Standardised method for reporting exercise programmes: protocol for a modified Delphi study.

PubMed

Slade, Susan C; Dionne, Clermont E; Underwood, Martin; Buchbinder, Rachelle

2014-12-30

Exercise is integral to health across the lifespan and important for people with chronic health conditions. A systematic review of exercise trials for chronic conditions reported suboptimal descriptions of the evaluated interventions and concluded that this hinders interpretation and replication. The aim of this project is to develop a standardised method for reporting essential exercise programme details being evaluated in clinical trials. A modified Delphi technique will be used to gain consensus among international exercise experts. We will use three sequential rounds of anonymous online questionnaires to refine a standardised checklist. A draft checklist of potentially relevant items was developed based on the results of a systematic review of exercise systematic reviews. An international panel of experts was identified by exercise systematic review authorship, established international profile in exercise research and practice and by peer referral. In round 1, the international panel of experts will be asked to rate the importance of each draft item and provide additional suggestions for revisions or new items. Consensus will be considered reached if at least 70% of the panel strongly agree/disagree that an item should be included or excluded. Where agreement is not reached or there are suggestions for altered or new items, these will be taken to round 2 together with an aggregated summary of round 1 responses. Following the second round, a ranking of item importance will be made to rationalise the number of items. The final template will be distributed to panel members for approval. Ethics approval was received from The Cabrini Institute Ethics Committee, Melbourne, Australia (HREC 02-07-04-14). We plan to use a stepwise process to develop and refine a standardised and internationally agreed template for explicit reporting of exercise programmes. The template will be generalisable across all types of exercise interventions. The findings will be disseminated through peer-reviewed publications and conference presentations. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Informatics in radiology: An open-source and open-access cancer biomedical informatics grid annotation and image markup template builder.

PubMed

Mongkolwat, Pattanasak; Channin, David S; Kleper, Vladimir; Rubin, Daniel L

2012-01-01

In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and image markup (AIM), a project supported by the National Cancer Institute's cancer biomedical informatics grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible.

Informatics in Radiology: An Open-Source and Open-Access Cancer Biomedical Informatics Grid Annotation and Image Markup Template Builder

PubMed Central

Channin, David S.; Rubin, Vladimir Kleper Daniel L.

2012-01-01

In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and Image Markup (AIM), a project supported by the National Cancer Institute’s cancer Biomedical Informatics Grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible. © RSNA, 2012 PMID:22556315

Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions

NASA Astrophysics Data System (ADS)

Chaudhari, Rajan; Heim, Andrew J.; Li, Zhijun

2015-05-01

Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy of "modeling first, refinement next". In the present work, we developed an alternative modeling approach through the novel application of available multiple templates. First, conserved inter-residue interactions are derived from each additional template through conservation analysis of each template-target pairwise alignment. Then, these interactions are converted into distance restraints and incorporated in the homology modeling process. This approach was applied to modeling of the human β2 adrenergic receptor using the bovin rhodopsin and the human protease-activated receptor 1 as templates and improved model quality was demonstrated compared to the homology model generated by standard single-template and multiple-template methods. This method of "refined restraints first, modeling next", provides a fast and complementary way to the current modeling approaches. It allows rational identification and implementation of additional conserved distance restraints extracted from multiple templates and/or experimental data, and has the potential to be applicable to modeling of all helical transmembrane proteins.

Mapping of a standard documentation template to the ICF core sets for arthritis and low back pain.

PubMed

Escorpizo, Reuben; Davis, Kandace; Stumbo, Teri

2010-12-01

To identify the contents of a documentation template in The Guide to Physical Therapist Practice using the International Classification of Functioning, Disability, and Health (ICF) Core Sets for rheumatoid arthritis, osteoarthritis, and low back pain (LBP) as reference. Concepts were identified from items of an outpatient documentation template and mapped to the ICF using established linking rules. The ICF categories that were linked were compared with existing arthritis and LBP Core Sets. Based on the ICF, the template had the highest number (29%) of linked categories under Activities and participation while Body structures had the least (17%). ICF categories in the arthritis and LBP Core Sets had a 37-55% match with the ICF categories found in the template. We found 164 concepts that were not classified or not defined and 37 as personal factors. The arthritis and LBP Core Sets were reflected in the contents of the template. ICF categories in the Core Sets were reflected in the template (demonstrating up to 55% match). Potential integration of ICF in documentation templates could be explored and examined in the future to enhance clinical encounters and multidisciplinary communication. Copyright © 2010 John Wiley & Sons, Ltd.

Template-based de novo design for type II kinase inhibitors and its extented application to acetylcholinesterase inhibitors.

PubMed

Su, Bo-Han; Huang, Yi-Syuan; Chang, Chia-Yun; Tu, Yi-Shu; Tseng, Yufeng J

2013-10-31

There is a compelling need to discover type II inhibitors targeting the unique DFG-out inactive kinase conformation since they are likely to possess greater potency and selectivity relative to traditional type I inhibitors. Using a known inhibitor, such as a currently available and approved drug or inhibitor, as a template to design new drugs via computational de novo design is helpful when working with known ligand-receptor interactions. This study proposes a new template-based de novo design protocol to discover new inhibitors that preserve and also optimize the binding interactions of the type II kinase template. First, sorafenib (Nexavar) and nilotinib (Tasigna), two type II inhibitors with different ligand-receptor interactions, were selected as the template compounds. The five-step protocol can reassemble each drug from a large fragment library. Our procedure demonstrates that the selected template compounds can be successfully reassembled while the key ligand-receptor interactions are preserved. Furthermore, to demonstrate that the algorithm is able to construct more potent compounds, we considered kinase inhibitors and other protein dataset, acetylcholinesterase (AChE) inhibitors. The de novo optimization was initiated using a template compound possessing a less than optimal activity from a series of aminoisoquinoline and TAK-285 inhibiting type II kinases, and E2020 derivatives inhibiting AChE respectively. Three compounds with greater potency than the template compound were discovered that were also included in the original congeneric series. This template-based lead optimization protocol with the fragment library can help to design compounds with preferred binding interactions of known inhibitors automatically and further optimize the compounds in the binding pockets.

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

PubMed Central

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

Where the item still rules supreme: Time-based selection, enumeration, pre-attentive processing and the target template?

PubMed

Watson, Derrick G

2017-01-01

I propose that there remains a central role for the item (or its equivalent) in a wider range of search and search-related tasks/functions than might be conveyed by the article. I consider the functional relationship between the framework and some aspects of previous theories, and suggest some challenges that the new framework might encounter.

Reinforced self-assembly of donor-acceptor π-conjugated molecules to DNA templates by dipole-dipole interactions together with complementary hydrogen bonding interactions for biomimetics.

PubMed

Yang, Wanggui; Chen, Yali; Wong, Man Shing; Lo, Pik Kwan

2012-10-08

One of the most important criteria for the successful DNA-templated polymerization to generate fully synthetic biomimetic polymers is to design the complementary structural monomers, which assemble to the templates strongly and precisely before carrying polymerization. In this study, water-soluble, laterally thymine-substituted donor-acceptor π-conjugated molecules were designed and synthesized to self-assemble with complementary oligoadenines templates, dA(20) and dA(40), into stable and tubular assemblies through noncovalent interactions including π-π stacking, dipole-dipole interactions, and the complementary adenine-thymine (A-T) hydrogen-bonding. UV-vis, fluorescence, circular dichroism (CD), atomic force microscopy (AFM), and transmission electron microscopy (TEM) techniques were used to investigate the formation of highly robust nanofibrous structures. Our results have demonstrated for the first time that the dipole-dipole interactions are stronger and useful to reinforce the assembly of donor-acceptor π-conjugated molecules to DNA templates and the formation of the stable and robust supramolecular nanofibrous complexes together with the complementary hydrogen bonding interactions. This provides an initial step toward DNA-templated polymerization to create fully synthetic DNA-mimetic polymers for biotechnological applications. This study also presents an opportunity to precisely position donor-acceptor type molecules in a controlled manner and tailor-make advanced materials for various biotechnological applications.

Influence of solvent polarity and supersaturation on template-induced nucleation of carbamazepine crystal polymorphs

NASA Astrophysics Data System (ADS)

Parambil, Jose V.; Poornachary, Sendhil K.; Tan, Reginald B. H.; Heng, Jerry Y. Y.

2017-07-01

Studies on the use of template surfaces to induce heterogeneous crystal nucleation have gained momentum in recent years-with potential applications in selective crystallisation of polymorphs and in the generation of seed crystals in a continuous crystallisation process. In developing a template-assisted solution crystallisation process, the kinetics of homogeneous versus heterogeneous crystal nucleation could be influenced by solute-solvent, solute-template, and solvent-template interactions. In this study, we report the effect of solvents of varying polarity on the nucleation of carbamazepine (CBZ) crystal polymorphs, a model active pharmaceutical ingredient. The experimental results demonstrate that functionalised template surfaces are effective in promoting crystallisation of either the metastable (form II) or stable (form III) polymorphs of CBZ only in moderately (methanol, ethanol, isopropanol) and low polar (toluene) solvents. A solvent with high polarity (acetonitrile) is thought to mask the template effect on heterogeneous nucleation due to strong solute-solvent and solvent-template interactions. The current study highlights that a quality-by-design (QbD) approach-considering the synergistic effects of solute concentration, solvent type, solution temperature, and template surface chemistry on crystal nucleation-is critical to the development of a template-induced crystallisation process.

Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template

PubMed Central

Rutvisuttinunt, Wiriya; Meyer, Peter R.; Scott, Walter A.

2008-01-01

Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively. PMID:18974785

Two new templates for epidemiology applications: linked micromap plots and conditioned choropleth maps.

PubMed

Carr, D B; Wallin, J F; Carr, D A

This paper describes two interactive templates for representing spatially indexed estimates. Both templates use a matrix layout of small panels. The first template, called linked micromap plots, can represent multivariate estimates associated with each spatially indexed study unit. The second template, called conditioned choropleth maps, shows the connection between a dependent variable, as represented in a classed choropleth map, and two explanatory variables. The paper describes the cognitive considerations that motivate the layouts and representation details. The discussion also addresses topics of data quality and access, hypothesis generation, and interactive features such as pan and zoom and dynamic conditioning via sliders. The examples show epidemiological (mortality rates) and environmental (toxic concentrations) applications. Copyright 2000 John Wiley & Sons, Ltd.

Stampless fabrication of sheet bars using disposable templates

NASA Astrophysics Data System (ADS)

Smolentsev, V. P.; Safonov, S. V.; Smolentsev, E. V.; Fedonin, O. N.

2016-04-01

The article is devoted to the new method of small-scale fabrication of sheet bars. The procedure is performed by using disposable overlay templates, or those associated with a sheet, which parameters are obtained directly from the drawing. The proposed method used as a substitution of die cutting enables to intensify the preparatory technological process, which is particularly effective when launching the market-oriented items into production. It significantly increases the competitiveness of mechanical engineering and creates the conditions for technical support of present-day flexible production systems.

Whatever you do, don't look at the...: Evaluating guidance by an exclusionary attentional template.

PubMed

Beck, Valerie M; Luck, Steven J; Hollingworth, Andrew

2018-04-01

People can use a target template consisting of one or more features to guide attention and gaze to matching objects in a search array. But can we also use feature information to guide attention away from known irrelevant items? Some studies found a benefit from foreknowledge of a distractor feature, whereas others found a cost. Importantly, previous work has largely relied on end-of-trial manual responses; it is unclear how feature-guided avoidance might unfold as candidate objects are inspected. In the current experiments, participants were cued with a distractor feature to avoid, then performed a visual search task while eye movements were recorded. Participants initially fixated a to-be-avoided object more frequently than predicted by chance, but they also demonstrated avoidance of cue-matching objects later in the trial. When provided more time between cue stimulus and search array, participants continued to be initially captured by a cued-color item. Furthermore, avoidance of cue-matching objects later in the trial was not contingent on initial capture by a cue-matching object. These results suggest that the conflicting findings in previous negative-cue experiments may be explained by a mixture of two independent processes: initial attentional capture by memory-matching items and later avoidance of known irrelevant items. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Template-Based Modeling of Protein-RNA Interactions.

PubMed

Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong

2016-09-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.

Consensus on Exercise Reporting Template (CERT): Explanation and Elaboration Statement.

PubMed

Slade, Susan C; Dionne, Clermont E; Underwood, Martin; Buchbinder, Rachelle

2016-10-05

Exercise is effective for prevention and management of acute and chronic health conditions. However, trial descriptions of exercise interventions are often suboptimal, leaving readers unclear about the content of effective programmes. To address this, the 16-item internationally endorsed Consensus on Exercise Reporting Template (CERT) was developed. The aim is to present the final template and provide an Explanation and Elaboration Statement to operationalise the CERT. Development of the CERT was based on the EQUATOR Network methodological framework for developing reporting guidelines. We used a modified Delphi technique to gain consensus of international exercise experts and conducted 3 sequential rounds of anonymous online questionnaires and a Delphi workshop. The 16-item CERT is the minimum data set considered necessary to report exercise interventions. The contents may be included in online supplementary material, published as a protocol or located on websites and other electronic repositories. The Explanation and Elaboration Statement is intended to enhance the use, understanding and dissemination of the CERT and presents the meaning and rationale for each item, together with examples of good reporting. The CERT is designed specifically for the reporting of exercise programmes across all evaluative study designs for exercise research. The CERT can be used by authors to structure intervention reports, by reviewers and editors to assess completeness of exercise descriptions and by readers to facilitate the use of the published information. The CERT has the potential to increase clinical uptake of effective exercise programmes, enable research replication, reduce research waste and improve patient outcomes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Nucleocapsid Protein Annealing of a Primer-Template Enhances (+)-Strand DNA Synthesis and Fidelity by HIV-1 Reverse Transcriptase†

PubMed Central

Kim, Jiae; Roberts, Anne; Yuan, Hua; Xiong, Yong; Anderson, Karen S.

2012-01-01

Human immunodeficiency virus type-1 (HIV-1) requires reverse transcriptase (RT) and HIV-1 nucleocapsid protein (NCp7) for proper viral replication. HIV-1 NCp7 has been shown to enhance various steps in reverse transcription including tRNA initiation and strand transfer which may be mediated through interactions with RT as well as RNA and DNA oligonucleotides. With the use of DNA oligonucleotides, we have examined the interaction of NCp7 with RT and the kinetics of reverse transcription during (+)-strand synthesis with an NCp7-facilitated annealed primer-template. Using a pre-steady state kinetics approach, the NCp7-annealed primer-template has a substantial increase (3-7 fold) in the rate of incorporation (kpol) by RT as compared to heat annealed primer-template with single nucleotide incorporation. There was also a 2-fold increase in the binding affinity constant (Kd) of the nucleotide. These differences in kpol and Kd were not through direct interactions between HIV-1 RT and NCp7. When examining extension by RT, the data suggests that the NCp7-annealed primer-template facilitates the formation of a longer product more quickly compared to the heat annealed primer-template. This enhancement in rate is mediated through interactions with NCp7’s zinc fingers and N-terminal domain and nucleic acids. The NCp7-annealed primer-template also enhances the fidelity of RT (3-fold) by slowing the rate of incorporation of an incorrect nucleotide. Taken together, this study elucidates a new role of NCp7 by facilitating DNA-directed DNA synthesis during reverse transcription by HIV-1 RT that may translate into enhanced viral fitness and offers an avenue to exploit for targeted therapeutic intervention against HIV. PMID:22210155

Template-Based Modeling of Protein-RNA Interactions

PubMed Central

Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.

2016-01-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342

Sequence of events in measles virus replication: role of phosphoprotein-nucleocapsid interactions.

PubMed

Brunel, Joanna; Chopy, Damien; Dosnon, Marion; Bloyet, Louis-Marie; Devaux, Patricia; Urzua, Erica; Cattaneo, Roberto; Longhi, Sonia; Gerlier, Denis

2014-09-01

The genome of nonsegmented negative-strand RNA viruses is tightly embedded within a nucleocapsid made of a nucleoprotein (N) homopolymer. To ensure processive RNA synthesis, the viral polymerase L in complex with its cofactor phosphoprotein (P) binds the nucleocapsid that constitutes the functional template. Measles virus P and N interact through two binding sites. While binding of the P amino terminus with the core of N (NCORE) prevents illegitimate encapsidation of cellular RNA, the interaction between their C-terminal domains, P(XD) and N(TAIL) is required for viral RNA synthesis. To investigate the binding dynamics between the two latter domains, the P(XD) F497 residue that makes multiple hydrophobic intramolecular interactions was mutated. Using a quantitative mammalian protein complementation assay and recombinant viruses, we found that an increase in P(XD)-to-N(TAIL) binding strength is associated with a slower transcript accumulation rate and that abolishing the interaction renders the polymerase nonfunctional. The use of a newly developed system allowing conditional expression of wild-type or mutated P genes, revealed that the loss of the P(XD)-N(TAIL) interaction results in reduced transcription by preformed transcriptases, suggesting reduced engagement on the genomic template. These intracellular data indicate that the viral polymerase entry into and progression along its genomic template relies on a protein-protein interaction that serves as a tightly controlled dynamic anchor. Mononegavirales have a unique machinery to replicate RNA. Processivity of their polymerase is only achieved when the genome template is entirely embedded into a helical homopolymer of nucleoproteins that constitutes the nucleocapsid. The polymerase binds to the nucleocapsid template through the phosphoprotein. How the polymerase complex enters and travels along the nucleocapsid template to ensure uninterrupted synthesis of up to ∼ 6,700-nucleotide messenger RNAs from six to ten consecutive genes is unknown. Using a quantitative protein complementation assay and a biGene-biSilencing system allowing conditional expression of two P genes copies, the role of the P-to-N interaction in polymerase function was further characterized. We report here a dynamic protein anchoring mechanism that differs from all other known polymerases that rely only onto a sustained and direct binding to their nucleic acid template. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Attentional Control via Parallel Target-Templates in Dual-Target Search

PubMed Central

Barrett, Doug J. K.; Zobay, Oliver

2014-01-01

Simultaneous search for two targets has been shown to be slower and less accurate than independent searches for the same two targets. Recent research suggests this ‘dual-target cost’ may be attributable to a limit in the number of target-templates than can guide search at any one time. The current study investigated this possibility by comparing behavioural responses during single- and dual-target searches for targets defined by their orientation. The results revealed an increase in reaction times for dual- compared to single-target searches that was largely independent of the number of items in the display. Response accuracy also decreased on dual- compared to single-target searches: dual-target accuracy was higher than predicted by a model restricting search guidance to a single target-template and lower than predicted by a model simulating two independent single-target searches. These results are consistent with a parallel model of dual-target search in which attentional control is exerted by more than one target-template at a time. The requirement to maintain two target-templates simultaneously, however, appears to impose a reduction in the specificity of the memory representation that guides search for each target. PMID:24489793

75 FR 26740 - Notice of Proposed Information Collection Requests

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-12

... Financial Statements and Compliance Audits. Frequency: Annually. Affected Public: Businesses or other for... designed to facilitate the submission of compliance and financial statement audits, expedite the review of... regulations. eZ-Audit has a minimal number of financial template line items and general information questions...

Influence of dipolar interactions on the angular-dependent coercivity of nickel nanocylinders

NASA Astrophysics Data System (ADS)

Bender, P.; Krämer, F.; Tschöpe, A.; Birringer, R.

2015-04-01

In this study the influence of dipolar interactions on the orientation-dependent magnetization behavior of an ensemble of single-domain nickel nanorods was investigated. The rods were synthesized by electrodeposition of nickel into porous alumina templates. Some of the rods were released from the oxide and embedded in gelatine hydrogels (ferrogel) at a sufficiently large average interparticle distance to suppress dipolar interactions. By comparing the orientation-dependent hystereses of the two ensembles in the template and the gel-matrix it could be shown that the dipolar interactions in the template considerably alter the functional form of the angular-dependent coercivity. Analysis of the magnetization curves for an angle of 60° between the rod-axes and the field revealed a significantly reduced coercivity of the template compared to the ferrogel, which could be directly attributed to a stray field induced magnetization reversal of a steadily increasing number of rods with increasing field strength. The magnetization curve of the template could be approximated by a weighted linear superposition of the hysteresis branches of the ferrogel. The magnetization reversal process of the rods was investigated by analyzing the angular-dependent coercivity of the non-interacting nanorods. Comparison of the functional form with analytical models and micromagnetic simulations emphasized the assumption of a localized magnetization reversal. Additionally, it could be shown that the nucleation field of rods with diameters in the range 18-29 nm tends to increase with increasing diameter.

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

PubMed

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.

Synthesis and characterization of inorganic materials precipitated into polymeric and novel liquid crystalline systems

NASA Astrophysics Data System (ADS)

Lubeck, Christopher Ryan

The use of nanostructured, hybrid materials possesses great future potential. Many examples of nanostructured materials exist within nature, such as animal bone, animal teeth, and seashells. This research, inspired by nature, strove to mimic salient properties of natural materials, utilizing methods observed within nature to produce materials. Further, this research increased the functionality of the templates from "mere" template to functional participant. Different chemical methods to produce hybrid materials were employed within this research to achieve these goals. First, electro-osmosis was utilized to drive ions into a polymeric matrix to form hybrid inorganic polymer material, creating a material inspired by naturally occurring bone or seashell in which the inorganic component provides strength and the polymeric material decreases the brittleness of the combined hybrid material. Second, self-assembled amphiphiles, forming higher ordered structures, acted as a template for inorganic cadmium sulfide. Electronically active molecules based on ethylene oxide and aniline segments were synthesized to create interaction between the templating material and the resulting inorganic cadmium sulfide. The templating process utilized self-assembly to create the inorganic structure through the interaction of the amphiphiles with water. The use of self-assembly is itself inspired by nature. Self-assembled structures are observed within living cells as cell walls and cell membranes are created through hydrophilic and hydrophobic interactions. Finally, the mesostructured inorganic cadmium sulfide was itself utilized as a template to form mesostructured copper sulfide.

Asymmetric Flasklike Hollow Carbonaceous Nanoparticles Fabricated by the Synergistic Interaction between Soft Template and Biomass.

PubMed

Chen, Chunhong; Wang, Haiyan; Han, Chuanlong; Deng, Jiang; Wang, Jing; Li, Mingming; Tang, Minghui; Jin, Haiyan; Wang, Yong

2017-02-22

The soft template method is broadly applied to the fabrication of hollow-structured nanomaterials. However, due to the instability and the typical spherical shape of these soft templates, the resultant particles have a spherical morphology with a wide size distribution. Herein, we developed a sustainable route to fabricate asymmetric flasklike hollow carbonaceous structures with a highly uniform morphology and a narrow size distribution using the soft template method. A dynamic growth mechanism induced by the synergetic interactions between template and biomass is proposed. The precursors (ribose) provide an acidic environment for sodium oleate during the hydrothermal process in which oleic acid nanoemulsions are initially formed and serve as both template and benign solvent for the amphiphilic derivatives of the precursor. Simultaneously, the cosurfactant P123 facilitates the uniform dispersion of the nanoemulsion and is believed to cause the carbonaceous shells to rupture, providing openings through which the intermediates can enter. These subtle interactions facilitate the formation of the flasklike, asymmetric, hollow, carbonaceous nanoparticles. Furthermore, this unique structure contributes to the high surface area (2335 m 2 g -1 ) of the flasklike carbon particles, which enhances the performance of supercapacitors. These findings may open up an exciting field for exploring anisotropic carbonaceous nanomaterials and for understanding the related mechanisms to provide guidance for the design of increasingly complex carbonaceous materials.

The Student Writing Toolkit: Enhancing Undergraduate Teaching of Scientific Writing in the Biological Sciences

ERIC Educational Resources Information Center

Dirrigl, Frank J., Jr.; Noe, Mark

2014-01-01

Teaching scientific writing in biology classes is challenging for both students and instructors. This article offers and reviews several useful "toolkit" items that improve student writing. These include sentence and paper-length templates, funnelling and compartmentalisation, and preparing compendiums of corrections. In addition,…

Authenticating concealed private data while maintaining concealment

DOEpatents

Thomas, Edward V [Albuquerque, NM; Draelos, Timothy J [Albuquerque, NM

2007-06-26

A method of and system for authenticating concealed and statistically varying multi-dimensional data comprising: acquiring an initial measurement of an item, wherein the initial measurement is subject to measurement error; applying a transformation to the initial measurement to generate reference template data; acquiring a subsequent measurement of an item, wherein the subsequent measurement is subject to measurement error; applying the transformation to the subsequent measurement; and calculating a Euclidean distance metric between the transformed measurements; wherein the calculated Euclidean distance metric is identical to a Euclidean distance metric between the measurement prior to transformation.

Quality indicators for learner-centered postgraduate medical e-learning.

PubMed

de Leeuw, Robert A; Westerman, Michiel; Scheele, Fedde

2017-04-27

The objectives of this study were to identify the needs and expectations of learners and educational experts in postgraduate medical e-learning, and to contribute to the current literature. We performed four focus-group discussions with e-learning end-users (learners) and didactic experts. The participants were postgraduate learners with varying levels of experience, educational experts from a Dutch e-learning task group, and commercial experts from a Dutch e-learning company. Verbatim transcribed interview recordings were analyzed using King's template analysis. The initial template was created with reference to recent literature on postgraduate medical e-learning quality indicators. The transcripts were coded, after which the emerging differences in template interpretation were discussed until a consensus was reached within the team. The final template consisted of three domains of positive e-learning influencers (motivators, learning enhancers, and real-world translation) and three domains of negatively influential parameters (barriers, learning discouragers, and poor preparation). The interpretation of the final template showed three subjects which form the basis of e-learning, namely, Motivate, Learn and Apply. This study forms a basis for learning in general and could be applied to many educational instruments. Individual characteristics should be adapted to the target audience. Three subjects form the basis of, and six themes cover all items needed for, good (enough) postgraduate e-learning. Further research should be carried out with learners and real-world e-learning to validate this template.

Advances in nanosized zeolites

NASA Astrophysics Data System (ADS)

Mintova, Svetlana; Gilson, Jean-Pierre; Valtchev, Valentin

2013-07-01

This review highlights recent developments in the synthesis of nanosized zeolites. The strategies available for their preparation (organic-template assisted, organic-template free, and alternative procedures) are discussed. Major breakthroughs achieved by the so-called zeolite crystal engineering and encompass items such as mastering and using the physicochemical properties of the precursor synthesis gel/suspension, optimizing the use of silicon and aluminium precursor sources, the rational use of organic templates and structure-directing inorganic cations, and careful adjustment of synthesis conditions (temperature, pressure, time, heating processes from conventional to microwave and sonication) are addressed. An on-going broad and deep fundamental understanding of the crystallization process, explaining the influence of all variables of this complex set of reactions, underpins an even more rational design of nanosized zeolites with exceptional properties. Finally, the advantages and limitations of these methods are addressed with particular attention to their industrial prospects and utilization in existing and advanced applications.

On the influence of crosslinker on template complexation in molecularly imprinted polymers: a computational study of prepolymerization mixture events with correlations to template-polymer recognition behavior and NMR spectroscopic studies.

PubMed

Shoravi, Siamak; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A

2014-06-12

Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer-crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity.

Customization of electronic medical record templates to improve end-user satisfaction.

PubMed

Gardner, Carrie Lee; Pearce, Patricia F

2013-03-01

Since 2004, increasing importance has been placed on the adoption of electronic medical records by healthcare providers for documentation of patient care. Recent federal regulations have shifted the focus from adoption alone to meaningful use of an electronic medical record system. As proposed by the Technology Acceptance Model, the behavioral intention to use technology is determined by the person's attitude toward usage. The purpose of this quality improvement project was to devise and implement customized templates into an existent electronic medical record system in a single clinic and measure the satisfaction of the clinic providers with the system before and after implementation. Provider satisfaction with the electronic medical record system was evaluated prior to and following template implementation using the current version 7.0 of the Questionnaire for User Interaction Satisfaction tool. Provider comments and improvement in the Questionnaire for User Interaction Satisfaction levels of rankings following template implementation indicated a positive perspective by the providers in regard to the templates and customization of the system.

Understanding the General Packing Rearrangements Required for Successful Template Based Modeling of Protein Structure from a CASP Experiment

PubMed Central

Day, Ryan; Joo, Hyun; Chavan, Archana; Lennox, Kristin P.; Chen, Ann; Dahl, David B.; Vannucci, Marina; Tsai, Jerry W.

2012-01-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. PMID:23266765

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

PubMed

Day, Ryan; Joo, Hyun; Chavan, Archana C; Lennox, Kristin P; Chen, Y Ann; Dahl, David B; Vannucci, Marina; Tsai, Jerry W

2013-02-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. Copyright © 2012 Elsevier Ltd. All rights reserved.

Template-based structure modeling of protein-protein interactions

PubMed Central

Szilagyi, Andras; Zhang, Yang

2014-01-01

The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement. PMID:24721449

Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I.

PubMed Central

Odelberg, S J; Weiss, R B; Hata, A; White, R

1995-01-01

Recombinant DNA molecules are often generated during the polymerase chain reaction (PCR) when partially homologous templates are available [e.g., see Pääbo et al. (1990) J. Biol. Chem. 265, 4718-4721]. It has been suggested that these recombinant molecules are a consequence of truncated extension products annealing to partially homologous templates on subsequent PCR cycles. However, we demonstrate here that recombinants can be generated during a single round of primer extension in the absence of subsequent heat denaturation, indicating that template-switching produces some of these recombinant molecules. Two types of template-switches were observed: (i) switches to pre-existing templates and (ii) switches to the complementary nascent strand. Recombination is reduced several fold when the complementary template strands are physically separated by attachment to streptavidin magnetic beads. This result supports the hypothesis that either the polymerase or at least one of the two extending strands switches templates during DNA synthesis and that interaction between the complementary template strands is necessary for efficient template-switching. Images PMID:7596836

Effects of Ignoring Item Interaction on Item Parameter Estimation and Detection of Interacting Items

ERIC Educational Resources Information Center

Chen, Cheng-Te; Wang, Wen-Chung

2007-01-01

This study explores the effects of ignoring item interaction on item parameter estimation and the efficiency of using the local dependence index Q[subscript 3] and the SAS NLMIXED procedure to detect item interaction under the three-parameter logistic model and the generalized partial credit model. Through simulations, it was found that ignoring…

Using Arden Syntax for the Generation of Intelligent Intensive Care Discharge Letters.

PubMed

Kraus, Stefan; Castellanos, Ixchel; Albermann, Matthias; Schuettler, Christina; Prokosch, Hans-Ulrich; Staudigel, Martin; Toddenroth, Dennis

2016-01-01

Discharge letters are an important means of communication between physicians and nurses from intensive care units and their colleagues from normal wards. The patient data management system (PDMS) used at our local intensive care units provides an export tool to create discharge letters by inserting data items from electronic medical records into predefined templates. Local intensivists criticized the limitations of this tool regarding the identification and the further processing of clinically relevant data items for a flexible creation of discharge letters. As our PDMS supports Arden Syntax, and the demanded functionalities are well within the scope of this standard, we set out to investigate the suitability of Arden Syntax for the generation of discharge letters. To provide an easy-to-understand facility for integrating data items into document templates, we created an Arden Syntax interface function which replaces the names of previously defined variables with their content in a way that permits arbitrary custom formatting by clinical users. Our approach facilitates the creation of flexible text sections by conditional statements, as well as the integration of arbitrary HTML code and dynamically generated graphs. The resulting prototype enables clinical users to apply the full set of Arden Syntax language constructs to identify and process relevant data items in a way that far exceeds the capabilities of the PDMS export tool. The generation of discharge letters is an uncommon area of application for Arden Syntax, considerably differing from its original purpose. However, we found our prototype well suited for this task and plan to evaluate it in clinical production after the next major release change of our PDMS.

Automatic capture of attention by conceptually generated working memory templates.

PubMed

Sun, Sol Z; Shen, Jenny; Shaw, Mark; Cant, Jonathan S; Ferber, Susanne

2015-08-01

Many theories of attention propose that the contents of working memory (WM) can act as an attentional template, which biases processing in favor of perceptually similar inputs. While support has been found for this claim, it is unclear how attentional templates are generated when searching real-world environments. We hypothesized that in naturalistic settings, attentional templates are commonly generated from conceptual knowledge, an idea consistent with sensorimotor models of knowledge representation. Participants performed a visual search task in the delay period of a WM task, where the item in memory was either a colored disk or a word associated with a color concept (e.g., "Rose," associated with red). During search, we manipulated whether a singleton distractor in the array matched the contents of WM. Overall, we found that search times were impaired in the presence of a memory-matching distractor. Furthermore, the degree of impairment did not differ based on the contents of WM. Put differently, regardless of whether participants were maintaining a perceptually colored disk identical to the singleton distractor, or whether they were simply maintaining a word associated with the color of the distractor, the magnitude of attentional capture was the same. Our results suggest that attentional templates can be generated from conceptual knowledge, in the physical absence of the visual feature.

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

PubMed Central

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

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

PubMed

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.

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches

PubMed Central

Green, Stefan J.; Venkatramanan, Raghavee; Naqib, Ankur

2015-01-01

The polymerase chain reaction (PCR) is sensitive to mismatches between primer and template, and mismatches can lead to inefficient amplification of targeted regions of DNA template. In PCRs in which a degenerate primer pool is employed, each primer can behave differently. Therefore, inefficiencies due to different primer melting temperatures within a degenerate primer pool, in addition to mismatches between primer binding sites and primers, can lead to a distortion of the true relative abundance of targets in the original DNA pool. A theoretical analysis indicated that a combination of primer-template and primer-amplicon interactions during PCR cycles 3–12 is potentially responsible for this distortion. To test this hypothesis, we developed a novel amplification strategy, entitled “Polymerase-exonuclease (PEX) PCR”, in which primer-template interactions and primer-amplicon interactions are separated. The PEX PCR method substantially and significantly improved the evenness of recovery of sequences from a mock community of known composition, and allowed for amplification of templates with introduced mismatches near the 3’ end of the primer annealing sites. When the PEX PCR method was applied to genomic DNA extracted from complex environmental samples, a significant shift in the observed microbial community was detected. Furthermore, the PEX PCR method provides a mechanism to identify which primers in a primer pool are annealing to target gDNA. Primer utilization patterns revealed that at high annealing temperatures in the PEX PCR method, perfect match annealing predominates, while at lower annealing temperatures, primers with up to four mismatches with templates can contribute substantially to amplification. The PEX PCR method is simple to perform, is limited to PCR mixes and a single exonuclease step which can be performed without reaction cleanup, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible. PMID:25996930

Quality indicators for learner-centered postgraduate medical e-learning

PubMed Central

Westerman, Michiel; Scheele, Fedde

2017-01-01

Objectives The objectives of this study were to identify the needs and expectations of learners and educational experts in postgraduate medical e-learning, and to contribute to the current literature. Methods We performed four focus-group discussions with e-learning end-users (learners) and didactic experts. The participants were postgraduate learners with varying levels of experience, educational experts from a Dutch e-learning task group, and commercial experts from a Dutch e-learning company. Verbatim transcribed interview recordings were analyzed using King’s template analysis. The initial template was created with reference to recent literature on postgraduate medical e-learning quality indicators. The transcripts were coded, after which the emerging differences in template interpretation were discussed until a consensus was reached within the team. Results The final template consisted of three domains of positive e-learning influencers (motivators, learning enhancers, and real-world translation) and three domains of negatively influential parameters (barriers, learning discouragers, and poor preparation). The interpretation of the final template showed three subjects which form the basis of e-learning, namely, Motivate, Learn and Apply. Conclusions This study forms a basis for learning in general and could be applied to many educational instruments. Individual characteristics should be adapted to the target audience. Three subjects form the basis of, and six themes cover all items needed for, good (enough) postgraduate e-learning. Further research should be carried out with learners and real-world e-learning to validate this template. PMID:28456781

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

PubMed

Xue, Li C; Rodrigues, João P G L M; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2017-05-01

Although many advanced and sophisticated ab initio approaches 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 exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon-alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein-protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein-protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models. © The Author 2016. Published by Oxford University Press.

Synthesis and characterization of amorphous mesoporous silica using TEMPO-functionalized amphiphilic templates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vries, Wilke de; Doerenkamp, Carsten; Zeng, Zhaoyang

Inorganic–organic hybrid materials based on amorphous mesoporous silica containing organized nitroxide radicals within its mesopores have been prepared using the micellar self-assembly of TEOS solutions containing the nitroxide functionalized amphiphile (4-(N,N-dimethyl-N-hexadecylammonium)-2,2,6, 6-tetramethyl-piperidin-N-oxyl-iodide) (CAT-16). This template has been used both in its pure form and in various mixtures with cetyl trimethylammonium bromide (CTAB). The samples have been characterized by chemical analysis, N{sub 2} sorption studies, magnetic susceptibility measurements, and various spectroscopic methods. While electron paramagnetic resonance (EPR) spectra indicate that the strength of the intermolecular spin–spin interactions can be controlled via the CAT-16/CTAB ratio, nuclear magnetic resonance (NMR) data suggest thatmore » these interactions are too weak to facilitate cooperative magnetism. - Graphical abstract: The amphiphilic radical CAT-16 is used as a template for the synthesis of amorphous mesoporous silica. The resulting paramagnetic hybrid materials are characterized by BET, FTIR, NMR, EPR and magnetic susceptibility studies. - Highlights: • Amphiphilic CAT-16 as a template for mesoporous silica. • Comprehensive structural characterization by BET, FTIR; EPR and NMR. • Strength of radical-radical interactions tuable within CAT-16/CTAB mixtures.« less

Intergenerational families of holocaust survivors: designing and piloting a family resilience template.

PubMed

Isserman, Nancy; Greene, Roberta R; Bowen, Sheryl Perlmutter; Hollander-Goldfein, Bea; Cohen, Harriet

2014-01-01

Researchers from the Templeton study, "Forgiveness, Resiliency, and Survivorship Among Holocaust Survivors," and the Transcending Trauma Project, combined efforts to examine six transcripts of interviews with survivors of the Nazi Holocaust. The researchers focused on the nature of parent-child family dynamics before, during, and after the Holocaust. They refined a Family Resilience Template (FRT) originally based on an ecological-systems design, adding an attachment theory component and a quantitative methodology. The goal of the research project was to pilot the FRT by further defining terms and adding a Quality of Family Dynamics Paradigm to encompass an intergenerational dimension. The researchers arrived at a consensus of item definitions, establishing the initial face validity of the FRT.

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

PubMed Central

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong

2017-01-01

Abstract Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein–protein and protein–DNA benchmarks and performed better than template-based modeling on the three protein–RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. PMID:28521030

Searching while loaded: Visual working memory does not interfere with hybrid search efficiency but hybrid search uses working memory capacity.

PubMed

Drew, Trafton; Boettcher, Sage E P; Wolfe, Jeremy M

2016-02-01

In "hybrid search" tasks, such as finding items on a grocery list, one must search the scene for targets while also searching the list in memory. How is the representation of a visual item compared with the representations of items in the memory set? Predominant theories would propose a role for visual working memory (VWM) either as the site of the comparison or as a conduit between visual and memory systems. In seven experiments, we loaded VWM in different ways and found little or no effect on hybrid search performance. However, the presence of a hybrid search task did reduce the measured capacity of VWM by a constant amount regardless of the size of the memory or visual sets. These data are broadly consistent with an account in which VWM must dedicate a fixed amount of its capacity to passing visual representations to long-term memory for comparison to the items in the memory set. The data cast doubt on models in which the search template resides in VWM or where memory set item representations are moved from LTM through VWM to earlier areas for comparison to visual items.

Recombinant viral RdRps can initiate RNA synthesis from circular templates

PubMed Central

RANJITH-KUMAR, C.T.; KAO, C.C.

2006-01-01

The crystal structure of the recombinant hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) revealed extensive interactions between the fingers and the thumb subdomains, resulting in a closed conformation with an established template channel that should specifically accept single-stranded templates. We made circularized RNA templates and found that they were efficiently used by the HCV RdRp to synthesize product RNAs that are significantly longer than the template, suggesting that RdRp could exist in an open conformation prior to template binding. RNA synthesis using circular RNA templates had properties similar to those previously documented for linear RNA, including a need for higher GTP concentration for initiation, usage of GTP analogs, sensitivity to salt, and involvement of active-site residues for product formation. Some products were resistant to challenge with the template competitor heparin, indicating that the elongation complexes remain bound to template and are competent for RNA synthesis. Other products were not elongated in the presence of heparin, indicating that the elongation complex was terminated. Lastly, recombinant RdRps from two other flaviviruses and from the Pseudomonas phage φ6 also could use circular RNA templates for RNA-dependent RNA synthesis, although the φ6 RdRp could only use circular RNAs made from the 3′-terminal sequence of the φ6 genome. PMID:16373481

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

DOE PAGES

Jones, Susan; Thornton, Janet M.

2003-01-01

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. Inmore » this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.« less

Affordance Templates for Shared Robot Control

NASA Technical Reports Server (NTRS)

Hart, Stephen; Dinh, Paul; Hambuchen, Kim

2014-01-01

This paper introduces the Affordance Template framework used to supervise task behaviors on the NASA-JSC Valkyrie robot at the 2013 DARPA Robotics Challenge (DRC) Trials. This framework provides graphical interfaces to human supervisors that are adjustable based on the run-time environmental context (e.g., size, location, and shape of objects that the robot must interact with, etc.). Additional improvements, described below, inject degrees of autonomy into instantiations of affordance templates at run-time in order to enable efficient human supervision of the robot for accomplishing tasks.

Risk based decision tool for space exploration missions

NASA Technical Reports Server (NTRS)

Meshkat, Leila; Cornford, Steve; Moran, Terrence

2003-01-01

This paper presents an approach and corresponding tool to assess and analyze the risks involved in a mission during the pre-phase A design process. This approach is based on creating a risk template for each subsystem expert involved in the mission design process and defining appropriate interactions between the templates.

Program Helps Standardize Documentation Of Software

NASA Technical Reports Server (NTRS)

Howe, G.

1994-01-01

Intelligent Documentation Management System, IDMS, computer program developed to assist project managers in implementing information system documentation standard known as NASA-STD-2100-91, NASA STD, COS-10300, of NASA's Software Management and Assurance Program. Standard consists of data-item descriptions or templates, each of which governs particular component of software documentation. IDMS helps program manager in tailoring documentation standard to project. Written in C language.

Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis.

PubMed

Mahajan, Gaurang; Mande, Shekhar C

2017-04-04

A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies towards this end. Several sequence-based in silico approaches tap the existing data on experimentally validated protein-protein interactions (PPIs); these PPIs serve as templates from which novel interactions between pathogen and host are inferred. Such comparative approaches typically make use of local sequence alignment, which, in the absence of structural details about the interfaces mediating the template interactions, could lead to incorrect inferences, particularly when multi-domain proteins are involved. We propose leveraging the domain-domain interaction (DDI) information in PDB complexes to score and prioritize candidate PPIs between host and pathogen proteomes based on targeted sequence-level comparisons. Our method picks out a small set of human-MTB protein pairs as candidates for physical interactions, and the use of functional meta-data suggests that some of them could contribute to the in vivo molecular cross-talk between pathogen and host that regulates the course of the infection. Further, we present numerical data for Pfam domain families that highlights interaction specificity on the domain level. Not every instance of a pair of domains, for which interaction evidence has been found in a few instances (i.e. structures), is likely to functionally interact. Our sorting approach scores candidates according to how "distant" they are in sequence space from known examples of DDIs (templates). Thus, it provides a natural way to deal with the heterogeneity in domain-level interactions. Our method represents a more informed application of local alignment to the sequence-based search for potential human-microbial interactions that uses available PPI data as a prior. Our approach is somewhat limited in its sensitivity by the restricted size and diversity of the template dataset, but, given the rapid accumulation of solved protein complex structures, its scope and utility are expected to keep steadily improving.

Rapid top-down control over template-guided attention shifts to multiple objects.

PubMed

Grubert, Anna; Fahrenfort, Johannes; Olivers, Christian N L; Eimer, Martin

2017-02-01

Previous research has shown that when observers search for targets defined by a particular colour, attention can be directed rapidly and independently to two target objects that appear in close temporal proximity. We investigated how such rapid attention shifts are modulated by task instructions to selectively attend versus ignore one of these objects. Two search displays that both contained a colour-defined target and a distractor in a different colour were presented in rapid succession, with a stimulus onset asynchrony (SOA) of 100ms. In different blocks, participants were instructed to attend and respond to target-colour objects in the first display and to ignore these objects in the second display, or vice versa. N2pc components were measured to track the allocation of spatial attention to target-colour objects in these two displays. When participants responded to the second display, irrelevant target-colour objects in the first display still triggered N2pc components, demonstrating task-set contingent attentional capture while a feature-specific target template is active. Critically, when participants responded to the first display instead, no N2pc was elicited by target-colour items in the second display, indicating that they no longer rapidly captured attention. However, these items still elicited a longer-latency contralateral negativity (SPCN component), suggesting that attention was oriented towards template-matching objects in working memory. This dissociation between N2pc and SPCN components shows that rapid attentional capture and subsequent attentional selection processes within working memory can be independent. We suggest that early attentional orienting mechanisms can be inhibited when task-set matching objects are no longer task-relevant, and that this type of inhibitory control is a rapid but transient process. Copyright © 2016 Elsevier Inc. All rights reserved.

Enhancing requirements engineering for patient registry software systems with evidence-based components.

PubMed

Lindoerfer, Doris; Mansmann, Ulrich

2017-07-01

Patient registries are instrumental for medical research. Often their structures are complex and their implementations use composite software systems to meet the wide spectrum of challenges. Commercial and open-source systems are available for registry implementation, but many research groups develop their own systems. Methodological approaches in the selection of software as well as the construction of proprietary systems are needed. We propose an evidence-based checklist, summarizing essential items for patient registry software systems (CIPROS), to accelerate the requirements engineering process. Requirements engineering activities for software systems follow traditional software requirements elicitation methods, general software requirements specification (SRS) templates, and standards. We performed a multistep procedure to develop a specific evidence-based CIPROS checklist: (1) A systematic literature review to build a comprehensive collection of technical concepts, (2) a qualitative content analysis to define a catalogue of relevant criteria, and (3) a checklist to construct a minimal appraisal standard. CIPROS is based on 64 publications and covers twelve sections with a total of 72 items. CIPROS also defines software requirements. Comparing CIPROS with traditional software requirements elicitation methods, SRS templates and standards show a broad consensus but differences in issues regarding registry-specific aspects. Using an evidence-based approach to requirements engineering for registry software adds aspects to the traditional methods and accelerates the software engineering process for registry software. The method we used to construct CIPROS serves as a potential template for creating evidence-based checklists in other fields. The CIPROS list supports developers in assessing requirements for existing systems and formulating requirements for their own systems, while strengthening the reporting of patient registry software system descriptions. It may be a first step to create standards for patient registry software system assessments. Copyright © 2017 Elsevier Inc. All rights reserved.

Kaizen practice in healthcare: a qualitative analysis of hospital employees' suggestions for improvement

PubMed Central

Mazzocato, Pamela; Stenfors-Hayes, Terese; von Thiele Schwarz, Ulrica; Hasson, Henna

2016-01-01

Objectives Kaizen, or continuous improvement, lies at the core of lean. Kaizen is implemented through practices that enable employees to propose ideas for improvement and solve problems. The aim of this study is to describe the types of issues and improvement suggestions that hospital employees feel empowered to address through kaizen practices in order to understand when and how kaizen is used in healthcare. Methods We analysed 186 structured kaizen documents containing improvement suggestions that were produced by 165 employees at a Swedish hospital. Directed content analysis was used to categorise the suggestions into following categories: type of situation (proactive or reactive) triggering an action; type of process addressed (technical/administrative, support and clinical); complexity level (simple or complex); and type of outcomes aimed for (operational or sociotechnical). Compliance to the kaizen template was calculated. Results 72% of the improvement suggestions were reactions to a perceived problem. Support, technical and administrative, and primary clinical processes were involved in 47%, 38% and 16% of the suggestions, respectively. The majority of the kaizen documents addressed simple situations and focused on operational outcomes. The degree of compliance to the kaizen template was high for several items concerning the identification of problems and the proposed solutions, and low for items related to the test and implementation of solutions. Conclusions There is a need to combine kaizen practices with improvement and innovation practices that help staff and managers to address complex issues, such as the improvement of clinical care processes. The limited focus on sociotechnical aspects and the partial compliance to kaizen templates may indicate a limited understanding of the entire kaizen process and of how it relates to the overall organisational goals. This in turn can hamper the sustainability of kaizen practices and results. PMID:27473953

Rational computational design for the development of andrographolide molecularly imprinted polymer

NASA Astrophysics Data System (ADS)

Krishnan, Hemavathi; Islam, K. M. Shafiqul; Hamzah, Zainab; Ahmad, Mohd Noor

2017-10-01

Andrographolide is a popular medicinal compound derived from Andrographis Paniculata (AP). Molecularly Imprint Polymer (MIP) is a "Lock and Key" approach, where MIP is the lock and Andrographolide is the key which fits to the MIP lock by both physically and chemically. MIP will be used as selective extraction tool to enrich Andrographolide bioactive compound. Pre-polymerization step is crucial to design MIP. This work investigates molecular interactions and the Gibbs free binding energies on the development of MIP. The structure of Andrographolide (template) and functional monomers were drawn in HyperChem 8.0.10. A hybrid quantum chemical model was used with a few functional monomers. Possible conformations of template and functional monomer as 1:n (n < 4) were designed and simulated to geometrically optimize the complex to the lowest energy in gas phase. The Gibbs free binding energies of each conformation were calculated using semi-empirical PM3 simulation method. Results proved that functional monomers that contain carboxylic group shows higher binding energy compared to those with amine functional group. Itaconic acid (IA) chosen as the best functional monomer at optimum ratio (1:3) of template: monomer to prepare andrographolide MIP. This study demonstrates the importance of studying intermolecular interaction among template, functional monomer and template-monomer ratio in developing MIP.

Anisotropic metal growth on phospholipid nanodiscs via lipid bilayer expansion

PubMed Central

Oertel, Jana; Keller, Adrian; Prinz, Julia; Schreiber, Benjamin; Hübner, René; Kerbusch, Jochen; Bald, Ilko; Fahmy, Karim

2016-01-01

Self-assembling biomolecules provide attractive templates for the preparation of metallic nanostructures. However, the intuitive transfer of the “outer shape” of the assembled macromolecules to the final metallic particle depends on the intermolecular forces among the biomolecules which compete with interactions between template molecules and the metal during metallization. The shape of the bio-template may thus be more dynamic than generally assumed. Here, we have studied the metallization of phospholipid nanodiscs which are discoidal particles of ~10 nm diameter containing a lipid bilayer ~5 nm thick. Using negatively charged lipids, electrostatic adsorption of amine-coated Au nanoparticles was achieved and followed by electroless gold deposition. Whereas Au nanoparticle adsorption preserves the shape of the bio-template, metallization proceeds via invasion of Au into the hydrophobic core of the nanodisc. Thereby, the lipidic phase induces a lateral growth that increases the diameter but not the original thickness of the template. Infrared spectroscopy reveals lipid expansion and suggests the existence of internal gaps in the metallized nanodiscs, which is confirmed by surface-enhanced Raman scattering from the encapsulated lipids. Interference of metallic growth with non-covalent interactions can thus become itself a shape-determining factor in the metallization of particularly soft and structurally anisotropic biomaterials. PMID:27216789

A template-based approach for responsibility management in executable business processes

NASA Astrophysics Data System (ADS)

Cabanillas, Cristina; Resinas, Manuel; Ruiz-Cortés, Antonio

2018-05-01

Process-oriented organisations need to manage the different types of responsibilities their employees may have w.r.t. the activities involved in their business processes. Despite several approaches provide support for responsibility modelling, in current Business Process Management Systems (BPMS) the only responsibility considered at runtime is the one related to performing the work required for activity completion. Others like accountability or consultation must be implemented by manually adding activities in the executable process model, which is time-consuming and error-prone. In this paper, we address this limitation by enabling current BPMS to execute processes in which people with different responsibilities interact to complete the activities. We introduce a metamodel based on Responsibility Assignment Matrices (RAM) to model the responsibility assignment for each activity, and a flexible template-based mechanism that automatically transforms such information into BPMN elements, which can be interpreted and executed by a BPMS. Thus, our approach does not enforce any specific behaviour for the different responsibilities but new templates can be modelled to specify the interaction that best suits the activity requirements. Furthermore, libraries of templates can be created and reused in different processes. We provide a reference implementation and build a library of templates for a well-known set of responsibilities.

Ottawa Model of Implementation Leadership and Implementation Leadership Scale: mapping concepts for developing and evaluating theory-based leadership interventions.

PubMed

Gifford, Wendy; Graham, Ian D; Ehrhart, Mark G; Davies, Barbara L; Aarons, Gregory A

2017-01-01

Leadership in health care is instrumental to creating a supportive organizational environment and positive staff attitudes for implementing evidence-based practices to improve patient care and outcomes. The purpose of this study is to demonstrate the alignment of the Ottawa Model of Implementation Leadership (O-MILe), a theoretical model for developing implementation leadership, with the Implementation Leadership Scale (ILS), an empirically validated tool for measuring implementation leadership. A secondary objective is to describe the methodological process for aligning concepts of a theoretical model with an independently established measurement tool for evaluating theory-based interventions. Modified template analysis was conducted to deductively map items of the ILS onto concepts of the O-MILe. An iterative process was used in which the model and scale developers (n=5) appraised the relevance, conceptual clarity, and fit of each ILS items with the O-MILe concepts through individual feedback and group discussions until consensus was reached. All 12 items of the ILS correspond to at least one O-MILe concept, demonstrating compatibility of the ILS as a measurement tool for the O-MILe theoretical constructs. The O-MILe provides a theoretical basis for developing implementation leadership, and the ILS is a compatible tool for measuring leadership based on the O-MILe. Used together, the O-MILe and ILS provide an evidence- and theory-based approach for developing and measuring leadership for implementing evidence-based practices in health care. Template analysis offers a convenient approach for determining the compatibility of independently developed evaluation tools to test theoretical models.

Ottawa Model of Implementation Leadership and Implementation Leadership Scale: mapping concepts for developing and evaluating theory-based leadership interventions

PubMed Central

Gifford, Wendy; Graham, Ian D; Ehrhart, Mark G; Davies, Barbara L; Aarons, Gregory A

2017-01-01

Purpose Leadership in health care is instrumental to creating a supportive organizational environment and positive staff attitudes for implementing evidence-based practices to improve patient care and outcomes. The purpose of this study is to demonstrate the alignment of the Ottawa Model of Implementation Leadership (O-MILe), a theoretical model for developing implementation leadership, with the Implementation Leadership Scale (ILS), an empirically validated tool for measuring implementation leadership. A secondary objective is to describe the methodological process for aligning concepts of a theoretical model with an independently established measurement tool for evaluating theory-based interventions. Methods Modified template analysis was conducted to deductively map items of the ILS onto concepts of the O-MILe. An iterative process was used in which the model and scale developers (n=5) appraised the relevance, conceptual clarity, and fit of each ILS items with the O-MILe concepts through individual feedback and group discussions until consensus was reached. Results All 12 items of the ILS correspond to at least one O-MILe concept, demonstrating compatibility of the ILS as a measurement tool for the O-MILe theoretical constructs. Conclusion The O-MILe provides a theoretical basis for developing implementation leadership, and the ILS is a compatible tool for measuring leadership based on the O-MILe. Used together, the O-MILe and ILS provide an evidence- and theory-based approach for developing and measuring leadership for implementing evidence-based practices in health care. Template analysis offers a convenient approach for determining the compatibility of independently developed evaluation tools to test theoretical models. PMID:29355212

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

PubMed

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

2017-07-03

Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein-protein and protein-DNA benchmarks and performed better than template-based modeling on the three protein-RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed

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.

Chondroitin sulfate template-mediated biomimetic synthesis of nano-flake hydroxyapatite

NASA Astrophysics Data System (ADS)

He, Dan; Xiao, Xiufeng; Liu, Fang; Liu, Rongfang

2008-11-01

By Ca(NO 3) 2·4H 2O and (NH 4) 3PO 4·3H 2O as reagents and chondroitin sulfate (ChS) as a template, nano-flake hydroxyapatite (HA) is synthesized using a biomimetic method according to the biomineralization theory. HA crystals obtained are characterized in crystalline phase, microstructure, chemical composition and morphology by X-ray diffraction (XRD), Fourier transform infrared spectroscope (FTIR), transmission electron microscopy (TEM) and elemental analysis respectively. UV-vis spectrum is adopted to investigate interactions between functional groups ChS and HA. The results show that HA crystal nucleation and growth take place in chemical interactions between HA crystals and ChS as a template. And elemental analysis indicates that obtained HA contains a small amount of ChS. Furthermore, ChS concentration significantly affects the morphology of HA crystals. Staple-fiber-like HA crystals can be obtained at a low concentration in ChS, and flake-like HA crystals synthesized at a high concentration (≥0.5 wt.%) of ChS as a template.

Pre-Incubation of Auric Acid with DNA Is Unnecessary for the Formation of DNA-Templated Gold Nanoclusters.

PubMed

Chen, Yang; Tao, Guangyu; Lin, Ruoyun; Pei, Xiaojing; Liu, Feng; Li, Na

2016-06-06

The rationale for the preparation of DNA-templated gold nanoclusters (DNA-Au NCs) has not been well understood, thereby slowing down the advancement of the synthesis and applications of DNA-Au NCs. The interaction between metal ions and the DNA template seems to be the key factor for the successful preparation of DNA-templated metal nanoclusters. With the help of circular dichroism in this contribution, we put efforts into interrogating the necessity of pre-incubation of HAuCl4 with poly-adenine template in the formation of Au NCs by citrate reduction. Our results revealed that the pre-incubation of HAuCl4 with poly-adenine is not favorable for the formation of Au NCs, which is distinctly different from the formation process for silver nanoclusters. It is our hope that this study can provide guidance in the preparation of Au NCs with more DNA templates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Template Recognition Mechanisms by Replicase Proteins Differ between Bipartite Positive-Strand Genomic RNAs of a Plant Virus▿

PubMed Central

Iwakawa, Hiro-oki; Mine, Akira; Hyodo, Kiwamu; An, Mengnan; Kaido, Masanori; Mise, Kazuyuki; Okuno, Tetsuro

2011-01-01

Recognition of RNA templates by viral replicase proteins is one of the key steps in the replication process of all RNA viruses. However, the mechanisms underlying this phenomenon, including primary RNA elements that are recognized by the viral replicase proteins, are not well understood. Here, we used aptamer pulldown assays with membrane fractionation and protein-RNA coimmunoprecipitation in a cell-free viral translation/replication system to investigate how viral replicase proteins recognize the bipartite genomic RNAs of the Red clover necrotic mosaic virus (RCNMV). RCNMV replicase proteins bound specifically to a Y-shaped RNA element (YRE) located in the 3′ untranslated region (UTR) of RNA2, which also interacted with the 480-kDa replicase complexes that contain viral and host proteins. The replicase-YRE interaction recruited RNA2 to the membrane fraction. Conversely, RNA1 fragments failed to interact with the replicase proteins supplied in trans. The results of protein-RNA coimmunoprecipitation assays suggest that RNA1 interacts with the replicase proteins coupled with their translation. Thus, the initial template recognition mechanisms employed by the replicase differ between RCNMV bipartite genomic RNAs and RNA elements are primary determinants of the differential replication mechanism. PMID:20980498

Herpes Simplex Virus Processivity Factor UL42 Imparts Increased DNA-Binding Specificity to the Viral DNA Polymerase and Decreased Dissociation from Primer-Template without Reducing the Elongation Rate

PubMed Central

Weisshart, Klaus; Chow, Connie S.; Coen, Donald M.

1999-01-01

Herpes simplex virus DNA polymerase consists of a catalytic subunit, Pol, and a processivity subunit, UL42, that, unlike other established processivity factors, binds DNA directly. We used gel retardation and filter-binding assays to investigate how UL42 affects the polymerase-DNA interaction. The Pol/UL42 heterodimer bound more tightly to DNA in a primer-template configuration than to single-stranded DNA (ssDNA), while Pol alone bound more tightly to ssDNA than to DNA in a primer-template configuration. The affinity of Pol/UL42 for ssDNA was reduced severalfold relative to that of Pol, while the affinity of Pol/UL42 for primer-template DNA was increased ∼15-fold relative to that of Pol. The affinity of Pol/UL42 for circular double-stranded DNA (dsDNA) was reduced drastically relative to that of UL42, but the affinity of Pol/UL42 for short primer-templates was increased modestly relative to that of UL42. Pol/UL42 associated with primer-template DNA ∼2-fold faster than did Pol and dissociated ∼10-fold more slowly, resulting in a half-life of 2 h and a subnanomolar Kd. Despite such stable binding, rapid-quench analysis revealed that the rates of elongation of Pol/UL42 and Pol were essentially the same, ∼30 nucleotides/s. Taken together, these studies indicate that (i) Pol/UL42 is more likely than its subunits to associate with DNA in a primer-template configuration rather than nonspecifically to either ssDNA or dsDNA, and (ii) UL42 reduces the rate of dissociation from primer-template DNA but not the rate of elongation. Two models of polymerase-DNA interactions during replication that may explain these findings are presented. PMID:9847307

Nanopolyaniline as immobilization template for signal enhancement of surface plasmon resonance biosensor - A preliminary study

NASA Astrophysics Data System (ADS)

Kamarun, Dzaraini; Abdul Azem, Nor Hazirah Kamel; Sarijo, Siti Halimah; Mohd, Ahmad Faiza; Abdullah @ Mohd Noor, Mashita

2012-07-01

A technique for the enhancement of Surface Plasmon Resonance (SPR) signal for sensing biomolecular interactions is described. Polyaniline (PANI) of particle size in the range of 1 to 15 nm was synthesized and used as the template for the immobilization of protein molecules. Biomolecular interactions of unbound and PANI-bound proteins with antibody molecules were SPR-monitored using a model system comprising of Bovine Serum Albumin (BSA) and anti BSA. A 7-fold increased in the signal was recorded from interactions of the PANI-bound BSA with anti BSA compared to the interactions of its unbound counterpart. This preliminary observation provides new avenue in immunosensor technology for improving the detection sensitivity of SPR biosensor; and thereby increasing the lower detection limit of biomolecules.

