. X-ray diffraction and imaging techniques were used to alucidate the microstructures, morphologies and chemical compositions of the nano wires produced. Due to their large surface area-to-volume ratios, and therefore high sensitivities, these functional nano structures have useful applications as critical components in nano sensor devices and various areas of nano technology. Potential applications include as hydrogen gas sensors in nuclear power plant for monitoring structural integrity of reactor components and containment building, as well as environmental monitoring of air pollution and leakages of toxic gases and chemicals. (Author)

Julius – a template based supplementary electronic health record system

Directory of Open Access Journals (Sweden)

Klein Gunnar O

2007-05-01

Full Text Available Abstract Background EHR systems are widely used in hospitals and primary care centres but it is usually difficult to share information and to collect patient data for clinical research. This is partly due to the different proprietary information models and inconsistent data quality. Our objective was to provide a more flexible solution enabling the clinicians to define which data to be recorded and shared for both routine documentation and clinical studies. The data should be possible to reuse through a common set of variable definitions providing a consistent nomenclature and validation of data. Another objective was that the templates used for the data entry and presentation should be possible to use in combination with the existing EHR systems. Methods We have designed and developed a template based system (called Julius that was integrated with existing EHR systems. The system is driven by the medical domain knowledge defined by clinicians in the form of templates and variable definitions stored in a common data repository. The system architecture consists of three layers. The presentation layer is purely web-based, which facilitates integration with existing EHR products. The domain layer consists of the template design system, a variable/clinical concept definition system, the transformation and validation logic all implemented in Java. The data source layer utilizes an object relational mapping tool and a relational database. Results The Julius system has been implemented, tested and deployed to three health care units in Stockholm, Sweden. The initial responses from the pilot users were positive. The template system facilitates patient data collection in many ways. The experience of using the template system suggests that enabling the clinicians to be in control of the system, is a good way to add supplementary functionality to the present EHR systems. Conclusion The approach of the template system in combination with various local EHR

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA.

Science.gov (United States)

Khodakov, Dmitriy A; Khodakova, Anastasia S; Huang, David M; Linacre, Adrian; Ellis, Amanda V

2015-03-04

Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.

Design and Fabrication of a Precision Template for Spine Surgery Using Selective Laser Melting (SLM).

Science.gov (United States)

Wang, Di; Wang, Yimeng; Wang, Jianhua; Song, Changhui; Yang, Yongqiang; Zhang, Zimian; Lin, Hui; Zhen, Yongqiang; Liao, Suixiang

2016-07-22

In order to meet the clinical requirements of spine surgery, this paper proposes the fabrication of the customized template for spine surgery through computer-aided design. A 3D metal printing-selective laser melting (SLM) technique was employed to directly fabricate the 316L stainless steel template, and the metal template with tiny locating holes was used as an auxiliary tool to insert spinal screws inside the patient's body. To guarantee accurate fabrication of the template for cervical vertebra operation, the contact face was placed upwards to improve the joint quality between the template and the cervical vertebra. The joint surface of the printed template had a roughness of Ra = 13 ± 2 μm. After abrasive blasting, the surface roughness was Ra = 7 ± 0.5 μm. The surgical metal template was bound with the 3D-printed Acrylonitrile Butadiene Styrene (ABS) plastic model. The micro-hardness values determined at the cross-sections of SLM-processed samples varied from HV0.3 250 to HV0.3 280, and the measured tensile strength was in the range of 450 MPa to 560 MPa, which showed that the template had requisite strength. Finally, the metal template was clinically used in the patient's surgical operation, and the screws were inserted precisely as the result of using the auxiliary template. The geometrical parameters of the template hole (e.g., diameter and wall thickness) were optimized, and measures were taken to optimize the key geometrical units (e.g., hole units) in metal 3D printing. Compared to the traditional technology of screw insertion, the use of the surgical metal template enabled the screws to be inserted more easily and accurately during spinal surgery. However, the design of the high-quality template should fully take into account the clinical demands of surgeons, as well as the advice of the designing engineers and operating technicians.