Interactions Between Item Content And Group Membership on Achievement Test Items.

ERIC Educational Resources Information Center

Linn, Robert L.; Harnisch, Delwyn L.

The purpose of this investigation was to examine the interaction of item content and group membership on achievement test items. Estimates of the parameters of the three parameter logistic model were obtained on the 46 item math test for the sample of eighth grade students (N = 2055) participating in the Illinois Inventory of Educational Progress,…

Engineering topochemical polymerizations using block copolymer templates.

PubMed

Zhu, Liangliang; Tran, Helen; Beyer, Frederick L; Walck, Scott D; Li, Xin; Agren, Hans; Killops, Kato L; Campos, Luis M

2014-09-24

With the aim to achieve rapid and efficient topochemical polymerizations in the solid state, via solution-based processing of thin films, we report the integration of a diphenyldiacetylene monomer and a poly(styrene-b-acrylic acid) block copolymer template for the generation of supramolecular architectural photopolymerizable materials. This strategy takes advantage of non-covalent interactions to template a topochemical photopolymerization that yields a polydiphenyldiacetylene (PDPDA) derivative. In thin films, it was found that hierarchical self-assembly of the diacetylene monomers by microphase segregation of the block copolymer template enhances the topochemical photopolymerization, which is complete within a 20 s exposure to UV light. Moreover, UV-active cross-linkable groups were incorporated within the block copolymer template to create micropatterns of PDPDA by photolithography, in the same step as the polymerization reaction. The materials design and processing may find potential uses in the microfabrication of sensors and other important areas that benefit from solution-based processing of flexible conjugated materials.

Experiment Management System for the SND Detector

NASA Astrophysics Data System (ADS)

Pugachev, K.

2017-10-01

We present a new experiment management system for the SND detector at the VEPP-2000 collider (Novosibirsk). An important part to report about is access to experimental databases (configuration, conditions and metadata). The system is designed in client-server architecture. User interaction comes true using web-interface. The server side includes several logical layers: user interface templates; template variables description and initialization; implementation details. The templates are meant to involve as less IT knowledge as possible. Experiment configuration, conditions and metadata are stored in a database. To implement the server side Node.js, a modern JavaScript framework, has been chosen. A new template engine having an interesting feature is designed. A part of the system is put into production. It includes templates dealing with showing and editing first level trigger configuration and equipment configuration and also showing experiment metadata and experiment conditions data index.

Synthesis and characterization of MAA-based molecularly-imprinted polymer (MIP) with D-glucose template

NASA Astrophysics Data System (ADS)

Yanti; Nurhayati, T.; Royani, I.; Widayani; Khairurrijal

2016-08-01

In this study, molecularly-imprinted polymer (MIP) was prepared by using a D-glucose template and a methacrylic acid (MAA) functional monomer. The obtained MIP was characterized using X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy techniques to study the template imprinting results. For comparison, similar characterizations were also carried out for the respective non imprinted polymer (NIP). It was found that the polymer has semicrystalline structure, with crystallinity degree of the unleached- polymer, the NIP, and the MIP is 62.40%, 62.97%, and 63.47%, respectively. XRD patterns showed that the intensity peaks increases as D-glucose content decreases. The FTIR spectra of the MIP indicate the detail interaction of template and functional monomer.

Acetylation of nucleosomal histones by p300 facilitates transcription from tax-responsive human T-cell leukemia virus type 1 chromatin template.

PubMed

Lu, Hanxin; Pise-Masison, Cynthia A; Fletcher, Terace M; Schiltz, R Louis; Nagaich, Akhilesh K; Radonovich, Michael; Hager, Gordon; Cole, Philip A; Brady, John N

2002-07-01

Expression of human T-cell leukemia virus type 1 (HTLV-1) is regulated by the viral transcriptional activator Tax. Tax activates viral transcription through interaction with the cellular transcription factor CREB and the coactivators CBP/p300. One key property of the coactivators is the presence of histone acetyltransferase (HAT) activity, which enables p300/CBP to modify nucleosome structure. The data presented in this manuscript demonstrate that full-length p300 and CBP facilitate transcription of a reconstituted chromatin template in the presence of Tax and CREB. The ability of p300 and CBP to activate transcription from the chromatin template is dependent upon the HAT activity. Moreover, the coactivator HAT activity must be tethered to the template by Tax and CREB, since a p300 mutant that fails to interact with Tax did not facilitate transcription or acetylate histones. p300 acetylates histones H3 and H4 within nucleosomes located in the promoter and 5' proximal regions of the template. Nucleosome acetylation is accompanied by an increase in the level of binding of RNA polymerase II transcription factor TFIID and RNA polymerase II to the promoter. Interestingly, we found distinct transcriptional activities between CBP and p300. CBP, but not p300, possesses an N-terminal activation domain which directly activates Tax-mediated HTLV-1 transcription from a naked DNA template. Finally, using the chromatin immunoprecipitation assay, we provide the first direct experimental evidence that p300 and CBP are associated with the HTLV-1 long terminal repeat in vivo.

Template-Framework Interactions in Tetraethylammonium-Directed Zeolite Synthesis

DOE PAGES

Schmidt, Joel E.; Fu, Donglong; Deem, Michael W.; ...

2016-11-22

Zeolites, having widespread applications in chemical industries, are often synthesized using organic templates. These can be cost-prohibitive, motivating investigations into their role in promoting crystallization. Herein, the relationship between framework structure, chemical composition, synthesis conditions and the conformation of the occluded, economical template tetraethylammonium (TEA +) has been systematically examined by experimental and computational means. The results show two distinct regimes of occluded conformer tendencies: 1) In frameworks with a large stabilization energy difference, only a single conformer was found (BEA, LTA and MFI). 2) In the frameworks with small stabilization energy differences (AEI, AFI, CHA and MOR), less thanmore » the interconversion of TEA + in solution, a heteroatom-dependent (Al, B, Co, Mn, Ti, Zn) distribution of conformers was observed. Our findings demonstrate that host–guest chemistry principles, including electrostatic interactions and coordination chemistry, are as important as ideal pore-filling.« less

The Affordance Template ROS Package for Robot Task Programming

NASA Technical Reports Server (NTRS)

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.

Fabrication of CoFe2O4 ferrite nanowire arrays in porous silicon template and their local magnetic properties

NASA Astrophysics Data System (ADS)

Hui, Zheng; Man-Gui, Han; Long-Jiang, Deng

2016-02-01

CoFe2O4 ferrite nanowire arrays are fabricated in porous silicon templates. The porous silicon templates are prepared via metal-assisted chemical etching with gold (Au) nanoparticles as the catalyst. Subsequently, CoFe2O4 ferrite nanowires are successfully synthesized into porous silicon templates by the sol-gel method. The magnetic hysteresis loop of nanowire array shows an isotropic feature of magnetic properties. The coercivity and squareness ratio (Mr/Ms) of ensemble nanowires are found to be 630 Oe (1 Oe, = 79.5775 A·m-1 and 0.4 respectively. However, the first-order reversal curve (FORC) is adopted to reveal the probability density function of local magnetostatic properties (i.e., interwire interaction field and coercivity). The FORC diagram shows an obvious distribution feature for interaction field and coercivity. The local coercivity with a value of about 1000 Oe is found to have the highest probability. Project supported by the National Natural Science Foundation of China (Grant No. 61271039), the Scientific Projects of Sichuan Province, China (Grant No. 2015HH0016), and the Natural Science Foundations of Zhejiang Province, China (Grant Nos. LQ12E02001 and Y107255).

Virtual imprinting as a tool to design efficient MIPs for photosynthesis-inhibiting herbicides.

PubMed

Breton, Florent; Rouillon, Regis; Piletska, Elena V; Karim, Kal; Guerreiro, Antonio; Chianella, Iva; Piletsky, Sergey A

2007-04-15

Molecular modelling and computational screening were used to identify functional monomers capable of interacting with several different photosynthesis-inhibiting herbicides. The process involved the design of a virtual library of molecular models of functional monomers containing polymerizable residues and residues able to interact with the template through electrostatic, hydrophobic, Van der Waals forces and dipole-dipole interactions. Each of the entries in the virtual library was probed for its possible interactions with molecular models of the template molecules. It was anticipated that the monomers giving the highest binding score would represent good candidates for the preparation of affinity polymers. Strong interactions were computationally determined between acidic functional monomers like methacrylic acid (MAA) or itaconic acid (IA) with triazines, and between vinylimidazole with bentazone and bromoxynil. Nevertheless, weaker interactions were seen with phenylureas. The corresponding blank polymers were prepared using the selected monomers and tested in the solid phase extraction (SPE) of herbicides from chloroform solutions. A good correlation was found between the binding score of the monomers and the affinities of the corresponding polymers. The use of computationally designed blanks can potentially eliminate the need for molecular imprinting, (adding a template to the monomer mixture to create specific binding sites). Data also showed that some monomers have a natural selectivity for some herbicides, which can be further enhanced by imprinting. Thus, in regard to retention on the blank polymer, we can estimate if the resulting imprinted polymer will be effective or not.

Mechanisms of triggering H1 helix in prion proteins unfolding revealed by molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Tseng, Chih-Yuan; Lee, H. C.

2006-03-01

In template-assistance model, normal Prion protein (PrP^C), the pathogen to cause several prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to infectious prion (PrP^Sc) through a transient interaction with PrP^Sc. Furthermore, conventional studies showed S1-H1-S2 region in PrP^C to be the template of S1-S2 β-sheet in PrP^Sc, and Prion protein's conformational conversion may involve an unfolding of H1 and refolding into β-sheet. Here we prepare several mouse prion peptides that contain S1-H1-S2 region with specific different structures, which are corresponding to specific interactions, to investigate possible mechanisms to trigger H1 α-helix unfolding process via molecular dynamic simulation. Three properties, conformational transition, salt-bridge in H1, and hydrophobic solvent accessible surface (SAS) are analyzed. From these studies, we found the interaction that triggers H1 unfolding to be the one that causes dihedral angle at residue Asn^143 changes. Whereas interactions that cause S1 segment's conformational changes play a minor in this process. These studies offers an additional evidence for template-assistance model.

A Delphi study among internal medicine clinicians to determine which therapeutic information is essential to record in a medical record.

PubMed

van Unen, Robert J; Tichelaar, Jelle; Nanayakkara, Prabath W B; van Agtmael, Michiel A; Richir, Milan C; de Vries, Theo P G M

2015-12-01

Several studies have demonstrated that using a template for recording general and diagnostic information in the medical record (MR) improves the completeness of MR documentation, communication between doctors, and performance of doctors. However, little is known about how therapeutic information should be structured in the MR. The aim of this study was to investigate which specific therapeutic information registrars and consultants in internal medicine consider essential to record in the MR. Therefore, we carried out a 2-round Internet Delphi study. Fifty-nine items were assessed on a 5-point scale; an item was considered important if ≥ 80% of the respondents awarded it a score of 4 or 5. In total, 26 registrars and 30 consultants in internal medicine completed both rounds of the study. Overall, they considered it essential to include information about 11 items in the MR. Subgroup analyses revealed that the registrars considered 8 additional items essential, whereas the consultants considered 1 additional item essential to record. Study findings can be used as a starting point to develop a structured section of the MR for therapeutic information for both paper and electronic MRs. This section should contain at least 11 items considered essential by registrars and clinical consultants in internal medicine. © 2015, The American College of Clinical Pharmacology.

Automated Scoring of an Interactive Geometry Item: A Proof-of-Concept

ERIC Educational Resources Information Center

Masters, Jessica

2010-01-01

An online interactive geometry item was developed to explore students' abilities to create prototypical and "tilted" rectangles out of line segments. The item was administered to 1,002 students. The responses to the item were hand-coded as correct, incorrect, or incorrect with possible evidence of a misconception. A variation of the nearest…

Evidence for negative feature guidance in visual search is explained by spatial recoding.

PubMed

Beck, Valerie M; Hollingworth, Andrew

2015-10-01

Theories of attention and visual search explain how attention is guided toward objects with known target features. But can attention be directed away from objects with a feature known to be associated only with distractors? Most studies have found that the demand to maintain the to-be-avoided feature in visual working memory biases attention toward matching objects rather than away from them. In contrast, Arita, Carlisle, and Woodman (2012) claimed that attention can be configured to selectively avoid objects that match a cued distractor color, and they reported evidence that this type of negative cue generates search benefits. However, the colors of the search array items in Arita et al. (2012) were segregated by hemifield (e.g., blue items on the left, red on the right), which allowed for a strategy of translating the feature-cue information into a simple spatial template (e.g., avoid right, or attend left). In the present study, we replicated the negative cue benefit using the Arita et al. (2012), method (albeit within a subset of participants who reliably used the color cues to guide attention). Then, we eliminated the benefit by using search arrays that could not be grouped by hemifield. Our results suggest that feature-guided avoidance is implemented only indirectly, in this case by translating feature-cue information into a spatial template. (c) 2015 APA, all rights reserved).

Formation of Polymer Particles by Direct Polymerization on the Surface of a Supramolecular Template.

PubMed

Schmuck, Carsten; Li, Mao; Zellermann, Elio

2018-04-06

Formation of polymeric materials on the surface of supramolecular assemblies is rather challenging due to the often weak non-covalent interactions between the self-assembled template and the monomers before polymerization. We herein describe that the introduction of a supramolecular anion recognition motif, the guanidiniocarbonyl pyrrole cation (GCP), into a short Fmoc-dipeptide 1 leads to self-assembled spherical nanoparticles in aqueous solution. Onto the surface of these nanoparticles negatively charged diacetylene monomers can be attached which after UV polymerization lead to the formation of a polymer shell around the self-assembled template. The hybrid supramolecular and polymeric nanoparticles demonstrated intriguing thermal hysteresis phenomenon. The template nanoparticle could be disassembled through the treatment with organic base which cleaved the Fmoc moiety on 1. This strategy thus showed that a supramolecular anion recognition motif allows the post-assembly formation of polymeric nanomaterials from anionic monomers around a cationic self-assembled template. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Template-constrained macrocyclic peptides prepared from native, unprotected precursors

PubMed Central

Lawson, Kenneth V.; Rose, Tristan E.; Harran, Patrick G.

2013-01-01

Peptide–protein interactions are important mediators of cellular-signaling events. Consensus binding motifs (also known as short linear motifs) within these contacts underpin molecular recognition, yet have poor pharmacological properties as discrete species. Here, we present methods to transform intact peptides into stable, templated macrocycles. Two simple steps install the template. The key reaction is a palladium-catalyzed macrocyclization. The catalysis has broad scope and efficiently forms large rings by engaging native peptide functionality including phenols, imidazoles, amines, and carboxylic acids without the necessity of protecting groups. The tunable reactivity of the template gives the process special utility. Defined changes in reaction conditions markedly alter chemoselectivity. In all cases examined, cyclization occurs rapidly and in high yield at room temperature, regardless of peptide composition or chain length. We show that conformational restraints imparted by the template stabilize secondary structure and enhance proteolytic stability in vitro. Palladium-catalyzed internal cinnamylation is a strong complement to existing methods for peptide modification. PMID:24043790

Dual soft-template system based on colloidal chemistry for the synthesis of hollow mesoporous silica nanoparticles.

PubMed

Li, Yunqi; Bastakoti, Bishnu Prasad; Imura, Masataka; Tang, Jing; Aldalbahi, Ali; Torad, Nagy L; Yamauchi, Yusuke

2015-04-20

A new dual soft-template system comprising the asymmetric triblock copolymer poly(styrene-b-2-vinyl pyridine-b-ethylene oxide) (PS-b-P2VP-b-PEO) and the cationic surfactant cetyltrimethylammonium bromide (CTAB) is used to synthesize hollow mesoporous silica (HMS) nanoparticles with a center void of around 17 nm. The stable PS-b-P2VP-b-PEO polymeric micelle serves as a template to form the hollow interior, while the CTAB surfactant serves as a template to form mesopores in the shells. The P2VP blocks on the polymeric micelles can interact with positively charged CTA(+) ions via negatively charged hydrolyzed silica species. Thus, dual soft-templates clearly have different roles for the preparation of the HMS nanoparticles. Interestingly, the thicknesses of the mesoporous shell are tunable by varying the amounts of TEOS and CTAB. This study provides new insight on the preparation of mesoporous materials based on colloidal chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymerase ribozyme efficiency increased by G/T-rich DNA oligonucleotides

PubMed Central

Yao, Chengguo; Müller, Ulrich F.

2011-01-01

The RNA world hypothesis states that the early evolution of life went through a stage where RNA served as genome and as catalyst. The replication of RNA world organisms would have been facilitated by ribozymes that catalyze RNA polymerization. To recapitulate an RNA world in the laboratory, a series of RNA polymerase ribozymes was developed previously. However, these ribozymes have a polymerization efficiency that is too low for self-replication, and the most efficient ribozymes prefer one specific template sequence. The limiting factor for polymerization efficiency is the weak sequence-independent binding to its primer/template substrate. Most of the known polymerase ribozymes bind an RNA heptanucleotide to form the P2 duplex on the ribozyme. By modifying this heptanucleotide, we were able to significantly increase polymerization efficiency. Truncations at the 3′-terminus of this heptanucleotide increased full-length primer extension by 10-fold, on a specific template sequence. In contrast, polymerization on several different template sequences was improved dramatically by replacing the RNA heptanucleotide with DNA oligomers containing randomized sequences of 15 nt. The presence of G and T in the random sequences was sufficient for this effect, with an optimal composition of 60% G and 40% T. Our results indicate that these DNA sequences function by establishing many weak and nonspecific base-pairing interactions to the single-stranded portion of the template. Such low-specificity interactions could have had important functions in an RNA world. PMID:21622900

The effects of implementing a point-of-care electronic template to prompt routine anxiety and depression screening in patients consulting for osteoarthritis (the Primary Care Osteoarthritis Trial): A cluster randomised trial in primary care.

PubMed

Mallen, Christian D; Nicholl, Barbara I; Lewis, Martyn; Bartlam, Bernadette; Green, Daniel; Jowett, Sue; Kigozi, Jesse; Belcher, John; Clarkson, Kris; Lingard, Zoe; Pope, Christopher; Chew-Graham, Carolyn A; Croft, Peter; Hay, Elaine M; Peat, George

2017-04-01

This study aimed to evaluate whether prompting general practitioners (GPs) to routinely assess and manage anxiety and depression in patients consulting with osteoarthritis (OA) improves pain outcomes. We conducted a cluster randomised controlled trial involving 45 English general practices. In intervention practices, patients aged ≥45 y consulting with OA received point-of-care anxiety and depression screening by the GP, prompted by an automated electronic template comprising five questions (a two-item Patient Health Questionnaire-2 for depression, a two-item Generalized Anxiety Disorder-2 questionnaire for anxiety, and a question about current pain intensity [0-10 numerical rating scale]). The template signposted GPs to follow National Institute for Health and Care Excellence clinical guidelines for anxiety, depression, and OA and was supported by a brief training package. The template in control practices prompted GPs to ask the pain intensity question only. The primary outcome was patient-reported current pain intensity post-consultation and at 3-, 6-, and 12-mo follow-up. Secondary outcomes included pain-related disability, anxiety, depression, and general health. During the trial period, 7,279 patients aged ≥45 y consulted with a relevant OA-related code, and 4,240 patients were deemed potentially eligible by participating GPs. Templates were completed for 2,042 patients (1,339 [31.6%] in the control arm and 703 [23.1%] in the intervention arm). Of these 2,042 patients, 1,412 returned questionnaires (501 [71.3%] from 20 intervention practices, 911 [68.0%] from 24 control practices). Follow-up rates were similar in both arms, totalling 1,093 (77.4%) at 3 mo, 1,064 (75.4%) at 6 mo, and 1,017 (72.0%) at 12 mo. For the primary endpoint, multilevel modelling yielded significantly higher average pain intensity across follow-up to 12 mo in the intervention group than the control group (adjusted mean difference 0.31; 95% CI 0.04, 0.59). Secondary outcomes were consistent with the primary outcome measure in reflecting better outcomes as a whole for the control group than the intervention group. Anxiety and depression scores did not reduce following the intervention. The main limitations of this study are two potential sources of bias: an imbalance in cluster size (mean practice size 7,397 [intervention] versus 5,850 [control]) and a difference in the proportion of patients for whom the GP deactivated the template (33.6% [intervention] versus 27.8% [control]). In this study, we observed no beneficial effect on pain outcomes of prompting GPs to routinely screen for and manage comorbid anxiety and depression in patients presenting with symptoms due to OA, with those in the intervention group reporting statistically significantly higher average pain scores over the four follow-up time points than those in the control group. ISRCTN registry ISRCTN40721988.

Binding of transcription termination protein nun to nascent RNA and template DNA.

PubMed

Watnick, R S; Gottesman, M E

1999-12-17

The amino-terminal arginine-rich motif of coliphage HK022 Nun binds phage lambda nascent transcript, whereas the carboxyl-terminal domain interacts with RNA polymerase (RNAP) and blocks transcription elongation. RNA binding is inhibited by zinc (Zn2+) and stimulated by Escherichia coli NusA. To study these interactions, the Nun carboxyl terminus was extended by a cysteine residue conjugated to a photochemical cross-linker. The carboxyl terminus contacted NusA and made Zn2+-dependent intramolecular contacts. When Nun was added to a paused transcription elongation complex, it cross-linked to the DNA template. Nun may arrest transcription by anchoring RNAP to DNA.

Graphene sheets stabilized on genetically engineered M13 viral templates as conducting frameworks for hybrid energy-storage materials.

PubMed

Oh, Dahyun; Dang, Xiangnan; Yi, Hyunjung; Allen, Mark A; Xu, Kang; Lee, Yun Jung; Belcher, Angela M

2012-04-10

Utilization of the material-specific peptide-substrate interactions of M13 virus broadens colloidal stability window of graphene. The homogeneous distribution of graphene is maintained in weak acids and increased ionic strengths by complexing with virus. This graphene/virus conducting template is utilized in the synthesis of energy-storage materials to increase the conductivity of the composite electrode. Successful formation of the hybrid biological template is demonstrated by the mineralization of bismuth oxyfluoride as a cathode material for lithium-ion batteries, with increased loading and improved electronic conductivity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mineralization and optical characterization of copper oxide nanoparticles using a high aspect ratio bio-template

NASA Astrophysics Data System (ADS)

Zaman, Mohammed Shahriar; Haberer, Elaine D.

2014-10-01

Organized chains of copper oxide nanoparticles were synthesized, without palladium (Pd) activation, using the M13 filamentous virus as a biological template. The interaction of Cu precursor ions with the negatively charged viral coat proteins were studied with Fourier transform infrared spectroscopy, transmission electron microscopy, and energy dispersive x-ray spectroscopy. Discrete nanoparticles with an average diameter of 4.5 nm and narrow size distribution were closely spaced along the length of the high aspect ratio templates. The synthesized material was identified as a mixture of cubic Cu2O and monoclinic CuO. UV/Vis absorption measurements were completed and a direct optical band gap of 2.87 eV was determined using Tauc's method. This value was slightly larger than bulk, signaling quantum confinement effects within the templated materials.

Mineralization and optical characterization of copper oxide nanoparticles using a high aspect ratio bio-template

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaman, Mohammed Shahriar; Haberer, Elaine D., E-mail: haberer@ucr.edu; Materials Science and Engineering Program, University of California, Riverside, California 92521

Organized chains of copper oxide nanoparticles were synthesized, without palladium (Pd) activation, using the M13 filamentous virus as a biological template. The interaction of Cu precursor ions with the negatively charged viral coat proteins were studied with Fourier transform infrared spectroscopy, transmission electron microscopy, and energy dispersive x-ray spectroscopy. Discrete nanoparticles with an average diameter of 4.5 nm and narrow size distribution were closely spaced along the length of the high aspect ratio templates. The synthesized material was identified as a mixture of cubic Cu₂O and monoclinic CuO. UV/Vis absorption measurements were completed and a direct optical band gap ofmore » 2.87 eV was determined using Tauc's method. This value was slightly larger than bulk, signaling quantum confinement effects within the templated materials.« less

Cytoskeleton-mediated templating of complex cellulose-scaffolded extracellular structure and its association with oikosins in the urochordate Oikopleura.

PubMed

Sagane, Yoshimasa; Hosp, Julia; Zech, Karin; Thompson, Eric M

2011-05-01

Oriented cellulose deposition is critical to plant patterning and models suggest microtubules constrain cellulose synthase movements through the plasma membrane. Though widespread in plants, urochordates are the only animals that synthesize cellulose. We characterized the distinctive cellulose microfibril scaffold of the larvacean house and its interaction with house structural proteins (oikosins). Targeted disruption of cytoskeletal elements, secretory pathways, and plasma membrane organization, suggested a working model for templating extracellular cellulose microfibrils from animal cells that shows both convergence and differences to plant models. Specialized cortical F-actin arrays template microfibril orientation and glycosylphosphatidylinositol-anchored proteins in lipid rafts may act as scaffolding proteins in microfibril elongation. Microtubules deliver and maintain cellulose synthase complexes to specific cell membrane sites rather than orienting their movement through the membrane. Oikosins are incorporated into house compartments directly above their corresponding cellular field of expression and interact with the cellulose scaffold to a variable extent.

An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Daisy  W.; Borek, Dominika; Luthra, Priya

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNP NTD complex, solved to 3.7 Å resolution, reveals how NPBP peptidemore » occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.« less

An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions

DOE PAGES

Leung, Daisy  W.; Borek, Dominika; Luthra, Priya; ...

2015-04-01

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNP NTD complex, solved to 3.7 Å resolution, reveals how NPBP peptidemore » occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.« less

An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.

PubMed

Leung, Daisy W; Borek, Dominika; Luthra, Priya; Binning, Jennifer M; Anantpadma, Manu; Liu, Gai; Harvey, Ian B; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; Shabman, Reed S; Chiu, Wah; Davey, Robert A; Otwinowski, Zbyszek; Basler, Christopher F; Amarasinghe, Gaya K

2015-04-21

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Kaizen practice in healthcare: a qualitative analysis of hospital employees' suggestions for improvement.

PubMed

Mazzocato, Pamela; Stenfors-Hayes, Terese; von Thiele Schwarz, Ulrica; Hasson, Henna; Nyström, Monica Elisabeth

2016-07-29

Kaizen, or continuous improvement, lies at the core of lean. Kaizen is implemented through practices that enable employees to propose ideas for improvement and solve problems. The aim of this study is to describe the types of issues and improvement suggestions that hospital employees feel empowered to address through kaizen practices in order to understand when and how kaizen is used in healthcare. We analysed 186 structured kaizen documents containing improvement suggestions that were produced by 165 employees at a Swedish hospital. Directed content analysis was used to categorise the suggestions into following categories: type of situation (proactive or reactive) triggering an action; type of process addressed (technical/administrative, support and clinical); complexity level (simple or complex); and type of outcomes aimed for (operational or sociotechnical). Compliance to the kaizen template was calculated. 72% of the improvement suggestions were reactions to a perceived problem. Support, technical and administrative, and primary clinical processes were involved in 47%, 38% and 16% of the suggestions, respectively. The majority of the kaizen documents addressed simple situations and focused on operational outcomes. The degree of compliance to the kaizen template was high for several items concerning the identification of problems and the proposed solutions, and low for items related to the test and implementation of solutions. There is a need to combine kaizen practices with improvement and innovation practices that help staff and managers to address complex issues, such as the improvement of clinical care processes. The limited focus on sociotechnical aspects and the partial compliance to kaizen templates may indicate a limited understanding of the entire kaizen process and of how it relates to the overall organisational goals. This in turn can hamper the sustainability of kaizen practices and results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

NASA Astrophysics Data System (ADS)

Sherly, K. B.; Rakesh, K.

2014-01-01

Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl2ṡ8H2O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with the theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.

Identification of Critical Residues for the Tight Binding of Both Correct and Incorrect Nucleotides to Human DNA Polymerase λ

PubMed Central

Brown, Jessica A.; Pack, Lindsey R.; Sherrer, Shanen M.; Kshetry, Ajay K.; Newmister, Sean A.; Fowler, Jason D.; Taylor, John-Stephen; Suo, Zucai

2010-01-01

DNA polymerase λ (Pol λ) is a novel X-family DNA polymerase that shares 34% sequence identity with DNA polymerase β (Pol β). Pre-steady state kinetic studies have shown that the Pol λ•DNA complex binds both correct and incorrect nucleotides 130-fold tighter on average than the Pol β•DNA complex, although, the base substitution fidelity of both polymerases is 10−4 to 10−5. To better understand Pol λ’s tight nucleotide binding affinity, we created single- and double-substitution mutants of Pol λ to disrupt interactions between active site residues and an incoming nucleotide or a template base. Single-turnover kinetic assays showed that Pol λ binds to an incoming nucleotide via cooperative interactions with active site residues (R386, R420, K422, Y505, F506, A510, and R514). Disrupting protein interactions with an incoming correct or incorrect nucleotide impacted binding with each of the common structural moieties in the following order: triphosphate ≫ base > ribose. In addition, the loss of Watson-Crick hydrogen bonding between the nucleotide and template base led to a moderate increase in the Kd. The fidelity of Pol λ was maintained predominantly by a single residue, R517, which has minor groove interactions with the DNA template. PMID:20851705

Interactions between visual working memory representations.

PubMed

Bae, Gi-Yeul; Luck, Steven J

2017-11-01

We investigated whether the representations of different objects are maintained independently in working memory or interact with each other. Observers were shown two sequentially presented orientations and required to reproduce each orientation after a delay. The sequential presentation minimized perceptual interactions so that we could isolate interactions between memory representations per se. We found that similar orientations were repelled from each other whereas dissimilar orientations were attracted to each other. In addition, when one of the items was given greater attentional priority by means of a cue, the representation of the high-priority item was not influenced very much by the orientation of the low-priority item, but the representation of the low-priority item was strongly influenced by the orientation of the high-priority item. This indicates that attention modulates the interactions between working memory representations. In addition, errors in the reported orientations of the two objects were positively correlated under some conditions, suggesting that representations of distinct objects may become grouped together in memory. Together, these results demonstrate that working-memory representations are not independent but instead interact with each other in a manner that depends on attentional priority.

Formation of Helically Structured Chitin/CaCO3 Hybrids through an Approach Inspired by the Biomineralization Processes of Crustacean Cuticles.

PubMed

Matsumura, Shunichi; Kajiyama, Satoshi; Nishimura, Tatsuya; Kato, Takashi

2015-10-01

Chitin/CaCO3 hybrids with helical structures are formed through a biomineralization-inspired crystallization process under ambient conditions. Liquid-crystalline chitin whiskers are used as helically ordered templates. The liquid-crystalline structures are stabilized by acidic polymer networks which interact with the chitin templates. The crystallization of CaCO3 is conducted by soaking the templates in the colloidal suspension of amorphous CaCO3 (ACC) at room temperature. At the initial stage of crystallization, ACC particles are introduced inside the templates, and they crystallize to CaCO3 nanocrystals. The acidic polymer networks induce CaCO3 crystallization. The characterization of the resultant hybrids reveals that they possess helical order and homogeneous hybrid structures of chitin and CaCO3 , which resemble the structure and composition of the exoskeleton of crustaceans. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inhibition of RNA-Dependent DNA Polymerase of Avian Myeloblastosis Virus by Pyran Copolymer

PubMed Central

Papas, Takis S.; Pry, Thomas W.; Chirigos, Michael A.

1974-01-01

Pyran copolymer, a known immunostimulator, was found to be a potent inhibitor of purified DNA polymerase (deoxynucleosidetriphosphate: DNA deoxynucleotidyltransferase; EC 2.7.7.7) isolated from avian myeloblastosis virus. Unlike other inhibitors, pyran showed unique features of inhibition. It interacts with the polymerase at a region other than the template site. The inhibitory effect was overcome only by excess enzyme and not affected by excess template. The degree of inhibition was not template specific for the templates tested: 70S RNA from avian myeloblastosis virus, synthetic hybrid poly(rA)·oligo(dT)10, synthetic copolymer poly(dA-dT), and activated calf-thymus DNA. The observed rate of inhibition by pyran was shown to vary with the different polymerases tested. Inhibition was shown with all oncornaviral polymerases and, to a lesser extent, with mammalian polymerases. However, two of the three bacterial polymerases, by contrast, showed a marked activation. PMID:4131275

Poly(cyclohexylethylene)- block-poly(ethylene oxide) block polymers for metal oxide templating

DOE PAGES

Schulze, Morgan W.; Sinturel, Christophe; Hillmyer, Marc A.

2015-09-01

A series of poly(cyclohexylethylene)- block-poly(ethylene oxide) (CEO) diblock copolymers were synthesized through tandem anionic polymerizations and heterogeneous catalytic hydrogenation. Solvent-annealed CEO diblock films were used to template dense arrays of inorganic oxide nanodots via simple spin coating of an inorganic precursor solution atop the ordered film. The substantial chemical dissimilarity of the two blocks enables (i) selective inclusion of the inorganic precursor within the PEO domain and (ii) the formation of exceptionally small feature sizes due to a relatively large interaction parameter estimated from mean-field analysis of the order–disorder transition temperatures of compositionally symmetric samples. UV/ozone treatment following incorporation producesmore » an ordered arrangement of oxide nanodots and simultaneously removes the block polymer template. However, we report the smallest particles (6 ± 1 nm) templated from a selective precursor insertion method to date using a block polymer scaffold.« less

Reading of the non-template DNA by transcription elongation factors.

PubMed

Svetlov, Vladimir; Nudler, Evgeny

2018-05-14

Unlike transcription initiation and termination, which have easily discernable signals such as promoters and terminators, elongation is regulated through a dynamic network involving RNA/DNA pause signals and states- rather than sequence-specific protein interactions. A report by Nedialkov et al. (in press) provides experimental evidence for sequence-specific recruitment of elongation factor RfaH to transcribing RNA polymerase (RNAP) and outlines the mechanism of gene expression regulation by restraint ("locking") of the DNA non-template strand. According to this model, the elongation complex pauses at the so called "operon polarity sequence" (found in some long bacterial operons coding for virulence genes), when the usually flexible non-template DNA strand adopts a distinct hairpin-loop conformation on the surface of transcribing RNAP. Sequence-specific binding of RfaH to this DNA segment facilitates conversion of RfaH from its inactive closed to its active open conformation. The interaction network formed between RfaH, non-template DNA, and RNAP locks DNA in a conformation that renders the elongation complex resistant to pausing and termination. The effects of such locking on transcript elongation can be mimicked by restraint of the non-template strand due to its shortening. This work advances our understanding of regulation of transcript elongation and has important implications for the action of general transcription factors, such as NusG, which lack apparent sequence-specificity, as well as for the mechanisms of other processes linked to transcription such as transcription-coupled DNA repair. This article is protected by copyright. All rights reserved. © 2018 John Wiley & Sons Ltd.

Rational design of molecularly imprinted polymer: the choice of cross-linker.

PubMed

Muhammad, Turghun; Nur, Zohre; Piletska, Elena V; Yimit, Osmanjan; Piletsky, Sergey A

2012-06-07

The paper describes a rational approach for the selection of cross-linkers during the development of molecularly imprinted polymers (MIPs). As a model system for this research MIPs specific for the drug zidovudine (AZT) were designed and tested. Three cross-linkers trimethylolpropane trimethacrylate (TRIM), ethylene glycol dimethacrylate (EGDMA) and divinylbenzene (DVB) were studied. The analogue of zidovudine (AZT) ester (AZT-ES) was used as a dummy template. The imprinting factors for all of the polymers in the static adsorption experiments were calculated. The data on the AZT adsorption by control polymers (CP), which were prepared with different cross-linkers without a functional monomer, was also analyzed. DVB was found to be more inert towards zidovudine than EGDMA and TRIM, which was confirmed by both molecular modelling and adsorption experiments. It was demonstrated that DVB-based polymers had a higher imprinting factor (I = 1.85) compared with other tested cross-linked polymers. It was suggested that the selection of the cross-linker should be based on the strength of the interaction with the template: the cross-linker which displays lower binding of the template should be preferential because it generates MIPs with lower non-specific binding and a higher imprinting factor, and therefore specificity. Which cross-linker to use for the preparation of any particular MIP can be determined by analysis of the interactions between the cross-linker and template. This could be done either virtually using computational modelling or by template adsorption using a small library of polymers prepared using different cross-linkers.

Switch from translation to RNA replication in a positive-stranded RNA virus

PubMed Central

Gamarnik, Andrea V.; Andino, Raul

1998-01-01

In positive-stranded viruses, the genomic RNA serves as a template for both translation and RNA replication. Using poliovirus as a model, we examined the interaction between these two processes. We show that the RNA polymerase is unable to replicate RNA templates undergoing translation. We discovered that an RNA structure at the 5′ end of the viral genome, next to the internal ribosomal entry site, carries signals that control both viral translation and RNA synthesis. The interaction of this RNA structure with the cellular factor PCBP up-regulates viral translation, while the binding of the viral protein 3CD represses translation and promotes negative-strand RNA synthesis. We propose that the interaction of 3CD with this RNA structure controls whether the genomic RNA is used for translation or RNA replication. PMID:9694795

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

PubMed Central

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

1975-01-01

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. Images PLATE 1 PMID:1218090

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

PubMed

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.

Template-free electrochemical nanofabrication of polyaniline nanobrush and hybrid polyaniline with carbon nanohorns for supercapacitors.

PubMed

Wei, Di; Wang, Haolan; Hiralal, Pritesh; Andrew, Piers; Ryhänen, Tapani; Hayashi, Yasuhiko; Amaratunga, Gehan A J

2010-10-29

Polyaniline (PANI) nanobrushes were synthesized by template-free electrochemical galvanostatic methods. When the same method was applied to the carbon nanohorn (CNH) solution containing aniline monomers, a hybrid nanostructure containing PANI and CNHs was enabled after electropolymerization. This is the first report on the template-free method to make PANI nanobrushes and homogeneous hybrid soft matter (PANI) with carbon nanoparticles. Raman spectroscopy was used to analyze the interaction between CNH and PANI. Electrochemical nanofabrication offers simplicity and good control when used to make electronic devices. Both of these materials were applied in supercapacitors and an improvement capacitive current by using the hybrid material was observed.

Template-free electrochemical nanofabrication of polyaniline nanobrush and hybrid polyaniline with carbon nanohorns for supercapacitors

NASA Astrophysics Data System (ADS)

Wei, Di; Wang, Haolan; Hiralal, Pritesh; Andrew, Piers; Ryhänen, Tapani; Hayashi, Yasuhiko; Amaratunga, Gehan A. J.

2010-10-01

Polyaniline (PANI) nanobrushes were synthesized by template-free electrochemical galvanostatic methods. When the same method was applied to the carbon nanohorn (CNH) solution containing aniline monomers, a hybrid nanostructure containing PANI and CNHs was enabled after electropolymerization. This is the first report on the template-free method to make PANI nanobrushes and homogeneous hybrid soft matter (PANI) with carbon nanoparticles. Raman spectroscopy was used to analyze the interaction between CNH and PANI. Electrochemical nanofabrication offers simplicity and good control when used to make electronic devices. Both of these materials were applied in supercapacitors and an improvement capacitive current by using the hybrid material was observed.

Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints

PubMed Central

Day, Ryan; Qu, Xiaotao; Swanson, Rosemarie; Bohannan, Zach; Bliss, Robert

2011-01-01

Abstract Most current template-based structure prediction methods concentrate on finding the correct backbone conformation and then packing sidechains within that backbone. Our packing-based method derives distance constraints from conserved relative packing groups (RPGs). In our refinement approach, the RPGs provide a level of resolution that restrains global topology while allowing conformational sampling. In this study, we test our template-based structure prediction method using 51 prediction units from CASP7 experiments. RPG-based constraints are able to substantially improve approximately two-thirds of starting templates. Upon deeper investigation, we find that true positive spatial constraints, especially those non-local in sequence, derived from the RPGs were important to building nearer native models. Surprisingly, the fraction of incorrect or false positive constraints does not strongly influence the quality of the final candidate. This result indicates that our RPG-based true positive constraints sample the self-consistent, cooperative interactions of the native structure. The lack of such reinforcing cooperativity explains the weaker effect of false positive constraints. Generally, these findings are encouraging indications that RPGs will improve template-based structure prediction. PMID:21210729

Sources of Interactional Problems in a Survey of Racial/Ethnic Discrimination

PubMed Central

Johnson, Timothy P.; Shariff-Marco, Salma; Willis, Gordon; Cho, Young Ik; Breen, Nancy; Gee, Gilbert C.; Krieger, Nancy; Grant, David; Alegria, Margarita; Mays, Vickie M.; Williams, David R.; Landrine, Hope; Liu, Benmei; Reeve, Bryce B.; Takeuchi, David; Ponce, Ninez A.

2014-01-01

Cross-cultural variability in respondent processing of survey questions may bias results from multiethnic samples. We analyzed behavior codes, which identify difficulties in the interactions of respondents and interviewers, from a discrimination module contained within a field test of the 2007 California Health Interview Survey. In all, 553 (English) telephone interviews yielded 13,999 interactions involving 22 items. Multilevel logistic regression modeling revealed that respondent age and several item characteristics (response format, customized questions, length, and first item with new response format), but not race/ethnicity, were associated with interactional problems. These findings suggest that item function within a multi-cultural, albeit English language, survey may be largely influenced by question features, as opposed to respondent characteristics such as race/ethnicity. PMID:26166949

Selection, constraint, and the evolution of coloration in African starlings.

PubMed

Maia, Rafael; Rubenstein, Dustin R; Shawkey, Matthew D

2016-05-01

Colorful plumage plays a prominent role in the evolution of birds, influencing communication (sexual/social selection), and crypsis (natural selection). Comparative studies have focused primarily on these selective pressures, but the mechanisms underlying color production can also be important by constraining the color gamut upon which selection acts. Iridescence is particularly interesting to study the interaction between selection and color-producing mechanisms because a broad range of colors can be produced with a shared template, and innovations to this template further expand this by increasing the parameters interacting to produce colors. We examine the patterns of ornamentation and dichromatism evolution in African starlings, a group remarkably diverse in color production mechanisms, social systems, and ecologies. We find that the presence of iridescence is ancestral to the group, being predominantly lost in females and cooperative breeders, as well as species with less labile templates. Color-producing mechanisms interact and are the main predictors of plumage ornamentation and elaboration, with little influence of selective pressures in their evolution. Dichromatism, however is influenced by social system and the loss of iridescence. Our results show the importance of considering both selection and constraints, and the different roles that they may have, in the evolution of ornamentation and dimorphism. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Decomposing the interaction between retention interval and study/test practice: The role of retrievability

PubMed Central

Jang, Yoonhee; Wixted, John T.; Pecher, Diane; Zeelenberg, René; Huber, David E.

2012-01-01

Even without feedback, test practice enhances delayed performance compared to study practice, but the size of the effect is variable across studies. We investigated the benefit of testing, separating initially retrievable items from initially non-retrievable items. In two experiments, an initial test determined item retrievability. Retrievable or non-retrievable items were subsequently presented for repeated study or test practice. Collapsing across items, in Experiment 1, we obtained the typical crossover interaction between retention interval and practice type. For retrievable items, however, the crossover interaction was quantitatively different, with a small study benefit for an immediate test and a larger testing benefit after a delay. For non-retrievable items, there was a large study benefit for an immediate test, but one week later there was no difference between the study and test practice conditions. In Experiment 2, initially non-retrievable items were given additional study followed by either an immediate test or even more additional study, and one week later performance did not differ between the two conditions. These results indicate that the effect size of study/test practice is due to the relative contribution of retrievable and non-retrievable items. PMID:22304454

Decomposing the interaction between retention interval and study/test practice: the role of retrievability.

PubMed

Jang, Yoonhee; Wixted, John T; Pecher, Diane; Zeelenberg, René; Huber, David E

2012-01-01

Even without feedback, test practice enhances delayed performance compared to study practice, but the size of the effect is variable across studies. We investigated the benefit of testing, separating initially retrievable items from initially nonretrievable items. In two experiments, an initial test determined item retrievability. Retrievable or nonretrievable items were subsequently presented for repeated study or test practice. Collapsing across items, in Experiment 1, we obtained the typical cross-over interaction between retention interval and practice type. For retrievable items, however, the cross-over interaction was quantitatively different, with a small study benefit for an immediate test and a larger testing benefit after a delay. For nonretrievable items, there was a large study benefit for an immediate test, but one week later there was no difference between the study and test practice conditions. In Experiment 2, initially nonretrievable items were given additional study followed by either an immediate test or even more additional study, and one week later performance did not differ between the two conditions. These results indicate that the effect size of study/test practice is due to the relative contribution of retrievable and nonretrievable items.

RPA physically interacts with the human DNA glycosylase NEIL1 to regulate excision of oxidative DNA base damage in primer-template structures.

PubMed

Theriot, Corey A; Hegde, Muralidhar L; Hazra, Tapas K; Mitra, Sankar

2010-06-04

The human DNA glycosylase NEIL1, activated during the S-phase, has been shown to excise oxidized base lesions in single-strand DNA substrates. Furthermore, our previous work demonstrating functional interaction of NEIL1 with PCNA and flap endonuclease 1 (FEN1) suggested its involvement in replication-associated repair. Here we show interaction of NEIL1 with replication protein A (RPA), the heterotrimeric single-strand DNA binding protein that is essential for replication and other DNA transactions. The NEIL1 immunocomplex isolated from human cells contains RPA, and its abundance in the complex increases after exposure to oxidative stress. NEIL1 directly interacts with the large subunit of RPA (K(d) approximately 20 nM) via the common interacting interface (residues 312-349) in NEIL1's disordered C-terminal region. RPA inhibits the base excision activity of both wild-type NEIL1 (389 residues) and its C-terminal deletion CDelta78 mutant (lacking the interaction domain) for repairing 5-hydroxyuracil (5-OHU) in a primer-template structure mimicking the DNA replication fork. This inhibition is reduced when the damage is located near the primer-template junction. Contrarily, RPA moderately stimulates wild-type NEIL1 but not the CDelta78 mutant when 5-OHU is located within the duplex region. While NEIL1 is inhibited by both RPA and Escherichia coli single-strand DNA binding protein, only inhibition by RPA is relieved by PCNA. These results showing modulation of NEIL1's activity on single-stranded DNA substrate by RPA and PCNA support NEIL1's involvement in repairing the replicating genome. Copyright 2010 Elsevier B.V. All rights reserved.

Headgroup effects of template monolayers on the adsorption behavior and conformation of glucose oxidase adsorbed at air/liquid interfaces.

PubMed

Wang, Ke-Hsuan; Syu, Mei-Jywan; Chang, Chien-Hsiang; Lee, Yuh-Lang

2011-06-21

Stearic acid (SA) and octadecylamine (ODA) monolayers at the air/liquid interface were used as template layers to adsorb glucose oxidase (GOx) from aqueous solution. The effect of the template monolayers on the adsorption behavior of GOx was studied in terms of the variation of surface pressure, the evolution of surface morphology observed by BAM and AFM, and the conformation of adsorbed GOx. The results show that the presence of a template monolayer can enhance the adsorption rate of GOx; furthermore, ODA has a higher ability, compared to SA, to adsorb GOx, which is attributed to the electrostatic attractive interaction between ODA and GOx. For adsorption performed on a bare surface or on an SA monolayer, the surface pressure approaches an equilibrium value (ca. 8 mN/m) after 2 to 3 h of adsorption and remains nearly constant in the following adsorption process. For the adsorption on an ODA monolayer, the surface pressure will increase further 1 to 2 h after approaching the first equilibrium pressure, which is termed the second adsorption stage. The measurement of circular dichroism (CD) spectroscopy indicates that the Langmuir-Blodgett films of adsorbed GOx transferred at the first equilibrium state (π = 8 mN/m) have mainly a β-sheet conformation, which is independent of the type of template monolayers. However, the ODA/GOx LB film transferred at the second adsorption stage has mainly an α-helix conformation. It is concluded that the specific interaction between ODA and GOx not only leads to a higher adsorption rate and adsorbed amount of GOx but also induces a conformation change in adsorbed GOx from β-sheet to α-helix. The present results indicate that is possible to control the conformation of adsorbed protein by selecting the appropriate template monolayer. © 2011 American Chemical Society

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

PubMed

Lee, Hasup; Baek, Minkyung; Lee, Gyu Rie; Park, Sangwoo; Seok, Chaok

2017-03-01

Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Preparation of "dummy" l-phenylalanine molecularly imprinted microspheres by using ionic liquid as a template and functional monomer.

PubMed

Li, Ji; Hu, Xiaoling; Guan, Ping; Song, Dongmen; Qian, Liwei; Du, Chunbao; Song, Renyuan; Wang, Chaoli

2015-07-07

In this study, dummy imprinting technology was employed for the preparation of l-phenylalanine-imprinted microspheres. Ionic liquids were utilized as both a "dummy" template and functional monomer, and 4-vinylpyridine and ethylene glycol dimethacrylate were used as the assistant monomer and cross-linker, respectively, for preparing a surface-imprinted polymer on poly(divinylbenzene) microspheres. By the results obtained by theoretical investigation, the interaction between the template and monomer complex was improved as compared with that between the template and the traditional l-phenylalanine-imprinted polymer. The batch experiments indicated that the imprinting factor reached 2.5. Scatchard analysis demonstrated that the obtained "dummy" molecularly imprinted microspheres exhibited an affinity of 77.4 M·10 -4 , significantly higher that of a traditional polymer directly prepared by l-phenylalanine, which is in agreement with theoretical results. Competitive adsorption experiments also showed that the molecularly imprinted polymer with the dummy template effectively isolated l-phenylalanine from l-histidine and l-tryptophan with separation factors of 5.68 and 2.68, respectively. All these results demonstrated that the polymerizable ionic liquid as the dummy template could enhance the affinity and selectivity of molecularly imprinted polymer, thereby promoting the development of imprinting technology for biomolecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical Epitaxial Growth of Gold Nanoparticle Arrays.

PubMed

Huang, Ningfeng; Martínez, Luis Javier; Jaquay, Eric; Nakano, Aiichiro; Povinelli, Michelle L

2015-09-09

We use an optical analogue of epitaxial growth to assemble gold nanoparticles into 2D arrays. Particles are attracted to a growth template via optical forces and interact through optical binding. Competition between effects determines the final particle arrangements. We use a Monte Carlo model to design a template that favors growth of hexagonal particle arrays. We experimentally demonstrate growth of a highly stable array of 50 gold particles with 200 nm diameter, spaced by 1.1 μm.

Interfacial Interaction in Anodic Aluminum Oxide Templates Modifies Morphology, Surface Area, and Crystallization of Polyamide-6 Nanofibers.

PubMed

Xue, Junhui; Xu, Yizhuang; Jin, Zhaoxia

2016-03-08

Here, we demonstrated that, when the precipitation process of polyamide-6 (PA6) solution happens in cylindrical channels of an anodized aluminum oxide membrane (AAO), interface interactions between a solid surface, solvent, non-solvent, and PA6 will influence the obtained polymer nanostructures, resulting in complex morphologies, increased surface area, and crystallization changes. With the enhancing interaction of PA6 and the AAO surface, the morphology of PA6 nanostructures changes from solid nanofibers, mesoporous, to bamboo-like, while at the same time, metastable γ-phase domains increase in these PA6 nanostructures. Brunauer-Emmett-Teller (BET) surface areas of solid, bamboo-like, and mesoporous PA6 nanofibers rise from 16, 20.9, to 25 m(2)/g. This study shows that interfacial interaction in AAO template fabrication can be used in manipulating the morphology and crystallization of one-dimensional polymer nanostructures. It also provides us a simple and novel method to create porous PA6 nanofibers with a large surface area.

Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherly, K. B.; Rakesh, K.

Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl{sub 2}⋅8H{sub 2}O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with themore » theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.« less

Mapping monomeric threading to protein-protein structure prediction.

PubMed

Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

2013-03-25

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD <2.5 Å by SPRING is 134% and 167% higher than these competing methods. SPRING is controlled with ZDOCK on 77 docking benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

Structure and properties of hybrid biopolymer particles fabricated by co-precipitation cross-linking dissolution procedure.

PubMed

Xiong, Yu; Georgieva, Radostina; Steffen, Axel; Smuda, Kathrin; Bäumler, Hans

2018-03-15

The Co-precipitation Crosslinking Dissolution technique (CCD-technique) allows a few-steps fabrication of particles composed of different biopolymers and bioactive agents under mild conditions. Morphology and properties of the fabricated biopolymer particles depend on the fabrication conditions, the nature of the biopolymers and additives, but also on the choice of the inorganic templates for co-precipitation. Here, we investigate the influence of an acidic biopolymer, hyaluronic acid (HA), on the formation of particles from bovine hemoglobin and bovine serum albumin applying co-precipitation with CaCO 3 and MnCO 3 . CaCO 3 templated biopolymer particles are almost spherical with particle size from 2 to 20 µm and protein entrapment efficiency from 13 to 77%. Presence of HA causes significant structural changes of the particles and decreasing protein entrapment efficiency. In contrast, MnCO 3 templated particles exhibit uniform peanut shape and submicron size with remarkably high protein entrapment efficiency of nearly 100%. Addition of HA has no influence on the protein entrapment efficiency or on morphology and size of the particles. These effects can be attributed to the strong interaction of Mn 2+ with proteins and much weaker interaction with HA. Therefore, entrapment efficiency, size and structure of biopolymer particles can be optimized by varying the mineral templates and additives. Copyright © 2017 Elsevier Inc. All rights reserved.

The Architecture Based Design Method

DTIC Science & Technology

2000-01-01

implementation of components of different types. The software templates include a description of how components interact with shared services and also include citizenship responsibilities for components.

Spontaneous emergence of catalytic cycles with colloidal spheres

NASA Astrophysics Data System (ADS)

Zeravcic, Zorana; Brenner, Michael P.

2017-04-01

Colloidal particles endowed with specific time-dependent interactions are a promising route for realizing artificial materials that have the properties of living ones. Previous work has demonstrated how this system can give rise to self-replication. Here, we introduce the process of colloidal catalysis, in which clusters of particles catalyze the creation of other clusters through templating reactions. Surprisingly, we find that simple templating rules generically lead to the production of huge numbers of clusters. The templating reactions among this sea of clusters give rise to an exponentially growing catalytic cycle, a specific realization of Dyson’s notion of an exponentially growing metabolism. We demonstrate this behavior with a fixed set of interactions between particles chosen to allow a catalysis of a specific six-particle cluster from a specific seven-particle cluster, yet giving rise to the catalytic production of a sea of clusters of sizes between 2 and 11 particles. The fact that an exponentially growing cycle emerges naturally from such a simple scheme demonstrates that the emergence of exponentially growing metabolisms could be simpler than previously imagined.

Directed self-assembly of diblock copolymers in cylindrical confinement: effect of underfilling and air-polymer interactions on configurations

NASA Astrophysics Data System (ADS)

Carpenter, Corinne L.; Delaney, Kris T.; Laachi, Nabil; Fredrickson, Glenn H.

2015-03-01

Directed self-assembly (DSA) of block copolymers has attracted attention for its use as a simple, cost- effective patterning tool for creating vertical interconnect access (VIA) channels in nanoelectronic devices.1, 2 This technique supplements existing lithographic technologies to allow for the creation of high-resolution cylindrical holes whose diameter and placement can be precisely controlled. In this study, we use self-consistent field theory (SCFT) simulations to investigate the equilibrium configurations of under-filled DSA systems with air-polymer interactions. We report on a series of SCFT simulations of our three species (PMMA-b-PS diblock and air) model in cylindrical confinement to explore the role of template diameter, under-fill fraction (i.e. volume fraction of air), air-polymer surface interaction and polymer-side wall/substrate interactions on equilibrium morphologies in an under-filled template with a free top surface. We identify parameters and system configurations where a meniscus appears and explore cases with PMMA-attractive, PS-attractive, and all-neutral walls to understand the effects of wall properties on meniscus geometry and DSA morphology. An important outcome is an understanding of the parameters that control the contact angle of the meniscus with the wall, as it is one of the simplest quantitative measures of the meniscus shape. Ultimately, we seek to identify DSA formulations, templates, and surface treatments with predictable central cylinder diameter and a shallow contact angle, as these factors would facilitate broad process windows and ease of manufacturing.

Refining and validating the Social Interaction Anxiety Scale and the Social Phobia Scale.

PubMed

Carleton, R Nicholas; Collimore, Kelsey C; Asmundson, Gordon J G; McCabe, Randi E; Rowa, Karen; Antony, Martin M

2009-01-01

The Social Interaction Anxiety Scale and Social Phobia Scale are companion measures for assessing symptoms of social anxiety and social phobia. The scales have good reliability and validity across several samples, however, exploratory and confirmatory factor analyses have yielded solutions comprising substantially different item content and factor structures. These discrepancies are likely the result of analyzing items from each scale separately or simultaneously. The current investigation sets out to assess items from those scales, both simultaneously and separately, using exploratory and confirmatory factor analyses in an effort to resolve the factor structure. Participants consisted of a clinical sample (n 5353; 54% women) and an undergraduate sample (n 5317; 75% women) who completed the Social Interaction Anxiety Scale and Social Phobia Scale, along with additional fear-related measures to assess convergent and discriminant validity. A three-factor solution with a reduced set of items was found to be most stable, irrespective of whether the items from each scale are assessed together or separately. Items from the Social Interaction Anxiety Scale represented one factor, whereas items from the Social Phobia Scale represented two other factors. Initial support for scale and factor validity, along with implications and recommendations for future research, is provided. (c) 2009 Wiley-Liss, Inc.

The Effects of Item Format and Cognitive Domain on Students' Science Performance in TIMSS 2011

NASA Astrophysics Data System (ADS)

Liou, Pey-Yan; Bulut, Okan

2017-12-01

The purpose of this study was to examine eighth-grade students' science performance in terms of two test design components, item format, and cognitive domain. The portion of Taiwanese data came from the 2011 administration of the Trends in International Mathematics and Science Study (TIMSS), one of the major international large-scale assessments in science. The item difficulty analysis was initially applied to show the proportion of correct items. A regression-based cumulative link mixed modeling (CLMM) approach was further utilized to estimate the impact of item format, cognitive domain, and their interaction on the students' science scores. The results of the proportion-correct statistics showed that constructed-response items were more difficult than multiple-choice items, and that the reasoning cognitive domain items were more difficult compared to the items in the applying and knowing domains. In terms of the CLMM results, students tended to obtain higher scores when answering constructed-response items as well as items in the applying cognitive domain. When the two predictors and the interaction term were included together, the directions and magnitudes of the predictors on student science performance changed substantially. Plausible explanations for the complex nature of the effects of the two test-design predictors on student science performance are discussed. The results provide practical, empirical-based evidence for test developers, teachers, and stakeholders to be aware of the differential function of item format, cognitive domain, and their interaction in students' science performance.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis.

PubMed

Pham, Phuong; Seitz, Erica M; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

2002-08-20

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD'(2)C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are "nonfilamentous". That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3' primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis

PubMed Central

Pham, Phuong; Seitz, Erica M.; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M.; Goodman, Myron F.

2002-01-01

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD′2C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are “nonfilamentous”. That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3′ primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3′ filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis. PMID:12177433

Supercooling of Hydrogen on Template Materials to Deterministically Seed Ignition-Quality Solid Fuel Layers

DOE PAGES

Shin, S. J.; Zepeda-Ruiz, L. A.; Lee, J. R. I.; ...

2016-09-01

In this study, we explored templating effects of various materials for hydrogen (H 2 and D 2) solidification by measuring the degree of supercooling required for liquid hydrogen to solidify below each triple point. The results show high supercooling (>100 mK) for most metallic, covalent, and ionic solids, and low supercooling (<100 mK) for van der Waals (vdW) solids. We attribute the low supercooling of vdW solids to the weak interaction of the substrate and hydrogen. Highly ordered pyrolytic graphite showed the lowest supercooling among materials that are solid at room temperature, but did not exhibit a templating effect withinmore » a fill-tube and capsule assembly.« less

Development of knowledge tests for multi-disciplinary emergency training: a review and an example.

PubMed

Sørensen, J L; Thellesen, L; Strandbygaard, J; Svendsen, K D; Christensen, K B; Johansen, M; Langhoff-Roos, P; Ekelund, K; Ottesen, B; Van Der Vleuten, C

2015-01-01

The literature is sparse on written test development in a post-graduate multi-disciplinary setting. Developing and evaluating knowledge tests for use in multi-disciplinary post-graduate training is challenging. The objective of this study was to describe the process of developing and evaluating a multiple-choice question (MCQ) test for use in a multi-disciplinary training program in obstetric-anesthesia emergencies. A multi-disciplinary working committee with 12 members representing six professional healthcare groups and another 28 participants were involved. Recurrent revisions of the MCQ items were undertaken followed by a statistical analysis. The MCQ items were developed stepwise, including decisions on aims and content, followed by testing for face and content validity, construct validity, item-total correlation, and reliability. To obtain acceptable content validity, 40 out of originally 50 items were included in the final MCQ test. The MCQ test was able to distinguish between levels of competence, and good construct validity was indicated by a significant difference in the mean score between consultants and first-year trainees, as well as between first-year trainees and medical and midwifery students. Evaluation of the item-total correlation analysis in the 40 items set revealed that 11 items needed re-evaluation, four of which addressed content issues in local clinical guidelines. A Cronbach's alpha of 0.83 for reliability was found, which is acceptable. Content and construct validity and reliability were acceptable. The presented template for the development of this MCQ test could be useful to others when developing knowledge tests and may enhance the overall quality of test development. © 2014 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results inmore » highly aligned, highly crystalline donor-acceptor polymer thin films over large area (41cm 2) and promoted charge transport along both the polymer backbone and the π-π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment.« less

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

PubMed Central

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; Qu, Ge; Zhang, Fengjiao; Zhao, Xikang; Mei, Jianguo; Zuo, Jian-Min; Shukla, Diwakar; Diao, Ying

2017-01-01

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results in highly aligned, highly crystalline donor–acceptor polymer thin films over large area (>1 cm2) and promoted charge transport along both the polymer backbone and the π–π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment. PMID:28703136

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

DOE PAGES

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; ...

2017-07-13

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results inmore » highly aligned, highly crystalline donor-acceptor polymer thin films over large area (41cm 2) and promoted charge transport along both the polymer backbone and the π-π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment.« less

Physical controls on directed virus assembly at nanoscale chemical templates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheung, C L; Chung, S; Chatterji, A

2006-05-10

Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In-situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, andmore » drove 1D and 2D condensation at subcritical volume fractions. The growth kinetics followed a t{sup 1/2} law controlled by the slow diffusion of viruses. The lateral expansion of virus clusters that initially form on the 1D templates following introduction of polyethylene glycol (PEG) into the solution suggests a significant role for weak interaction.« less

Self-replication with magnetic dipolar colloids

NASA Astrophysics Data System (ADS)

Dempster, Joshua M.; Zhang, Rui; Olvera de la Cruz, Monica

2015-10-01

Colloidal self-replication represents an exciting research frontier in soft matter physics. Currently, all reported self-replication schemes involve coating colloidal particles with stimuli-responsive molecules to allow switchable interactions. In this paper, we introduce a scheme using ferromagnetic dipolar colloids and preprogrammed external magnetic fields to create an autonomous self-replication system. Interparticle dipole-dipole forces and periodically varying weak-strong magnetic fields cooperate to drive colloid monomers from the solute onto templates, bind them into replicas, and dissolve template complexes. We present three general design principles for autonomous linear replicators, derived from a focused study of a minimalist sphere-dimer magnetic system in which single binding sites allow formation of dimeric templates. We show via statistical models and computer simulations that our system exhibits nonlinear growth of templates and produces nearly exponential growth (low error rate) upon adding an optimized competing electrostatic potential. We devise experimental strategies for constructing the required magnetic colloids based on documented laboratory techniques. We also present qualitative ideas about building more complex self-replicating structures utilizing magnetic colloids.

High-resolution physical and functional mapping of the template adjacent DNA binding site in catalytically active telomerase.

PubMed

Romi, Erez; Baran, Nava; Gantman, Marina; Shmoish, Michael; Min, Bosun; Collins, Kathleen; Manor, Haim

2007-05-22

Telomerase is a cellular reverse transcriptase, which utilizes an integral RNA template to extend single-stranded telomeric DNA. We used site-specific photocrosslinking to map interactions between DNA primers and the catalytic protein subunit (tTERT) of Tetrahymena thermophila telomerase in functional enzyme complexes. Our assays reveal contact of the single-stranded DNA adjacent to the primer-template hybrid and tTERT residue W187 at the periphery of the N-terminal domain. This contact was detected in complexes with three different registers of template in the active site, suggesting that it is maintained throughout synthesis of a complete telomeric repeat. Substitution of nearby residue Q168, but not W187, alters the K(m) for primer elongation, implying that it plays a role in the DNA recognition. These findings are the first to directly demonstrate the physical location of TERT-DNA contacts in catalytically active telomerase and to identify amino acid determinants of DNA binding affinity. Our data also suggest a movement of the TERT active site relative to the template-adjacent single-stranded DNA binding site within a cycle of repeat synthesis.

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

NASA Astrophysics Data System (ADS)

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.

Conducting a successful residency research project.

PubMed

Barletta, Jeffrey F

2008-08-15

The residency research project can be a challenging endeavor for pharmacy residents since they typically have limited experience in this area. Furthermore, as the number of accredited residency programs has increased, so has the demand for preceptors with research experience. This review is intended to assist the resident and preceptor by providing steps and guidance with conducting a successful residency research project. Items such as idea generation, proposing the right type of project, departmental review, and project management skills are discussed and guidance with writing the research protocol is provided. Items that must be addressed in every research protocol are described and a generalized protocol template is presented. In addition, the institutional review board review process is described and tips and pointers for obtaining approval are included. Finally, useful tools and resources are provided that can be used up front or throughout each phase of the research project.

Guidelines for evaluating the educational performance of medical school faculty: priming a national conversation.

PubMed

Baldwin, Constance; Chandran, Latha; Gusic, Maryellen

2011-01-01

The academic community needs a sound framework for the promotion and advancement of educators. The Group on Educational Affairs of the Association of American Medical Colleges organized a consensus conference that affirmed the use of five domains for documenting the quantity and quality of scholarly engagement in educational activities: teaching, curriculum, advising/mentoring, educational leadership/administration, and learner assessment. In this article, we offer detailed guidelines to evaluate these five domains of educator performance and the essential elements of scholarly activity. The guidelines are adapted from our developmental educator portfolio template and educator portfolio analysis tool, previously published in MedEdPORTAL. A short tool for educator performance evaluation that summarizes items in the guidelines is proposed for discussion. Our goal in this article is to itemize criteria for systematic faculty evaluation that can be applied in any institutional setting to assist promotion decision makers in their task of evaluating medical school faculty.

Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials.

PubMed

Hesemann, Peter; Nguyen, Thy Phung; Hankari, Samir El

2014-04-11

The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS) recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA), mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the "anionic templating" strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches.

Linear pi-Acceptor-Templated Dynamic Clipping to Macrobicycles and[2]Rotaxanes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klivansky, Liana M.; Koshkakaryan, Gayane; Cao, Dennis

2009-04-30

Functional rotaxanes are one of the representative nanoscale molecular machines that have found applications in many areas, including molecular electronics, nanoelectromechanical systems (NEMS), photo controllable smart surfaces, and nanovalves. With the advent of molecular recognition and self-assembly, such molecular compounds can now be obtained efficiently through template-directed synthesis. One of the common strategies of making [2]rotaxanes involves the clipping of a macrocycle around a preformed dumbbell-shaped template in a [1+1] or [2+2] manner. While early examples were based on irreversible kinetic pathway through covalent bond formation, recent advances on reversible dynamic covalent chemistry (DCC) has attracted great attention to thismore » field. By virtue of thermodynamically controlled equilibria, DCC has provided highly efficient and versatile synthetic routes in the selection of specific products from a complex system. Among the several reversible reactions in the category of DCC reactions, the imine formation has proven to be very versatile in macrocyclization to give complex interlocked molecular compounds. Cryptands are three dimensional bicyclic hosts with preorganized cavities capable of inclusion of ions and small molecules. Replacing the nitrogen bridgeheads in common cryptands with aromatic ring systems gives cyclophane-based macrobicycles. The introduction of aromatic ring systems into a preorganized cage-like geometry facilitates ion-{pi} interactions and {pi}-{pi} interactions, resulting in novel metal sandwiches, fluoride receptors, and host-guest complexes. In particular, the seminal work by Gibson, Huang and coworkers on cryptand complexation with paraquat and diquat guests have resulted in the efficient synthesis of mechanically interlocked rotaxanes. The synthesis of cyclophane-based macrobicycles, however, was mostly realized through multiple reaction steps and in high-dilution conditions, which often suffered from low yield and tedious workup. Thus, a one-step, five-component [2+3] clipping reaction that can give the desired macrobicycle is highly desirable. We are motivated by a {pi}-guest templating protocol, because not only {pi}-{pi} interactions can contribute to the formation of macrobicycles, but also the resulting host-guest system holds great promise as a forerunner in the construction of interlocked molecules. (Scheme 1c) Very simple precursors, namely 1,3,5-benzenetrialdehyde (1) and 2,2{prime}-(ethylenedioxy)diethylamine (2) were chosen as the components for desired macrobicycle. (Scheme 2) The formation of six imine bonds would connect the five components to give a macrobicycle while extending the conjugation in the C{sub 3}-symmetric aromatic 'ceiling' and 'floor', which is suitable for enhancing the {pi}-{pi} interactions with a complementary aromatic template. Meanwhile, the ethylene glycol 'pillars' can provide sufficient flexibility, proper spacing, and polar binding sites to assist guest encapsulation. Initial screening of ?-templates engaged several C{sub 3} symmetric aromatic compounds in order to match the symmetry of the desired macrobicycle, which only resulted in nonspecific mixtures. It was found instead that linear bipyridinium (BPY) containing guests effectively templated the [2+3] clipping reaction. Based on this protocol, a [2]rotaxane was successfully assembled as the single product from the six-component reaction.« less

Mutational analysis reveals a noncontractile but interactive role of actin and profilin in viral RNA-dependent RNA synthesis.

PubMed

Harpen, Mary; Barik, Tiasha; Musiyenko, Alla; Barik, Sailen

2009-11-01

As obligatory parasites, viruses co-opt a variety of cellular functions for robust replication. The expression of the nonsegmented negative-strand RNA genome of respiratory syncytial virus (RSV), a significant pediatric pathogen, absolutely requires actin and is stimulated by the actin-regulatory protein profilin. As actin is a major contractile protein, it was important to determine whether the known functional domains of actin and profilin were important for their ability to activate RSV transcription. Analyses of recombinant mutants in a reconstituted RSV transcription system suggested that the divalent-cation-binding domain of actin is critically needed for binding to the RSV genome template and for the activation of viral RNA synthesis. In contrast, the nucleotide-binding domain and the N-terminal acidic domain were needed neither for template binding nor for transcription. Specific surface residues of actin, required for actin-actin contact during filamentation, were also nonessential for viral transcription. Unlike actin, profilin did not directly bind to the viral template but was recruited by actin. Mutation of the interactive residues of actin or profilin, resulting in the loss of actin-profilin binding, also abolished profilin's ability to stimulate viral transcription. Together, these results suggest that actin acts as a classical transcription factor for the virus by divalent-cation-dependent binding to the viral template and that profilin acts as a transcriptional cofactor, in part by associating with actin. This essential viral role of actin is independent of its contractile cellular role.

Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments.

PubMed

Potapov, V; Reichmann, D; Abramovich, R; Filchtinski, D; Zohar, N; Ben Halevy, D; Edelman, M; Sobolev, V; Schreiber, G

2008-12-05

A new method is presented for the redesign of protein-protein interfaces, resulting in specificity of the designed pair while maintaining high affinity. The design is based on modular interface architecture and was carried out on the interaction between TEM1 beta-lactamase and its inhibitor protein, beta-lactamase inhibitor protein. The interface between these two proteins is composed of several mostly independent modules. We previously showed that it is possible to delete a complete module without affecting the overall structure of the interface. Here, we replace a complete module with structure fragments taken from nonrelated proteins. Nature-optimized fragments were chosen from 10(7) starting templates found in the Protein Data Bank. A procedure was then developed to identify sets of interacting template residues with a backbone arrangement mimicking the original module. This generated a final list of 361 putative replacement modules that were ranked using a novel scoring function based on grouped atom-atom contact surface areas. The top-ranked designed complex exhibited an affinity of at least the wild-type level and a mode of binding that was remarkably specific despite the absence of negative design in the procedure. In retrospect, the combined application of three factors led to the success of the design approach: utilizing the modular construction of the interface, capitalizing on native rather than artificial templates, and ranking with an accurate atom-atom contact surface scoring function.

Control of Orientation and Morphology of Crystals Grown Under Organic Templates

NASA Astrophysics Data System (ADS)

Stripe, Benjamin

Living creatures demonstrate an extraordinary ability to both grow and control the growth of inorganic crystals. These biominerals are found almost everywhere in nature from simple plants and plankton to our own teeth and bones. A great deal of research has been focused on how living creatures are able to achieve such control over the shape, size, orientation, and arrangement of these biominerals. Many studies have been done demonstrating the effects the presence of organic molecules can have on the morphology of nucleating inorganic crystals. These studies have led to the use of ordered arrays of biological molecules as templates to select the orientation of the crystals. Such experiments have had amazing success cataloging monolayers, orientations and morphologies of crystals grown beneath them. However, despite several decades of work, the exact mechanisms by which the orientation and morphology of crystals is selected by organic templates are still not known. The present study attempts to explain the complex interactions that take place at the template surface and decide the orientations and morphologies of the crystals that nucleate there. To do this, scanning electron microscopy (SEM), grazing incidence x-ray diffraction (GID), and x-ray reflectivity have been used to probe the templates and nucleating crystals in situ. The experiments described here seek to move beyond the well-studied two-component systems. In many of these two-component systems a single template and a single type of crystal are grown, and often many claims and comparisons are made about monolayer charge, crystal surface energies, stereochemical recognition, and lattice matches. However, almost all of the claims and comparisons are between systems that are different enough that assumptions about relative charge, strain, recognition, and lattice dynamics are either unfounded or poorly supported. To bridge this gap in the comparison of these different two-component systems the studies presented here are tunable three-component systems. These experiments allow for either continuously adjusting the template by means of two miscible monolayers or adjusting the growing crystals by incorporation of secondary ions. In either case, the idea is the same: we can more accurately compare two-component systems and isolate the controlling factor in the selection of orientation and morphology of the nucleating crystals. The results of these studies have shown that there is a complex interplay of charge, lattice parameters and kinetics. Despite this, we have been able to show that well-oriented growth of single non-dendritic crystals is limited to a fairly small range of surface charges and relative growth kinetics. Within this range, variations in the growing crystals can be seen based on changes in the average lattice parameters despite there being no evidence of direct epitaxy. Theories have evolved around the idea of stereochemical matching between the template and nucleating surface. These theories correlate the template molecular tilt to the orientation relative to the nucleation plane. However, these theories are not supported by the results presented in this manuscript. The data presented in this manuscript are suggestive of far more complex interfacial interactions involving an intermediary amorphous precursor, or possible networks of hydrated or hydrogen bonded ions than has been suggested in previous studies. Excitingly, it appears to be possible to control the selection of orientation using these multicomponent systems despite the complex interactions at the surface.

An audit of nursing reports for First-Tier Tribunals in a secure inpatient service.

PubMed

Haw, C

2015-08-01

Very little research has been conducted into the role of nurses in relation to patients' mental health tribunals (known in some countries as review panels). In England nurses are playing an increasingly important role in giving evidence at tribunals and, since October 2013, are required to provide much more detailed written reports than previously. This is the first published study to examine the content of nursing tribunal reports. Overall, the quality of nursing reports was patchy and not as good as those of psychiatrists or social workers, but there was improvement when the audit was repeated. Writing reports for tribunals is a comparatively new and perhaps unfamiliar requirement for nursing staff. Nurses need training in report writing and protected time and a quiet area to write reports. Providing these things is a real challenge on busy inpatient wards. In October 2013, the Tribunals Judiciary of England issued a new practice direction stipulating how tribunal reports should be completed. This paper aimed to study the quality of nursing tribunal reports in a secure inpatient service before and after the introduction of the latest practice direction and the issuing of a local template to aid report writing. A total of 160 reports (80 written in 2013 and 80 in 2014) were scored on the presence of 24 key items derived from the latest practice direction. The quality of nursing reports improved in the re-audit from an average of 36.3% of key items present to 51.3% but still lagged behind that of medical and social circumstances reports. Even in the second audit, few reports were signed or commented on why the patient should remain detained. Report length increased from a mean of 2.9 to 4.0 pages but only 27.5% of reports used the template despite widespread publicity. Use of the template resulted in better quality reports. Among other interventions, a training programme in report writing is now underway to assist nurses with meeting the new practice direction requirements. Nurses also need supervision, protected time and a quiet area for report writing. © 2015 John Wiley & Sons Ltd.

Systematic Heuristic Evaluation of Computerized Consultation Order Templates: Clinicians' and Human Factors Engineers' Perspectives.

PubMed

Savoy, April; Patel, Himalaya; Flanagan, Mindy E; Weiner, Michael; Russ, Alissa L

2017-08-01

We assessed the usability of consultation order templates and identified problems to prioritize in design efforts for improving referral communication. With a sample of 26 consultation order templates, three evaluators performed a usability heuristic evaluation. The evaluation used 14 domain-independent heuristics and the following three supplemental references: 1 new domain-specific heuristic, 6 usability goals, and coded clinicians' statements regarding ease of use for 10 sampled templates. Evaluators found 201 violations, a mean of 7.7 violations per template. Minor violations outnumbered major violations almost twofold, 115 (57%) to 62 (31%). Approximately 68% of violations were linked to 5 heuristics: aesthetic and minimalist design (17%), error prevention (16%), consistency and standards (14%), recognition rather than recall (11%), and meet referrers' information needs (10%). Severe violations were attributed mostly to meet referrers' information needs and recognition rather than recall. Recorded violations yielded potential negative consequences for efficiency, effectiveness, safety, learnability, and utility. Evaluators and clinicians demonstrated 80% agreement in usability assessment. Based on frequency and severity of usability heuristic violations, the consultation order templates reviewed may impede clinical efficiency and risk patient safety. Results support the following design considerations: communicate consultants' requirements, facilitate information seeking, and support communication. While the most frequent heuristic violations involved interaction design and presentation, the most severe violations lacked information desired by referring clinicians. Violations related to templates' inability to support referring clinicians' information needs had the greatest potential negative impact on efficiency and safety usability goals. Heuristics should be prioritized in future design efforts.

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation.

PubMed

Branson, Oscar; Bonnin, Elisa A; Perea, Daniel E; Spero, Howard J; Zhu, Zihua; Winters, Maria; Hönisch, Bärbel; Russell, Ann D; Fehrenbacher, Jennifer S; Gagnon, Alexander C

2016-11-15

Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales. Understanding the role of templates in biomineral nucleation, and their importance in skeletal geochemistry requires an integrated, multiscale approach, which can place atom-scale observations of organic-mineral interfaces within a broader structural and geochemical context. Here we map the chemistry of an embedded organic template structure within a carbonate skeleton of the foraminifera Orbulina universa using both atom probe tomography (APT), a 3D chemical imaging technique with Ångström-level spatial resolution, and time-of-flight secondary ionization mass spectrometry (ToF-SIMS), a 2D chemical imaging technique with submicron resolution. We quantitatively link these observations, revealing that the organic template in O. universa is uniquely enriched in both Na and Mg, and contributes to intraskeletal chemical heterogeneity. Our APT analyses reveal the cation composition of the organic surface, offering evidence to suggest that cations other than Ca 2+ , previously considered passive spectator ions in biomineral templating, may be important in defining the energetics of carbonate nucleation on organic templates.

Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking.

PubMed

Yan, Yumeng; Wen, Zeyu; Wang, Xinxiang; Huang, Sheng-You

2017-03-01

Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and more experimental binding information ranging from mutagenesis data to three-dimensional structures of protein complexes are becoming available. Therefore, how to appropriately incorporate the biological information into traditional ab initio docking has been an important issue and challenge in the field of protein-protein docking. To address these challenges, we have developed a Hybrid DOCKing protocol of template-based and template-free approaches, referred to as HDOCK. The basic procedure of HDOCK is to model the structures of individual components based on the template complex by a template-based method if a template is available; otherwise, the component structures will be modeled based on monomer proteins by regular homology modeling. Then, the complex structure of the component models is predicted by traditional protein-protein docking. With the HDOCK protocol, we have participated in the CPARI experiment for rounds 28-35. Out of the 25 CASP-CAPRI targets for oligomer modeling, our HDOCK protocol predicted correct models for 16 targets, ranking one of the top algorithms in this challenge. Our docking method also made correct predictions on other CAPRI challenges such as protein-peptide binding for 6 out of 8 targets and water predictions for 2 out of 2 targets. The advantage of our hybrid docking approach over pure template-based docking was further confirmed by a comparative evaluation on 20 CASP-CAPRI targets. Proteins 2017; 85:497-512. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An Investigation of the Impact of Guessing on Coefficient α and Reliability

PubMed Central

2014-01-01

Guessing is known to influence the test reliability of multiple-choice tests. Although there are many studies that have examined the impact of guessing, they used rather restrictive assumptions (e.g., parallel test assumptions, homogeneous inter-item correlations, homogeneous item difficulty, and homogeneous guessing levels across items) to evaluate the relation between guessing and test reliability. Based on the item response theory (IRT) framework, this study investigated the extent of the impact of guessing on reliability under more realistic conditions where item difficulty, item discrimination, and guessing levels actually vary across items with three different test lengths (TL). By accommodating multiple item characteristics simultaneously, this study also focused on examining interaction effects between guessing and other variables entered in the simulation to be more realistic. The simulation of the more realistic conditions and calculations of reliability and classical test theory (CTT) item statistics were facilitated by expressing CTT item statistics, coefficient α, and reliability in terms of IRT model parameters. In addition to the general negative impact of guessing on reliability, results showed interaction effects between TL and guessing and between guessing and test difficulty.

Assembly of Multi-Phthalocyanines on a Porphyrin Template by Fourfold Rotaxane Formation.

PubMed

Yamada, Yasuyuki; Kato, Tatsuhisa; Tanaka, Kentaro

2016-08-22

A stacked assembly composed of a porphyrin and two phthalocyanines was prepared through fourfold rotaxane formation. Two phthalocyanine molecules, bearing four 24-crown-8 units, were assembled onto a porphyrin template incorporating four sidechains with two dialkylammonium ions each through pseudorotaxane formation between crown ether units and ammonium ions. The Staudinger phosphite reaction, as the stoppering reaction, resulted in the formation of the stacked heterotrimer composed of a porphyrin and two phthalocyanines connected through a fourfold rotaxane structure. UV/Vis spectroscopic and electrochemical studies of the heterotrimer indicated that there is a significant electronic interaction between the two phthalocyanine units due to the close stacking. The electrochemical oxidation process of the stacked heterotrimer was studied by cyclic voltammetry and spectroelectrochemistry. Electron paramagnetic resonance (EPR) spectroscopy of a dinuclear Cu(II) complex, in which two Cu(II) phthalocyanines were assembled on a metal-free porphyrin template, revealed that two Cu(II) phthalocyanines were located within the stacking distance, which resulted in an antiferromagnetic interaction between the two S=1/2 spins in the ground state of the Cu(2+) ions in the heterotrimer. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A prototype of a beam steering assistant tool for accelerator operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

M. Bickley; P. Chevtsov

2006-10-24

The CEBAF accelerator provides nuclear physics experiments at Jefferson Lab with high quality electron beams. Three experimental end stations can simultaneously receive the beams with different energies and intensities. For each operational mode, the accelerator setup procedures are complicated and require very careful checking of beam spot sizes and positions on multiple beam viewers. To simplify these procedures and make them reproducible, a beam steering assistant GUI tool has been created. The tool is implemented as a multi-window control screen. The screen has an interactive graphical object window, which is an overlay on top of a digitized live video imagemore » from a beam viewer. It allows a user to easily create and edit any graphical objects consisting of text, ellipses, and lines, right above the live beam viewer image and then save them in a file that is called a beam steering template. The template can show, for example, the area within which the beam must always be on the viewer. Later, this template can be loaded in the interactive graphical object window to help accelerator operators steer the beam to the specified area on the viewer.« less

Structure based drug design: development of potent and selective factor IXa (FIXa) inhibitors.

PubMed

Wang, Shouming; Beck, Richard; Burd, Andrew; Blench, Toby; Marlin, Frederic; Ayele, Tenagne; Buxton, Stuart; Dagostin, Claudio; Malic, Maja; Joshi, Rina; Barry, John; Sajad, Mohammed; Cheung, Chiming; Shaikh, Shaheda; Chahwala, Suresh; Chander, Chaman; Baumgartner, Christine; Holthoff, Hans-Peter; Murray, Elizabeth; Blackney, Michael; Giddings, Amanda

2010-02-25

On the basis of our understanding on the binding interactions of the benzothiophene template within the FIXa active site by X-ray crystallography and molecular modeling studies, we developed our SAR strategy by targeting the 4-position of the template to access the S1 beta and S2-S4 sites. A number of highly selective and potent factor Xa (FXa) and FIXa inhibitors were identified by simple switch of functional groups with conformational changes toward the S2-S4 sites.

An alternative for presenting interactive dynamic data sets in electronic presentations: a scrollable flash movie loop.

PubMed

Yam, Chun-Shan

2007-11-01

The purpose of this article is to describe an alternative for creating scrollable movie loops for electronic presentations including PowerPoint. The alternative provided in this article enables academic radiologists to present scrollable movie loops in PowerPoint. The scrolling capability is created using Flash ActionScript. A Flash template with the required ActionScript code is provided. Users can simply download the template and follow the step-by-step demonstration to create scrollable movie loops. No previous ActionScript programming knowledge is necessary.

Final Scientific Report - Electromagnetic Interactions in Self-Assembled Metallo-Dielectric Biomaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dragnea, Bogdan G.

Achievements which resulted from previous DOE funding include: templated virus-like particle assembly thermodynamics, development of single particle photothermal absorption spectroscopy and dark- field spectroscopy instrumentation for the measurement of optical properties of virus-like nanoparticles, electromagnetic simulations of coupled nanoparticle cluster systems, virus contact mechanics, energy transfer and fluorescence quenching in multichromophore systems supported on biomolecular templates, and photo physical work on virus-aptamer systems. A current total of eight published research articles and a book chapter are acknowledging DOE support for the period 2013-2016.

Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models

NASA Astrophysics Data System (ADS)

Comitani, Federico; Cohen, Netta; Ashby, Jamie; Botten, Dominic; Lummis, Sarah C. R.; Molteni, Carla

2014-01-01

The resistance to dieldrin (RDL) receptor is an insect pentameric ligand-gated ion channel (pLGIC). It is activated by the neurotransmitter γ-aminobutyric acid (GABA) binding to its extracellular domain; hence elucidating the atomistic details of this interaction is important for understanding how the RDL receptor functions. As no high resolution structures are currently available, we built homology models of the extracellular domain of the RDL receptor using different templates, including the widely used acetylcholine binding protein and two pLGICs, the Erwinia Chrysanthemi ligand-gated ion channel (ELIC) and the more recently resolved GluCl. We then docked GABA into the selected three dimensional structures, which we used as starting points for classical molecular dynamics simulations. This allowed us to analyze in detail the behavior of GABA in the binding sites, including the hydrogen bond and cation-π interaction networks it formed, the conformers it visited and the possible role of water molecules in mediating the interactions; we also estimated the binding free energies. The models were all stable and showed common features, including interactions consistent with experimental data and similar to other pLGICs; differences could be attributed to the quality of the models, which increases with increasing sequence identity, and the use of a pLGIC template. We supplemented the molecular dynamics information with metadynamics, a rare event method, by exploring the free energy landscape of GABA binding to the RDL receptor. Overall, we show that the GluCl template provided the best models. GABA forming direct salt-bridges with Arg211 and Glu204, and cation-π interactions with an aromatic cage including Tyr109, Phe206 and Tyr254, represents a favorable binding arrangement, and the interaction with Glu204 can also be mediated by a water molecule.

Usability of Interactive Item Types and Tools Introduced in the New GRE® Revised General Test. ETS GRE® Board Research Report. ETS GRE®-14-05. ETS Research Report. RR-14-28

ERIC Educational Resources Information Center

Swiggett, Wanda D.; Kotloff, Laurie; Ezzo, Chelsea; Adler, Rachel; Oliveri, Maria Elena

2014-01-01

The computer-based "Graduate Record Examinations"® ("GRE"®) revised General Test includes interactive item types and testing environment tools (e.g., test navigation, on-screen calculator, and help). How well do test takers understand these innovations? If test takers do not understand the new item types, these innovations may…

Excellent reliability of the Hamilton Depression Rating Scale (HDRS-21) in Indonesia after training.

PubMed

Istriana, Erita; Kurnia, Ade; Weijers, Annelies; Hidayat, Teddy; Pinxten, Lucas; de Jong, Cor; Schellekens, Arnt

2013-09-01

The Hamilton Depression Rating Scale (HDRS) is the most widely used depression rating scale worldwide. Reliability of HDRS has been reported mainly from Western countries. The current study tested the reliability of HDRS ratings among psychiatric residents in Indonesia, before and after HDRS training. The hypotheses were that: (i) prior to the training reliability of HDRS ratings is poor; and (ii) HDRS training can improve reliability of HDRS ratings to excellent levels. Furthermore, we explored cultural validity at item level. Videotaped HDRS interviews were rated by 30 psychiatric residents before and after 1 day of HDRS training. Based on a gold standard rating, percentage correct ratings and deviation from the standard were calculated. Correct ratings increased from 83% to 99% at item level and from 70% to 100% for the total rating. The average deviation from the gold standard rating improved from 0.07 to 0.02 at item level and from 2.97 to 0.46 for the total rating. HDRS assessment by psychiatric trainees in Indonesia without prior training is unreliable. A short, evidence-based HDRS training improves reliability to near perfect levels. The outlined training program could serve as a template for HDRS trainings. HDRS items that may be less valid for assessment of depression severity in Indonesia are discussed. Copyright © 2013 Wiley Publishing Asia Pty Ltd.

Dewetting of polymer thin films on modified curved surfaces: preparation of polymer nanoparticles with asymmetric shapes by anodic aluminum oxide templates.

PubMed

Liu, Chih-Ting; Tsai, Chia-Chan; Chu, Chien-Wei; Chi, Mu-Huan; Chung, Pei-Yun; Chen, Jiun-Tai

2018-04-18

We study the dewetting behaviors of poly(methyl methacrylate) (PMMA) thin films coated in the cylindrical nanopores of anodic aluminum oxide (AAO) templates by thermal annealing. Self-assembled monolayers (SAMs) of n-octadecyltrichlorosilane (ODTS) are introduced to modify the pore surfaces of the AAO templates to induce the dewetting process. By using scanning electron microscopy (SEM), the dewetting-induced morphology transformation from the PMMA thin films to PMMA nanoparticles with asymmetric shapes can be observed. The sizes of the PMMA nanoparticles can be controlled by the original PMMA solution concentrations. The dewetting phenomena on the modified nanopores are explained by taking into account the excess intermolecular interaction free energy (ΔG). This work opens a new possibility for creating polymer nanoparticles with asymmetric shapes in confined geometries.

Tailoring uniform gold nanoparticle arrays and nanoporous films for next-generation optoelectronic devices

NASA Astrophysics Data System (ADS)

Farid, Sidra; Kuljic, Rade; Poduri, Shripriya; Dutta, Mitra; Darling, Seth B.

2018-06-01

High-density arrays of gold nanodots and nanoholes on indium tin oxide (ITO)-coated glass surfaces are fabricated using a nanoporous template fabricated by the self-assembly of diblock copolymers of poly (styrene-block-methyl methacrylate) (PS-b-PMMA) structures. By balancing the interfacial interactions between the polymer blocks and the substrate using random copolymer, cylindrical block copolymer microdomains oriented perpendicular to the plane of the substrate have been obtained. Nanoporous PS films are created by selectively etching PMMA cylinders, a straightforward route to form highly ordered nanoscale porous films. Deposition of gold on the template followed by lift off and sonication leaves a highly dense array of gold nanodots. These materials can serve as templates for the vapor-liquid-solid (VLS) growth of semiconductor nanorod arrays for next generation hybrid optoelectronic applications.

Experimental and Computational Exploration of para-Selective Silylation with a Hydrogen-Bonded Template.

PubMed

Maji, Arun; Guin, Srimanta; Feng, Sheng; Dahiya, Amit; Singh, Vikas Kumar; Liu, Peng; Maiti, Debabrata

2017-11-20

The regioselective conversion of C-H bonds into C-Si bonds is extremely important owing to the natural abundance and non-toxicity of silicon. Classical silylation reactions often suffer from poor functional group compatibility, low atom economy, and insufficient regioselectivity. Herein, we disclose a template-assisted method for the regioselective para silylation of toluene derivatives. A new template was designed, and the origin of selectivity was analyzed experimentally and computationally. An interesting substrate-solvent hydrogen-bonding interaction was observed. Kinetic, spectroscopic, and computational studies shed light on the reaction mechanism. The synthetic significance of this strategy was highlighted by the generation of a precursor of a potential lipophilic bioisostere of γ-aminobutyric acid (GABA), various late-stage diversifications, and by mimicking enzymatic transformations. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fabrication and electrical properties of textured strontium(0.53)barium(0.47)niobium(2)oxygen(6) ceramics prepared by templated grain growth

NASA Astrophysics Data System (ADS)

Duran, Cihangir

Sr0.53Ba0.47Nb2O6 (SBN53) ceramics were textured by the templated grain growth (TGG), in a matrix of SrNb2O6 and BaNb2O6 powders. Acicular KSr2Nb5O15 (KSN) template particles, synthesized by a molten salt process, were used to texture the samples in the c direction (i.e., [001]). Template growth was assisted by adding V2O5 as a liquid phase former for some compositions. The texture fraction also increased with higher sintering temperatures or times and with initial template concentration due to the preferential growth of the template particles. When V2O5 was present, SBN53 phase formation initiated on the KSN templates and texture development started at temperatures as low as 950°C. Phase formation in the V2O5-free samples, however, initiated in the matrix (i.e., independent of the KSN templates). The liquid phase adversely affected the template growth by favoring anisotropic grain growth in the matrix, which caused lower texture fraction and broader texture distribution in [001] at low template concentrations. Increased template-template interaction (e.g., tangling) during tape casting also resulted in broader texture distribution. Therefore, an optimum template content was found to be ˜10--15 wt%. However, a texture fraction of 0.93 to 0.98 was obtained using only 5 wt% templates when anisotropic matrix grain growth was prevented. Phase evolution was studied in the randomly oriented samples as a function of quenching temperature, heating rate, and liquid phase, using KSN powder (rather than acicular particles) as a seed material. The formation temperature for SBN53 was lowered substantially by adding more seeds, decreasing the heating rate, and introducing a liquid. The temperature decreased from 1260°C for the samples with no seeds to 1130°C for the samples with 15.4 wt% seeds + 0.8 mol% V2O5 at a heating rate of 4°C/min. For the V2O5-free samples, the activation energy was considerably lowered from 554 +/- 15 kJ/mol for the samples with no seeds to 241 +/- 17 kJ/mol for the samples with 15.4 wt% seeds. The dielectric and piezoelectric properties were enhanced in samples with better orientation (i.e., high texture fraction (f) and narrow degree of orientation parameter (r) in the texture direction). The presence of nonferroelectric phases (V2O5 or Nb2O5-based) at the grain boundaries suppressed the observed dielectric properties, especially at the transition temperature. (Abstract shortened by UMI.)

Mechanism of transcription termination by RNA polymerase III utilizes a nontemplate-strand sequence-specific signal element

PubMed Central

Arimbasseri, Aneeshkumar G.; Maraia, Richard J.

2015-01-01

SUMMARY Understanding the mechanism of transcription termination by a eukaryotic RNA polymerase (RNAP) has been limited by lack of a characterizable intermediate that reflects transition from an elongation complex to a true termination event. While other multisubunit RNAPs require multipartite cis-signals and/or ancillary factors to mediate pausing and release of the nascent transcript from the clutches of these enzymes, RNAP III does so with precision and efficiency on a simple oligo(dT) tract, independent of other cis-elements or trans-factors. We report a RNAP III pre-termination complex that reveals termination mechanisms controlled by sequence-specific elements in the non-template strand. Furthermore, the TFIIF-like, RNAP III subunit, C37 is required for this function of the non-template strand signal. The results reveal the RNAP III terminator as an information-rich control element. While the template strand promotes destabilization via a weak oligo(rU:dA) hybrid, the non-template strand provides distinct sequence-specific destabilizing information through interactions with the C37 subunit. PMID:25959395

Rapid, High Affinity Binding by a Fluorescein Templated Copolymer Combining Covalent, Hydrophobic, and Acid–Base Noncovalent Crosslinks

PubMed Central

Timberman, Anthony; Yang, Rongfang; Papantones, Alex; Seitz, W. Rudolf

2018-01-01

A new type of biomimetic templated copolymer has been prepared by reverse addition fragmentation chain transfer polymerization (RAFT) in dioxane. The initial formulation includes the template fluorescein, N-isopropylacrylamide (NIPAM, 84 mol %), methacrylic acid (MAA, 5-mol %), 4-vinylpyridine (4-VP, 9 mmol %), and N,N′-methylenebis(acrylamide) (MBA, 2 mol %). PolyNIPAM is a thermosensitive polymer that comes out of aqueous solution above its lower critical solution temperature forming hydrophobic ‘crosslinks’. MAA and 4-VP interact in dioxane forming acid–base crosslinks. The excess 4-VP serves as a recognition monomer organizing around the template fluorescein to form a binding site that is held in place by the noncovalent and covalent crosslinks. The MBA is a covalent crosslinker. The RAFT agent in the resulting copolylmer was reduced to a thiol and attached to gold nanoparticles. The gold nanoparticle bound copolymer binds fluorescein completely in less than two seconds with an affinity constant greater than 108 M−1. A reference copolymer prepared with the same monomers by the same procedure binds fluorescein much more weakly. PMID:29693601

A comparison of different functions for predicted protein model quality assessment.

PubMed

Li, Juan; Fang, Huisheng

2016-07-01

In protein structure prediction, a considerable number of models are usually produced by either the Template-Based Method (TBM) or the ab initio prediction. The purpose of this study is to find the critical parameter in assessing the quality of the predicted models. A non-redundant template library was developed and 138 target sequences were modeled. The target sequences were all distant from the proteins in the template library and were aligned with template library proteins on the basis of the transformation matrix. The quality of each model was first assessed with QMEAN and its six parameters, which are C_β interaction energy (C_beta), all-atom pairwise energy (PE), solvation energy (SE), torsion angle energy (TAE), secondary structure agreement (SSA), and solvent accessibility agreement (SAE). Finally, the alignment score (score) was also used to assess the quality of model. Hence, a total of eight parameters (i.e., QMEAN, C_beta, PE, SE, TAE, SSA, SAE, score) were independently used to assess the quality of each model. The results indicate that SSA is the best parameter to estimate the quality of the model.

Parallel interactive retrieval of item and associative information from event memory.

PubMed

Cox, Gregory E; Criss, Amy H

2017-09-01

Memory contains information about individual events (items) and combinations of events (associations). Despite the fundamental importance of this distinction, it remains unclear exactly how these two kinds of information are stored and whether different processes are used to retrieve them. We use both model-independent qualitative properties of response dynamics and quantitative modeling of individuals to address these issues. Item and associative information are not independent and they are retrieved concurrently via interacting processes. During retrieval, matching item and associative information mutually facilitate one another to yield an amplified holistic signal. Modeling of individuals suggests that this kind of facilitation between item and associative retrieval is a ubiquitous feature of human memory. Copyright © 2017 Elsevier Inc. All rights reserved.

The factor structure and screening utility of the Social Interaction Anxiety Scale.

PubMed

Rodebaugh, Thomas L; Woods, Carol M; Heimberg, Richard G; Liebowitz, Michael R; Schneier, Franklin R

2006-06-01

The widely used Social Interaction Anxiety Scale (SIAS; R. P. Mattick & J. C. Clarke, 1998) possesses favorable psychometric properties, but questions remain concerning its factor structure and item properties. Analyses included 445 people with social anxiety disorder and 1,689 undergraduates. Simple unifactorial models fit poorly, and models that accounted for differences due to item wording (i.e., reverse scoring) provided superior fit. It was further found that clients and undergraduates approached some items differently, and the SIAS may be somewhat overly conservative in selecting analogue participants from an undergraduate sample. Overall, this study provides support for the excellent properties of the SIAS's straightforwardly worded items, although questions remain regarding its reverse-scored items. Copyright 2006 APA, all rights reserved.

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation

PubMed Central

Bonnin, Elisa A.; Perea, Daniel E.; Spero, Howard J.; Zhu, Zihua; Winters, Maria; Hönisch, Bärbel; Russell, Ann D.; Fehrenbacher, Jennifer S.; Gagnon, Alexander C.

2016-01-01

Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales. Understanding the role of templates in biomineral nucleation, and their importance in skeletal geochemistry requires an integrated, multiscale approach, which can place atom-scale observations of organic-mineral interfaces within a broader structural and geochemical context. Here we map the chemistry of an embedded organic template structure within a carbonate skeleton of the foraminifera Orbulina universa using both atom probe tomography (APT), a 3D chemical imaging technique with Ångström-level spatial resolution, and time-of-flight secondary ionization mass spectrometry (ToF-SIMS), a 2D chemical imaging technique with submicron resolution. We quantitatively link these observations, revealing that the organic template in O. universa is uniquely enriched in both Na and Mg, and contributes to intraskeletal chemical heterogeneity. Our APT analyses reveal the cation composition of the organic surface, offering evidence to suggest that cations other than Ca2+, previously considered passive spectator ions in biomineral templating, may be important in defining the energetics of carbonate nucleation on organic templates. PMID:27794119

Preparation of molecularly imprinted polymers specific to glycoproteins, glycans and monosaccharides via boronate affinity controllable-oriented surface imprinting.

PubMed

Xing, Rongrong; Wang, Shuangshou; Bie, Zijun; He, Hui; Liu, Zhen

2017-05-01

Molecularly imprinted polymers (MIPs) are materials that are designed to be receptors for a template molecule (e.g., a protein). They are made by polymerizing the polymerizable reagents in the presence of the template; when the template is removed, the material can be used for many applications that would traditionally use antibodies. Thus, MIPs are biomimetic of antibodies and in this capacity have found wide applications, such as sensing, separation and diagnosis. However, many imprinting approaches are uncontrollable, and facile imprinting approaches widely applicable to a large variety of templates remain limited. We developed an approach called boronate affinity controllable-oriented surface imprinting, which allows for easy and efficient preparation of MIPs specific to glycoproteins, glycans and monosaccharides. This approach relies on immobilization of a template (glycoprotein, glycan or monosaccharide) on a boronic-acid-functionalized substrate through boronate affinity interaction, followed by self-polymerization of biocompatible monomer(s) to form an imprinting layer on the substrate with appropriate thickness. Imprinting in this approach is performed in a controllable manner, permitting the thickness of the imprinting layer to be fine-tuned according to the molecular size of the template by adjusting the imprinting time. This not only simplifies the imprinting procedure but also makes the approach widely applicable to a large range of sugar-containing biomolecules. MIPs prepared by this approach exhibit excellent binding properties and can be applied to complex real samples. The MIPs prepared by this protocol have been used in affinity separation, disease diagnosis and bioimaging. The entire protocol, including preparation, property characterization and performance evaluation, takes ∼3-8 d, depending on the type of substrate and template used.

Protein-Containing Multilayer Capsules by Templating on Mesoporous CaCO3 Particles: POST- and PRE-Loading Approaches.

PubMed

Balabushevich, Nadezhda G; Lopez de Guerenu, Anna V; Feoktistova, Natalia A; Skirtach, Andre G; Volodkin, Dmitry

2016-01-01

Encapsulation of model proteins (catalase, insulin, aprotinin) into multilayer dextran sulphate/protamin capsules by templating on CaCO3 microparticles is investigated employing: (i) PRE-loading into CaCO3 particles by adsorption or co-synthesis and (ii) POST-loading into performed capsules. Protein encapsulation is governed by both its size and electrostatic interactions with the carbonate microparticles and multilayer shell. PRE-loading enables improved encapsulation compared to POST-loading (catalase content in capsules 630 and 70 mg · g(-1)). Bioactivity of encapsulated protein is not affected by interaction with multilayers but may be reduced at slightly alkaline pH due to CaCO3 hydrolysis. This study might help to successfully encapsulate fragile bio-macromolecules into multilayer capsules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Workload and Interaction: Unisa's Signature Courses--A Design Template for Transitioning to Online DE?

ERIC Educational Resources Information Center

Hülsmann, Thomas; Shabalala, Lindiwe

2016-01-01

The principal contradiction of online distance education is the disparity that exists between economies of scale and the new interactive capabilities of digital technologies. This is particularly felt where mega-universities in developing countries seek to make better use of these affordances while at the same time protecting their economies of…

Fabrication of Au- and Ag–SiO{sub 2} inverse opals having both localized surface plasmon resonance and Bragg diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erola, Markus O.A.; Philip, Anish; Ahmed, Tanzir

The inverse opal films of SiO{sub 2} containing metal nanoparticles can have both the localized surface plasmon resonance (LSPR) of metal nanoparticles and the Bragg diffraction of inverse opal crystals of SiO{sub 2}, which are very useful properties for applications, such as tunable photonic structures, catalysts and sensors. However, effective processes for fabrication of these films from colloidal particles have rarely been reported. In our study, two methods for preparation of inverse opal films of SiO{sub 2} with three different crystal sizes and containing gold or silver nanoparticles (NPs) via self-assembly using electrostatic interactions and capillary forces are reported. Themore » Bragg diffraction of inverse opal films of SiO{sub 2} in the presence and absence of the template was measured and predicted on the basis of with UV–vis spectroscopy and scanning electron microscopy. The preparation methods used provided good-quality inverse opal SiO{sub 2} films containing highly dispersed, plasmonic AuNPs or AgNPs and having both Bragg diffractions and LSPRs. - Graphical abstract: For syntheses of SiO{sub 2} inverse opals containing Au/Ag nanoparticles two approaches and three template sizes were employed. Self-assembly of template molecules and metal nanoparticles occurred using electrostatic interactions and capillary forces. Both the Bragg diffraction of the photonic crystal and the localized surface plasmon resonance of Au/Ag nanoparticles were detected. - Highlights: • Fabrication methods of silica inverse opals containing metal nanoparticles studied. • Three template sizes used to produce SiO{sub 2} inverse opals with Au/Ag nanoparticles. • PS templates with Au nanoparticles adsorbed used in formation of inverse opals. • Ag particles infiltrated in inverse opals with capillary and electrostatic forces. • Bragg diffractions of IOs and surface plasmon resonances of nanoparticles observed.« less

Computational design and fabrication of core-shell magnetic molecularly imprinted polymer for dispersive micro-solid-phase extraction coupled with high-performance liquid chromatography for the determination of rhodamine 6G.

PubMed

Xie, Jin; Xie, Jie; Deng, Jian; Fang, Xiangfang; Zhao, Haiqing; Qian, Duo; Wang, Hongjuan

2016-06-01

A novel core-shell magnetic nano-adsorbent with surface molecularly imprinted polymer coating was fabricated and then applied to dispersive micro-solid-phase extraction followed by determination of rhodamine 6G using high-performance liquid chromatography. The molecularly imprinted polymer coating was prepared by copolymerization of dopamine and m-aminophenylboronic acid (functional monomers), in the presence of rhodamine 6G (template). The selection of the suitable functional monomers was based on the interaction between different monomers and the template using the density functional theory. The ratios of the monomers to template were further optimized by an OA9 (3(4) ) orthogonal array design. The binding performances of the adsorbent were evaluated by static, kinetic, and selective adsorption experiments. The results reveal that the adsorbent possesses remarkable affinity and binding specificity for rhodamine 6G because of the enhanced Lewis acid-base interaction between the B(Ш) embedded in the imprinted cavities and the template. The nano-adsorbent was successfully applied to dispersive micro-solid-phase extraction coupled to high-performance liquid chromatography for the trace determination of rhodamine 6G in samples with a detection limit of 2.7 nmol/L. Spiked recoveries ranged from 93.0-99.1, 89.5-92.7, and 86.9-105% in river water, matrimony vine and paprika samples, respectively, with relative standard deviations of less than 4.3%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Improvement of Automated Spectral Identification Tool ASERA

NASA Astrophysics Data System (ADS)

Yuan, Hailong; zhang, Yanxia

2015-08-01

The regular survey of Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) has acquired over four millions spectra of celestial objects by the summer of 2014, covering about a third of the whole sky area. More spectra will be obtained as the survey projects (eg. LAMOST, SDSS) keeps going on. To effectively make use of the massive spectral data, various advanced data analysis methods and technologies are in great requirement. ASERA, A Spectrum Eye Recognition Assistant, provides a simple convenient solution for the user to access spectra from LAMOST and SDSS, identify their types (QSO, galaxy, and various types of stars) and estimate their redshifts in an interactive graphic interface. The toolkit is at first especially designed for quasar identification. By shifting the quasar template overlaping the target spectrum interactively, one can easily find out the best broad emission line position and the redshift value. Now, besides the quasar template, various templates for different types of galaxies (early type, later type, starburst, bulge, elliptical and luminous red galaxies) and stars (O, B, A, F, G, K, M, WD, CV, Double Stars and Emission-Line-Objects) are added. We also have developed many new useful functionalities for inspecting and analyzing spectra, such as zooming, line fitting, smoothing and automatic result saving. The target information from input catalogues and data processing result from the pipeline as well as fitting parameters for various types of templates, can be presented at the same time. Several volume processing components are developed to support the cooperation with MySQL database, internet resources and SSAP services. ASERA will be a strong helper for astronomers to recognize spectra.

Engineering Plasmonic Nanocrystal Coupling through Template-Assisted Self-Assembly

NASA Astrophysics Data System (ADS)

Greybush, Nicholas J.

The construction of materials from nanocrystal building blocks represents a powerful new paradigm for materials design. Just as nature's materials orchestrate intricate combinations of atoms from the library of the periodic table, nanocrystal "metamaterials" integrate individual nanocrystals into larger architectures with emergent collective properties. The individual nanocrystal "meta-atoms" that make up these materials are themselves each a nanoscale atomic system with tailorable size, shape, and elemental composition, enabling the creation of hierarchical materials with predesigned structure at multiple length scales. However, an improved fundamental understanding of the interactions among individual nanocrystals is needed in order to translate this structural control into enhanced functionality. The ability to form precise arrangements of nanocrystals and measure their collective properties is therefore essential for the continued development of nanocrystal metamaterials. In this dissertation, we utilize template-assisted self-assembly and spatially-resolved spectroscopy to form and characterize individual nanocrystal oligomers. At the intersection of "top-down" and "bottom-up" nanoscale patterning schemes, template-assisted self-assembly combines the design freedom of lithography with the chemical control of colloidal synthesis to achieve unique nanocrystal configurations. Here, we employ shape-selective templates to assemble new plasmonic structures, including heterodimers of Au nanorods and upconversion phosphors, a series of hexagonally-packed Au nanocrystal oligomers, and triangular formations of Au nanorods. Through experimental analysis and numerical simulation, we elucidate the means through which inter-nanocrystal coupling imparts collective optical properties to the plasmonic assemblies. Our self-assembly and measurement strategy offers a versatile platform for exploring optical interactions in a wide range of material systems and application areas.

Time limits during visual foraging reveal flexible working memory templates.

PubMed

Kristjánsson, Tómas; Thornton, Ian M; Kristjánsson, Árni

2018-06-01

During difficult foraging tasks, humans rarely switch between target categories, but switch frequently during easier foraging. Does this reflect fundamental limits on visual working memory (VWM) capacity or simply strategic choice due to effort? Our participants performed time-limited or unlimited foraging tasks where they tapped stimuli from 2 target categories while avoiding items from 2 distractor categories. These time limits should have no effect if capacity imposes limits on VWM representations but more flexible VWM could allow observers to use VWM according to task demands in each case. We found that with time limits, participants switched more frequently and switch-costs became much smaller than during unlimited foraging. Observers can therefore switch between complex (conjunction) target categories when needed. We propose that while maintaining many complex templates in working memory is effortful and observers avoid this, they can do so if this fits task demands, showing the flexibility of working memory representations used for visual exploration. This is in contrast with recent proposals, and we discuss the implications of these findings for theoretical accounts of working memory. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

PubMed

Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

2002-08-01

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Organic materials as templates for the formation of mesoporous inorganic materials and ordered inorganic nanocomposites

NASA Astrophysics Data System (ADS)

Ziegler, Christopher R.

Hierarchically structured inorganic materials are everywhere in nature. From unicellular aquatic algae such as diatoms to the bones and/or cartilage that comprise the skeletal systems of vertebrates. Complex mechanisms involving site-specific chemistries and precision kinetics are responsible for the formation of such structures. In the synthetic realm, reproduction of even the most basic hierarchical structure effortlessly produced in nature is difficult. However, through the utilization of self-assembling structures or "templates", such as polymers or amphiphilic surfactants, combined with some favorable interaction between a chosen inorganic, the potential exists to imprint an inorganic material with a morphology dictated via synthetic molecular self-assembly. In doing so, a very basic hierarchical structure is formed on the angstrom and nanometer scales. The work presented herein utilizes the self-assembly of either surfactants or block copolymers with the desired inorganic or inorganic precursor to form templated inorganic structures. Specifically, mesoporous silica spheres and copolymer directed calcium phosphate-polymer composites were formed through the co-assembly of an organic template and a precursor to form the desired mesostructured inorganic. For the case of the mesoporous silica spheres, a silica precursor was mixed with cetyltrimethylammonium bromide and cysteamine, a highly effective biomimetic catalyst for the conversion of alkoxysilanes to silica. Through charge-based interactions between anionic silica species and the micelle-forming cationic surfactant, ordered silica structures resulted. The incorporation of a novel, effective catalyst was found to form highly condensed silica spheres for potential application as catalyst supports or an encapsulation media. Ordered calcium phosphate-polymer composites were formed using two routes. Both routes take advantage of hydrogen bonding and ionic interactions between the calcium and phosphate precursors and the self-assembling copolymer template. Some evidence suggests that the copolymer morphology remained in the composite despite the known tendency for calcium phosphates to form highly elongated crystalline structures with time, as is commonly the case for synthetic hydroxyapatites. Such materials have obvious application as bone grafts and bone coatings due, in part, to the osteoconductive nature of calcium phosphate as well as to the mesoporosity generated through the cooperative assembly of the block copolymer and the inorganic. Future work, including potential experiments to determine osteoconductivity of as-prepared composites, is also presented herein.

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

PubMed

Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John T

2015-08-01

Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for HiTS-RAP that can be completed in about a month (8 d hands-on time). This includes the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, HiTS and protein binding with a GAIIx instrument, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, quantitative analysis of RNA on a massively parallel array (RNA-MaP) and RNA Bind-n-Seq (RBNS), for quantitative analysis of RNA-protein interactions.

Clinical validation of a non-heteronormative version of the Social Interaction Anxiety Scale (SIAS).

PubMed

Lindner, Philip; Martell, Christopher; Bergström, Jan; Andersson, Gerhard; Carlbring, Per

2013-12-19

Despite welcomed changes in societal attitudes and practices towards sexual minorities, instances of heteronormativity can still be found within healthcare and research. The Social Interaction Anxiety Scale (SIAS) is a valid and reliable self-rating scale of social anxiety, which includes one item (number 14) with an explicit heteronormative assumption about the respondent's sexual orientation. This heteronormative phrasing may confuse, insult or alienate sexual minority respondents. A clinically validated version of the SIAS featuring a non-heteronormative phrasing of item 14 is thus needed. 129 participants with diagnosed social anxiety disorder, enrolled in an Internet-based intervention trial, were randomly assigned to responding to the SIAS featuring either the original or a novel non-heteronormative phrasing of item 14, and then answered the other item version. Within-subject, correlation between item versions was calculated and the two scores were statistically compared. The two items' correlations with the other SIAS items and other psychiatric rating scales were also statistically compared. Item versions were highly correlated and scores did not differ statistically. The two items' correlations with other measures did not differ statistically either. The SIAS can be revised with a non-heteronormative formulation of item 14 with psychometric equivalence on item and scale level. Implications for other psychiatric instruments with heteronormative phrasings are discussed.

The reverse of social anxiety is not always the opposite: the reverse-scored items of the social interaction anxiety scale do not belong.

PubMed

Rodebaugh, Thomas L; Woods, Carol M; Heimberg, Richard G

2007-06-01

Although well-used and empirically supported, the Social Interaction Anxiety Scale (SIAS) has a questionable factor structure and includes reverse-scored items with questionable utility. Here, using samples of undergraduates and a sample of clients with social anxiety disorder, we extend previous work that opened the question of whether the reverse-scored items belong on the scale. First, we successfully confirmed the factor structure obtained in previous samples. Second, we found the reverse-scored items to show consistently weaker relationships with a variety of comparison measures. Third, we demonstrated that removing the reverse-scored questions generally helps rather than hinders the psychometric performance of the SIAS total score. Fourth, we found that the reverse-scored items show a strong relationship with the normal personality characteristic of extraversion, suggesting that the reverse-scored items may primarily assess extraversion. Given the above results, we suggest investigators consider performing data analyses using only the straightforwardly worded items of the SIAS.

What's in a Topic? Exploring the Interaction between Test-Taker Age and Item Content in High-Stakes Testing

ERIC Educational Resources Information Center

Banerjee, Jayanti; Papageorgiou, Spiros

2016-01-01

The research reported in this article investigates differential item functioning (DIF) in a listening comprehension test. The study explores the relationship between test-taker age and the items' language domains across multiple test forms. The data comprise test-taker responses (N = 2,861) to a total of 133 unique items, 46 items of which were…

Multidimensional Extension of Multiple Indicators Multiple Causes Models to Detect DIF

ERIC Educational Resources Information Center

Lee, Soo; Bulut, Okan; Suh, Youngsuk

2017-01-01

A number of studies have found multiple indicators multiple causes (MIMIC) models to be an effective tool in detecting uniform differential item functioning (DIF) for individual items and item bundles. A recently developed MIMIC-interaction model is capable of detecting both uniform and nonuniform DIF in the unidimensional item response theory…

A focus on polarity: Investigating the role of orientation cues in mediating student performance on mRNA synthesis tasks in an introductory cell and molecular biology course.

PubMed

Olimpo, Jeffrey T; Quijas, Daniel A; Quintana, Anita M

2017-11-01

The central dogma has served as a foundational model for information flow, exchange, and storage in the biological sciences for several decades. Despite its continued importance, however, recent research suggests that novices in the domain possess several misconceptions regarding the aforementioned processes, including those pertaining specifically to the formation of messenger ribonucleic acid (mRNA) transcripts. In the present study, we sought to expand upon these observations through exploration of the influence of orientation cues on students' aptitude at synthesizing mRNAs from provided deoxyribonucleic acid (DNA) template strands. Data indicated that participants (n = 45) were proficient at solving tasks of this nature when the DNA template strand and the mRNA molecule were represented in an antiparallel orientation. In contrast, participants' performance decreased significantly on items in which the mRNA was depicted in a parallel orientation relative to the DNA template strand. Furthermore, participants' Grade Point Average, self-reported confidence in understanding the transcriptional process, and spatial ability were found to mediate their performance on the mRNA synthesis tasks. Collectively, these data reaffirm the need for future research and pedagogical interventions designed to enhance students' comprehension of the central dogma in a manner that makes transparent its relevance to real-world scientific phenomena. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):501-508, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.

PubMed

Djokic-Petrovic, Marija; Cvjetkovic, Vladimir; Yang, Jeremy; Zivanovic, Marko; Wild, David J

2017-09-20

There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel "similar data items detection" algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust.

Fissile interrogation using gamma rays from oxygen

DOEpatents

Smith, Donald; Micklich, Bradley J.; Fessler, Andreas

2004-04-20

The subject apparatus provides a means to identify the presence of fissionable material or other nuclear material contained within an item to be tested. The system employs a portable accelerator to accelerate and direct protons to a fluorine-compound target. The interaction of the protons with the fluorine-compound target produces gamma rays which are directed at the item to be tested. If the item to be tested contains either a fissionable material or other nuclear material the interaction of the gamma rays with the material contained within the test item with result in the production of neutrons. A system of neutron detectors is positioned to intercept any neutrons generated by the test item. The results from the neutron detectors are analyzed to determine the presence of a fissionable material or other nuclear material.

MTA Computer Based Evaluation System.

ERIC Educational Resources Information Center

Brenner, Lisa P.; And Others

The MTA PLATO-based evaluation system, which has been implemented by a consortium of schools of medical technology, is designed to be general-purpose, modular, data-driven, and interactive, and to accommodate other national and local item banks. The system provides a comprehensive interactive item-banking system in conjunction with online student…

ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery.

PubMed

Partl, Christian; Lex, Alexander; Streit, Marc; Strobelt, Hendrik; Wassermann, Anne-Mai; Pfister, Hanspeter; Schmalstieg, Dieter

2014-12-01

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets. At its core ConTour lists all items of each dataset in a column. Relationships between the columns are revealed through interaction: selecting one or multiple items in one column highlights and re-sorts the items in other columns. Filters based on relationships enable drilling down into the large data space. To identify interesting items in the first place, ConTour employs advanced sorting strategies, including strategies based on connectivity strength and uniqueness, as well as sorting based on item attributes. ConTour also introduces interactive nesting of columns, a powerful method to show the related items of a child column for each item in the parent column. Within the columns, ConTour shows rich attribute data about the items as well as information about the connection strengths to other datasets. Finally, ConTour provides a number of detail views, which can show items from multiple datasets and their associated data at the same time. We demonstrate the utility of our system in case studies conducted with a team of chemical biologists, who investigate the effects of chemical compounds on cells and need to understand the underlying mechanisms.