Performance Evaluation of Fusing Protected Fingerprint Minutiae Templates on the Decision Level

Directory of Open Access Journals (Sweden)

Raymond N. J. Veldhuis

2012-04-01

Full Text Available In a biometric authentication system using protected templates, a pseudonymous identifier is the part of a protected template that can be directly compared. Each compared pair of pseudonymous identifiers results in a decision testing whether both identifiers are derived from the same biometric characteristic. Compared to an unprotected system, most existing biometric template protection methods cause to a certain extent degradation in biometric performance. Fusion is therefore a promising way to enhance the biometric performance in template-protected biometric systems. Compared to feature level fusion and score level fusion, decision level fusion has not only the least fusion complexity, but also the maximum interoperability across different biometric features, template protection and recognition algorithms, templates formats, and comparison score rules. However, performance improvement via decision level fusion is not obvious. It is influenced by both the dependency and the performance gap among the conducted tests for fusion. We investigate in this paper several fusion scenarios (multi-sample, multi-instance, multi-sensor, multi-algorithm, and their combinations on the binary decision level, and evaluate their biometric performance and fusion efficiency on a multi-sensor fingerprint database with 71,994 samples.

Performance Evaluation of Fusing Protected Fingerprint Minutiae Templates on the Decision Level

Science.gov (United States)

Yang, Bian; Busch, Christoph; de Groot, Koen; Xu, Haiyun; Veldhuis, Raymond N. J.

2012-01-01

In a biometric authentication system using protected templates, a pseudonymous identifier is the part of a protected template that can be directly compared. Each compared pair of pseudonymous identifiers results in a decision testing whether both identifiers are derived from the same biometric characteristic. Compared to an unprotected system, most existing biometric template protection methods cause to a certain extent degradation in biometric performance. Fusion is therefore a promising way to enhance the biometric performance in template-protected biometric systems. Compared to feature level fusion and score level fusion, decision level fusion has not only the least fusion complexity, but also the maximum interoperability across different biometric features, template protection and recognition algorithms, templates formats, and comparison score rules. However, performance improvement via decision level fusion is not obvious. It is influenced by both the dependency and the performance gap among the conducted tests for fusion. We investigate in this paper several fusion scenarios (multi-sample, multi-instance, multi-sensor, multi-algorithm, and their combinations) on the binary decision level, and evaluate their biometric performance and fusion efficiency on a multi-sensor fingerprint database with 71,994 samples. PMID:22778583

[A population genetic study of 22 autosomal loci of single nucleotide polymorphisms].

Science.gov (United States)

Tang, Jian-pin; Jiang, Feng-hui; Shi, Mei-sen; Xu, Chuan-chao; Chen, Rui; Lai, Xiao-pin

2012-12-01

To evaluate polymorphisms and forensic efficiency of 22 non-binary single nucleotide polymorphism (SNP) loci. One hundred ethnic Han Chinese individuals were recruited from Dongguan, Guangdong. The 22 loci were genotyped with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Nine loci were found with a single allele, 4 loci were found to be biallelic, whilst 9 loci were found to have 3 alleles. For 13 polymorphic loci, the combined discrimination power and power of exclusion were 0.999 98 and 0.9330, respectively. For the 9 non-biallelic loci, the combined discrimination power and power of exclusion were 0.9998 and 0.8956, respectively. For motherless cases, the combined power of exclusion was 0.6405 for 13 polymorphic SNPs and 0.6405 for 9 non-binary SNPs. Non-binary loci have a greater discrimination power and exclusion power per SNP.

Identification of cyclic nucleotide gated channels using regular expressions

KAUST Repository

Zelman, Alice K.; Dawe, Adam Sean; Berkowitz, Gerald A.

2013-01-01

Cyclic nucleotide-gated channels (CNGCs) are nonselective cation channels found in plants, animals, and some bacteria. They have a six-transmembrane/one- pore structure, a cytosolic cyclic nucleotide-binding domain, and a cytosolic calmodulin

Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions.

Science.gov (United States)

Hesketh, Andy; Vergnano, Marta; Wan, Chris; Oliver, Stephen G

2017-07-25

cells recover. Despite the importance of this process, the broader impact of bacterial nucleotides on the functioning of eukaryotic cells remains poorly defined. To address this, we genetically modified cells of the eukaryote Saccharomyces cerevisiae (baker's yeast) to produce three of these molecules (cdiAMP, cdiGMP, and ppGpp) and used the engineered strains as model systems to characterize the effects of the molecules on the cells. In addition to demonstrating that the nucleotides are each capable of adversely affecting yeast cell function and growth, we also identified the cellular functions important for mitigating the damage caused, suggesting possible modes of action. This study expands our understanding of the molecular interactions that can take place between bacterial and eukaryotic cells. Copyright © 2017 Hesketh et al.