Exploring problem solving strategies on multiple-choice science items: Comparing native Spanish-speaking English Language Learners and mainstream monolinguals

NASA Astrophysics Data System (ADS)

Kachchaf, Rachel Rae

The purpose of this study was to compare how English language learners (ELLs) and monolingual English speakers solved multiple-choice items administered with and without a new form of testing accommodation---vignette illustration (VI). By incorporating theories from second language acquisition, bilingualism, and sociolinguistics, this study was able to gain more accurate and comprehensive input into the ways students interacted with items. This mixed methods study used verbal protocols to elicit the thinking processes of thirty-six native Spanish-speaking English language learners (ELLs), and 36 native-English speaking non-ELLs when solving multiple-choice science items. Results from both qualitative and quantitative analyses show that ELLs used a wider variety of actions oriented to making sense of the items than non-ELLs. In contrast, non-ELLs used more problem solving strategies than ELLs. There were no statistically significant differences in student performance based on the interaction of presence of illustration and linguistic status or the main effect of presence of illustration. However, there were significant differences based on the main effect of linguistic status. An interaction between the characteristics of the students, the items, and the illustrations indicates considerable heterogeneity in the ways in which students from both linguistic groups think about and respond to science test items. The results of this study speak to the need for more research involving ELLs in the process of test development to create test items that do not require ELLs to carry out significantly more actions to make sense of the item than monolingual students.

On the Relationship Between Tooth Shape and Masticatory Efficiency: A Finite Element Study.

PubMed

Berthaume, Michael A

2016-05-01

Dental topography has successfully linked disparate tooth shapes to distinct dietary categories, but not to masticatory efficiency. Here, the relationship between four dental topographic metrics and brittle food item breakdown efficiency during compressive biting was investigated using a parametric finite element model of a bunodont molar. Food item breakdown efficiency was chosen to represent masticatory efficiency as it isolated tooth-food item interactions, where most other categories of masticatory efficiency include several aspects of the masticatory process. As relative food item size may affect the presence/absence of any relationship, four isometrically scaled, hemispherical, proxy food items were considered. Topographic metrics were uncorrelated to food item breakdown efficiency irrespective of relative food item size, and dental topographic metrics were largely uncorrelated to one another. The lack of a correlation between topographic metrics and food item breakdown efficiency is not unexpected as not all food items break down in the same manner (e.g., nuts are crushed, leaves are sheared), and only one food item shape was considered. In addition, food item breakdown efficiency describes tooth-food item interactions and requires location and shape specific information, which are absent from dental topographic metrics. This makes it unlikely any one efficiency metric will be correlated to all topographic metrics. These results emphasize the need to take into account how food items break down during biting, ingestion, and mastication when investigating the mechanical relationship between food item shape, size, mechanical properties, and breakdown, and tooth shape. © 2016 Wiley Periodicals, Inc.

Student Perceptions of Chemistry Laboratory Learning Environments, Student-Teacher Interactions and Attitudes in Secondary School Gifted Education Classes in Singapore

NASA Astrophysics Data System (ADS)

Lang, Quek Choon; Wong, Angela F. L.; Fraser, Barry J.

2005-09-01

This study investigated the chemistry laboratory classroom environment, teacher-student interactions and student attitudes towards chemistry among 497 gifted and non-gifted secondary-school students in Singapore. The data were collected using the 35-item Chemistry Laboratory Environment Inventory (CLEI), the 48-item Questionnaire on Teacher Interaction (QTI) and the 30-item Questionnaire on Chemistry-Related Attitudes (QOCRA). Results supported the validity and reliability of the CLEI and QTI for this sample. Stream (gifted versus non-gifted) and gender differences were found in actual and preferred chemistry laboratory classroom environments and teacher-student interactions. Some statistically significant associations of modest magnitude were found between students' attitudes towards chemistry and both the laboratory classroom environment and the interpersonal behaviour of chemistry teachers. Suggestions for improving chemistry laboratory classroom environments and the teacher-student interactions for gifted students are provided.

CAD system for footwear design based on whole real 3D data of last surface

NASA Astrophysics Data System (ADS)

Song, Wanzhong; Su, Xianyu

2000-10-01

Two major parts of application of CAD in footwear design are studied: the development of last surface; computer-aided design of planar shoe-template. A new quasi-experiential development algorithm of last surface based on triangulation approximation is presented. This development algorithm consumes less time and does not need any interactive operation for precisely development compared with other development algorithm of last surface. Based on this algorithm, a software, SHOEMAKERTM, which contains computer aided automatic measurement, automatic development of last surface and computer aide design of shoe-template has been developed.

Band gap variations in ferritin-templated nanocrystals

NASA Astrophysics Data System (ADS)

Colton, John; Erickson, Stephen; Smith, Trevor; Watt, Richard

2014-03-01

Ferritin is a 12 nm diameter protein shell with an 8 nm ``cage'' inside that can be used as a template for nanoparticle formation. The native particle is an iron oxide, ferrihydrite, but can be altered or replaced. We have used optical absorption spectroscopy to study the band gap of the ferrihydrite nanoparticles as they age (and become more crystalline), and as they respond to surface interactions with ions in solution. We will also present results of particle composition variations due to incorporation of oxo-anions into the interior of the nanoparticles and substitution of iron with other metals such as cobalt and manganese.

RNA Study Using DNA Nanotechnology.

PubMed

Tadakuma, Hisashi; Masubuchi, Takeya; Ueda, Takuya

2016-01-01

Transcription is one of the fundamental steps of gene expression, where RNA polymerases (RNAPs) bind to their template genes and make RNAs. In addition to RNAP and the template gene, many molecules such as transcription factors are involved. The interaction and the effect of these factors depend on the geometry. Molecular layout of these factors, RNAP and gene is thus important. DNA nanotechnology is a promising technology that allows controlling of the molecular layout in the range of nanometer to micrometer scale with nanometer resolution; thus, it is expected to expand the RNA study beyond the current limit. Copyright © 2016 Elsevier Inc. All rights reserved.

The application of CuAAC 'click' chemistry to catenane and rotaxane synthesis.

PubMed

Hänni, Kevin D; Leigh, David A

2010-04-01

The copper(I)-catalysed azide-alkyne cycloaddition (the CuAAC 'click' reaction) is proving to be a powerful new tool for the construction of mechanically interlocked molecular-level architectures. The reaction is highly selective for the functional groups involved (terminal alkynes and azides) and the experimental conditions are mild and compatible with the weak and reversible intermolecular interactions generally used to template the assembly of interlocked structures. Since the CuAAC reaction was introduced as a means of making rotaxanes by an 'active template' mechanism in 2006, it has proven effective for the synthesis of numerous different types of rotaxanes, catenanes and molecular shuttles by passive as well as active template strategies. Mechanistic insights into the CuAAC reaction itself have been provided by unexpected results encountered during the preparation of rotaxanes. In this tutorial review we highlight the rapidly increasing utility and future potential of the CuAAC reaction in mechanically interlocked molecule synthesis.

Nanospace-Mediated Self-Organization of Nanoparticles in Flexible Porous Polymer Templates.

PubMed

Kuroda, Yoshiyuki; Muto, Itaru; Shimojima, Atsushi; Wada, Hiroaki; Kuroda, Kazuyuki

2017-09-12

Self-organization is a fundamental process for the construction of complex hierarchically ordered nanostructures, which are widespread in biological systems. However, precise control of size, shape, and surface properties is required for self-organization of nanoparticles. Here, we demonstrate a novel self-organization phenomenon mediated by flexible nanospaces in templates. Inorganic nanoparticles (e.g., silica, zirconia, and titania) are deposited in porous polymer thin films with randomly distributed pores on the surface, leaving a partially filled nanospace in each pore. Heating at temperatures beyond the glass transition temperature of the template leads to self-organization of the inorganic nanoparticles into one-dimensional chainlike networks. The self-organization is mediated by the deformation and fusion of the residual nanospaces, and it can be rationally controlled by sequential heat treatments. These results show that a nanospace, defined by the nonexistence of matter, interacts indirectly with matter and can be used as a component of self-organization systems.

Design reflowable digital book template

NASA Astrophysics Data System (ADS)

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.

Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

NASA Astrophysics Data System (ADS)

Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

2013-12-01

Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

Templated synthesis of copper(II) azacyclam complexes using urea as a locking fragment and their metal-enhanced binding tendencies towards anions.

PubMed

Boiocchi, Massimo; Fabbrizzi, Luigi; Garolfi, Mauro; Licchelli, Maurizio; Mosca, Lorenzo; Zanini, Cristina

2009-10-26

Copper(II) azacyclam complexes 3(2+) and 4(2+) were obtained through a metal-templated procedure involving the pertinent open-chain tetramine, formaldehyde and a phenylurea derivative as a locking fragment. Both metal complexes can establish interactions with anions through the metal centre and the amide NH group. Equilibrium studies in DMSO by a spectrophotometric titration technique were carried out to assess the affinity of 3(2+) and 4(2+) towards anions. While the NH group of an amide model compound and the metal centre of the plain Cu(II)(azacyclam)(2+) complex do not interact at all with anions, 3(2+) and 4(2+) establish strong interactions with oxo anions, profiting from a pronounced cooperative effect. In particular, 1) they form stable 1:1 and 1:2 complexes with H(2)PO(4) (-) ions in a stepwise mode with both hydrogen-bonding and metal-ligand interactions, and 2) in the presence of CH(3)COO(-), they undergo deprotonation of the amido NH group and thus profit from axial coordination of the partially negatively charged carbonyl oxygen atom in a scorpionate binding mode.

Two Pathways to Stimulus Encoding in Category Learning?

PubMed Central

Davis, Tyler; Love, Bradley C.; Maddox, W. Todd

2008-01-01

Category learning theorists tacitly assume that stimuli are encoded by a single pathway. Motivated by theories of object recognition, we evaluate a dual-pathway account of stimulus encoding. The part-based pathway establishes mappings between sensory input and symbols that encode discrete stimulus features, whereas the image-based pathway applies holistic templates to sensory input. Our experiments use rule-plus-exception structures in which one exception item in each category violates a salient regularity and must be distinguished from other items. In Experiment 1, we find that discrete representations are crucial for recognition of exceptions following brief training. Experiments 2 and 3 involve multi-session training regimens designed to encourage either part or image-based encoding. We find that both pathways are able to support exception encoding, but have unique characteristics. We speculate that one advantage of the part-based pathway is the ability to generalize across domains, whereas the image-based pathway provides faster and more effortless recognition. PMID:19460948

Quantitative Assessment of RNA-Protein Interactions with High Throughput Sequencing - RNA Affinity Profiling (HiTS-RAP)

PubMed Central

Ozer, Abdullah; Tome, Jacob M.; Friedman, Robin C.; Gheba, Dan; Schroth, Gary P.; Lis, John T.

2016-01-01

Because RNA-protein interactions play a central role in a wide-array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the High Throughput Sequencing-RNA Affinity Profiling (HiTS-RAP) assay, which couples sequencing on an Illumina GAIIx with the quantitative assessment of one or several proteins’ interactions with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of EGFP and NELF-E proteins with their corresponding canonical and mutant RNA aptamers. Here, we provide a detailed protocol for HiTS-RAP, which can be completed in about a month (8 days hands-on time) including the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, high-throughput sequencing and protein binding with GAIIx, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, RNA-MaP and RBNS. A successful HiTS-RAP experiment provides the sequence and binding curves for approximately 200 million RNAs in a single experiment. PMID:26182240

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

PubMed

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.

Engineering fluorescent poly(dopamine) capsules.

PubMed

Chen, Xi; Yan, Yan; Müllner, Markus; van Koeverden, Martin P; Noi, Ka Fung; Zhu, Wei; Caruso, Frank

2014-03-18

The recent development of poly(dopamine) (PDA) capsules provides new opportunities for their application in biology and medicine. To advance the biomedical application of PDA capsules, strategies that enable the preparation of fluorescently labeled PDA (F-PDA) capsules are required, as this will allow evaluation of their cellular interactions using a range of fluorescence-based techniques. Herein, we report a facile approach for the fabrication of F-PDA capsules via the polymerization of dopamine (DA) on sacrificial templates in the presence of hydrogen peroxide (H2O2). F-PDA capsules with well-defined sizes are prepared by templating different organic and inorganic particles. The resulting F-PDA capsules show negligible cytotoxicity in HeLa cells after incubation for 48 h. We also demonstrate visualization of the F-PDA capsules following internalization by HeLa cells using conventional fluorescence microscopy, en route toward detailed investigations on their biological interactions.

Fabrication of nanocomposites by collagen templated synthesis of layered double hydroxides assisted by an acrylic silane coupling agent

NASA Astrophysics Data System (ADS)

Sun, Yanqing; Zhou, Yuming; Wang, Zhiqiang; Ye, Xiaoyun

2009-02-01

The purpose of this study was to control the fabrication of nanocomposites at the nanoscale interface by collagen templated synthesis of Zn-Al layered double hydroxides (LDHs) assisted by γ-methacryloxypropyl trimethoxy silane (KH570) with further treatment of graft polymerization. The results show that collagen directs the growth of LDHs into curved nanorods by length of 300 nm in perfect consistency with collagen chain in both the size and flexility under the essential hydrophobic environment on the solid surface provided by KH570. The nanorods are aggregated into thin curved platelets due to strong interaction between collagen molecules themselves and strong interaction between collagen and LDH sheets. By further treatment of graft polymerization, the adjacent curved platelets encircle into numerous hollows via chemical linkage, achieving polyporous nanocomposites. Nanohybrid materials with this structure are especially interesting for applications as biosensors or supported catalysis.

Dentist-assistant communication style: perceived gender differences in The Netherlands and Northern Ireland.

PubMed

Gorter, Ronald C; Freeman, Ruth

2005-04-01

To assess communication style differences with the (female) dental assistant, as perceived by male and female dentists. Data were collected from 216 Dutch (male: 99; female: 117) and 261 Northern Irish (male: 135; female: 126) dentists (overall response rate: 60%). Respondents filled in a self-report questionnaire (one follow-up mailing), with 22 items on staff communication style. Using principal component analysis, four distinguishable factors could be extracted: businesslike leadership style (seven items, Cronbach's alpha = 0.87), friendly leadership style (seven items, alpha = 0.87), professional interacting style (four items, alpha = 0.83) and gender interacting style (four items, alpha = 0.83). manova indicated a main effect for gender [F(8,946) = 10.905, P < 0.001] and for country [F(4,474) =4.197, P = 0.002] on the communication style scales. Male dentists, compared with female colleagues, showed higher mean scores on businesslike leadership style and gender interacting style, whereas female dentists showed higher mean scores on friendly leadership style and professional interacting style. Dutch dentists showed higher mean scores on friendly leadership style and professional interacting style than their Northern Irish colleagues. No interaction effect between gender and country was found. Dentist's age and length of assistant's employment (in years) partly explained differences in means. Male and female dentists perceive their communication with the assistant differently; male dentists tend to be influenced by the gender differences, female dentists by striving for friendliness. Some country differences were found. Increasing influx of young female dentists underlines the relevance of this topic in dental education and for future research.

Item Response Models for Local Dependence among Multiple Ratings

ERIC Educational Resources Information Center

Wang, Wen-Chung; Su, Chi-Ming; Qiu, Xue-Lan

2014-01-01

Ratings given to the same item response may have a stronger correlation than those given to different item responses, especially when raters interact with one another before giving ratings. The rater bundle model was developed to account for such local dependence by forming multiple ratings given to an item response as a bundle and assigning…

Comparing short forms of the Social Interaction Anxiety Scale and the Social Phobia Scale.

PubMed

Carleton, R Nicholas; Thibodeau, Michel A; Weeks, Justin W; Teale Sapach, Michelle J N; McEvoy, Peter M; Horswill, Samantha C; Heimberg, Richard G

2014-12-01

The Social Interaction Anxiety Scale (SIAS) and the Social Phobia Scale (SPS; Mattick & Clarke, 1998) are companion scales developed to measure anxiety in social interaction and performance situations, respectively. The measures have strong discriminant and convergent validity; however, their factor structures remain debated, and furthermore, the combined administration length (i.e., 39 items) can be prohibitive for some settings. There have been 4 attempts to assess the factor structures of the scales and reduce the item content: the 14-item Social Interaction Phobia Scale (SIPS; Carleton et al., 2009), the 12-item SIAS-6/SPS-6 (Peters, Sunderland, Andrews, Rapee, & Mattick, 2012), the 21-item abbreviated SIAS/SPS (ASIAS/ASPS; Kupper & Denollet, 2012), and the 12-item Readability SIAS and SPS (RSIAS/RSPS; Fergus, Valentiner, McGrath, Gier-Lonsway, & Kim, 2012). The current study compared the short forms on (a) factor structure, (b) ability to distinguish between clinical and non-clinical populations, (c) sensitivity to change following therapy, and (d) convergent validity with related measures. Participants included 3,607 undergraduate students (55% women) and 283 patients with social anxiety disorder (43% women). Results of confirmatory factor analyses, sensitivity analyses, and correlation analyses support the robust utility of items in the SIPS and the SPS-6 and SIAS-6 relative to the other short forms; furthermore, the SIPS and the SPS-6 and SIAS-6 were also supported by convergent validity analyses within the undergraduate sample. The RSIAS/RSPS and the ASIAS/ASPS were least supported, based on the current results and the principle of parsimony. Accordingly, researchers and clinicians should consider carefully which of the short forms will best suit their needs. (c) 2014 APA, all rights reserved.

Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues.

PubMed

Killelea, Tom; Ghosh, Samantak; Tan, Samuel S; Heslop, Pauline; Firbank, Susan J; Kool, Eric T; Connolly, Bernard A

2010-07-13

Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describe uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at position 2 explains the stimulation of the polymerase 3'-5' proofreading exonuclease, observed with deaminated bases at this location. A beta-hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double-stranded DNA. This denatures the two complementary primer bases and directs the resulting 3' single-stranded extension toward the exonuclease active site. Finally, the relative importance of hydrogen bonding and shape fit in determining selectivity for deaminated bases has been examined using nonpolar isosteres. Affinity for both 2,4-difluorobenzene and fluorobenzimidazole, non-hydrogen bonding shape mimics of uracil and hypoxanthine, respectively, is strongly diminished, suggesting polar protein-base contacts are important. However, residual interaction with 2,4-difluorobenzene is seen, confirming a role for shape recognition.

Lean thinking transformation of the unsedated upper gastrointestinal endoscopy pathway improves efficiency and is associated with high levels of patient satisfaction.

PubMed

Hydes, Theresa; Hansi, Navjyot; Trebble, Timothy M

2012-01-01

Upper gastrointestinal (UGI) endoscopy is a routine healthcare procedure with a defined patient pathway. The objective of this study was to redesign this pathway for unsedated patients using lean thinking transformation to focus on patient-derived value-adding steps, remove waste and create a more efficient process. This was to form the basis of a pathway template that was transferrable to other endoscopy units. A literature search of patient expectations for UGI endoscopy identified patient-derived value. A value stream map was created of the current pathway. The minimum and maximum time per step, bottlenecks and staff-staff interactions were recorded. This information was used for service transformation using lean thinking. A patient pathway template was created and implemented into a secondary unit. Questionnaire studies were performed to assess patient satisfaction. In the primary unit the patient pathway reduced from 19 to 11 steps with a reduction in the maximum lead time from 375 to 80 min following lean thinking transformation. The minimum value/lead time ratio increased from 24% to 49%. The patient pathway was redesigned as a 'cellular' system with minimised patient and staff travelling distances, waiting times, paperwork and handoffs. Nursing staff requirements reduced by 25%. Patient-prioritised aspects of care were emphasised with increased patient-endoscopist interaction time. The template was successfully introduced into a second unit with an overall positive patient satisfaction rating of 95%. Lean thinking transformation of the unsedated UGI endoscopy pathway results in reduced waiting times, reduced staffing requirements and improved patient flow and can form the basis of a pathway template which may be successfully transferred into alternative endoscopy environments with high levels of patient satisfaction.

Clinical staging and operative reporting for multi-institutional trials in head and neck squamous cell carcinoma.

PubMed

Weymuller, E A

1997-12-01

A Strategic Planning Conference (jointly supported by NCI and NIDCD) was convened to consider potential improvements in surgical patient data for multi-institutional trials. The thesis underlying this project is that inadequacies in staging, pretreatment patient stratification, and the details of surgical resection may have obscured the detection of treatment effect. The goals of this project were multiple: (1) to consider the utility of new clinical stratification variables, (2) to increase the precision of tumor staging, and (3) to improve operative reporting for multi-institutional trials in head and neck cancer. The conference attendees came to a number of important conclusions: (1) TNM status is inadequate for describing head and neck cancer in a multi-institutional trial setting. A detailed anatomic reporting scheme is proposed; (2) comorbidity measures should be included as patient descriptors, especially those that meet the criteria "definitely important and easy to obtain"; (3) surgical reporting in multi-institutional trials should use a format that is compatible with computer analysis and use the same items as the revised (anatomic) staging system; (4) the surgeon should be personally responsible for data coding and should interact directly with the pathologist in marking the surgical specimen; (5) pathologic reporting should use an anatomic template identical to the staging and operative reporting formats.

Developing Teaching Strategies in the EHR Era: A Survey of GME Experts.

PubMed

Atwater, Amber R; Rudd, Mariah; Brown, Audrey; Wiener, John S; Benjamin, Robert; Lee, W Robert; Rosdahl, Jullia A

2016-10-01

There is limited information on the impact of widespread adoption of the electronic health record (EHR) on graduate medical education (GME). To identify areas of consensus by education experts, where the use of EHR impacts GME, with the goal of developing strategies and tools to enhance GME teaching and learning in the EHR environment. Information was solicited from experienced US physician educators who use EPIC EHR following 3 steps: 2 rounds of online surveys using the Delphi technique, followed by telephone interviews. The survey contained 3 stem questions and 52 items with Likert-scale responses. Consensus was defined by predetermined cutoffs. A second survey reassessed items for which consensus was not initially achieved. Common themes to improve GME in settings with an EHR were compiled from the telephone interviews. The panel included 19 physicians in 15 states in Round 1, 12 in Round 2, and 10 for the interviews. Ten items were found important for teaching and learning: balancing focus on EHR documentation with patient engagement achieved 100% consensus. Other items achieving consensus included adequate learning time, balancing EHR data with verbal history and physical examination, communicating clinical thought processes, hands-on EHR practice, minimizing data repetition, and development of shortcuts and templates. Teaching strategies incorporating both online software and face-to-face solutions were identified during the interviews. New strategies are needed for effective teaching and learning of residents and fellows, capitalizing on the potential of the EHR, while minimizing any unintended negative impact on medical education.

Kinetic Basis of Nucleotide Selection Employed by a Protein Template-Dependent DNA Polymerase†

PubMed Central

Brown, Jessica A.; Fowler, Jason D.; Suo, Zucai

2010-01-01

Rev1, a Y-family DNA polymerase, contributes to spontaneous and DNA damage-induced mutagenic events. In this paper, we have employed pre-steady state kinetic methodology to establish a kinetic basis for nucleotide selection by human Rev1, a unique nucleotidyl transferase that uses a protein template-directed mechanism to preferentially instruct dCTP incorporation. This work demonstrated that the high incorporation efficiency of dCTP is dependent on both substrates: an incoming dCTP and a templating base dG. The extremely low base substitution fidelity of human Rev1 (100 to 10-5) was due to the preferred misincorporation of dCTP with templating bases dA, dT, and dC over correct dNTPs. Using non-natural nucleotide analogs, we showed that hydrogen bonding interactions between residue R357 of human Rev1 and an incoming dNTP are not essential for DNA synthesis. Lastly, human Rev1 discriminates between ribonucleotides and deoxyribonucleotides mainly by reducing the rate of incorporation, and the sugar selectivity of human Rev1 is sensitive to both the size and orientation of the 2′-substituent of a ribonucleotide. PMID:20518555

An In Vitro RNA Synthesis Assay for Rabies Virus Defines Ribonucleoprotein Interactions Critical for Polymerase Activity.

PubMed

Morin, Benjamin; Liang, Bo; Gardner, Erica; Ross, Robin A; Whelan, Sean P J

2017-01-01

We report an in vitro RNA synthesis assay for the RNA-dependent RNA polymerase (RdRP) of rabies virus (RABV). We expressed RABV large polymerase protein (L) in insect cells from a recombinant baculovirus vector and the phosphoprotein cofactor (P) in Escherichia coli and purified the resulting proteins by affinity and size exclusion chromatography. Using chemically synthesized short RNA corresponding to the first 19 nucleotides (nt) of the rabies virus genome, we demonstrate that L alone initiates synthesis on naked RNA and that P serves to enhance the initiation and processivity of the RdRP. The L-P complex lacks full processivity, which we interpret to reflect the lack of the viral nucleocapsid protein (N) on the template. Using this assay, we define the requirements in P for stimulation of RdRP activity as residues 11 to 50 of P and formally demonstrate that ribavirin triphosphate (RTP) inhibits the RdRP. By comparing the properties of RABV RdRP with those of the related rhabdovirus, vesicular stomatitis virus (VSV), we demonstrate that both polymerases can copy the heterologous promoter sequence. The requirements for engagement of the N-RNA template of VSV by its polymerase are provided by the C-terminal domain (CTD) of P. A chimeric RABV P protein in which the oligomerization domain (OD) and the CTD were replaced by those of VSV P stimulated RABV RdRP activity on naked RNA but was insufficient to permit initiation on the VSV N-RNA template. This result implies that interactions between L and the template N are also required for initiation of RNA synthesis, extending our knowledge of ribonucleoprotein interactions that are critical for gene expression. The current understanding of the structural and functional significance of the components of the rabies virus replication machinery is incomplete. Although structures are available for the nucleocapsid protein in complex with RNA, and also for portions of P, information on both the structure and function of the L protein is lacking. This study reports the expression and purification of the full-length L protein of RABV and the characterization of its RdRP activity in vitro The study provides a new assay that has utility for screening inhibitors and understanding their mechanisms of action, as well as defining new interactions that are required for RdRP activity. Copyright © 2016 American Society for Microbiology.

Accuracy and Variability of Item Parameter Estimates from Marginal Maximum a Posteriori Estimation and Bayesian Inference via Gibbs Samplers

ERIC Educational Resources Information Center

Wu, Yi-Fang

2015-01-01

Item response theory (IRT) uses a family of statistical models for estimating stable characteristics of items and examinees and defining how these characteristics interact in describing item and test performance. With a focus on the three-parameter logistic IRT (Birnbaum, 1968; Lord, 1980) model, the current study examines the accuracy and…

Rapid Forgetting Results From Competition Over Time Between Items in Visual Working Memory

PubMed Central

2016-01-01

Working memory is now established as a fundamental cognitive process across a range of species. Loss of information held in working memory has the potential to disrupt many aspects of cognitive function. However, despite its significance, the mechanisms underlying rapid forgetting remain unclear, with intense recent debate as to whether it is interference between stored items that leads to loss of information or simply temporal decay. Here we show that both factors are essential and interact in a highly specific manner. Although a single item can be maintained in memory with high fidelity, multiple items compete in working memory, progressively degrading each other’s representations as time passes. Specifically, interaction between items is associated with both worsening precision and increased reporting errors of object features over time. Importantly, during the period of maintenance, although items are no longer visible, maintenance resources can be selectively redeployed to protect the probability to recall the correct feature and the precision with which cued items can be recalled, as if it was the only item in memory. These findings reveal that the biased competition concept could be applied not only to perceptual processes but also to active maintenance of working memory representations over time. PMID:27668485

Crisis checklists for in-hospital emergencies: expert consensus, simulation testing and recommendations for a template determined by a multi-institutional and multi-disciplinary learning collaborative.

PubMed

Subbe, Christian P; Kellett, John; Barach, Paul; Chaloner, Catriona; Cleaver, Hayley; Cooksley, Tim; Korsten, Erik; Croke, Eilish; Davis, Elinor; De Bie, Ashley Jr; Durham, Lesley; Hancock, Chris; Hartin, Jilian; Savijn, Tracy; Welch, John

2017-05-08

'Failure to rescue' of hospitalized patients with deteriorating physiology on general wards is caused by a complex array of organisational, technical and cultural failures including a lack of standardized team and individual expected responses and actions. The aim of this study using a learning collaborative method was to develop consensus recomendations on the utility and effectiveness of checklists as training and operational tools to assist in improving the skills of general ward staff on the effective rescue of patients with abnormal physiology. A scoping study of the literature was followed by a multi-institutional and multi-disciplinary international learning collaborative. We sought to achieve a consensus on procedures and clinical simulation technology to determine the requirements, develop and test a safe using a checklist template that is rapidly accessible to assist in emergency management of common events for general ward use. Safety considerations about deteriorating patients were agreed upon and summarized. A consensus was achieved among an international group of experts on currently available checklist formats performing poorly in simulation testing as first responders in general ward clinical crises. The Crisis Checklist Collaborative ratified a consensus template for a general ward checklist that provides a list of issues for first responders to address (i.e. 'Check In'), a list of prompts regarding common omissions (i.e. 'Stop & Think'), and, a list of items required for the safe "handover" of patients that remain on the general ward (i.e. 'Check Out'). Simulation usability assessment of the template demonstrated feasibility for clinical management of deteriorating patients. Emergency checklists custom-designed for general ward patients have the potential to guide the treatment speed and reliability of responses for emergency management of patients with abnormal physiology while minimizing the risk of adverse events. Interventional trials are needed.

Testing the Effects of Interactive Courseware Template for the Learning of History among Form One Students

ERIC Educational Resources Information Center

bin Mohamad, Rossafri; Muninday, Balakrishnan; Govindasamy, Malliga

2010-01-01

This article presents a study on the use of multimedia technology for the teaching of Form (Grade) One history, which is a form of narrative subject in nature. Specifically, it is to study the viability of multimedia materials in supporting active learning for subjects which are in narrative form. Due to the scarcity of interactive multimedia…

Controllable synthesis of mesoporous carbon nanospheres and Fe-N/carbon nanospheres as efficient oxygen reduction electrocatalysts

NASA Astrophysics Data System (ADS)

Wei, Jing; Liang, Yan; Zhang, Xinyi; Simon, George P.; Zhao, Dongyuan; Zhang, Jin; Jiang, Sanping; Wang, Huanting

2015-03-01

The synthesis of mesoporous carbon nanospheres (MCNs), especially with diameters below 200 nm remains a great challenge due to weak interactions between the carbon precursors and soft templates, as well as the uncontrollable cross-linking rate of carbon precursors. Herein, we demonstrate a simple acid-assisted, hydrothermal synthesis approach to synthesizing such uniform MCNs with well controlled diameters ranging from 20 to 150 nm under highly acidic conditions (2 M HCl). Both the carbon precursor and the template are partly protonated under such conditions and show additional Coulombic interactions with chloride ions (acts as mediators). This kind of enhanced interaction is similar to that of the ``I+X-S+'' mechanism in the synthesis of mesoporous metal oxide, which can effectively retard the cross-linking rate of resol molecules and avoid macroscopic phase separation during the hydrothermal synthesis. Due to their uniform spherical morphology, small diameter, and high surface areas, MCNs can be modified with Fe and N species via impregnation of cheap precursors (ferric nitrate and dicyandiamide), which are further converted into nonprecious electrocatalysts for oxygen reduction reactions. The resulting Fe-N/MCNs exhibit high catalytic activities, long-term stability and improved methanol tolerance under alkaline conditions, which can be potentially used in direct methanol fuel cells and metal-air batteries.The synthesis of mesoporous carbon nanospheres (MCNs), especially with diameters below 200 nm remains a great challenge due to weak interactions between the carbon precursors and soft templates, as well as the uncontrollable cross-linking rate of carbon precursors. Herein, we demonstrate a simple acid-assisted, hydrothermal synthesis approach to synthesizing such uniform MCNs with well controlled diameters ranging from 20 to 150 nm under highly acidic conditions (2 M HCl). Both the carbon precursor and the template are partly protonated under such conditions and show additional Coulombic interactions with chloride ions (acts as mediators). This kind of enhanced interaction is similar to that of the ``I+X-S+'' mechanism in the synthesis of mesoporous metal oxide, which can effectively retard the cross-linking rate of resol molecules and avoid macroscopic phase separation during the hydrothermal synthesis. Due to their uniform spherical morphology, small diameter, and high surface areas, MCNs can be modified with Fe and N species via impregnation of cheap precursors (ferric nitrate and dicyandiamide), which are further converted into nonprecious electrocatalysts for oxygen reduction reactions. The resulting Fe-N/MCNs exhibit high catalytic activities, long-term stability and improved methanol tolerance under alkaline conditions, which can be potentially used in direct methanol fuel cells and metal-air batteries. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00331h

Method of data mining including determining multidimensional coordinates of each item using a predetermined scalar similarity value for each item pair

DOEpatents

Meyers, Charles E.; Davidson, George S.; Johnson, David K.; Hendrickson, Bruce A.; Wylie, Brian N.

1999-01-01

A method of data mining represents related items in a multidimensional space. Distance between items in the multidimensional space corresponds to the extent of relationship between the items. The user can select portions of the space to perceive. The user also can interact with and control the communication of the space, focusing attention on aspects of the space of most interest. The multidimensional spatial representation allows more ready comprehension of the structure of the relationships among the items.

Effect of length and location of edentulous area on the accuracy of prosthetic treatment plan incorporation into cone-beam computed tomography scans.

PubMed

Jamjoom, Faris Z; Kim, Do-Gyoon; Lee, Damian J; McGlumphy, Edwin A; Yilmaz, Burak

2018-02-05

Effects of length and location of the edentulous area on the accuracy of prosthetic treatment plan incorporation into cone-beam computed tomography (CBCT) scans has not been investigated. To evaluate the effect of length and location of the edentulous area on the accuracy of prosthetic treatment plan incorporation into CBCT scans using different methods. Direct digital scans of a completely dentate master model with removable radiopaque teeth were made using an intraoral scanner, and digital scans of stone duplicates of the master model were made using a laboratory scanner. Specific teeth were removed to simulate different clinical situations and their CBCT scans were made. Surface scans were registered onto the CBCT scans. Radiographic templates for each clinical situation were also fabricated and used during CBCT scans of the master models. Using metrology software, three-dimensional (3D) deviation was measured on standard tesselation language (STL) files created from the CBCT scans against an STL file of the master model created from a CBCT scan. Statistical analysis was done using the MIXED procedure in a statistical software and Tukey HSD test (α =.05). The interaction between location and method was significant (P = .009). Location had no significant effect on registration methods (P > .05), but on the radiographic templates (P = .011). Length of the edentulous area did not have any significant effect (P > .05). Accuracy of digital image registration methods was similar and higher than that of radiographic templates in all clinical situations. Tooth-bound radiographic templates were significantly more accurate than the free-end templates. The results of this study suggest using image registration instead of radiographic templates when planning dental implants, particularly in free-end situations. © 2018 Wiley Periodicals, Inc.

Was that cheating? Perceptions vary by sex, attachment anxiety, and behavior.

PubMed

Kruger, Daniel J; Fisher, Maryanna L; Edelstein, Robin S; Chopik, William J; Fitzgerald, Carey J; Stout, Sarah L

2013-02-13

We generated an inventory of 27 interpersonal behaviors and examined the extent to which participants judged each behavior as cheating on a long-term partner. We predicted variation in these judgments based on participant sex and attachment insecurity. Ratings for items ranged considerably; participants rated sexual behaviors as most indicative of cheating, then erotic behaviors, followed by behaviors consistent with a romantic relationship, and then behaviors related to financial support. Women rated ten items higher than did men, and men's ratings were higher on a minor financial support item. Higher attachment anxiety was associated with higher ratings for 18 of 27 behaviors; higher attachment avoidance was associated with lower scores on five items and higher scores on one item. Principle Axis Factoring identified three dimensions; sexual interaction, behaviors indicating close relationships, and casual social interaction. We discuss these results using the framework of attachment theory and sex-specific mating strategies.

Enhanced magnetic performance of metal-organic nanowire arrays by FeCo/polypyrrole co-electrodeposition

NASA Astrophysics Data System (ADS)

Luo, X. J.; Xia, W. B.; Gao, J. L.; Zhang, S. Y.; Li, Y. L.; Tang, S. L.; Du, Y. W.

2013-05-01

FeCo/polypyrrole (PPy) composite nanowire array, which shows enhanced magnetic remanence and coercivity along the nanowires, was fabricated by AC electrodeposition using anodic aluminum oxide templates. High resolution transmission electron microscopy shows that PPy grows on the surface of FeCo nanowires forming a coaxial nanowire structure, with a coating layer of about 4 nm. It suggests that the decreased dipolar interaction due to the reduced nanowire diameters is responsible for the enhancement of magnetic performance. The possible mechanism of this coating may be that PPy is inclined to nucleate along the pore wall of the templates.

The origin of polynucleotide-directed protein synthesis

NASA Technical Reports Server (NTRS)

Orgel, Leslie E.

1989-01-01

If protein synthesis evolved in an RNA world it was probably preceded by simpler processes by means of which interaction with amino acids conferred selective advantage on replicating RNA molecules. It is suggested that at first the simple attachment of amino acids to the 2'(3') termini of RNA templates favored initiation of replication at the end of the template rather than at internal positions. The second stage in the evolution of protein synthesis would probably have been the association of pairs of charged RNA adaptors in such a way as to favor noncoded formation of peptides. Only after this process had become efficient could coded synthesis have begun.

Interaction between numbers and size during visual search.

PubMed

Krause, Florian; Bekkering, Harold; Pratt, Jay; Lindemann, Oliver

2017-05-01

The current study investigates an interaction between numbers and physical size (i.e. size congruity) in visual search. In three experiments, participants had to detect a physically large (or small) target item among physically small (or large) distractors in a search task comprising single-digit numbers. The relative numerical size of the digits was varied, such that the target item was either among the numerically large or small numbers in the search display and the relation between numerical and physical size was either congruent or incongruent. Perceptual differences of the stimuli were controlled by a condition in which participants had to search for a differently coloured target item with the same physical size and by the usage of LCD-style numbers that were matched in visual similarity by shape transformations. The results of all three experiments consistently revealed that detecting a physically large target item is significantly faster when the numerical size of the target item is large as well (congruent), compared to when it is small (incongruent). This novel finding of a size congruity effect in visual search demonstrates an interaction between numerical and physical size in an experimental setting beyond typically used binary comparison tasks, and provides important new evidence for the notion of shared cognitive codes for numbers and sensorimotor magnitudes. Theoretical consequences for recent models on attention, magnitude representation and their interactions are discussed.

Dimensional structure of the Social Interaction Anxiety Scale according to the analysis of data obtained with a German version.

PubMed

Eidecker, Judith; Glöckner-Rist, Angelika; Gerlach, Alexander L

2010-08-01

The Social Interaction and Anxiety Scale (SIAS) is widely used to assess social interaction anxiety. Yet its dimensional structure is still not well-defined. Especially, the conceptual pertinence of three negatively keyed items has been challenged. In this study, dimensionality of the answers of a student sample to a German SIAS version was first analyzed exploratorily. Subsequently, we tested confirmatorily several measurement models specifying different SIAS dimensions, and investigated how these relate to extraversion. The most reasonable model was cross-validated relying on data from healthy controls and social phobia sufferers. All analyses involved methods suited for an adequate handling of ordinal data. The findings confirm that three negatively keyed items are dubious indicators of social interaction anxiety. Thus, only the remaining 17 items should be used for this purpose in future studies. Analyses of their psychometric properties show, in addition, that they apparently tap three different facets of social interaction anxiety. (c) 2010 Elsevier Ltd. All rights reserved.

Template-directed deposition of amyloid

NASA Astrophysics Data System (ADS)

Ha, Chanki

The formation of amyloid plaques in tissue is a pathological feature of many neurodegenerative diseases. Amyloid deposition, the process of amyloid plaque growth by the association of individual soluble amyloid molecules with a pre-existing amyloid template (i.e. plaque), is known to be critical for amyloid formation in vivo. In order to characterize amyloid deposition, we developed novel, synthetic amyloid templates like amyloid plaques in the human Alzheimer's brain by attaching amyloid seeds covalently onto an N-hydroxysuccinimide-activated surface. Amyloid plaques with a characteristic beta-sheet structure formed through a conformational rearrangement of soluble insulin or Abeta monomers upon interaction with the template. The amyloid deposition rate followed saturation kinetics with respect to insulin concentration in the solution. According to visualization of temporal evolution of Abeta plaque deposition on a template, it was found that mature amyloid plaques serve as a sink of soluble Abeta in a solution as well as a reservoir of small aggregates such as oligomers and protofibrils. Quantitative analysis of seeding efficiencies of three different Abeta species revealed that oligomeric forms of Abeta act more efficiently as seeds than monomers or fibrils do. Furthermore, studies on the interaction between Abeta40 and 42 showed an important role of Abeta42 in amyloid deposition. A slightly acidic condition was found to be unfavorable for amyloid plaque formation. Effects of metal ions on amyloid deposition indicated that Fe3+, but not Cu3 and Zn2+, is important for the deposition of amyloid plaques. The binding of Fe3+ to Abeta42 peptide was confirmed by using SIMS analysis. Zn2+ induced nonfibrillar amorphous aggregates, but the release of Zn2+ from Abeta42 deposits by Fe3+ triggered the formation of amyloid fibers. Effects or metal ion chelators such as ethylenediamine tetraacetic acid, deferoxamine, and clioquinol on amyloid deposition were tested to determine if they can be effective in preventing the deposition of amyloid plaques. The results may give insights into understanding the effects of environmental factors on amyloid plaque deposition and important information for therapeutic development for Alzheimer's disease.

Generation And Understanding Of Natural Language Using Information In A Frame Structure

NASA Astrophysics Data System (ADS)

Perkins, Walton A.

1989-03-01

Many expert systems and relational database systems store factual information in the form of attributes values of objects. Problems arise in transforming from that attribute (frame) database representation into English surface structure and in transforming the English surface structure into a representation that references information in the frame database. In this paper we consider mainly the generation process, as it is this area in which we have made the most significant progress. In its interaction with the user, the expert system must generate questions, declarations, and uncertain declarations. Attributes such as COLOR, LENGTH, and ILLUMINATION can be referenced using the template: " of " for both questions and declarations. However, many other attributes, such as RATTLES, in "What is RATTLES of the light bulb?", and HAS_STREP_THROAT in, "HAS_STREP_THROAT of Dan is true." do not fit this template. We examined over 300 attributes from several knowledge bases and have grouped them into 16 classes. For each class there is one "question" template, one "declaration" template, and one "uncertain declaration" template for generating English surface structure. The internal databases identifiers (e.g., HAS_STREP_THROAT and DISEASE_35) must also be replaced by output synonyms. Classifying each attribute in combination with synonym translation remarkably improved the English surface structure that the system generated. In the area of understanding, synonym translation and knowledge of the attribute properties, such as legal values, has resulted in a robust database query capability.

Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials

PubMed Central

Hesemann, Peter; Nguyen, Thy Phung; Hankari, Samir El

2014-01-01

The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS) recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA), mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the “anionic templating” strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches. PMID:28788602

The guidance of spatial attention during visual search for color combinations and color configurations.

PubMed

Berggren, Nick; Eimer, Martin

2016-09-01

Representations of target-defining features (attentional templates) guide the selection of target objects in visual search. We used behavioral and electrophysiological measures to investigate how such search templates control the allocation of attention in search tasks where targets are defined by the combination of 2 colors or by a specific spatial configuration of these colors. Target displays were preceded by spatially uninformative cue displays that contained items in 1 or both target-defining colors. Experiments 1 and 2 demonstrated that, during search for color combinations, attention is initially allocated independently and in parallel to all objects with target-matching colors, but is then rapidly withdrawn from objects that only have 1 of the 2 target colors. In Experiment 3, targets were defined by a particular spatial configuration of 2 colors, and could be accompanied by nontarget objects with a different configuration of the same colors. Attentional guidance processes were unable to distinguish between these 2 types of objects. Both attracted attention equally when they appeared in a cue display, and both received parallel focal-attentional processing and were encoded into working memory when they were presented in the same target display. Results demonstrate that attention can be guided simultaneously by multiple features from the same dimension, but that these guidance processes have no access to the spatial-configural properties of target objects. They suggest that attentional templates do not represent target objects in an integrated pictorial fashion, but contain separate representations of target-defining features. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Visual working memory simultaneously guides facilitation and inhibition during visual search.

PubMed

Dube, Blaire; Basciano, April; Emrich, Stephen M; Al-Aidroos, Naseem

2016-07-01

During visual search, visual working memory (VWM) supports the guidance of attention in two ways: It stores the identity of the search target, facilitating the selection of matching stimuli in the search array, and it maintains a record of the distractors processed during search so that they can be inhibited. In two experiments, we investigated whether the full contents of VWM can be used to support both of these abilities simultaneously. In Experiment 1, participants completed a preview search task in which (a) a subset of search distractors appeared before the remainder of the search items, affording participants the opportunity to inhibit them, and (b) the search target varied from trial to trial, requiring the search target template to be maintained in VWM. We observed the established signature of VWM-based inhibition-reduced ability to ignore previewed distractors when the number of distractors exceeds VWM's capacity-suggesting that VWM can serve this role while also representing the target template. In Experiment 2, we replicated Experiment 1, but added to the search displays a singleton distractor that sometimes matched the color (a task-irrelevant feature) of the search target, to evaluate capture. We again observed the signature of VWM-based preview inhibition along with attentional capture by (and, thus, facilitation of) singletons matching the target template. These findings indicate that more than one VWM representation can bias attention at a time, and that these representations can separately affect selection through either facilitation or inhibition, placing constraints on existing models of the VWM-based guidance of attention.

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

PubMed

Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

2013-01-01

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures.

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

PubMed Central

Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

2013-01-01

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures. PMID:23516343

Quantum dot nanocrystals having guanosine imprinted nanoshell for DNA recognition.

PubMed

Diltemiz, Sibel Emir; Say, Ridvan; Büyüktiryaki, Sibel; Hür, Deniz; Denizli, Adil; Ersöz, Arzu

2008-05-30

Molecular imprinted polymers (MIPs) as a recognition element for sensors are increasingly of interest and MIP nanoparticles have started to appear in the literature. In this study, we have proposed a novel thiol ligand-capping method with polymerizable methacryloylamido-cysteine (MAC) attached to CdS quantum dots (QDs), reminiscent of a self-assembled monolayer and have reconstructed surface shell by synthetic host polymers based on molecular imprinting method for DNA recognition. In this method, methacryloylamidohistidine-platinium (MAH-Pt(II)) is used as a new metal-chelating monomer via metal coordination-chelation interactions and guanosine templates of DNA. Nanoshell sensors with guanosine templates give a cavity that is selective for guanosine and its analogues. The guanosine can simultaneously chelate to Pt(II) metal ion and fit into the shape-selective cavity. Thus, the interaction between Pt(II) ion and free coordination spheres has an effect on the binding ability of the CdS QD nanosensor. The binding affinity of the guanosine imprinted nanocrystals has investigated by using the Langmuir and Scatchard methods, and experiments have shown the shape-selective cavity formation with O6 and N7 of a guanosine nucleotide (K(a) = 4.841x10(6) mol L(-1)) and a free guanine base (K(a) = 0.894x10(6) mol L(-1)). Additionally, the guanosine template of the nanocrystals is more favored for single stranded DNA compared to double stranded DNA.

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

PubMed

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.

Evaluation of Two Methods for Modeling Measurement Errors When Testing Interaction Effects with Observed Composite Scores

ERIC Educational Resources Information Center

Hsiao, Yu-Yu; Kwok, Oi-Man; Lai, Mark H. C.

2018-01-01

Path models with observed composites based on multiple items (e.g., mean or sum score of the items) are commonly used to test interaction effects. Under this practice, researchers generally assume that the observed composites are measured without errors. In this study, we reviewed and evaluated two alternative methods within the structural…

Averaged head phantoms from magnetic resonance images of Korean children and young adults

NASA Astrophysics Data System (ADS)

Han, Miran; Lee, Ae-Kyoung; Choi, Hyung-Do; Jung, Yong Wook; Park, Jin Seo

2018-02-01

Increased use of mobile phones raises concerns about the health risks of electromagnetic radiation. Phantom heads are routinely used for radiofrequency dosimetry simulations, and the purpose of this study was to construct averaged phantom heads for children and young adults. Using magnetic resonance images (MRI), sectioned cadaver images, and a hybrid approach, we initially built template phantoms representing 6-, 9-, 12-, 15-year-old children and young adults. Our subsequent approach revised the template phantoms using 29 averaged items that were identified by averaging the MRI data from 500 children and young adults. In females, the brain size and cranium thickness peaked in the early teens and then decreased. This is contrary to what was observed in males, where brain size and cranium thicknesses either plateaued or grew continuously. The overall shape of brains was spherical in children and became ellipsoidal by adulthood. In this study, we devised a method to build averaged phantom heads by constructing surface and voxel models. The surface model could be used for phantom manipulation, whereas the voxel model could be used for compliance test of specific absorption rate (SAR) for users of mobile phones or other electronic devices.

PREP: Portal for Readiness Exercises & Planning v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noel, Todd; Le, Tam; McNeil, Carrie

2016-10-28

The software includes a web-based template for recording actions taken during emergency preparedness exercises and planning workshops. In addition, a virtual outbreak prevention simulation exercise is also included. Both tools interact with a server which records user decisions and communications.

Synaptic efficacy shapes resource limitations in working memory.

PubMed

Krishnan, Nikhil; Poll, Daniel B; Kilpatrick, Zachary P

2018-06-01

Working memory (WM) is limited in its temporal length and capacity. Classic conceptions of WM capacity assume the system possesses a finite number of slots, but recent evidence suggests WM may be a continuous resource. Resource models typically assume there is no hard upper bound on the number of items that can be stored, but WM fidelity decreases with the number of items. We analyze a neural field model of multi-item WM that associates each item with the location of a bump in a finite spatial domain, considering items that span a one-dimensional continuous feature space. Our analysis relates the neural architecture of the network to accumulated errors and capacity limitations arising during the delay period of a multi-item WM task. Networks with stronger synapses support wider bumps that interact more, whereas networks with weaker synapses support narrower bumps that are more susceptible to noise perturbations. There is an optimal synaptic strength that both limits bump interaction events and the effects of noise perturbations. This optimum shifts to weaker synapses as the number of items stored in the network is increased. Our model not only provides a circuit-based explanation for WM capacity, but also speaks to how capacity relates to the arrangement of stored items in a feature space.

Rapid forgetting results from competition over time between items in visual working memory.

PubMed

Pertzov, Yoni; Manohar, Sanjay; Husain, Masud

2017-04-01

Working memory is now established as a fundamental cognitive process across a range of species. Loss of information held in working memory has the potential to disrupt many aspects of cognitive function. However, despite its significance, the mechanisms underlying rapid forgetting remain unclear, with intense recent debate as to whether it is interference between stored items that leads to loss of information or simply temporal decay. Here we show that both factors are essential and interact in a highly specific manner. Although a single item can be maintained in memory with high fidelity, multiple items compete in working memory, progressively degrading each other's representations as time passes. Specifically, interaction between items is associated with both worsening precision and increased reporting errors of object features over time. Importantly, during the period of maintenance, although items are no longer visible, maintenance resources can be selectively redeployed to protect the probability to recall the correct feature and the precision with which cued items can be recalled, as if it was the only item in memory. These findings reveal that the biased competition concept could be applied not only to perceptual processes but also to active maintenance of working memory representations over time. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Au-coated 3-D nanoporous titania layer prepared using polystyrene-b-poly(2-vinylpyridine) block copolymer nanoparticles.

PubMed

Shin, Won-Jeong; Basarir, Fevzihan; Yoon, Tae-Ho; Lee, Jae-Suk

2009-04-09

New nanoporous structures of Au-coated titania layers were prepared by using amphiphilic block copolymer nanoparticles as a template. A 3-D template composed of self-assembled quaternized polystyrene-b-poly(2-vinylpyridine) (Q-PS-b-P2VP) block copolymer nanoparticles below 100 nm was prepared. The core-shell-type nanoparticles were well ordered three-dimensionally using the vertical immersion method on the substrate. The polar solvents were added to the polymer solution to prevent particle merging at 40 degrees C when considering the interaction between polymer nanoparticles and solvents. Furthermore, Au-coated PS-b-P2VP nanoparticles were prepared using thiol-capped Au nanoparticles (3 nm). The 3-D arrays with Au-coated PS-b-P2VP nanoparticles as a template contributed to the preparation of the nanoporous Au-coated titania layer. Therefore, the nanoporous Au-coated titania layer was fabricated by removing PS-b-P2VP block copolymer nanoparticles by oxygen plasma etching.

Block Copolymer-Templated Approach to Nanopatterned Metal-Organic Framework Films.

PubMed

Zhou, Meimei; Wu, Yi-Nan; Wu, Baozhen; Yin, Xianpeng; Gao, Ning; Li, Fengting; Li, Guangtao

2017-08-17

The fabrication of patterned metal-organic framework (MOF) films with precisely controlled nanoscale resolution has been a fundamental challenge in nanoscience and nanotechnology. In this study, nanopatterned MOF films were fabricated using a layer-by-layer (LBL) growth method on functional templates (such as a bicontinuous nanoporous membrane or a structure with highly long-range-ordered nanoscopic channels parallel to the underlying substrate) generated by the microphase separation of polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) block copolymers. HKUST-1 can be directly deposited on the templates without any chemical modification because the pyridine groups in P2VP interact with metal ions via metal-BCP complexes. As a result, nanopatterned HKUST-1 films with feature sizes below 50 nm and controllable thicknesses can be fabricated by controlling the number of LBL growth cycles. The proposed fabrication method further extends the applications of MOFs in various fields. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel electrochemiluminescence of silver nanoclusters fabricated on triplex DNA scaffolds for label-free detection of biothiols.

PubMed

Feng, Lingyan; Wu, Li; Xing, Feifei; Hu, Lianzhe; Ren, Jinsong; Qu, Xiaogang

2017-12-15

Electrochemiluminescence (ECL) of metal nanoclusters and their application have been widely reported due to the good biocompatibility, fascinating electrocatalytic activity and so on. Using DNA as synthesis template opens new opportunities to modulate the physical properties of AgNCs. Triplex DNA has been reported for the site-specific, homogeneous and highly stable silver nanoclusters (AgNCs) fabrication from our recent research. Here we further explore their extraordinary ECL properties and applications in biosensor utilization. By reasonable design of DNA sequence, AgNCs were obtained in the predefined position of CG.C + sites of triplex DNA, and the ECL emission at a low potential was observed with this novel DNA template. Finally, a simple and label-free method was developed for biothiols detection based on the enhanced catalytic reaction and a robust interaction between the triplex-AgNCs and cysteine, by influencing the microenvironment provided by DNA template. Copyright © 2017 Elsevier B.V. All rights reserved.

An organic dye-polymer (phenol red-poly (vinyl alcohol)) composite architecture towards tunable -optical and -saturable absorption characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sreedhar, Sreeja, E-mail: sreejasreedhar83@gmail.com; Muneera, C. I., E-mail: drcimuneera@hotmail.com; Illyaskutty, Navas

2016-05-21

Herein, we demonstrate that blending an organic dye (guest/filler), with a vinyl polymer (host template), is an inexpensive and simple approach for the fabrication of multifunctional photonic materials which could display an enhancement in the desirable properties of the constituent materials and, at the same time provide novel synergistic properties for the guest-host system. A new guest-host nanocomposite system comprising Phenol Red dye and poly (vinyl alcohol) as guest and host template, respectively, which exhibits tunable optical characteristics and saturable absorption behavior, is introduced. The dependence of local electronic environment provided by the polymer template and the interactions of themore » polymer molecules with the encapsulated guest molecules on the observed optical/nonlinear absorption behavior is discussed. An understanding of the tunability of the optical/ photophysical processes, with respect to the filler content, as discussed herein could help in the design of improved optical materials for several photonic device applications like organic light emitting diodes and saturable absorbers.« less

Surface-Casting Synthesis of Mesoporous Zirconia with a CMK-5-Like Structure and High Surface Area.

PubMed

Gu, Dong; Schmidt, Wolfgang; Pichler, Christian M; Bongard, Hans-Josef; Spliethoff, Bernd; Asahina, Shunsuke; Cao, Zhengwen; Terasaki, Osamu; Schüth, Ferdi

2017-09-04

About 15 years ago, the Ryoo group described the synthesis of CMK-5, a material consisting of a hexagonal arrangement of carbon nanotubes. Extension of the surface casting synthesis to oxide compositions, however, was not possible so far, in spite of many attempts. Here it is demonstrated, that crystalline mesoporous hollow zirconia materials with very high surface areas up to 400 m 2  g -1 , and in selected cases in the form of CMK-5-like, are indeed accessible via such a surface casting process. The key for the successful synthesis is an increased interaction between the silica hard template surface and the zirconia precursor species by using silanol group-rich mesoporous silica as a hard template. The surface areas of the obtained zirconias exceed those of conventionally hard-templated ones by a factor of two to three. The surface casting process seems to be applicable also to other oxide materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of molecular imprinting polymers for extraction of gallic acid from urine.

PubMed

Bhawani, Showkat Ahmad; Sen, Tham Soon; Ibrahim, Mohammad Nasir Mohammad

2018-02-21

The molecularly imprinted polymers for gallic acid were synthesized by precipitation polymerization. During the process of synthesis a non-covalent approach was used for the interaction of template and monomer. In the polymerization process, gallic acid was used as a template, acrylic acid as a functional monomer, ethylene glycol dimethacrylate as a cross-linker and 2,2'-azobisisobutyronitrile as an initiator and acetonitrile as a solvent. The synthesized imprinted and non-imprinted polymer particles were characterized by using Fourier-transform infrared spectroscopy and scanning electron microscopy. The rebinding efficiency of synthesized polymer particles was evaluated by batch binding assay. The highly selective imprinted polymer for gallic acid was MIPI1 with a composition (molar ratio) of 1:4:20, template: monomer: cross-linker, respectively. The MIPI1 showed highest binding efficiency (79.50%) as compared to other imprinted and non-imprinted polymers. The highly selective imprinted polymers have successfully extracted about 80% of gallic acid from spiked urine sample.

Molecularly imprinted solid-phase extraction sorbent for the clean-up of chlorinated phenoxyacids from aqueous samples.

PubMed

Baggiani, C; Giovannoli, C; Anfossi, L; Tozzi, C

2001-12-14

A molecularly imprinted polymer (MIP) was synthesized using the herbicide 2,4,5-trichlorophenoxyacetic acid as a template, 4-vinylpyridine as an interacting monomer, ethylendimethacrylate as a cross-linker and a methanol-water mixture as a porogen. The binding properties and the selectivity of the polymer towards the template were investigated by frontal and zonal liquid chromatography. The polymer was used as a solid-phase extraction material for the clean-up of the template molecule and some related herbicides (2,4-dichlorophenoxyacetic acid, fenoprop, dichlorprop) from river water samples at a concentration level of ng/ml with quantitative recoveries comparable with those obtained with a traditional C18 reversed-phase column when analyzed by capillary electrophoresis. The results obtained show that the MIP-based approach to the solid-phase extraction is comparable with the more traditional solid-phase extraction with C18 reversed-phase columns in terms of recovery, but it is superior in terms of sample clean-up.

Highly Ordered Block Copolymer Templates for the Generation of Nanostructured Materials

NASA Astrophysics Data System (ADS)

Bhoje Gowd, E.; Nandan, Bhanu; Bigall, Nadja C.; Eychmuller, Alexander; Stamm, Manfred

2009-03-01

Among many different types of self-assembled materials, block copolymers have attracted immense interest for applications in nanotechnology. Block copolymer thin film can be used as a template for patterning of hard inorganic materials such as metal nanoparticles. In the present work, we demonstrate a new approach to fabricate highly ordered arrays of nanoscopic inorganic dots and wires using switchable block copolymer thin films. Various inorganic nanoparticles from a simple aqueous solution were directly deposited on the surface reconstructed block copolymer templates. The preferential interaction of the nanoparticles with one of the blocks is mainly responsible for the lateral distribution of the nanoparticles in addition to the capillary forces. Subsequent stabilization by UV-irradiation followed by pyrolysis in air at 450 ^oC removes the polymer to produce highly ordered metallic nanostructures. This method is highly versatile as the procedure used here is simple, eco-friendly and provides a facile approach to fabricate a broad range of nanoscaled architectures with tunable lateral spacing.

When will bigger be (recalled) better? The influence of category size on JOLs depends on test format.

PubMed

Hourihan, Kathleen L; Tullis, Jonathan G

2015-08-01

Although it is well known that organized lists of words (e.g., categories) are recalled better than unrelated lists, little research has examined whether participants can predict how categorical relatedness influences recall. In two experiments, participants studied lists of words that included items from big categories (12 items), small categories (4 items), and unrelated items, and provided immediate JOLs. In Experiment 1, free recall was highest for items from large categories and lowest for unrelated items. Importantly, participants were sensitive to the effects of category size on recall, with JOLs to items from big categories actually increasing over the study list. In Experiment 2, one group of participants was cued to recall all exemplars from the categories in a blocked manner, whereas the other group was cued in a random order. As expected, the random group did not show the recall benefit for big categories over small categories observed in free recall, while the blocked group did. Critically, the pattern of metacognitive judgments closely matched actual cued recall performance. Participants' JOLs were sensitive to the interaction between category size and output order, demonstrating a relatively sophisticated strategy that incorporates the interaction of multiple extrinsic cues in predicting recall.

Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues†

PubMed Central

Killelea, Tom; Ghosh, Samantak; Tan, Samuel S.; Heslop, Pauline; Firbank, Susan; Kool, Eric T.; Connolly, Bernard A.

2010-01-01

Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describes uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at the +2 position explains the stimulation of the polymerase 3′-5′ proof reading exonuclease, observed with deaminated bases at this location. A β hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double stranded DNA. This denatures the two complementary primer bases and directs the resulting 3′ single-stranded extension towards the exonuclease active site. Finally the relative importance of hydrogen bonding and shape fit in determining selectivity for deaminated bases has been examined using non-polar isosteres. Affinity for both 2,4 difluorobenzene and fluorobenzimidazole, non-hydrogen bonding shape mimics of uracil and hypoxanthine respectively, is strongly diminished, suggesting polar protein-base contacts are important. However, residual interaction with 2,4 difluorobenzene is seen, confirming a role for shape recognition. PMID:20527806

Negative Affect Impairs Associative Memory but Not Item Memory

ERIC Educational Resources Information Center

Bisby, James A.; Burgess, Neil

2014-01-01

The formation of associations between items and their context has been proposed to rely on mechanisms distinct from those supporting memory for a single item. Although emotional experiences can profoundly affect memory, our understanding of how it interacts with different aspects of memory remains unclear. We performed three experiments to examine…

Cluster Analysis for Cognitive Diagnosis: Theory and Applications

ERIC Educational Resources Information Center

Chiu, Chia-Yi; Douglas, Jeffrey A.; Li, Xiaodong

2009-01-01

Latent class models for cognitive diagnosis often begin with specification of a matrix that indicates which attributes or skills are needed for each item. Then by imposing restrictions that take this into account, along with a theory governing how subjects interact with items, parametric formulations of item response functions are derived and…

Differential Item Functioning Amplification and Cancellation in a Reading Test

ERIC Educational Resources Information Center

Bao, Han; Dayton, C. Mitchell; Hendrickson, Amy B.

2009-01-01

When testlet effects and item idiosyncratic features are both considered to be the reasons of DIF in educational tests using testlets (Wainer & Kiely, 1987) or item bundles (Rosenbaum, 1988), it is interesting to investigate the phenomena of DIF amplification and cancellation due to the interactive effects of these two factors. This research…

Heterocentric language in commonly used measures of social anxiety: recommended alternate wording.

PubMed

Weiss, Brandon J; Hope, Debra A; Capozzoli, Michelle C

2013-03-01

A number of self-report measures of social anxiety contain language that appears to assume heterosexuality. It is unclear how such items should be answered by individuals who are not exclusively heterosexual, which may lead to inaccurate measurement of symptoms, perpetuation of stigma, and alienation of respondents. More specific wording could improve measurement accuracy for sexual minorities as well as heterosexual respondents. Gender-neutral wording was developed for items containing the phrase "opposite sex" in commonly used self-report measures of social anxiety (Interaction Anxiousness Scale [Leary, 1983], Social Avoidance and Distress Scale [Watson & Friend, 1969], Social Interaction Anxiety Scale [Mattick & Clarke, 1998], and Social Phobia and Anxiety Inventory [Turner, Beidel, Dancu, & Stanley, 1989]). Undergraduate college students (N=405; mean age=19.88, SD=2.05) completed measures containing original and revised items. Overall, results indicated that the alternate-worded items demonstrated equivalent or slightly stronger psychometric properties compared to original items. Select alternate-worded items are recommended for clinical and research use, and directions for future research are recommended. Copyright © 2012. Published by Elsevier Ltd.

Innovative testing of spatial ability: interactive responding and the use of complex stimuli material.

PubMed

Jelínek, Martin; Květon, Petr; Vobořil, Dalibor

2015-02-01

Despite initial expectations, which have emerged with the advancement of computer technology over the last decade of the twentieth century, scientific literature does not contain many relevant references regarding the development and use of innovative items in psychological testing. Our study presents and evaluates two novel item types. One item type is derived from a standard schematic test item used for the assessment of the spatial perception aspect of spatial ability, enhanced by an interactive response module. The performance on this item type is correlated with the performance on its paper and pencil counterpart. The other innovative item type used complex stimuli in the form of a short video of a ride through a city presented in an on-route perspective, which is intended to measure navigation skills and the ability to keep oneself oriented in space. In this case, the scores were related to the capacity of visuo-spatial working memory and also to the overall score in the paper/pencil test of spatial ability. The second relationship was moderated by gender.

Structural Features of a Picornavirus Polymerase Involved in the Polyadenylation of Viral RNA

PubMed Central

Kempf, Brian J.; Kelly, Michelle M.; Springer, Courtney L.; Peersen, Olve B.

2013-01-01

Picornaviruses have 3′ polyadenylated RNA genomes, but the mechanisms by which these genomes are polyadenylated during viral replication remain obscure. Based on prior studies, we proposed a model wherein the poliovirus RNA-dependent RNA polymerase (3Dpol) uses a reiterative transcription mechanism while replicating the poly(A) and poly(U) portions of viral RNA templates. To further test this model, we examined whether mutations in 3Dpol influenced the polyadenylation of virion RNA. We identified nine alanine substitution mutations in 3Dpol that resulted in shorter or longer 3′ poly(A) tails in virion RNA. These mutations could disrupt structural features of 3Dpol required for the recruitment of a cellular poly(A) polymerase; however, the structural orientation of these residues suggests a direct role of 3Dpol in the polyadenylation of RNA genomes. Reaction mixtures containing purified 3Dpol and a template RNA with a defined poly(U) sequence provided data consistent with a template-dependent reiterative transcription mechanism for polyadenylation. The phylogenetically conserved structural features of 3Dpol involved in the polyadenylation of virion RNA include a thumb domain alpha helix that is positioned in the minor groove of the double-stranded RNA product and lysine and arginine residues that interact with the phosphates of both the RNA template and product strands. PMID:23468507

Distribution of acetylated histones resulting from Gal4-VP16 recruitment of SAGA and NuA4 complexes

PubMed Central

Vignali, Marissa; Steger, David J.; Neely, Kristen E.; Workman, Jerry L.

2000-01-01

We analyzed the targeting of histone acetyltransferase (HAT) complexes by DNA-binding activators during transcriptional activation and the resulting distribution of acetylated histones. An in vitro competition assay was developed to acetylate and transcribe a nucleosomal array template in the presence of excess non-specific chromatin, which mimics in vivo conditions. Stimulation of transcription from the nucleosomal array template under competitive conditions by the SAGA and NuA4 HAT complexes depended on the presence of the Gal4-VP16 activator, which recognizes sites in the promoter and directly interacts with these HATs. Importantly, the stimulation of transcription by SAGA and NuA4 depended on the presence of Gal4-VP16 during histone acetylation, and Gal4-VP16-bound nucleosomal templates were acetylated preferentially by SAGA and NuA4 relative to the competitor chromatin. While targeting of the SAGA complex led to H3 acetylation of promoter-proximal nucleosomes, targeting of the NuA4 complex led to a broader domain of H4 acetylation of >3 kbp. Thus, either promoter-proximal H3 acetylation by SAGA or broadly distributed acetylation of H4 by NuA4 activated transcription from chromatin templates. PMID:10835360

Synthesis of thermo-responsive bovine hemoglobin imprinted nanoparticles by combining ionic liquid immobilization with aqueous precipitation polymerization.

PubMed

Wang, Yongmei; Yang, Chongchong; Sun, Yan; Qiu, Fengtao; Xiang, Yang; Fu, Guoqi

2018-02-01

Surface molecular imprinting over functionalized nanoparticles has proved to be an effective approach for construction of artificial nanomaterials for protein recognition. Herein, we report a strategy for synthesis of core-shell protein-imprinted nanoparticles by the functionalization of nano-cores with ionic liquids followed by aqueous precipitation polymerization to build thermo-responsive imprinted polymer nano-shells. The immobilized ionic liquids can form multiple interactions with the protein template. The polymerization process can produce thermo-reversible physical crosslinks, which are advantageous to enhancing imprinting and facilitating template removal. With bovine hemoglobin as a model template, the imprinted nanoparticles showed temperature-sensitivity in both dispersion behaviors and rebinding capacities. Compared with the ionic-liquid-modified core nanoparticles, the imprinted particles exhibited greatly increased selectivity and two orders of magnitude higher binding affinity for the template protein. The imprinted nanoparticles achieved relatively high imprinting factor up to 5.0 and specific rebinding capacity of 67.7 mg/g, respectively. These nanoparticles also demonstrated rapid rebinding kinetics and good reproducibility after five cycles of adsorption-regeneration. Therefore, the presented approach may be viable for the fabrication of high-performance protein-imprinted nanoparticles with temperature sensitivity. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomimetic nanoparticles with polynucleotide and PEG mixed-monolayers enhance calcium phosphate mineralization

NASA Astrophysics Data System (ADS)

Vasconcellos, Kayla B.; McHugh, Sean M.; Dapsis, Katherine J.; Petty, Alexander R.; Gerdon, Aren E.

2013-09-01

Biomineralization of hydroxyapatite (Ca10(PO4)6(OH)2) is of significant importance in biomedical applications such as bone and dental repair, and biomimetic control of mineral formation may lead to more effective restorative procedures. Gold nanoparticles are functional scaffolds on which to assemble multi-component monolayers capable of mimicking protein activity in the templated synthesis of calcium phosphate. The goal of this research was to explore nanoparticle templates with mixed-monolayers of uncharged polar polyethylene glycol (PEG) molecules and highly charged polynucleotide and amino acid molecules in their ability to influence mineralization rates and mineral particle size and morphology. This research demonstrates through time-resolved optical density and dynamic light scattering measurements that the combination of tiopronin, PEG, and DNA presented on a nanoparticle surface decreases nanoparticle aggregation from 59 to 21 nm solvated radius, increases mineralization kinetics from 1.5 × 10-3 to 3.1 × 10-3 OD/min, and decreases mineral particle size from 685 to 442 nm average radius. FT-IR and TEM data demonstrate that mineralized material, while initially amorphous, transforms to a semi-crystalline material when guided by template interactions. This demonstrates that surface-tailored monolayer protected cluster scaffolds are successful and controllable mineralization templates with further potential for biomedical applications involving calcium phosphate and other biomaterials.

Atomic Resolution Description of the Interaction between the Nucleoprotein and Phosphoprotein of Hendra Virus

PubMed Central

Yabukarski, Filip; Blocquel, David; Schneider, Robert; Tarbouriech, Nicolas; Papageorgiou, Nicolas; Ruigrok, Rob W. H.; Jamin, Marc; Jensen, Malene Ringkjøbing; Longhi, Sonia; Blackledge, Martin

2013-01-01

Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, NTAIL, of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered NTAIL domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between NTAIL and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of NTAIL upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to NTAIL without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae. PMID:24086133

Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus.

PubMed

Communie, Guillaume; Habchi, Johnny; Yabukarski, Filip; Blocquel, David; Schneider, Robert; Tarbouriech, Nicolas; Papageorgiou, Nicolas; Ruigrok, Rob W H; Jamin, Marc; Jensen, Malene Ringkjøbing; Longhi, Sonia; Blackledge, Martin

2013-01-01

Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL), of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL) domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL) and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of N(TAIL) upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL) without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae.

Transportable Applications Environment (TAE) Tenth Users' Conference

NASA Technical Reports Server (NTRS)

Rouff, Chris (Editor); Harris, Elfrieda (Editor); Yeager, Arleen (Editor)

1993-01-01

Conference proceedings are represented in graphic visual-aid form. Presentation and panel discussion topics include user experiences with C++ and Ada; the design and interaction of the user interface; the history and goals of TAE; commercialization and testing of TAE Plus; Computer-Human Interaction Models (CHIMES); data driven objects; item-to-item connections and object dependencies; and integration with other software. There follows a list of conference attendees.

The Reverse of Social Anxiety Is Not Always the Opposite: The Reverse-Scored Items of the Social Interaction Anxiety Scale Do Not Belong

ERIC Educational Resources Information Center

Rodebaugh, Thomas L.; Woods, Carol M.; Heimberg, Richard G.

2007-01-01

Although well-used and empirically supported, the Social Interaction Anxiety Scale (SIAS) has a questionable factor structure and includes reverse-scored items with questionable utility. Here, using samples of undergraduates and a sample of clients with social anxiety disorder, we extend previous work that opened the question of whether the…

Sunshine, Bugs and Trout.

ERIC Educational Resources Information Center

Cushing, C. E.

1995-01-01

Provides a "template" for how a stream ecosystem functions. Discusses the physical and chemical factors of geology, light, current velocity, temperature, and energy sources. Describes functional groups of aquatic insects and the River Continuum Concept, a model of interaction that explains the spatial occurrence of aquatic insects. (LZ)

One-step template-free synthesis of 3D functionalized flower-like boron nitride nanosheets for NH3 and CO2 adsorption.

PubMed

Yang, Chen; Wang, Jinfeng; Chen, Ying; Liu, Dan; Huang, Shaoming; Lei, Weiwei

2018-06-14

3D functionalized flower-like boron nitride nanosheets (FBNNSs) were synthesized by a novel template-free method involving "cylinder compressing". Due to the high surface area (1114 m2 g-1), pore volume (0.7 cm3 g-1), hierarchical pore distributions, and abundant edge groups (-OH and -NH2), the 3D functionalized FBNNSs displayed excellent NH3 and CO2 adsorption up to 91 mg g-1 and 37.9 cc g-1 (74.4 mg g-1) at 1 bar, respectively. Moreover, the reusable performance of the material for gas adsorption was maintained for 10 cycles, indicating the stable structure of the FBNNSs. In addition, the adsorption mechanism was mainly explained by Lewis acid/base interactions, weak van der Waals interactions, and H-bonds. The combination of the enhanced adsorption capacity, excellent regenerability, and extraordinary chemical and thermal stability means that 3D FBNNSs possess huge potential for implementation in practical NH3 and CO2 capture.

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble

PubMed Central

Barnes, Christopher O.; Calero, Monica; Malik, Indranil; Graham, Brian W.; Spahr, Henrik; Lin, Guowu; Cohen, Aina; Brown, Ian S.; Zhang, Qiangmin; Pullara, Filippo; Trakselis, Michael A.; Kaplan, Craig D.; Calero, Guillermo

2015-01-01

Summary Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop-1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the Trigger Loop (TL), allowing visualization of its open state. Overall, our observations suggest that “open/closed” conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation. PMID:26186291

New evidence on the validity of the Arnett Caregiver Interaction Scale: Results from the Early Childhood Longitudinal Study-Birth Cohort

PubMed Central

Colwell, Nicole; Gordon, Rachel A.; Fujimoto, Ken; Kaestner, Robert; Korenman, Sanders

2013-01-01

The Arnett Caregiver Interaction Scale (CIS) has been widely used in research studies to measure the quality of caregiver–child interactions. The scale was modeled on a well-established theory of parenting, but there are few psychometric studies of its validity. We applied factor analyses and item response theory methods to assess the psychometric properties of the Arnett CIS in a national sample of toddlers in home-based care and preschoolers in center-based care from the Early Childhood Longitudinal Study-Birth Cohort. We found that a bifactor structure (one common factor and a second set of specific factors) best fits the data. In the Arnett CIS, the bifactor model distinguishes a common substantive dimension from two methodological dimensions (for positively and negatively oriented items). Despite the good fit of this model, the items are skewed (most teachers/caregivers display positive interactions with children) and, as a result, the Arnett CIS is not well suited to distinguish between caregivers who are “highly” versus “moderately” positive in their interactions with children, according to the items on the scale. Regression-adjusted associations between the Arnett CIS and child outcomes are small, especially for preschoolers in centers. We encourage future scale development work on measures of child care quality by early childhood scholars. PMID:24058264

Interaction between Air Bubbles and Superhydrophobic Surfaces in Aqueous Solutions.

PubMed

Shi, Chen; Cui, Xin; Zhang, Xurui; Tchoukov, Plamen; Liu, Qingxia; Encinas, Noemi; Paven, Maxime; Geyer, Florian; Vollmer, Doris; Xu, Zhenghe; Butt, Hans-Jürgen; Zeng, Hongbo

2015-07-07

Superhydrophobic surfaces are usually characterized by a high apparent contact angle of water drops in air. Here we analyze the inverse situation: Rather than focusing on water repellency in air, we measure the attractive interaction of air bubbles and superhydrophobic surfaces in water. Forces were measured between microbubbles with radii R of 40-90 μm attached to an atomic force microscope cantilever and submerged superhydrophobic surfaces. In addition, forces between macroscopic bubbles (R = 1.2 mm) at the end of capillaries and superhydrophobic surfaces were measured. As superhydrophobic surfaces we applied soot-templated surfaces, nanofilament surfaces, micropillar arrays with flat top faces, and decorated micropillars. Depending on the specific structure of the superhydrophobic surfaces and the presence and amount of entrapped air, different interactions were observed. Soot-templated surfaces in the Cassie state showed superaerophilic behavior: Once the electrostatic double-layer force and a hydrodynamic repulsion were overcome, bubbles jumped onto the surface and fully merged with the entrapped air. On nanofilaments and micropillar arrays we observed in addition the formation of sessile bubbles with finite contact angles below 90° or the attachment of bubbles, which retained their spherical shape.

Metalloporphyrin probes for antimalarial drug action.

PubMed

Ziegler, James; Pasierb, Lisa; Cole, Kelly A; Wright, David W

2003-09-01

Metal-substituted protoporphyrin IXs (Co(III)PPIX (1), Cr(III)PPIX (2), Mn(III)PPIX (3), Cu(II)PPIX (4), Mg(II)PPIX (5), Zn(II)PPIX (6) and Sn(IV)PPIX (7)), phthalocyanine tetrasulfonates (PcS (8) and Ni(II)PcS (9)), and anionic and cationic porphyrins (meso-tetra(4-sulfonatophenyl)porphine (TPPS4, 10), meso-tetra(4-carboxyphenyl)porphine (TPPC4, 11), tetrakis(4-N-trimethylaminophenyl)porphine (TMAP, 12) and meso-tetra(N-methyl-4-pyridyl)porphine (TMPyP4, 13)) have been used as probes to compare two different assays for the inhibition of beta-hematin formation. The results demonstrate that the efficacy of these probes in either the beta-hematin inhibition assay (9, 7, 6, 5>4>11, 3>10, 8>2, 1; 12 and 13 did not inhibit.) or the bionucleating template assay (8>1>11>9, 2>4>3>7>10>5>6; 12 and 13 did not inhibit.) differ significantly. These differences are examined in light of possible interactions between the inhibitor probes, heme, beta-hematin and the bionucleating template. This detailed analysis highlights the fact that while dominant modes of interactions may be occasionally identified, the precise mechanism of inhibition undoubtedly consists of the interplay between multiple interactions.

eMontage: An Architecture for Rapid Integration of Situational Awareness Data at the Edge

DTIC Science & Technology

2013-05-01

Request Response Interaction Android Client Dispatcher Servlet Spring MVC Controller Camel Producer Template Camel Route Remote Data Service - REST...8SATURN 2013© 2013 Carnegie Mellon University Publish Subscribe Interaction Android Client Dispatcher Servlet Spring MVC Controller Remote Data...set ..., "’"C oUkRelw•b J’- - ’ ~ ’~------’ ~-------- ’-------~ , Parse XML into a single Java XML Document object. -=--:=’ Software Engineering

Template-based synthesis and magnetic properties of Mn-Zn ferrite nanotube and nanowire arrays

NASA Astrophysics Data System (ADS)

Guo, Limin; Wang, Xiaohui; Zhong, Caifu; Li, Longtu

2012-01-01

Template-based electrophoretic deposition of Mn-Zn ferrite nanotubes (NTs) and nanowires (NWs) were achieved using anodic alumina oxide (AAO) membranes. The effect of electrophoretic current and deposition time on the morphology of the tubes was investigated. The samples show cubic spinel structure with no preferred orientation. Room-temperature magnetic properties of the Mn-Zn ferrite NT/NW arrays were studied. The magnetic easy axis parallels the NT/NW's channel axis attributing to the large shape anisotropy in this direction, especially for the NTs with a small wall thickness. Magnetocrystalline anisotropy and magnetostatic interactions were found dominant in the samples when applied field was perpendicular to the channel axis.

Spacecraft control center automation using the generic inferential executor (GENIE)

NASA Technical Reports Server (NTRS)

Hartley, Jonathan; Luczak, Ed; Stump, Doug

1996-01-01

The increasing requirement to dramatically reduce the cost of mission operations led to increased emphasis on automation technology. The expert system technology used at the Goddard Space Flight Center (MD) is currently being applied to the automation of spacecraft control center activities. The generic inferential executor (GENIE) is a tool which allows pass automation applications to be constructed. The pass script templates constructed encode the tasks necessary to mimic flight operations team interactions with the spacecraft during a pass. These templates can be configured with data specific to a particular pass. Animated graphical displays illustrate the progress during the pass. The first GENIE application automates passes of the solar, anomalous and magnetospheric particle explorer (SAMPEX) spacecraft.

Constructing molecular structures on periodic superstructure of graphene/Ru(0001)

PubMed Central

Li, Geng; Huang, Li; Xu, Wenyan; Que, Yande; Zhang, Yi; Lu, Jianchen; Du, Shixuan; Liu, Yunqi; Gao, Hong-Jun

2014-01-01

We review the way to fabricate large-scale, high-quality and single crystalline graphene epitaxially grown on Ru(0001) substrate. A moiré pattern of the graphene/Ru(0001) is formed due to the lattice mismatch between graphene and Ru(0001). This superstructure gives rise to surface charge redistribution and could behave as an ordered quantum dot array, which results in a perfect template to guide the assembly of organic molecular structures. Molecules, for example iron phthalocyanine and C60, on this template show how the molecule–substrate interaction makes different superstructures. These results show the possibility of constructing ordered molecular structures on graphene/Ru(0001), which is helpful for practical applications in the future. PMID:24615151

Assessing the factor structure of the Chinese conformity to masculine norms inventory.

PubMed

Rochelle, Tina L; Yim, K H

2015-01-01

The purpose of the present study was to examine the factor structure and assess the reliability of the Chinese Conformity to Masculine Norms Inventory-46 (CCMNI-46). Using a cohort of 254 Hong Kong-born Chinese males, scale reliability determination involved the internal consistencies of the entire instrument. Ages of respondents ranged from 18 to 81 years (M = 38.05; SD = 17.3). Confirmatory factor analysis provided support for the psychometric properties of the CCMNI-46, thus confirming the multidimensional structure of the CMNI-46 and the replicability of the CMNI using a Hong Kong Chinese sample. All items loaded onto the corresponding factor with the exception of one item from the emotional control subscale. The overall reliability of the CCMNI-46 was lower than previous Western studies and may well reflect the subtle diversity of masculinity across cultures. The findings offered psychometric support for use of the CCMNI-46 in research and practice regarding Hong Kong Chinese masculinity. The CCMNI-46 provides a useful template for the operationalization of masculine norms in Chinese society.

"How Do I Quantify This?" Students Reflect on Survey Items Related to Diversity and Cross-Racial Interaction

ERIC Educational Resources Information Center

Park, Julie J.; Buckley, Jessica Belue; Koo, Katie

2017-01-01

Given the critical significance of empirical studies of diversity, it is important for researchers and assessment practitioners to gain insight into how students are interpreting and answering survey items that have noteworthy implications for policy and practice. To examine how students make meaning of survey items related to diversity, we…

Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.

PubMed

Kumar, Avishek; Campitelli, Paul; Thorpe, M F; Ozkan, S Banu

2015-12-01

The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled. © 2015 Wiley Periodicals, Inc.

Development and preliminary evaluation of an ultrasonic motor actuated needle guide for 3T MRI-guided transperineal prostate interventions

NASA Astrophysics Data System (ADS)

Song, Sang-Eun; Tokuda, Junichi; Tuncali, Kemal; Tempany, Clare; Hata, Nobuhiko

2012-02-01

Image guided prostate interventions have been accelerated by Magnetic Resonance Imaging (MRI) and robotic technologies in the past few years. However, transrectal ultrasound (TRUS) guided procedure still remains as vast majority in clinical practice due to engineering and clinical complexity of the MRI-guided robotic interventions. Subsequently, great advantages and increasing availability of MRI have not been utilized at its maximum capacity in clinic. To benefit patients from the advantages of MRI, we developed an MRI-compatible motorized needle guide device "Smart Template" that resembles a conventional prostate template to perform MRI-guided prostate interventions with minimal changes in the clinical procedure. The requirements and specifications of the Smart Template were identified from our latest MRI-guided intervention system that has been clinically used in manual mode for prostate biopsy. Smart Template consists of vertical and horizontal crossbars that are driven by two ultrasonic motors via timing-belt and mitergear transmissions. Navigation software that controls the crossbar position to provide needle insertion positions was also developed. The software can be operated independently or interactively with an open-source navigation software, 3D Slicer, that has been developed for prostate intervention. As preliminary evaluation, MRI distortion and SNR test were conducted. Significant MRI distortion was found close to the threaded brass alloy components of the template. However, the affected volume was limited outside the clinical region of interest. SNR values over routine MRI scan sequences for prostate biopsy indicated insignificant image degradation during the presence of the robotic system and actuation of the ultrasonic motors.

An Interactive Design Space Supporting Development of Vehicle Architecture Concept Models

DTIC Science & Technology

2011-06-17

ponents that are not designed to carry structural loads in the assembly, such as seats and other trim items. However, these inertial items have an...Denver, Colorado, USA IMECE2011-64510 AN INTERACTIVE DESIGN SPACE SUPPORTING DEVELOPMENT OF VEHICLE ARCHITECTURE CONCEPT MODELS Gary Osborne...early in the development cycle. Optimization taking place later in the cycle usually occurs at the detail design level, and tends to result in

Effects of cerebellar nuclear inactivation on the learning of a complex forelimb movement in cats.

PubMed

Wang, J J; Shimansky, Y; Bracha, V; Bloedel, J R

1998-05-01

The purpose of this study was to determine the effects of inactivating concurrently the cerebellar interposed and dentate nuclei on the capacity of cats to acquire and retain a complex, goal-directed forelimb movement. To assess the effects on acquisition, cats were required to learn to move a vertical manipulandum bar through a two-segment template with a shape approximating an inverted "L" after the injection of muscimol (saline for the control group) in the interposed and dentate cerebellar nuclei. During training periods, they were exposed progressively to more difficult templates, which were created by decreasing the angle between the two segments of the template. After determining the most difficult template the injected animals could learn within the specified time and performance constraints, the retraining phase of the experiment was initiated in which the cats were required to execute the same sequence of templates in the absence of any injection. This stage of the experiment assessed retention and determined the extent of any relearning required to execute the task at criterion levels. Next, the animals were overtrained without any injection on the most difficult template they could perform. Finally, to determine the effects of nuclear inactivation on retention after extensive retraining, their capacity to perform the same template was determined after muscimol injection in the interposed and dentate nuclei. The findings show that during the inactivation of the dentate and interposed nuclei the animals could learn to execute the more difficult templates. However, when required to execute the most difficult template learned under muscimol on the day after injections were discontinued, the cats had to "relearn" (reacquire) the movement. Finally, when the cerebellar nuclei were inactivated after the animals learned the task in the absence of any injections during the retraining phase, retention was not blocked. The data indicate that the intermediate and lateral cerebellum are not required either for learning this type of complex voluntary movement or for retaining the capacity to perform the task once it is learned. Nevertheless, when the cerebellum becomes available for executing a task learned in the absence of this structure, reacquisition of the behavior usually is necessary. It is hypothesized that the relearning observed after acquisition during muscimol inactivation reflects the tendency of the system to incorporate the cerebellum into the interactions responsible for the learning and performance of a motor sequence that is optimal for executing the task.

In-service documentation tools and statements on palliative sedation in Germany--do they meet the EAPC framework recommendations? A qualitative document analysis.

PubMed

Stiel, Stephanie; Heckel, Maria; Christensen, Britta; Ostgathe, Christoph; Klein, Carsten

2016-01-01

Numerous (inter-)national guidelines and frameworks have been developed to provide recommendations for the application of palliative sedation (PS). However, they are still not widely known, and large variations in PS clinical practice can be found. This study aims to collect and describe contents from documents used in clinical practice and to compare to what extent they match the European Association for Palliative Care (EAPC) framework recommendations. In a national survey on PS in Germany 2012, participants were asked to upload their in-service templates, assessment tools, specific protocols, and in-service statements for the application and documentation of PS. These documents are analyzed by using systematic structured content analysis. Three hundred seven content units of 52 provided documents were coded. The analyzed templates are very heterogeneous and also contain items not mentioned in the EAPC framework. Among 11 scales for the evaluation of sedation level, the Ramsey Sedation Score (n = 5) and the Richmond-Agitation-Sedation-Scale (n = 2) were found most often. For symptom assessment, three different scales were provided one time respectively. In all six PS statements, the common core elements were possible indications for PS, instructions on dose titration, patient monitoring, and care. Wide congruency exists for physical and psychological indications. Most documents coincide on midazolam as a preferred drug and basic monitoring in regular intervals. Aspects such as pre-emptive discussion of the potential role of sedation, informational needs of relatives, and care for the medical professionals are mentioned rarely. The analyzed templates do neglect some points of the EAPC recommendations. However, they expand the ten-point scheme of the framework in some details. The findings may facilitate the development of standardized consensus documentation and monitoring draft as an operational statement.

"Tipping" Teachers toward Change: Developing Leadership Characteristics through Book Club

ERIC Educational Resources Information Center

Klinker, JoAnn Franklin; Watson, Patricia A.; Furgerson, Paige; Halsey, Pamela; Janisch, Carole

2010-01-01

Teacher leadership is difficult because teachers often lack encouragement and opportunities to implement ideas that deliberately and strategically interact with and tap power structures in schools. In this study, a book club of university faculty and middle school teachers provided teacher leaders with a template for change around concepts…

Experiences with Reusable E-Learning Objects: From Theory to Practice.

ERIC Educational Resources Information Center

Muzio, Jeanette A.; Heins, Tanya; Mundell, Roger

2002-01-01

Explains reusable electronic learning objects (ELOs) that are stored in a database and discusses the practical application of creating and reusing ELOs at Royal Roads University (Canada). Highlights include ELOs and the instructional design of online courses; and examples of using templates to develop interactive ELOs. (Author/LRW)

Item Order, Response Format, and Examinee Sex and Handedness and Performance on a Multiple-Choice Test.

ERIC Educational Resources Information Center

Kleinke, David J.

Four forms of a 36-item adaptation of the Stanford Achievement Test were administered to 484 fourth graders. External factors potentially influencing test performance were examined, namely: (1) item order (easy-to-difficult vs. uniform); (2) response location (left column vs. right column); (3) handedness which may interact with response location;…

Plasma Interactions With Spacecraft

DTIC Science & Technology

2009-04-01

software core 3 Table 2. N2kDB classes 8 Table 3. N2kDB Application Programmer Interface 11 Table 4. How to get number of items from N2kDB 14 Table 5...grid, timesteps, and pages of particles. Table 4 specifies how these functions are used to get useful quantities. The Getcount function gets the...number of items with data item names that start with the specified string. 13 Table 4. How to get number of items from N2kDB. Function Specifics

Strategy combination during execution of memory strategies in young and older adults.

PubMed

Hinault, Thomas; Lemaire, Patrick; Touron, Dayna

2017-05-01

The present study investigated whether people can combine two memory strategies to encode pairs of words more efficiently than with a single strategy, and age-related differences in such strategy combination. Young and older adults were asked to encode pairs of words (e.g., satellite-tunnel). For each item, participants were told to use either the interactive-imagery strategy (e.g., mentally visualising the two words and making them interact), the sentence-generation strategy (i.e., generate a sentence linking the two words), or with strategy combination (i.e., generating a sentence while mentally visualising it). Participants obtained better recall performance on items encoded with strategy combination than on items encoded with interactive-imagery or sentence-generation strategies. Moreover, we found age-related decline in such strategy combination. These findings have important implications to further our understanding of execution of memory strategies, and suggest that strategy combination occurs in a variety of cognitive domains.

Testosterone treatment and MMPI-2 improvement in transgender men: a prospective controlled study.

PubMed

Keo-Meier, Colton L; Herman, Levi I; Reisner, Sari L; Pardo, Seth T; Sharp, Carla; Babcock, Julia C

2015-02-01

Most transgender men desire to receive testosterone treatment in order to masculinize their bodies. In this study, we aimed to investigate the short-term effects of testosterone treatment on psychological functioning in transgender men. This is the 1st controlled prospective follow-up study to examine such effects. We examined a sample of transgender men (n = 48) and nontransgender male (n = 53) and female (n = 62) matched controls (mean age = 26.6 years; 74% White). We asked participants to complete the Minnesota Multiphasic Personality Inventory (2nd ed., or MMPI-2; Butcher, Graham, Tellegen, Dahlstrom, & Kaemmer, 2001) to assess psychological functioning at baseline and at the acute posttreatment follow-up (3 months after testosterone initiation). Regression models tested (a) Gender × Time interaction effects comparing divergent mean response profiles across measurements by gender identity; (b) changes in psychological functioning scores for acute postintervention measurements, adjusting for baseline measures, comparing transgender men with their matched nontransgender male and female controls and adjusting for baseline scores; and (c) changes in meeting clinical psychopathological thresholds. Statistically significant changes in MMPI-2 scale scores were found at 3-month follow-up after initiating testosterone treatment relative to baseline for transgender men compared with female controls (female template): reductions in Hypochondria (p < .05), Depression (p < .05), Hysteria (p < .05), and Paranoia (p < .01); and increases in Masculinity-Femininity scores (p < .01). Gender × Time interaction effects were found for Hysteria (p < .05) and Paranoia (p < .01) relative to female controls (female template) and for Hypochondria (p < .05), Depression (p < .01), Hysteria (p < .01), Psychopathic Deviate (p < .05), Paranoia (p < .01), Psychasthenia (p < .01), and Schizophrenia (p < .01) compared with male controls (male template). In addition, the proportion of transgender men presenting with co-occurring psychopathology significantly decreased from baseline compared with 3-month follow-up relative to controls (p < .05). Findings suggest that testosterone treatment resulted in increased levels of psychological functioning on multiple domains in transgender men relative to nontransgender controls. These findings differed in comparisons of transgender men with female controls using the female template and with male controls using the male template. No iatrogenic effects of testosterone were found. These findings suggest a direct positive effect of 3 months of testosterone treatment on psychological functioning in transgender men. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Surface-imprinted microspheres prepared by a template-oriented method for the chiral separation of amlodipine.

PubMed

Lai, Shenzhi; Ouyang, Xiaoli; Cai, Changqun; Xu, Wensheng; Chen, Chunyan; Chen, Xiaoming

2017-05-01

The surface imprinting technique has been developed to overcome the mass-transfer difficulty, but the utilization ratio of template molecules in the imprinting procedure still remains a challengeable task to be improved. In this work, specifically designed surface-imprinted microspheres were prepared by a template-oriented method for enantioseparation of amlodipine besylate. Submicron mesoporous silica microspheres were surface-modified with double bonds, followed by polymerizing methacrylic acid to generate carboxyl modified mesoporous silica microspheres (PMAA@SiO 2 ). Afterwards, PMAA@SiO 2 was densely adsorbed with (S)-amlodipine molecules to immobilize template molecules through multiple hydrogen bonding interactions. Then surface molecular imprinting was carried out by cross-linking the carboxyl group of PMAA@SiO 2 with ethylene glycol diglycidyl ether. The surface-imprinted microspheres showed fast binding kinetics of only 20 min for equilibrium adsorption, and the saturation adsorption capacity reached 137 mg/g. The imprinted materials displayed appreciable chiral separation ability when used as column chromatography for enantioseparation of amlodipine from amlodipine besylate, and the enantiomeric excess of (S)-amlodipine reached 13.8% with only 2.3 cm column length by no extra chiral additives. Besides, the imprinted materials exhibited excellent reusability, and this allows the potential application for amplification production of amlodipine enantiomer. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two Different Template Replicators Coexisting in the Same Protocell: Stochastic Simulation of an Extended Chemoton Model

PubMed Central

Zachar, István; Fedor, Anna; Szathmáry, Eörs

2011-01-01

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix. PMID:21818258

Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.

PubMed

Zachar, István; Fedor, Anna; Szathmáry, Eörs

2011-01-01

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.

Directed self-assembly of virus particles at nanoscale chemical templates

NASA Astrophysics Data System (ADS)

Chung, Sung-Wook; Cheung, Chin Li; Chatterji, Anju; Lin, Tianwei; Johnson, Jack; de Yoreo, Jim

2006-03-01

Because viruses can be site-specifically engineered to present catalytic, electronic, and optical moieties, they are attractive as building blocks for hierarchical nanostructures. We report results using scanned probe nanolithography to direct virus organization into 1D and 2D patterns and in situ AFM investigations of organization dynamics as pattern geometry, inter-viral potential, virus flux, and virus-pattern interaction are varied. Cowpea Mosaic Virus was modified to present surface sites with histidine (His) or cysteine (Cys) groups. Flat gold substrates were patterned with 10-100nm features of alkyl thiols terminated by Ni-NTA or meleimide groups to reversibly and irreversibly bind to the Hys and Cys groups, respectively. We show how assembly kinetics, degree of ordering and cluster-size distribution at these templates depend on the control parameters and present a physical picture of virus assembly at templates that incorporates growth dynamics of small-molecule epitaxial systems and condensation dynamics of colloidal systems. This work was performed under the auspices of the U. S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.

Cell-free system for synthesizing membrane proteins cell free method for synthesizing membrane proteins

DOEpatents

Laible, Philip D; Hanson, Deborah K

2013-06-04

The invention provides an in vitro method for producing proteins, membrane proteins, membrane-associated proteins, and soluble proteins that interact with membrane-associated proteins for assembly into an oligomeric complex or that require association with a membrane for proper folding. The method comprises, supplying intracytoplasmic membranes from organisms; modifying protein composition of intracytoplasmic membranes from organism by modifying DNA to delete genes encoding functions of the organism not associated with the formation of the intracytoplasmic membranes; generating appropriate DNA or RNA templates that encode the target protein; and mixing the intracytoplasmic membranes with the template and a transcription/translation-competent cellular extract to cause simultaneous production of the membrane proteins and encapsulation of the membrane proteins within the intracytoplasmic membranes.

Scale Refinement and Initial Evaluation of a Behavioral Health Function Measurement Tool for Work Disability Evaluation

PubMed Central

Marfeo, Elizabeth E.; Ni, Pengsheng; Bogusz, Kara; Meterko, Mark; McDonough, Christine M.; Chan, Leighton; Rasch, Elizabeth K.; Brandt, Diane E.; Jette, Alan M.

2014-01-01

Objectives To use item response theory (IRT) data simulations to construct and perform initial psychometric testing of a newly developed instrument, the Social Security Administration Behavioral Health Function (SSA-BH) instrument, that aims to assess behavioral health functioning relevant to the context of work. Design Cross-sectional survey followed by item response theory (IRT) calibration data simulations Setting Community Participants A sample of individuals applying for SSA disability benefits, claimants (N=1015), and a normative comparative sample of US adults (N=1000) Interventions None. Main Outcome Measure Social Security Administration Behavioral Health Function (SSA-BH) measurement instrument Results Item response theory analyses supported the unidimensionality of four SSA-BH scales: Mood and Emotions (35 items), Self-Efficacy (23 items), Social Interactions (6 items), and Behavioral Control (15 items). All SSA-BH scales demonstrated strong psychometric properties including reliability, accuracy, and breadth of coverage. High correlations of the simulated 5- or 10- item CATs with the full item bank indicated robust ability of the CAT approach to comprehensively characterize behavioral health function along four distinct dimensions. Conclusions Initial testing and evaluation of the SSA-BH instrument demonstrated good accuracy, reliability, and content coverage along all four scales. Behavioral function profiles of SSA claimants were generated and compared to age and sex matched norms along four scales: Mood and Emotions, Behavioral Control, Social Interactions, and Self-Efficacy. Utilizing the CAT based approach offers the ability to collect standardized, comprehensive functional information about claimants in an efficient way, which may prove useful in the context of the SSA’s work disability programs. PMID:23542404

Development of a new assessment scale for measuring interaction during staff-assisted transfer of residents in dementia special care units.

PubMed

Thunborg, Charlotta; von Heideken Wågert, Petra; Götell, Eva; Ivarsson, Ann-Britt; Söderlund, Anne

2015-02-10

Mobility problems and cognitive deficits related to transferring or moving persons suffering from dementia are associated with dependency. Physical assistance provided by staff is an important component of residents' maintenance of mobility in dementia care facilities. Unfortunately, hands-on assistance during transfers is also a source of confusion in persons with dementia, as well as a source of strain in the caregiver. The bidirectional effect of actions in a dementia care dyad involved in transfer is complicated to evaluate. This study aimed to develop an assessment scale for measuring actions related to transferring persons with dementia by dementia care dyads. This study was performed in four phases and guided by the framework of the biopsychosocial model and the approach presented by Social Cognitive Theory. These frameworks provided a starting point for understanding reciprocal effects in dyadic interaction. The four phases were 1) a literature review identifying existing assessment scales; 2) analyses of video-recorded transfer of persons with dementia for further generation of items, 3) computing the item content validity index of the 93 proposed items by 15 experts; and 4) expert opinion on the response scale and feasibility testing of the new assessment scale by video observation of the transfer situations. The development process resulted in a 17-item scale with a seven-point response scale. The scale consists of two sections. One section is related to transfer-related actions (e.g., capability of communication, motor skills performance, and cognitive functioning) of the person with dementia. The other section addresses the caregivers' facilitative actions (e.g., preparedness of transfer aids, interactional skills, and means of communication and interaction). The literature review and video recordings provided ideas for the item pool. Expert opinion decreased the number of items by relevance ratings and qualitative feedback. No further development of items was performed after feasibility testing of the scale. To enable assessment of transfer-related actions in dementia care dyads, our new scale shows potential for bridging the gap in this area. Results from this study could provide health care professionals working in dementia care facilities with a useful tool for assessing transfer-related actions.

Molecular identification of python species: development and validation of a novel assay for forensic investigations.

PubMed

Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

2015-05-01

Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Nursing Care Interpersonal Relationship Questionnaire: elaboration and validation.

PubMed

Borges, José Wicto Pereira; Moreira, Thereza Maria Magalhães; Andrade, Dalton Franscisco de

2018-01-08

to elaborate an instrument for the measurement of the interpersonal relationship in nursing care through the Item Response Theory, and the validation thereof. methodological study, which followed the three poles of psychometry: theoretical, empirical and analytical. The Nursing Care Interpersonal Relationship Questionnaire was developed in light of the Imogene King's Interpersonal Conceptual Model and the psychometric properties were studied through the Item Response Theory in a sample of 950 patients attended in Primary, Secondary and Tertiary Health Care. the final instrument consisted of 31 items, with Cronbach's alpha of 0.90 and McDonald's Omega of 0.92. The parameters of the Item Response Theory demonstrated high discrimination in 28 items, being developed a five-level interpretive scale. At the first level, the communication process begins, gaining a wealth of interaction. Subsequent levels demonstrate qualitatively the points of effectiveness of the interpersonal relationship with the involvement of behaviors related to the concepts of transaction and interaction, followed by the concept of role. the instrument was created and proved to be consistent to measure interpersonal relationship in nursing care, as it presented adequate reliability and validity parameters.

Reporting of Telehealth-Delivered Dietary Intervention Trials in Chronic Disease: Systematic Review.

PubMed

Warner, Molly M; Kelly, Jaimon T; Reidlinger, Dianne P; Hoffmann, Tammy C; Campbell, Katrina L

2017-12-11

Telehealth-delivered dietary interventions are effective for chronic disease management and are an emerging area of clinical practice. However, to apply interventions from the research setting in clinical practice, health professionals need details of each intervention component. The aim of this study was to evaluate the completeness of intervention reporting in published dietary chronic disease management trials that used telehealth delivery methods. Eligible randomized controlled trial publications were identified through a systematic review. The completeness of reporting of experimental and comparison interventions was assessed by two independent assessors using the Template for Intervention Description and Replication (TIDieR) checklist that consists of 12 items including intervention rationale, materials used, procedures, providers, delivery mode, location, when and how much intervention delivered, intervention tailoring, intervention modifications, and fidelity. Where reporting was incomplete, further information was sought from additional published material and through email correspondence with trial authors. Within the 37 eligible trials, there were 49 experimental interventions and 37 comparison interventions. One trial reported every TIDieR item for their experimental intervention. No publications reported every item for the comparison intervention. For the experimental interventions, the most commonly reported items were location (96%), mode of delivery (98%), and rationale for the essential intervention elements (96%). Least reported items for experimental interventions were modifications (2%) and intervention material descriptions (39%) and where to access them (20%). Of the 37 authors, 14 responded with further information, and 8 could not be contacted. Many details of the experimental and comparison interventions in telehealth-delivered dietary chronic disease management trials are incompletely reported. This prevents accurate interpretation of trial results and implementation of effective interventions in clinical practice. ©Molly M Warner, Jaimon T Kelly, Dianne P Reidlinger, Tammy C Hoffmann, Katrina L Campbell. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 11.12.2017.

FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.

PubMed

Michino, Mayako; Chen, Jianhan; Stevens, Raymond C; Brooks, Charles L

2010-08-01

Building reliable structural models of G protein-coupled receptors (GPCRs) is a difficult task because of the paucity of suitable templates, low sequence identity, and the wide variety of ligand specificities within the superfamily. Template-based modeling is known to be the most successful method for protein structure prediction. However, refinement of homology models within 1-3 A C alpha RMSD of the native structure remains a major challenge. Here, we address this problem by developing a novel protocol (foldGPCR) for modeling the transmembrane (TM) region of GPCRs in complex with a ligand, aimed to accurately model the structural divergence between the template and target in the TM helices. The protocol is based on predicted conserved inter-residue contacts between the template and target, and exploits an all-atom implicit membrane force field. The placement of the ligand in the binding pocket is guided by biochemical data. The foldGPCR protocol is implemented by a stepwise hierarchical approach, in which the TM helical bundle and the ligand are assembled by simulated annealing trials in the first step, and the receptor-ligand complex is refined with replica exchange sampling in the second step. The protocol is applied to model the human beta(2)-adrenergic receptor (beta(2)AR) bound to carazolol, using contacts derived from the template structure of bovine rhodopsin. Comparison with the X-ray crystal structure of the beta(2)AR shows that our protocol is particularly successful in accurately capturing helix backbone irregularities and helix-helix packing interactions that distinguish rhodopsin from beta(2)AR. (c) 2010 Wiley-Liss, Inc.

Recycling of surfactant template in mesoporous MCM-41 synthesis

NASA Astrophysics Data System (ADS)

Lai, J. Y.; Twaiq, F.; Ngu, L. H.

2017-06-01

The recycling of surfactant template is investigated through the reuse of the surfactant template in the mesoporous MCM-41 synthesis process. In the synthesis of MCM-41, tetraethylorthosilicate (TEOS) solution in water was utilized as the silica source while hexadecyltrimethylammonium bromide (CTAB) solution in ethyl alcohol was used as a surfactant template. The synthesized gel is formed thoroughly by mixing the two solutions under acid conditions with a pH value of 0.5 for 1 hour and kept for crystallization for 48 hours. The as-synthesized MCM-41 powder is recovered by filtration while the filtrate (mother liquor) was then reused for the second synthesis cycle. The synthesis procedure was repeated till no further solid product was formed. The synthesized gel was not produced in the unifying solution in the fifth cycle of MCM-41 synthesis. The quality of the calcined MCM-41 powder produced in each synthesis cycle was evaluated by calculating the amount of MCM-41 produced and the surface area of the powder product. The result showed that 1.28, 0.37, 1.64, 1.90 and 0.037 g were obtained in the 1st, 2nd, 3rd, 4th and 5th synthesis cycle, respectively. The surface area of the powder produced was found to be 1170, 916, 728, and 508 m2/g for 1st, 2nd, 3rd and 4th respectively. The concentration of the surfactant template has reached value lower than the critical micelle concentration (CMC) and remained constant after the 4th cycle. There was no further formation of gel due to low availability in the interaction between silicate anions and surfactant cations when the amount of TEOS was fixed for every synthesis cycle.

One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting.

PubMed

Ensslen, Philipp; Wagenknecht, Hans-Achim

2015-10-20

Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.

Development of a templated approach to fabricate diamond patterns on various substrates.

PubMed

Shimoni, Olga; Cervenka, Jiri; Karle, Timothy J; Fox, Kate; Gibson, Brant C; Tomljenovic-Hanic, Snjezana; Greentree, Andrew D; Prawer, Steven

2014-06-11

We demonstrate a robust templated approach to pattern thin films of chemical vapor deposited nanocrystalline diamond grown from monodispersed nanodiamond (mdND) seeds. The method works on a range of substrates, and we herein demonstrate the method using silicon, aluminum nitride (AlN), and sapphire substrates. Patterns are defined using photo- and e-beam lithography, which are seeded with mdND colloids and subsequently introduced into microwave assisted chemical vapor deposition reactor to grow patterned nanocrystalline diamond films. In this study, we investigate various factors that affect the selective seeding of different substrates to create high quality diamond thin films, including mdND surface termination, zeta potential, surface treatment, and plasma cleaning. Although the electrostatic interaction between mdND colloids and substrates is the main process driving adherence, we found that chemical reaction (esterification) or hydrogen bonding can potentially dominate the seeding process. Leveraging the knowledge on these different interactions, we optimize fabrication protocols to eliminate unwanted diamond nucleation outside the patterned areas. Furthermore, we have achieved the deposition of patterned diamond films and arrays over a range of feature sizes. This study contributes to a comprehensive understanding of the mdND-substrate interaction that will enable the fabrication of integrated nanocrystalline diamond thin films for microelectronics, sensors, and tissue culturing applications.

Controllable synthesis of mesoporous carbon nanospheres and Fe-N/carbon nanospheres as efficient oxygen reduction electrocatalysts.

PubMed

Wei, Jing; Liang, Yan; Zhang, Xinyi; Simon, George P; Zhao, Dongyuan; Zhang, Jin; Jiang, Sanping; Wang, Huanting

2015-04-14

The synthesis of mesoporous carbon nanospheres (MCNs), especially with diameters below 200 nm remains a great challenge due to weak interactions between the carbon precursors and soft templates, as well as the uncontrollable cross-linking rate of carbon precursors. Herein, we demonstrate a simple acid-assisted, hydrothermal synthesis approach to synthesizing such uniform MCNs with well controlled diameters ranging from 20 to 150 nm under highly acidic conditions (2 M HCl). Both the carbon precursor and the template are partly protonated under such conditions and show additional Coulombic interactions with chloride ions (acts as mediators). This kind of enhanced interaction is similar to that of the "I(+)X(-)S(+)" mechanism in the synthesis of mesoporous metal oxide, which can effectively retard the cross-linking rate of resol molecules and avoid macroscopic phase separation during the hydrothermal synthesis. Due to their uniform spherical morphology, small diameter, and high surface areas, MCNs can be modified with Fe and N species via impregnation of cheap precursors (ferric nitrate and dicyandiamide), which are further converted into nonprecious electrocatalysts for oxygen reduction reactions. The resulting Fe-N/MCNs exhibit high catalytic activities, long-term stability and improved methanol tolerance under alkaline conditions, which can be potentially used in direct methanol fuel cells and metal-air batteries.

Williams Holistic Approach Model (WHAM): Sustainable University Leadership from the Perspective of a Woman Physicist

ERIC Educational Resources Information Center

Williams, Elvira S.

2010-01-01

University leadership from career and organizational viewpoints are discussed from the perspective of a woman physicist. Laws of physics are used, through appropriate analogies, as templates for structuring useful life lessons on holistic WHAM leadership. Interactive university skill sets and program policies based on holistic WHAM approaches are…

The Pre-Designed Lesson: Teaching with Transdisciplinary Pedagogical Templates (TPTs)

ERIC Educational Resources Information Center

Dobozy, Eva

2017-01-01

An ongoing challenge in higher education is the support of educators in their development of effective pedagogies. The field of educational research and practice referred to as Learning Design may be able to help educators with no or limited pedagogical training deliver highly interactive and contemporary teaching and learning offerings. The…

Wetland soils, hydrology and geomorphology

Treesearch

C. Rhett Jackson; James A. Thompson; Randall K. Kolka

2014-01-01

The hydrology, soils, and watershed processes of a wetland all interact with vegetation and animals over time to create the dynamic physical template upon which a wetland's ecosystem is based (Fig. 2.1). With respect to many ecosystem processes, the physical factors defining a wetland environment at any particular time are often treated as independent variables,...

Piezoelectric Templates - New Views on Biomineralization and Biomimetics.

PubMed

Stitz, Nina; Eiben, Sabine; Atanasova, Petia; Domingo, Neus; Leineweber, Andreas; Burghard, Zaklina; Bill, Joachim

2016-05-23

Biomineralization in general is based on electrostatic interactions and molecular recognition of organic and inorganic phases. These principles of biomineralization have also been utilized and transferred to bio-inspired synthesis of functional materials during the past decades. Proteins involved in both, biomineralization and bio-inspired processes, are often piezoelectric due to their dipolar character hinting to the impact of a template's piezoelectricity on mineralization processes. However, the piezoelectric contribution on the mineralization process and especially the interaction of organic and inorganic phases is hardly considered so far. We herein report the successful use of the intrinsic piezoelectric properties of tobacco mosaic virus (TMV) to synthesize piezoelectric ZnO. Such films show a two-fold increase of the piezoelectric coefficient up to 7.2 pm V(-1) compared to films synthesized on non-piezoelectric templates. By utilizing the intrinsic piezoelectricity of a biotemplate, we thus established a novel synthesis pathway towards functional materials, which sheds light on the whole field of biomimetics. The obtained results are of even broader and general interest since they are providing a new, more comprehensive insight into the mechanisms involved into biomineralization in living nature.

Prospects for cosmological collider physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meerburg, P. Daniel; Münchmeyer, Moritz; Muñoz, Julian B.

2017-03-01

It is generally expected that heavy fields are present during inflation, which can leave their imprint in late-time cosmological observables. The main signature of these fields is a small amount of distinctly shaped non-Gaussianity, which if detected, would provide a wealth of information about the particle spectrum of the inflationary Universe. Here we investigate to what extent these signatures can be detected or constrained using futuristic 21-cm surveys. We construct model-independent templates that extract the squeezed-limit behavior of the bispectrum, and examine their overlap with standard inflationary shapes and secondary non-Gaussianities. We then use these templates to forecast detection thresholdsmore » for different masses and couplings using a 3D reconstruction of modes during the dark ages ( z ∼ 30–100). We consider interactions of several broad classes of models and quantify their detectability as a function of the baseline of a dark ages interferometer. Our analysis shows that there exists the tantalizing possibility of discovering new particles with different masses and interactions with future 21-cm surveys.« less

Superconductivity: A Continuous Surprise or ``How I Learned to Love the Surprises''

NASA Astrophysics Data System (ADS)

Dynes, Robert

2011-03-01

When I was invited to give this talk, I thought I would talk about new materials, or new opportunities, or the electron-phonon interaction, or non electron phonon interactions. Then when I looked at the speakers in this symposium and the subjects that they were scheduled to talk about, I realized that they were better equipped to talk individually about each of these subjects than I was, and it was my role to introduce the subject and give a perspective on the future of research and applications in superconductivity. My experience over the past decades has been that it is very dangerous to make predictions in this field. There are many examples of our distinguished colleagues who have engaged in this practice only to be proven wrong by surprise after surprise Fortunately, this has not harmed their reputations or their courage to continue to make predictions. In this talk I will reflect on my personal experience over several decades of research in superconductivity and how my own thinking has changed. Hopefully, I will Transmit a flavor of this field and stimulate other younger investigators to be adventuresome Prepare the audience for the talks that follow Motivate the following speakers to reveal their own predictions and surprises.

Identification of putative agouti-related protein(87-132)-melanocortin-4 receptor interactions by homology molecular modeling and validation using chimeric peptide ligands.

PubMed

Wilczynski, Andrzej; Wang, Xiang S; Joseph, Christine G; Xiang, Zhimin; Bauzo, Rayna M; Scott, Joseph W; Sorensen, Nicholas B; Shaw, Amanda M; Millard, William J; Richards, Nigel G; Haskell-Luevano, Carrie

2004-04-22

Agouti-related protein (AGRP) is one of only two naturally known antagonists of G-protein-coupled receptors (GPCRs) identified to date. Specifically, AGRP antagonizes the brain melanocortin-3 and -4 receptors involved in energy homeostasis. Alpha-melanocyte stimulating hormone (alpha-MSH) is one of the known endogenous agonists for these melanocortin receptors. Insight into putative interactions between the antagonist AGRP amino acids with the melanocortin-4 receptor (MC4R) may be important for the design of unique ligands for the treatment of obesity related diseases and is currently lacking in the literature. A three-dimensional homology molecular model of the mouse MC4 receptor complex with the hAGRP(87-132) ligand docked into the receptor has been developed to identify putative antagonist ligand-receptor interactions. Key putative AGRP-MC4R interactions include the Arg111 of hAGRP(87-132) interacting in a negatively charged pocket located in a cavity formed by transmembrane spanning (TM) helices 1, 2, 3, and 7, capped by the acidic first extracellular loop (EL1) and specifically with the conserved melanocortin receptor residues mMC4R Glu92 (TM2), mMC4R Asp114 (TM3), and mMC4R Asp118 (TM3). Additionally, Phe112 and Phe113 of hAGRP(87-132) putatively interact with an aromatic hydrophobic pocket formed by the mMC4 receptor residues Phe176 (TM4), Phe193 (TM5), Phe253 (TM6), and Phe254 (TM6). To validate the AGRP-mMC4R model complex presented herein from a ligand perspective, we generated nine chimeric peptide ligands based on a modified antagonist template of the hAGRP(109-118) (Tyr-c[Asp-Arg-Phe-Phe-Asn-Ala-Phe-Dpr]-Tyr-NH(2)). In these chimeric ligands, the antagonist AGRP Arg-Phe-Phe residues were replaced by the melanocortin agonist His/D-Phe-Arg-Trp amino acids. These peptides resulted in agonist activity at the mouse melanocortin receptors (mMC1R and mMC3-5Rs). The most notable results include the identification of a novel subnanomolar melanocortin peptide template Tyr-c[Asp-His-DPhe-Arg-Trp-Asn-Ala-Phe-Dpr]-Tyr-NH(2) that is equipotent to alpha-MSH at the mMC1, mMC3, and mMC5 receptors but is 30-fold more potent than alpha-MSH at the mMC4R. Additionally, these studies identified a new and novel >200-fold MC4R versus MC3R selective peptide Tyr-c[Asp-D-Phe-Arg-Trp-Asn-Ala-Phe-Dpr]-Tyr-NH(2) template. Furthermore, when the His-DPhe-Arg-Trp sequence is used to replace the hAGRP Arg-Phe-Phe residues in the "mini"-AGRP (hAGRP87-120, C105A) template, a potent nanomolar agonist resulted at the mMC1R and MC3-5Rs.

Characterization and modification of phage T7 DNA polymerase for use in DNA sequencing; Progress report, June 1, 1990--May 31, 1993

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richardson, C.C.

1993-12-31

This project focuses on the DNA polymerase (gene 5 protein) of phage T7 for use in DNA sequence analysis. Gene 5 protein interacts with accessory proteins to acquire properties essential for DNA replication. One goal is to understand these interactions in order to modify the proteins for use in DNA sequencing. E. coli thioredoxin, binds to gene 5 protein and clamps it to a primer-template. They have analyzed the binding of gene 5 protein-thioredoxin to primer-templates and have defined the optimal conditions to form an extremely stable complex with a dNTP in the polymerase catalytic site. The spatial proximity ofmore » these components has been determined using fluorescence emission anisotropy. The T7 DNA binding protein, the gene 2.5 protein, interacts with gene 5 protein and gene 4 protein to increase processivity and primer synthesis, respectively. Mutant gene 2.5 proteins have been isolated that do not interact with T7 DNA polymerase and can not support T7 growth. The nucleotide binding site of the T7 helicase has been identified and mutations affecting the site provide information on how the hydrolysis of NTPs fuel its unidirectional translocation. The sequence, GTC, has been shown to be necessary and sufficient for recognition by the T7 primase. The T7 gene 5.5 protein interacts with the E. coli nucleoid protein, H-NS, and also overcomes the phage {lambda} rex restriction system.« less

IDSP- INTERACTIVE DIGITAL SIGNAL PROCESSOR

NASA Technical Reports Server (NTRS)

Mish, W. H.

1994-01-01

The Interactive Digital Signal Processor, IDSP, consists of a set of time series analysis "operators" based on the various algorithms commonly used for digital signal analysis work. The processing of a digital time series to extract information is usually achieved by the application of a number of fairly standard operations. However, it is often desirable to "experiment" with various operations and combinations of operations to explore their effect on the results. IDSP is designed to provide an interactive and easy-to-use system for this type of digital time series analysis. The IDSP operators can be applied in any sensible order (even recursively), and can be applied to single time series or to simultaneous time series. IDSP is being used extensively to process data obtained from scientific instruments onboard spacecraft. It is also an excellent teaching tool for demonstrating the application of time series operators to artificially-generated signals. IDSP currently includes over 43 standard operators. Processing operators provide for Fourier transformation operations, design and application of digital filters, and Eigenvalue analysis. Additional support operators provide for data editing, display of information, graphical output, and batch operation. User-developed operators can be easily interfaced with the system to provide for expansion and experimentation. Each operator application generates one or more output files from an input file. The processing of a file can involve many operators in a complex application. IDSP maintains historical information as an integral part of each file so that the user can display the operator history of the file at any time during an interactive analysis. IDSP is written in VAX FORTRAN 77 for interactive or batch execution and has been implemented on a DEC VAX-11/780 operating under VMS. The IDSP system generates graphics output for a variety of graphics systems. The program requires the use of Versaplot and Template plotting routines and IMSL Math/Library routines. These software packages are not included in IDSP. The virtual memory requirement for the program is approximately 2.36 MB. The IDSP system was developed in 1982 and was last updated in 1986. Versaplot is a registered trademark of Versatec Inc. Template is a registered trademark of Template Graphics Software Inc. IMSL Math/Library is a registered trademark of IMSL Inc.