Nucleotide Metabolism and its Control in Lactic Acid Bacteria

DEFF Research Database (Denmark)

Kilstrup, Mogens; Hammer, Karin; Jensen, Peter Ruhdal

2005-01-01

Most metabolic reactions are connected through either their utilization of nucleotides or their utilization of nucleotides or their regulation by these metabolites. In this review the biosynthetic pathways for pyrimidine and purine metabolism in lactic acid bacteria are described including...... the interconversion pathways, the formation of deoxyribonucleotides and the salvage pathways for use of exogenous precursors. The data for the enzymatic and the genetic regulation of these pathways are reviewed, as well as the gene organizations in different lactic acid bacteria. Mutant phenotypes and methods...... for manipulation of nucleotide pools are also discussed. Our aim is to provide an overview of the physiology and genetics of nucleotide metabolism and its regulation that will facilitate the interpretation of data arising from genetics, metabolomics, proteomics, and transcriptomics in lactic acid bacteria....

Synthesis of boron nitride nanotubes with SiC nanowire as template

International Nuclear Information System (INIS)

Zhong, B.; Song, L.; Huang, X.X.; Wen, G.W.; Xia, L.

2011-01-01

Highlights: → Boron nitride nanotubes (BNNTs) have been fabricated using SiC nanowires as template. → SiC nanowires could be effectively etched out by the vapors decomposed from ammonia borane, leading to the formation of BNNTs. → A template self-sacrificing mechanism is responsible for the formation of BNNTs. -- Abstract: A novel template method for the preparation of boron nitride nanotubes (BNNTs) using SiC nanowire as template and ammonia borane as precursor is reported. We find out that the SiC nanowires could be effectively etched out by the vapors decomposed from ammonia borane, leading to the formation of BNNTs. The as-prepared products are well characterized by means of complementary analytical techniques. A possible formation mechanism is disclosed. The method developed here paves the way for large scale production of BNNTs.

Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

Energy Technology Data Exchange (ETDEWEB)

Baak, M., E-mail: max.baak@cern.ch [CERN, CH-1211 Geneva 23 (Switzerland); Gadatsch, S., E-mail: stefan.gadatsch@nikhef.nl [Nikhef, PO Box 41882, 1009 DB Amsterdam (Netherlands); Harrington, R. [School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, Scotland (United Kingdom); Verkerke, W. [Nikhef, PO Box 41882, 1009 DB Amsterdam (Netherlands)

2015-01-21

A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates are often required to model the impact of systematic uncertainties.

Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

International Nuclear Information System (INIS)

Baak, M.; Gadatsch, S.; Harrington, R.; Verkerke, W.

2015-01-01

A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates are often required to model the impact of systematic uncertainties

Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

CERN Document Server

Baak, Max; Harrington, Robert; Verkerke, Wouter

2014-01-01

A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates is often required to model the impact of systematic uncertainties.

Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

CERN Document Server

Baak, Max; Harrington, Robert; Verkerke, Wouter

2015-01-01

A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates is often required to model the impact of systematic uncertainties.

Fabrication of porous zirconia using filter paper template

International Nuclear Information System (INIS)

Deng Yuhua; Wei Pan

2005-01-01

In this work, porous zirconia ceramic was synthesized using filter papers as a template. Special attention is paid to whether the structural of the filter paper can be transferred to the zirconia structure. Microstructure of so synthesized porous zirconia was observed with SEM and the phase was determined by XRD. The surface area and the pore were investigated with an automatic volumetric sorption analyzer. It has been found that the morphology of the template transmit to the porous zirconia quite well. (orig.)

The Role of Morphology in Word Recognition of Hebrew as a Templatic Language

Science.gov (United States)

Oganyan, Marina

2017-01-01

Research on recognition of complex words has primarily focused on affixational complexity in concatenative languages. This dissertation investigates both templatic and affixational complexity in Hebrew, a templatic language, with particular focus on the role of the root and template morphemes in recognition. It also explores the role of morphology…

Non-detectable levels of 6-thioguanine nucleotides and 6-methylmercaptopurine in a patient treated with azathioprine: a case report

Science.gov (United States)