Storyboard Development for Interactive Multimedia Training.

ERIC Educational Resources Information Center

Orr, Kay L.; And Others

1994-01-01

Discusses procedures for storyboard development and provides guidelines for designing interactive multimedia courseware, including interactivity, learner control, feedback, visual elements, motion video, graphics/animation, text, audio, and programming. A topical bibliography that lists 98 items is included. (LRW)

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II[OPEN

PubMed Central

Qu, Jie; Ji, Shaoyi; Wallace, Andrew J.; Wu, Jian; Li, Yi; Gopalan, Venkat; Ding, Biao

2016-01-01

Some DNA-dependent RNA polymerases (DdRPs) possess RNA-dependent RNA polymerase activity, as was first discovered in the replication of Potato spindle tuber viroid (PSTVd) RNA genome in tomato (Solanum lycopersicum). Recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. Here, we used PSTVd as a model to uncover auxiliary factors essential for RNA-templated transcription by DdRP. PSTVd replication in the nucleoplasm generates (−)-PSTVd intermediates and (+)-PSTVd copies. We found that the Nicotiana benthamiana canonical 9-zinc finger (ZF) Transcription Factor IIIA (TFIIIA-9ZF) as well as its variant TFIIIA-7ZF interacted with (+)-PSTVd, but only TFIIIA-7ZF interacted with (−)-PSTVd. Suppression of TFIIIA-7ZF reduced PSTVd replication, and overexpression of TFIIIA-7ZF enhanced PSTVd replication in planta. Consistent with the locale of PSTVd replication, TFIIIA-7ZF was found in the nucleoplasm and nucleolus, in contrast to the strictly nucleolar localization of TFIIIA-9ZF. Footprinting assays revealed that only TFIIIA-7ZF bound to a region of PSTVd critical for initiating transcription. Furthermore, TFIIIA-7ZF strongly enhanced the in vitro transcription of circular (+)-PSTVd by partially purified Pol II. Together, our results identify TFIIIA-7ZF as a dedicated cellular transcription factor that acts in DdRP-catalyzed RNA-templated transcription, highlighting both the extraordinary evolutionary adaptation of viroids and the potential of DdRPs for a broader role in cellular processes. PMID:27113774

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.

PubMed

Tome, Jacob M; Ozer, Abdullah; Pagano, John M; Gheba, Dan; Schroth, Gary P; Lis, John T

2014-06-01

RNA-protein interactions play critical roles in gene regulation, but methods to quantitatively analyze these interactions at a large scale are lacking. We have developed a high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay by adapting a high-throughput DNA sequencer to quantify the binding of fluorescently labeled protein to millions of RNAs anchored to sequenced cDNA templates. Using HiTS-RAP, we measured the affinity of mutagenized libraries of GFP-binding and NELF-E-binding aptamers to their respective targets and identified critical regions of interaction. Mutations additively affected the affinity of the NELF-E-binding aptamer, whose interaction depended mainly on a single-stranded RNA motif, but not that of the GFP aptamer, whose interaction depended primarily on secondary structure.

Rehabilitation Aids.

ERIC Educational Resources Information Center

National Center on Educational Media and Materials for the Handicapped, Columbus, OH.

Selected from the National Instructional Materials Information System (NIMIS)--a computer based on-line interactive retrieval system on special education materials--the bibliography covers 40 equipment items for rehabilitation and physical therapy programs for all levels of handicapped children. Described are such items as a handygym, a suspension…

RNA Nanotechnology: Engineering, Assembly and Applications in Detection, Gene Delivery and Therapy

PubMed Central

Guo, Peixuan

2010-01-01

Biological macromolecules including DNA, RNA, and proteins, have intrinsic features that make them potential building blocks for the bottom-up fabrication of nanodevices. RNA is unique in nanoscale fabrication due to its amazing diversity of function and structure. RNA molecules can be designed and manipulated with a level of simplicity characteristic of DNA while possessing versatility in structure and function similar to that of proteins. RNA molecules typically contain a large variety of single stranded loops suitable for inter- and intra-molecular interaction. These loops can serve as mounting dovetails obviating the need for external linking dowels in fabrication and assembly. The self-assembly of nanoparticles from RNA involves cooperative interaction of individual RNA molecules that spontaneously assemble in a predefined manner to form a larger two- or three-dimensional structure. Within the realm of self-assembly there are two main categories, namely template and non-template. Template assembly involves interaction of RNA molecules under the influence of specific external sequence, forces, or spatial constraints such as RNA transcription, hybridization, replication, annealing, molding, or replicas. In contrast, non-template assembly involves formation of a larger structure by individual components without the influence of external forces. Examples of non-template assembly are ligation, chemical conjugation, covalent linkage, and loop/loop interaction of RNA, especially the formation of RNA multimeric complexes. The best characterized RNA multiplier and the first to be described in RNA nanotechnological application is the motor pRNA of bacteriophage phi29 which form dimers, trimers, and hexamers, via hand-in-hand interaction. phi29 pRNA can be redesigned to form a variety of structures and shapes including twins, tetramers, rods, triangles, and 3D arrays several microns in size via interaction of programmed helical regions and loops. 3D RNA array formation requires a defined nucleotide number for twisting and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH. Both the therapeutic siRNA or ribozyme and a receptor-binding RNA aptamer or other ligands have been engineered into individual pRNAs. Individual chimeric RNA building blocks harboring siRNA or other therapeutic molecules have been fabricated subsequently into a trimer through hand-in-hand interaction of the engineered right and left interlocking RNA loops. The incubation of these particles containing the receptor-binding aptamer or other ligands results in the binding and co-entry of trivalent therapeutic particles into cells. Such particles were subsequently shown to modulate the apoptosis of cancer cells in both cell cultures and animal trials. The use of such antigen-free 20–40 nm particles holds promise for the repeated long-term treatment of chronic diseases. Other potentially useful RNA molecules that form multimers include HIV RNA that contain kissing loop to form dimers, tecto-RNA that forms a “jigsaw puzzle,” and the Drosophila bicoid mRNA that forms multimers via “hand-by-arm” interactions. Applications of RNA molecules involving replication, molding, embossing, and other related techniques, have recently been described that allow the utilization of a variety of materials to enhance diversity and resolution of nanomaterials. It should eventually be possible to adapt RNA to facilitate construction of ordered, patterned, or pre-programmed arrays or superstructures. Given the potential for 3D fabrication, the chance to produce reversible self-assembly, and the ability of self-repair, editing and replication, RNA self-assembly will play an increasingly significant role in integrated biological nanofabrication. A random 100-nucleotide RNA library may exist in 1.6 × 1060 varieties with multifarious structure to serve as a vital system for efficient fabrication, with a complexity and diversity far exceeding that of any current nanoscale system. This review covers the basic concepts of RNA structure and function, certain methods for the study of RNA structure, the approaches for engineering or fabricating RNA into nanoparticles or arrays, and special features of RNA molecules that form multimers. The most recent development in exploration of RNA nanoparticles for pathogen detection, drug/gene delivery, and therapeutic application is also introduced in this review. PMID:16430131

Contextual behavior and neural circuits

PubMed Central

Lee, Inah; Lee, Choong-Hee

2013-01-01

Animals including humans engage in goal-directed behavior flexibly in response to items and their background, which is called contextual behavior in this review. Although the concept of context has long been studied, there are differences among researchers in defining and experimenting with the concept. The current review aims to provide a categorical framework within which not only the neural mechanisms of contextual information processing but also the contextual behavior can be studied in more concrete ways. For this purpose, we categorize contextual behavior into three subcategories as follows by considering the types of interactions among context, item, and response: contextual response selection, contextual item selection, and contextual item–response selection. Contextual response selection refers to the animal emitting different types of responses to the same item depending on the context in the background. Contextual item selection occurs when there are multiple items that need to be chosen in a contextual manner. Finally, when multiple items and multiple contexts are involved, contextual item–response selection takes place whereby the animal either chooses an item or inhibits such a response depending on item–context paired association. The literature suggests that the rhinal cortical regions and the hippocampal formation play key roles in mnemonically categorizing and recognizing contextual representations and the associated items. In addition, it appears that the fronto-striatal cortical loops in connection with the contextual information-processing areas critically control the flexible deployment of adaptive action sets and motor responses for maximizing goals. We suggest that contextual information processing should be investigated in experimental settings where contextual stimuli and resulting behaviors are clearly defined and measurable, considering the dynamic top-down and bottom-up interactions among the neural systems for contextual behavior. PMID:23675321

Quality of physical therapy from a patient's perspective; factor analysis on web-based survey data revealed three dimensions on patient experiences with physical therapy.

PubMed

Scholte, Marijn; Calsbeek, Hilly; Nijhuis-van der Sanden, Maria W G; Braspenning, Jozé

2014-06-18

Assessing quality of care from the patient's perspective has changed from patient satisfaction to the more general term patient experience, as satisfaction measures turned out to be less discriminative due to high scores. Literature describes four to ten dimensions of patient experience, tailored to specific conditions or types of care. Given the administrative burden on patients, less dimensions and items could increase feasibility. Ten dimensions of patient experiences with physical therapy (PT) were proposed in the Netherlands in a consensus-based process with patients, physical therapists, health insurers, and policy makers. The aim of this paper is to detect the number of dimensions from data of a field study using factor analysis at item level. A web-based survey yielded data of 2,221 patients from 52 PT practices on 41 items. Principal component factor analysis at item level was used to assess the proposed distinction between the ten dimensions. Factor analysis revealed two dimensions: 'personal interaction' and 'practice organisation'. The dimension 'patient reported outcome' was artificially established. The three dimensions 'personal interaction' (14 items) (median(practice level) = 91.1; IQR = 2.4), 'practice organisation' (9 items) (median(practice level) = 88.9; IQR = 6.0) and 'outcome' (3 items) (median(practice level) = 80.6; IQR = 19.5) reduced the number of dimensions from ten to three and the number of items by more than a third. Factor analysis revealed three dimensions and achieved an item reduction of more than a third. It is a relevant step in the development process of a quality measurement tool to reduce respondent burden, increase clarity, and promote feasibility.

Molecular mechanism of transcription inhibition by phage T7 gp2 protein.

PubMed

Mekler, Vladimir; Minakhin, Leonid; Sheppard, Carol; Wigneshweraraj, Sivaramesh; Severinov, Konstantin

2011-11-11

Escherichia coli T7 bacteriophage gp2 protein is a potent inhibitor of host RNA polymerase (RNAP). gp2 inhibits formation of open promoter complex by binding to the β' jaw, an RNAP domain that interacts with downstream promoter DNA. Here, we used an engineered promoter with an optimized sequence to obtain and characterize a specific promoter complex containing RNAP and gp2. In this complex, localized melting of promoter DNA is initiated but does not propagate to include the point of the transcription start. As a result, the complex is transcriptionally inactive. Using a highly sensitive RNAP beacon assay, we performed quantitative real-time measurements of specific binding of the RNAP-gp2 complex to promoter DNA and various promoter fragments. In this way, the effect of gp2 on RNAP interaction with promoters was dissected. As expected, gp2 greatly decreased RNAP affinity to downstream promoter duplex. However, gp2 also inhibited RNAP binding to promoter fragments that lacked downstream promoter DNA that interacts with the β' jaw. The inhibition was caused by gp2-mediated decrease of the RNAP binding affinity to template and non-template strand segments of the transcription bubble downstream of the -10 promoter element. The inhibition of RNAP interactions with single-stranded segments of the transcription bubble by gp2 is a novel effect, which may occur via allosteric mechanism that is set in motion by the gp2 binding to the β' jaw. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evaluation of the Edinburgh Post Natal Depression Scale using Rasch analysis

PubMed Central

Pallant, Julie F; Miller, Renée L; Tennant, Alan

2006-01-01

Background The Edinburgh Postnatal Depression Scale (EPDS) is a 10 item self-rating post-natal depression scale which has seen widespread use in epidemiological and clinical studies. Concern has been raised over the validity of the EPDS as a single summed scale, with suggestions that it measures two separate aspects, one of depressive feelings, the other of anxiety. Methods As part of a larger cross-sectional study conducted in Melbourne, Australia, a community sample (324 women, ranging in age from 18 to 44 years: mean = 32 yrs, SD = 4.6), was obtained by inviting primiparous women to participate voluntarily in this study. Data from the EPDS were fitted to the Rasch measurement model and tested for appropriate category ordering, for item bias through Differential Item Functioning (DIF) analysis, and for unidimensionality through tests of the assumption of local independence. Results Rasch analysis of the data from the ten item scale initially demonstrated a lack of fit to the model with a significant Item-Trait Interaction total chi-square (chi Square = 82.8, df = 40; p < .001). Removal of two items (items 7 and 8) resulted in a non-significant Item-Trait Interaction total chi-square with a residual mean value for items of -0.467 with a standard deviation of 0.850, showing fit to the model. No DIF existed in the final 8-item scale (EPDS-8) and all items showed fit to model expectations. Principal Components Analysis of the residuals supported the local independence assumption, and unidimensionality of the revised EPDS-8 scale. Revised cut points were identified for EPDS-8 to maintain the case identification of the original scale. Conclusion The results of this study suggest that EPDS, in its original 10 item form, is not a viable scale for the unidimensional measurement of depression. Rasch analysis suggests that a revised eight item version (EPDS-8) would provide a more psychometrically robust scale. The revised cut points of 7/8 and 9/10 for the EPDS-8 show high levels of agreement with the original case identification for the EPDS-10. PMID:16768803

Examining relations of entertainment with social interaction motives and team identification.

PubMed

Gau, Li-Shiue; Wann, Daniel L; James, Jeffrey D

2010-10-01

The goal was to investigate a potential causal pattern between the motives of sport spectators and team identification by using a cross-lagged panel design. Questionnaires were completed by 229 participants at the beginning and end of one NCAA (National Collegiate Athletic Association) college football season for 4 mo. in the USA. The questionnaire included three items for each motive (Social Interaction and Entertainment), three items measuring team identification, and demographic items. The relation of Entertainment at Time 1 to team identification at Time 2 was larger than the relation of team identification at Time 1 to Entertainment at Time 2. This suggests that the motivation of Entertainment may lead to the formation of team identification more than team identification leads to Entertainment. However, the motive of Social Interaction did not show the same pattern. As results of this study suggested some spectator sport motives might lead to identification with a team, the hypothesis that all motives would be the basis of team identification might not be correct.

Red-luminescent europium (III) doped silica nanoshells: synthesis, characterization, and their interaction with HeLa cells

NASA Astrophysics Data System (ADS)

Yang, Jian; Sandoval, Sergio; Alfaro, Jesus G.; Aschemeyer, Sharraya; Liberman, Alex; Martin, David T.; Makale, Milan; Kummel, Andrew C.; Trogler, William C.

2011-06-01

A simple method to fabricate Eu3+ doped silica nanoshells particles with 100 and 200 nm diameters is reported. Amino polystyrene beads were used as templates, and an 8 to 10 nm thick silica gel coating was formed by the sol-gel reaction. After removing the template by calcination, porous dehydrated silica gel nanoshells of uniform size were obtained. The Eu3+ doped silica nanoshells exhibited a red emission at 615 nm on UV excitation. The porous structure of the silica shell wall was characterized by transmission electron microscopy measurements, while particle size and zeta potentials of the particles suspended in aqueous solution were characterized by dynamic light scattering. Two-photon microscopy was used to image the nanoshells after assimilation by HeLa cancer cells.

Light-assisted, templated self-assembly of gold nanoparticle chains.

PubMed

Jaquay, Eric; Martínez, Luis Javier; Huang, Ningfeng; Mejia, Camilo A; Sarkar, Debarghya; Povinelli, Michelle L

2014-09-10

We experimentally demonstrate the technique of light-assisted, templated self-assembly (LATS) to trap and assemble 200 nm diameter gold nanoparticles. We excite a guided-resonance mode of a photonic-crystal slab with 1.55 μm laser light to create an array of optical traps. Unlike our previous demonstration of LATS with polystyrene particles, we find that the interparticle interactions play a significant role in the resulting particle patterns. Despite a two-dimensionally periodic intensity profile in the slab, the particles form one-dimensional chains whose orientations can be controlled by the incident polarization of the light. The formation of chains can be understood in terms of a competition between the gradient force due to the excitation of the mode in the slab and optical binding between particles.

Ligand exchange and MIP-based paraoxon memories onto QCM sensor

NASA Astrophysics Data System (ADS)

Birlik Özkütük, Ebru; Emir Diltemiz, Sibel; Özalp, Elif; Uzun, Lokman; Ersöz, Arzu

2015-04-01

In this study, we have aimed to prepare quartz crystal microbalance (QCM) sensor using paraoxon-imprinted particles. Firstly, methacryloyl antipyrine (MAAP)-based metal-chelate-coordinated pre-complex has been prepared and used for paraoxon templation. Then, paraoxon-imprinted nanofilms were formed on QCM sensor after modification of the gold surfaces with allyl mercaptan. By this way, specific and selective memories, which depend on metal-chelate interactions between Eu(III) ions and template, for paraoxon molecules have been obtained on the electrode surface. QCM sensor has characterized using AFM and ellipsometer. The detection limit and the affinity constant have found to be 0.09 μM and 5.71 × 103 M-1 for MAAP-Eu paraoxon-based nanofilm, respectively. The specificity of the QCM sensor has shown using parathion as a competitor molecule.

Mesoporous Akaganeite of Adjustable Pore Size Synthesized using Mixed Templates

NASA Astrophysics Data System (ADS)

Zhang, Y.; Ge, D. L.; Ren, H. P.; Fan, Y. J.; Wu, L. M.; Sun, Z. X.

2017-12-01

Mesoporous akaganeite with large and adjustable pore size was synthesized through a co-template method, which was achieved by the combined interaction between PEG2000 and alkyl amines with different lengths of the straight carbon chain. The characterized results indicate that the synthesized samples show comparatively narrow BJH pore size distributions and centered at 14.3 nm when PEG and HEPA was used, and it could be enlarged to 16.8 and 19.4 nm respectively through changing the alkyl amines to DDA and HDA. Meanwhile, all the synthesized akaganeite possess relativity high specific surface area ranging from 183 to 281 m2/g and high total pore volume of 0.98 to 1.5 cm3/g. A possible mechanism leading to the pore size changing was also proposed.

Site-Specific Colloidal Crystal Nucleation by Template-enhanced Particle Transport

NASA Astrophysics Data System (ADS)

Mishra, Chandan K.; Sood, A. K.; Ganapathy, Rajesh

The deliberate positioning of nano- and microstructures on surfaces is often a prerequisite for fabricating functional devices. While template-assisted nucleation is a promising route to self-assemble these structures, its success hinges on particles reaching target sites prior to nucleation and for nano/microscale particles, this is hampered by their small surface mobilities. We tailored surface features, which in the presence of attractive depletion interactions not only directed micrometer-sized colloids to specific sites but also subsequently guided their growth into ordered crystalline arrays of well-defined size and symmetry. By following the nucleation kinetics with single-particle resolution, we demonstrate control over nucleation density in a growth regime that has hitherto remained inaccessible. Our findings pave the way towards realizing non-trivial surface architectures composed of complex colloids/nanoparticles as well.

Integrating Nanostructured Artificial Receptors with Whispering Gallery Mode Optical Microresonators via Inorganic Molecular Imprinting Techniques

PubMed Central

Hammond, G. Denise; Vojta, Adam L.; Grant, Sheila A.; Hunt, Heather K.

2016-01-01

The creation of label-free biosensors capable of accurately detecting trace contaminants, particularly small organic molecules, is of significant interest for applications in environmental monitoring. This is achieved by pairing a high-sensitivity signal transducer with a biorecognition element that imparts selectivity towards the compound of interest. However, many environmental pollutants do not have corresponding biorecognition elements. Fortunately, biomimetic chemistries, such as molecular imprinting, allow for the design of artificial receptors with very high selectivity for the target. Here, we perform a proof-of-concept study to show how artificial receptors may be created from inorganic silanes using the molecular imprinting technique and paired with high-sensitivity transducers without loss of device performance. Silica microsphere Whispering Gallery Mode optical microresonators are coated with a silica thin film templated by a small fluorescent dye, fluorescein isothiocyanate, which serves as our model target. Oxygen plasma degradation and solvent extraction of the template are compared. Extracted optical devices are interacted with the template molecule to confirm successful sorption of the template. Surface characterization is accomplished via fluorescence and optical microscopy, ellipsometry, optical profilometry, and contact angle measurements. The quality factors of the devices are measured to evaluate the impact of the coating on device sensitivity. The resulting devices show uniform surface coating with no microstructural damage with Q factors above 106. This is the first report demonstrating the integration of these devices with molecular imprinting techniques, and could lead to new routes to biosensor creation for environmental monitoring. PMID:27314397

Fabrication of Protein Microparticles and Microcapsules with Biomolecular Tools

NASA Astrophysics Data System (ADS)

Cheung, Kwan Yee; Lai, Kwok Kei; Mak, Wing Cheung

2018-05-01

Microparticles have attracted much attention for medical, analytical and biological applications. Calcium carbonate (CaCO3) templating method with the advantages of having narrow size distribution, controlled morphology and good biocompatibility that has been widely used for the synthesis of various protein-based microparticles. Despite CaCO3 template is biocompatible, most of the conventional methods to create stable protein microparticles are mainly driven by chemical crosslink reagents which may induce potential harmful effect and remains undesirable especially for biomedical or clinical applications. In this article, we demonstrate the fabrication of protein microparticles and microcapsules with an innovative method using biomolecular tools such as enzymes and affinity molecules to trigger the assembling of protein molecules within a porous CaCO3 template followed by a template removal step. We demonstrated the enzyme-assisted fabrication of collagen microparticles triggered by transglutaminase, as well as the affinity-assisted fabrication of BSA-biotin avidin microcapsules triggered by biotin-avidin affinity interaction, respectively. Based on the different protein assemble mechanisms, the collagen microparticles appeared as a solid-structured particles, while the BSA-biotin avidin microcapsules appeared as hollow-structured morphology. The fabrication procedures are simple and robust that allows producing protein microparticles or microcapsules under mild conditions at physiological pH and temperature. In addition, the microparticle morphologies, protein compositions and the assemble mechanisms were studied. Our technology provides a facile approach to design and fabricate protein microparticles and microcapsules that are useful in the area of biomaterials, pharmaceuticals and analytical chemistry.

Repositioning Titanium: An In Vitro Evaluation of Laser-Generated Microporous, Microrough Titanium Templates As a Potential Bridging Interface for Enhanced Osseointegration and Durability of Implants

PubMed Central

Tang, Daniel; Yang, Liang-Yo; Ou, Keng-Liang; Oreffo, Richard O. C.

2017-01-01

Although titanium alloys remain the preferred biomaterials for the manufacture of biomedical implants today, such devices can fail within 15 years of implantation due to inadequate osseointegration. Furthermore, wear debris toxicity due to alloy metal ion release has been found to cause side-effects including neurotoxicity and chronic inflammation. Titanium, with its known biocompatibility, corrosion resistance, and high elastic modulus, could if harnessed in the form of a superficial scaffold or bridging device, resolve such issues. A novel three-dimensional culture approach was used to investigate the potential osteoinductive and osseointegrative capabilities of a laser-generated microporous, microrough medical grade IV titanium template on human skeletal stem cells (SSCs). Human SSCs seeded on a rough 90-µm pore surface of ethylene oxide-sterilized templates were observed to be strongly adherent, and to display early osteogenic differentiation, despite their inverted culture in basal conditions over 21 days. Limited cellular migration across the template surface highlighted the importance of high surface wettability in maximizing cell adhesion, spreading and cell-biomaterial interaction, while restricted cell ingrowth within the conical-shaped pores underlined the crucial role of pore geometry and size in determining the extent of osseointegration of an implant device. The overall findings indicate that titanium only devices, with appropriate optimizations to porosity and surface wettability, could yet play a major role in improving the long-term efficacy, durability, and safety of future implant technology. PMID:29322044

GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors.

PubMed

Worth, Catherine L; Kreuchwig, Franziska; Tiemann, Johanna K S; Kreuchwig, Annika; Ritschel, Michele; Kleinau, Gunnar; Hildebrand, Peter W; Krause, Gerd

2017-07-03

G-protein coupled receptors (GPCRs) are key players in signal transduction and therefore a large proportion of pharmaceutical drugs target these receptors. Structural data of GPCRs are sparse yet important for elucidating the molecular basis of GPCR-related diseases and for performing structure-based drug design. To ameliorate this problem, GPCR-SSFE 2.0 (http://www.ssfa-7tmr.de/ssfe2/), an intuitive web server dedicated to providing three-dimensional Class A GPCR homology models has been developed. The updated web server includes 27 inactive template structures and incorporates various new functionalities. Uniquely, it uses a fingerprint correlation scoring strategy for identifying the optimal templates, which we demonstrate captures structural features that sequence similarity alone is unable to do. Template selection is carried out separately for each helix, allowing both single-template models and fragment-based models to be built. Additionally, GPCR-SSFE 2.0 stores a comprehensive set of pre-calculated and downloadable homology models and also incorporates interactive loop modeling using the tool SL2, allowing knowledge-based input by the user to guide the selection process. For visual analysis, the NGL viewer is embedded into the result pages. Finally, blind-testing using two recently published structures shows that GPCR-SSFE 2.0 performs comparably or better than other state-of-the art GPCR modeling web servers. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Zinc-binding Domain of the Bacteriophage T7 DNA Primase Modulates Binding to the DNA Template*

PubMed Central

Lee, Seung-Joo; Zhu, Bin; Akabayov, Barak; Richardson, Charles C.

2012-01-01

The zinc-binding domain (ZBD) of prokaryotic DNA primases has been postulated to be crucial for recognition of specific sequences in the single-stranded DNA template. To determine the molecular basis for this role in recognition, we carried out homolog-scanning mutagenesis of the zinc-binding domain of DNA primase of bacteriophage T7 using a bacterial homolog from Geobacillus stearothermophilus. The ability of T7 DNA primase to catalyze template-directed oligoribonucleotide synthesis is eliminated by substitution of any five-amino acid residue-long segment within the ZBD. The most significant defect occurs upon substitution of a region (Pro-16 to Cys-20) spanning two cysteines that coordinate the zinc ion. The role of this region in primase function was further investigated by generating a protein library composed of multiple amino acid substitutions for Pro-16, Asp-18, and Asn-19 followed by genetic screening for functional proteins. Examination of proteins selected from the screening reveals no change in sequence-specific recognition. However, the more positively charged residues in the region facilitate DNA binding, leading to more efficient oligoribonucleotide synthesis on short templates. The results suggest that the zinc-binding mode alone is not responsible for sequence recognition, but rather its interaction with the RNA polymerase domain is critical for DNA binding and for sequence recognition. Consequently, any alteration in the ZBD that disturbs its conformation leads to loss of DNA-dependent oligoribonucleotide synthesis. PMID:23024359

Nursing Care Interpersonal Relationship Questionnaire: elaboration and validation 1

PubMed Central

Borges, José Wicto Pereira; Moreira, Thereza Maria Magalhães; de Andrade, Dalton Franscisco

2018-01-01

ABSTRACT Objective: to elaborate an instrument for the measurement of the interpersonal relationship in nursing care through the Item Response Theory, and the validation thereof. Method: methodological study, which followed the three poles of psychometry: theoretical, empirical and analytical. The Nursing Care Interpersonal Relationship Questionnaire was developed in light of the Imogene King’s Interpersonal Conceptual Model and the psychometric properties were studied through the Item Response Theory in a sample of 950 patients attended in Primary, Secondary and Tertiary Health Care. Results: the final instrument consisted of 31 items, with Cronbach’s alpha of 0.90 and McDonald’s Omega of 0.92. The parameters of the Item Response Theory demonstrated high discrimination in 28 items, being developed a five-level interpretive scale. At the first level, the communication process begins, gaining a wealth of interaction. Subsequent levels demonstrate qualitatively the points of effectiveness of the interpersonal relationship with the involvement of behaviors related to the concepts of transaction and interaction, followed by the concept of role. Conclusion: the instrument was created and proved to be consistent to measure interpersonal relationship in nursing care, as it presented adequate reliability and validity parameters. PMID:29319743

Technology for Musicianship: Using the Internet for Music Instruction.

ERIC Educational Resources Information Center

Kassner, Kirk

2001-01-01

Presents descriptions of using the Internet for music instruction by Laura Ferguson, James F. Daugherty, and Sandi MacLeod. Covers topics such as steps for creating and publishing movies on a Web site, a template for electronic learning called ChoirONLINE based on the creative use of interactive Web forms, and the Vermont MIDI Project. (CMK)

Brain Basis of Early Parent-Infant Interactions: Psychology, Physiology, and "in vivo" Functional Neuroimaging Studies

ERIC Educational Resources Information Center

Swain, James E.; Lorberbaum, Jeffrey P.; Kose, Samet; Strathearn, Lane

2007-01-01

Parenting behavior critically shapes human infants' current and future behavior. The parent-infant relationship provides infants with their first social experiences, forming templates of what they can expect from others and how to best meet others' expectations. In this review, we focus on the neurobiology of parenting behavior, including our own…

Restricted interests and teacher presentation of items.

PubMed

Stocco, Corey S; Thompson, Rachel H; Rodriguez, Nicole M

2011-01-01

Restricted and repetitive behavior (RRB) is more pervasive, prevalent, frequent, and severe in individuals with autism spectrum disorders (ASDs) than in their typical peers. One subtype of RRB is restricted interests in items or activities, which is evident in the manner in which individuals engage with items (e.g., repetitious wheel spinning), the types of items or activities they select (e.g., preoccupation with a phone book), or the range of items or activities they select (i.e., narrow range of items). We sought to describe the relation between restricted interests and teacher presentation of items. Overall, we observed 5 teachers interacting with 2 pairs of students diagnosed with an ASD. Each pair included 1 student with restricted interests. During these observations, teachers were free to present any items from an array of 4 stimuli selected by experimenters. We recorded student responses to teacher presentation of items and analyzed the data to determine the relation between teacher presentation of items and the consequences for presentation provided by the students. Teacher presentation of items corresponded with differential responses provided by students with ASD, and those with restricted preferences experienced a narrower array of items.

Online Calibration of Polytomous Items Under the Generalized Partial Credit Model

PubMed Central

Zheng, Yi

2016-01-01

Online calibration is a technology-enhanced architecture for item calibration in computerized adaptive tests (CATs). Many CATs are administered continuously over a long term and rely on large item banks. To ensure test validity, these item banks need to be frequently replenished with new items, and these new items need to be pretested before being used operationally. Online calibration dynamically embeds pretest items in operational tests and calibrates their parameters as response data are gradually obtained through the continuous test administration. This study extends existing formulas, procedures, and algorithms for dichotomous item response theory models to the generalized partial credit model, a popular model for items scored in more than two categories. A simulation study was conducted to investigate the developed algorithms and procedures under a variety of conditions, including two estimation algorithms, three pretest item selection methods, three seeding locations, two numbers of score categories, and three calibration sample sizes. Results demonstrated acceptable estimation accuracy of the two estimation algorithms in some of the simulated conditions. A variety of findings were also revealed for the interacted effects of included factors, and recommendations were made respectively. PMID:29881063

Construction of population-specific Indian MRI brain template: Morphometric comparison with Chinese and Caucasian templates.

PubMed

Bhalerao, Gaurav Vivek; Parlikar, Rujuta; Agrawal, Rimjhim; Shivakumar, Venkataram; Kalmady, Sunil V; Rao, Naren P; Agarwal, Sri Mahavir; Narayanaswamy, Janardhanan C; Reddy, Y C Janardhan; Venkatasubramanian, Ganesan

2018-06-01

Spatial normalization of brain MR images is highly dependent on the choice of target brain template. Morphological differences caused by factors like genetic and environmental exposures, generates a necessity to construct population specific brain templates. Brain image analysis performed using brain templates from Caucasian population may not be appropriate for non-Caucasian population. In this study, our objective was to construct an Indian brain template from a large population (N = 157 subjects) and compare the morphometric parameters of this template with that of Chinese-56 and MNI-152 templates. In addition, using an independent MRI data of 15 Indian subjects, we also evaluated the potential registration accuracy differences using these three templates. Indian brain template was constructed using iterative routines as per established procedures. We compared our Indian template with standard MNI-152 template and Chinese template by measuring global brain features. We also examined accuracy of registration by aligning 15 new Indian brains to Indian, Chinese and MNI templates. Furthermore, we supported our measurement protocol with inter-rater and intra-rater reliability analysis. Our results showed that there were significant differences in global brain features of Indian template in comparison with Chinese and MNI brain templates. The results of registration accuracy analysis revealed that fewer deformations are required when Indian brains are registered to Indian template as compared to Chinese and MNI templates. This study concludes that population specific Indian template is likely to be more appropriate for structural and functional image analysis of Indian population. Copyright © 2018 Elsevier B.V. All rights reserved.

Perception that "everything requires a lot of effort": transcultural SCL-25 item validation.

PubMed

Moreau, Nicolas; Hassan, Ghayda; Rousseau, Cécile; Chenguiti, Khalid

2009-09-01

This brief report illustrates how the migration context can affect specific item validity of mental health measures. The SCL-25 was administered to 432 recently settled immigrants (220 Haitian and 212 Arabs). We performed descriptive analyses, as well as Infit and Outfit statistics analyses using WINSTEPS Rasch Measurement Software based on Item Response Theory. The participants' comments about the item You feel everything requires a lot of effort in the SCL-25 were also qualitatively analyzed. Results revealed that the item You feel everything requires a lot of effort is an outlier and does not adjust in an expected and valid fashion with its cluster items, as it is over-endorsed by Haitian and Arab healthy participants. Our study thus shows that, in transcultural mental health research, the cultural and migratory contexts may interact and significantly influence the meaning of some symptom items and consequently, the validity of symptom scales.

Social desirability in personality inventories: Symptoms, diagnosis and prescribed cure

PubMed Central

Bäckström, Martin; Björklund, Fredrik

2013-01-01

An analysis of social desirability in personality assessment is presented. Starting with the symptoms, Study 1 showed that mean ratings of graded personality items are moderately to strongly linearly related to social desirability (Self Deception, Impression formation, and the first Principal Component), suggesting that item popularity may be a useful heuristic tool for identifying items which elicit socially desirable responding. We diagnose the cause of socially desirable responding as an interaction between the evaluative content of the item and enhancement motivation in the rater. Study 2 introduced a possible cure; evaluative neutralization of items. To test the feasibility of the method lay psychometricians (undergraduates) reformulated existing personality test items according to written instructions. The new items were indeed lower in social desirability while essentially retaining the five factor structure and reliability of the inventory. We conclude that although neutralization is no miracle cure, it is simple and has beneficial effects. PMID:23252410

Activation of remote meta-C-H bonds assisted by an end-on template.

PubMed

Leow, Dasheng; Li, Gang; Mei, Tian-Sheng; Yu, Jin-Quan

2012-06-27

Functionalization of unactivated carbon-hydrogen (C-H) single bonds is an efficient strategy for rapid generation of complex molecules from simpler ones. However, it is difficult to achieve selectivity when multiple inequivalent C-H bonds are present in the target molecule. The usual approach is to use σ-chelating directing groups, which lead to ortho-selectivity through the formation of a conformationally rigid six- or seven-membered cyclic pre-transition state. Despite the broad utility of this approach, proximity-driven reactivity prevents the activation of remote C-H bonds. Here we report a class of easily removable nitrile-containing templates that direct the activation of distal meta-C-H bonds (more than ten bonds away) of a tethered arene. We attribute this new mode of C-H activation to a weak 'end-on' interaction between the linear nitrile group and the metal centre. The 'end-on' coordination geometry relieves the strain of the cyclophane-like pre-transition state of the meta-C-H activation event. In addition, this template overrides the intrinsic electronic and steric biases as well as ortho-directing effects with two broadly useful classes of arene substrates (toluene derivatives and hydrocinnamic acids).

Synthesis and characterization of guar-alginate hybrid bead templated mercury sorbing titania spheres.

PubMed

Singh, Vandana; Preeti; Singh, Angela; Singh, Devendra; Singh, Yadveer; Pandey, Arvind Kumar

2015-01-01

Present communication reports on the synthesis and characterization of Hg(II) sorbing millimeter sized porous titania spheres (TSP). The synthesis utilizes guar gum-alginate hybrid beads as sacrificial template to polymerize titanium(IV) isopropoxide. The hybrid beads are crafted by pouring guar-alginate mixed solution to calcium bath. The mechanical strength of the beads depended on guar to alginate ratio in the mixed solution. The equal weight ratio of the two polysaccharides is appropriate for adequate mechanical strength beads. The unique performance of the templating beads is attributed to the synergistic interaction between guar gum and sodium alginate. FTIR, BET, SEM, TEM, XRD, TGA, and DTG analyses have been used for the characterization of the optimum performance TSP (TSPAG2). TSPAG2 is a mesoporous material that has higher surface area and narrower pore size distribution than pure alginate derived titania spheres (TSPA). TEM study demonstrated that TSPAG2 spheres are constituted of aggregated TiO2 nanoparticles of ∼ 10 nm size. TSPAG2 is able to capture >95% Hg(II) from synthetic Hg(II) solution in 10h at pH 5 as opposed to only 68% removal by TSPA. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection and Counting of Orchard Trees from Vhr Images Using a Geometrical-Optical Model and Marked Template Matching

NASA Astrophysics Data System (ADS)

Maillard, Philippe; Gomes, Marília F.

2016-06-01

This article presents an original algorithm created to detect and count trees in orchards using very high resolution images. The algorithm is based on an adaptation of the "template matching" image processing approach, in which the template is based on a "geometricaloptical" model created from a series of parameters, such as illumination angles, maximum and ambient radiance, and tree size specifications. The algorithm is tested on four images from different regions of the world and different crop types. These images all have < 1 meter spatial resolution and were downloaded from the GoogleEarth application. Results show that the algorithm is very efficient at detecting and counting trees as long as their spectral and spatial characteristics are relatively constant. For walnut, mango and orange trees, the overall accuracy was clearly above 90%. However, the overall success rate for apple trees fell under 75%. It appears that the openness of the apple tree crown is most probably responsible for this poorer result. The algorithm is fully explained with a step-by-step description. At this stage, the algorithm still requires quite a bit of user interaction. The automatic determination of most of the required parameters is under development.

A simulation study of fast neutron interrogation for standoff detection of improvised explosive devices

NASA Astrophysics Data System (ADS)

Heider, S. A.; Dunn, W. L.

2015-11-01

The signature-based radiation-scanning technique utilizes radiation detector responses, called "signatures," and compares these to "templates" in order to differentiate targets that contain certain materials, such as explosives or drugs, from those that do not. Our investigations are aimed at the detection of nitrogen-rich explosives contained in improvised explosive devices. We use the term "clutter" to refer to any non-explosive materials with which the interrogating radiation may interact between source and detector. To deal with the many target types and clutter configurations that may be encountered in the field, the use of "artificial templates" is proposed. The MCNP code was used to simulate 14.1 MeV neutron source beams incident on one type of target containing various clutter and sample materials. Signatures due to inelastic-scatter and prompt-capture gamma rays from hydrogen, carbon, nitrogen, and oxygen and two scattered neutron signatures were considered. Targets containing explosive materials in the presence of clutter were able to be identified from targets that contained only non-explosive ("inert") materials. This study demonstrates that a finite number of artificial templates is sufficient for IED detection with fairly good sensitivity and specificity.

Formalizing an integrative, multidisciplinary cancer therapy discovery workflow

PubMed Central

McGuire, Mary F.; Enderling, Heiko; Wallace, Dorothy I.; Batra, Jaspreet; Jordan, Marie; Kumar, Sushil; Panetta, John C.; Pasquier, Eddy

2014-01-01

Although many clinicians and researchers work to understand cancer, there has been limited success to effectively combine forces and collaborate over time, distance, data and budget constraints. Here we present a workflow template for multidisciplinary cancer therapy that was developed during the 2nd Annual Workshop on Cancer Systems Biology sponsored by Tufts University, Boston, MA in July 2012. The template was applied to the development of a metronomic therapy backbone for neuroblastoma. Three primary groups were identified: clinicians, biologists, and scientists (mathematicians, computer scientists, physicists and engineers). The workflow described their integrative interactions; parallel or sequential processes; data sources and computational tools at different stages as well as the iterative nature of therapeutic development from clinical observations to in vitro, in vivo, and clinical trials. We found that theoreticians in dialog with experimentalists could develop calibrated and parameterized predictive models that inform and formalize sets of testable hypotheses, thus speeding up discovery and validation while reducing laboratory resources and costs. The developed template outlines an interdisciplinary collaboration workflow designed to systematically investigate the mechanistic underpinnings of a new therapy and validate that therapy to advance development and clinical acceptance. PMID:23955390

Novelty of Dynamic Process in the Synthesis of Biocompatible Silica Nanotubes by Biomimetic Glycyldodecylamide as a Soft Template.

PubMed

Choi, Hyejung; Kim, Joong-Jo; Mo, Yong-Hwan; Reddy, Benjaram M; Park, Sang-Eon

2017-10-10

A dynamic process in the synthesis of silica nanotubes (SNTs) by utilizing glycyldodecylamide (GDA) as a soft template was thoroughly investigated. The morphological evolution from GDA to SNTs was deeply explored to elucidate the formation mechanism for optimizing the synthesis procedure. Various analytical tools, namely, XRD, FTIR, SEM, TEM, Z-potential, and N 2 adsorption/desorption isotherms, were employed during the synthesis procedure. The interactive structure of GDA was also investigated using TEM-EDX as a function of aging time. These studies revealed the stepwise morphology of nanograin, nanofiber, curved plate, and nanotube in the ethanol/water solution when aged at room temperature. The supramolecular GDA molded the vesicle type nanostructure which was surrounded by silica and facilitated the formation of uniform SNTs. The stimulus for GDA to be curved into a vesicle was the intermolecular hydrogen bonding between adjacent amide groups of the template molecules. This was illustrated by FTIR spectra of GDA-silica intermediate by detecting the transition of amide I peak from 1678 to 1635 cm -1 . The effect of hydrogen bonding became stronger when the sample was aged.

Wave Energy Prize - General Information

DOE Data Explorer

Scharmen, Wesley

2016-12-01

All the informational files, templates, rules and guidelines for Wave Energy Prize (WEP), including the Wave Energy Prize Rules, Participant Terms and Conditions Template, WEC Prize Name, Logo, Branding, WEC Publicity, Technical Submission Template , Numerical Modeling Template, SSTF Submission Template, 1/20th Scale Model Design and Construction Plan Template, Final Report template, and Webinars.

Coaxial Lithography

NASA Astrophysics Data System (ADS)

Ozel, Tuncay

The optical and electrical properties of heterogeneous nanowires are profoundly related to their composition and nanoscale architecture. However, the intrinsic constraints of conventional synthetic and lithographic techniques have limited the types of multi-compositional nanowires that can be realized and studied in the laboratory. This thesis focuses on bridging templated electrochemical synthesis and lithography for expanding current synthetic capabilities with respect to materials generality and the ability to tailor two-dimensional growth in the formation of core-shell structures for the rational design and preparation of nanowires with very complex architectures that cannot be made by any other techniques. Chapter 1 introduces plasmonics, templated electrochemical synthesis, and on-wire lithography concepts and their significances within chemistry and materials science. Chapter 2 details a powerful technique for the deposition of metals and semiconductors with nanometer resolution in segment and gap lengths using on-wire lithography, which serves as a new platform to explore plasmon-exciton interactions in the form of long-range optical nanoscale rulers. Chapter 3 highlights an approach for the electrochemical synthesis of solution dispersible core-shell polymeric and inorganic semiconductor nanowires with metallic leads. A photodetector based on a single core-shell semiconductor nanowire is presented to demonstrate the functionality of the nanowires produced using this approach. Chapter 4 describes a new materials general technique, termed coaxial lithography (COAL), bridging templated electrochemical synthesis and lithography for generating coaxial nanowires in a parallel fashion with sub-10 nanometer resolution in both axial and radial dimensions. Combinations of coaxial nanowires composed of metals, metal oxides, metal chalcogenides, conjugated polymers, and a core/shell semiconductor nanowire with an embedded plasmonic nanoring are presented to demonstrate the possibilities afforded by COAL. Chapter 5 addresses the use of COAL for the synthesis of solution dispersible metal nanorings and nanotubes with exceptional architectural tailorability of inner diameter, outer diameter, and length leading to precise spectral control over the resulting plasmonic fields ranging from visible to the near-IR. Chapter 6 is an outlook on templated electrochemical synthesis using coaxial lithography and highlights a few promising applications from nanoparticle assembly to light-matter interactions.

Developing an interactive mobile phone self-report system for self-management of hypertension. Part 2: content validity and usability.

PubMed

Bengtsson, Ulrika; Kjellgren, Karin; Höfer, Stefan; Taft, Charles; Ring, Lena

2014-10-01

Self-management support tools using technology may improve adherence to hypertension treatment. There is a need for user-friendly tools facilitating patients' understanding of the interconnections between blood pressure, wellbeing and lifestyle. This study aimed to examine comprehension, comprehensiveness and relevance of items, and further to evaluate the usability and reliability of an interactive hypertension-specific mobile phone self-report system. Areas important in supporting self-management and candidate items were derived from five focus group interviews with patients and healthcare professionals (n = 27), supplemented by a literature review. Items and response formats were drafted to meet specifications for mobile phone administration and were integrated into a mobile phone data-capture system. Content validity and usability were assessed iteratively in four rounds of cognitive interviews with patients (n = 21) and healthcare professionals (n = 4). Reliability was examined using a test-retest. Focus group analyses yielded six areas covered by 16 items. The cognitive interviews showed satisfactory item comprehension, relevance and coverage; however, one item was added. The mobile phone self-report system was reliable and perceived easy to use. The mobile phone self-report system appears efficiently to capture information relevant in patients' self-management of hypertension. Future studies need to evaluate the effectiveness of this tool in improving self-management of hypertension in clinical practice.

Handbook of Polytomous Item Response Theory Models

ERIC Educational Resources Information Center

Nering, Michael L., Ed.; Ostini, Remo, Ed.

2010-01-01

This comprehensive "Handbook" focuses on the most used polytomous item response theory (IRT) models. These models help us understand the interaction between examinees and test questions where the questions have various response categories. The book reviews all of the major models and includes discussions about how and where the models…

A Computerized Interactive Vocabulary Development System for Advanced Learners.

ERIC Educational Resources Information Center

Kukulska-Hulme, Agnes

1988-01-01

Argues that the process of recording newly encountered vocabulary items in a typical language learning situation can be improved through a computerized system of vocabulary storage based on database management software that improves the discovery and recording of meaning, subsequent retrieval of items for productive use, and memory retention.…

Self-assembled chiral helical nanofibers by amphiphilic dipeptide derived from d- or l-threonine and application as a template for the synthesis of Au and Ag nanoparticles.

PubMed

Zhang, Han; Xin, Xia; Sun, Jichao; Zhao, Liupeng; Shen, Jinglin; Song, Zhaohua; Yuan, Shiling

2016-12-15

The discovery of a class of self-assembling peptides that spontaneously undergo self-organization into well-ordered structures opened a new avenue for molecular fabrication of biological materials. In this paper, the structure controlled helical nanofibers were prepared by two artificial β-sheet dipeptides with long alkyl chains derived from l- and d-threonine (Thr) and sodium hydroxide (NaOH). These helical nanofibers have been characterized using transmission electron microscopy (TEM), field emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, and X-ray powder diffraction (XRD). It was demonstrated that the helicity of the nanofibers could be easily controlled by changing the chirality of the constituent amino acids in the peptide species (d- or l-threonine). Moreover, the hydrogen bonding interactions between the amide groups as well as the hydrophobic interactions among the alkyl chains play important roles in the self-assembly process. It also can be observed that with the passage of time, the hydrogen bonding interactions between the individual nanofiber induced the conversion from nanofibers to nanobelts. Particularly, gold and silver nanoparticles performed good catalytic ability were synthesized using the assembled nanofibers as template. Copyright © 2016 Elsevier Inc. All rights reserved.

Student perceptions of gamified audience response system interactions in large group lectures and via lecture capture technology.

PubMed

Pettit, Robin K; McCoy, Lise; Kinney, Marjorie; Schwartz, Frederic N

2015-05-22

Higher education students have positive attitudes about the use of audience response systems (ARS), but even technology-enhanced lessons can become tiresome if the pedagogical approach is exactly the same with each implementation. Gamification is the notion that gaming mechanics can be applied to routine activities. In this study, TurningPoint (TP) ARS interactions were gamified and implemented in 22 large group medical microbiology lectures throughout an integrated year 1 osteopathic medical school curriculum. A 32-item questionnaire was used to measure students' perceptions of the gamified TP interactions at the end of their first year. The survey instrument generated both Likert scale and open-ended response data that addressed game design and variety, engagement and learning features, use of TP questions after class, and any value of lecture capture technology for reviewing these interactive presentations. The Chi Square Test was used to analyze grouped responses to Likert scale questions. Responses to open-ended prompts were categorized using open-coding. Ninety-one students out of 106 (86 %) responded to the survey. A significant majority of the respondents agreed or strongly agreed that the games were engaging, and an effective learning tool. The questionnaire investigated the degree to which specific features of these interactions were engaging (nine items) and promoted learning (seven items). The most highly ranked engagement aspects were peer competition and focus on the activity (tied for highest ranking), and the most highly ranked learning aspect was applying theoretical knowledge to clinical scenarios. Another notable item was the variety of interactions, which ranked in the top three in both the engagement and learning categories. Open-ended comments shed light on how students use TP questions for exam preparation, and revealed engaging and non-engaging attributes of these interactive sessions for students who review them via lecture capture. Students clearly valued the engagement and learning aspects of gamified TP interactions. The overwhelming majority of students surveyed in this study were engaged by the variety of TP games, and gained an interest in microbiology. The methods described in this study may be useful for other educators wishing to expand the utility of ARS in their classrooms.

Conversion of Radiology Reporting Templates to the MRRT Standard.

PubMed

Kahn, Charles E; Genereaux, Brad; Langlotz, Curtis P

2015-10-01

In 2013, the Integrating the Healthcare Enterprise (IHE) Radiology workgroup developed the Management of Radiology Report Templates (MRRT) profile, which defines both the format of radiology reporting templates using an extension of Hypertext Markup Language version 5 (HTML5), and the transportation mechanism to query, retrieve, and store these templates. Of 200 English-language report templates published by the Radiological Society of North America (RSNA), initially encoded as text and in an XML schema language, 168 have been converted successfully into MRRT using a combination of automated processes and manual editing; conversion of the remaining 32 templates is in progress. The automated conversion process applied Extensible Stylesheet Language Transformation (XSLT) scripts, an XML parsing engine, and a Java servlet. The templates were validated for proper HTML5 and MRRT syntax using web-based services. The MRRT templates allow radiologists to share best-practice templates across organizations and have been uploaded to the template library to supersede the prior XML-format templates. By using MRRT transactions and MRRT-format templates, radiologists will be able to directly import and apply templates from the RSNA Report Template Library in their own MRRT-compatible vendor systems. The availability of MRRT-format reporting templates will stimulate adoption of the MRRT standard and is expected to advance the sharing and use of templates to improve the quality of radiology reports.

Cloning nanocrystal morphology with soft templates

NASA Astrophysics Data System (ADS)

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.

Visualization of Documents and Concepts in Neuroinformatics with the 3D-SE Viewer

PubMed Central

Naud, Antoine; Usui, Shiro; Ueda, Naonori; Taniguchi, Tatsuki

2007-01-01

A new interactive visualization tool is proposed for mining text data from various fields of neuroscience. Applications to several text datasets are presented to demonstrate the capability of the proposed interactive tool to visualize complex relationships between pairs of lexical entities (with some semantic contents) such as terms, keywords, posters, or papers' abstracts. Implemented as a Java applet, this tool is based on the spherical embedding (SE) algorithm, which was designed for the visualization of bipartite graphs. Items such as words and documents are linked on the basis of occurrence relationships, which can be represented in a bipartite graph. These items are visualized by embedding the vertices of the bipartite graph on spheres in a three-dimensional (3-D) space. The main advantage of the proposed visualization tool is that 3-D layouts can convey more information than planar or linear displays of items or graphs. Different kinds of information extracted from texts, such as keywords, indexing terms, or topics are visualized, allowing interactive browsing of various fields of research featured by keywords, topics, or research teams. A typical use of the 3D-SE viewer is quick browsing of topics displayed on a sphere, then selecting one or several item(s) displays links to related terms on another sphere representing, e.g., documents or abstracts, and provides direct online access to the document source in a database, such as the Visiome Platform or the SfN Annual Meeting. Developed as a Java applet, it operates as a tool on top of existing resources. PMID:18974802

Visualization of Documents and Concepts in Neuroinformatics with the 3D-SE Viewer.

PubMed

Naud, Antoine; Usui, Shiro; Ueda, Naonori; Taniguchi, Tatsuki

2007-01-01

A new interactive visualization tool is proposed for mining text data from various fields of neuroscience. Applications to several text datasets are presented to demonstrate the capability of the proposed interactive tool to visualize complex relationships between pairs of lexical entities (with some semantic contents) such as terms, keywords, posters, or papers' abstracts. Implemented as a Java applet, this tool is based on the spherical embedding (SE) algorithm, which was designed for the visualization of bipartite graphs. Items such as words and documents are linked on the basis of occurrence relationships, which can be represented in a bipartite graph. These items are visualized by embedding the vertices of the bipartite graph on spheres in a three-dimensional (3-D) space. The main advantage of the proposed visualization tool is that 3-D layouts can convey more information than planar or linear displays of items or graphs. Different kinds of information extracted from texts, such as keywords, indexing terms, or topics are visualized, allowing interactive browsing of various fields of research featured by keywords, topics, or research teams. A typical use of the 3D-SE viewer is quick browsing of topics displayed on a sphere, then selecting one or several item(s) displays links to related terms on another sphere representing, e.g., documents or abstracts, and provides direct online access to the document source in a database, such as the Visiome Platform or the SfN Annual Meeting. Developed as a Java applet, it operates as a tool on top of existing resources.

Structure-Templated Predictions of Novel Protein Interactions from Sequence Information

PubMed Central

Betel, Doron; Breitkreuz, Kevin E; Isserlin, Ruth; Dewar-Darch, Danielle; Tyers, Mike; Hogue, Christopher W. V

2007-01-01

The multitude of functions performed in the cell are largely controlled by a set of carefully orchestrated protein interactions often facilitated by specific binding of conserved domains in the interacting proteins. Interacting domains commonly exhibit distinct binding specificity to short and conserved recognition peptides called binding profiles. Although many conserved domains are known in nature, only a few have well-characterized binding profiles. Here, we describe a novel predictive method known as domain–motif interactions from structural topology (D-MIST) for elucidating the binding profiles of interacting domains. A set of domains and their corresponding binding profiles were derived from extant protein structures and protein interaction data and then used to predict novel protein interactions in yeast. A number of the predicted interactions were verified experimentally, including new interactions of the mitotic exit network, RNA polymerases, nucleotide metabolism enzymes, and the chaperone complex. These results demonstrate that new protein interactions can be predicted exclusively from sequence information. PMID:17892321

A pilot study of a heuristic algorithm for novel template identification from VA electronic medical record text.

PubMed

Redd, Andrew M; Gundlapalli, Adi V; Divita, Guy; Carter, Marjorie E; Tran, Le-Thuy; Samore, Matthew H

2017-07-01

Templates in text notes pose challenges for automated information extraction algorithms. We propose a method that identifies novel templates in plain text medical notes. The identification can then be used to either include or exclude templates when processing notes for information extraction. The two-module method is based on the framework of information foraging and addresses the hypothesis that documents containing templates and the templates within those documents can be identified by common features. The first module takes documents from the corpus and groups those with common templates. This is accomplished through a binned word count hierarchical clustering algorithm. The second module extracts the templates. It uses the groupings and performs a longest common subsequence (LCS) algorithm to obtain the constituent parts of the templates. The method was developed and tested on a random document corpus of 750 notes derived from a large database of US Department of Veterans Affairs (VA) electronic medical notes. The grouping module, using hierarchical clustering, identified 23 groups with 3 documents or more, consisting of 120 documents from the 750 documents in our test corpus. Of these, 18 groups had at least one common template that was present in all documents in the group for a positive predictive value of 78%. The LCS extraction module performed with 100% positive predictive value, 94% sensitivity, and 83% negative predictive value. The human review determined that in 4 groups the template covered the entire document, with the remaining 14 groups containing a common section template. Among documents with templates, the number of templates per document ranged from 1 to 14. The mean and median number of templates per group was 5.9 and 5, respectively. The grouping method was successful in finding like documents containing templates. Of the groups of documents containing templates, the LCS module was successful in deciphering text belonging to the template and text that was extraneous. Major obstacles to improved performance included documents composed of multiple templates, templates that included other templates embedded within them, and variants of templates. We demonstrate proof of concept of the grouping and extraction method of identifying templates in electronic medical records in this pilot study and propose methods to improve performance and scaling up. Published by Elsevier Inc.

Nanoparticles Affect PCR Primarily via Surface Interactions with PCR Components: Using Amino-Modified Silica-Coated Magnetic Nanoparticles as a Main Model.

PubMed

Bai, Yalong; Cui, Yan; Paoli, George C; Shi, Chunlei; Wang, Dapeng; Shi, Xianming

2015-06-24

Nanomaterials have been widely reported to affect the polymerase chain reaction (PCR). However, many studies in which these effects were observed were not comprehensive, and many of the proposed mechanisms have been primarily speculative. In this work, we used amino-modified silica-coated magnetic nanoparticles (ASMNPs, which can be collected very easily using an external magnetic field) as a model and compared them with gold nanoparticles (AuNPs, which have been studied extensively) to reveal the mechanisms by which nanoparticles affect PCR. We found that nanoparticles affect PCR primarily by binding to PCR components: (1) inhibition, (2) specifity, and (3) efficiency and yield of PCR are impacted. (1) Excess nanomaterials inhibit PCR by adsorbing to DNA polymerase, Mg(2+), oligonucleotide primers, or DNA templates. Nanoparticle surface-active groups are particularly important to this effect. (2, a) Nanomaterials do not inhibit nonspecific amplification products caused by false priming as previously surmised. It was shown that relatively low concentrations of nanoparticles inhibited the amplification of long amplicons, and increasing the amount of nanoparticles inhibited the amplification of short amplicons. This concentration phenomenon appears to be the result of the formation of "joints" upon the adsorption of ASMNPs to DNA templates. (b) Nanomaterials are able to inhibit nonspecific amplification products due to incomplete amplification by preferably adsorbing single-stranded incomplete amplification products. (3) Some types of nanomaterials, such as AuNPs, enhance the efficiency and yield of PCR because these types of nanoparticles can adsorb to single-stranded DNA more strongly than to double-stranded DNA. This behavior assists in the rapid and thorough denaturation of double-stranded DNA templates. Therefore, the interaction between the surface of nanoparticles and PCR components is sufficient to explain most of the effects of nanoparticles on PCR.

Mutational Analysis of Influenza A Virus Nucleoprotein: Identification of Mutations That Affect RNA Replication

PubMed Central

Mena, Ignacio; Jambrina, Enrique; Albo, Carmen; Perales, Beatriz; Ortín, Juan; Arrese, Marta; Vallejo, Dolores; Portela, Agustín

1999-01-01

The influenza A virus nucleoprotein (NP) is a multifunctional polypeptide which plays a pivotal role in virus replication. To get information on the domains and specific residues involved in the different NP activities, we describe here the preparation and characterization of 20 influenza A virus mutant NPs. The mutations, mostly single-amino-acid substitutions, were introduced in a cDNA copy of the A/Victoria/3/75 NP gene and, in most cases, affected residues located in regions that were highly conserved across the NPs of influenza A, B, and C viruses. The mutant NPs were characterized (i) in vivo (cell culture) by analyzing their intracellular localization and their functionality in replication, transcription, and expression of model RNA templates; and (ii) in vitro by analyzing their RNA-binding and sedimentation properties. The results obtained allowed us to identify both a mutant protein that accumulated in the cytoplasm and mutations that altered the functionality and/or the oligomerization state of the NP polypeptide. Among the mutations that reduced the NP capability to express chloramphenicol acetyltransferase protein from a model viral RNA (vRNA) template, some displayed a temperature-sensitive phenotype. Interestingly, four mutant NPs, which showed a reduced functionality in synthesizing cRNA molecules from a vRNA template, were fully competent to reconstitute complementary ribonucleoproteins (cRNPs) capable of synthesizing vRNAs, which in turn yielded mRNA molecules. Based on the phenotype of these mutants and on previously published observations, it is proposed that these mutant NPs have a reduced capability to interact with the polymerase complex and that this NP-polymerase interaction is responsible for making vRNPs switch from mRNA to cRNA synthesis. PMID:9882320

Identifying Drug-Target Interactions with Decision Templates.