Wong, D R; den Dulk, M O; Derijks, L J J; Gemmeke, E H K M; Hooymans, P M

2007-01-01

in the liver. 6-MP is then further catabolised by xanthine-oxidase (XO) and TPMT or anabolised by hypoxanthine phosphoribosyl transferase (HPRT). Remarkably, treatment with 6-MP in combination with the XO-inhibitor allopurinol resulted in a myelotoxic 6TGN level in the first week after start of treatment. There are two hypotheses on the mechanism by which this finding could be explained. First, an ‘ultra-high’ XO activity results in a direct and complete conversion of 6-MP into 6-thiouric acid. Secondly, AZA is not converted into 6-MP. Consequently, there is no formation of active thiopurine nucleotides out of 6-MP. Also, a combination of these two mechanisms could lead to a decreased formation of active thiopurine metabolites. Conclusion: Our finding indicates non-conventional insights in the biotransformation of AZA contributing to an interindividual variation in thiopurine metabolism.

External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

DEFF Research Database (Denmark)

Kalle, Elena; Gulevich, Alexander; Rensing, Christopher Günther T

2013-01-01

as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples......In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur....... This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control...

Effects of hypokinesia on cyclic nucleotides and hormonal regulation ...

African Journals Online (AJOL)

PTH), calcitonin (CT), cyclic nucleotides (cAMP, cGMP) and calcium in the blood of rats, while in urine - phosphate, calcium and cyclic nucleotides. Design: Laboratory based experiment. Setting: Laboratory in the Department of Biochemistry, ...

International developments in openEHR archetypes and templates.

Science.gov (United States)

Leslie, Heather

Electronic Health Records (EHRs) are a complex knowledge domain. The ability to design EHRs to cope with the changing nature of health knowledge, and to be shareable, has been elusive. A recent pilot study1 tested the applicability of the CEN 13606 as an electronic health record standard. Using openEHR archetypes and tools2, 650 clinical content specifi cations (archetypes) were created (e.g. for blood pressure) and re-used across all clinical specialties and contexts. Groups of archetypes were aggregated in templates to support clinical information gathering or viewing (e.g. 80 separate archetypes make up the routine antenatal visit record). Over 60 templates were created for use in the emergency department, antenatal care and delivery of an infant, and paediatric hearing loss assessment. The primary goal is to define a logical clinical record architecture for the NHS but potentially, with archetypes as the keystone, shareable EHRs will also be attainable. Archetype and template development work is ongoing, with associated evaluation occurring in parallel.

Addition of magnetic markers for non-destructive evaluation of polymer composites

Directory of Open Access Journals (Sweden)

Ana Paula Pereira Fulco

2011-12-01

Full Text Available Polymer composite pipes are an appealing option as a substitute for conventional steel pipes, particularly due to their inherent corrosion resistance. However, the composite pipes currently used do not allow non-destructive evaluation (NDE using instrumented devices which operate with magnetic sensors. The present work aims at the development of polymer composites with the addition magnetic markers to allow the application non-destructive evaluation techniques which use magnetic sensors. Glass-polyester composite flat, circular plates were fabricated with the addition of ferrite particles (barium ferrite and strontium ferrite and four types of notches were introduced on the plates' surfaces. The influence of these notches on the measured magnetic properties of each material was measured. X-ray diffraction (XRD, X-ray fluorescence (XRF and Brunauer, Emmett, and Teller (BET nitrogen adsorption were used for the characterization of the ferrite particles. Particle dispersion in the polymer matrix was analyzed by scanning electron microscopy (SEM. According to the results, a particular variation in magnetic field was detected over the region surrounding each type of notch. The results suggest that the proposed technique has great potential for damage detection in polymer composites using magnetic sensors and thus constitute a valuable contribution which may ultimately lead to the development of non-destructive evaluation techniques for assessing the structural integrity polymer composite pipes.

Caprine Butchery and Bone Modification Templates: A step towards standardisation

Directory of Open Access Journals (Sweden)

Peter Popkin

2005-03-01

Full Text Available Widely accepted zooarchaeological procedure for recording butchery marks and other types of bone modification involves two processes: Drawing the bone showing the exact location and orientation of the modification and recording all of the information about the bone and its modification into an electronic database. No recording templates have ever been published, however, resulting in individual zooarchaeologists repeating the effort of developing their own templates or drawings for each bone in an assemblage showing a modification. Both of these tasks are time consuming and lead to inconsistencies in recording and quantification methods. To help alleviate this problem a series of caprine (sheep and goat bone templates have been created. These templates show every bone in a goat skeleton, apart from the skull, from six views at life-size when printed on A4 paper. They have intentionally been produced with a minimum of detail (without shading or stippling etc. so that the recorded butchery marks and bone modifications will be clearly visible. Because the skeletal morphology of sheep and goats is so similar these templates may be used interchangeably for either species. They may also be used for many other artiodactyl species such as cattle and deer as no scale has been indicated. The study of butchery marks and bone modification has the potential to provide zooarchaeologists with information about taphonomy, site formation processes, burial/ritual practices, human behaviour, ancient technologies and possibly ethnicity amongst other things, but only if the recording of these bone modifications is undertaken in a standardised fashion across the field. While much effort has been directed towards standardising the recognition and classification of various bone modifications, the recording of these modifications regularly occurs in various ways. Using standardised recording templates will save valuable time and help to alleviate problems of data

Lack of effect of dietary nucleotide supplementation on erythrocyte 2,3-diphosphoglycerate concentration. A study on preterm neonates.

Science.gov (United States)

Scopesi, Fabio; Canini, Silvana; Arioni, Cesare; Mazzella, Massimo; Gazzolo, Diego; Lantieri, Pasquale B; Bonacci, Wanda; Serra, Giovanni

2006-06-01

Recently we demonstrated an increased 2,3-diphosphoglycerate (2,3-DPG) erythrocyte concentration in rat pups subjected to nucleotide-enriched artificial feeding. The present study was carried out to test the hypothesis that a possible increase in 2,3-DPG concentration can also be obtained in human neonates who are fed nucleotide-enriched formula. Preterm neonates born or referred to the neonatal intensive care unit of the G. Gaslini Hospital, Genoa University, with a gestational age >30 weeks and <37 weeks were enrolled in our randomized trial. Recruitment took place within 48-72 hours from birth. Only newborns of mothers deciding not to breast-feed were eligible to be randomized for the supplemented group (FN) or non-supplemented group (RF). Breast-fed newborns were considered the control group (C). The study window (for supplementation and blood samples) was restricted to the first two weeks following birth (from the 2nd (t1) to the 16th (t2) day of life). At the end of our study, only 21 neonates were eligible for statistical analysis. The stimulating action of dietary nucleotides on 2,3-DPG concentration failed to be demonstrated; increases in 2,3-DPG concentration that were observed in newborns fed with nucleotide supplemented formula (FN) were comparable to those observed in newborns fed with regular formula (RF) and breast-fed newborns. The EC recommendation for the amount of nucleotides allowed in formula milk does not seem to be high enough to have positive effects on 2,3-DPG synthesis. Whether this possible 'pharmacological' effect can be achieved by a higher intake of ingested nucleotides and/or a change in the proportions of single nucleotides contained in milk formulas remain interesting end points to be elucidated.

A flexible, bolaamphiphilic template for mesoporous silicas.

Science.gov (United States)

Yuen, Alexander K L; Heinroth, Falk; Ward, Antony J; Masters, Anthony F; Maschmeyer, Thomas

2013-08-28

A novel symmetrical bolaamphiphile, containing two N-methylimidazolium head-groups bridged by a 32-methylene linker, was synthesized and characterized. A variety of mesoporous silicas was prepared using the bolaamphiphile as a "soft template". The effects of absolute surfactant concentration and synthesis conditions upon the morphologies of these silicas were investigated. For a given surfactant concentration, particle morphology; pore size; and pore ordering were modified through control of the template to silica-precursor ratio and synthesis conditions. Observed morphologies included: lenticular core-shell nanoparticles and decorticated globules, truncated hexagonal plates, and sheets. In all cases the mesopores are aligned along the shortest axis of the nanomaterial. Decorticated materials displayed surface areas of up to 1200 m(2) g(-1) and pore diameters (D(BJH)) of 24-28 Å. Small-angle X-ray diffraction and transmission electron microscopy measurements revealed that the majority of the materials has elliptical pores arranged in rectangular lattices (c2mm). Adoption of this symmetry group is a result of the template aggregate deformation from a regular hexagonal phase of cylindrical rods to a ribbon phase under the synthetic conditions.

Rational design of mesoporous metals and related nanomaterials by a soft-template approach.