PubMed

Yan, Xiao-Ying; Zhang, Shao-Wu

2018-01-01

During the development process of new drugs, identification of the drug-target interactions wins primary concerns. However, the chemical or biological experiments bear the limitation in coverage as well as the huge cost of both time and money. Based on drug similarity and target similarity, chemogenomic methods can be able to predict potential drug-target interactions (DTIs) on a large scale and have no luxurious need about target structures or ligand entries. In order to reflect the cases that the drugs having variant structures interact with common targets and the targets having dissimilar sequences interact with same drugs. In addition, though several other similarity metrics have been developed to predict DTIs, the combination of multiple similarity metrics (especially heterogeneous similarities) is too naïve to sufficiently explore the multiple similarities. In this paper, based on Gene Ontology and pathway annotation, we introduce two novel target similarity metrics to address above issues. More importantly, we propose a more effective strategy via decision template to integrate multiple classifiers designed with multiple similarity metrics. In the scenarios that predict existing targets for new drugs and predict approved drugs for new protein targets, the results on the DTI benchmark datasets show that our target similarity metrics are able to enhance the predictive accuracies in two scenarios. And the elaborate fusion strategy of multiple classifiers has better predictive power than the naïve combination of multiple similarity metrics. Compared with other two state-of-the-art approaches on the four popular benchmark datasets of binary drug-target interactions, our method achieves the best results in terms of AUC and AUPR for predicting available targets for new drugs (S2), and predicting approved drugs for new protein targets (S3).These results demonstrate that our method can effectively predict the drug-target interactions. The software package can freely available at https://github.com/NwpuSY/DT_all.git for academic users. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Fast template matching with polynomials.

PubMed

Omachi, Shinichiro; Omachi, Masako

2007-08-01

Template matching is widely used for many applications in image and signal processing. This paper proposes a novel template matching algorithm, called algebraic template matching. Given a template and an input image, algebraic template matching efficiently calculates similarities between the template and the partial images of the input image, for various widths and heights. The partial image most similar to the template image is detected from the input image for any location, width, and height. In the proposed algorithm, a polynomial that approximates the template image is used to match the input image instead of the template image. The proposed algorithm is effective especially when the width and height of the template image differ from the partial image to be matched. An algorithm using the Legendre polynomial is proposed for efficient approximation of the template image. This algorithm not only reduces computational costs, but also improves the quality of the approximated image. It is shown theoretically and experimentally that the computational cost of the proposed algorithm is much smaller than the existing methods.

Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene.

PubMed

Cleland, Dougal; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A; McCluskey, Adam

2014-02-07

The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer-template (FM-T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with trimethylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2.8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the π-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to π-π stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level of interference from other MIP synthesis components. The effect on PFS-1 interaction by MeOH was significantly lower and thus this system was not adversely affected.

User productivity as a function of AutoCAD interface design.

PubMed

Mitta, D A; Flores, P L

1995-12-01

Increased operator productivity is a desired outcome of user-CAD interaction scenarios. Two objectives of this research were to (1) define a measure of operator productivity and (2) empirically investigate the potential effects of CAD interface design on operator productivity, where productivity is defined as the percentage of a drawing session correctly completed per unit time. Here, AutoCAD provides the CAD environment of interest. Productivity with respect to two AutoCAD interface designs (menu, template) and three task types (draw, dimension, display) was investigated. Analysis of user productivity data revealed significantly higher productivity under the menu interface condition than under the template interface condition. A significant effect of task type was also discovered, where user productivity under display tasks was higher than productivity under the draw and dimension tasks. Implications of these results are presented.

Negative regulation of retrovirus expression in embryonal carcinoma cells mediated by an intragenic domain.

PubMed

Loh, T P; Sievert, L L; Scott, R W

1988-11-01

An intragenic region spanning the tRNA primer binding site of a Moloney murine leukemia virus recombinant retrovirus was found to restrict expression specifically in embryonal carcinoma (EC) cells. When the inhibitory domain was present, the levels of steady-state RNA synthesized from integrated recombinant templates in stable cotransformation assays were reduced 20-fold in EC cells but not in C2 myoblast cells. Transient-cotransfection assays showed that repression of a template containing the EC-specific inhibitory component was relieved by an excess of specific competitor DNA. In addition, repression mediated by the inhibitory component was orientation independent. This evidence demonstrates the presence of a saturable, trans-acting negative regulatory factor(s) in EC cells and suggests that the interaction of the factor(s) with the intragenic inhibitory component occurs at the DNA level.

Genes, Culture and Conservatism-A Psychometric-Genetic Approach.

PubMed

Schwabe, Inga; Jonker, Wilfried; van den Berg, Stéphanie M

2016-07-01

The Wilson-Patterson conservatism scale was psychometrically evaluated using homogeneity analysis and item response theory models. Results showed that this scale actually measures two different aspects in people: on the one hand people vary in their agreement with either conservative or liberal catch-phrases and on the other hand people vary in their use of the "?" response category of the scale. A 9-item subscale was constructed, consisting of items that seemed to measure liberalism, and this subscale was subsequently used in a biometric analysis including genotype-environment interaction, correcting for non-homogeneous measurement error. Biometric results showed significant genetic and shared environmental influences, and significant genotype-environment interaction effects, suggesting that individuals with a genetic predisposition for conservatism show more non-shared variance but less shared variance than individuals with a genetic predisposition for liberalism.

The construction of MRI brain/head templates for Chinese children from 7 to 16 years of age

PubMed Central

Xie, Wanze; Richards, John E.; Lei, Du; Zhu, Hongyan; Lee, Kang; Gong, Qiyong

2015-01-01

Population-specific brain templates that provide detailed brain information are beneficial to both structural and functional neuroimaging research. However, age-specific MRI templates have not been constructed for Chinese or any Asian developmental populations. This study developed novel T1-weighted average brain and head templates for Chinese children from 7 to 16 years of age in two-year increments using high quality magnetic resonance imaging (MRI) and well-validated image analysis techniques. A total of 138 Chinese children (51 F/87 M) were included in this study. The internally and externally validated registrations show that these Chinese age-specific templates fit Chinese children’s MR images significantly better than age-specific templates created from U.S. children, or adult templates based on either Chinese or North American adults. It implies that age-inappropriate (e.g., the Chinese56 template, the US20–24 template) and nationality-inappropriate brain templates (e.g., U.S. children’s templates, the US20–24 template) do not provide optimal reference MRIs for processing MR brain images of Chinese pediatric populations. Thus, our age-specific MRI templates are the first of the kind and should be useful in neuroimaging studies with children from Chinese or other Asian populations. These templates can also serve as the foundations for the construction of more comprehensive sets of nationality-specific templates for Asian developmental populations. These templates are available for use in our database. PMID:26343862

Graphene/MoS2 heterostructures as templates for growing two-dimensional metals: Predictions from ab initio calculations

NASA Astrophysics Data System (ADS)

Šljivančanin, Željko; Belić, Milivoj

2017-09-01

Preparation of single-atom-thick layers of ordinary metals has been a challenging task since their closely packed atoms lack layered structure with highly anisotropic bonding. Using computational modeling based on density functional theory we showed that graphene/MoS2 heterostructures can be used as suitable templates to grow stable two-dimensional (2D) clusters, as well as extended monoatomic layers of metals with nonlayered structure in the bulk. Considering gold and lithium as two metals with markedly different properties, we found that Li intercalants strengthen coupling between graphene (G) and MoS2, mainly due to electrostatic attraction of 2D materials with positively charged Li atoms. However, intercalation with large Au atoms gives rise to a significant increase in the distance between G and MoS2 and thus, weakens their interaction. In addition to strong preference for 2D growth, we demonstrated that Au intercalants weakly interact with both G and MoS2, and hence G /MoS2 vertical heterostructures could be a promising framework to prepare gold 2D structures with electronic properties closely resembling those of the hypothetical free-standing hexagonal gold monolayer.

Human PrimPol activity is enhanced by RPA.

PubMed

Martínez-Jiménez, María I; Lahera, Antonio; Blanco, Luis

2017-04-10

Human PrimPol is a primase belonging to the AEP superfamily with the unique ability to synthesize DNA primers de novo, and a non-processive DNA polymerase able to bypass certain DNA lesions. PrimPol facilitates both mitochondrial and nuclear replication fork progression either acting as a conventional TLS polymerase, or repriming downstream of blocking lesions. In vivo assays have shown that PrimPol is rapidly recruited to sites of DNA damage by interaction with the human replication protein A (RPA). In agreement with previous findings, we show here that the higher affinity of RPA for ssDNA inhibits PrimPol activities in short ssDNA templates. In contrast, once the amount of ssDNA increases up to a length in which both proteins can simultaneously bind ssDNA, as expected during replicative stress conditions, PrimPol and RPA functionally interact, and their binding capacities are mutually enhanced. When using M13 ssDNA as template, RPA stimulated both the primase and polymerase activities of PrimPol, either alone or in synergy with Polε. These new findings supports the existence of a functional PrimPol/RPA association that allows repriming at the exposed ssDNA regions formed in the leading strand upon replicase stalling.

Structure of human DNA polymerase iota and the mechanism of DNA synthesis.

PubMed

Makarova, A V; Kulbachinskiy, A V

2012-06-01

Cellular DNA polymerases belong to several families and carry out different functions. Highly accurate replicative DNA polymerases play the major role in cell genome replication. A number of new specialized DNA polymerases were discovered at the turn of XX-XXI centuries and have been intensively studied during the last decade. Due to the special structure of the active site, these enzymes efficiently perform synthesis on damaged DNA but are characterized by low fidelity. Human DNA polymerase iota (Pol ι) belongs to the Y-family of specialized DNA polymerases and is one of the most error-prone enzymes involved in DNA synthesis. In contrast to other DNA polymerases, Pol ι is able to use noncanonical Hoogsteen interactions for nucleotide base pairing. This allows it to incorporate nucleotides opposite various lesions in the DNA template that impair Watson-Crick interactions. Based on the data of X-ray structural analysis of Pol ι in complexes with various DNA templates and dNTP substrates, we consider the structural peculiarities of the Pol ι active site and discuss possible mechanisms that ensure the unique behavior of the enzyme on damaged and undamaged DNA.

Feasibility of using touch screen technology for early cognitive assessment in children.

PubMed

Twomey, Deirdre M; Wrigley, Conal; Ahearne, Caroline; Murphy, Raegan; De Haan, Michelle; Marlow, Neil; Murray, Deirdre M

2018-03-13

To explore the feasibility of using a touch screen assessment tool to measure cognitive capacity in toddlers. 112 typically developing children with a median age of 31 months (IQR: 26-34) interacted with a touch screen cognitive assessment tool. We examined the sensitivity of the tool to age-related changes in cognition by comparing the number of items completed, speed of task completion and accuracy in two age groups; 24-29 months versus 30-36 months. Children aged 30-36 months completed more tasks (median: 18, IQR: 18-18) than those aged 24-29 months (median: 17, IQR: 15-18). Older children also completed two of the three working memory tasks and an object permanence task faster than their younger peers. Children became faster at completing the working memory items with each exposure and registered similar completion times on the hidden object retrieval items, despite task demands being twofold on the second exposure. A novel item required children to integrate what they had learnt on preceding items. The older group was more likely to complete this item and to do so faster than the younger group. Children as young as 24 months can complete items requiring cognitive engagement on a touch screen device, with no verbal instruction and minimal child-administrator interaction. This paves the way for using touch screen technology for language and administrator independent developmental assessment in toddlers. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Rasch validation of the Chinese parent-child interaction scale (CPCIS).

PubMed

Ip, Patrick; Tso, Winnie; Rao, Nirmala; Ho, Frederick Ka Wing; Chan, Ko Ling; Fu, King Wa; Li, Sophia Ling; Goh, Winnie; Wong, Wilfred Hing-Sang; Chow, Chun Bong

2018-03-15

Proper parent-child interaction is crucial for child development, but an assessment tool in Chinese is currently lacking. This study aimed to develop and validate a parent-reported parent-child interaction scale for Chinese preschool children. The Chinese parent-child interaction scale (CPCIS) was designed by an expert panel based on the literature and clinical observations in the Chinese context. The initial CPCIS had 14 parent-child interactive activity items. Psychometric properties of the CPCIS were examined using the Rasch model and confirmatory factor analysis (CFA). Convergent validity was investigated by the associations between CPCIS and family income, maternal education level, and children's school readiness. The study recruited 567 Chinese parent-child pairs from diverse socioeconomic backgrounds, who completed the CPCIS. Six out of the 14 items in the initial CPCIS were dropped due to suboptimal fit values. The refined 8-item CPCIS was shown to be valid and reliable by Rasch models and CFA. The person separation reliability and Cronbach's α of the CPCIS were 0.81 and 0.82, respectively. The CPCIS scores were positively associated with family's socioeconomic status (η 2  = 0.05, P < 0.001), maternal education level (η 2  = 0.08, P < 0.001), and children's school readiness (η 2  = 0.01, P < 0.01). CPCIS is an easily administered, valid, and reliable tool for the assessment of parent-child interactions in Chinese families.

Biometric template transformation: a security analysis

NASA Astrophysics Data System (ADS)

Nagar, Abhishek; Nandakumar, Karthik; Jain, Anil K.

2010-01-01

One of the critical steps in designing a secure biometric system is protecting the templates of the users that are stored either in a central database or on smart cards. If a biometric template is compromised, it leads to serious security and privacy threats because unlike passwords, it is not possible for a legitimate user to revoke his biometric identifiers and switch to another set of uncompromised identifiers. One methodology for biometric template protection is the template transformation approach, where the template, consisting of the features extracted from the biometric trait, is transformed using parameters derived from a user specific password or key. Only the transformed template is stored and matching is performed directly in the transformed domain. In this paper, we formally investigate the security strength of template transformation techniques and define six metrics that facilitate a holistic security evaluation. Furthermore, we analyze the security of two wellknown template transformation techniques, namely, Biohashing and cancelable fingerprint templates based on the proposed metrics. Our analysis indicates that both these schemes are vulnerable to intrusion and linkage attacks because it is relatively easy to obtain either a close approximation of the original template (Biohashing) or a pre-image of the transformed template (cancelable fingerprints). We argue that the security strength of template transformation techniques must consider also consider the computational complexity of obtaining a complete pre-image of the transformed template in addition to the complexity of recovering the original biometric template.

The Role of Standardized and Study-specific Human Brain Diffusion Tensor Templates in Inter-subject Spatial Normalization

PubMed Central

Zhang, Shengwei; Arfanakis, Konstantinos

2012-01-01

Purpose To investigate the effect of standardized and study-specific human brain diffusion tensor templates on the accuracy of spatial normalization, without ignoring the important roles of data quality and registration algorithm effectiveness. Materials and Methods Two groups of diffusion tensor imaging (DTI) datasets, with and without visible artifacts, were normalized to two standardized diffusion tensor templates (IIT2, ICBM81) as well as study-specific templates, using three registration approaches. The accuracy of inter-subject spatial normalization was compared across templates, using the most effective registration technique for each template and group of data. Results It was demonstrated that, for DTI data with visible artifacts, the study-specific template resulted in significantly higher spatial normalization accuracy than standardized templates. However, for data without visible artifacts, the study-specific template and the standardized template of higher quality (IIT2) resulted in similar normalization accuracy. Conclusion For DTI data with visible artifacts, a carefully constructed study-specific template may achieve higher normalization accuracy than that of standardized templates. However, as DTI data quality improves, a high-quality standardized template may be more advantageous than a study-specific template, since in addition to high normalization accuracy, it provides a standard reference across studies, as well as automated localization/segmentation when accompanied by anatomical labels. PMID:23034880

Virtual Screening of Peptide and Peptidomimetic Fragments Targeted to Inhibit Bacterial Dithiol Oxidase DsbA.

PubMed

Duprez, Wilko; Bachu, Prabhakar; Stoermer, Martin J; Tay, Stephanie; McMahon, Róisín M; Fairlie, David P; Martin, Jennifer L

2015-01-01

Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to address the growing problem of antibiotic resistance. The periplasmic oxidative folding system in Gram-negative bacteria represents a possible target for anti-virulence antibacterials. By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized. Here, we undertook the design of peptidomimetic inhibitors targeting the interaction between the two key enzymes of oxidative folding, DsbA and DsbB, with the ultimate goal of preventing virulence factor assembly. Structures of DsbB--or peptides--complexed with DsbA revealed key interactions with the DsbA active site cysteine, and with a hydrophobic groove adjacent to the active site. The present work aimed to discover peptidomimetics that target the hydrophobic groove to generate non-covalent DsbA inhibitors. The previously reported structure of a Proteus mirabilis DsbA active site cysteine mutant, in a non-covalent complex with the heptapeptide PWATCDS, was used as an in silico template for virtual screening of a peptidomimetic fragment library. The highest scoring fragment compound and nine derivatives were synthesized and evaluated for DsbA binding and inhibition. These experiments discovered peptidomimetic fragments with inhibitory activity at millimolar concentrations. Although only weakly potent relative to larger covalent peptide inhibitors that interact through the active site cysteine, these fragments offer new opportunities as templates to build non-covalent inhibitors. The results suggest that non-covalent peptidomimetics may need to interact with sites beyond the hydrophobic groove in order to produce potent DsbA inhibitors.

Tyrosine Templating in the Self-Assembly and Crystallization of Silk Fibroin.

PubMed

Partlow, Benjamin P; Bagheri, Mehran; Harden, James L; Kaplan, David L

2016-11-14

Native silk fibers exhibit strength and toughness that rival those of the best synthetic fibers. Despite significant research, further insight is still needed to understand the mechanisms by which silkworms are capable of spinning such tough fibers. Here we propose that π-π and π-OH group interactions of tyrosine side chains provide templating effects, such that the crystal-forming domains are in registration, thereby fostering the self-assembly of the spinning dope. Intrinsic fluorescence measurements, in conjunction with circular dichroism, showed that during self-assembly of regenerated silk solutions, the tyrosine residues were localized in a more hydrophobic local environment, suggesting preferential assembly. In situ Fourier transform infrared spectroscopy indicated that cross-linking of the tyrosine residues resulted in the development of extended β-sheet structure. Additionally, control of cross-link density directly influenced the degree of crystallinity upon drying. Molecular dynamics simulations were performed on silk mimetic peptides in order to more thoroughly understand the role of tyrosines. The results indicated that tyrosine residues tended to transiently colocate in solution due to π-π interactions and hydrogen bonds with adjacent residues and with the peptide backbone. These more stable tyrosine interactions resulted in reduced lateral chain fluctuations and increased incidence of coordinated intrachain association, while introduction of a dityrosine bond directly promoted the formation of β-sheet structures. In total, the experimental and modeling data support a critical role for tyrosine-tyrosine interactions as a key early feature in the self-assembly of regenerated silk protein chains and therefore are important in the robust and unusual mechanical properties ultimately achieved in the process.

Rational design and synthesis of water-compatible molecularly imprinted polymers for selective solid phase extraction of amiodarone.

PubMed

Muhammad, Turghun; Cui, Liu; Jide, Wang; Piletska, Elena V; Guerreiro, Antonio R; Piletsky, Sergey A

2012-01-04

Novel water-compatible molecularly imprinted polymers (MIPs) selective for amiodarone (AD) were designed via a new methodology which relies on screening library of non-imprinted polymers (NIPs). The NIP library consisted of eighteen cross-linked co-polymers synthesized from monomers commonly used in molecular imprinting. The binding capacity of each polymer in the library was analyzed in two different solvents. Binding in water was used to assess non-specific (hydrophobic) interactions and binding in an appropriate organic solvent was used to assess specific interactions. A good correlation was found between the screening tests and modeling of monomer-template interactions performed using computational approach. Additionally, analysis of template-monomer interactions was performed using UV-vis spectroscopy. As the result, 4-vinylpyridine (4-VP) was selected as the best monomer for developing MIP for AD. The 4-VP-based polymers demonstrated imprinting factor equal 3.9. The polymers performance in SPE was evaluated using AD and its structural analogues. The recovery of AD was as high as 96% when extracted from spiked phosphate buffer (pH 4.5) solution and 82.1% from spiked serum samples. The developed MIP shown as a material with specific binding to AD, comparing to its structural analogues, 1-(2-diethylaminoethoxy)-2,6-diiodo-4-nitrobenzene and lidocaine, which shown 9.9% and 25.4% of recovery from the buffer solution, correspondingly. We believe that the screening of NIP library could be proposed as an alternative to commonly used computational and combinatorial approaches. Copyright © 2011 Elsevier B.V. All rights reserved.

Remote detection of weak aftershocks of the DPRK underground explosions using waveform cross correlation

NASA Astrophysics Data System (ADS)

Le Bras, R.; Rozhkov, M.; Bobrov, D.; Kitov, I. O.; Sanina, I.

2017-12-01

Association of weak seismic signals generated by low-magnitude aftershocks of the DPRK underground tests into event hypotheses represent a challenge for routine automatic and interactive processing at the International Data Centre (IDC) of the Comprehensive Nuclear-Test-Ban Treaty Organization, due to the relatively low station density of the International Monitoring System (IMS) seismic network. Since 2011, as an alternative, the IDC has been testing various prototype techniques of signal detection and event creation based on waveform cross correlation. Using signals measured by seismic stations of the IMS from DPRK explosions as waveform templates, the IDC detected several small (estimated mb between 2.2 and 3.6) seismic events after two DPRK tests conducted on September 9, 2016 and September 3, 2017. The obtained detections were associated with reliable event hypothesis and then used to locate these events relative to the epicenters of the DPRK explosions. We observe high similarity of the detected signals with the corresponding waveform templates. The newly found signals also correlate well between themselves. In addition, the values of the signal-to-noise ratios (SNR) estimated using the traces of cross correlation coefficients, increase with template length (from 5 s to 150 s), providing strong evidence in favour of their spatial closeness, which allows interpreting them as explosion aftershocks. We estimated the relative magnitudes of all aftershocks using the ratio of RMS amplitudes of the master and slave signal in the cross correlation windows characterized by the highest SNR. Additional waveform data from regional non-IMS stations MDJ and SEHB provide independent validation of these aftershock hypotheses. Since waveform templates from any single master event may be sub-efficient at some stations, we have also developed a method of joint usage of the DPRK and the biggest aftershocks templates to build more robust event hypotheses.

PoLi: A Virtual Screening Pipeline Based On Template Pocket And Ligand Similarity

PubMed Central

Roy, Ambrish; Srinivasan, Bharath; Skolnick, Jeffrey

2015-01-01

Often in pharmaceutical research, the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand binding pockets in proteins is small. PoLi identifies similar ligand binding pockets in a holo-template protein library, selectively copies relevant parts of template ligands and uses them for VS. In practice, PoLi is a hybrid structure and ligand based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6 respectively, in the top 1% of the screened library. In contrast, traditional docking based VS using AutoDock Vina and homology-based VS using FINDSITEfilt have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods. PMID:26225536

Acetate templating on digital images is more accurate than computer-based templating for total hip arthroplasty.

PubMed

Petretta, Robert; Strelzow, Jason; Ohly, Nicholas E; Misur, Peter; Masri, Bassam A

2015-12-01

Templating is an important aspect of preoperative planning for total hip arthroplasty and can help determine the size and positioning of the prosthesis. Historically, templating has been performed using acetate templates over printed radiographs. As a result of the increasing use of digital imaging, surgeons now either obtain additional printed radiographs solely for templating purposes or use specialized digital templating software, both of which carry additional cost. The purposes of this study was to compare acetate templating of digitally calibrated images on an LCD monitor to digital templating in terms of (1) accuracy; (2) reproducibility; and (3) time efficiency. Acetate onlay templating was performed directly over digital radiographs on an LCD monitor and was compared with digital templating. Five separate observers participated in this study templating on 52 total hip arthroplasties. For the acetate templating, the digital images were magnified to the scaled reference on the templates provided by the manufacturer (ratio 1.2:1) before templating using a 25-mm marker as a reference. Both the acetate and digital templating results were then compared with the actual implanted components to determine accuracy. Interobserver and intraobserver variability was determined by an intraclass correlation coefficient. Observers recorded time to complete templating from the time of complete upload of patients' imaging onto the system to completion of templating. Both acetate and digital templates demonstrated moderate accuracy in predicting within one size of the eventual implanted acetabular cup (77% [199 of 260]; 70% [181 of 260], respectively; p = 0.050; 95% confidence interval [CI], 0.058-0.32), whereas acetate templating was better at predicting the femoral stem compared to digital templating (75% [195 of 260]; 60% [155 of 260], respectively; p < 0.001; 95% CI, 0.084-0.32). Acetate templating showed moderate to substantial interobserver agreement (cup intraclass correlation coefficient [ICC] = 0.55; 95% CI, 0.14-0.86; femoral ICC = 0.75; 95% CI, 0.39-0.95) and both methods showed almost perfect intraobserver agreement in reproducibility (acetate cup ICC = 0.82; 95% CI, 0.66-0.97; acetate femoral ICC = 0.86; 95% CI, 0.74-0.97; digital cup ICC = 0.82; 95% CI, 0.68-0.97; digital femoral ICC = 0.88; 95% CI, 0.77-1.0). Acetate templating could be performed more quickly (acetate mean 119 seconds; range, 37-220 seconds versus 154 seconds; range, 73-343 seconds; p < 0.001). Acetate onlay templating on digitally calibrated images can be a reliable substitute for digital templating using specialized software. It is quicker to perform and much less expensive. Hospitals and practices need not purchase expensive software, particularly at lower volume centers. Level III, diagnostic study.

Model-Based Collaborative Filtering Analysis of Student Response Data: Machine-Learning Item Response Theory

ERIC Educational Resources Information Center

Bergner, Yoav; Droschler, Stefan; Kortemeyer, Gerd; Rayyan, Saif; Seaton, Daniel; Pritchard, David E.

2012-01-01

We apply collaborative filtering (CF) to dichotomously scored student response data (right, wrong, or no interaction), finding optimal parameters for each student and item based on cross-validated prediction accuracy. The approach is naturally suited to comparing different models, both unidimensional and multidimensional in ability, including a…

Ethnic Pride and Cardiovascular Health among Mexican American Adults along the U.S.-Mexico Border

ERIC Educational Resources Information Center

de Heer, Hendrik Dirk; Balcazar, Hector G; Lee Rosenthal, E.; Cardenas, Victor M; Schulz, Leslie O.

2011-01-01

This study addressed the association between items from the General Acculturation Index (GAI) and cardiovascular health. Specifically, we assessed whether ethnic pride was associated with health outcomes after controlling for items regarding language, place where the childhood was spent, and ethnic interaction. The study was a cross-sectional…

Encoding Strategy Changes and Spacing Effects in the Free Recall of Unmixed Lists

ERIC Educational Resources Information Center

Delaney, P.F.; Knowles, M.E.

2005-01-01

Memory for repeated items often improves when repetitions are separated by other items-a phenomenon called the spacing effect. In two experiments, we explored the complex interaction between study strategies, serial position, and spacing effects. When people studied several unmixed lists, they initially used mainly rote rehearsal, but some people…

The Role of Abstract Syntactic Knowledge in Language Acquisition: A Reply to Tomasello (2000).

ERIC Educational Resources Information Center

Fisher, Cynthia

2002-01-01

Argues that Tomasello's (2000) interpretation of young children's conservatism in language production depends on questionable premises. Reviews evidence against the assumptions, showing that children learn item-specific facts about verbs and other lexical items. Asserts that researchers must explore the interactions of lexical and more abstract…

The Development and Experimental Analysis of a Self-Instructional Program in Graphical Kinematics.

ERIC Educational Resources Information Center

Nee, John G.

A project to help vocational-technical teachers in the development and experimental analysis of self-instructional programs is presented. The emphasis in developing the program was on maximizing effectiveness and efficiency of program-learner interaction as measured by criterion items. These items emphasized cognitive content dealing with the…

Development of the Enzyme-Substrate Interactions Concept Inventory

ERIC Educational Resources Information Center

Bretz, Stacey Lowery; Linenberger, Kimberly J.

2012-01-01

Enzyme function is central to student understanding of multiple topics within the biochemistry curriculum. In particular, students must understand how enzymes and substrates interact with one another. This manuscript describes the development of a 15-item Enzyme-Substrate Interactions Concept Inventory (ESICI) that measures student understanding…

An Agent-Based Modeling Template for a Cohort of Veterans with Diabetic Retinopathy.

PubMed

Day, Theodore Eugene; Ravi, Nathan; Xian, Hong; Brugh, Ann

2013-01-01

Agent-based models are valuable for examining systems where large numbers of discrete individuals interact with each other, or with some environment. Diabetic Veterans seeking eye care at a Veterans Administration hospital represent one such cohort. The objective of this study was to develop an agent-based template to be used as a model for a patient with diabetic retinopathy (DR). This template may be replicated arbitrarily many times in order to generate a large cohort which is representative of a real-world population, upon which in-silico experimentation may be conducted. Agent-based template development was performed in java-based computer simulation suite AnyLogic Professional 6.6. The model was informed by medical data abstracted from 535 patient records representing a retrospective cohort of current patients of the VA St. Louis Healthcare System Eye clinic. Logistic regression was performed to determine the predictors associated with advancing stages of DR. Predicted probabilities obtained from logistic regression were used to generate the stage of DR in the simulated cohort. The simulated cohort of DR patients exhibited no significant deviation from the test population of real-world patients in proportion of stage of DR, duration of diabetes mellitus (DM), or the other abstracted predictors. Simulated patients after 10 years were significantly more likely to exhibit proliferative DR (P<0.001). Agent-based modeling is an emerging platform, capable of simulating large cohorts of individuals based on manageable data abstraction efforts. The modeling method described may be useful in simulating many different conditions where course of disease is described in categorical stages.

LipidPioneer: A Comprehensive User-Generated Exact Mass Template for Lipidomics

PubMed Central

Ulmer, Candice Z.; Koelmel, Jeremy P.; Ragland, Jared M.; Garrett, Timothy J.

2017-01-01

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. PMID:28074328

Targeting Neuroblastoma Cell Surface Proteins: Recommendations for Homology Modeling of hNET, ALK, and TrkB.

PubMed

Haddad, Yazan; Heger, Zbyněk; Adam, Vojtech

2017-01-01

Targeted therapy is a promising approach for treatment of neuroblastoma as evident from the large number of targeting agents employed in clinical practice today. In the absence of known crystal structures, researchers rely on homology modeling to construct template-based theoretical structures for drug design and testing. Here, we discuss three candidate cell surface proteins that are suitable for homology modeling: human norepinephrine transporter (hNET), anaplastic lymphoma kinase (ALK), and neurotrophic tyrosine kinase receptor 2 (NTRK2 or TrkB). When choosing templates, both sequence identity and structure quality are important for homology modeling and pose the first of many challenges in the modeling process. Homology modeling of hNET can be improved using template models of dopamine and serotonin transporters instead of the leucine transporter (LeuT). The extracellular domains of ALK and TrkB are yet to be exploited by homology modeling. There are several idiosyncrasies that require direct attention throughout the process of model construction, evaluation and refinement. Shifts/gaps in the alignment between the template and target, backbone outliers and side-chain rotamer outliers are among the main sources of physical errors in the structures. Low-conserved regions can be refined with loop modeling method. Residue hydrophobicity, accessibility to bound metals or glycosylation can aid in model refinement. We recommend resolving these idiosyncrasies as part of "good modeling practice" to obtain highest quality model. Decreasing physical errors in protein structures plays major role in the development of targeting agents and understanding of chemical interactions at the molecular level.

Acetic and Acrylic Acid Molecular Imprinted Model Silicone Hydrogel Materials for Ciprofloxacin-HCl Delivery

PubMed Central

Hui, Alex; Sheardown, Heather; Jones, Lyndon

2012-01-01

Contact lenses, as an alternative drug delivery vehicle for the eye compared to eye drops, are desirable due to potential advantages in dosing regimen, bioavailability and patient tolerance/compliance. The challenge has been to engineer and develop these materials to sustain drug delivery to the eye for a long period of time. In this study, model silicone hydrogel materials were created using a molecular imprinting strategy to deliver the antibiotic ciprofloxacin. Acetic and acrylic acid were used as the functional monomers, to interact with the ciprofloxacin template to efficiently create recognition cavities within the final polymerized material. Synthesized materials were loaded with 9.06 mM, 0.10 mM and 0.025 mM solutions of ciprofloxacin, and the release of ciprofloxacin into an artificial tear solution was monitored over time. The materials were shown to release for periods varying from 3 to 14 days, dependent on the loading solution, functional monomer concentration and functional monomer:template ratio, with materials with greater monomer:template ratio (8:1 and 16:1 imprinted) tending to release for longer periods of time. Materials with a lower monomer:template ratio (4:1 imprinted) tended to release comparatively greater amounts of ciprofloxacin into solution, but the release was somewhat shorter. The total amount of drug released from the imprinted materials was sufficient to reach levels relevant to inhibit the growth of common ocular isolates of bacteria. This work is one of the first to demonstrate the feasibility of molecular imprinting in model silicone hydrogel-type materials. PMID:28817033

Development of a consensus core dataset in juvenile dermatomyositis for clinical use to inform research

PubMed Central

McCann, Liza J; Pilkington, Clarissa A; Huber, Adam M; Ravelli, Angelo; Appelbe, Duncan; Kirkham, Jamie J; Williamson, Paula R; Aggarwal, Amita; Christopher-Stine, Lisa; Constantin, Tamas; Feldman, Brian M; Lundberg, Ingrid; Maillard, Sue; Mathiesen, Pernille; Murphy, Ruth; Pachman, Lauren M; Reed, Ann M; Rider, Lisa G; van Royen-Kerkof, Annet; Russo, Ricardo; Spinty, Stefan; Wedderburn, Lucy R

2018-01-01

Objectives This study aimed to develop consensus on an internationally agreed dataset for juvenile dermatomyositis (JDM), designed for clinical use, to enhance collaborative research and allow integration of data between centres. Methods A prototype dataset was developed through a formal process that included analysing items within existing databases of patients with idiopathic inflammatory myopathies. This template was used to aid a structured multistage consensus process. Exploiting Delphi methodology, two web-based questionnaires were distributed to healthcare professionals caring for patients with JDM identified through email distribution lists of international paediatric rheumatology and myositis research groups. A separate questionnaire was sent to parents of children with JDM and patients with JDM, identified through established research networks and patient support groups. The results of these parallel processes informed a face-to-face nominal group consensus meeting of international myositis experts, tasked with defining the content of the dataset. This developed dataset was tested in routine clinical practice before review and finalisation. Results A dataset containing 123 items was formulated with an accompanying glossary. Demographic and diagnostic data are contained within form A collected at baseline visit only, disease activity measures are included within form B collected at every visit and disease damage items within form C collected at baseline and annual visits thereafter. Conclusions Through a robust international process, a consensus dataset for JDM has been formulated that can capture disease activity and damage over time. This dataset can be incorporated into national and international collaborative efforts, including existing clinical research databases. PMID:29084729

Development of a fragile X syndrome (FXS) knowledge scale: towards a modified multidimensional measure of informed choice for FXS population carrier screening.

PubMed

Ames, Alice G; Jaques, Alice; Ukoumunne, Obioha C; Archibald, Alison D; Duncan, Rony E; Emery, Jon; Metcalfe, Sylvia A

2015-02-01

Genetic carrier screening is increasingly possible for many conditions, but it is important to ensure decisions are informed. The multidimensional measure of informed choice (MMIC) is a quantitative instrument developed to evaluate informed choice in prenatal screening for Down syndrome, measuring knowledge, attitudes and uptake. To apply the MMIC in other screening settings, the knowledge scale must be modified. To develop and validate a modified MMIC knowledge scale for use with women undergoing carrier screening for fragile X syndrome (FXS). Responses to MMIC items were collected through questionnaires as part of a FXS carrier screening pilot study in a preconception setting in Melbourne, Australia. Ten knowledge scale items were developed using a modified Delphi technique. Cronbach's alpha and factor analysis were used to validate the new FXS knowledge scale. We summarized the knowledge, attitudes and informed choice status based on the modified MMIC. Two hundred and eighty-five women were recruited, 241 eligible questionnaires were complete for analysis. The FXS knowledge scale items measured one salient construct and were internally consistent (alpha = 0.70). 71% (172/241) of participants were classified as having good knowledge, 70% (169/241) had positive attitudes and 27% (65/241) made an informed choice to accept or decline screening. We present the development of a knowledge scale as part of a MMIC to evaluate informed choice in population carrier screening for FXS. This can be used as a template by other researchers to develop knowledge scales for other conditions for use in the MMIC. © 2012 John Wiley & Sons Ltd.

Effects of long-term representations on free recall of unrelated words

PubMed Central

Katkov, Mikhail; Romani, Sandro

2015-01-01

Human memory stores vast amounts of information. Yet recalling this information is often challenging when specific cues are lacking. Here we consider an associative model of retrieval where each recalled item triggers the recall of the next item based on the similarity between their long-term neuronal representations. The model predicts that different items stored in memory have different probability to be recalled depending on the size of their representation. Moreover, items with high recall probability tend to be recalled earlier and suppress other items. We performed an analysis of a large data set on free recall and found a highly specific pattern of statistical dependencies predicted by the model, in particular negative correlations between the number of words recalled and their average recall probability. Taken together, experimental and modeling results presented here reveal complex interactions between memory items during recall that severely constrain recall capacity. PMID:25593296

Teaching children with autism to engage in peer-directed mands using a picture exchange communication system.

PubMed

Paden, Amber R; Kodak, Tiffany; Fisher, Wayne W; Gawley-Bullington, Elizabeth M; Bouxsein, Kelly J

2012-01-01

We evaluated differential reinforcement of alternative behavior (DRA) plus prompting to increase peer-directed mands for preferred items using a picture exchange communication system (PECS). Two nonvocal individuals with autism participated. Independent mands with a peer increased with the implementation of DRA plus prompting for both participants. In addition, peers engaged in brief social interactions following the majority of mands for leisure items. These results suggest that teaching children to use PECS with peers may be one way to increase manding and social interactions in individuals with limited or no vocal repertoire.

TEACHING CHILDREN WITH AUTISM TO ENGAGE IN PEER-DIRECTED MANDS USING A PICTURE EXCHANGE COMMUNICATION SYSTEM

PubMed Central

Paden, Amber R; Kodak, Tiffany; Fisher, Wayne W; Gawley-Bullington, Elizabeth M; Bouxsein, Kelly J

2012-01-01

We evaluated differential reinforcement of alternative behavior (DRA) plus prompting to increase peer-directed mands for preferred items using a picture exchange communication system (PECS). Two nonvocal individuals with autism participated. Independent mands with a peer increased with the implementation of DRA plus prompting for both participants. In addition, peers engaged in brief social interactions following the majority of mands for leisure items. These results suggest that teaching children to use PECS with peers may be one way to increase manding and social interactions in individuals with limited or no vocal repertoire. PMID:22844150

Teacher-Student Interaction and Gifted Students' Attitudes toward Chemistry in Laboratory Classrooms in Singapore

ERIC Educational Resources Information Center

Lang, Quek Choon; Wong, Angela F. L.; Fraser, Barry J.

2005-01-01

This study investigated associations between teacher-student interaction and students' attitudes towards chemistry among 497 tenth grade students from three independent schools in Singapore. Analyses supported the reliability and validity of a 48-item version of the Questionnaire on Teacher Interaction (QTI). Statistically significant gender…

Imagining Garage Start-Ups: Interactive Effects of Imaginative Capacities on Entrepreneurial Intention

ERIC Educational Resources Information Center

Chang, Chi-Cheng; Yao, Shu-Nung; Chen, Shi-An; King, Jung-Tai; Liang, Chaoyun

2016-01-01

This article describes a structural examination of the interaction among different imaginative capacities and the entrepreneurial intention of electrical and computer engineering students. Two studies were combined to confirm the factor structure of survey items and test the hypothesised interaction model. The results indicated that imaginative…

Group Trust, Communication Media, and Interactivity: Toward an Integrated Model of Online Collaborative Learning

ERIC Educational Resources Information Center

Du, Jianxia; Wang, Chuang; Zhou, Mingming; Xu, Jianzhong; Fan, Xitao; Lei, Saosan

2018-01-01

The present investigation examines the multidimensional relationships among several critical components in online collaborative learning, including group trust, communication media, and interactivity. Four hundred eleven university students from 103 groups in the United States responded survey items on online collaboration, interactivity,…

Radio-nuclide mixture identification using medium energy resolution detectors

DOEpatents

Nelson, Karl Einar

2013-09-17

According to one embodiment, a method for identifying radio-nuclides includes receiving spectral data, extracting a feature set from the spectral data comparable to a plurality of templates in a template library, and using a branch and bound method to determine a probable template match based on the feature set and templates in the template library. In another embodiment, a device for identifying unknown radio-nuclides includes a processor, a multi-channel analyzer, and a memory operatively coupled to the processor, the memory having computer readable code stored thereon. The computer readable code is configured, when executed by the processor, to receive spectral data, to extract a feature set from the spectral data comparable to a plurality of templates in a template library, and to use a branch and bound method to determine a probable template match based on the feature set and templates in the template library.

Introducing the Postsecondary Instructional Practices Survey (PIPS): A Concise, Interdisciplinary, and Easy-to-Score Survey

PubMed Central

Walter, Emily M.; Henderson, Charles R.; Beach, Andrea L.; Williams, Cody T.

2016-01-01

Researchers, administrators, and policy makers need valid and reliable information about teaching practices. The Postsecondary Instructional Practices Survey (PIPS) is designed to measure the instructional practices of postsecondary instructors from any discipline. The PIPS has 24 instructional practice statements and nine demographic questions. Users calculate PIPS scores by an intuitive proportion-based scoring convention. Factor analyses from 72 departments at four institutions (N = 891) support a 2- or 5-factor solution for the PIPS; both models include all 24 instructional practice items and have good model fit statistics. Factors in the 2-factor model include (a) instructor-centered practices, nine items; and (b) student-centered practices, 13 items. Factors in the 5-factor model include (a) student–student interactions, six items; (b) content delivery, four items; (c) formative assessment, five items; (d) student-content engagement, five items; and (e) summative assessment, four items. In this article, we describe our development and validation processes, provide scoring conventions and outputs for results, and describe wider applications of the instrument. PMID:27810868

Development of Total Knee Replacement Digital Templating Software

NASA Astrophysics Data System (ADS)

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.

Procedural justice and layoff survivors' commitment: a quantitative review.

PubMed

Grubb, W Lee

2006-10-01

Layoffs are common in today's organizations. Most studies that have examined the correlation between procedural justice and the organizational commitment of layoff survivors have yielded positive correlations, but the magnitude of the correlations varies widely. This study is the first to estimate the population correlation and to identify the primary sources that cause variation in the correlation across studies. The results indicated that justice and commitment correlations can always be expected to be positive. Based on a total sample size of 9080 individuals, the estimated mean population correlation was .34. Variation was primarily explained by attributes of the justice measure where multiple items scales and scales composed of both interactional and procedural justice items yielded higher correlations than single item measures. Therefore, it is important that employers recognize the substantial assuaging affect that procedural and interactional justice can have on survivors' organizational commitment.

Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation.

PubMed

Utecht, Joseph; Brochhausen, Mathias; Judkins, John; Schneider, Jodi; Boyce, Richard D

2017-01-01

In this research we aim to demonstrate that an ontology-based system can categorize potential drug-drug interaction (PDDI) evidence items into complex types based on a small set of simple questions. Such a method could increase the transparency and reliability of PDDI evidence evaluation, while also reducing the variations in content and seriousness ratings present in PDDI knowledge bases. We extended the DIDEO ontology with 44 formal evidence type definitions. We then manually annotated the evidence types of 30 evidence items. We tested an RDF/OWL representation of answers to a small number of simple questions about each of these 30 evidence items and showed that automatic inference can determine the detailed evidence types based on this small number of simpler questions. These results show proof-of-concept for a decision support infrastructure that frees the evidence evaluator from mastering relatively complex written evidence type definitions.

Enhanced ICBM Diffusion Tensor Template of the Human Brain

PubMed Central

Zhang, Shengwei; Peng, Huiling; Dawe, Robert J.; Arfanakis, Konstantinos

2010-01-01

Development of a diffusion tensor (DT) template that is representative of the micro-architecture of the human brain is crucial for comparisons of neuronal structural integrity and brain connectivity across populations, as well as for the generation of a detailed white matter atlas. Furthermore, a DT template in ICBM space may simplify consolidation of information from DT, anatomical and functional MRI studies. The previously developed “IIT DT brain template” was produced in ICBM-152 space, based on a large number of subjects from a limited age-range, using data with minimal image artifacts, and non-linear registration. That template was characterized by higher image sharpness, provided the ability to distinguish smaller white matter fiber structures, and contained fewer image artifacts, than several previously published DT templates. However, low-dimensional registration was used in the development of that template, which led to a mismatch of DT information across subjects, eventually manifested as loss of local diffusion information and errors in the final tensors. Also, low-dimensional registration led to a mismatch of the anatomy in the IIT and ICBM-152 templates. In this work, a significantly improved DT brain template in ICBM-152 space was developed, using high-dimensional non-linear registration and the raw data collected for the purposes of the IIT template. The accuracy of inter-subject DT matching was significantly increased compared to that achieved for the development of the IIT template. Consequently, the new template contained DT information that was more representative of single-subject human brain data, and was characterized by higher image sharpness than the IIT template. Furthermore, a bootstrap approach demonstrated that the variance of tensor characteristics was lower in the new template. Additionally, compared to the IIT template, brain anatomy in the new template more accurately matched ICBM-152 space. Finally, spatial normalization of a number of DT datasets through registration to the new and existing IIT templates was improved when using the new template. PMID:20851772

Dakota Graphical User Interface v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Friedman-Hill, Ernest; Glickman, Matthew; Gibson, Marcus

Graphical analysis environment for Sandia’s Dakota software for optimization and uncertainty quantification. The Dakota GUI is an interactive graphical analysis environment for creating, running, and interpreting Dakota optimization and uncertainty quantification studies. It includes problem (Dakota study) set-up, option specification, simulation interfacing, analysis execution, and results visualization. Through the use of wizards, templates, and views, Dakota GUI helps uses navigate Dakota’s complex capability landscape.

Active Wiki Knowledge Repository

DTIC Science & Technology

2012-10-01

data using SPARQL queries or RESTful web-services; ‘gardening’ tools for examining the semantically tagged content in the wiki; high-level language tool...Tagging & RDF triple-store Fusion and inferences for collaboration Tools for Consuming Data SPARQL queries or RESTful WS Inference & Gardening tools...other stores using AW SPARQL queries and rendering templates; and 4) Interactively share maps and other content using annotation tools to post notes

Effect of heparin and heparan sulphate on open promoter complex formation for a simple tandem gene model using ex situ atomic force microscopy.

PubMed

Chammas, Oliver; Bonass, William A; Thomson, Neil H

2017-05-01

The influence of heparin and heparan sulphate (HepS) on the appearance and analysis of open promoter complex (RP o ) formation by E. coli RNA polymerase (RNAP) holoenzyme (σ 70 RNAP) on linear DNA using ex situ imaging by atomic force microscopy (AFM) has been investigated. Introducing heparin or HepS into the reaction mix significantly reduces non-specific interactions of the σ 70 RNAP and RNAP after RP o formation allowing for better interpretation of complexes shown within AFM images, particularly on DNA templates containing more than one promoter. Previous expectation was that negatively charged polysaccharides, often used as competitive inhibitors of σRNAP binding and RP o formation, would also inhibit binding of the DNA template to the mica support surface and thereby lower the imaging yield of active RNAP-DNA complexes. We found that the reverse of this was true, and that the yield of RP o formation detected by AFM, for a simple tandem gene model containing two λ PR promoters, increased. Moreover and unexpectedly, HepS was more efficient than heparin, with both of them having a dispersive effect on the sample, minimising unwanted RNAP-RNAP interactions as well as non-specific interactions between the RNAP and DNA template. The success of this method relied on the observation that E. coli RNAP has the highest affinity for the mica surface of all the molecular components. For our system, the affinity of the three constituent biopolymers to muscovite mica was RNAP>Heparin or HepS>DNA. While we observed that heparin and HepS can inhibit DNA binding to the mica, the presence of E. coli RNAP overcomes this effect allowing a greater yield of RP o s for AFM analysis. This method can be extended to other DNA binding proteins and enzymes, which have an affinity to mica higher than DNA, to improve sample preparation for AFM studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Elucidating the 3D structures of Al(iii)-Aβ complexes: a template free strategy based on the pre-organization hypothesis.

PubMed

Mujika, Jon I; Rodríguez-Guerra Pedregal, Jaime; Lopez, Xabier; Ugalde, Jesus M; Rodríguez-Santiago, Luis; Sodupe, Mariona; Maréchal, Jean-Didier

2017-07-01

Senile plaques are extracellular deposits found in patients with Alzheimer's Disease (AD) and are mainly formed by insoluble fibrils of β-amyloid (Aβ) peptides. The mechanistic details about how AD develops are not fully understood yet, but metals such as Cu, Zn, or Fe are proposed to have a non-innocent role. Many studies have also linked the non biological metal aluminum with AD, a species whose concentration in the environment and food has been constantly increasing since the industrial revolution. Gaining a molecular picture of how Al(iii) interacts with an Aβ peptide is of fundamental interest to improve understanding of the many variables in the evolution of AD. So far, no consensus has been reached on how this metal interacts with Aβ, partially due to the experimental complexity of detecting and quantifying the resulting Al(iii)-Aβ complexes. Computational chemistry arises as a powerful alternative to investigate how Al(iii) can interact with Aβ peptides, as suitable strategies could shed light on the metal-peptide description at the molecular level. However, the absence of any reliable template that could be used for the modeling of the metallopeptide structure makes computational insight extremely difficult. Here, we present a novel strategy to generate accurate 3D models of the Al(iii)-Aβ complexes, which still circumvents first principles simulations of metal binding to peptides of Aβ. The key to this approach lies in the identification of experimental structures of the isolated peptide that are favourably pre-organized for the binding of a given metal in configurations of the first coordination sphere that were previously identified as the most stable with amino acid models. This approach solves the problem of the absence of clear structural templates for novel metallopeptide constructs. The posterior refinement of the structures via QM/MM and MD calculations allows us to provide, for the first time, physically sound models for Al(iii)-Aβ complexes with a 1 : 1 stoichiometry, where up to three carboxylic groups are involved in the metal binding, with a clear preference towards Glu3, Asp7, and Glu11.

Reporting of interventions and "standard of care" control arms in pediatric clinical trials: a quantitative analysis.

PubMed

Yu, Ashley M; Balasubramanaiam, Bannuya; Offringa, Martin; Kelly, Lauren E

2018-06-13

In pediatric medicine, the usual treatment received by children ("standard of care") varies across centers. Evaluations of new treatments often compare to the existing "standard of care" to determine if a treatment is more effective, has a better safety profile, or costs less. The objective of our study was to evaluate intervention and "standard of care" control arms reported in published pediatric clinical trials. Pediatric clinical trials, published in 2014, reporting the use of a "standard of care" control arm were included. Duplicate assessment of reporting completeness was done using the 12-item TIDieR (Template for Intervention Description and Replication) checklist for both the "standard of care" control arms and intervention arms within the same published study. Following screening, 214 pediatric trials in diverse therapeutic areas were included. Several different terms were used to describe "standard of care." There was a significant difference between the mean reported TIDieR checklist items of "standard of care" control arms (5.81 (SD 2.13) and intervention arms (8.45 (SD 1.39, p < 0.0001). Reporting of intervention and "standard of care" control arms in pediatric clinical trials should be improved as current "standard of care" reporting deficiencies limit reproducibility of research and may ultimately contribute to research waste.

Measurement of Teen Dating Violence Attitudes: An Item Response Theory Evaluation of Differential Item Functioning According to Gender

ERIC Educational Resources Information Center

Edelen, Maria Orlando; McCaffrey, Daniel F.; Marshall, Grant N.; Jaycox, Lisa H.

2009-01-01

Accurate assessment of attitudes about intimate partner violence is important for evaluation of prevention and early intervention programs. Assessment of attitudes about cross-gender interactions is particularly susceptible to bias because it requires specifying the gender of the perpetrator and the victim. As it is likely that respondents will…

Network Approach to Autistic Traits: Group and Subgroup Analyses of ADOS Item Scores

ERIC Educational Resources Information Center

Anderson, George M.; Montazeri, Farhad; de Bildt, Annelies

2015-01-01

A network conceptualization might contribute to understanding the occurrence and interacting nature of behavioral traits in the autism realm. Networks were constructed based on correlations of item scores of the Autism Diagnostic Observation Schedule for Modules 1, 2 and 3 obtained for a group of 477 Dutch individuals with developmental disorders.…

Managing a Test Item Bank on a Microcomputer: Can It Help You and Your Students?

ERIC Educational Resources Information Center

Peterson, Julian A.; Meister, Lynn L.

1983-01-01

Describes a test item bank developed by the Association for Medical School Departments of Biochemistry (Texas). Programs (written in Pascal) allow self-evaluation by interactive student access to questions randomly selected from a chosen category. Potential users of the system (having student, manager, and instructor modes) are invited to contact…

Design Patterns for Digital Item Types in Higher Education

ERIC Educational Resources Information Center

Draaijer, S.; Hartog, R. J. M.

2007-01-01

A set of design patterns for digital item types has been developed in response to challenges identified in various projects by teachers in higher education. The goal of the projects in question was to design and develop formative and summative tests, and to develop interactive learning material in the form of quizzes. The subject domains involved…

An Analysis of Variance Approach for the Estimation of Response Time Distributions in Tests

ERIC Educational Resources Information Center

Attali, Yigal

2010-01-01

Generalizability theory and analysis of variance methods are employed, together with the concept of objective time pressure, to estimate response time distributions and the degree of time pressure in timed tests. By estimating response time variance components due to person, item, and their interaction, and fixed effects due to item types and…

Effects of interactive instructional techniques in a web-based peripheral nervous system component for human anatomy.

PubMed

Allen, Edwin B; Walls, Richard T; Reilly, Frank D

2008-02-01

This study investigated the effects of interactive instructional techniques in a web-based peripheral nervous system (PNS) component of a first year medical school human anatomy course. Existing data from 9 years of instruction involving 856 students were used to determine (1) the effect of web-based interactive instructional techniques on written exam item performance and (2) differences between student opinions of the benefit level of five different types of interactive learning objects used. The interactive learning objects included Patient Case studies, review Games, Simulated Interactive Patients (SIP), Flashcards, and unit Quizzes. Exam item analysis scores were found to be significantly higher (p < 0.05) for students receiving the instructional treatment incorporating the web-based interactive learning objects than for students not receiving this treatment. Questionnaires using a five-point Likert scale were analysed to determine student opinion ratings of the interactive learning objects. Students reported favorably on the benefit level of all learning objects. Students rated the benefit level of the Simulated Interactive Patients (SIP) highest, and this rating was significantly higher (p < 0.05) than all other learning objects. This study suggests that web-based interactive instructional techniques improve student exam performance. Students indicated a strong acceptance of Simulated Interactive Patient learning objects.

BSA modification to reduce CTAB induced nonspecificity and cytotoxicity of aptamer-conjugated gold nanorods

NASA Astrophysics Data System (ADS)

Yasun, Emir; Li, Chunmei; Barut, Inci; Janvier, Denisse; Qiu, Liping; Cui, Cheng; Tan, Weihong

2015-05-01

Aptamer-conjugated gold nanorods (AuNRs) are excellent candidates for targeted hyperthermia therapy of cancer cells. However, in high concentrations of AuNRs, aptamer conjugation alone fails to result in highly cell-specific AuNRs due to the presence of positively charged cetyltrimethylammonium bromide (CTAB) as a templating surfactant. Besides causing nonspecific electrostatic interactions with the cell surfaces, CTAB can also be cytotoxic, leading to uncontrolled cell death. To avoid the nonspecific interactions and cytotoxicity triggered by CTAB, we report the further biologically inspired modification of aptamer-conjugated AuNRs with bovine serum albumin (BSA) protein. Following this modification, interaction between CTAB and the cell surface was efficiently blocked, thereby dramatically reducing the side effects of CTAB. This approach may provide a general and simple method to avoid one of the most serious issues in biomedical applications of nanomaterials: nonspecific binding of the nanomaterials with biological cells.Aptamer-conjugated gold nanorods (AuNRs) are excellent candidates for targeted hyperthermia therapy of cancer cells. However, in high concentrations of AuNRs, aptamer conjugation alone fails to result in highly cell-specific AuNRs due to the presence of positively charged cetyltrimethylammonium bromide (CTAB) as a templating surfactant. Besides causing nonspecific electrostatic interactions with the cell surfaces, CTAB can also be cytotoxic, leading to uncontrolled cell death. To avoid the nonspecific interactions and cytotoxicity triggered by CTAB, we report the further biologically inspired modification of aptamer-conjugated AuNRs with bovine serum albumin (BSA) protein. Following this modification, interaction between CTAB and the cell surface was efficiently blocked, thereby dramatically reducing the side effects of CTAB. This approach may provide a general and simple method to avoid one of the most serious issues in biomedical applications of nanomaterials: nonspecific binding of the nanomaterials with biological cells. Electronic supplementary information (ESI) available: Fig. S-1 to S-6 are included. See DOI: 10.1039/c5nr01704a

Information sensing and interactive technology of Internet of Things

NASA Astrophysics Data System (ADS)

Xiao, Zhiliang

2017-11-01

With the rapid development of economic, the Internet of Things based on Internet technology is more and more concerned by all circles of society, and the Internet of Things begins to penetrate into various fields of society. The Internet of things is an extension of the Internet, the difference between the Internet and the Internet of Things is that the purpose of things aims to achieve the exchange and exchange of information and data, contract the people and goods through a variety of technologies and equipment from items to items. Information perception and interaction technology are two very important technologies in the development of things, but also is the important technology in the history of the development of network technology. This paper briefly analyzes the characteristics of the original information perception, and the difference between the interactive technology of the Internet of Things and the human-computer interaction technology. On this basis, this paper mainly elaborates from the two aspects of information perception and interactive technology.

Development and initial validation of the Pharmacist Frequency of Interprofessional Collaboration Instrument (FICI-P) in primary care.

PubMed

Van, Connie; Costa, Daniel; Mitchell, Bernadette; Abbott, Penny; Krass, Ines

2012-01-01

Existing validated measures of pharmacist-physician collaboration focus on measuring attitudes toward collaboration and do not measure frequency of collaborative interactions. To develop and validate an instrument to measure the frequency of collaboration between pharmacists and general practitioners (GPs) from the pharmacist's perspective. An 11-item Pharmacist Frequency of Interprofessional Collaboration Instrument (FICI-P) was developed and administered to 586 pharmacists in 8 divisions of general practice in New South Wales, Australia. The initial items were informed by a review of the literature in addition to interviews of pharmacists and GPs. Items were subjected to principal component and Rasch analyses to determine each item's and the overall measure's psychometric properties and for any needed refinements. Two hundred and twenty four (38%) of pharmacist surveys were completed and returned. Principal component analysis suggested removal of 1 item for a final 1-factor solution. The refined 10-item FICI-P demonstrated internal consistency reliability at Cronbach's alpha=0.90. After collapsing the original 5-point response scale to a 4-point response scale, the refined FICI-P demonstrated fit to the Rasch model. Criterion validity of the FICI-P was supported by the correlation of FICI-P scores with scores on a previously validated Physician-Pharmacist Collaboration Instrument. Validity was also supported by predicted differences in FICI-P scores between subgroups of respondents stratified on age, colocation with GPs, and interactions during the intern-training period. The refined 10-item FICI-P was shown to have good internal consistency, criterion validity, and fit to the Rasch model. The creation of such a tool may allow for the measure of impact in the evaluation of interventions designed to improve interprofessional collaboration between GPs and pharmacists. Copyright © 2012 Elsevier Inc. All rights reserved.

Scale refinement and initial evaluation of a behavioral health function measurement tool for work disability evaluation.

PubMed

Marfeo, Elizabeth E; Ni, Pengsheng; Haley, Stephen M; Bogusz, Kara; Meterko, Mark; McDonough, Christine M; Chan, Leighton; Rasch, Elizabeth K; Brandt, Diane E; Jette, Alan M

2013-09-01

To use item response theory (IRT) data simulations to construct and perform initial psychometric testing of a newly developed instrument, the Social Security Administration Behavioral Health Function (SSA-BH) instrument, that aims to assess behavioral health functioning relevant to the context of work. Cross-sectional survey followed by IRT calibration data simulations. Community. Sample of individuals applying for Social Security Administration disability benefits: claimants (n=1015) and a normative comparative sample of U.S. adults (n=1000). None. SSA-BH measurement instrument. IRT analyses supported the unidimensionality of 4 SSA-BH scales: mood and emotions (35 items), self-efficacy (23 items), social interactions (6 items), and behavioral control (15 items). All SSA-BH scales demonstrated strong psychometric properties including reliability, accuracy, and breadth of coverage. High correlations of the simulated 5- or 10-item computer adaptive tests with the full item bank indicated robust ability of the computer adaptive testing approach to comprehensively characterize behavioral health function along 4 distinct dimensions. Initial testing and evaluation of the SSA-BH instrument demonstrated good accuracy, reliability, and content coverage along all 4 scales. Behavioral function profiles of Social Security Administration claimants were generated and compared with age- and sex-matched norms along 4 scales: mood and emotions, behavioral control, social interactions, and self-efficacy. Using the computer adaptive test-based approach offers the ability to collect standardized, comprehensive functional information about claimants in an efficient way, which may prove useful in the context of the Social Security Administration's work disability programs. Copyright © 2013 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Functional Programming with C++ Template Metaprograms

NASA Astrophysics Data System (ADS)

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.

Modeling complexes of modeled proteins.

PubMed

Anishchenko, Ivan; Kundrotas, Petras J; Vakser, Ilya A

2017-03-01

Structural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein-protein complexes. Thus, structural modeling of protein-protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such "double" modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template-based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å C α RMSD. Many template-based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5-6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template-based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470-478. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

PubMed

Akhter, Nasrin; Shehu, Amarda

2018-01-19

Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

Facile synthesis of functionalized ionic surfactant templated mesoporous silica for incorporation of poorly water-soluble drug.