Science.gov (United States)

Yamauchi, Yusuke; Kuroda, Kazuyuki

2008-04-07

We review recent developments in the preparation of mesoporous metals and related metal-based nanomaterials. Among the many types of mesoporous materials, mesoporous metals hold promise for a wide range of potential applications, such as in electronic devices, magnetic recording media, and metal catalysts, owing to their metallic frameworks. Mesoporous metals with highly ordered networks and narrow pore-size distributions have traditionally been produced by using mesoporous silica as a hard template. This method involves the formation of an original template followed by deposition of metals within the mesopores and subsequent removal of the template. Another synthetic method is the direct-template approach from lyotropic liquid crystals (LLCs) made of nonionic surfactants at high concentrations. Direct-template synthesis creates a novel avenue for the production of mesoporous metals as well as related metal-based nanomaterials. Many mesoporous metals have been prepared by the chemical or electrochemical reduction of metal salts dissolved in aqueous LLC domains. As a soft template, LLCs are more versatile and therefore more advantageous than hard templates. It is possible to produce various nanostructures (e.g., lamellar, 2D hexagonal (p6mm), and 3D cubic (Ia\\3d)), nanoparticles, and nanotubes simply by controlling the composition of the reaction bath.

Compatibility of Anti-Wear Additives with Non-Ferrous Engine Bearing Alloys

Energy Technology Data Exchange (ETDEWEB)

Qu, Jun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Zhou, Yan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-01-01

Investigate the compatibility of engine lubricant antiwear (AW) additives, specifically conventional zinc dialkyldithiophosphate (ZDDP) and newly developed ionic liquids (ILs), with selected non-ferrous engine bearing alloys, specifically aluminum and bronze alloys that are commonly used in connecting rod end journal bearings and bushings, to gain fundamental understanding to guide future development of engine lubricants

Fabricating hydroxyapatite nanorods using a biomacromolecule template

Energy Technology Data Exchange (ETDEWEB)

Zhu Aiping, E-mail: apzhu@yzu.edu.cn [College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002 (China); Lu Yan; Si Yunfeng [College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002 (China); Dai Sheng [School of Chemical Engineering, University of Adelaide, Adelaide, SA 5005 (Australia)

2011-02-01

Rod-like hydroxyapatite (HAp) nanoparticles with various aspect ratios are synthesized by means of low-temperature hydrothermal method in the presence of a N-[(2-hydroxy-3-trimethylammonium) propyl]chitosan chloride (HTCC) template. The synthesized HAps were examined by X-ray diffraction (XRD), Fourier transform infrared spectrophotometer (FTIR) and transmission electron microscopy (TEM) techniques. The results reveal that HAps are rod-like monocrystals, where the size and morphology can be tailored by varying synthesis conditions, such as pH, hydrothermal synthesis temperature and the ratio of PO{sub 4}{sup 3-} to the quaternary ammonium in HTCC. The mechanism of HTCC template on HAp nanorod preparation is analyzed.

Fabricating hydroxyapatite nanorods using a biomacromolecule template

International Nuclear Information System (INIS)

Zhu Aiping; Lu Yan; Si Yunfeng; Dai Sheng

2011-01-01

Rod-like hydroxyapatite (HAp) nanoparticles with various aspect ratios are synthesized by means of low-temperature hydrothermal method in the presence of a N-[(2-hydroxy-3-trimethylammonium) propyl]chitosan chloride (HTCC) template. The synthesized HAps were examined by X-ray diffraction (XRD), Fourier transform infrared spectrophotometer (FTIR) and transmission electron microscopy (TEM) techniques. The results reveal that HAps are rod-like monocrystals, where the size and morphology can be tailored by varying synthesis conditions, such as pH, hydrothermal synthesis temperature and the ratio of PO 4 3- to the quaternary ammonium in HTCC. The mechanism of HTCC template on HAp nanorod preparation is analyzed.

Frabicating hydroxyapatite nanorods using a biomacromolecule template

Science.gov (United States)

Zhu, Aiping; Lu, Yan; Si, Yunfeng; Dai, Sheng

2011-02-01

Rod-like hydroxyapatite (HAp) nanoparticles with various aspect ratios are synthesized by means of low-temperature hydrothermal method in the presence of a N-[(2-hydroxy-3-trimethylammonium) propyl]chitosan chloride (HTCC) template. The synthesized HAps were examined by X-ray diffraction (XRD), Fourier transform infrared spectrophotometer (FTIR) and transmission electron microscopy (TEM) techniques. The results reveal that HAps are rod-like monocrystals, where the size and morphology can be tailored by varying synthesis conditions, such as pH, hydrothermal synthesis temperature and the ratio of PO43- to the quaternary ammonium in HTCC. The mechanism of HTCC template on HAp nanorod preparation is analyzed.

Crosslinked Aspartic Acids as Helix-Nucleating Templates.

Science.gov (United States)

Zhao, Hui; Liu, Qi-Song; Geng, Hao; Tian, Yuan; Cheng, Min; Jiang, Yan-Hong; Xie, Ming-Sheng; Niu, Xiao-Gang; Jiang, Fan; Zhang, Ya-Ou; Lao, Yuan-Zhi; Wu, Yun-Dong; Xu, Nai-Han; Li, Zi-Gang

2016-09-19

Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational study of textured ferroelectric polycrystals: Dielectric and piezoelectric properties of template-matrix composites

Science.gov (United States)

Zhou, Jie E.; Yan, Yongke; Priya, Shashank; Wang, Yu U.

2017-01-01

Quantitative relationships between processing, microstructure, and properties in textured ferroelectric polycrystals and the underlying responsible mechanisms are investigated by phase field modeling and computer simulation. This study focuses on three important aspects of textured ferroelectric ceramics: (i) grain microstructure evolution during templated grain growth processing, (ii) crystallographic texture development as a function of volume fraction and seed size of the templates, and (iii) dielectric and piezoelectric properties of the obtained template-matrix composites of textured polycrystals. Findings on the third aspect are presented here, while an accompanying paper of this work reports findings on the first two aspects. In this paper, the competing effects of crystallographic texture and template seed volume fraction on the dielectric and piezoelectric properties of ferroelectric polycrystals are investigated. The phase field model of ferroelectric composites consisting of template seeds embedded in matrix grains is developed to simulate domain evolution, polarization-electric field (P-E), and strain-electric field (ɛ-E) hysteresis loops. The coercive field, remnant polarization, dielectric permittivity, piezoelectric coefficient, and dissipation factor are studied as a function of grain texture and template seed volume fraction. It is found that, while crystallographic texture significantly improves the polycrystal properties towards those of single crystals, a higher volume fraction of template seeds tends to decrease the electromechanical properties, thus canceling the advantage of ferroelectric polycrystals textured by templated grain growth processing. This competing detrimental effect is shown to arise from the composite effect, where the template phase possesses material properties inferior to the matrix phase, causing mechanical clamping and charge accumulation at inter-phase interfaces between matrix and template inclusions. The computational

Single Nucleotide Polymorphism

DEFF Research Database (Denmark)

Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

2014-01-01

Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...... of SNPs. This will allow acquisition of more information from the sample materials and open up for new possibilities as well as new challenges....

A novel ethanol templating synthesis of ordered lamellar superstructured crystalline zirconia

Energy Technology Data Exchange (ETDEWEB)

Liu Chao, E-mail: liuchao_tj@yahoo.com; Wang Bin [Key Laboratory for New Type of Functional Materials in Hebei Province, Hebei University of Technology (China); Ji Xiujie, E-mail: jxjchem@yahoo.com [State Key Laboratory of Hollow Fiber Membrane Materials and Processes, Tianjin Polytechnic University (China); Zhao Shanshan; Wu Jie; Jia Jianlong; Ma Dongxia [Key Laboratory for New Type of Functional Materials in Hebei Province, Hebei University of Technology (China)

2012-03-15

Soft template technique has attracted great interest, because it is a facile, inexpensive and efficient synthesis strategy for ordered superstructural systems. Here, a novel ethanol template was used to synthesize the ordered lamellar superstructured crystalline zirconia (L{alpha}-ZrO{sub 2}) without post-treatments and surfactants. ZrOCl{sub 2} and NaOH were served as Zr source and precipitant, respectively. XRD analysis showed that L{alpha}-ZrO{sub 2} is crystalline. XPS spectra indicated the physical adsorption of ethanol molecules in L{alpha}-ZrO{sub 2}. TEM further observed and proved the 1.36-nm period of superstructure detected and calculated by SAXRD (1.35 nm), which is composed of 0.68-nm thick ZrO{sub 2} and pore alternatively. In contrast, the template-free ZrO{sub 2} (TF-ZrO{sub 2}) presents no superstructure and is poorly crystallized. As a soft template, ethanol presents the roles of (i) inducing the growth of zirconia layers, (ii) directing the self-assembly of ordered lamellar superstructure, and (iii) decreasing the crystallization temperature. The possible mechanism of ethanol serving as a soft template was proposed and discussed in thermodynamics.