PubMed

Li, Jing; Xu, Lu; Yang, Baixue; Wang, Hongyu; Bao, Zhihong; Pan, Weisan; Li, Sanming

2015-08-15

The present paper reported amino group functionalized anionic surfactant templated mesoporous silica (Amino-AMS) for loading and release of poorly water-soluble drug indomethacin (IMC) and carboxyl group functionalized cationic surfactant templated mesoporous silica (Carboxyl-CMS) for loading and release of poorly water-soluble drug famotidine (FMT). Herein, Amino-AMS and Carboxyl-CMS were facilely synthesized using co-condensation method through two types of silane coupling agent. Amino-AMS was spherical nanoparticles, and Carboxyl-CMS was well-formed spherical nanosphere with a thin layer presented at the edge. Drug loading capacity was obviously enhanced when using Amino-AMS and Carboxyl-CMS as drug carriers due to the stronger hydrogen bonding force formed between surface modified carrier and drug. Amino-AMS and Carboxyl-CMS had the ability to transform crystalline state of loaded drug from crystalline phase to amorphous phase. Therefore, IMC loaded Amino-AMS presented obviously faster release than IMC because amorphous phase of IMC favored its dissolution. The application of asymmetric membrane capsule delayed FMT release significantly, and Carboxyl-CMS favored sustained release of FMT due to its long mesoporous channels and strong interaction formed between its carboxyl group and amino group of FMT. Copyright © 2015 Elsevier B.V. All rights reserved.

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

PubMed Central

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2015-01-01

Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

Patterned assembly of colloidal particles by confined dewetting lithography.

PubMed

Celio, Hugo; Barton, Emily; Stevenson, Keith J

2006-12-19

We report the assembly of colloidal particles into confined arrangements and patterns on various cleaned and chemically modified solid substrates using a method which we term "confined dewetting lithography" or CDL for short. The experimental setup for CDL is a simple deposition cell where an aqueous suspension of colloidal particles (e.g., polystyrene spheres) is placed between a floating deposition template (i.e., metal microgrid) and the solid substrate. The voids of the deposition template serve as an array of micrometer-sized reservoirs where several hydrodynamic processes are confined. These processes include water evaporation, meniscus formation, convective flow, rupturing, dewetting, and capillary-bridge formation. We discuss the optimal conditions where the CDL has a high efficiency to deposit intricate patterns of colloidal particles using polystyrene spheres (PS; 4.5, 2.0, 1.7, 0.11, 0.064 microm diameter) and square and hexagonal deposition templates as model systems. We find that the optimization conditions of the CDL method, when using submicrometer, sulfate-functionalized PS particles, are primarily dependent on minimizing attractive particle-substrate interactions. The CDL methodology described herein presents a relatively simple and rapid method to assemble virtually any geometric pattern, including more complex patterns assembled using PS particles with different diameters, from aqueous suspensions by choosing suitable conditions and materials.

The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA.

PubMed

Schüller, Andreas; Suhartono, Marcel; Fechner, Uli; Tanrikulu, Yusuf; Breitung, Sven; Scheffer, Ute; Göbel, Michael W; Schneider, Gisbert

2008-02-01

Principles of fragment-based molecular design are presented and discussed in the context of de novo drug design. The underlying idea is to dissect known drug molecules in fragments by straightforward pseudo-retro-synthesis. The resulting building blocks are then used for automated assembly of new molecules. A particular question has been whether this approach is actually able to perform scaffold-hopping. A prospective case study illustrates the usefulness of fragment-based de novo design for finding new scaffolds. We were able to identify a novel ligand disrupting the interaction between the Tat peptide and TAR RNA, which is part of the human immunodeficiency virus (HIV-1) mRNA. Using a single template structure (acetylpromazine) as reference molecule and a topological pharmacophore descriptor (CATS), new chemotypes were automatically generated by our de novo design software Flux. Flux features an evolutionary algorithm for fragment-based compound assembly and optimization. Pharmacophore superimposition and docking into the target RNA suggest perfect matching between the template molecule and the designed compound. Chemical synthesis was straightforward, and bioactivity of the designed molecule was confirmed in a FRET assay. This study demonstrates the practicability of de novo design to generating RNA ligands containing novel molecular scaffolds.

Role of the C-terminal residue of the DNA polymerase of bacteriophage T7.

PubMed

Kumar, J K; Tabor, S; Richardson, C C

2001-09-14

The crystal structure of the DNA polymerase encoded by gene 5 of bacteriophage T7, in a complex with its processivity factor, Escherichia coli thioredoxin, a primer-template, and an incoming deoxynucleoside triphosphate reveals a putative hydrogen bond between the C-terminal residue, histidine 704 of gene 5 protein, and an oxygen atom on the penultimate phosphate diester of the primer strand. Elimination of this electrostatic interaction by replacing His(704) with alanine renders the phage nonviable, and no DNA synthesis is observed in vivo. Polymerase activity of the genetically altered enzyme on primed M13 DNA is only 12% of the wild-type enzyme, and its processivity is drastically reduced. Kinetic parameters for binding a primer-template (K(D)(app)), nucleotide binding (K(m)), and k(off) for dissociation of the altered polymerase from a primer-template are not significantly different from that of wild-type T7 DNA polymerase. However, the decrease in polymerase activity is concomitant with increased hydrolytic activity, judging from the turnover of nucleoside triphosphate into the corresponding nucleoside monophosphate (percentage of turnover, 65%) during DNA synthesis. Biochemical data along with structural observations imply that the terminal amino acid residue of T7 DNA polymerase plays a critical role in partitioning DNA between the polymerase and exonuclease sites.

RNA synthetic mechanisms employed by diverse families of RNA viruses.

PubMed

McDonald, Sarah M

2013-01-01

RNA viruses are ubiquitous in nature, infecting every known organism on the planet. These viruses can also be notorious human pathogens with significant medical and economic burdens. Central to the lifecycle of an RNA virus is the synthesis of new RNA molecules, a process that is mediated by specialized virally encoded enzymes called RNA-dependent RNA polymerases (RdRps). RdRps directly catalyze phosphodiester bond formation between nucleoside triphosphates in an RNA-templated manner. These enzymes are strikingly conserved in their structural and functional features, even among diverse RNA viruses belonging to different families. During host cell infection, the activities of viral RdRps are often regulated by viral cofactor proteins. Cofactors can modulate the type and timing of RNA synthesis by directly engaging the RdRp and/or by indirectly affecting its capacity to recognize template RNA. High-resolution structures of RdRps as apoenzymes, bound to RNA templates, in the midst of catalysis, and/or interacting with regulatory cofactor proteins, have dramatically increased our understanding of viral RNA synthetic mechanisms. Combined with elegant biochemical studies, such structures are providing a scientific platform for the rational design of antiviral agents aimed at preventing and treating RNA virus-induced diseases. Copyright © 2013 John Wiley & Sons, Ltd.

Improved prediction of antibody VL–VH orientation

PubMed Central

Marze, Nicholas A.; Lyskov, Sergey; Gray, Jeffrey J.

2016-01-01

Antibodies are important immune molecules with high commercial value and therapeutic interest because of their ability to bind diverse antigens. Computational prediction of antibody structure can quickly reveal valuable information about the nature of these antigen-binding interactions, but only if the models are of sufficient quality. To achieve high model quality during complementarity-determining region (CDR) structural prediction, one must account for the VL–VH orientation. We developed a novel four-metric VL–VH orientation coordinate frame. Additionally, we extended the CDR grafting protocol in RosettaAntibody with a new method that diversifies VL–VH orientation by using 10 VL–VH orientation templates rather than a single one. We tested the multiple-template grafting protocol on two datasets of known antibody crystal structures. During the template-grafting phase, the new protocol improved the fraction of accurate VL–VH orientation predictions from only 26% (12/46) to 72% (33/46) of targets. After the full RosettaAntibody protocol, including CDR H3 remodeling and VL–VH re-orientation, the new protocol produced more candidate structures with accurate VL–VH orientation than the standard protocol in 43/46 targets (93%). The improved ability to predict VL–VH orientation will bolster predictions of other parts of the paratope, including the conformation of CDR H3, a grand challenge of antibody homology modeling. PMID:27276984

Structure investigation of fluorinated aluminophosphate ULM-3 Al templated by 3-methylaminopropylamine

NASA Astrophysics Data System (ADS)

Zabukovec Logar, Natasa; Mali, Gregor; Rajic, Nevenka; Jevtic, Sanja; Rangus, Mojca; Golobic, Amalija; Kaucic, Venceslav

2010-05-01

A single-crystal X-ray diffraction analysis of an open-framework aluminophosphate ULM-3 Al prepared by 3-methylaminopropylamine (MAPA) as structure-directing agent revealed an orthorhombic Pcab symmetry ( a=9.9949(4) Å, b=15.8229(7) Å, c=18.1963(5) Å, R=0.0648, Z=8, unit cell formula [Al 24P 24O 96F 16·C 32H 112N 16]), which differs from the Pbc2 1 symmetry of the structural analogue prepared in the presence of 1,4-diaminobutane. The 27Al, 31P, 19F, 13C and 1H NMR investigations, which were performed to study in detail MAPA arrangement inside the framework as well as the interactions of MAPA with the aluminophosphate host, confirmed the crystal symmetry and the proposed hydrogen bonding scheme between the template and the framework.

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozden, Sehmus; Macwan, Isaac G.; Owuor, Peter S.

It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamicsmore » simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. Furthermore, the 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications.« less

Conducting real-time multiplayer experiments on the web.

PubMed

Hawkins, Robert X D

2015-12-01

Group behavior experiments require potentially large numbers of participants to interact in real time with perfect information about one another. In this paper, we address the methodological challenge of developing and conducting such experiments on the web, thereby broadening access to online labor markets as well as allowing for participation through mobile devices. In particular, we combine a set of recent web development technologies, including Node.js with the Socket.io module, HTML5 canvas, and jQuery, to provide a secure platform for pedagogical demonstrations and scalable, unsupervised experiment administration. Template code is provided for an example real-time behavioral game theory experiment which automatically pairs participants into dyads and places them into a virtual world. In total, this treatment is intended to allow those with a background in non-web-based programming to modify the template, which handles the technical server-client networking details, for their own experiments.

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

PubMed

Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

2017-05-05

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

Tellurium nano-structure based NO gas sensor.

PubMed

Kumar, Vivek; Sen, Shashwati; Sharma, M; Muthe, K P; Jagannath; Gaur, N K; Gupta, S K

2009-09-01

Tellurium nanotubes were grown on bare and silver/gold nanoparticle (nucleation centers) deposited silicon substrates by vacuum deposition technique at a substrate temperature of 100 degrees C under high vacuum conditions. Silver and gold nanoparticles prepared on (111) oriented silicon substrates were found to act as nucleation centers for growth of Tellurium nanostructures. Density of nanotubes was found to increase while their diameter reduced when grown using metallic nanoparticle template. These Te nanostructures were investigated for their gas sensitivity. Tellurium nanotubes on Ag templates showed better response to NO in comparison to H2S and NH3 gases. Selectivity in response to NO was improved in comparison to Te thin film sensors reported earlier. The gas sensing mechanism was investigated using Raman and X-ray photoelectron spectroscopy techniques. The interaction of NO is seen to yield increased adsorption of oxygen that in turn increases hole density and conductivity in the material.

Classifying the auditory P300 using mobile EEG recordings without calibration phase.

PubMed

Zink, R; Hunyádi, B; Van Huffel, S; De Vos, M

2015-08-01

One of the major drawbacks in mobile EEG Brain Computer Interfaces (BCI) is the need for subject specific training data to train a classifier. By removing the need for supervised classification and calibration phase, new users could start immediate interaction with a BCI. We propose a solution to exploit the structural difference by means of canonical polyadic decomposition (CPD) for three-class auditory oddball data without the need for subject-specific information. We achieve this by adding average event-related-potential (ERP) templates to the CPD model. This constitutes a novel similarity measure between single-trial pairs and known-templates, which results in a fast and interpretable classifier. These results have similar accuracy to those of the supervised and cross-validated stepwise LDA approach but without the need for having subject-dependent data. Therefore the described CPD method has a significant practical advantage over the traditional and widely used approach.

Engineered Metal-Phenolic Capsules Show Tunable Targeted Delivery to Cancer Cells.

PubMed

Ju, Yi; Cui, Jiwei; Sun, Huanli; Müllner, Markus; Dai, Yunlu; Guo, Junling; Bertleff-Zieschang, Nadja; Suma, Tomoya; Richardson, Joseph J; Caruso, Frank

2016-06-13

We engineered metal-phenolic capsules with both high targeting and low nonspecific cell binding properties. The capsules were prepared by coating phenolic-functionalized hyaluronic acid (HA) and poly(ethylene glycol) (PEG) on calcium carbonate templates, followed by cross-linking the phenolic groups with metal ions and removing the templates. The incorporation of HA significantly enhanced binding and association with a CD44 overexpressing (CD44+) cancer cell line, while the incorporation of PEG reduced nonspecific interactions with a CD44 minimal-expressing (CD44-) cell line. Moreover, high specific targeting to CD44+ cells can be balanced with low nonspecific binding to CD44- cells simply by using an optimized feed-ratio of HA and PEG to vary the content of HA and PEG incorporated into the capsules. Loading an anticancer drug (i.e., doxorubicin) into the obtained capsules resulted in significantly higher cytotoxicity to CD44+ cells but lower cytotoxicity to CD44- cells.

A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

NASA Technical Reports Server (NTRS)

Setlik, R. F.; Meyer, D. J.; Shibata, M.; Roskwitalski, R.; Ornstein, R. L.; Rein, R.

1994-01-01

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.

PubMed

Xing, Li; McDonald, Joseph J; Kolodziej, Steve A; Kurumbail, Ravi G; Williams, Jennifer M; Warren, Chad J; O'Neal, Janet M; Skepner, Jill E; Roberds, Steven L

2011-03-10

Structure-based virtual screening was applied to design combinatorial libraries to discover novel and potent soluble epoxide hydrolase (sEH) inhibitors. X-ray crystal structures revealed unique interactions for a benzoxazole template in addition to the conserved hydrogen bonds with the catalytic machinery of sEH. By exploitation of the favorable binding elements, two iterations of library design based on amide coupling were employed, guided principally by the docking results of the enumerated virtual products. Biological screening of the libraries demonstrated as high as 90% hit rate, of which over two dozen compounds were single digit nanomolar sEH inhibitors by IC(50) determination. In total the library design and synthesis produced more than 300 submicromolar sEH inhibitors. In cellular systems consistent activities were demonstrated with biochemical measurements. The SAR understanding of the benzoxazole template provides valuable insights into discovery of novel sEH inhibitors as therapeutic agents.

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

DOE PAGES

Ozden, Sehmus; Macwan, Isaac G.; Owuor, Peter S.; ...

2017-08-29

It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamicsmore » simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. Furthermore, the 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications.« less

DNA-Templated Molecular Silver Fluorophores

PubMed Central

Petty, Jeffrey T.; Story, Sandra P.; Hsiang, Jung-Cheng; Dickson, Robert M.

2013-01-01

Conductive and plasmon-supporting noble metals exhibit an especially wide range of size-dependent properties, with discrete electronic levels, strong optical absorption, and efficient radiative relaxation dominating optical behavior at the ~10-atom cluster scale. In this Perspective, we describe the formation and stabilization of silver clusters using DNA templates and highlight the distinct spectroscopic and photophysical properties of the resulting hybrid fluorophores. Strong visible to near-IR emission from DNA-encapsulated silver clusters ranging in size from 5–11 atoms has been produced and characterized. Importantly, this strong Ag cluster fluorescence can be directly modulated and selectively recovered by optically controlling the dark state residence, even when faced with an overwhelming background. The strength and sequence sensitivity of the oligonucleotide-Ag interaction suggests strategies for fine tuning and stabilizing cluster-based emitters in a host of sensing and biolabeling applications that would benefit from brighter, more photostable, and quantifiable emitters in high background environments. PMID:23745165

RECURSIVE PROTEIN MODELING: A DIVIDE AND CONQUER STRATEGY FOR PROTEIN STRUCTURE PREDICTION AND ITS CASE STUDY IN CASP9

PubMed Central

CHENG, JIANLIN; EICKHOLT, JESSE; WANG, ZHENG; DENG, XIN

2013-01-01

After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of structural modeling, two types of modeling techniques — template-based modeling and template-free modeling — have been developed. Template-based modeling can often generate a moderate- to high-resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling, such as fragment-based assembly, may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e. certain) and template-free (i.e. uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can signicantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction. PMID:22809379

Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization

NASA Astrophysics Data System (ADS)

Elkin, Carl D.; Zuccola, Harmon J.; Hogle, James M.; Joseph-McCarthy, Diane

2000-11-01

Hepatitis delta virus (HDV) encodes a single polypeptide called hepatitis delta antigen (DAg). Dimerization of DAg is required for viral replication. The structure of the dimerization region, residues 12 to 60, consists of an anti-parallel coiled coil [Zuccola et al., Structure, 6 (1998) 821]. Multiple Copy Simultaneous Searches (MCSS) of the hydrophobic core region formed by the bend in the helix of one monomer of this structure were carried out for many diverse functional groups. Six critical interaction sites were identified. The Protein Data Bank was searched for backbone templates to use in the subsequent design process by matching to these sites. A 14 residue helix expected to bind to the d-isomer of the target structure was selected as the template. Over 200 000 mutant sequences of this peptide were generated based on the MCSS results. A secondary structure prediction algorithm was used to screen all sequences, and in general only those that were predicted to be highly helical were retained. Approximately 100 of these 14-mers were model built as d-peptides and docked with the l-isomer of the target monomer. Based on calculated interaction energies, predicted helicity, and intrahelical salt bridge patterns, a small number of peptides were selected as the most promising candidates. The ligand design approach presented here is the computational analogue of mirror image phage display. The results have been used to characterize the interactions responsible for formation of this model anti-parallel coiled coil and to suggest potential ligands to disrupt it.

Prediction of IOI-HA scores using speech reception thresholds and speech discrimination scores in quiet.

PubMed

Brännström, K Jonas; Lantz, Johannes; Nielsen, Lars Holme; Olsen, Steen Østergaard

2014-02-01

Outcome measures can be used to improve the quality of the rehabilitation by identifying and understanding which variables influence the outcome. This information can be used to improve outcomes for clients. In clinical practice, pure-tone audiometry, speech reception thresholds (SRTs), and speech discrimination scores (SDSs) in quiet or in noise are common assessments made prior to hearing aid (HA) fittings. It is not known whether SRT and SDS in quiet relate to HA outcome measured with the International Outcome Inventory for Hearing Aids (IOI-HA). The aim of the present study was to investigate the relationship between pure-tone average (PTA), SRT, and SDS in quiet and IOI-HA in both first-time and experienced HA users. SRT and SDS were measured in a sample of HA users who also responded to the IOI-HA. Fifty-eight Danish-speaking adult HA users. The psychometric properties were evaluated and compared to previous studies using the IOI-HA. The associations and differences between the outcome scores and a number of descriptive variables (age, gender, fitted monaurally/binaurally with HA, first-time/experienced HA users, years of HA use, time since last HA fitting, best ear PTA, best ear SRT, or best ear SDS) were examined. A multiple forward stepwise regression analysis was conducted using scores on the separate IOI-HA items, the global score, and scores on the introspection and interaction subscales as dependent variables to examine whether the descriptive variables could predict these outcome measures. Scores on single IOI-HA items, the global score, and scores on the introspection (items 1, 2, 4, and 7) and interaction (items 3, 5, and 6) subscales closely resemble those previously reported. Multiple regression analysis showed that the best ear SDS predicts about 18-19% of the outcome on items 3 and 5 separately, and about 16% on the interaction subscale (sum of items 3, 5, and 6) CONCLUSIONS: The best ears SDS explains some of the variance displayed in the IOI-HA global score and the interaction subscale. The relation between SDS and IOI-HA suggests that a poor unaided SDS might in itself be a limiting factor for the HA rehabilitation efficacy and hence the IOI-HA outcome. The clinician could use this information to align the user's HA expectations to what is within possible reach. American Academy of Audiology.

Multivariate analysis of fears in dental phobic patients according to a reduced FSS-II scale.

PubMed

Hakeberg, M; Gustafsson, J E; Berggren, U; Carlsson, S G

1995-10-01

This study analyzed and assessed dimensions of a questionnaire developed to measure general fears and phobias. A previous factor analysis among 109 dental phobics had revealed a five-factor structure with 22 items and an explained total variance of 54%. The present study analyzed the same material using a multivariate statistical procedure (LISREL) to reveal structural latent variables. The LISREL analysis, based on the correlation matrix, yielded a chi-square of 216.6 with 195 degrees of freedom (P = 0.138) and showed a model with seven latent variables. One was a general fear factor correlated to all 22 items. The other six factors concerned "Illness & Death" (5 items), "Failures & Embarrassment" (5 items), "Social situations" (5 items), "Physical injuries" (4 items), "Animals & Natural phenomena" (4 items). One item (opposite sex) was included in both "Failures & Embarrassment" and "Social situations". The last factor, "Social interaction", combined all the items in "Failures & Embarrassment" and "Social situations" (9 items). In conclusion, this multivariate statistical analysis (LISREL) revealed and confirmed a factor structure similar to our previous study, but added two important dimensions not shown with a traditional factor analysis. This reduced FSS-II version measures general fears and phobias and may be used on a routine clinical basis as well as in dental phobia research.

Optimized Periocular Template Selection for Human Recognition

PubMed Central

Sa, Pankaj K.; Majhi, Banshidhar

2013-01-01

A novel approach for selecting a rectangular template around periocular region optimally potential for human recognition is proposed. A comparatively larger template of periocular image than the optimal one can be slightly more potent for recognition, but the larger template heavily slows down the biometric system by making feature extraction computationally intensive and increasing the database size. A smaller template, on the contrary, cannot yield desirable recognition though the smaller template performs faster due to low computation for feature extraction. These two contradictory objectives (namely, (a) to minimize the size of periocular template and (b) to maximize the recognition through the template) are aimed to be optimized through the proposed research. This paper proposes four different approaches for dynamic optimal template selection from periocular region. The proposed methods are tested on publicly available unconstrained UBIRISv2 and FERET databases and satisfactory results have been achieved. Thus obtained template can be used for recognition of individuals in an organization and can be generalized to recognize every citizen of a nation. PMID:23984370

Negative affect impairs associative memory but not item memory.

PubMed

Bisby, James A; Burgess, Neil

2013-12-17

The formation of associations between items and their context has been proposed to rely on mechanisms distinct from those supporting memory for a single item. Although emotional experiences can profoundly affect memory, our understanding of how it interacts with different aspects of memory remains unclear. We performed three experiments to examine the effects of emotion on memory for items and their associations. By presenting neutral and negative items with background contexts, Experiment 1 demonstrated that item memory was facilitated by emotional affect, whereas memory for an associated context was reduced. In Experiment 2, arousal was manipulated independently of the memoranda, by a threat of shock, whereby encoding trials occurred under conditions of threat or safety. Memory for context was equally impaired by the presence of negative affect, whether induced by threat of shock or a negative item, relative to retrieval of the context of a neutral item in safety. In Experiment 3, participants were presented with neutral and negative items as paired associates, including all combinations of neutral and negative items. The results showed both above effects: compared to a neutral item, memory for the associate of a negative item (a second item here, context in Experiments 1 and 2) is impaired, whereas retrieval of the item itself is enhanced. Our findings suggest that negative affect impairs associative memory while recognition of a negative item is enhanced. They support dual-processing models in which negative affect or stress impairs hippocampal-dependent associative memory while the storage of negative sensory/perceptual representations is spared or even strengthened.

Population differences in brain morphology: Need for population specific brain template.

PubMed

Rao, Naren P; Jeelani, Haris; Achalia, Rashmin; Achalia, Garima; Jacob, Arpitha; Bharath, Rose Dawn; Varambally, Shivarama; Venkatasubramanian, Ganesan; K Yalavarthy, Phaneendra

2017-07-30

Brain templates provide a standard anatomical platform for population based morphometric assessments. Typically, standard brain templates for such assessments are created using Caucasian brains, which may not be ideal to analyze brains from other ethnicities. To effectively demonstrate this, we compared brain morphometric differences between T1 weighted structural MRI images of 27 healthy Indian and Caucasian subjects of similar age and same sex ratio. Furthermore, a population specific brain template was created from MRI images of healthy Indian subjects and compared with standard Montreal Neurological Institute (MNI-152) template. We also examined the accuracy of registration of by acquiring a different T1 weighted MRI data set and registering them to newly created Indian template and MNI-152 template. The statistical analysis indicates significant difference in global brain measures and regional brain structures of Indian and Caucasian subjects. Specifically, the global brain measurements of the Indian brain template were smaller than that of the MNI template. Also, Indian brain images were better realigned to the newly created template than to the MNI-152 template. The notable variations in Indian and Caucasian brains convey the need to build a population specific Indian brain template and atlas. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Variance in predicted cup size by 2-dimensional vs 3-dimensional computerized tomography-based templating in primary total hip arthroplasty.

PubMed

Osmani, Feroz A; Thakkar, Savyasachi; Ramme, Austin; Elbuluk, Ameer; Wojack, Paul; Vigdorchik, Jonathan M

2017-12-01

Preoperative total hip arthroplasty templating can be performed with radiographs using acetate prints, digital viewing software, or with computed tomography (CT) images. Our hypothesis is that 3D templating is more precise and accurate with cup size prediction as compared to 2D templating with acetate prints and digital templating software. Data collected from 45 patients undergoing robotic-assisted total hip arthroplasty compared cup sizes templated on acetate prints and OrthoView software to MAKOplasty software that uses CT scan. Kappa analysis determined strength of agreement between each templating modality and the final size used. t tests compared mean cup-size variance from the final size for each templating technique. Interclass correlation coefficient (ICC) determined reliability of digital and acetate planning by comparing predictions of the operating surgeon and a blinded adult reconstructive fellow. The Kappa values for CT-guided, digital, and acetate templating with the final size was 0.974, 0.233, and 0.262, respectively. Both digital and acetate templating significantly overpredicted cup size, compared to CT-guided methods ( P < .001). There was no significant difference between digital and acetate templating ( P  = .117). Interclass correlation coefficient value for digital and acetate templating was 0.928 and 0.931, respectively. CT-guided planning more accurately predicts hip implant cup size when compared to the significant overpredictions of digital and acetate templating. CT-guided templating may also lead to better outcomes due to bone stock preservation from a smaller and more accurate cup size predicted than that of digital and acetate predictions.

Development of nanoimprint lithography templates for the contact hole layer application (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ichimura, Koji; Hikichi, Ryugo; Harada, Saburo; Kanno, Koichi; Kurihara, Masaaki; Hayashi, Naoya

2017-04-01

Nanoimprint lithography, NIL, is gathering much attention as one of the most potential candidates for the next generation lithography for semiconductor. This technology needs no pattern data modification for exposure, simpler exposure system, and single step patterning process without any coat/develop truck, and has potential of cost effective patterning rather than very complex optical lithography and/or EUV lithography. NIL working templates are made by the replication of the EB written high quality master templates. Fabrication of high resolution master templates is one of the most important issues. Since NIL is 1:1 pattern transfer process, master templates have 4 times higher resolution compared with photomasks. Another key is to maintain the quality of the master templates in replication process. NIL process is applied for the template replication and this imprint process determines most of the performance of the replicated templates. Expectations to the NIL are not only high resolution line and spaces but also the contact hole layer application. Conventional ArF-i lithography has a certain limit in size and pitch for contact hole fabrication. On the other hand, NIL has good pattern fidelity for contact hole fabrication at smaller sizes and pitches compared with conventional optical lithography. Regarding the tone of the templates for contact hole, there are the possibilities of both tone, the hole template and the pillar template, depending on the processes of the wafer side. We have succeeded to fabricate both types of templates at 2xnm in size. In this presentation, we will be discussing fabrication or our replica template for the contact hole layer application. Both tone of the template fabrication will be presented as well as the performance of the replica templates. We will also discuss the resolution improvement of the hole master templates by using various e-beam exposure technologies.

Exploring the Technical Adequacy of the Family Interaction Inventory.

ERIC Educational Resources Information Center

Robinson, Christopher S.; And Others

There are no available measures that assess family interaction from a comprehensive theoretical perspective. This study reports analyses of the measurement integrity of scores from a measure developed to offer a comprehensive assessment. The preliminary version of the Family Interaction Inventory (FII) is a 24-scale instrument with 5 items per…

The views of healthcare professionals, drug developers and regulators on information about older people needed for rational drug prescription.

PubMed

Beers, Erna; Egberts, Toine C G; Leufkens, Hubert G M; Jansen, Paul A F

2013-01-01

The ICH E7 guideline intends to improve the knowledge about medicines in geriatric patients. As a legislative document, it might not reflect the needs of healthcare professionals. This study investigated what information healthcare professionals, regulatory agencies and pharmaceutical industries consider necessary for rational drug prescribing to older individuals. A 29-item-questionnaire was composed, considering the representation in trials, pharmacokinetics, efficacy, safety, and convenience of use in older individuals, with space for additions. Forty-three European professionals with an interest in medication for older individuals were included. In order to investigate their relevance, five items were included in a second questionnaire, with 11 control items. Median scores, differences between clinical and non-clinical respondents and response consistency were analysed. Consistency was present in 10 control items. Therefore, all items of the first questionnaire and the five additional items were analysed. Thirty-seven (86%) respondents returned the first questionnaire; 31/37 (84%) the second. Information about age-related differences in adverse events, locomotor effects, drug-disease interactions, dosing instructions, and information about the proportion of included 65+ patients was considered necessary by most respondents. Clinicians considered information significantly more important than the non-clinical respondents about the inclusion of 75+, time-until-benefit in older people, anticholinergic effects, drug-disease interactions, and convenience of use. Main study limitations are the focus on information for daily practice, while the ICH E7 guideline is a legislative document focused on market approval of a new medicine. Also, a questionnaire with a Likert scale has its limitations; this was addressed by providing space for comments. This study reveals that items considered necessary are currently not included in the ICH E7 guideline. Also, clinicians' and non-clinicians' opinions differed significantly in 15% of the items. Therefore, all stakeholders should collaborate to improve the availability of information for the rational prescribing to older individuals.

The Views of Healthcare Professionals, Drug Developers and Regulators on Information about Older People Needed for Rational Drug Prescription

PubMed Central

Beers, Erna; Egberts, Toine C. G.; Leufkens, Hubert G. M.; Jansen, Paul A. F.

2013-01-01

Background The ICH E7 guideline intends to improve the knowledge about medicines in geriatric patients. As a legislative document, it might not reflect the needs of healthcare professionals. This study investigated what information healthcare professionals, regulatory agencies and pharmaceutical industries consider necessary for rational drug prescribing to older individuals. Methods and Findings A 29-item-questionnaire was composed, considering the representation in trials, pharmacokinetics, efficacy, safety, and convenience of use in older individuals, with space for additions. Forty-three European professionals with an interest in medication for older individuals were included. In order to investigate their relevance, five items were included in a second questionnaire, with 11 control items. Median scores, differences between clinical and non-clinical respondents and response consistency were analysed. Consistency was present in 10 control items. Therefore, all items of the first questionnaire and the five additional items were analysed. Thirty-seven (86%) respondents returned the first questionnaire; 31/37 (84%) the second. Information about age-related differences in adverse events, locomotor effects, drug-disease interactions, dosing instructions, and information about the proportion of included 65+ patients was considered necessary by most respondents. Clinicians considered information significantly more important than the non-clinical respondents about the inclusion of 75+, time-until-benefit in older people, anticholinergic effects, drug-disease interactions, and convenience of use. Main study limitations are the focus on information for daily practice, while the ICH E7 guideline is a legislative document focused on market approval of a new medicine. Also, a questionnaire with a Likert scale has its limitations; this was addressed by providing space for comments. Conclusions This study reveals that items considered necessary are currently not included in the ICH E7 guideline. Also, clinicians’ and non-clinicians’ opinions differed significantly in 15% of the items. Therefore, all stakeholders should collaborate to improve the availability of information for the rational prescribing to older individuals. PMID:23977208

US Federal LCA Commons Life Cycle Inventory Unit Process Template

EPA Science Inventory

The US Federal LCA Commons Life Cycle Inventory Unit Process Template is a multi-sheet Excel template for life cycle inventory data, metadata and other documentation. The template comes as a package that consistent of three parts: (1) the main template itself for life cycle inven...

Target templates: the precision of mental representations affects attentional guidance and decision-making in visual search.

PubMed

Hout, Michael C; Goldinger, Stephen D

2015-01-01

When people look for things in the environment, they use target templates-mental representations of the objects they are attempting to locate-to guide attention and to assess incoming visual input as potential targets. However, unlike laboratory participants, searchers in the real world rarely have perfect knowledge regarding the potential appearance of targets. In seven experiments, we examined how the precision of target templates affects the ability to conduct visual search. Specifically, we degraded template precision in two ways: 1) by contaminating searchers' templates with inaccurate features, and 2) by introducing extraneous features to the template that were unhelpful. We recorded eye movements to allow inferences regarding the relative extents to which attentional guidance and decision-making are hindered by template imprecision. Our findings support a dual-function theory of the target template and highlight the importance of examining template precision in visual search.

Biometric templates selection and update using quality measures

NASA Astrophysics Data System (ADS)

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.

Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor

PubMed Central

Bertaccini, Edward J.; Yoluk, Ozge; Lindahl, Erik R.; Trudell, James R.

2013-01-01

Background Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). While its molecular structure remains unknown, significant progress has been made towards understanding its interactions with anesthetics via molecular modeling. Methods The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50’s. Results Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between alpha and beta subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Conclusion Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed correlation of ligand docking scores with experimentally measured GABAaR potentiation. PMID:23770602

Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor.

PubMed

Bertaccini, Edward J; Yoluk, Ozge; Lindahl, Erik R; Trudell, James R

2013-11-01

Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). Although its molecular structure remains unknown, significant progress has been made toward understanding its interactions with anesthetics via molecular modeling. The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH-sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50s. Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between α and β subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed a correlation of ligand docking scores with experimentally measured GABAaR potentiation.

Directed-assembly of ordered nanoparticle arrays exploiting multiple adsorption mechanisms on a self-assembling biological template

NASA Astrophysics Data System (ADS)

Shindel, Matthew M.

Developing processes to fabricate inorganic architectures with designer functionalities at increasingly minute length-scales is of chief concern in the fields of nanotechnology and nanoscience. This enterprise requires assembly mechanisms with the capacity to tailor both the spatial arrangement and material composition of a system's constituent building blocks. To this end, significant advances can be made by turning to biology, as the natural world has evolved the ability to generate intricate nanostructures, which can potentially be employed as templates for inorganic nanosystems. We explore this biotemplating methodology using two-dimensional streptavidin crystals, investigating the ability of the protein lattice to direct the assembly of ordered metallic nanoparticle arrays. We demonstrate that the adsorption of nanoparticles on the protein monolayer can be induced through both electrostatic and molecular recognition (ligand-receptor) interactions. Furthermore, the dynamics of adsorption can be modulated through both environmental factors (e.g. pH), and by tailoring particle surface chemistry. When the characteristic nanoparticle size is on the order of the biotemplate's unit-cell dimension, electrostatically-mediated adsorption occurs in a site-specific manner. The nanoparticles exhibit a pronounced preference for adhering to the areas between protein molecules. The two-dimensional structure of the resultant nanoparticle ensemble consequently conforms to that of the underlying protein crystal. Through theoretical calculations, simulation and experiment, we show that interparticle spacing in the templated array is influenced by the screened-coulombic repulsion between particles, and can thus be tuned by controlling ionic strength during deposition. Templating ordered nanoparticle arrays via ligand-receptor mediated adsorption, and the constrained growth of metallic nanoparticles directly on the protein lattice from ionic precursors are also examined. Overall, this work demonstrates that the streptavidin crystal system possesses unique utility for nanoscale, directed-assembly applications.

A Microwell-Printing Fabrication Strategy for the On-Chip Templated Biosynthesis of Protein Microarrays for Surface Plasmon Resonance Imaging

PubMed Central

Manuel, Gerald; Lupták, Andrej; Corn, Robert M.

2017-01-01

A two-step templated, ribosomal biosynthesis/printing method for the fabrication of protein microarrays for surface plasmon resonance imaging (SPRI) measurements is demonstrated. In the first step, a sixteen component microarray of proteins is created in microwells by cell free on chip protein synthesis; each microwell contains both an in vitro transcription and translation (IVTT) solution and 350 femtomoles of a specific DNA template sequence that together are used to create approximately 40 picomoles of a specific hexahistidine-tagged protein. In the second step, the protein microwell array is used to contact print one or more protein microarrays onto nitrilotriacetic acid (NTA)-functionalized gold thin film SPRI chips for real-time SPRI surface bioaffinity adsorption measurements. Even though each microwell array element only contains approximately 40 picomoles of protein, the concentration is sufficiently high for the efficient bioaffinity adsorption and capture of the approximately 100 femtomoles of hexahistidine-tagged protein required to create each SPRI microarray element. As a first example, the protein biosynthesis process is verified with fluorescence imaging measurements of a microwell array containing His-tagged green fluorescent protein (GFP), yellow fluorescent protein (YFP) and mCherry (RFP), and then the fidelity of SPRI chips printed from this protein microwell array is ascertained by measuring the real-time adsorption of various antibodies specific to these three structurally related proteins. This greatly simplified two-step synthesis/printing fabrication methodology eliminates most of the handling, purification and processing steps normally required in the synthesis of multiple protein probes, and enables the rapid fabrication of SPRI protein microarrays from DNA templates for the study of protein-protein bioaffinity interactions. PMID:28706572

Fast and accurate semi-automated segmentation method of spinal cord MR images at 3T applied to the construction of a cervical spinal cord template.

PubMed

El Mendili, Mohamed-Mounir; Chen, Raphaël; Tiret, Brice; Villard, Noémie; Trunet, Stéphanie; Pélégrini-Issac, Mélanie; Lehéricy, Stéphane; Pradat, Pierre-François; Benali, Habib

2015-01-01

To design a fast and accurate semi-automated segmentation method for spinal cord 3T MR images and to construct a template of the cervical spinal cord. A semi-automated double threshold-based method (DTbM) was proposed enabling both cross-sectional and volumetric measures from 3D T2-weighted turbo spin echo MR scans of the spinal cord at 3T. Eighty-two healthy subjects, 10 patients with amyotrophic lateral sclerosis, 10 with spinal muscular atrophy and 10 with spinal cord injuries were studied. DTbM was compared with active surface method (ASM), threshold-based method (TbM) and manual outlining (ground truth). Accuracy of segmentations was scored visually by a radiologist in cervical and thoracic cord regions. Accuracy was also quantified at the cervical and thoracic levels as well as at C2 vertebral level. To construct a cervical template from healthy subjects' images (n=59), a standardization pipeline was designed leading to well-centered straight spinal cord images and accurate probability tissue map. Visual scoring showed better performance for DTbM than for ASM. Mean Dice similarity coefficient (DSC) was 95.71% for DTbM and 90.78% for ASM at the cervical level and 94.27% for DTbM and 89.93% for ASM at the thoracic level. Finally, at C2 vertebral level, mean DSC was 97.98% for DTbM compared with 98.02% for TbM and 96.76% for ASM. DTbM showed similar accuracy compared with TbM, but with the advantage of limited manual interaction. A semi-automated segmentation method with limited manual intervention was introduced and validated on 3T images, enabling the construction of a cervical spinal cord template.

Confidence Bounds and Power for the Reliability of Observational Measures on the Quality of a Social Setting

ERIC Educational Resources Information Center

Shin, Yongyun; Raudenbush, Stephen W.

2012-01-01

Social scientists are frequently interested in assessing the qualities of social settings such as classrooms, schools, neighborhoods, or day care centers. The most common procedure requires observers to rate social interactions within these settings on multiple items and then to combine the item responses to obtain a summary measure of setting…

Comparing Cognitive Models of Domain Mastery and Task Performance in Algebra: Validity Evidence for a State Assessment

ERIC Educational Resources Information Center

Warner, Zachary B.

2013-01-01

This study compared an expert-based cognitive model of domain mastery with student-based cognitive models of task performance for Integrated Algebra. Interpretations of student test results are limited by experts' hypotheses of how students interact with the items. In reality, the cognitive processes that students use to solve each item may be…

Comparison of Fixed-Item and Response-Sensitive Versions of an Online Tutorial

ERIC Educational Resources Information Center

Grant, Lyle K.; Courtoreille, Marni

2007-01-01

This study is a comparison of 2 versions of an Internet-based tutorial that teaches the behavior-analysis concept of positive reinforcement. A fixed-item group of students studied a version of the tutorial that included 14 interactive examples and nonexamples of the concept. A response-sensitive group of students studied a different version of the…

Impact of Missing Data on the Detection of Differential Item Functioning: The Case of Mantel-Haenszel and Logistic Regression Analysis

ERIC Educational Resources Information Center

Robitzsch, Alexander; Rupp, Andre A.

2009-01-01

This article describes the results of a simulation study to investigate the impact of missing data on the detection of differential item functioning (DIF). Specifically, it investigates how four methods for dealing with missing data (listwise deletion, zero imputation, two-way imputation, response function imputation) interact with two methods of…

Interactions between spontaneous instantiations to the basic level and post-event suggestions.

PubMed

Pansky, Ainat; Tenenboim, Einat

2011-11-01

Extensive research shows that post-event suggestions can distort the memory for a target event. In this study we examined the effect of such suggestions as they interact with the products of a spontaneous memory process: instantiation of abstract information to an intermediate level of abstractness, the basic level (Pansky & Koriat, 2004 ). Participants read a narrative containing items presented at the superordinate level (e.g., FRUIT), were exposed to suggestions that referred to these items at the basic level (e.g., APPLE), and were finally asked to recall the original items. We found that the tendency to instantiate spontaneously in the control (non-misleading) condition, particularly over time, increased following exposure to suggestions that were likely to coincide with those instantiations. Exposure to such suggestions, either immediately or following a 24-hour delay, reduced subsequent correct recall of the original items only if the suggested information coincided with the information one tends to instantiate spontaneously in a given context. Suggestibility, in this case, was particularly pronounced and phenomenologically compelling in terms of remember/know judgements. The findings are taken to imply that effects of post-event suggestions can be understood in terms of the constructive processes that set the stage for their occurrence.

Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication

PubMed Central

Martinez, Matthew P.; Wacker, Amanda L.; Bruck, Irina; Kaplan, Daniel L.

2017-01-01

The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described. PMID:28383499

Development and evaluation of an interactive electronic laboratory manual for cooperative learning of medical histology.

PubMed

Khalil, Mohammed K; Kirkley, Debbie L; Kibble, Jonathan D

2013-01-01

This article describes the development of an interactive computer-based laboratory manual, created to facilitate the teaching and learning of medical histology. The overarching goal of developing the manual is to facilitate self-directed group interactivities that actively engage students during laboratory sessions. The design of the manual includes guided instruction for students to navigate virtual slides, exercises for students to monitor learning, and cases to provide clinical relevance. At the end of the laboratory activities, student groups can generate a laboratory report that may be used to provide formative feedback. The instructional value of the manual was evaluated by a questionnaire containing both closed-ended and open-ended items. Closed-ended items using a five-point Likert-scale assessed the format and navigation, instructional contents, group process, and learning process. Open-ended items assessed student's perception on the effectiveness of the manual in facilitating their learning. After implementation for two consecutive years, student evaluation of the manual was highly positive and indicated that it facilitated their learning by reinforcing and clarifying classroom sessions, improved their understanding, facilitated active and cooperative learning, and supported self-monitoring of their learning. Copyright © 2013 American Association of Anatomists.

Initial evaluation of an interactive test of sentence gist recognition.

PubMed

Tye-Murray, N; Witt, S; Castelloe, J

1996-12-01

The laser videodisc-based Sentence Gist Recognition (SGR) test consists of sets of topically related sentences that are cued by short film clips. Clients respond to test items by selecting picture illustrations and may interact with the talker by using repair strategies when they do not recognize a test item. The two experiments, involving 40 and 35 adult subjects, respectively, indicated that the SGR may better predict subjective measures of speechreading and listening performance than more traditional audiologic sentence and nonsense syllable tests. Data from cochlear implant users indicated that the SGR accounted for a greater percentage of the variance for selected items of the Communication Profile for the Hearing-Impaired and the Speechreading Questionnaire for Cochlear-Implant Users than two other audiologic tests. As in previous work, subjects were most apt to ask the talker to repeat an utterance that they did not recognize than to ask the talker to restructure it. It is suggested that the SGR may reflect the interactive nature of conversation and provide a simulated real-world listening and/or speechreading task. The principles underlaying this test are consistent with the development of other computer technologies and concepts, such as compact discinteractive and virtual reality.

Electronic Quality of Life Assessment Using Computer-Adaptive Testing

PubMed Central

2016-01-01

Background Quality of life (QoL) questionnaires are desirable for clinical practice but can be time-consuming to administer and interpret, making their widespread adoption difficult. Objective Our aim was to assess the performance of the World Health Organization Quality of Life (WHOQOL)-100 questionnaire as four item banks to facilitate adaptive testing using simulated computer adaptive tests (CATs) for physical, psychological, social, and environmental QoL. Methods We used data from the UK WHOQOL-100 questionnaire (N=320) to calibrate item banks using item response theory, which included psychometric assessments of differential item functioning, local dependency, unidimensionality, and reliability. We simulated CATs to assess the number of items administered before prespecified levels of reliability was met. Results The item banks (40 items) all displayed good model fit (P>.01) and were unidimensional (fewer than 5% of t tests significant), reliable (Person Separation Index>.70), and free from differential item functioning (no significant analysis of variance interaction) or local dependency (residual correlations < +.20). When matched for reliability, the item banks were between 45% and 75% shorter than paper-based WHOQOL measures. Across the four domains, a high standard of reliability (alpha>.90) could be gained with a median of 9 items. Conclusions Using CAT, simulated assessments were as reliable as paper-based forms of the WHOQOL with a fraction of the number of items. These properties suggest that these item banks are suitable for computerized adaptive assessment. These item banks have the potential for international development using existing alternative language versions of the WHOQOL items. PMID:27694100

Effect of Body Mass Index on Digital Templating for Total Hip Arthroplasty.

PubMed

Sershon, Robert A; Diaz, Alejandro; Bohl, Daniel D; Levine, Brett R

2017-03-01

Digital templating is becoming more prevalent in orthopedics. Recent investigations report high accuracy using digital templating in total hip arthroplasty (THA); however, the effect of body mass index (BMI) on templating accuracy is not well described. Digital radiographs of 603 consecutive patients (645 hips) undergoing primary THA by a single surgeon were digitally templated using OrthoView (Jacksonville, FL). A 25-mm metallic sphere was used as a calibration marker. Preoperative digital hip templates were compared with the final implant size. Hips were stratified into groups based on BMI: BMI <30 (315), BMI 30-35 (132), BMI 35-40 (97), and BMI >40 (101). Accuracy between templating and final size did not vary by BMI for acetabular or femoral components. Digital templating was within 2 sizes of the final acetabular and femoral implants in 99.1% and 97.1% of cases, respectively. Digital templating is an effective means of predicting the final size of THA components. BMI does not appear to play a major role in altering THA digital templating accuracy. Copyright © 2016 Elsevier Inc. All rights reserved.

Real-Time Tracking by Double Templates Matching Based on Timed Motion History Image with HSV Feature

PubMed Central

Li, Zhiyong; Li, Pengfei; Yu, Xiaoping; Hashem, Mervat

2014-01-01

It is a challenge to represent the target appearance model for moving object tracking under complex environment. This study presents a novel method with appearance model described by double templates based on timed motion history image with HSV color histogram feature (tMHI-HSV). The main components include offline template and online template initialization, tMHI-HSV-based candidate patches feature histograms calculation, double templates matching (DTM) for object location, and templates updating. Firstly, we initialize the target object region and calculate its HSV color histogram feature as offline template and online template. Secondly, the tMHI-HSV is used to segment the motion region and calculate these candidate object patches' color histograms to represent their appearance models. Finally, we utilize the DTM method to trace the target and update the offline template and online template real-timely. The experimental results show that the proposed method can efficiently handle the scale variation and pose change of the rigid and nonrigid objects, even in illumination change and occlusion visual environment. PMID:24592185

A multi-factor Rasch scale for artistic judgment.

PubMed

Bezruczko, Nikolaus

2002-01-01

Measurement properties are reported for a combined scale of abstract and figurative artistic judgment aptitude items. Abstract items are synthetic, rule-based images from Visual Designs Test which implements a statistical algorithm to control design complexity and redundancy, and figurative items are canvas paintings in five styles, Fauvism, Post-Impressionism, Surrealism, Renaissance, and Baroque especially created for this research. The paintings integrate syntactic structure from VDT Abstract designs with thematic content for each style at four levels of complexity while controlling redundancy. Trained test administrators collected preference for synthetic abstract designs and authentic figurative art from 462 examinees in Johnson O'Connor Research Foundation testing offices in Boston, New York, Chicago, and Dallas. The Rasch model replicated measurement properties for VDT Abstract items and identified an item hierarchy that was statistically invariant between genders and generally stable across age for new, authentic figurative items. Further examination of the figurative item hierarchy revealed that complexity interacts with style and meaning. Sound measurement properties for a combined VDT Abstract and Figurative scale shows promise for a comprehensive artistic judgment construct.

Staphylococcus aureus recovery from cotton towels.

PubMed

Oller, Anna R; Mitchell, Ashley

2009-04-30

Staphylococcus aureus is an emerging pathogen afflicting healthy individuals without known risk factors, and methicillin-resistant Staphylococcus aureus has been shown to colonize multiple family members sharing households. Because household items such as towels are often shared by family members, this study investigated whether cotton towel absorbency or washing conditions affect Staphylococcus aureus cell viability or cell retention, and whether the levels may be sufficient for person-to-person transmission. Staphylococcus aureus ATCC 25923 was added to a 48 mm(2) template area on three cotton towel types (terry, pima, and Egyptian), and subjected to hand washing, without manual wringing, in three conditions (water only, bleach addition, or liquid detergent addition). Serial dilutions plated onto mannitol salt plates quantified bacteria for inoculations, pre- and post-wash water samples, towel surfaces, and hand transfer. Hand transfer of bacteria was determined on towels immediately, one, 24, and 48 hours post inoculation. Bleach (p < or = .05) was the most effective at reducing bacterial viability on all towel types compared to detergent and water. Although not statistically significant, more Staphylococcus colonies were recovered from higher absorbency towels and from inside directly inoculated template areas. A paired t-test showed a difference between immediate and one-hour CFUs versus 24- and 48-hour recoveries (0.0002) for hand transfers. Cell viability decreased for over 48 hours on towels, but sufficient quantities may remain for colonization. More absorbent towels may harbor more Staphylococci than less absorbent ones, and may serve as a transmission mechanism for the bacterium.

Discovery and X-ray crystallographic analysis of a spiropiperidine iminohydantoin inhibitor of beta-secretase.

PubMed

Barrow, James C; Stauffer, Shaun R; Rittle, Kenneth E; Ngo, Phung L; Yang, ZhiQiang; Selnick, Harold G; Graham, Samuel L; Munshi, Sanjeev; McGaughey, Georgia B; Holloway, M Katharine; Simon, Adam J; Price, Eric A; Sankaranarayanan, Sethu; Colussi, Dennis; Tugusheva, Katherine; Lai, Ming-Tain; Espeseth, Amy S; Xu, Min; Huang, Qian; Wolfe, Abigail; Pietrak, Beth; Zuck, Paul; Levorse, Dorothy A; Hazuda, Daria; Vacca, Joseph P

2008-10-23

A high-throughput screen at 100 microM inhibitor concentration for the BACE-1 enzyme revealed a novel spiropiperidine iminohydantoin aspartyl protease inhibitor template. An X-ray cocrystal structure with BACE-1 revealed a novel mode of binding whereby the inhibitor interacts with the catalytic aspartates via bridging water molecules. Using the crystal structure as a guide, potent compounds with good brain penetration were designed.

The Self-Assembly of Particles with Multipolar Interactions

DTIC Science & Technology

2004-01-01

the LATEX template in which this thesis has been written. I also thank Kevin Van Workum and Jack Douglas for contributing simulation work and some...of the computational expense of simulating such complex self-assembly systems at the molecular level and a desire to understand the self-assembly at...Dissertation directed by: Professor Wolfgang Losert Department of Physics In this thesis , we describe results from investigations of the self-assembly of

Implantation of Fe3O4 Nanoparticles in Shells of Au@m-SiO2 Yolk@Shell Nanocatalysts with Both Improved Recyclability and Catalytic Activity.

PubMed

Li, Yanan; Jin, Chenjing; Yuan, Ganyin; Han, Jie; Wang, Minggui; Guo, Rong

2017-08-01

Multifunctional nanocatalysts of Au@Fe 3 O 4 /m-SiO 2 yolk@shell hybrids had been developed through a template-assisted synthesis, where Fe 3 O 4 nanoparticles (∼12 nm) and m-SiO 2 shells were sequentially assembled on surfaces of Au/SiO 2 core/shell templates, followed by selective etching of the inner SiO 2 cores, leading to the formation of Au@Fe 3 O 4 /m-SiO 2 yolk@shell hybrids. The Fe 3 O 4 nanoparticles were implanted in the inner surfaces of m-SiO 2 shells with partially exposed surfaces to the inner cavity. The novel design not only ensures a high surface area (540.0 m 2 /g) and saturation magnetization (48.6 emu/g) of the hybrids but also enables interaction between Au and Fe 3 O 4 nanoparticles. Catalytic tests toward the reduction of 4-nitrophenol in the presence of NaBH 4 indicated that Au@Fe 3 O 4 /m-SiO 2 yolk@shell nanocatalysts not only showed high stability and recyclability but also maintained improved catalytic activity as a result of the synergetic effect resulting from Au and Fe 3 O 4 interactions.

An Absolute Phase Space for the Physicality of Matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valentine, John S.

2010-12-22

We define an abstract and absolute phase space (''APS'') for sub-quantum intrinsic wave states, in three axes, each mapping directly to a duality having fundamental ontological basis. Many aspects of quantum physics emerge from the interaction algebra and a model deduced from principles of 'unique solvability' and 'identifiable entity', and we reconstruct previously abstract fundamental principles and phenomena from these new foundations. The physical model defines bosons as virtual continuous waves pairs in the APS, and fermions as real self-quantizing snapshots of those waves when simple conditions are met. The abstraction and physical model define a template for the constitutionmore » of all fermions, a template for all the standard fundamental bosons and their local interactions, in a common framework and compactified phase space for all forms of real matter and virtual vacuum energy, and a distinct algebra for observables and unobservables. To illustrate our scheme's potential, we provide examples of slit experiment variations (where the model finds theoretical basis for interference only occurring between two final sources), QCD (where we may model most attributes known to QCD, and a new view on entanglement), and we suggest approaches for other varied applications. We believe this is a viable candidate for further exploration as a foundational proposition for physics.« less

Templated and template-free fabrication strategies for zero-dimensional hollow MOF superstructures.

PubMed

Kim, Hyehyun; Lah, Myoung Soo

2017-05-16

Various fabrication strategies for hollow metal-organic framework (MOF) superstructures are reviewed and classified using various types of external templates and their properties. Hollow MOF superstructures have also been prepared without external templates, wherein unstable intermediates obtained during reactions convert to the final hollow MOF superstructures. Many hollow MOF superstructures have been fabricated using hard templates. After the core-shell core@MOF structure was prepared using a hard template, the core was selectively etched to generate a hollow MOF superstructure. Another approach for generating hollow superstructures is to use a solid reactant as a sacrificial template; this method requires no additional etching process. Soft templates such as discontinuous liquid/emulsion droplets and gas bubbles in a continuous soft phase have also been employed to prepare hollow MOF superstructures.

The longer we have to forget the more we remember: The ironic effect of postcue duration in item-based directed forgetting.

PubMed

Bancroft, Tyler D; Hockley, William E; Farquhar, Riley

2013-05-01

The effects of the duration of remember and forget cues were examined to test the differential rehearsal account of item-based directed forgetting. In Experiments 1 and 2, cues were shown for 300, 600, or 900 ms, and a directed forgetting effect (better recognition of remember than forget items) was found at each duration. In addition, recognition of both remember and forget items increased with cue duration. These 2 effects did not interact. The results of Experiment 2 further showed that memory for the cue associated with the study items increased with cue duration as well. The results of Experiment 1 were replicated in Experiment 3 for cue durations of 1, 2, and 3 s. Finally, a similar pattern of results was found for cue durations of 2, 4, and 6 s for associative recognition of random word pairs. If subjects cannot immediately terminate the processing of forget items, the lingering processing of these items is as beneficial as the continued processing of remember items. Alternatively, subjects may use inefficient or counterproductive strategies that ironically improve memory for the information they wish to forget.

Anxiety and fear. Discriminant validity in the child and adolescent practitioner's perspective.

PubMed

Pavuluri, Mani N; Henry, David; Allen, Kathleen

2002-12-01

We assessed the ability of child and adolescent practitioners to discriminate between anxiety items from the Revised Children's Manifest Anxiety Scale (RCMAS) and fear items from the Fear Survey Schedule for Children-Revised (FSSC-R). In addition, we examined the effects age, gender, nationality, and therapeutic orientation on discrimination ability. Child and adolescent psychiatrists and psychologists from two university hospitals in Australia and the USA completed a questionnaire comprised of items randomly chosen from the RCMAS and the FSSC-R. Clinicians rated each item on the extent to which the item represented the construct of anxiety or fear, using a 7-point Likert-type scale. Clinicians were more accurate in their perceptions of anxiety than in their perceptions of fear. Clinicians with a psychodynamic orientation were more likely to perceive an item as describing anxiety, and were less likely to identify fear. There was a significant interaction between age, scale and perception, with the youngest clinicians showing the greatest perceptual differentiation between the fear and anxiety items. The results suggest a need to develop common terminology among researchers and clinicians, develop scales with items specific to the pathology they intend to measure, and consider the variables influencing the clinicians rating them.

Integration of EEG lead placement templates into traditional technologist-based staffing models reduces costs in continuous video-EEG monitoring service.

PubMed

Kolls, Brad J; Lai, Amy H; Srinivas, Anang A; Reid, Robert R

2014-06-01

The purpose of this study was to determine the relative cost reductions within different staffing models for continuous video-electroencephalography (cvEEG) service by introducing a template system for 10/20 lead application. We compared six staffing models using decision tree modeling based on historical service line utilization data from the cvEEG service at our center. Templates were integrated into technologist-based service lines in six different ways. The six models studied were templates for all studies, templates for intensive care unit (ICU) studies, templates for on-call studies, templates for studies of ≤ 24-hour duration, technologists for on-call studies, and technologists for all studies. Cost was linearly related to the study volume for all models with the "templates for all" model incurring the lowest cost. The "technologists for all" model carried the greatest cost. Direct cost comparison shows that any introduction of templates results in cost savings, with the templates being used for patients located in the ICU being the second most cost efficient and the most practical of the combined models to implement. Cost difference between the highest and lowest cost models under the base case produced an annual estimated savings of $267,574. Implementation of the ICU template model at our institution under base case conditions would result in a $205,230 savings over our current "technologist for all" model. Any implementation of templates into a technologist-based cvEEG service line results in cost savings, with the most significant annual savings coming from using the templates for all studies, but the most practical implementation approach with the second highest cost reduction being the template used in the ICU. The lowered costs determined in this work suggest that a template-based cvEEG service could be supported at smaller centers with significantly reduced costs and could allow for broader use of cvEEG patient monitoring.

Comparing a volume based template approach and ultrasound guided freehand approach in multicatheter interstitial accelerated partial breast irradiation.

PubMed

Koh, Vicky Y; Buhari, Shaik A; Tan, Poh Wee; Tan, Yun Inn; Leong, Yuh Fun; Earnest, Arul; Tang, Johann I

2014-06-01

Currently, there are two described methods of catheter insertion for women undergoing multicatheter interstitial accelerated partial breast irradiation (APBI). These are a volume based template approach (template) and a non-template ultrasound guidance freehand approach (non-template). We aim to compare dosimetric endpoints between the template and non-template approach. Twenty patients, who received adjuvant multicatheter interstitial APBI between August 2008 to March 2010 formed the study cohort. Dosimetric planning was based on the RTOG 04-13 protocol. For standardization, the planning target volume evaluation (PTV-Eval) and organs at risk were contoured with the assistance of the attending surgeon. Dosimetric endpoints include D90 of the PTV-Eval, Dose Homogeneity Index (DHI), V200, maximum skin dose (MSD), and maximum chest wall dose (MCD). A median of 18 catheters was used per patient. The dose prescribed was 34 Gy in 10 fractions BID over 5 days. The average breast volume was 846 cm(3) (526-1384) for the entire cohort and there was no difference between the two groups (p = 0.6). Insertion time was significantly longer for the non-template approach (mean 150 minutes) compared to the template approach (mean: 90 minutes) (p = 0.02). The planning time was also significantly longer for the non-template approach (mean: 240 minutes) compared to the template approach (mean: 150 minutes) (p < 0.01). The template approach yielded a higher D90 (mean: 95%) compared to the non-template approach (mean: 92%) (p < 0.01). There were no differences in DHI (p = 0.14), V200 (p = 0.21), MSD (p = 0.7), and MCD (p = 0.8). Compared to the non-template approach, the template approach offered significant shorter insertion and planning times with significantly improved dosimetric PTV-Eval coverage without significantly compromising organs at risk dosimetrically.